Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 124 of 349
Found at i:39519260 original size:37 final size:37
Alignment explanation
Indices: 39519207--39519343 Score: 247
Period size: 37 Copynumber: 3.7 Consensus size: 37
39519197 CGAATAGTCC
* *
39519207 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
39519244 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
39519281 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
39519318 CCACACGTAGTCATCGAGTCTTACCC
1 CCACACGTAGTCATCGGGTCTTACCC
39519344 AGAATATATT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:39519572 original size:48 final size:48
Alignment explanation
Indices: 39519515--39519922 Score: 744
Period size: 48 Copynumber: 8.5 Consensus size: 48
39519505 CTAGCCGAAT
*
39519515 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCG
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
* *
39519563 CATTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
39519611 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
39519659 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
39519707 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
39519755 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
39519803 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
39519851 CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
39519899 CATTAGCCATTCGGCTTTACCACA
1 CACTAGCCATTCGGCTTTACCACA
39519923 CACATATATA
Statistics
Matches: 354, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 354 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.34
Consensus pattern (48 bp):
CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
Found at i:39522550 original size:27 final size:27
Alignment explanation
Indices: 39522492--39522554 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
39522482 TAAATAACAC
*
39522492 TAATTAAATTAATTAAAGAATACAAAA
1 TAATCAAATTAATTAAAGAATACAAAA
*
39522519 TAATCAAATATAATTATAGAATA-AGAAA
1 TAATCAAAT-TAATTAAAGAATACA-AAA
39522547 -AATCAAAT
1 TAATCAAAT
39522555 GCACATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (27 bp):
TAATCAAATTAATTAAAGAATACAAAA
Found at i:39523423 original size:40 final size:40
Alignment explanation
Indices: 39523368--39523447 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
39523358 ATAAAATTAA
*
39523368 ACTCATCAATGATAGAATTTATTAAAAATTCTTAAACTAT
1 ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
39523408 ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
1 ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
39523448 TTTTTTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (40 bp):
ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
Found at i:39525520 original size:68 final size:69
Alignment explanation
Indices: 39525395--39525529 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
39525385 TGATTAAACT
* * * *
39525395 TAATCACTTTAATATTAAATTAATATAATACTTATCAGGATGAATATTAGATTAAATTTAATATT
1 TAATAACTTTAACATTAAATTAATAAAATACTTATCAGGATGAATATTAAATTAAATTTAATATT
39525460 AAGA
66 AAGA
39525464 TAATAACTTTAACATTAAATTAATAAAATA-TTATCAAGG-T-AAGTATTAAATTAAATTTAATA
1 TAATAACTTTAACATTAAATTAATAAAATACTTATC-AGGATGAA-TATTAAATTAAATTTAATA
39525526 TTAA
64 TTAA
39525530 ATATATTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 2 0.03
68 28 0.47
69 30 0.50
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (69 bp):
TAATAACTTTAACATTAAATTAATAAAATACTTATCAGGATGAATATTAAATTAAATTTAATATT
AAGA
Found at i:39527035 original size:55 final size:55
Alignment explanation
Indices: 39526959--39527069 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
39526949 GAATCAAATG
39526959 CTCATTTTGATTTTTTTATGAGATTACGAACTCGTTTAAATTATCTATTGAAGTA
1 CTCATTTTGATTTTTTTATGAGATTACGAACTCGTTTAAATTATCTATTGAAGTA
39527014 CTCATTTTGATTTTTTTATGAGATTACGAACTCGTTTAAATTATCTATTGAAGTA
1 CTCATTTTGATTTTTTTATGAGATTACGAACTCGTTTAAATTATCTATTGAAGTA
39527069 C
1 C
39527070 GTTGTCTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.47
Consensus pattern (55 bp):
CTCATTTTGATTTTTTTATGAGATTACGAACTCGTTTAAATTATCTATTGAAGTA
Found at i:39527956 original size:17 final size:17
Alignment explanation
Indices: 39527914--39527952 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
39527904 CTTCATCAAT
*
39527914 TCTTTGTTAAAAAATAA
1 TCTTTATTAAAAAATAA
39527931 TCTTTATTAAAAAATAA
1 TCTTTATTAAAAAATAA
39527948 T-TTTA
1 TCTTTA
39527953 ATTATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (17 bp):
TCTTTATTAAAAAATAA
Found at i:39528811 original size:30 final size:30
Alignment explanation
Indices: 39528772--39528828 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
39528762 TTTTATAAAT
39528772 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
39528802 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
39528829 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:39529397 original size:24 final size:24
Alignment explanation
Indices: 39529368--39529415 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39529358 TTTAATTTCA
39529368 AATATAATTATAGAAAATTAAAAT
1 AATATAATTATAGAAAATTAAAAT
39529392 AATATAATTATAGAAAATTAAAAT
1 AATATAATTATAGAAAATTAAAAT
39529416 GGTTTAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AATATAATTATAGAAAATTAAAAT
Found at i:39551851 original size:6 final size:6
Alignment explanation
Indices: 39551840--39551871 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39551830 TCTTCCTTTT
39551840 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TG
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TG
39551872 GCCTCTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:39566475 original size:21 final size:21
Alignment explanation
Indices: 39566451--39566492 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39566441 GTTTACCTAT
39566451 ATGGTTGCAACTTGAGGTATA
1 ATGGTTGCAACTTGAGGTATA
39566472 ATGGTTGCAACTTGAGGTATA
1 ATGGTTGCAACTTGAGGTATA
39566493 CTTAATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (21 bp):
ATGGTTGCAACTTGAGGTATA
Found at i:39568924 original size:22 final size:21
Alignment explanation
Indices: 39568869--39568926 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
39568859 TCTTTTAACA
39568869 CATAAACATTCAATTATATTGG
1 CATAAACA-TCAATTATATTGG
* *
39568891 CACAACCAATCAATTATATTGG
1 CATAAAC-ATCAATTATATTGG
39568913 CATAATACATCAAT
1 CATAA-ACATCAAT
39568927 AGAAATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (21 bp):
CATAAACATCAATTATATTGG
Found at i:39570379 original size:23 final size:23
Alignment explanation
Indices: 39570349--39570421 Score: 146
Period size: 23 Copynumber: 3.2 Consensus size: 23
39570339 AGTGAAAAAT
39570349 GAGTGAAAAGTGAGGTAGTTGCA
1 GAGTGAAAAGTGAGGTAGTTGCA
39570372 GAGTGAAAAGTGAGGTAGTTGCA
1 GAGTGAAAAGTGAGGTAGTTGCA
39570395 GAGTGAAAAGTGAGGTAGTTGCA
1 GAGTGAAAAGTGAGGTAGTTGCA
39570418 GAGT
1 GAGT
39570422 TTTTAAAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.22
Consensus pattern (23 bp):
GAGTGAAAAGTGAGGTAGTTGCA
Found at i:39572943 original size:21 final size:21
Alignment explanation
Indices: 39572906--39572945 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39572896 GGGATTAAAT
*
39572906 CAAAATATAAAATAAATAACA
1 CAAAATATAAAAAAAATAACA
39572927 CAAAAT-TAAATAAAAATAA
1 CAAAATATAAA-AAAAATAA
39572946 AGACAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
CAAAATATAAAAAAAATAACA
Found at i:39576502 original size:19 final size:20
Alignment explanation
Indices: 39576478--39576515 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39576468 GGTACCACCA
39576478 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39576497 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39576516 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39576866 original size:42 final size:42
Alignment explanation
Indices: 39576819--39576985 Score: 192
Period size: 42 Copynumber: 3.8 Consensus size: 42
39576809 GACGGATCTC
39576819 GAACTCGGACTCAACTCAACGAGTTCGCATGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGCATGCATCCATAAGT
* * * *
39576861 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGCATG-C-A--TCCA--TAAGT
39576908 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTC-G-CA--TGCATCCATAAGT
*
39576954 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGCATGC
39576986 TCAACCATCC
Statistics
Matches: 105, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 33 0.31
43 1 0.01
44 2 0.02
45 3 0.03
46 29 0.28
47 29 0.28
48 3 0.03
49 2 0.02
50 1 0.01
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (42 bp):
GAACTCGGACTCAACTCAACGAGTTCGCATGCATCCATAAGT
Found at i:39576871 original size:72 final size:75
Alignment explanation
Indices: 39576743--39576882 Score: 232
Period size: 72 Copynumber: 1.9 Consensus size: 75
39576733 GCCCCTAAGT
*
39576743 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTC-AGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
39576808 CGACGGATCTC
65 CGACGGATCTC
*
39576819 GAACTCGGACTCAACTCAACGAGTTC-GC-AT-GCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCAGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
39576881 GA
66 GA
39576883 GTTCGGATGC
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
72 34 0.55
73 1 0.02
74 2 0.03
76 25 0.40
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (75 bp):
GAACTCGGACTCAACTCAACGAGCTCAGCGATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GACGGATCTC
Found at i:39576913 original size:47 final size:49
Alignment explanation
Indices: 39576850--39576985 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 49
39576840 AGTTCGCATG
*
39576850 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA
1 CATCCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTA
* * *
39576900 CAT-C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTG
1 CATCCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTA
*
39576943 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CATCCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
39576986 TCAACCATCC
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
43 6 0.08
44 2 0.03
45 2 0.03
46 29 0.39
47 29 0.39
48 2 0.03
49 1 0.01
50 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (49 bp):
CATCCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTA
Found at i:39576973 original size:93 final size:89
Alignment explanation
Indices: 39576818--39576985 Score: 300
Period size: 93 Copynumber: 1.8 Consensus size: 89
39576808 CGACGGATCT
39576818 CGAACTCGGACTCAACTCAACGAGTTCGCATGCATCCATAAGTGAACTCGGACTCAACTCAACGA
1 CGAACTCGGACTCAACTCAACGAGTTCGCATGCATCCATAAGTGAACTCGGACTCAACTCAACGA
39576883 GTTCGGATGCCTAGTTACATCTCA
66 GTTCGGATGCCTAGTTACATCTCA
39576907 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTC-G-CA--TGCATCCATAAGTGAACTCGGACTCAACTCA
39576972 ACGAGTTCGGATGC
62 ACGAGTTCGGATGC
39576986 TCAACCATCC
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
89 27 0.36
90 1 0.01
91 2 0.03
93 45 0.60
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (89 bp):
CGAACTCGGACTCAACTCAACGAGTTCGCATGCATCCATAAGTGAACTCGGACTCAACTCAACGA
GTTCGGATGCCTAGTTACATCTCA
Found at i:39586535 original size:93 final size:91
Alignment explanation
Indices: 39586376--39586544 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 91
39586366 CGCCCTAAGT
* *
39586376 GAACTCGGACTCAACTCAACGAGCTGAGCGTTCTCATCCATAAGTGAACTCGGACTCAACTAAAC
1 GAACTCGGACTCAACTCAACGAGCGGAGCATTCTCATCCATAAGTGAACTCGGACTCAACTAAAC
39586441 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAG-TCGGATGCCTAGTTACATCTCAC
* *
39586468 GAACTCGGACTCAACTCAACGAGTTCGGA-CATT-TGCATCCATAAGTGAACTTGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAG--CGGAGCATTCT-CATCCATAAGTGAACTCGGACTCAACTA
39586531 AACGAGTCGGATGC
63 AACGAGTCGGATGC
39586545 TCAACCATCC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
92 32 0.46
93 35 0.50
94 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCGGAGCATTCTCATCCATAAGTGAACTCGGACTCAACTAAAC
GAGTCGGATGCCTAGTTACATCTCAC
Found at i:39588344 original size:38 final size:39
Alignment explanation
Indices: 39588277--39588376 Score: 157
Period size: 38 Copynumber: 2.6 Consensus size: 39
39588267 AACATGTTTT
*
39588277 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
39588316 TGAGTATTGTGATAT-TGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
39588354 TAAGTATTATGATATAGTGCTTA
1 TGAGTATTGTGATATA-TGCTTA
39588377 CCCGAAACTC
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.62
39 15 0.27
40 6 0.11
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:39590080 original size:19 final size:20
Alignment explanation
Indices: 39590056--39590093 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39590046 GGTACCACCA
39590056 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39590075 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39590094 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39590434 original size:93 final size:93
Alignment explanation
Indices: 39590322--39590492 Score: 276
Period size: 93 Copynumber: 1.8 Consensus size: 93
39590312 GCCCCTAAGT
*
39590322 GAACTCGGACTCAACTCAACGAGCTT--GAGCGTTCT-CATCCATAAGTGAACTCGGACTCAACT
1 GAACTCGGACTCAACTCAACGAG-TTCGGA-CATT-TGCATCCATAAGTGAACTCGGACTCAACT
39590384 CAACGAGTTCGGATGCCTAGTTACATCTCAC
63 CAACGAGTTCGGATGCCTAGTTACATCTCAC
*
39590415 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
39590480 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39590493 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
92 3 0.04
93 68 0.93
94 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39590488 original size:46 final size:46
Alignment explanation
Indices: 39590317--39590489 Score: 196
Period size: 46 Copynumber: 3.7 Consensus size: 46
39590307 AACCCGCCCC
*
39590317 TAAGTGAACTCGGACTCAACTCAACGAGCTT--GAGCGTTCTCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGAGCATT-TCATCCA
*
39590363 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTTCATCCA
* *
39590411 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTT-CATCCA
*
39590456 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39590490 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 8, Indels: 20
0.80 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 56 0.51
47 31 0.28
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTCATCCA
Found at i:39590946 original size:30 final size:30
Alignment explanation
Indices: 39590912--39590971 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39590902 ATTTAATACG
39590912 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
39590942 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
39590972 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:39592309 original size:39 final size:39
Alignment explanation
Indices: 39592250--39592390 Score: 219
Period size: 39 Copynumber: 3.6 Consensus size: 39
39592240 AACATGTTTT
*
39592250 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
39592289 TGAGTATTGTGATATTTGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
39592328 TAAGTATTATGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
39592367 TGTGTAATGTGATACATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
39592391 AGTGAATATG
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:39594616 original size:43 final size:43
Alignment explanation
Indices: 39594537--39594723 Score: 230
Period size: 43 Copynumber: 4.3 Consensus size: 43
39594527 GCCGCAAAAC
* * * * *
39594537 TTAGCGGCGTTTTTTCGAAAAAAAGGCCACTAAAGACTAGGACTT
1 TTAGCGGCG-CTTTTC-TAAAAAACGCCGCTAAAGACCAGGACTT
* *
39594582 TTAGCTGCGCTTTTTTAAAAAACGCCGCTAAAGACCAGGACTT
1 TTAGCGGCGCTTTTCTAAAAAACGCCGCTAAAGACCAGGACTT
*
39594625 TTAGCGGCGCTTTTCTAAAAAACACCGCTAAAGACCAGGACTT
1 TTAGCGGCGCTTTTCTAAAAAACGCCGCTAAAGACCAGGACTT
* ** * *
39594668 TTCGCGGCGCTTTTCCCACAAACGCCGCTAAAGTCCAGGACTT
1 TTAGCGGCGCTTTTCTAAAAAACGCCGCTAAAGACCAGGACTT
*
39594711 TTCGCGGCGCTTT
1 TTAGCGGCGCTTT
39594724 CCCGCAAACG
Statistics
Matches: 126, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 114 0.90
44 4 0.03
45 8 0.06
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGCTTTTCTAAAAAACGCCGCTAAAGACCAGGACTT
Found at i:39594738 original size:42 final size:43
Alignment explanation
Indices: 39594566--39594742 Score: 221
Period size: 43 Copynumber: 4.1 Consensus size: 43
39594556 AAAAAGGCCA
* * * *** *
39594566 CTAAAGACTAGGACTTTTAGCTGCGCTTTTTTAAAAAACGCCG
1 CTAAAGACCAGGACTTTTCGCGGCGCTTTTCCCACAAACGCCG
* ** * *
39594609 CTAAAGACCAGGACTTTTAGCGGCGCTTTTCTAAAAAACACCG
1 CTAAAGACCAGGACTTTTCGCGGCGCTTTTCCCACAAACGCCG
39594652 CTAAAGACCAGGACTTTTCGCGGCGCTTTTCCCACAAACGCCG
1 CTAAAGACCAGGACTTTTCGCGGCGCTTTTCCCACAAACGCCG
* *
39594695 CTAAAGTCCAGGACTTTTCGCGGCGC-TTTCCCGCAAACGCCG
1 CTAAAGACCAGGACTTTTCGCGGCGCTTTTCCCACAAACGCCG
39594737 CTAAAG
1 CTAAAG
39594743 GTCATAAAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 21 0.17
43 102 0.83
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
CTAAAGACCAGGACTTTTCGCGGCGCTTTTCCCACAAACGCCG
Found at i:39596804 original size:22 final size:22
Alignment explanation
Indices: 39596778--39596822 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39596768 CTAATATATG
39596778 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39596800 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39596822 T
1 T
39596823 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39600576 original size:22 final size:22
Alignment explanation
Indices: 39600548--39600592 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39600538 AGGGGGAGTG
39600548 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39600570 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39600592 T
1 T
39600593 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39602551 original size:16 final size:16
Alignment explanation
Indices: 39602530--39602561 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39602520 AAATATTAAA
*
39602530 TTTTTAAGTTTTTTAT
1 TTTTTAAATTTTTTAT
39602546 TTTTTAAATTTTTTAT
1 TTTTTAAATTTTTTAT
39602562 GAATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTAAATTTTTTAT
Found at i:39603188 original size:7 final size:7
Alignment explanation
Indices: 39603176--39603276 Score: 69
Period size: 7 Copynumber: 14.1 Consensus size: 7
39603166 ACTAACTAAT
39603176 CTAAACC
1 CTAAACC
39603183 CTAAACTC
1 CTAAAC-C
*
39603191 CTAATCC
1 CTAAACC
*
39603198 CTAAACA
1 CTAAACC
*
39603205 TTAAACC
1 CTAAACC
*
39603212 CTAAAAC
1 CTAAACC
*
39603219 ATAAACC
1 CTAAACC
*
39603226 CTGAACC
1 CTAAACC
*
39603233 CTGAACC
1 CTAAACC
* *
39603240 ATGAACCC
1 CT-AAACC
*
39603248 CTAACCC
1 CTAAACC
39603255 CT-AACAC
1 CTAAAC-C
39603262 CTAAACC
1 CTAAACC
*
39603269 TTAAACC
1 CTAAACC
39603276 C
1 C
39603277 CAACCCTTAA
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
6 2 0.03
7 57 0.79
8 13 0.18
ACGTcount: A:0.41, C:0.39, G:0.03, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:39603215 original size:14 final size:14
Alignment explanation
Indices: 39603177--39603227 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
39603167 CTAACTAATC
39603177 TAAACCCTAAAC-T
1 TAAACCCTAAACAT
*
39603190 CCTAATCCCTAAACAT
1 --TAAACCCTAAACAT
39603206 TAAACCCTAAAACA-
1 TAAACCCT-AAACAT
39603220 TAAACCCT
1 TAAACCCT
39603228 GAACCCTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 15 0.47
15 16 0.50
16 1 0.03
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACAT
Found at i:39603428 original size:41 final size:41
Alignment explanation
Indices: 39603367--39603503 Score: 240
Period size: 41 Copynumber: 3.4 Consensus size: 41
39603357 CTAGTTGGTA
39603367 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGG
*
39603408 TCTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGG
39603449 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCT-G
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGG
* *
39603489 TTTTTAGCGCCGTTT
1 TCTTTAGCGGCGTTT
39603504 TAACAAAAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 14 0.15
41 78 0.85
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (41 bp):
TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGG
Found at i:39603558 original size:81 final size:81
Alignment explanation
Indices: 39603367--39603544 Score: 250
Period size: 82 Copynumber: 2.2 Consensus size: 81
39603357 CTAGTTGGTA
* * * *
39603367 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCT-GTTTTTAGCGCCGTTTTACAAAAAA
*
39603432 CGCCGCTAATGCTCTGG
65 CGCCGCTAATGCTCTAG
39603449 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGCCGTTTTAACAAAAAA
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGCCGTTTT-ACAAAAAA
* *
39603514 TGCCGCTATTGCTC-AG
65 CGCCGCTAATGCTCTAG
* *
39603530 TTTTTAGTGGCGTTT
1 TCTTTAGCGGCGTTT
39603545 TTGTCAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
81 29 0.34
82 57 0.66
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (81 bp):
TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGCCGTTTTACAAAAAAC
GCCGCTAATGCTCTAG
Found at i:39604866 original size:18 final size:18
Alignment explanation
Indices: 39604840--39604874 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39604830 TTGTCCCCAA
39604840 TATCAATACAAAAAATGT
1 TATCAATACAAAAAATGT
* *
39604858 TATCGATACCAAAAATG
1 TATCAATACAAAAAATG
39604875 CATTCTGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (18 bp):
TATCAATACAAAAAATGT
Found at i:39605143 original size:12 final size:12
Alignment explanation
Indices: 39605126--39605151 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39605116 CTTCATATGA
39605126 TACCAAAATAAG
1 TACCAAAATAAG
39605138 TACCAAAATAAG
1 TACCAAAATAAG
39605150 TA
1 TA
39605152 AAGTTTTCAT
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:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (12 bp):
TACCAAAATAAG
Found at i:39605379 original size:27 final size:27
Alignment explanation
Indices: 39605341--39605395 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
39605331 TAAAAACAAC
39605341 TTAGTAAGTACTTCAAGAATTTAATGA
1 TTAGTAAGTACTTCAAGAATTTAATGA
*
39605368 TTAGTAAGTACTTTAAGAATTTAATGA
1 TTAGTAAGTACTTCAAGAATTTAATGA
39605395 T
1 T
39605396 AAGCCTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (27 bp):
TTAGTAAGTACTTCAAGAATTTAATGA
Found at i:39607309 original size:170 final size:170
Alignment explanation
Indices: 39607008--39607329 Score: 452
Period size: 170 Copynumber: 1.9 Consensus size: 170
39606998 CTTTTATAGT
* * * *
39607008 TTTTACGATTTAGTCCTTGTATTTTAATTACTAATCGTCTAATAAAATTACCTAACCAAATCTCG
1 TTTTACGATTTAGTCCTTGTACTTTAAGTACTAATCGTCTAATAAAATTACCTAACCAAAACTCA
* * * * *
39607073 ATATAAATCTCAAGTAAGCTCATAAATATTAGTAATTAATATTTACTGAATCGATTATTGGTATA
66 ATATAAATCTAAAGTAAGCTCATAAATATTAATAATTAATATTTACGGAATCAATGATTGGTATA
*
39607138 CGGTGTTCTGAAACAATCATTTTTGGTACACTTTTGCAAA
131 CGGAGTTCTGAAACAATCATTTTTGGTACACTTTTGCAAA
* * * *
39607178 TTTTATGATTTAGTCCTTGTACTTTAAGTACTAGTTGTCTACTAAAATTA-CTAGACCAAAACTC
1 TTTTACGATTTAGTCCTTGTACTTTAAGTACTAATCGTCTAATAAAATTACCTA-ACCAAAACTC
39607242 AATATAAATCTAAAGTTAA-CTCATAAATATTAATAATTAATATTTACGGAATCAATGATCT-GT
65 AATATAAATCTAAAG-TAAGCTCATAAATATTAATAATTAATATTTACGGAATCAATGAT-TGGT
* *
39607305 ATACGGAGTTCTGGAACCATCATTT
128 ATACGGAGTTCTGAAACAATCATTT
39607330 CTAGTGCCAC
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
169 3 0.02
170 126 0.95
171 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (170 bp):
TTTTACGATTTAGTCCTTGTACTTTAAGTACTAATCGTCTAATAAAATTACCTAACCAAAACTCA
ATATAAATCTAAAGTAAGCTCATAAATATTAATAATTAATATTTACGGAATCAATGATTGGTATA
CGGAGTTCTGAAACAATCATTTTTGGTACACTTTTGCAAA
Found at i:39608173 original size:49 final size:49
Alignment explanation
Indices: 39608116--39608221 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 49
39608106 GGAAGACAAG
* * *
39608116 TGTCGCGACACCCAACTTCGAGCTGTCAGAAGTTCCATTTGATGTTCAA
1 TGTCGCGACACCCAACTTCGAGCTATCAGAAATCCCATTTGATGTTCAA
*
39608165 TGTCGCGACACCCAACTTTGAGCTATCAGAAATCCCATTTGATGTTCAA
1 TGTCGCGACACCCAACTTCGAGCTATCAGAAATCCCATTTGATGTTCAA
*
39608214 TGACGCGA
1 TGTCGCGA
39608222 GACCTATATC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (49 bp):
TGTCGCGACACCCAACTTCGAGCTATCAGAAATCCCATTTGATGTTCAA
Found at i:39609407 original size:27 final size:26
Alignment explanation
Indices: 39609369--39609484 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 26
39609359 CAGCATGGCT
* *
39609369 ACCAGAACAGATAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
*
39609395 ACCAGATACAGATAATCGTGGTAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
39609423 ACCAGAACAGATATATGTGGCAGAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* * *
39609450 ACCAGATCAGATATTTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
39609477 ACCAGAAC
1 ACCAGAAC
39609485 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 6 0.08
27 57 0.72
28 16 0.20
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:39609428 original size:54 final size:54
Alignment explanation
Indices: 39609369--39609484 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
39609359 CAGCATGGCT
* *
39609369 ACCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGCC
1 ACCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCC
* * * *
39609423 ACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCC
1 ACCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCC
39609477 ACCAGAAC
1 ACCAGAAC
39609485 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (54 bp):
ACCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCC
Found at i:39611142 original size:26 final size:26
Alignment explanation
Indices: 39611102--39611211 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
39611092 CATGAAATTC
39611102 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
39611128 TTACCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
39611154 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
39611180 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
39611206 TTATCA
1 TTATCA
39611212 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:39618021 original size:48 final size:48
Alignment explanation
Indices: 39617969--39618090 Score: 156
Period size: 48 Copynumber: 2.5 Consensus size: 48
39617959 AGATCCCATG
* *
39617969 TAAGACCATGTCTAGGACATGGCATTGGCATCGAGATGAGAT-CTCGTA
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAG-TGCTAGTA
* * * * * *
39618017 TAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGTGCTAGTA
39618065 TAAGACCATGTCTGGGACATGGCATT
1 TAAGACCATGTCTGGGACATGGCATT
39618091 ATTATGAGAC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 1 0.02
48 63 0.98
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGTGCTAGTA
Found at i:39621446 original size:25 final size:26
Alignment explanation
Indices: 39621412--39621466 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 26
39621402 TGAAATGCCC
39621412 ATCATAGAACATTTACCTAACCC-TT
1 ATCATAGAACATTTACCTAACCCATT
*
39621437 ATCATGGAACATTTACCTAACCCATT
1 ATCATAGAACATTTACCTAACCCATT
39621463 ATCA
1 ATCA
39621467 ATTTTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.31
Consensus pattern (26 bp):
ATCATAGAACATTTACCTAACCCATT
Found at i:39625384 original size:12 final size:12
Alignment explanation
Indices: 39625367--39625397 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39625357 AGTACTACCT
39625367 CGGCCTCGACCA
1 CGGCCTCGACCA
39625379 CGGCCTCGACCA
1 CGGCCTCGACCA
*
39625391 CAGCCTC
1 CGGCCTC
39625398 TTCCCCGAGT
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:0.16, C:0.52, G:0.23, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:39627026 original size:26 final size:26
Alignment explanation
Indices: 39626997--39627049 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
39626987 TCAAACATGC
*
39626997 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGAT-AATTTAACTCCTAGGGGT
* *
39627023 ATTTCGATAATTTATCTCCTAGGGGT
1 ATTTAGATAATTTAACTCCTAGGGGT
39627049 A
1 A
39627050 AAATTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAGATAATTTAACTCCTAGGGGT
Found at i:39627342 original size:8 final size:8
Alignment explanation
Indices: 39627329--39627356 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
39627319 AAAATACTGA
39627329 TTTTCGGC
1 TTTTCGGC
39627337 TTTTCGGC
1 TTTTCGGC
39627345 TTTTCGGC
1 TTTTCGGC
39627353 TTTT
1 TTTT
39627357 GCCGATCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.57
Consensus pattern (8 bp):
TTTTCGGC
Found at i:39628566 original size:26 final size:26
Alignment explanation
Indices: 39628536--39628591 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
39628526 TGAAATGCCC
39628536 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACATAACCCATT
*
39628562 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACATAACCCATT
39628588 ATCA
1 ATCA
39628592 ATTTTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACATAACCCATT
Found at i:39632392 original size:29 final size:31
Alignment explanation
Indices: 39632360--39632417 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
39632350 TCTGCATTAT
*
39632360 ATATATATGCTGAA-TT-AAGT-TGTAAAAGA
1 ATATAAATG-TGAAGTTGAAGTATGTAAAAGA
39632389 ATATAAATGTGAAGTTGAAGTATGTAAAA
1 ATATAAATGTGAAGTTGAAGTATGTAAAA
39632418 TATGAACTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 4 0.16
31 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (31 bp):
ATATAAATGTGAAGTTGAAGTATGTAAAAGA
Found at i:39636020 original size:40 final size:40
Alignment explanation
Indices: 39635957--39636049 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
39635947 ATCTCCGTCT
* * **
39635957 AACCCAACACACC-A-TGTGGGGATAAAATTGACCCACCC
1 AACCCTACACACCAAGTATGGGGATAAAATCAACCCACCC
* *
39635995 ATCCCTACACACCAAGTATGGGGATAAAATCAACCCATCC
1 AACCCTACACACCAAGTATGGGGATAAAATCAACCCACCC
39636035 AACCCTACACACCAA
1 AACCCTACACACCAA
39636050 ATGGTACCGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
38 11 0.24
39 1 0.02
40 34 0.74
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14
Consensus pattern (40 bp):
AACCCTACACACCAAGTATGGGGATAAAATCAACCCACCC
Found at i:39642373 original size:25 final size:25
Alignment explanation
Indices: 39642326--39642373 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
39642316 TTCAGTTTAC
*
39642326 ACTACCTAAAGTGTTTCAGTAACGT
1 ACTACCTAAAGTGTCTCAGTAACGT
*
39642351 ACTACCTATAGTAGTCTCA-TAAC
1 ACTACCTAAAGT-GTCTCAGTAAC
39642374 ACATACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (25 bp):
ACTACCTAAAGTGTCTCAGTAACGT
Found at i:39645132 original size:25 final size:24
Alignment explanation
Indices: 39645101--39645149 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
39645091 ACCCTTCTCA
*
39645101 TCTCTTCACTT-CTTTCTCATTTTTC
1 TCTCTTCA-TTCCCTTCT-ATTTTTC
39645126 TCTCTTCATTCCCTTCTATTTTTC
1 TCTCTTCATTCCCTTCTATTTTTC
39645150 ATTGTTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (24 bp):
TCTCTTCATTCCCTTCTATTTTTC
Found at i:39645379 original size:11 final size:11
Alignment explanation
Indices: 39645356--39645389 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39645346 ATGTCAAATC
*
39645356 ATCAAGAATAA
1 ATCAAGAACAA
*
39645367 ATTAAGAACAA
1 ATCAAGAACAA
39645378 ATCAAGAACAA
1 ATCAAGAACAA
39645389 A
1 A
39645390 AATAGATGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (11 bp):
ATCAAGAACAA
Found at i:39650351 original size:19 final size:19
Alignment explanation
Indices: 39650327--39650377 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
39650317 GTTGTGAATA
39650327 GGCCAAATGGGCCGAAATG
1 GGCCAAATGGGCCGAAATG
*
39650346 GGCCAAATGGGCCGGAATG
1 GGCCAAATGGGCCGAAATG
*
39650365 GGCTAAATGGGCC
1 GGCCAAATGGGCC
39650378 CGATGGGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.39, T:0.12
Consensus pattern (19 bp):
GGCCAAATGGGCCGAAATG
Found at i:39650353 original size:9 final size:9
Alignment explanation
Indices: 39650327--39650377 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
39650317 GTTGTGAATA
39650327 GGCCAAATG
1 GGCCAAATG
39650336 GGCCGAAATG
1 GGCC-AAATG
39650346 GGCCAAATG
1 GGCCAAATG
*
39650355 GGCCGGAATG
1 GGCC-AAATG
*
39650365 GGCTAAATG
1 GGCCAAATG
39650374 GGCC
1 GGCC
39650378 CGATGGGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.27, C:0.22, G:0.39, T:0.12
Consensus pattern (9 bp):
GGCCAAATG
Found at i:39650486 original size:28 final size:28
Alignment explanation
Indices: 39650455--39650571 Score: 123
Period size: 28 Copynumber: 4.1 Consensus size: 28
39650445 GTGAGCATGA
39650455 ATAT-AATGTGATTTGGGCCAGATGGGCC
1 ATATAAATGTGA-TTGGGCCAGATGGGCC
* *
39650483 ATATAAATGAGATTGGGCCTGATGGGCC
1 ATATAAATGTGATTGGGCCAGATGGGCC
* *
39650511 ATATGAACATG-AATTGGGCCGGATGGGCC
1 ATAT-AA-ATGTGATTGGGCCAGATGGGCC
* *
39650540 ATATAAATGGGATTGGG-CATAGTGGGCC
1 ATATAAATGTGATTGGGCCAGA-TGGGCC
39650568 ATAT
1 ATAT
39650572 GCATGTATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.06
28 41 0.53
29 28 0.36
30 3 0.04
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCAGATGGGCC
Found at i:39650535 original size:29 final size:28
Alignment explanation
Indices: 39650467--39650571 Score: 133
Period size: 28 Copynumber: 3.7 Consensus size: 28
39650457 ATAATGTGAT
39650467 TTGGGCCAGATGGGCCATATAAATGAGA
1 TTGGGCCAGATGGGCCATATAAATGAGA
*
39650495 TTGGGCCTGATGGGCCATATGAACATGA-A
1 TTGGGCCAGATGGGCCATAT-AA-ATGAGA
* *
39650524 TTGGGCCGGATGGGCCATATAAATGGGA
1 TTGGGCCAGATGGGCCATATAAATGAGA
*
39650552 TTGGG-CATAGTGGGCCATAT
1 TTGGGCCAGA-TGGGCCATAT
39650572 GCATGTATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.07
28 37 0.54
29 22 0.32
30 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.24
Consensus pattern (28 bp):
TTGGGCCAGATGGGCCATATAAATGAGA
Found at i:39653049 original size:20 final size:20
Alignment explanation
Indices: 39653024--39653068 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
39653014 TATACGAAAA
*
39653024 TTAAAACTTTAAAACTTTAT
1 TTAAAACCTTAAAACTTTAT
*
39653044 TTAAAACCTTAAAATTTTAT
1 TTAAAACCTTAAAACTTTAT
39653064 TTAAA
1 TTAAA
39653069 GAATCAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAACCTTAAAACTTTAT
Found at i:39653315 original size:11 final size:11
Alignment explanation
Indices: 39653292--39653325 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39653282 ATGTCAAATC
*
39653292 ATCAAGAATAA
1 ATCAAGAACAA
*
39653303 ATTAAGAACAA
1 ATCAAGAACAA
39653314 ATCAAGAACAA
1 ATCAAGAACAA
39653325 A
1 A
39653326 ACTGGATGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (11 bp):
ATCAAGAACAA
Found at i:39659858 original size:49 final size:49
Alignment explanation
Indices: 39659784--39659881 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
39659774 TTGAACCGAA
*
39659784 GAGATTGGTCCAAAAGACTGTATGATGCTTTATGGGCCTACAAGACAAC
1 GAGATTGGTCCAAAAGACTGGATGATGCTTTATGGGCCTACAAGACAAC
* *
39659833 GAGATTGGTCCAAAAGATTGGATGATGCTTTATGGGCCTACAGGACAAC
1 GAGATTGGTCCAAAAGACTGGATGATGCTTTATGGGCCTACAAGACAAC
39659882 ATACAAGACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (49 bp):
GAGATTGGTCCAAAAGACTGGATGATGCTTTATGGGCCTACAAGACAAC
Found at i:39660131 original size:22 final size:22
Alignment explanation
Indices: 39660073--39660125 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
39660063 AAAATTGACT
39660073 TTTAGCGACATTTTTTAAGGTC
1 TTTAGCGACATTTTTTAAGGTC
*
39660095 TTTAGCGGCATTTTTTAAGGTC
1 TTTAGCGACATTTTTTAAGGTC
39660117 TTTAGCGAC
1 TTTAGCGAC
39660126 GCTTTTAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (22 bp):
TTTAGCGACATTTTTTAAGGTC
Found at i:39660133 original size:21 final size:22
Alignment explanation
Indices: 39660073--39660134 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
39660063 AAAATTGACT
**
39660073 TTTAGCGACATTTTTTAAGGTC
1 TTTAGCGACAGCTTTTAAGGTC
* **
39660095 TTTAGCGGCATTTTTTAAGGTC
1 TTTAGCGACAGCTTTTAAGGTC
39660117 TTTAGCGAC-GCTTTTAAG
1 TTTAGCGACAGCTTTTAAG
39660135 CGCCGCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (22 bp):
TTTAGCGACAGCTTTTAAGGTC
Found at i:39660262 original size:43 final size:43
Alignment explanation
Indices: 39660214--39660397 Score: 205
Period size: 43 Copynumber: 4.3 Consensus size: 43
39660204 TATTTAAAAA
*
39660214 AAACGCCGCTAAAGATCAAAACCTATAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGATCAAGACCTATAGCGACGCTTTTTCCAC
*
39660257 AAACGCCGCTAAAGATCAAGACCTAT-GACAACGC-TTTTCCTAC
1 AAACGCCGCTAAAGATCAAGACCTATAG-CGACGCTTTTTCC-AC
** * * *
39660300 AAACGCTACTAAAGATCACGACCTTTAGCGACGCTTTTT-TAC
1 AAACGCCGCTAAAGATCAAGACCTATAGCGACGCTTTTTCCAC
* * * *
39660342 AAATGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTTCCA-
1 AAACGCCGCTAAAGATCAAGACCTATAGCGACGC-TTTTTCCAC
*
39660385 AAATGCCGCTAAA
1 AAACGCCGCTAAA
39660398 AGTCATGAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
42 39 0.32
43 77 0.63
44 6 0.05
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCAAGACCTATAGCGACGCTTTTTCCAC
Found at i:39661939 original size:6 final size:6
Alignment explanation
Indices: 39661930--39661964 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
39661920 AAAATTGATG
39661930 AATTTA AATTTA GAATTTA AATTTA GAATTTA AAT
1 AATTTA AATTTA -AATTTA AATTTA -AATTTA AAT
39661965 ATTATGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 15 0.56
7 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:39661947 original size:13 final size:13
Alignment explanation
Indices: 39661929--39661964 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
39661919 AAAAATTGAT
39661929 GAATTTAAATTTA
1 GAATTTAAATTTA
39661942 GAATTTAAATTTA
1 GAATTTAAATTTA
39661955 GAATTTAAAT
1 GAATTTAAAT
39661965 ATTATGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
GAATTTAAATTTA
Found at i:39664550 original size:19 final size:19
Alignment explanation
Indices: 39664528--39664572 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
39664518 TTTTTAACTA
*
39664528 TTTTATATTTTATTTTTAT
1 TTTTATATTTCATTTTTAT
*
39664547 TTTTGTATTTCATTTTTAT
1 TTTTATATTTCATTTTTAT
39664566 TTGTTAT
1 TT-TTAT
39664573 CAATGTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTATATTTCATTTTTAT
Found at i:39664954 original size:7 final size:7
Alignment explanation
Indices: 39664918--39664956 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
39664908 ATATAAATCA
39664918 TTAACCC
1 TTAACCC
*
39664925 TGAACCC
1 TTAACCC
*
39664932 ATAACCC
1 TTAACCC
*
39664939 ATAACCC
1 TTAACCC
39664946 TTAACCC
1 TTAACCC
39664953 TTAA
1 TTAA
39664957 ACTTTAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.36, C:0.38, G:0.03, T:0.23
Consensus pattern (7 bp):
TTAACCC
Found at i:39665256 original size:15 final size:15
Alignment explanation
Indices: 39665242--39665274 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39665232 CCCTAACCCT
39665242 TAAA-CCATAATCCC
1 TAAACCCATAATCCC
*
39665256 TAAACCCATAATCCA
1 TAAACCCATAATCCC
39665271 TAAA
1 TAAA
39665275 ACTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAACCCATAATCCC
Found at i:39665271 original size:22 final size:21
Alignment explanation
Indices: 39665232--39665273 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
39665222 AATCTTAGAC
*
39665232 CCCTAACCCTTAAACCATAAT
1 CCCTAACCCATAAACCATAAT
*
39665253 CCCTAAACCCATAATCCATAA
1 CCCT-AACCCATAAACCATAA
39665274 AACTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (21 bp):
CCCTAACCCATAAACCATAAT
Found at i:39665518 original size:22 final size:21
Alignment explanation
Indices: 39665490--39665536 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39665480 TTTAAGATTT
* *
39665490 TTTAAGGTTTAGGAGTTTAGTG
1 TTTAAGGATTA-GAGATTAGTG
*
39665512 TTTAAGGATTATAGATTAGTG
1 TTTAAGGATTAGAGATTAGTG
39665533 TTTA
1 TTTA
39665537 TGATTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTAGAGATTAGTG
Found at i:39665640 original size:41 final size:40
Alignment explanation
Indices: 39665577--39665754 Score: 250
Period size: 41 Copynumber: 4.4 Consensus size: 40
39665567 GTTATATGAC
* * *
39665577 TTTTA-CGGCGTTTTCCCGAAAGCCCCGCTAATGCTCCGAT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCC-AT
* *
39665617 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATACTCCGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCC-AT
*
39665658 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTCAGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCA-T
*
39665699 TTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCTCAT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC-CAT
39665740 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
39665755 TGGTAAAACG
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
40 5 0.04
41 117 0.94
42 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCAT
Found at i:39665767 original size:82 final size:81
Alignment explanation
Indices: 39665577--39665801 Score: 267
Period size: 82 Copynumber: 2.8 Consensus size: 81
39665567 GTTATATGAC
* * * * *
39665577 TTTTA-CGGCGTTTTCCCGAAAGCCCCGCTAATGCTCCGATTTTTAGCGGCGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCAG-TTTTTAGCGGCATTTTACCAAAAGC
*
39665641 GCCGCTAATACTCCGGT
65 GCCGCTAATACTCCGAT
39665658 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTCAGTTTTTAGCGGCATTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGC-TCAGTTTTTAGCGGCATTTTACCAAAAGC
*
39665723 GCCGCTAATGCTCTC-AT
65 GCCGCTAATACTC-CGAT
*** * * * *
39665740 TTTTAGCGGCGTTTTTGGTAAAA-CGCCGCTATTGCTCTGTTTTTAGCAGCATTTTAACAAAA
1 TTTTAGCGGCG-TTTTACCAAAAGCGCCGCTAATGCTCAGTTTTTAGCGGCATTTTACCAAAA
39665802 AATGCCGCTA
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
81 29 0.23
82 85 0.67
83 12 0.10
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (81 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCAGTTTTTAGCGGCATTTTACCAAAAGCG
CCGCTAATACTCCGAT
Found at i:39665826 original size:123 final size:122
Alignment explanation
Indices: 39665577--39665816 Score: 279
Period size: 123 Copynumber: 2.0 Consensus size: 122
39665567 GTTATATGAC
* * *
39665577 TTTTACGGCGTTTTCCCGAAAGCCCCGCTAATGCTCCGATTTTTAGCGGCGTTTTACCAAAAGCG
1 TTTTACGGCATTTTACCAAAAGCCCCGCTAATGCTCCGATTTTTAGCGGCGTTTTACCAAAAGCG
* * * *
39665642 CCGCTAATACTCCGGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTCAGT
66 CCGCTAATACTCCGGTTTTTAGCAGCATTTTACAAAAAACGCCGCTAATGCTTCAGT
* ***
39665699 TTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCTC-ATTTTTAGCGGCGTTTTTGGTAAAA
1 TTTTA-CGGCATTTTACCAAAAGCCCCGCTAATGCTC-CGATTTTTAGCGGCG-TTTTACCAAAA
* * * * *
39665763 -CGCCGCTATTGCT-CTGTTTTTAGCAGCATTTTAACAAAAAATGCCGCTATTGCT
63 GCGCCGCTAATACTCCGGTTTTTAGCAGCATTTT-ACAAAAAACGCCGCTAATGCT
39665817 CTATGTTTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
122 21 0.21
123 68 0.69
124 9 0.09
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (122 bp):
TTTTACGGCATTTTACCAAAAGCCCCGCTAATGCTCCGATTTTTAGCGGCGTTTTACCAAAAGCG
CCGCTAATACTCCGGTTTTTAGCAGCATTTTACAAAAAACGCCGCTAATGCTTCAGT
Found at i:39665864 original size:12 final size:12
Alignment explanation
Indices: 39665849--39665874 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39665839 TGTTTTTGGT
39665849 AAAACGCCGCTA
1 AAAACGCCGCTA
39665861 AAAACGCCGCTA
1 AAAACGCCGCTA
39665873 AA
1 AA
39665875 GCCCTGTTTT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:39666524 original size:301 final size:301
Alignment explanation
Indices: 39665982--39666538 Score: 985
Period size: 301 Copynumber: 1.9 Consensus size: 301
39665972 ATTTGAGTTC
39665982 TTTCCAGGTAAGTTAAAATCACATTGGTCCGGTCCATTTGTGATTCACCGATTTTATCCATACGG
1 TTTCCAGGTAAGTTAAAATCACATTGGTCCGGTCCATTTGTGATTCACCGATTTTATCCATACGG
39666047 AGTTGTCAAACTTCAAAGTAAGAGAGGCAATTTTTTTAAGTTAATGCTCATCGCTCAAAACAATA
66 AGTTGTCAAACTTCAAAGTAAGAGAGGCAATTTTTTTAAGTTAATGCTCATCGCTCAAAACAATA
*
39666112 CTGGGGAGATAAAATTGAAAGGGATCAAATCTAATTCATTTTATCAGATGATTAATTTTTCTTGT
131 CTGGGGAGATAAAATTGAAAGGGATCAAATCTAATTCATTTTATCAGATGATTAATTTTTCTTAT
39666177 TTTCCTTTTTAAATAAATCATTTAGGGTATATTTTTGGGATTAGTATGTTTTAATAAATTCGAAG
196 TTTCCTTTTTAAATAAATCATTTAGGGTATATTTTTGGGATTAGTATGTTTTAATAAATTCGAAG
39666242 CAGGTCAGCAAGTCTTGTTATTCAATTCCAAATTAAGGTTT
261 CAGGTCAGCAAGTCTTGTTATTCAATTCCAAATTAAGGTTT
*
39666283 TTTCCAGGTAAGTTAAAATCACATTGGTTCGGTCCATTTGTGATTCACCGATTTTATCCATACGG
1 TTTCCAGGTAAGTTAAAATCACATTGGTCCGGTCCATTTGTGATTCACCGATTTTATCCATACGG
* * *
39666348 AGTTGTCGAACTTCAAAGTAAGAGAGGTAATTTTTTTGAGTTAATGCTCAAT-GCTCAAAACAAT
66 AGTTGTCAAACTTCAAAGTAAGAGAGGCAATTTTTTTAAGTTAATGCTC-ATCGCTCAAAACAAT
* **
39666412 ACTGGGGAGATAAAATTGAACA-GGATCATATCTCGTTCA-TTTATCAGATGATTAATTTTTCTT
130 ACTGGGGAGATAAAATTGAA-AGGGATCAAATCTAATTCATTTTATCAGATGATTAATTTTTCTT
*
39666475 ATTTTCCTTTTTAAATAAATTATTTAGGGTATATTTTTTGGGATTAGTATGTTTTAATAAATTC
194 ATTTTCCTTTTTAAATAAATCATTTAGGGTATA-TTTTTGGGATTAGTATGTTTTAATAAATTC
39666539 TGTCTAAGAG
Statistics
Matches: 244, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
300 55 0.23
301 186 0.76
302 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (301 bp):
TTTCCAGGTAAGTTAAAATCACATTGGTCCGGTCCATTTGTGATTCACCGATTTTATCCATACGG
AGTTGTCAAACTTCAAAGTAAGAGAGGCAATTTTTTTAAGTTAATGCTCATCGCTCAAAACAATA
CTGGGGAGATAAAATTGAAAGGGATCAAATCTAATTCATTTTATCAGATGATTAATTTTTCTTAT
TTTCCTTTTTAAATAAATCATTTAGGGTATATTTTTGGGATTAGTATGTTTTAATAAATTCGAAG
CAGGTCAGCAAGTCTTGTTATTCAATTCCAAATTAAGGTTT
Found at i:39670659 original size:22 final size:22
Alignment explanation
Indices: 39670633--39670677 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39670623 ATTATGTGTA
39670633 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
39670655 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
39670677 T
1 T
39670678 GGATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:39672707 original size:28 final size:27
Alignment explanation
Indices: 39672609--39672705 Score: 95
Period size: 28 Copynumber: 3.5 Consensus size: 27
39672599 TATATATGAC
* *
39672609 CCACTAGGCCCAATCTCTTTCATATGG
1 CCACTAGGCCCAATCACATTCATATGG
* * * *
39672636 CCCATTAGGCCCATTCACATTTATGTGG
1 -CCACTAGGCCCAATCACATTCATATGG
* *
39672664 CCTATTAGGCCCAAATCACATTCATACGG
1 CC-ACTAGGCCC-AATCACATTCATATGG
39672693 CCACTAGGCCCAA
1 CCACTAGGCCCAA
39672706 ATAACATTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 4 0.07
28 38 0.68
29 14 0.25
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (27 bp):
CCACTAGGCCCAATCACATTCATATGG
Found at i:39681357 original size:89 final size:89
Alignment explanation
Indices: 39681206--39681383 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
39681196 TCTTGATTCG
39681206 GTAGATTTTTAATCATTTTAACTTGGTTATATGTGGTATGTACTTTGGAGTGTCAAATGAATTGT
1 GTAGATTTTTAATCATTTTAACTTGGTTATATGTGGTATGTACTTTGGAGTGTCAAATGAATTGT
39681271 AATACCAAGTGTGTTTGAATTATA
66 AATACCAAGTGTGTTTGAATTATA
39681295 GTAGATTTTTAATCATTTTAACTTGGTTATATGTGGTATGTACTTTGGAGTGTCAAATGAATTGT
1 GTAGATTTTTAATCATTTTAACTTGGTTATATGTGGTATGTACTTTGGAGTGTCAAATGAATTGT
39681360 AATACCAAGTGTGTTTGAATTATA
66 AATACCAAGTGTGTTTGAATTATA
39681384 ATGATTATGG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (89 bp):
GTAGATTTTTAATCATTTTAACTTGGTTATATGTGGTATGTACTTTGGAGTGTCAAATGAATTGT
AATACCAAGTGTGTTTGAATTATA
Found at i:39681765 original size:7 final size:7
Alignment explanation
Indices: 39681755--39681788 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39681745 TACCACGAAT
*
39681755 ATGTGAT
1 ATGTGAG
*
39681762 ATGTAAG
1 ATGTGAG
39681769 ATGTGAG
1 ATGTGAG
39681776 ATGTGAG
1 ATGTGAG
39681783 ATGTGA
1 ATGTGA
39681789 TGACGAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (7 bp):
ATGTGAG
Found at i:39684713 original size:49 final size:48
Alignment explanation
Indices: 39684628--39684830 Score: 155
Period size: 49 Copynumber: 4.2 Consensus size: 48
39684618 TTCCAAACAT
* * * * *
39684628 GGTCTTACATTGACTCTC-ACATCTAAGTCGATGCCATGTCCCAGACA
1 GGTCTTACAATGACTTTCTACATCGAGGCCGATGCCATGTCCCAGACA
* *
39684675 GGTCTTACAATGACTTTCATACATCGAGGCCGATGCCATTTCCCAAACA
1 GGTCTTACAATGACTTTC-TACATCGAGGCCGATGCCATGTCCCAGACA
* * * * *
39684724 GGTCTTACAGTGGCTTT-TACTTATCTG-TGTCGATGGCATGTCCCAGACA
1 GGTCTTACAATGACTTTCTAC--ATC-GAGGCCGATGCCATGTCCCAGACA
* * **
39684773 GGTCTTAC-ATTAGCTTCCGTATC-TTTAGGCCGATGCCATGTCCCAGACA
1 GGTCTTACAATGA-CTTTC-TA-CATCGAGGCCGATGCCATGTCCCAGACA
*
39684822 AGTCTTACA
1 GGTCTTACA
39684831 CAGGCTCCCA
Statistics
Matches: 121, Mismatches: 24, Indels: 19
0.74 0.15 0.12
Matches are distributed among these distances:
47 19 0.16
48 1 0.01
49 97 0.80
50 1 0.01
51 2 0.02
52 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (48 bp):
GGTCTTACAATGACTTTCTACATCGAGGCCGATGCCATGTCCCAGACA
Found at i:39684803 original size:98 final size:98
Alignment explanation
Indices: 39684654--39684830 Score: 241
Period size: 98 Copynumber: 1.8 Consensus size: 98
39684644 TCACATCTAA
* *
39684654 GTCGATGCCATGTCCCAGACAGGTCTTACAATGACTTTCATACATCGAGGCCGATGCCATTTCCC
1 GTCGATGCCATGTCCCAGACAGGTCTTACAATGACTTCCATACATCGAGGCCGATGCCATGTCCC
*
39684719 AAACAGGTCTTACAGTGGCTTTTACTTATCTGT
66 AAACAAGTCTTACAGTGGCTTTTACTTATCTGT
* * * **
39684752 GTCGATGGCATGTCCCAGACAGGTCTTAC-ATTAGCTTCCGTATC-TTTAGGCCGATGCCATGTC
1 GTCGATGCCATGTCCCAGACAGGTCTTACAATGA-CTTCCATA-CATCGAGGCCGATGCCATGTC
*
39684815 CCAGACAAGTCTTACA
64 CCAAACAAGTCTTACA
39684831 CAGGCTCCCA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
97 3 0.04
98 64 0.94
99 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (98 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACAATGACTTCCATACATCGAGGCCGATGCCATGTCCC
AAACAAGTCTTACAGTGGCTTTTACTTATCTGT
Found at i:39684846 original size:98 final size:98
Alignment explanation
Indices: 39684654--39684879 Score: 224
Period size: 98 Copynumber: 2.3 Consensus size: 98
39684644 TCACATCTAA
* *
39684654 GTCGATGCCATGTCCCAGACAGGTCTTACAATGACTTTCATACATCGAGGCCGATGCCATTTCCC
1 GTCGATGCCATGTCCCAGACAGGTCTTACAATGACTTCCATACATCGAGGCCGATGCCATGTCCC
* ** ***
39684719 AAACAGGTCTTACAGTGGCTTTTACTTATCTGT
66 AAACAAGTCTTACACAGGCTCCCACTTATCTGT
* * * **
39684752 GTCGATGGCATGTCCCAGACAGGTCTTAC-ATTAGCTTCCGTATC-TTTAGGCCGATGCCATGTC
1 GTCGATGCCATGTCCCAGACAGGTCTTACAATGA-CTTCCATA-CATCGAGGCCGATGCCATGTC
* * **
39684815 CCAGACAAGTCTTACACAGGCTCCCATTTATCAAT
64 CCAAACAAGTCTTACACAGGCTCCCACTTATCTGT
** *
39684850 G-CTGATGCCATACCCCAGACAGGTTTTACA
1 GTC-GATGCCATGTCCCAGACAGGTCTTACA
39684880 CTAGCACACT
Statistics
Matches: 103, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
97 4 0.04
98 98 0.95
99 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (98 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACAATGACTTCCATACATCGAGGCCGATGCCATGTCCC
AAACAAGTCTTACACAGGCTCCCACTTATCTGT
Found at i:39686968 original size:40 final size:40
Alignment explanation
Indices: 39686883--39687023 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
39686873 AAACACATCA
* * * *
39686883 TTTTCATTTGTTACCCTTTTCAGTTAATATCCTTTTCAACA
1 TTTTCATTTGTTATCCTTTTCAGAT-ACATCCTTTTCAACC
* * *
39686924 TTTTCATTTGATATCCTTTTCGGGTACATCCTTTTCAACC
1 TTTTCATTTGTTATCCTTTTCAGATACATCCTTTTCAACC
* *
39686964 TTTTCATCTGTTATCCTTTTCAGATACTTCCTTTTCAACC
1 TTTTCATTTGTTATCCTTTTCAGATACATCCTTTTCAACC
*
39687004 TTTTAATTTGTTATCCTTTT
1 TTTTCATTTGTTATCCTTTT
39687024 TAACCCTTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 66 0.76
41 21 0.24
ACGTcount: A:0.18, C:0.23, G:0.06, T:0.52
Consensus pattern (40 bp):
TTTTCATTTGTTATCCTTTTCAGATACATCCTTTTCAACC
Found at i:39687022 original size:25 final size:25
Alignment explanation
Indices: 39686992--39687073 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
39686982 TTCAGATACT
* *
39686992 TCCTTTTCAACCTTTTAATTTGTTA
1 TCCTTTTTAACCTTTTCATTTGTTA
*
39687017 TCCTTTTTAACCCTTTCATTTGTTA
1 TCCTTTTTAACCTTTTCATTTGTTA
39687042 TCCTTTTTAACCTTTTCATTT-TTA
1 TCCTTTTTAACCTTTTCATTTGTTA
39687066 TCCTTTTT
1 TCCTTTTT
39687074 GGATAACTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 11 0.21
25 42 0.79
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (25 bp):
TCCTTTTTAACCTTTTCATTTGTTA
Found at i:39688484 original size:16 final size:17
Alignment explanation
Indices: 39688465--39688503 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
39688455 AGAATTAAAC
39688465 TTAACATTAA-CATTCA
1 TTAACATTAAGCATTCA
39688481 TTAA-ATTAAGCATTCA
1 TTAACATTAAGCATTCA
*
39688497 ATAACAT
1 TTAACAT
39688504 GCTTCCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 13 0.65
17 2 0.10
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAACATTAAGCATTCA
Found at i:39698786 original size:55 final size:56
Alignment explanation
Indices: 39698717--39698839 Score: 151
Period size: 55 Copynumber: 2.2 Consensus size: 56
39698707 CGATATGGCC
* * *
39698717 GTGGTTGAGCCTGCCAAAACAACACAGGCATGCGACATGCCCGTGTGGAAGAA-CA
1 GTGGTCGAGCCTGCCAAAACAACACAGGCATGCGACACGCCCATGTGGAAGAATCA
** * * *
39698772 GTGGTCGAGCCTGCCAAAACTGCACGGGCGTTCGACACGCCCATGTGGAAGAATCA
1 GTGGTCGAGCCTGCCAAAACAACACAGGCATGCGACACGCCCATGTGGAAGAATCA
*
39698828 -TGGTCGAACCTG
1 GTGGTCGAGCCTG
39698840 TTAAATTAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 56 0.97
56 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (56 bp):
GTGGTCGAGCCTGCCAAAACAACACAGGCATGCGACACGCCCATGTGGAAGAATCA
Found at i:39698857 original size:55 final size:56
Alignment explanation
Indices: 39698717--39698858 Score: 139
Period size: 55 Copynumber: 2.6 Consensus size: 56
39698707 CGATATGGCC
* * * * *
39698717 GTGGTTGAGCCTGCCAAAAC-AACACAGGCATGCGACATGCCCGTGTGGAAGAACA
1 GTGGTCGAACCTGCCAAAACTAACACAGGCGTGCGACACGCCCATGTGGAAGAACA
* * * *
39698772 GTGGTCGAGCCTGCCAAAACT-GCACGGGCGTTCGACACGCCCATGTGGAAGAATCA
1 GTGGTCGAACCTGCCAAAACTAACACAGGCGTGCGACACGCCCATGTGGAAGAA-CA
** *
39698828 -TGGTCGAACCTG-TTAAATTAACACAGGCGTG
1 GTGGTCGAACCTGCCAAAACTAACACAGGCGTG
39698859 GGGCTTGCAC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
54 4 0.06
55 64 0.91
56 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.29, T:0.18
Consensus pattern (56 bp):
GTGGTCGAACCTGCCAAAACTAACACAGGCGTGCGACACGCCCATGTGGAAGAACA
Found at i:39703999 original size:15 final size:15
Alignment explanation
Indices: 39703981--39704027 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
39703971 TATATTATAT
39703981 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * * *
39703996 TTCAATTAAAATGAT
1 TTCAATCAATATAAA
39704011 TTCAATCAATATAAA
1 TTCAATCAATATAAA
39704026 TT
1 TT
39704028 TGATAAATTC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:39705102 original size:13 final size:14
Alignment explanation
Indices: 39705084--39705112 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39705074 GATTAACTTC
39705084 ATAAATATTTT-TA
1 ATAAATATTTTCTA
39705097 ATAAATATTTTCTA
1 ATAAATATTTTCTA
39705111 AT
1 AT
39705113 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:39712482 original size:40 final size:41
Alignment explanation
Indices: 39712392--39712520 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 41
39712382 AAACACACCA
* * ** * * * *
39712392 TTTTCATTTGTTACCCTTTTTGGATAATATCCTTTACAGCA
1 TTTTCATTTGATATCCTTTTCAGATAACATCCTTTTCAACC
39712433 TTTTCATTTGATATCCTTTTC-GA-ATACATCCTTTTCAACC
1 TTTTCATTTGATATCCTTTTCAGATA-ACATCCTTTTCAACC
* * *
39712473 TTTTTATTTGCTATCCTTTTCAGATAACTTCCTTTTCAACC
1 TTTTCATTTGATATCCTTTTCAGATAACATCCTTTTCAACC
39712514 TTTTCAT
1 TTTTCAT
39712521 GGATTCAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 32 0.43
41 40 0.54
42 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.50
Consensus pattern (41 bp):
TTTTCATTTGATATCCTTTTCAGATAACATCCTTTTCAACC
Found at i:39715043 original size:21 final size:21
Alignment explanation
Indices: 39715019--39715065 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39715009 ACAATTATTG
*
39715019 TAATTGTGA-TTTGAGTTCTTA
1 TAATTGT-ATTTTAAGTTCTTA
*
39715040 TAATTGTATTTTAAGTTCTTT
1 TAATTGTATTTTAAGTTCTTA
39715061 TAATT
1 TAATT
39715066 TAGTTGGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (21 bp):
TAATTGTATTTTAAGTTCTTA
Found at i:39718030 original size:29 final size:28
Alignment explanation
Indices: 39717989--39718068 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 28
39717979 GACTGTAAAA
39717989 GTGATTGGGCCTAGTGGGCCATAT-AGAT
1 GTGATTGGGCCTAGTGGGCCATATGA-AT
*
39718017 GTGATTTGGGCCTAATGGGCCATATGAAT
1 GTGA-TTGGGCCTAGTGGGCCATATGAAT
*
39718046 GAGATTGGGCCTAGTGGGCCATA
1 GTGATTGGGCCTAGTGGGCCATA
39718069 AGCATGTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
28 22 0.47
29 24 0.51
30 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.28
Consensus pattern (28 bp):
GTGATTGGGCCTAGTGGGCCATATGAAT
Found at i:39725086 original size:47 final size:47
Alignment explanation
Indices: 39725014--39725238 Score: 193
Period size: 46 Copynumber: 4.9 Consensus size: 47
39725004 TCACTTGTGT
* * *
39725014 GAGCTAGAGTAAG-CCATGTCTGGGACATGCATTGG-ATACATTATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATACA-GATGA
* **
39725060 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATACAGATGA
* *
39725108 GTGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCT-CAAGACAT-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATAC-AG--ATGA
* * *
39725155 -AGCTAGTATAAGA-CATGTTTGGGACATGCATCGAC-TACGAGAT-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATAC-AGATGA
*
39725199 -TG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATA
1 GAGCT-AGTGTAAGACCATGTCTGGGACAT-GCATCGGCATA
39725239 GATATACTAT
Statistics
Matches: 149, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 12 0.08
45 14 0.09
46 64 0.43
47 30 0.20
48 25 0.17
49 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (47 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATACAGATGA
Found at i:39725160 original size:46 final size:47
Alignment explanation
Indices: 39725061--39725275 Score: 176
Period size: 46 Copynumber: 4.6 Consensus size: 47
39725051 ACATTATGAG
* * *
39725061 AGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCAT-TGAGATGA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAAGAGAT-A
* *
39725108 GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGACATA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-AAGAGATA
* * * *
39725155 AGCTAGTATAAGA-CATGTTTGGGACAT-GCATC-GACTACGAGATA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAAGAGATA
* * * *
39725199 TG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGATATACTA
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTA-AGAGA-TA
* *
39725248 TAACTTGTGTAAGACCATG-CTGGGACAT
1 -AGCTAGTGTAAGACCATGTCTGGGACAT
39725276 AGAGTCGATG
Statistics
Matches: 135, Mismatches: 22, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 15 0.11
45 16 0.12
46 43 0.32
47 17 0.13
48 18 0.13
49 11 0.08
50 13 0.10
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAAGAGATA
Found at i:39725233 original size:92 final size:94
Alignment explanation
Indices: 39725061--39725235 Score: 245
Period size: 92 Copynumber: 1.9 Consensus size: 94
39725051 ACATTATGAG
* * *
39725061 AGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGATGAGTGCTAGTGTAAGACATG
1 AGCTAGTATAAGACCATGTTTGGGACATGGCATCGACATCGAGATGAGTGCTAGTGTAAGACATG
39725126 TCTGGGACATGCATCGGCCTCAAGACATA
66 TCTGGGACATGCATCGGCCTCAAGACATA
39725155 AGCTAGTATAAGA-CATGTTTGGGACAT-GCATCGAC-TACGAGAT-A-TG-TCAGTGTAAGACC
1 AGCTAGTATAAGACCATGTTTGGGACATGGCATCGACAT-CGAGATGAGTGCT-AGTGTAAGA-C
39725214 ATGTCTGGGACATGGCATCGGC
63 ATGTCTGGGACAT-GCATCGGC
39725236 ATAGATATAC
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
89 1 0.01
90 11 0.15
91 16 0.22
92 20 0.27
93 14 0.19
94 12 0.16
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (94 bp):
AGCTAGTATAAGACCATGTTTGGGACATGGCATCGACATCGAGATGAGTGCTAGTGTAAGACATG
TCTGGGACATGCATCGGCCTCAAGACATA
Found at i:39727597 original size:46 final size:46
Alignment explanation
Indices: 39727521--39727637 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
39727511 GACGAGTGCT
* *
39727521 AGTGTAAGACATGTTTGGGACATGTATCGGCCT-CAAGACG-TAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACAAGACGAT-AGCC
* * *
39727567 AGTGTAAGACATGTCTGGGACATGCGTCGGCTACAAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGACGATAGCC
*
39727613 AGTGTAAGACCATGTCTGTGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
39727638 GCTTCAACTT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 2 0.03
46 45 0.73
47 15 0.24
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGACGATAGCC
Found at i:39740572 original size:4 final size:4
Alignment explanation
Indices: 39740563--39740587 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39740553 ATATTTATAC
39740563 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
39740588 CACCTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:39741614 original size:8 final size:8
Alignment explanation
Indices: 39741597--39741647 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
39741587 GTAGATCGGC
39741597 AAAAGCTG
1 AAAAGCTG
*
39741605 AAATGCTG
1 AAAAGCTG
39741613 AAAAG-TCG
1 AAAAGCT-G
39741621 AAAAGCTG
1 AAAAGCTG
*
39741629 AAATGCTG
1 AAAAGCTG
*
39741637 AAAAGCCG
1 AAAAGCTG
39741645 AAA
1 AAA
39741648 GTTTGGCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 1 0.03
8 34 0.94
9 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.24, T:0.14
Consensus pattern (8 bp):
AAAAGCTG
Found at i:39741629 original size:24 final size:24
Alignment explanation
Indices: 39741597--39741647 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
39741587 GTAGATCGGC
*
39741597 AAAAGCTGAAATGCTGAAAAGTCG
1 AAAAGCTGAAATGCTGAAAAGCCG
39741621 AAAAGCTGAAATGCTGAAAAGCCG
1 AAAAGCTGAAATGCTGAAAAGCCG
39741645 AAA
1 AAA
39741648 GTTTGGCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.14, G:0.24, T:0.14
Consensus pattern (24 bp):
AAAAGCTGAAATGCTGAAAAGCCG
Found at i:39741901 original size:29 final size:29
Alignment explanation
Indices: 39741859--39741974 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
39741849 GCGAGCATGA
*
39741859 ATATGAATGTGATTTGGGCCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
*
39741888 ATATAAATGTGATTTGGGTCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
** * * * *
39741917 ATATAAATGCAAATTAGGCCTAATCGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
* *
39741946 ATACAAATGTGA-TTGGGCCTGGTGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
39741974 A
1 A
39741975 GATACAGGTA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 13 0.18
29 58 0.82
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTGATGGGCC
Found at i:39742284 original size:26 final size:27
Alignment explanation
Indices: 39742255--39742309 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
39742245 AAACCCATAA
* * *
39742255 TAAAGG-AAAAATTATCAAAATGCCCC
1 TAAAGGCAAAAATGACCAAAATACCCC
*
39742281 TAAAGGCGAAAATGACCAAAATACCCC
1 TAAAGGCAAAAATGACCAAAATACCCC
39742308 TA
1 TA
39742310 TACGTTGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (27 bp):
TAAAGGCAAAAATGACCAAAATACCCC
Found at i:39742365 original size:11 final size:11
Alignment explanation
Indices: 39742349--39742373 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39742339 TATGTATATC
39742349 TACTGCATACA
1 TACTGCATACA
39742360 TACTGCATACA
1 TACTGCATACA
39742371 TAC
1 TAC
39742374 GATATTCTGT
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:0.28, G:0.08, T:0.28
Consensus pattern (11 bp):
TACTGCATACA
Found at i:39745737 original size:47 final size:44
Alignment explanation
Indices: 39745542--39745762 Score: 160
Period size: 46 Copynumber: 4.7 Consensus size: 44
39745532 CATTTGTGAG
* * *
39745542 AGCTAGTGTAAGACCATGTCTGCGACATGGCATCGGAATTGAGACGAGT
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC-GACTTGAGA-TA-T
* *
39745591 -GCTATTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGACGTA-
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGACTT-GAGA--TAT
* * ** *
39745636 AGCCAGTGTAAGACATGTCTGGGACATGCGTCGACTACAAGATGGT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGACT-TGAGAT-AT
*
39745682 AG-TCAGTGTAAGACCATGTCTGGGACATGGCTTCGACTTGAGATAT
1 AGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTTGAGATAT
* *
39745728 ACGCTAGTGTAAGATCGTGTCTGGGATATGACATC
1 A-GCTAGTGTAAGA-CATGTCTGGGACATG-CATC
39745763 AGCATCTTAC
Statistics
Matches: 138, Mismatches: 22, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
44 1 0.01
45 3 0.02
46 57 0.41
47 57 0.41
48 20 0.14
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (44 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGACTTGAGATAT
Found at i:39748434 original size:19 final size:20
Alignment explanation
Indices: 39748395--39748435 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39748385 TACAATCTAG
39748395 TAGCGGAAAAGTGATTTTTT
1 TAGCGGAAAAGTGATTTTTT
39748415 TAGCGGAAAAGTGATTTTTT
1 TAGCGGAAAAGTGATTTTTT
39748435 T
1 T
39748436 TTACTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.41
Consensus pattern (20 bp):
TAGCGGAAAAGTGATTTTTT
Found at i:39749086 original size:45 final size:45
Alignment explanation
Indices: 39749020--39749216 Score: 204
Period size: 45 Copynumber: 4.4 Consensus size: 45
39749010 CTGGTTTCAT
* *
39749020 AGATAAAATCTGCCACTAGGCTGTGGATGCACAACAAAAATTCAG-
1 AGATAAAACCTGCCACTAGGCTGTGGATACACAACAAAAATTC-GC
* * * *
39749065 AGATGAAACCTGTCACTAGGCTGTGGGTACACAGC-AAAATATCGC
1 AGATAAAACCTGCCACTAGGCTGTGGATACACAACAAAAAT-TCGC
** *
39749110 AGATAAAATTTGCCACTAGGCTGTGAATACACAACAAAAATTCGC
1 AGATAAAACCTGCCACTAGGCTGTGGATACACAACAAAAATTCGC
* * * * *
39749155 AGATGAAACCTGTCACT-GGCTGTGGGTACACAGC-AAAATATCAC
1 AGATAAAACCTGCCACTAGGCTGTGGATACACAACAAAAAT-TCGC
*
39749199 AGATAAAATCTGCCACTA
1 AGATAAAACCTGCCACTA
39749217 CATTGTAGAT
Statistics
Matches: 123, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
43 5 0.04
44 37 0.30
45 76 0.62
46 5 0.04
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (45 bp):
AGATAAAACCTGCCACTAGGCTGTGGATACACAACAAAAATTCGC
Found at i:39749143 original size:90 final size:89
Alignment explanation
Indices: 39749020--39749216 Score: 333
Period size: 90 Copynumber: 2.2 Consensus size: 89
39749010 CTGGTTTCAT
* *
39749020 AGATAAAATCTGCCACTAGGCTGTGGATGCACAACAAAAATTCAG-AGATGAAACCTGTCACTAG
1 AGATAAAATCTGCCACTAGGCTGTGAATACACAACAAAAATTC-GCAGATGAAACCTGTCACT-G
*
39749084 GCTGTGGGTACACAGCAAAATATCGC
64 GCTGTGGGTACACAGCAAAATATCAC
*
39749110 AGATAAAATTTGCCACTAGGCTGTGAATACACAACAAAAATTCGCAGATGAAACCTGTCACTGGC
1 AGATAAAATCTGCCACTAGGCTGTGAATACACAACAAAAATTCGCAGATGAAACCTGTCACTGGC
39749175 TGTGGGTACACAGCAAAATATCAC
66 TGTGGGTACACAGCAAAATATCAC
39749199 AGATAAAATCTGCCACTA
1 AGATAAAATCTGCCACTA
39749217 CATTGTAGAT
Statistics
Matches: 101, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
89 44 0.44
90 57 0.56
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (89 bp):
AGATAAAATCTGCCACTAGGCTGTGAATACACAACAAAAATTCGCAGATGAAACCTGTCACTGGC
TGTGGGTACACAGCAAAATATCAC
Found at i:39749232 original size:89 final size:89
Alignment explanation
Indices: 39749020--39749234 Score: 326
Period size: 89 Copynumber: 2.4 Consensus size: 89
39749010 CTGGTTTCAT
39749020 AGATAAAATCTGCCACTAGGCTGTGGATGCACAACAAAAATTCAGAGATGAAACCTGTCACTAGG
1 AGATAAAATCTGCCACTAGGCTGT-GATGCACAACAAAAATTCAGAGATGAAACCTGTCACTAGG
*
39749085 CTGTGGGTACACAGCAAAATATCGC
65 CTGTGGGTACACAGCAAAATATCAC
* *
39749110 AGATAAAATTTGCCACTAGGCTGTGAATACACAACAAAAATTC-GCAGATGAAACCTGTCACT-G
1 AGATAAAATCTGCCACTAGGCTGTG-ATGCACAACAAAAATTCAG-AGATGAAACCTGTCACTAG
39749173 GCTGTGGGTACACAGCAAAATATCAC
64 GCTGTGGGTACACAGCAAAATATCAC
***
39749199 AGATAAAATCTGCCACTACATTGTAGATGCACAACA
1 AGATAAAATCTGCCACTAGGCTGT-GATGCACAACA
39749235 TATTTGCAGG
Statistics
Matches: 114, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
89 57 0.50
90 57 0.50
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (89 bp):
AGATAAAATCTGCCACTAGGCTGTGATGCACAACAAAAATTCAGAGATGAAACCTGTCACTAGGC
TGTGGGTACACAGCAAAATATCAC
Found at i:39749780 original size:28 final size:27
Alignment explanation
Indices: 39749748--39749881 Score: 101
Period size: 28 Copynumber: 4.8 Consensus size: 27
39749738 AATTGTGGGT
* **
39749748 AAATTTGTAAAATTTGGAAAATAAGGGA
1 AAATTTGTAAAATCTAAAAAAT-AGGGA
39749776 AAATTTGTAAAATCTAAAAAATAGGGAA
1 AAATTTGTAAAATCTAAAAAATAGGG-A
** * *
39749804 AAAACTATAAAATCTAAAAAAATATAGGCA
1 AAATTTGTAAAATCT--AAAAA-ATAGGGA
* *
39749834 AAA-TTATAAAATCCAAAAAATAGGGGCA
1 AAATTTGTAAAATCTAAAAAATA-GGG-A
*
39749862 AAA-TTATAAAATCTAAAAAA
1 AAATTTGTAAAATCTAAAAAA
39749882 CAAGAAACAC
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
26 3 0.03
27 11 0.12
28 52 0.58
29 9 0.10
30 9 0.10
31 5 0.06
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.23
Consensus pattern (27 bp):
AAATTTGTAAAATCTAAAAAATAGGGA
Found at i:39749824 original size:29 final size:28
Alignment explanation
Indices: 39749765--39749881 Score: 123
Period size: 28 Copynumber: 4.1 Consensus size: 28
39749755 TAAAATTTGG
*
39749765 AAAATAAGGG-AAAATTTGTAAAATCT-AA
1 AAAAT-AGGGCAAAA-TTATAAAATCTAAA
* *
39749793 AAAATAGGGAAAAAACTATAAAATCTAAA
1 AAAATAGGG-CAAAATTATAAAATCTAAA
* *
39749822 AAAATATAGGCAAAATTATAAAATC-CAA
1 AAAATA-GGGCAAAATTATAAAATCTAAA
39749850 AAAATAGGGGCAAAATTATAAAATCTAAA
1 AAAATA-GGGCAAAATTATAAAATCTAAA
39749879 AAA
1 AAA
39749882 CAAGAAACAC
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
27 4 0.05
28 39 0.52
29 30 0.40
30 2 0.03
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.21
Consensus pattern (28 bp):
AAAATAGGGCAAAATTATAAAATCTAAA
Found at i:39749826 original size:57 final size:57
Alignment explanation
Indices: 39749765--39749881 Score: 164
Period size: 57 Copynumber: 2.1 Consensus size: 57
39749755 TAAAATTTGG
* * *
39749765 AAAATA-AGGGAAAATTTGTAAAATCTAAAAAATAGGGAAAAAACTATAAAATCTAAA
1 AAAATATAGGCAAAA-TTATAAAATCCAAAAAATAGGGAAAAAACTATAAAATCTAAA
** *
39749822 AAAATATAGGCAAAATTATAAAATCCAAAAAATAGGGGCAAAATTATAAAATCTAAA
1 AAAATATAGGCAAAATTATAAAATCCAAAAAATAGGGAAAAAACTATAAAATCTAAA
39749879 AAA
1 AAA
39749882 CAAGAAACAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 46 0.87
58 7 0.13
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.21
Consensus pattern (57 bp):
AAAATATAGGCAAAATTATAAAATCCAAAAAATAGGGAAAAAACTATAAAATCTAAA
Found at i:39751234 original size:38 final size:38
Alignment explanation
Indices: 39751183--39751259 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
39751173 ACAAAAATGG
39751183 TAAATTTTCAAAAATTTGACAGTATTATGAATTAGTAC
1 TAAATTTTCAAAAATTTGACAGTATTATGAATTAGTAC
39751221 TAAATTTTCAAAAATTTGACAGTATTATGAATTAGTAC
1 TAAATTTTCAAAAATTTGACAGTATTATGAATTAGTAC
39751259 T
1 T
39751260 TGGGCTAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (38 bp):
TAAATTTTCAAAAATTTGACAGTATTATGAATTAGTAC
Found at i:39756509 original size:34 final size:33
Alignment explanation
Indices: 39756471--39756551 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
39756461 TTAGCCCCTC
39756471 TTTCAGTAGCAGTAACAATCTGGG-CTTGAGCCCA
1 TTTCAGTA-CAGTAACAATCTGGGCCTT-AGCCCA
* * * *
39756505 TTTCAGTATTAGTGACAGTTTGGGCCTTAGCCCA
1 TTTCAGTA-CAGTAACAATCTGGGCCTTAGCCCA
39756539 TTTCAGTACAGTA
1 TTTCAGTACAGTA
39756552 TGCAAACACA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
33 3 0.08
34 33 0.85
35 3 0.08
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (33 bp):
TTTCAGTACAGTAACAATCTGGGCCTTAGCCCA
Found at i:39767337 original size:171 final size:170
Alignment explanation
Indices: 39767035--39767368 Score: 446
Period size: 171 Copynumber: 1.9 Consensus size: 170
39767025 TTTTGTAAGG
* * *
39767035 CATTTTCCAACTCTCACTAATCTTTCCCCCTTGCGCTGTTCTTCATCTTCCTTCTTCATCATCCA
1 CATTTTCCAACTCTCACCAATCTTT--CCCTAGCGCTGTACTTCATCTTCCTTCTTCATCATCCA
* *
39767100 GGTACTTTCCTCCTACTTCTTCTGTTCTTCATCTTTTAATTTTCTTTTTTCCTTAGCTTTTCGCA
64 GGTACTTTCCTCCTACTTCTTCTGTTCGTCATCTTTTAATTTTCTGTTTTCCTTAGCTTTTCGCA
*
39767165 TATCTTCTCTTCTCAGGGCTGCTGTTTCGTTTCGCTCTGTAA
129 TATCTTCTCTTCTCAGGGCTGCTGTTTCATTTCGCTCTGTAA
* *
39767207 CATTTTCCAACTCTCACCAATCTTT-CCTAGC-C-GTACTTCATCTTCCTTCTTCTTCATCTAGG
1 CATTTTCCAACTCTCACCAATCTTTCCCTAGCGCTGTACTTCATCTTCCTTCTTCATCATCCAGG
* *
39767269 TAACTTTTTTCCTTCTACTTCTTCTGTTGGTCATCTTTT-ATTTTC-GTTTTCCTTAG-TGTCTG
66 T-AC---TTTCCTCCTACTTCTTCTGTTCGTCATCTTTTAATTTTCTGTTTTCCTTAGCT-T-T-
*
39767331 TCGCATATCTTCTCTTCTCAGGGCTGTTGTTTCATTTC
124 TCGCATATCTTCTCTTCTCAGGGCTGCTGTTTCATTTC
39767369 ACTTAAATCT
Statistics
Matches: 144, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
167 28 0.19
168 4 0.03
169 16 0.11
170 7 0.05
171 65 0.45
172 24 0.17
ACGTcount: A:0.13, C:0.29, G:0.10, T:0.48
Consensus pattern (170 bp):
CATTTTCCAACTCTCACCAATCTTTCCCTAGCGCTGTACTTCATCTTCCTTCTTCATCATCCAGG
TACTTTCCTCCTACTTCTTCTGTTCGTCATCTTTTAATTTTCTGTTTTCCTTAGCTTTTCGCATA
TCTTCTCTTCTCAGGGCTGCTGTTTCATTTCGCTCTGTAA
Found at i:39771276 original size:21 final size:21
Alignment explanation
Indices: 39771252--39771327 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
39771242 GTCTTGAATT
39771252 TGTTAGATATTGAATTTTTTA
1 TGTTAGATATTGAATTTTTTA
* * * *
39771273 TGTTTTAAGCTTGTTAAATTTATTA
1 TG--TT-AG-ATATTGAATTTTTTA
39771298 TGTTAGATATTGAATTTATTTA
1 TGTTAGATATTGAATTT-TTTA
*
39771320 -GTTGGATA
1 TGTTAGATA
39771328 ATGATATTGA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 17 0.41
22 5 0.12
23 4 0.10
24 2 0.05
25 13 0.32
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (21 bp):
TGTTAGATATTGAATTTTTTA
Found at i:39772592 original size:20 final size:20
Alignment explanation
Indices: 39772567--39772606 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39772557 ATAATTTAAA
39772567 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
39772587 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
39772607 GTAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:39796144 original size:129 final size:128
Alignment explanation
Indices: 39795860--39796394 Score: 741
Period size: 128 Copynumber: 4.2 Consensus size: 128
39795850 ATTACGCACA
** * * *
39795860 TGCCATACACTTTATAATATGAATAAATCTATTTATGTGATACACATGACAGACAATAACTAAAG
1 TGCCATACAC-TT-TAATACAAACAAATCCATTTATGTGATACACATGACAGACAATAACCAAAG
* * *
39795925 AAATCTAAACTTGTCATACTCTTTGATACAAACAATAATCATATTTCAACAAATAAATTCAAACC
64 AAATCCAAACTTGCCATACTCTTTGATACAAATAATAATCATATTTCAACAAATAAATTCAAACC
* ** *
39795990 TACCATACACTTTAATACAAACAAATCCATTTATGTGATGTACATGACAGACAATAGCCAAAGAA
1 TGCCATACACTTTAATACAAACAAATCCATTTATGTGATACACATGACAGACAATAACCAAAGAA
* * * *
39796055 ATCCGAACATGCCATACTCTTTGATACAAAAAAAAAATCATATTTCAACAAATAAATTCAAACC
66 ATCCAAACTTGCCATACTCTTTGATAC-AAATAATAATCATATTTCAACAAATAAATTCAAACC
* *
39796119 TGCCATACACTTTAATACAAACAAATCCATTTATTTGATACACATGACAGACAATAATCAAAGAA
1 TGCCATACACTTTAATACAAACAAATCCATTTATGTGATACACATGACAGACAATAACCAAAGAA
* * *
39796184 ATCTAAACTTGCCTTACTCTTTGATACAAATAATAATCATATTTCAACAAATAAATTCAAACA
66 ATCCAAACTTGCCATACTCTTTGATACAAATAATAATCATATTTCAACAAATAAATTCAAACC
* * * * *
39796247 TGCCATACACTTTAACACAAACAAATCCATTTATGTGATGCACGTGATAGACAATAA-CAAAAAA
1 TGCCATACACTTTAATACAAACAAATCCATTTATGTGATACACATGACAGACAATAACCAAAGAA
* *
39796311 ATCCAAACCTACCATACTCTTTGATACAAATAATAATCATATTTCAACAAATAAA-TCTAAACC
66 ATCCAAACTTGCCATACTCTTTGATACAAATAATAATCATATTTCAACAAATAAATTC-AAACC
** *
39796374 TATCATATACTTTAATACAAA
1 TGCCATACACTTTAATACAAA
39796395 AAAGAATCAT
Statistics
Matches: 360, Mismatches: 43, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
126 2 0.01
127 78 0.22
128 153 0.43
129 118 0.33
130 9 0.03
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (128 bp):
TGCCATACACTTTAATACAAACAAATCCATTTATGTGATACACATGACAGACAATAACCAAAGAA
ATCCAAACTTGCCATACTCTTTGATACAAATAATAATCATATTTCAACAAATAAATTCAAACC
Found at i:39796367 original size:54 final size:54
Alignment explanation
Indices: 39796302--39796405 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
39796292 GATAGACAAT
* * *
39796302 AACAAAAAAATCCAAACCTACCATACT-CTTTGATACAAATAATAATCATATTTC
1 AACAAAAAAATCCAAACCTACCATA-TACTTTAATACAAAAAAGAATCATATTTC
* * *
39796356 AACAAATAAATCTAAACCTATCATATACTTTAATACAAAAAAGAATCATA
1 AACAAAAAAATCCAAACCTACCATATACTTTAATACAAAAAAGAATCATA
39796406 AACCTATGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 42 0.98
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (54 bp):
AACAAAAAAATCCAAACCTACCATATACTTTAATACAAAAAAGAATCATATTTC
Found at i:39797206 original size:17 final size:16
Alignment explanation
Indices: 39797181--39797228 Score: 78
Period size: 17 Copynumber: 2.9 Consensus size: 16
39797171 GAAAAAGAAT
39797181 TATTTTTTAATTTTAA
1 TATTTTTTAATTTTAA
39797197 TATATTTTTAATATTTAA
1 TAT-TTTTTAAT-TTTAA
39797215 TATTTTTTAATTTT
1 TATTTTTTAATTTT
39797229 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.20
17 16 0.53
18 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTTAATTTTAA
Found at i:39807315 original size:39 final size:39
Alignment explanation
Indices: 39807269--39807603 Score: 483
Period size: 39 Copynumber: 8.6 Consensus size: 39
39807259 GCTCTGGTGA
*
39807269 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTAT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
*
39807308 GCTTCAGTCAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
*
39807347 GCTTCAGTCAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* * *
39807386 GCTTCAG-TCGACCTTTGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAG-CCTTCGGGCTTCCGTTTAGCACTTCTGT
* *
39807425 GCTTCAGTCAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* *
39807464 GCTTCAGTCAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* *
39807503 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* ** *
39807542 GCTTCAGCTAAACTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
* **
39807581 GCTTCAGCTAAACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
39807604 AGATCACGAA
Statistics
Matches: 278, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
38 1 0.00
39 276 0.99
40 1 0.00
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
Done.