Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 35 of 120
Found at i:9495456 original size:21 final size:22
Alignment explanation
Indices: 9495431--9495475 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
9495421 AAAATAATTT
9495431 TTAAAAAATATAAA-TTAAAAA
1 TTAAAAAATATAAAGTTAAAAA
* *
9495452 TTAAAAAATCTAAAGTTTAAAA
1 TTAAAAAATATAAAGTTAAAAA
9495474 TT
1 TT
9495476 CATAAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAAATATAAAGTTAAAAA
Found at i:9496362 original size:22 final size:22
Alignment explanation
Indices: 9496319--9496362 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
9496309 AAATGACAAC
* * *
9496319 AAAACAGTAAAAAAATAGCAGT
1 AAAACAATAAAAAAACAACAGT
*
9496341 AAAACAATAACAAAACAACAGT
1 AAAACAATAAAAAAACAACAGT
9496363 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAACAATAAAAAAACAACAGT
Found at i:9511378 original size:18 final size:20
Alignment explanation
Indices: 9511341--9511379 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9511331 TGGCTTGGTA
*
9511341 ATTAATTATTTTTTTGAATT
1 ATTAATTATTTTTATGAATT
9511361 ATTAATT-TTTTTAT-AATT
1 ATTAATTATTTTTATGAATT
9511379 A
1 A
9511380 AATAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTAATTATTTTTATGAATT
Found at i:9513596 original size:4 final size:4
Alignment explanation
Indices: 9513587--9513612 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9513577 GGAAAAAAAT
9513587 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
9513613 AAGATAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:9515150 original size:15 final size:15
Alignment explanation
Indices: 9515129--9515218 Score: 126
Period size: 15 Copynumber: 6.0 Consensus size: 15
9515119 AGGGCCCCTC
*
9515129 TGCTGAAGGATCCGA
1 TGCTGAAGGACCCGA
*
9515144 GGCTGAAGGACCCGA
1 TGCTGAAGGACCCGA
*
9515159 TACTGAAGGACCCGA
1 TGCTGAAGGACCCGA
9515174 TGCTGAAGGACCCGA
1 TGCTGAAGGACCCGA
* *
9515189 TGCCGATGGACCCGA
1 TGCTGAAGGACCCGA
*
9515204 TGTTGAAGGACCCGA
1 TGCTGAAGGACCCGA
9515219 AGGTGATGAC
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 65 1.00
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.14
Consensus pattern (15 bp):
TGCTGAAGGACCCGA
Found at i:9518050 original size:9 final size:9
Alignment explanation
Indices: 9518036--9518093 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
9518026 TTTGGTTAAA
9518036 AATTAACCG
1 AATTAACCG
9518045 AATTAACCG
1 AATTAACCG
*
9518054 AATTACCCG
1 AATTAACCG
*
9518063 AATTACCCG
1 AATTAACCG
*
9518072 AATTACCCG
1 AATTAACCG
*
9518081 AATTAACCA
1 AATTAACCG
9518090 AATT
1 AATT
9518094 GAATCACTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:9518063 original size:18 final size:18
Alignment explanation
Indices: 9518036--9518093 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
9518026 TTTGGTTAAA
*
9518036 AATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
*
9518054 AATTACCCGAATTACCCG
1 AATTACCCGAATTAACCG
*
9518072 AATTACCCGAATTAACCA
1 AATTACCCGAATTAACCG
9518090 AATT
1 AATT
9518094 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:9518245 original size:18 final size:18
Alignment explanation
Indices: 9518206--9518248 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
9518196 TATGATTGGG
**
9518206 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGAATAA
*
9518224 TTGGGTTGGGTTGAATAC
1 TTGGGTTGGGTTGAATAA
9518242 TTGGGTT
1 TTGGGTT
9518249 TAGATTGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.44, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGAATAA
Found at i:9519518 original size:14 final size:14
Alignment explanation
Indices: 9519499--9519547 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
9519489 CATGGCCGTG
9519499 TGTCACACACGAGC
1 TGTCACACACGAGC
*
9519513 TGTCACACA-AATG-
1 TGTCACACACGA-GC
*
9519526 TGTCACACACGTGC
1 TGTCACACACGAGC
9519540 TGTCACAC
1 TGTCACAC
9519548 GGTTGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (14 bp):
TGTCACACACGAGC
Found at i:9519616 original size:29 final size:29
Alignment explanation
Indices: 9519496--9519607 Score: 147
Period size: 29 Copynumber: 3.9 Consensus size: 29
9519486 CCACATGGCC
* **
9519496 GTGTGTCACACACGAGCTGTCACAC--AA
1 GTGTGTCACACACGGGCTGTCACACGGTT
* *
9519523 ATGTGTCACACACGTGCTGTCACACGGTT
1 GTGTGTCACACACGGGCTGTCACACGGTT
* *
9519552 GTGTGTCACACACGGGCTATCACATGGTT
1 GTGTGTCACACACGGGCTGTCACACGGTT
9519581 GTGTGTCACACACGGGCTGTCACACGG
1 GTGTGTCACACACGGGCTGTCACACGG
9519608 CCGCATGTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.32
29 50 0.68
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23
Consensus pattern (29 bp):
GTGTGTCACACACGGGCTGTCACACGGTT
Found at i:9527402 original size:30 final size:30
Alignment explanation
Indices: 9527358--9527415 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9527348 CACAGTCTGG
*
9527358 CACATGGGCGTGTGTCCAACCCATGTGGCT
1 CACACGGGCGTGTGTCCAACCCATGTGGCT
* * *
9527388 CACACGGGCTTGTGTCCAGCCCGTGTGG
1 CACACGGGCGTGTGTCCAACCCATGTGG
9527416 AAATGCTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.22
Consensus pattern (30 bp):
CACACGGGCGTGTGTCCAACCCATGTGGCT
Found at i:9529248 original size:6 final size:6
Alignment explanation
Indices: 9529239--9529292 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
9529229 TAAGTCTAAG
* *
9529239 AAAATA AAAATA AAGCAACTA AAAACA AAAATA AAGATA AAAAT- AAAATA
1 AAAATA AAAATA AA--AA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
9529289 AAAA
1 AAAA
9529293 CGAAATAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.12
6 27 0.68
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:9529510 original size:18 final size:18
Alignment explanation
Indices: 9529441--9529512 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 18
9529431 AAAAAGGAAA
* * *
9529441 AAAATAAAATAGATTAGT
1 AAAATAAAATAAATAAAT
9529459 AAAATAAAACTAAATAATAT
1 AAAATAAAA-TAAATAA-AT
9529479 AATAGATAATAATAAATAAAT
1 AA-A-ATAA-AATAAATAAAT
9529500 AAAATAAAATAAA
1 AAAATAAAATAAA
9529513 GAAAAGTGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 15 0.33
19 9 0.20
20 4 0.09
21 5 0.11
22 11 0.24
23 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAATAAAATAAATAAAT
Found at i:9541170 original size:48 final size:48
Alignment explanation
Indices: 9541111--9541358 Score: 158
Period size: 48 Copynumber: 5.0 Consensus size: 48
9541101 GAGTAAAGTG
9541111 ACCCTACTCCCAGACACATGGGGGAGGCTTATGAAAAGTAATAATATA
1 ACCCTACTCCCAGACACATGGGGGAGGCTTATGAAAAGTAATAATATA
* * * *
9541159 ACCCTGCTCCCAGATGA-ATAGGGGGAAGCTTATGGAAAGTAATATTATAAATAATATA
1 ACCCTACTCCCAGA-CACAT-GGGGGAGGCTTAT-G--A--AA-A--GT-AATAATATA
* * * * * * *
9541217 ACCCTACTCTCAAACACAT-GTGAAGACTTATGGAAAGTATTAATATA
1 ACCCTACTCCCAGACACATGGGGGAGGCTTATGAAAAGTAATAATATA
** * ** * ** *
9541264 GTCTTGTTCCCAGACGCATGATGGAGGCTTACGAAAAGTAATAATATA
1 ACCCTACTCCCAGACACATGGGGGAGGCTTATGAAAAGTAATAATATA
* * * * *
9541312 ACCCTACTCTCAAACACATGGGGAAGGCTTACGAAAAGTAACAATAT
1 ACCCTACTCCCAGACACATGGGGGAGGCTTATGAAAAGTAATAATAT
9541359 TCTTGTATTT
Statistics
Matches: 146, Mismatches: 41, Indels: 26
0.69 0.19 0.12
Matches are distributed among these distances:
47 19 0.13
48 73 0.50
49 13 0.09
50 2 0.01
51 2 0.01
52 1 0.01
54 2 0.01
55 2 0.01
56 8 0.05
57 2 0.01
58 22 0.15
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (48 bp):
ACCCTACTCCCAGACACATGGGGGAGGCTTATGAAAAGTAATAATATA
Found at i:9542823 original size:18 final size:18
Alignment explanation
Indices: 9542800--9542837 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9542790 ACTATCAGCG
9542800 CTAGCCCAAGCGAGAGCC
1 CTAGCCCAAGCGAGAGCC
*
9542818 CTAGCCCAAGCGGGAGCC
1 CTAGCCCAAGCGAGAGCC
9542836 CT
1 CT
9542838 GAGGAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (18 bp):
CTAGCCCAAGCGAGAGCC
Found at i:9547048 original size:9 final size:9
Alignment explanation
Indices: 9547024--9547060 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
9547014 TGGGTTTTCG
*
9547024 AATTCAAAT
1 AATTCGAAT
*
9547033 AACTCGAAT
1 AATTCGAAT
9547042 AATTCGAAT
1 AATTCGAAT
9547051 AATTCGAAT
1 AATTCGAAT
9547060 A
1 A
9547061 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:9549548 original size:23 final size:23
Alignment explanation
Indices: 9549500--9549548 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9549490 AAAAATGCTA
* **
9549500 TTTTCTCACTGTTTTGATGTTGT
1 TTTTCTCACTGATTTGATGTCAT
*
9549523 TTTTCTCACTGATTTGTTGTCAT
1 TTTTCTCACTGATTTGATGTCAT
9549546 TTT
1 TTT
9549549 ACTATAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.61
Consensus pattern (23 bp):
TTTTCTCACTGATTTGATGTCAT
Found at i:9554901 original size:20 final size:20
Alignment explanation
Indices: 9554864--9554900 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
9554854 GAAAAAATAA
9554864 GAAATATTTGGAAATTTTAG
1 GAAATATTTGGAAATTTTAG
*
9554884 GAAA-ATTTTGAAATTTT
1 GAAATATTTGGAAATTTT
9554901 TGGACTACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (20 bp):
GAAATATTTGGAAATTTTAG
Found at i:9556045 original size:40 final size:40
Alignment explanation
Indices: 9555958--9556067 Score: 105
Period size: 40 Copynumber: 2.8 Consensus size: 40
9555948 AGATAAATAG
* * ** *
9555958 AACACACCAGACAGAAGCTCATAAAAGCTGATTTAACTAA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCAA
* * * *
9555998 AATACACCAAACAGAAGCTCATAAGAGCTGGTCCACCCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCAA
* * *
9556038 AACACACC-AATAGAAGCTTATAGGAGCTGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGA
9556068 ACAGAAGCTC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
39 18 0.32
40 38 0.68
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (40 bp):
AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCAA
Found at i:9556075 original size:21 final size:21
Alignment explanation
Indices: 9556049--9556109 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
9556039 ACACACCAAT
* *
9556049 AGAAGCTTATAGGAGCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
* *
9556070 AGAAGCTCATAAGTGCTTAAC
1 AGAAGCTCATAAGAGCTGAAC
*
9556091 AAAAGCTCATAAGAGCTGA
1 AGAAGCTCATAAGAGCTGA
9556110 TCCACCCGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:9558782 original size:14 final size:15
Alignment explanation
Indices: 9558763--9558805 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
9558753 ATAAAATTAT
9558763 TAAATATATATATA-
1 TAAATATATATATAG
9558777 TAAATATATATATATG
1 TAAATATATATATA-G
*
9558793 TAAGTATATATAT
1 TAAATATATATAT
9558806 TTACAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.54
16 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
TAAATATATATATAG
Found at i:9558787 original size:16 final size:16
Alignment explanation
Indices: 9558766--9558805 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9558756 AAATTATTAA
9558766 ATATATATATATAAAT
1 ATATATATATATAAAT
* *
9558782 ATATATATATGTAAGT
1 ATATATATATATAAAT
9558798 ATATATAT
1 ATATATAT
9558806 TTACAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATATATATATAAAT
Found at i:9558948 original size:3 final size:3
Alignment explanation
Indices: 9558940--9558993 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
9558930 GTAAATAAAA
* *
9558940 AAT AAT AAT AAT AAGGT AAGT AAT AAT AAT AAT GAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
9558988 AAT AAT
1 AAT AAT
9558994 GCTAAAACTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.84
4 4 0.09
5 3 0.07
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9558990 original size:18 final size:18
Alignment explanation
Indices: 9558939--9558990 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
9558929 GGTAAATAAA
*
9558939 AAATAATAATAATAAGGT
1 AAATAATAATAATAATGT
*
9558957 AAGTAATAATAATAATG-
1 AAATAATAATAATAATGT
9558974 ACAATAATAATAATAAT
1 A-AATAATAATAATAAT
9558991 AATGCTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (18 bp):
AAATAATAATAATAATGT
Found at i:9562932 original size:21 final size:21
Alignment explanation
Indices: 9562878--9562980 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 21
9562868 ATCAGTATAT
*
9562878 GACACAT-AAGTGCCTGAAAC
1 GACACATAAAGTGCCTGATAC
* * *
9562898 GACATATGATGTGCCTGATAC
1 GACACATAAAGTGCCTGATAC
9562919 -AGCACATAAAGTGCCTGAGATAC
1 GA-CACATAAAGTGCCT--GATAC
9562942 GACACATAAAGTGCCTGATGTAC
1 GACACATAAAGTGCCTGA--TAC
9562965 GACACATAAAGTGCCT
1 GACACATAAAGTGCCT
9562981 TATTGGCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.10
21 24 0.34
23 38 0.54
24 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (21 bp):
GACACATAAAGTGCCTGATAC
Found at i:9562974 original size:46 final size:42
Alignment explanation
Indices: 9562878--9562980 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
9562868 ATCAGTATAT
* * *
9562878 GACACAT-AAGTGCCTGAAACGACATATGATGTGCCTGATAC
1 GACACATAAAGTGCCTGAAACGACACATAAAGTGCCTGATAC
9562919 -AGCACATAAAGTGCCTGAGATACGACACATAAAGTGCCTGATGTAC
1 GA-CACATAAAGTGCCTGA-A-ACGACACATAAAGTGCCTGA--TAC
9562965 GACACATAAAGTGCCT
1 GACACATAAAGTGCCT
9562981 TATTGGCAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
40 1 0.02
41 5 0.10
42 10 0.19
43 1 0.02
44 17 0.33
46 17 0.33
47 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (42 bp):
GACACATAAAGTGCCTGAAACGACACATAAAGTGCCTGATAC
Found at i:9563254 original size:36 final size:37
Alignment explanation
Indices: 9563176--9563272 Score: 92
Period size: 36 Copynumber: 2.6 Consensus size: 37
9563166 AACACATATA
* **
9563176 TTTCAAATCCACATTTCAATTC-AATTTCACTTTTTCAC
1 TTTC-AAT-CACAATTCAATTCAAATTTCACTTTCCCAC
*
9563214 TTTCAATCACAATTCAATTCAAATTT-ACTTTCCCAT
1 TTTCAATCACAATTCAATTCAAATTTCACTTTCCCAC
*
9563250 TTTCAAGTCA-ATATTCATTTCAA
1 TTTCAA-TCACA-ATTCAATTCAA
9563273 TTCCACACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
36 26 0.51
37 21 0.41
38 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.01, T:0.43
Consensus pattern (37 bp):
TTTCAATCACAATTCAATTCAAATTTCACTTTCCCAC
Found at i:9563346 original size:16 final size:17
Alignment explanation
Indices: 9563325--9563356 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9563315 TAATAATAAT
9563325 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
9563341 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
9563357 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:9569472 original size:16 final size:16
Alignment explanation
Indices: 9569451--9569485 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9569441 AGTCCTTGTA
9569451 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
9569467 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
9569483 ATT
1 ATT
9569486 AAAATTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:9573372 original size:66 final size:66
Alignment explanation
Indices: 9573291--9573423 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 66
9573281 GAATTCTCTT
** *
9573291 TTTGCACTCTATCCTCCTTGTGCTTATAATGTCTCTTCTTGCAAGTTTCTTAATAAAAAGAAAAG
1 TTTGCACTCTATCCTCCTCCTGCTTATAACGTCTCTTCTTGCAAGTTTCTTAATAAAAAGAAAAG
9573356 G
66 G
* * * *
9573357 TTTGCACTCTATCCTCGTCCTGCTTATCACGTCTCTTTTTGCAAGTTTCTTAATAAAGAGAAAAG
1 TTTGCACTCTATCCTCCTCCTGCTTATAACGTCTCTTCTTGCAAGTTTCTTAATAAAAAGAAAAG
9573422 G
66 G
9573423 T
1 T
9573424 GAGTTAATCT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (66 bp):
TTTGCACTCTATCCTCCTCCTGCTTATAACGTCTCTTCTTGCAAGTTTCTTAATAAAAAGAAAAG
G
Found at i:9579167 original size:93 final size:93
Alignment explanation
Indices: 9579054--9579330 Score: 437
Period size: 93 Copynumber: 3.0 Consensus size: 93
9579044 TCATGGTCCA
* *
9579054 CAGAAGAAATCATTTCAGAAGCAACCAGGCCCTCGCCACTGGGCTCAGTTTCTTTAGCTTGCATA
1 CAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAGTTTCTTTAGCTTGCATA
* *
9579119 AAATGTTCGGCATGAGTTGTAACATCTG
66 AAATGTTCAGCATGAGTTGTAACACCTG
* *
9579147 CAGAAGAAATCATTTGAGAAGCAACCTGGCCCTCACCACTGGGCTCAGTTTCTTTAGCTTGAATA
1 CAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAGTTTCTTTAGCTTGCATA
9579212 AAATGTTCAGCATGAGTTGTAACACCTG
66 AAATGTTCAGCATGAGTTGTAACACCTG
* * * *
9579240 CAGAAGAAATCATTTTAGAAGCAACCTGGGCCTCAACACTGGCCTCAGTTTCTTTAGCTTGCATA
1 CAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAGTTTCTTTAGCTTGCATA
** *
9579305 AAATGTTCCCCGTGAGTTGTAACACC
66 AAATGTTCAGCATGAGTTGTAACACC
9579331 ATGTAATGAC
Statistics
Matches: 170, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 170 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (93 bp):
CAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAGTTTCTTTAGCTTGCATA
AAATGTTCAGCATGAGTTGTAACACCTG
Found at i:9580793 original size:81 final size:81
Alignment explanation
Indices: 9580657--9580856 Score: 215
Period size: 81 Copynumber: 2.5 Consensus size: 81
9580647 CAGAAGGATA
** * * *
9580657 AGAACTTTCGGCAACACTACCAGCATTCAAACTACCCGCAAGCCTAACAGAAGTAGAACTCACTG
1 AGAACTTGAGGCAACACTACCAGCATTAAAACTAGCTGCAAGCCTAACAGAAGTAGAACTCACTG
* *** *
9580722 CAGCACTGGAAGCTTT
66 CAACACCCAAAGCATT
* * * * *
9580738 AGAACTTGAGGCAACGCTACCAGCATTAAAACAAGCTGC-AGCACTACCAGCAGTAGAACTCATT
1 AGAACTTGAGGCAACACTACCAGCATTAAAACTAGCTGCAAGC-CTAACAGAAGTAGAACTCACT
9580802 GCAACACCCAAAGCATT
65 GCAACACCCAAAGCATT
* *
9580819 AGAACTTGTA-GCAAAACTACCAGCATTTAAACTAGCTG
1 AGAACTTG-AGGCAACACTACCAGCATTAAAACTAGCTG
9580857 TAACACCATC
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
80 3 0.03
81 94 0.96
82 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (81 bp):
AGAACTTGAGGCAACACTACCAGCATTAAAACTAGCTGCAAGCCTAACAGAAGTAGAACTCACTG
CAACACCCAAAGCATT
Found at i:9580947 original size:27 final size:26
Alignment explanation
Indices: 9580878--9581000 Score: 72
Period size: 27 Copynumber: 4.6 Consensus size: 26
9580868 GCATTGATAA
*
9580878 CACTGGT-TTTCGAACTCCCTAAA-ATTC
1 CACTGGTGTTT-GAACTCGCTAAACA--C
* ** *
9580905 CACTGTTGTTCAAACTCGCTACGACAC
1 CACTGGTGTTTGAACTCGCTA-AACAC
* *
9580932 CACTGGTGTTTGAACTGGCTAAAGCAT
1 CACTGGTGTTTGAACTCGCTAAA-CAC
** *
9580959 CACTGGTACTTGAACTCACTAAAACAC
1 CACTGGTGTTTGAACTCGCT-AAACAC
9580986 CACTGG-GTGTTGAAC
1 CACTGGTGT-TTGAAC
9581001 GCACTGCAAC
Statistics
Matches: 72, Mismatches: 18, Indels: 12
0.71 0.18 0.12
Matches are distributed among these distances:
26 1 0.01
27 64 0.89
28 6 0.08
29 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (26 bp):
CACTGGTGTTTGAACTCGCTAAACAC
Found at i:9585173 original size:16 final size:16
Alignment explanation
Indices: 9585154--9585198 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
9585144 AATAGGGCCA
9585154 TAATGAAATAGAGATG
1 TAATGAAATAGAGATG
* *
9585170 TAATGAAATGGAGTTG
1 TAATGAAATAGAGATG
* *
9585186 TACTAAAATAGAG
1 TAATGAAATAGAG
9585199 TTATAATCAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (16 bp):
TAATGAAATAGAGATG
Found at i:9585199 original size:16 final size:16
Alignment explanation
Indices: 9585154--9585205 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
9585144 AATAGGGCCA
* *
9585154 TAATGAAATAGAGATG
1 TAATAAAATAGAGTTG
* *
9585170 TAATGAAATGGAGTTG
1 TAATAAAATAGAGTTG
* *
9585186 TACTAAAATAGAGTTA
1 TAATAAAATAGAGTTG
9585202 TAAT
1 TAAT
9585206 CAGTAATTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (16 bp):
TAATAAAATAGAGTTG
Found at i:9585802 original size:69 final size:68
Alignment explanation
Indices: 9585721--9585856 Score: 245
Period size: 69 Copynumber: 2.0 Consensus size: 68
9585711 ATACATTAAC
* *
9585721 AAAAAGTTACATGATCTCGTTAGCTTATATGCCATAATCTATATGTTAAATTTTATAGCATCAAA
1 AAAAAGTTACATGATCTCATTAGCTTATATGCCATAATCTATATGTTAAATTTTACAGCAT-AAA
9585786 AAAT
65 AAAT
9585790 AAAAAGTTACATGATCTCATTAGCTTATATGCCATAATCTATATGTTAAATTTTACAGCATAAAA
1 AAAAAGTTACATGATCTCATTAGCTTATATGCCATAATCTATATGTTAAATTTTACAGCATAAAA
9585855 AA
66 AA
9585857 GTTATAACAG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 6 0.09
69 59 0.91
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (68 bp):
AAAAAGTTACATGATCTCATTAGCTTATATGCCATAATCTATATGTTAAATTTTACAGCATAAAA
AAT
Found at i:9590333 original size:9 final size:9
Alignment explanation
Indices: 9590315--9590369 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
9590305 CGAAGAAACA
*
9590315 TCATCATCC
1 TCATCGTCC
9590324 TCATCGTCC
1 TCATCGTCC
* *
9590333 TCAACGTCG
1 TCATCGTCC
9590342 TCATCGTCC
1 TCATCGTCC
*
9590351 TCATCGTCT
1 TCATCGTCC
9590360 TCATCGTCC
1 TCATCGTCC
9590369 T
1 T
9590370 TTTTGCAACC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.15, C:0.40, G:0.11, T:0.35
Consensus pattern (9 bp):
TCATCGTCC
Found at i:9592910 original size:13 final size:13
Alignment explanation
Indices: 9592843--9592910 Score: 77
Period size: 13 Copynumber: 5.2 Consensus size: 13
9592833 ATTTAATGTG
9592843 TATTAAAACAA-TA
1 TATTAAAA-AAGTA
9592856 TATTAAAAAAGTA
1 TATTAAAAAAGTA
* *
9592869 TATTTATAATAGTA
1 TA-TTAAAAAAGTA
9592883 TATTAAAACAA-TA
1 TATTAAAA-AAGTA
9592896 TATTAAAAAAGTA
1 TATTAAAAAAGTA
9592909 TA
1 TA
9592911 CATACATGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
12 4 0.09
13 31 0.66
14 12 0.26
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (13 bp):
TATTAAAAAAGTA
Found at i:9593037 original size:182 final size:182
Alignment explanation
Indices: 9592725--9593388 Score: 1292
Period size: 182 Copynumber: 3.6 Consensus size: 182
9592715 TATATACTTA
*
9592725 TATATATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
1 TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
*
9592790 GGTAAGTATATTAAAATTTGTTATAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
66 GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
9592855 ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
131 ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
9592907 TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
1 TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
9592972 GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
66 GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
9593037 ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
131 ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
9593089 TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
1 TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
9593154 GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
66 GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
9593219 ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
131 ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
*
9593271 TATACATACATGTATTAAAATTAAATAAGCTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
1 TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
*
9593336 GGTAAGTATATTAAAATTTGTTATAATACATTAGGACACCAACATTTAATGTG
66 GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTG
9593389 NNNNNNNNNN
Statistics
Matches: 478, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 478 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (182 bp):
TATACATACATGTATTAAAATTAAATAAACTTTCATACATAGTTTTCTAGTATTTTATTAAAAAC
GGTAAGTATATTAAAATTTGTTACAATACATTAGGACACCAACATTTAATGTGTATTAAAACAAT
ATATTAAAAAAGTATATTTATAATAGTATATTAAAACAATATATTAAAAAAG
Found at i:9593092 original size:13 final size:13
Alignment explanation
Indices: 9593025--9593092 Score: 77
Period size: 13 Copynumber: 5.2 Consensus size: 13
9593015 ATTTAATGTG
9593025 TATTAAAACAA-TA
1 TATTAAAA-AAGTA
9593038 TATTAAAAAAGTA
1 TATTAAAAAAGTA
* *
9593051 TATTTATAATAGTA
1 TA-TTAAAAAAGTA
9593065 TATTAAAACAA-TA
1 TATTAAAA-AAGTA
9593078 TATTAAAAAAGTA
1 TATTAAAAAAGTA
9593091 TA
1 TA
9593093 CATACATGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
12 4 0.09
13 31 0.66
14 12 0.26
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (13 bp):
TATTAAAAAAGTA
Found at i:9593274 original size:13 final size:13
Alignment explanation
Indices: 9593207--9593274 Score: 77
Period size: 13 Copynumber: 5.2 Consensus size: 13
9593197 ATTTAATGTG
9593207 TATTAAAACAA-TA
1 TATTAAAA-AAGTA
9593220 TATTAAAAAAGTA
1 TATTAAAAAAGTA
* *
9593233 TATTTATAATAGTA
1 TA-TTAAAAAAGTA
9593247 TATTAAAACAA-TA
1 TATTAAAA-AAGTA
9593260 TATTAAAAAAGTA
1 TATTAAAAAAGTA
9593273 TA
1 TA
9593275 CATACATGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
12 4 0.09
13 31 0.66
14 12 0.26
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (13 bp):
TATTAAAAAAGTA
Found at i:9593961 original size:11 final size:11
Alignment explanation
Indices: 9593930--9593967 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
9593920 AGGCAACAAC
9593930 AACAGATTATA
1 AACAGATTATA
*
9593941 AAGAAGATTATA
1 AA-CAGATTATA
9593953 AACAGATTATA
1 AACAGATTATA
9593964 AACA
1 AACA
9593968 AAAGACATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (11 bp):
AACAGATTATA
Found at i:9596404 original size:21 final size:21
Alignment explanation
Indices: 9596378--9596423 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
9596368 GTTTCTAATT
*
9596378 TCACCGCTACAGTACCCAATC
1 TCACCGCTACAGTAACCAATC
*
9596399 TCACCGCTACAGTAACTAATC
1 TCACCGCTACAGTAACCAATC
9596420 TCAC
1 TCAC
9596424 TGCCACCGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.39, G:0.09, T:0.22
Consensus pattern (21 bp):
TCACCGCTACAGTAACCAATC
Found at i:9610474 original size:31 final size:34
Alignment explanation
Indices: 9610421--9610491 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 34
9610411 AGAGGATTTT
*
9610421 GATTTTTGGGTTTAAAAGGGGA-G-AAA-TAAAA
1 GATTTTTGGGGTTAAAAGGGGAGGAAAAGTAAAA
9610452 GATTTTTGGGAGTTAAAA-GGGAGGAAAAGTAAAA
1 GATTTTTGGG-GTTAAAAGGGGAGGAAAAGTAAAA
9610486 -ATTTTT
1 GATTTTT
9610492 TGAGGTAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 14 0.40
32 7 0.20
33 9 0.26
34 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (34 bp):
GATTTTTGGGGTTAAAAGGGGAGGAAAAGTAAAA
Found at i:9617754 original size:22 final size:21
Alignment explanation
Indices: 9617729--9617775 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
9617719 AGACTAATTT
*
9617729 AAATAATAAAAATCTAAAAAAC
1 AAAT-ATAAAAATATAAAAAAC
**
9617751 AAAT-TGTAAATATAAAAAAC
1 AAATATAAAAATATAAAAAAC
9617771 AAATA
1 AAATA
9617776 GAATGTCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.81
22 4 0.19
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATATAAAAATATAAAAAAC
Found at i:9620886 original size:3 final size:3
Alignment explanation
Indices: 9620878--9620907 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9620868 CTGATAAAGG
9620878 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
9620908 CTTAAGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:9622546 original size:20 final size:20
Alignment explanation
Indices: 9622523--9622633 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
9622513 GGTCGAGCCA
9622523 CCAGTAATGCAAATAAACTG
1 CCAGTAATGCAAATAAACTG
* * **
9622543 CCAGTAGTGTAGAA-AAGTTG
1 CCAGTAATGCA-AATAAACTG
* *
9622563 CCAGTATTGCAGATAAACTG
1 CCAGTAATGCAAATAAACTG
*** * * *
9622583 CCAGTAATG-TGGTCAAGTCA
1 CCAGTAATGCAAATAAACT-G
*
9622603 CCAGTGATGCAAATAAACTG
1 CCAGTAATGCAAATAAACTG
9622623 CCAGTAATGCA
1 CCAGTAATGCA
9622634 GACAAGGCTA
Statistics
Matches: 64, Mismatches: 23, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
19 6 0.09
20 52 0.81
21 6 0.09
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
CCAGTAATGCAAATAAACTG
Found at i:9622567 original size:40 final size:40
Alignment explanation
Indices: 9622521--9622631 Score: 141
Period size: 40 Copynumber: 2.8 Consensus size: 40
9622511 GTGGTCGAGC
*
9622521 CACCAGTAATGCAAATAAACTGCCAGTAGTGTAGAAAAGT
1 CACCAGTAATGCAAATAAACTGCCAGTAATGTAGAAAAGT
** * * * **
9622561 TGCCAGTATTGCAGATAAACTGCCAGTAATGTGGTCAAGT
1 CACCAGTAATGCAAATAAACTGCCAGTAATGTAGAAAAGT
*
9622601 CACCAGTGATGCAAATAAACTGCCAGTAATG
1 CACCAGTAATGCAAATAAACTGCCAGTAATG
9622632 CAGACAAGGC
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (40 bp):
CACCAGTAATGCAAATAAACTGCCAGTAATGTAGAAAAGT
Found at i:9625362 original size:31 final size:31
Alignment explanation
Indices: 9625292--9625746 Score: 569
Period size: 31 Copynumber: 14.7 Consensus size: 31
9625282 GTATATGTTT
* *
9625292 TATACATTGCCAAATTTGATTTGTTTATAGATA
1 TATACATTGCCGAATTTGATTTGTATATAG--A
* * * *
9625325 TATACATTGCCAAAATTGATTTTTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
9625356 TATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
9625387 TATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
9625418 TATACATTGCCGAATTTGATTTGTATAT-GA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * ** *
9625448 TTGTACATTGTCGAATTTGATTTGTATAGGGT
1 -TATACATTGCCGAATTTGATTTGTATATAGA
*
9625480 TATACATTGCCGAATTTGATTTGCATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * * *
9625511 TATACATTG-TGGATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
9625541 TATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
9625572 TATACGTTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
9625602 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
9625633 TATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
9625664 TATTCATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
9625694 TATACATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
9625725 TATATATTGCTGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
9625747 AGCATTGGAT
Statistics
Matches: 372, Mismatches: 45, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
30 89 0.24
31 254 0.68
32 1 0.00
33 28 0.08
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:9625557 original size:61 final size:61
Alignment explanation
Indices: 9625292--9625746 Score: 567
Period size: 61 Copynumber: 7.4 Consensus size: 61
9625282 GTATATGTTT
* * * * * * *
9625292 TATACATTGCCAAATTTGATTTGTTTATAGATATATACATTGCCAAAATTGATTTTTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAG--ATATACATTG-CGAATTTGATTTGTATATGGA
* * *
9625356 TATACATTGCCGAATTTGAATTGTTTATAGATATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTG-CGAATTTGATTTGTATATGGA
* * *
9625418 TATACATTGCCGAATTTGATTTGTATAT-GATTGTACATTGTCGAATTTGATTTGTATAGGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA-TATACATTG-CGAATTTGATTTGTATATGGA
* * * *
9625480 TATACATTGCCGAATTTGATTTGCATATAGATATACATTGTGGATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCGAATTTGATTTGTATATGGA
* * *
9625541 TATACATTGCCGAATTTGATTTGTATATGGATATACGTTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTG-CGAATTTGATTTGTATATGGA
* *
9625602 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTG-CGAATTTGATTTGTATATGGA
* *
9625664 TATTCATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTG-CGAATTTGATTTGTATATGGA
* *
9625725 TATATATTGCTGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
9625747 AGCATTGGAT
Statistics
Matches: 352, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
61 177 0.50
62 145 0.41
63 2 0.01
64 28 0.08
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (61 bp):
TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCGAATTTGATTTGTATATGGA
Found at i:9625560 original size:92 final size:93
Alignment explanation
Indices: 9625292--9625746 Score: 612
Period size: 92 Copynumber: 4.9 Consensus size: 93
9625282 GTATATGTTT
* * * * * * * *
9625292 TATACATTGCCAAATTTGATTTGTTTATAGATATATACATTGCCAAAATTGATTTTTTTATAGAT
1 TATACATTGCCGAATTTGATTTGTATATAG--ATATACATTGCCGAATTTGATTTGTATATGGTT
* * *
9625357 ATACATTGCCGAATTTGAATTGTTTATAGA
64 ATACATTGCCGAATTTGATTTGTATATGGA
* * * * *
9625387 TATACATTGTCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATGATTGT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
* * *
9625452 ACATTGTCGAATTTGATTTGTATAGGGT
66 ACATTGCCGAATTTGATTTGTATATGGA
* * *
9625480 TATACATTGCCGAATTTGATTTGCATATAGATATACATTG-TGGATTTGATTTGTATATGGTTAT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
9625544 ACATTGCCGAATTTGATTTGTATATGGA
66 ACATTGCCGAATTTGATTTGTATATGGA
*
9625572 TATACGTTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
9625636 ACATTGCCGAATTTGATTTGTATATGGA
66 ACATTGCCGAATTTGATTTGTATATGGA
* * *
9625664 TATTCATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTCGTATATGGATAT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
* *
9625728 ATATTGCTGAA-TTGATTTG
66 ACATTGCCGAATTTGATTTG
9625747 AGCATTGGAT
Statistics
Matches: 319, Mismatches: 40, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
91 32 0.10
92 177 0.55
93 84 0.26
95 26 0.08
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (93 bp):
TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
ACATTGCCGAATTTGATTTGTATATGGA
Found at i:9630633 original size:43 final size:43
Alignment explanation
Indices: 9630582--9630680 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
9630572 TAGAAACAAA
* * *
9630582 CGCCGCTAAAGGTCACGGCCTTTAGCGGCGTTTGTGAATTGAG
1 CGCCGCTAAAGGTCAAGCCCTTTAGCGGCGTTTGTGAATTAAG
* **
9630625 CGCCGCTAAAAGTCAAGCCCTTTAGCGGCGTTTGTGGCTTAAG
1 CGCCGCTAAAGGTCAAGCCCTTTAGCGGCGTTTGTGAATTAAG
9630668 CGCCGCTAAAGGT
1 CGCCGCTAAAGGT
9630681 TATTATCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGGTCAAGCCCTTTAGCGGCGTTTGTGAATTAAG
Found at i:9630754 original size:43 final size:43
Alignment explanation
Indices: 9630687--9631065 Score: 187
Period size: 43 Copynumber: 8.8 Consensus size: 43
9630677 AGGTTATTAT
** *
9630687 CTTTAGCGGCGCTTAAACCTA-AAACGCCGCTAAAGAGCTTGAC
1 CTTTAGCGGCGCTTTCA-CTACAAACGCCGCTAAATAGCTTGAC
* * * *
9630730 CTTTAGCGGCGCTTTCACTAAAAACACCGC-AAAAAACATT-AGC
1 CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGC-TTGA-C
* * * * * *
9630773 CTATAGCGGCGCTTT-ATTTACAAATGCCACTAGATACCTTGAC
1 CTTTAGCGGCGCTTTCA-CTACAAACGCCGCTAAATAGCTTGAC
* * * * *
9630816 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAA-AACTCTAATT
1 CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGCT-TGA-C
*
9630860 TTTTAGCGGCGCTTTCACTACAAACGCCGC-AAATA-CATT-AGC
1 CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGC-TTGA-C
* * * * * *
9630902 CTATAGCGGCGCTTT-ATTTTCAAATGCCACTATATATG-TTGAC
1 CTTTAGCGGCGCTTTCA-CTACAAACGCCGCTAAATA-GCTTGAC
** *
9630945 CTTTAGCGGCGCTTTGGGC-ACAAACGCCGCTAAA-AGACCTTG-G
1 CTTTAGCGGCGCTTT-CACTACAAACGCCGCTAAATAG--CTTGAC
* * * * *
9630988 TTTTAGCGACGCTTTTCA-TAAAAACGCCACTAAAT-GCATTAAC
1 CTTTAGCGGCGC-TTTCACTACAAACGCCGCTAAATAGC-TTGAC
* *
9631031 CTTTAGCGGCACTTTTC-CCACAAACGCCGCTAAAT
1 CTTTAGCGGCGC-TTTCACTACAAACGCCGCTAAAT
9631066 TGAGCAGCTT
Statistics
Matches: 252, Mismatches: 57, Indels: 54
0.69 0.16 0.15
Matches are distributed among these distances:
41 3 0.01
42 39 0.15
43 168 0.67
44 42 0.17
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGCTTGAC
Found at i:9631005 original size:129 final size:129
Alignment explanation
Indices: 9630687--9631045 Score: 424
Period size: 129 Copynumber: 2.8 Consensus size: 129
9630677 AGGTTATTAT
** * *
9630687 CTTTAGCGGCGCTTAAACCTA-AAACGCCGCT-AAAGAGCTTGACCTTTAGCGGCGCTTTCACTA
1 CTTTAGCGGCGCTTTGACC-ACAAACGCCGCTAAAAGACCTTG-CTTTTAGCGGCGCTTTCACTA
* *
9630750 AAAACACCGCAAAAAACATTAGCCTATAGCGGCGCTTTATTTACAAATGCCACTAGATACCTTGA
64 AAAACGCCGCAAAATACATTAGCCTATAGCGGCGCTTTATTTACAAATGCCACTAGATACCTTGA
9630815 C
129 C
*
9630816 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAAA-ACTCTAAT-TTTTTAGCGGCGCTTTCACT
1 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAAAGAC-CT--TGCTTTTAGCGGCGCTTTCACT
* * * **
9630879 ACAAACGCCGC-AAATACATTAGCCTATAGCGGCGCTTTATTTTCAAATGCCACTATATATGTTG
63 AAAAACGCCGCAAAATACATTAGCCTATAGCGGCGCTTTATTTACAAATGCCACTAGATACCTTG
9630943 AC
128 AC
** * *
9630945 CTTTAGCGGCGCTTTGGGCACAAACGCCGCTAAAAGACCTTGGTTTTAGCGACGCTTTTCA-TAA
1 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAAAGACCTTGCTTTTAGCGGCGC-TTTCACTAA
* * * * * *
9631009 AAACGCCACTAAATGCATTAACCTTTAGCGGCACTTT
65 AAACGCCGCAAAATACATTAGCCTATAGCGGCGCTTT
9631046 TCCCACAAAC
Statistics
Matches: 199, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
127 1 0.01
128 22 0.11
129 141 0.71
130 34 0.17
132 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (129 bp):
CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAAAGACCTTGCTTTTAGCGGCGCTTTCACTAAA
AACGCCGCAAAATACATTAGCCTATAGCGGCGCTTTATTTACAAATGCCACTAGATACCTTGAC
Found at i:9633560 original size:24 final size:24
Alignment explanation
Indices: 9633533--9633638 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 24
9633523 TTTATTATTG
9633533 AAAATATACATGTTAATATTTAGA
1 AAAATATACATGTTAATATTTAGA
**
9633557 AAAATA-ACAT-TTACAATTATTTCTA
1 AAAATATACATGTT--AA-TATTTAGA
* * ** *
9633582 AAATTATAAAAATTATTA-TT-G-
1 AAAATATACATGTTAATATTTAGA
*
9633603 AAAATATAGATGTTAATATTTAGA
1 AAAATATACATGTTAATATTTAGA
9633627 AAAATA-ACATGT
1 AAAATATACATGT
9633639 ACAATTAGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 17
0.67 0.14 0.19
Matches are distributed among these distances:
21 13 0.21
22 4 0.07
23 12 0.20
24 16 0.26
25 12 0.20
26 2 0.03
27 2 0.03
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.38
Consensus pattern (24 bp):
AAAATATACATGTTAATATTTAGA
Found at i:9633576 original size:70 final size:70
Alignment explanation
Indices: 9633487--9633654 Score: 293
Period size: 70 Copynumber: 2.4 Consensus size: 70
9633477 GAAAATATAG
*
9633487 AAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAATAT
1 AAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAATATACATGTTAATAT
9633552 TTAGA
66 TTAGA
*
9633557 AAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAATATAGATGTTAATAT
1 AAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAATATACATGTTAATAT
9633622 TTAGA
66 TTAGA
*
9633627 AAAATAACATGTACAATTAGTTT-TAAAA
1 AAAATAACATTTACAATTA-TTTCTAAAA
9633655 ATTTCTAGAA
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
70 91 0.97
71 3 0.03
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (70 bp):
AAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAATATACATGTTAATAT
TTAGA
Found at i:9635108 original size:12 final size:12
Alignment explanation
Indices: 9635071--9635110 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
9635061 CAACCAGTTT
*
9635071 CAAACTTATGAA
1 CAAAATTATGAA
9635083 CAAAATTA-GTAA
1 CAAAATTATG-AA
9635095 CAAAATTATGAA
1 CAAAATTATGAA
9635107 CAAA
1 CAAA
9635111 CAGTATTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (12 bp):
CAAAATTATGAA
Found at i:9635497 original size:23 final size:23
Alignment explanation
Indices: 9635459--9635518 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
9635449 TTCTAGAATT
*
9635459 GGGGGATTTTTGGGGGAAAATTCG
1 GGGGGAATTTT-GGGGAAAATTCG
* *
9635483 GGGGGAATTTTGGGGATAATTTG
1 GGGGGAATTTTGGGGAAAATTCG
9635506 GGGGGAATTTTGG
1 GGGGGAATTTTGG
9635519 CTAAGTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 23 0.70
24 10 0.30
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.32
Consensus pattern (23 bp):
GGGGGAATTTTGGGGAAAATTCG
Found at i:9640769 original size:41 final size:42
Alignment explanation
Indices: 9640707--9640807 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 42
9640697 TTTATGTTTA
* * * *
9640707 CGTGTAAGACCATGTCTGGGATATTGTCATCG-TATTTGATT
1 CGTGCAAGACCATGTCTGGGATAGTGGCATCGATATGTGATT
*
9640748 CGTGCAAGACCCTGTCTGGGATAGTGGCATCGATATGTGATT
1 CGTGCAAGACCATGTCTGGGATAGTGGCATCGATATGTGATT
* * *
9640790 ACATGTAAGACCACGTCT
1 -CGTGCAAGACCATGTCT
9640808 AGGACGTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 28 0.57
42 8 0.16
43 13 0.27
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
CGTGCAAGACCATGTCTGGGATAGTGGCATCGATATGTGATT
Found at i:9640819 original size:43 final size:43
Alignment explanation
Indices: 9640650--9640822 Score: 147
Period size: 43 Copynumber: 4.1 Consensus size: 43
9640640 CATAGGATTT
* * * *
9640650 TCGATATGTGTTTTCGTGTAAGACCACATCTAGGACGTTGGTA
1 TCGATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCA
* * * * * ** *
9640693 TCGATTTATGTTTACGTGTAAGACCATGTCTGGGATATTGTCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCA
* * * *
9640736 TCG-TATTTGATT-CGTGCAAGACC-CTGTCTGGGATAG-TGGCA
1 TCGATATGTGATTACGTGTAAGACCAC-GTCTAGGA-CGTTGGCA
*
9640777 TCGATATGTGATTACATGTAAGACCACGTCTAGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCA
9640820 TCG
1 TCG
9640823 TACGAGCCTT
Statistics
Matches: 101, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
41 25 0.25
42 15 0.15
43 60 0.59
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCA
Found at i:9660032 original size:215 final size:214
Alignment explanation
Indices: 9659661--9660094 Score: 789
Period size: 215 Copynumber: 2.0 Consensus size: 214
9659651 TTTGGATATG
*
9659661 ATAGTAAAATTTTGAGCTTATAAGGTTATATAATGACATGTTATTATAGAGTAATTAGTGTATAT
1 ATAGTAAAATTTTGAGCTTATAAGGTTATATAATGACATGTAATTATAGAGTAATTAGTGTATAT
* *
9659726 ATATGGTCCAATTGGGAGATAGTTGGAAAGTATGGACATCACATATATAATAAGGGTAATTACAT
66 ATATGGTCCAAGTGGGAGATAGTTGGAAAGTATGGACATCACATATATAATAAAGGTAATTACAT
*
9659791 GTTATTATTTACTATCATAATAGGTTAGCCCAAATTAAAAGTGATCTAATTTGGTTAAGGTTTAT
131 GTTATTATTTACTATCATAATAGGTTAGCCCAAATTAAAAGTGATCTAATTTGATTAAGGTTT-T
* *
9659856 TGGGCTTTATTTTTTAAATA
195 TGGGCTTTAATTATTAAATA
9659876 ATAGTAAAATTTTGAGCTTATAAGGTTATATAATGACATGTAATTATAGAGTAATTAGTGTATAT
1 ATAGTAAAATTTTGAGCTTATAAGGTTATATAATGACATGTAATTATAGAGTAATTAGTGTATAT
*
9659941 ATATGGTCCAAGTGGGAGATTGTTGGAAAGTATGGACATCACATATATAATAAAGGTAATTACAT
66 ATATGGTCCAAGTGGGAGATAGTTGGAAAGTATGGACATCACATATATAATAAAGGTAATTACAT
9660006 GTTATTATTTACTATCATAATAGGTTAGCCCAAATTAAAAGTGATCTAATTTGATTAAGGTTTTT
131 GTTATTATTTACTATCATAATAGGTTAGCCCAAATTAAAAGTGATCTAATTTGATTAAGGTTTTT
9660071 GGGCTTTAATTATTAAATA
196 GGGCTTTAATTATTAAATA
9660090 A-AGTA
1 ATAGTA
9660095 TGGGTCAAAT
Statistics
Matches: 212, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
213 4 0.02
214 20 0.09
215 188 0.89
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (214 bp):
ATAGTAAAATTTTGAGCTTATAAGGTTATATAATGACATGTAATTATAGAGTAATTAGTGTATAT
ATATGGTCCAAGTGGGAGATAGTTGGAAAGTATGGACATCACATATATAATAAAGGTAATTACAT
GTTATTATTTACTATCATAATAGGTTAGCCCAAATTAAAAGTGATCTAATTTGATTAAGGTTTTT
GGGCTTTAATTATTAAATA
Found at i:9669198 original size:129 final size:129
Alignment explanation
Indices: 9668968--9669228 Score: 432
Period size: 129 Copynumber: 2.0 Consensus size: 129
9668958 CGTCGGGACT
* * * * *
9668968 GAGCCATAGAATGATACATTAGAAAATAGAACACTTATATACTTTTAACGGATAATTCGAATCGA
1 GAGCCATAGAATGATACAGTACAAAACAAAACACTTATAGACTTTTAACGGATAATTCGAATCGA
*
9669033 AAATAATTAACTATCATAATACGAATCACACATAACAAATTTAAACCTTTATCGAGCTTAATAC
66 AAATAATTAACTATCATAATACGAATCACACATAACAAATTTAAACCTTTATCGAGCTTAACAC
* * *
9669097 GAGCCATATAATGCTACAGTACAAAACAAAACACTTATAGACTTTTAACGGATAATTTGAATCGA
1 GAGCCATAGAATGATACAGTACAAAACAAAACACTTATAGACTTTTAACGGATAATTCGAATCGA
*
9669162 AAATAATTAACTATCATAATATGAATCACACATAACAAATTTAAACCTTTATCGAGCTTAACAC
66 AAATAATTAACTATCATAATACGAATCACACATAACAAATTTAAACCTTTATCGAGCTTAACAC
9669226 GAG
1 GAG
9669229 TTTACGTTAG
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (129 bp):
GAGCCATAGAATGATACAGTACAAAACAAAACACTTATAGACTTTTAACGGATAATTCGAATCGA
AAATAATTAACTATCATAATACGAATCACACATAACAAATTTAAACCTTTATCGAGCTTAACAC
Found at i:9669493 original size:138 final size:138
Alignment explanation
Indices: 9669245--9669521 Score: 518
Period size: 138 Copynumber: 2.0 Consensus size: 138
9669235 TTAGCTCTAA
9669245 AGCTAACCTAAAATCGAACAAGGACCAATCTGCAAAGGTTTTAAAAGTTCACAACGACATCGTGA
1 AGCTAACCTAAAATCGAACAAGGACCAATCTGCAAAGGTTTTAAAAGTTCACAACGACATCGTGA
* *
9669310 TGTTAGGGAGTTCTTCGTCGCGACGTCACCAAAATAGTTTGTCACGTCACGGCATCCATCTGTTC
66 TGTTAGGGAGTTCTTCGTCGCGACGTCACCAAAATAGTTTGTCACGTCACGGCATCCATCCGCTC
9669375 AATGTTGC
131 AATGTTGC
* *
9669383 AGCTAACCTGAAATTGAACAAGGACCAATCTGCAAAGGTTTTAAAAGTTCACAACGACATCGTGA
1 AGCTAACCTAAAATCGAACAAGGACCAATCTGCAAAGGTTTTAAAAGTTCACAACGACATCGTGA
9669448 TGTTAGGGAGTTCTTCGTCGCGACGTCACCAAAATAGTTTGTCACGTCACGGCATCCATCCGCTC
66 TGTTAGGGAGTTCTTCGTCGCGACGTCACCAAAATAGTTTGTCACGTCACGGCATCCATCCGCTC
9669513 AATGTTGC
131 AATGTTGC
9669521 A
1 A
9669522 ACATCACTCA
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (138 bp):
AGCTAACCTAAAATCGAACAAGGACCAATCTGCAAAGGTTTTAAAAGTTCACAACGACATCGTGA
TGTTAGGGAGTTCTTCGTCGCGACGTCACCAAAATAGTTTGTCACGTCACGGCATCCATCCGCTC
AATGTTGC
Found at i:9673927 original size:15 final size:15
Alignment explanation
Indices: 9673907--9673940 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
9673897 AACCAATTGG
*
9673907 ATGAGGATGGAGTAT
1 ATGAGGAAGGAGTAT
9673922 ATGAGGAAGGAGTAT
1 ATGAGGAAGGAGTAT
9673937 ATGA
1 ATGA
9673941 ACAATGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (15 bp):
ATGAGGAAGGAGTAT
Found at i:9676048 original size:13 final size:13
Alignment explanation
Indices: 9676032--9676076 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
9676022 TTTTTATTTT
9676032 TATTTTAAATATA
1 TATTTTAAATATA
* *
9676045 TATTTTTAAGACT-
1 TATTTTAAATA-TA
9676058 TATTTTAAATATA
1 TATTTTAAATATA
9676071 TATTTT
1 TATTTT
9676077 TAAGACTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
TATTTTAAATATA
Found at i:9676060 original size:26 final size:26
Alignment explanation
Indices: 9676031--9676090 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
9676021 TTTTTTATTT
9676031 TTATTTTAAATATATATTTTTAAGAC
1 TTATTTTAAATATATATTTTTAAGAC
9676057 TTATTTTAAATATATATTTTTAAGAC
1 TTATTTTAAATATATATTTTTAAGAC
9676083 TTATTTTA
1 TTATTTTA
9676091 TTTTTGGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (26 bp):
TTATTTTAAATATATATTTTTAAGAC
Found at i:9676087 original size:13 final size:13
Alignment explanation
Indices: 9676045--9676089 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
9676035 TTTAAATATA
9676045 TATTTTTAAGACT
1 TATTTTTAAGACT
* *
9676058 TATTTTAAATA-T
1 TATTTTTAAGACT
9676070 ATATTTTTAAGACT
1 -TATTTTTAAGACT
9676084 TATTTT
1 TATTTT
9676090 ATTTTTGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (13 bp):
TATTTTTAAGACT
Found at i:9676874 original size:15 final size:15
Alignment explanation
Indices: 9676854--9676887 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
9676844 GTACTAATCT
9676854 ATTTAGGTGTATATA
1 ATTTAGGTGTATATA
9676869 ATTTAGGTGTATATA
1 ATTTAGGTGTATATA
9676884 ATTT
1 ATTT
9676888 CTAGCTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (15 bp):
ATTTAGGTGTATATA
Found at i:9678530 original size:17 final size:18
Alignment explanation
Indices: 9678491--9678524 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9678481 GTGGTCAAAC
9678491 AATA-TAATAGAATAATA
1 AATATTAATAGAATAATA
9678508 AATATTAATA-AATAATA
1 AATATTAATAGAATAATA
9678525 TTTATTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AATATTAATAGAATAATA
Found at i:9689529 original size:25 final size:25
Alignment explanation
Indices: 9689500--9689651 Score: 87
Period size: 25 Copynumber: 6.0 Consensus size: 25
9689490 AAAGTAAACA
9689500 CAAATCCTCTAGAAAGCCTTTGTGG
1 CAAATCCTCTAGAAAGCCTTTGTGG
* * * * *
9689525 CAAATACTTTGGAAATCCTTTATGG
1 CAAATCCTCTAGAAAGCCTTTGTGG
* *
9689550 CAAA-CACACTAGAAAGCTTTTGTGG
1 CAAATC-CTCTAGAAAGCCTTTGTGG
** * * * *
9689575 TGAATACTTTGGAGTA-CCTTTGTGG
1 CAAATCCTCTAGA-AAGCCTTTGTGG
*
9689600 CGAAAT-CTCTGGAAAGCCTTTGTGG
1 C-AAATCCTCTAGAAAGCCTTTGTGG
9689625 CAAACTCTTTCTCTAG-AAGCCTTTGTG
1 CAAA-TC---CTCTAGAAAGCCTTTGTG
9689652 TCGTGTTACC
Statistics
Matches: 92, Mismatches: 25, Indels: 17
0.69 0.19 0.13
Matches are distributed among these distances:
24 4 0.04
25 68 0.74
26 4 0.04
28 11 0.12
29 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (25 bp):
CAAATCCTCTAGAAAGCCTTTGTGG
Found at i:9692154 original size:4 final size:4
Alignment explanation
Indices: 9692112--9692168 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
9692102 TCGATTGGAA
* * * * *
9692112 AATT ATTT AATT GATA AATT AATTT AGTT AATTT GATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AA-TT AATT AA-TT AATT AATT AATT AATT
9692162 AATT AAT
1 AATT AAT
9692169 ATTTAGTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 35 0.85
5 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:9695263 original size:6 final size:6
Alignment explanation
Indices: 9695252--9695280 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9695242 GGTTCTCTCC
9695252 AAAATG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAAT
9695281 TGACCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:9697428 original size:27 final size:27
Alignment explanation
Indices: 9697398--9697449 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
9697388 TAAATAAAAG
9697398 AACAT-AAATT-AAGAATTAAATTAAATT
1 AACATAAAATTAAAG-A-TAAATTAAATT
9697425 AACATAAAATTAAAGATAAATTAAA
1 AACATAAAATTAAAGATAAATTAAA
9697450 ATCAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 14 0.61
28 6 0.26
29 3 0.13
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (27 bp):
AACATAAAATTAAAGATAAATTAAATT
Found at i:9706695 original size:21 final size:21
Alignment explanation
Indices: 9706671--9706712 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9706661 CCCTCTACAC
9706671 GGGTGTGTGTAGCCTTCACAT
1 GGGTGTGTGTAGCCTTCACAT
*
9706692 GGGTGTGTGTGGCCTTCACAT
1 GGGTGTGTGTAGCCTTCACAT
9706713 AGACGTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.36, T:0.33
Consensus pattern (21 bp):
GGGTGTGTGTAGCCTTCACAT
Found at i:9706720 original size:21 final size:21
Alignment explanation
Indices: 9706675--9706720 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
9706665 CTACACGGGT
* **
9706675 GTGTGTAGCCTTCACATGGGT
1 GTGTGTAGCCTTCACATAGAC
*
9706696 GTGTGTGGCCTTCACATAGAC
1 GTGTGTAGCCTTCACATAGAC
9706717 GTGT
1 GTGT
9706721 AGACCCCCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (21 bp):
GTGTGTAGCCTTCACATAGAC
Found at i:9708589 original size:16 final size:16
Alignment explanation
Indices: 9708555--9708589 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9708545 TTTATTCTTC
*
9708555 ATTTATTATATTCTGT
1 ATTTATTATATTCTAT
*
9708571 ATTTATTATATTTTAT
1 ATTTATTATATTCTAT
9708587 ATT
1 ATT
9708590 ATAATTGGTT
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:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTTATTATATTCTAT
Found at i:9710783 original size:21 final size:21
Alignment explanation
Indices: 9710759--9710804 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
9710749 CCCTCTACAC
*
9710759 GGGTGTGTGTAGCCTTCACAT
1 GGGTATGTGTAGCCTTCACAT
*
9710780 GGGTATGTGTGGCCTTCACAT
1 GGGTATGTGTAGCCTTCACAT
9710801 GGGT
1 GGGT
9710805 TTGTAGACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.17, G:0.37, T:0.33
Consensus pattern (21 bp):
GGGTATGTGTAGCCTTCACAT
Found at i:9718358 original size:20 final size:21
Alignment explanation
Indices: 9718323--9718364 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9718313 CTACAACTAG
* *
9718323 TAGTTGCAGAAAAAATGTCAT
1 TAGTTACAGAAAAAATGACAT
9718344 TAGTTACAG-AAAAATGACAT
1 TAGTTACAGAAAAAATGACAT
9718364 T
1 T
9718365 CCTTTAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
TAGTTACAGAAAAAATGACAT
Found at i:9721988 original size:15 final size:16
Alignment explanation
Indices: 9721968--9721997 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9721958 TGGAAAAGTC
9721968 AAAATTA-TTTATTTT
1 AAAATTATTTTATTTT
9721983 AAAATTATTTTATTT
1 AAAATTATTTTATTT
9721998 AAATTCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AAAATTATTTTATTTT
Found at i:9722645 original size:22 final size:22
Alignment explanation
Indices: 9722620--9722669 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
9722610 TTATTAATTA
9722620 TATTTGGGAAATTTAGAA-AATC
1 TATTTGGGAAATTTA-AAGAATC
* *
9722642 TATTTGTGAACTTTAAAGAATC
1 TATTTGGGAAATTTAAAGAATC
9722664 TATTTG
1 TATTTG
9722670 ATGATGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (22 bp):
TATTTGGGAAATTTAAAGAATC
Found at i:9723157 original size:40 final size:40
Alignment explanation
Indices: 9723109--9723189 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
9723099 CAGTTTGTAA
* *
9723109 GCGATCTTTTGCGGACCCTTGAATGATTTTGTCTGTAAAT
1 GCGATCTTTTGCGAACCCTTGAATGATTTTGTCTATAAAT
9723149 GCGATCTTTTGCGAACCCTTGAATGATTTTGTCTATAAAT
1 GCGATCTTTTGCGAACCCTTGAATGATTTTGTCTATAAAT
9723189 G
1 G
9723190 ATCTGTAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (40 bp):
GCGATCTTTTGCGAACCCTTGAATGATTTTGTCTATAAAT
Found at i:9723205 original size:38 final size:38
Alignment explanation
Indices: 9723123--9723207 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 38
9723113 TCTTTTGCGG
* **
9723123 ACCCTTGAATGATTTTGTCTGTAAATGCGATCTTTTGCGA
1 ACCCTTGAATGATTTTGTCTATAAAT-CGATCTTAAGC-A
9723163 ACCCTTGAATGATTTTGTCTATAAAT-GATCTGTAAGTC-
1 ACCCTTGAATGATTTTGTCTATAAATCGATCT-TAAG-CA
9723201 ACCCTTG
1 ACCCTTG
9723208 TGAAGCACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 12 0.30
39 2 0.05
40 26 0.65
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (38 bp):
ACCCTTGAATGATTTTGTCTATAAATCGATCTTAAGCA
Found at i:9724220 original size:29 final size:28
Alignment explanation
Indices: 9724181--9724238 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
9724171 GTGAAATATT
9724181 TTTTTAATTTGATTAAA-ATAT-TTTTAA
1 TTTTTAATTTG-TTAAAGATATATTTTAA
9724208 TTTTTAATTTTTGTTAAAGATATATTTTAA
1 TTTTTAA--TTTGTTAAAGATATATTTTAA
9724238 T
1 T
9724239 ATTAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 7 0.26
28 5 0.19
29 8 0.30
30 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTTTAATTTGTTAAAGATATATTTTAA
Found at i:9726400 original size:35 final size:35
Alignment explanation
Indices: 9726360--9726448 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
9726350 ACAACAACAA
*
9726360 TTATAGGTCATTCGAGGCGACACCATGGAAACGAT
1 TTATAGGTCTTTCGAGGCGACACCATGGAAACGAT
** *** * * *
9726395 TTATAGGTCTTTCTCGGCGAGGTCGTGGGAATGAT
1 TTATAGGTCTTTCGAGGCGACACCATGGAAACGAT
9726430 TTATAGGTCTTTCGAGGCG
1 TTATAGGTCTTTCGAGGCG
9726449 GTAACTCCGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (35 bp):
TTATAGGTCTTTCGAGGCGACACCATGGAAACGAT
Found at i:9727802 original size:43 final size:43
Alignment explanation
Indices: 9727741--9727864 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
9727731 ATTTTCGATA
* *
9727741 TGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT
1 TGTGTTTACGAGTAAGACCACGTCTGGGACGTTGGCATCGACT
*
9727784 TGTGTTTACGAGTAAGACC-CTGTCTGGGACAG-TGGCATCGATT
1 TGTGTTTACGAGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT
** *
9727827 TGTGAATAC-ATGTAAGACCACATCTGGGACGTTGGCAT
1 TGTGTTTACGA-GTAAGACCACGTCTGGGACGTTGGCAT
9727865 TGTACGAGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.04
43 65 0.93
44 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
TGTGTTTACGAGTAAGACCACGTCTGGGACGTTGGCATCGACT
Found at i:9728505 original size:2 final size:2
Alignment explanation
Indices: 9728498--9728524 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9728488 GTTTTGGTAT
9728498 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9728525 TCGGTTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9731344 original size:67 final size:68
Alignment explanation
Indices: 9731248--9731418 Score: 181
Period size: 67 Copynumber: 2.5 Consensus size: 68
9731238 CATAACCGAA
* * * * * *
9731248 CTATTGTCTTACACAACATACCCCGTGTTTAAT-GTTC-TTGCGAACTCCATATGTTGCCATAGC
1 CTATGGTCTTACATAATATAACCCATGTTTAATCG-TCATGGCGAACTCCATATGTTGCCATAG-
*
9731311 TGA-G
64 TCACG
* * * *
9731315 CTATGGTCTTACATAATATAACCCATGTTT-ATCGTCATGGCGGACTTCATTTGTTTCCATAGTC
1 CTATGGTCTTACATAATATAACCCATGTTTAATCGTCATGGCGAACTCCATATGTTGCCATAGTC
9731379 ACG
66 ACG
9731382 CTATGGTCTTACATAATATAACCCCATGTTT-ATCGTC
1 CTATGGTCTTACATAATATAA-CCCATGTTTAATCGTC
9731419 CTGGTAGACT
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
66 6 0.07
67 68 0.76
68 15 0.17
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (68 bp):
CTATGGTCTTACATAATATAACCCATGTTTAATCGTCATGGCGAACTCCATATGTTGCCATAGTC
ACG
Found at i:9731521 original size:68 final size:68
Alignment explanation
Indices: 9731299--9731541 Score: 260
Period size: 68 Copynumber: 3.6 Consensus size: 68
9731289 GAACTCCATA
* * * * *
9731299 TGTTGCCATAGCTGA-GCTATGGTCTTACATAATATAACC-CATGTTTATCGTCATGGCGGACTT
1 TGTTGCCATAGC-CACGCTATGGTCTTACACAAAATAACCTCATGTTTATCGTCCTGGTGGACTT
*
9731362 CATT
65 TATT
* * * * * * *
9731366 TGTTTCCATAGTCACGCTATGGTCTTACATAATATAACCCCATGTTTATCGTCCTGGTAGACTCT
1 TGTTGCCATAGCCACGCTATGGTCTTACACAAAATAACCTCATGTTTATCGTCCTGGTGGACTTT
9731431 ATT
66 ATT
** * * *
9731434 TGTTAACATATCCATGCTATGGTCTTGCACAAAATAACCTCATGTTTATCGTCCTGGTGGACTTT
1 TGTTGCCATAGCCACGCTATGGTCTTACACAAAATAACCTCATGTTTATCGTCCTGGTGGACTTT
9731499 ATT
66 ATT
* *
9731502 TGTTGCCAAAGCCGA-GCTATGGTCTTATACAAAA-AACCTC
1 TGTTGCCATAGCC-ACGCTATGGTCTTACACAAAATAACCTC
9731542 TTTTGAGGTG
Statistics
Matches: 148, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
66 1 0.01
67 40 0.27
68 106 0.72
69 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (68 bp):
TGTTGCCATAGCCACGCTATGGTCTTACACAAAATAACCTCATGTTTATCGTCCTGGTGGACTTT
ATT
Found at i:9733020 original size:30 final size:33
Alignment explanation
Indices: 9732970--9733049 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 33
9732960 GTCTATATCT
* * *
9732970 TTATAATTTTAAAAAAATT-AAAT-T-ATTTTC
1 TTATTATTTTTAAAAAATTAAAATATAATTTTA
*
9733000 TTATTATTTTTAAAAGATTAAAATATAATTTTA
1 TTATTATTTTTAAAAAATTAAAATATAATTTTA
9733033 TTATTATTAATTTAAAA
1 TTATTATT--TTTAAAA
9733050 TTTTAACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 16 0.39
31 4 0.10
32 1 0.02
33 13 0.32
35 7 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
TTATTATTTTTAAAAAATTAAAATATAATTTTA
Found at i:9735603 original size:25 final size:23
Alignment explanation
Indices: 9735569--9735623 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
9735559 AAACAATCAA
9735569 ATATA-AATATTTCAGTTTTCTTAT
1 ATATATAATATTTCA-TTTTCTT-T
*
9735593 ATTTATAATATTTCATTTTCTTT
1 ATATATAATATTTCATTTTCTTT
9735616 ATATATAA
1 ATATATAA
9735624 AATCCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.29
24 11 0.39
25 9 0.32
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATATAATATTTCATTTTCTTT
Found at i:9735683 original size:14 final size:15
Alignment explanation
Indices: 9735653--9735686 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
9735643 TTTAGCTCGA
9735653 TATAATATATCCATT
1 TATAATATATCCATT
*
9735668 TATAATAT-TTCATT
1 TATAATATATCCATT
9735682 TATAA
1 TATAA
9735687 AATGCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATATATCCATT
Found at i:9735798 original size:29 final size:29
Alignment explanation
Indices: 9735756--9735811 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
9735746 AAAAGCCCTT
9735756 TTTTTTCAATATTTACCGAAATGGGCCGG
1 TTTTTTCAATATTTACCGAAATGGGCCGG
*
9735785 TTTTTT-AATTATTTACCGGAATGGGCC
1 TTTTTTCAA-TATTTACCGAAATGGGCC
9735812 ATTTTCCGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
TTTTTTCAATATTTACCGAAATGGGCCGG
Found at i:9736783 original size:29 final size:29
Alignment explanation
Indices: 9736749--9736804 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
9736739 CACGGAAAAT
9736749 GGCCCATTCCGGTAAATAATT-AAAAAACC
1 GGCCCATTCCGGTAAAT-ATTGAAAAAACC
*
9736778 GGCCCATTTCGGTAAATATTGAAAAAA
1 GGCCCATTCCGGTAAATATTGAAAAAA
9736805 AAAGGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATATTGAAAAAACC
Found at i:9738698 original size:67 final size:67
Alignment explanation
Indices: 9738587--9738712 Score: 207
Period size: 67 Copynumber: 1.9 Consensus size: 67
9738577 TTGAGGCCAA
* *
9738587 CTACAATGATATCGTGATACCGAGTAACGGGTATTATGAGACCGAGACCTCTAAAACTTTCAACC
1 CTACAATGATATCGCGATACCGAGTAACGGGTATTATGAGACCGAGACCCCTAAAACTTTCAACC
9738652 AG
66 AG
* * *
9738654 CTACAATGATATCGCGATACTGAGTAATGGGTATTATGATACCGAGACCCCTAAAACTT
1 CTACAATGATATCGCGATACCGAGTAACGGGTATTATGAGACCGAGACCCCTAAAACTT
9738713 CCAATCTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (67 bp):
CTACAATGATATCGCGATACCGAGTAACGGGTATTATGAGACCGAGACCCCTAAAACTTTCAACC
AG
Found at i:9738991 original size:25 final size:26
Alignment explanation
Indices: 9738947--9738996 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
9738937 AGGTTTGTTT
*
9738947 TCTTTTCATTTTTAAGTTAGATTTTC
1 TCTTTTCATTTTTAAATTAGATTTTC
9738973 TCTTTT-ATTTTTAAATTAGATTTT
1 TCTTTTCATTTTTAAATTAGATTTT
9738997 ATTTTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (26 bp):
TCTTTTCATTTTTAAATTAGATTTTC
Found at i:9757790 original size:27 final size:28
Alignment explanation
Indices: 9757692--9757791 Score: 132
Period size: 27 Copynumber: 3.6 Consensus size: 28
9757682 CAAAAAATAA
*
9757692 AAGCCTTTGTGGCAATCTATGAAAA-GG
1 AAGCCTTTGTGGCGATCTATGAAAATGG
** *
9757719 AAGCCTTTGTAACTATCTATGAAAATGG
1 AAGCCTTTGTGGCGATCTATGAAAATGG
9757747 AAGCCTTTGTGGCGATCTATGAAAATGG
1 AAGCCTTTGTGGCGATCTATGAAAATGG
* *
9757775 -AGCTTTTGTGGTGATCT
1 AAGCCTTTGTGGCGATCT
9757792 TTGTGGTGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 37 0.58
28 27 0.42
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (28 bp):
AAGCCTTTGTGGCGATCTATGAAAATGG
Found at i:9757796 original size:12 final size:12
Alignment explanation
Indices: 9757779--9757803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9757769 AAATGGAGCT
9757779 TTTGTGGTGATC
1 TTTGTGGTGATC
9757791 TTTGTGGTGATC
1 TTTGTGGTGATC
9757803 T
1 T
9757804 ATGAAAACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TTTGTGGTGATC
Found at i:9757805 original size:39 final size:39
Alignment explanation
Indices: 9757751--9757830 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
9757741 AAATGGAAGC
* * * *
9757751 CTTTGTGGCGATCTATGAAAATGGAGCTTTTGTGGTGAT
1 CTTTGTGGCGATCTATGAAAACGAAGCCTTTGTGGCGAT
*
9757790 CTTTGTGGTGATCTATGAAAACGAAGCCTTTGTGGCGAT
1 CTTTGTGGCGATCTATGAAAACGAAGCCTTTGTGGCGAT
9757829 CT
1 CT
9757831 ATGAAGGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (39 bp):
CTTTGTGGCGATCTATGAAAACGAAGCCTTTGTGGCGAT
Found at i:9757806 original size:94 final size:93
Alignment explanation
Indices: 9757696--9757878 Score: 235
Period size: 94 Copynumber: 2.0 Consensus size: 93
9757686 AAATAAAAGC
* * * * *
9757696 CTTTGTGGCAATCTATGAAAAGGAAGCCTTTGTAACTATCTATGAAAATGGAA-GCCTTTGTGGC
1 CTTTGTGGCAATCTATGAAAACGAAGCCTTTGTAACGATCTATG--AAGGGAATGCATTTATGGC
*
9757760 GATCTATGAAAATGG-AGCTTTTGTGGTGAT
64 GATCTATGAAAA-GGAAGCCTTTGTGGTGAT
** **
9757790 CTTTGTGGTGATCTATGAAAACGAAGCCTTTGTGGCGATCTATGAAGGGAATGCATTTATGGCGA
1 CTTTGTGGCAATCTATGAAAACGAAGCCTTTGTAACGATCTATGAAGGGAATGCATTTATGGCGA
9757855 TCTATGAAAAGGAAGCCTTTGTGG
66 TCTATGAAAAGGAAGCCTTTGTGG
9757879 CGTTCTATGA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
92 8 0.10
93 31 0.40
94 38 0.49
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (93 bp):
CTTTGTGGCAATCTATGAAAACGAAGCCTTTGTAACGATCTATGAAGGGAATGCATTTATGGCGA
TCTATGAAAAGGAAGCCTTTGTGGTGAT
Found at i:9757829 original size:27 final size:27
Alignment explanation
Indices: 9757790--9757889 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
9757780 TTGTGGTGAT
* *
9757790 CTTTGTGGTGATCTATGAAAACGAAGC
1 CTTTGTGGCGATCTATGAAAAGGAAGC
*
9757817 CTTTGTGGCGATCTATG-AAGGGAATGC
1 CTTTGTGGCGATCTATGAAAAGGAA-GC
* *
9757844 ATTTATGGCGATCTATGAAAAGGAAGC
1 CTTTGTGGCGATCTATGAAAAGGAAGC
*
9757871 CTTTGTGGCGTTCTATGAA
1 CTTTGTGGCGATCTATGAA
9757890 GGGAATACCT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 5 0.08
27 51 0.82
28 6 0.10
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
CTTTGTGGCGATCTATGAAAAGGAAGC
Found at i:9757857 original size:66 final size:66
Alignment explanation
Indices: 9757733--9757857 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
9757723 CTTTGTAACT
* * * * *
9757733 ATCTATGAAAATGGAAGCCTTTGTGGCGATCTATGAAAATGGAGCTTTTGTGGTGATCTTTGTGG
1 ATCTATGAAAATCGAAGCCTTTGTGGCGATCTATG-AAAGGGAGCATTTATGGCGATCTTTGTGG
9757798 TG
65 TG
9757800 ATCTATGAAAA-CGAAGCCTTTGTGGCGATCTATG-AAGGGAATGCATTTATGGCGATCT
1 ATCTATGAAAATCGAAGCCTTTGTGGCGATCTATGAAAGGG-A-GCATTTATGGCGATCT
9757858 ATGAAAAGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
64 4 0.08
65 1 0.02
66 35 0.69
67 11 0.22
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (66 bp):
ATCTATGAAAATCGAAGCCTTTGTGGCGATCTATGAAAGGGAGCATTTATGGCGATCTTTGTGGT
G
Found at i:9757900 original size:27 final size:27
Alignment explanation
Indices: 9757790--9757901 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
9757780 TTGTGGTGAT
* **
9757790 CTTTGTGGTGATCTATGAAAACGAA-GC
1 CTTTGTGGCGATCTATG-AAGGGAATGC
9757817 CTTTGTGGCGATCTATGAAGGGAATGC
1 CTTTGTGGCGATCTATGAAGGGAATGC
* * *
9757844 ATTTATGGCGATCTATGAAAAGGAA-GC
1 CTTTGTGGCGATCTATG-AAGGGAATGC
* *
9757871 CTTTGTGGCGTTCTATGAAGGGAATAC
1 CTTTGTGGCGATCTATGAAGGGAATGC
9757898 CTTT
1 CTTT
9757902 TGCGGCATGC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 11 0.15
27 54 0.76
28 6 0.08
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
CTTTGTGGCGATCTATGAAGGGAATGC
Found at i:9759661 original size:22 final size:22
Alignment explanation
Indices: 9759636--9759712 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
9759626 TTTTTAGAAA
9759636 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
9759658 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
9759680 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
9759702 CATGAGAGCTT
1 CATGAGAGCTT
9759713 CATTTTGGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:9760940 original size:16 final size:15
Alignment explanation
Indices: 9760902--9760940 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
9760892 AGACAGAAAG
9760902 TTTTATTTATTTCAT
1 TTTTATTTATTTCAT
* *
9760917 TTTGATTTAGTTTTAT
1 TTTTATTTA-TTTCAT
9760933 TTTTATTT
1 TTTTATTT
9760941 TTACTTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTTATTTATTTCAT
Found at i:9762868 original size:22 final size:23
Alignment explanation
Indices: 9762842--9762896 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
9762832 AGGATATGTT
**
9762842 TGATATGTTATGTGATAT-ACTC
1 TGATATGTTATAAGATATGACTC
* *
9762864 TGATATGCTATAAGATATGACTT
1 TGATATGTTATAAGATATGACTC
9762887 TGATATGTTA
1 TGATATGTTA
9762897 AGCAATATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (23 bp):
TGATATGTTATAAGATATGACTC
Found at i:9770728 original size:19 final size:17
Alignment explanation
Indices: 9770687--9770728 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
9770677 TGTTTCTTTG
*
9770687 CTCAAGCCGAGCCACCT
1 CTCAAGCCGAGCCACAT
9770704 -TCAAGCCGAGCCATCAT
1 CTCAAGCCGAGCCA-CAT
9770721 ACTCAAGC
1 -CTCAAGC
9770729 TATTCTGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
19 6 0.29
ACGTcount: A:0.29, C:0.40, G:0.17, T:0.14
Consensus pattern (17 bp):
CTCAAGCCGAGCCACAT
Found at i:9774191 original size:24 final size:24
Alignment explanation
Indices: 9774162--9774243 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
9774152 CAGTATAACG
*
9774162 GGAAGCTCATAAGAGCCATATTCA
1 GGAAGCTCATAAGAGCCATAATCA
** *
9774186 GGAAGCTCATGTGAGCCAATAAT-G
1 GGAAGCTCATAAGAGCC-ATAATCA
*
9774210 GGTAGCTC-TGAAGAGCCATTAATCA
1 GGAAGCTCAT-AAGAGCCA-TAATCA
9774235 GGAAGCTCA
1 GGAAGCTCA
9774244 AGATAGCCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
23 2 0.05
24 31 0.70
25 11 0.25
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:9791155 original size:36 final size:36
Alignment explanation
Indices: 9791115--9791192 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
9791105 CTCTGGAATC
*
9791115 AACACAACCTAAACTTGATACAAAAGAGAATCCCAA
1 AACACAACCTAAACCTGATACAAAAGAGAATCCCAA
**
9791151 AACACAACCTAAACCTGATACAAAAGAGAATCCTGA
1 AACACAACCTAAACCTGATACAAAAGAGAATCCCAA
9791187 AACACA
1 AACACA
9791193 GCCGGTGCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.53, C:0.26, G:0.09, T:0.13
Consensus pattern (36 bp):
AACACAACCTAAACCTGATACAAAAGAGAATCCCAA
Found at i:9798825 original size:9 final size:9
Alignment explanation
Indices: 9798811--9798861 Score: 93
Period size: 9 Copynumber: 5.7 Consensus size: 9
9798801 CATTAGGGAC
9798811 TAAATTGAA
1 TAAATTGAA
9798820 TAAATTGAA
1 TAAATTGAA
9798829 TAAATTGAA
1 TAAATTGAA
9798838 TAAATTGAA
1 TAAATTGAA
9798847 TAAATTGAA
1 TAAATTGAA
*
9798856 AAAATT
1 TAAATT
9798862 TCATGAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (9 bp):
TAAATTGAA
Found at i:9802380 original size:11 final size:12
Alignment explanation
Indices: 9802364--9802401 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
9802354 TATTTTTTAA
9802364 TTTTAAAATA-T
1 TTTTAAAATACT
9802375 TTTTAAAATACT
1 TTTTAAAATACT
*
9802387 TTTTTAAA-ACT
1 TTTTAAAATACT
9802398 TTTT
1 TTTT
9802402 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAAATACT
Found at i:9805808 original size:49 final size:49
Alignment explanation
Indices: 9805715--9805808 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
9805705 ATATCTATTT
* * *
9805715 AAAGGTTAAAAAAACTCATTCTAATCAATGTCAAATAGATGAAGTGTAG
1 AAAGGTTAAAAAAACTCATTCTAATCAATGTCAAACAAAAGAAGTGTAG
* * *
9805764 AAAGGTTGAAAAATA-TTATTCTATTCAATGTCAAACAAAAGAAGT
1 AAAGGTT-AAAAAAACTCATTCTAATCAATGTCAAACAAAAGAAGT
9805809 ATAATTCTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 32 0.84
50 6 0.16
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.28
Consensus pattern (49 bp):
AAAGGTTAAAAAAACTCATTCTAATCAATGTCAAACAAAAGAAGTGTAG
Found at i:9807932 original size:50 final size:50
Alignment explanation
Indices: 9807837--9807932 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
9807827 GGAAAGAGTT
* * * *
9807837 TACTCAGTTCAGCAGCCTTTCGGATCTATTCTAATTGATGTACTCAACTC
1 TACTCAGTTCAGCAGCCTTTCGGATCTATTCTAACTAAAGCACTCAACTC
* *
9807887 TACTCAGTTTAGCAGCCTTTCGGATCTATTCTGACTAAAGCACTCA
1 TACTCAGTTCAGCAGCCTTTCGGATCTATTCTAACTAAAGCACTCA
9807933 TCCGTTTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (50 bp):
TACTCAGTTCAGCAGCCTTTCGGATCTATTCTAACTAAAGCACTCAACTC
Found at i:9808693 original size:15 final size:15
Alignment explanation
Indices: 9808673--9808703 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9808663 TAAAATACTT
9808673 TTTAAATTTTTAAAA
1 TTTAAATTTTTAAAA
*
9808688 TTTAAATTTTTTAAA
1 TTTAAATTTTTAAAA
9808703 T
1 T
9808704 ACTAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATTTTTAAAA
Found at i:9808727 original size:16 final size:16
Alignment explanation
Indices: 9808706--9808738 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9808696 TTTTAAATAC
9808706 TAACAATTAATTTTAA
1 TAACAATTAATTTTAA
*
9808722 TAACAATTAGTTTTAA
1 TAACAATTAATTTTAA
9808738 T
1 T
9808739 TTTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
TAACAATTAATTTTAA
Found at i:9808737 original size:22 final size:22
Alignment explanation
Indices: 9808712--9808772 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
9808702 ATACTAACAA
* * *
9808712 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
9808734 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
9808756 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
9808773 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:9812270 original size:23 final size:23
Alignment explanation
Indices: 9812243--9812312 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
9812233 CAAATAAAAG
9812243 AAATATAATTCTATATGAATTTT
1 AAATATAATTCTATATGAATTTT
9812266 AAATATAATTCTATATGAATTTT
1 AAATATAATTCTATATGAATTTT
9812289 AAATATAATTCTATATGAATTTT
1 AAATATAATTCTATATGAATTTT
9812312 A
1 A
9812313 CTTTTATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
AAATATAATTCTATATGAATTTT
Found at i:9817959 original size:25 final size:25
Alignment explanation
Indices: 9817931--9817983 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
9817921 GGATCAGTTA
9817931 ATACTTAAATTAAATTATTCGAAAT
1 ATACTTAAATTAAATTATTCGAAAT
9817956 ATACTTAAATTAAATTATTCGAAAT
1 ATACTTAAATTAAATTATTCGAAAT
9817981 ATA
1 ATA
9817984 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATACTTAAATTAAATTATTCGAAAT
Found at i:9819204 original size:17 final size:17
Alignment explanation
Indices: 9819182--9819245 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
9819172 ATGCTATTTT
9819182 TTTTTAAT-TTTTATGAA
1 TTTTTAATATTTT-TGAA
9819199 TTTTT-ATATTTTATTGAA
1 TTTTTAATA-TTT-TTGAA
*
9819217 TTTTAAATATTTTT--A
1 TTTTTAATATTTTTGAA
*
9819232 TTTTTTATATTTTT
1 TTTTTAATATTTTT
9819246 TGAAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 13 0.32
16 2 0.05
17 7 0.17
18 14 0.35
19 4 0.10
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTAATATTTTTGAA
Found at i:9819246 original size:17 final size:17
Alignment explanation
Indices: 9819181--9819248 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
9819171 CATGCTATTT
9819181 TTTTTTA-ATTTTTATGA
1 TTTTTTATATTTTT-TGA
*
9819198 ATTTTTATATTTTATTGA
1 TTTTTTATATTTT-TTGA
* *
9819216 -ATTTTAAATATTTTT-A
1 TTTTTTATAT-TTTTTGA
9819232 TTTTTTATATTTTTTGA
1 TTTTTTATATTTTTTGA
9819249 AATTATTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 6 0.15
17 23 0.56
18 11 0.27
19 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTTTGA
Found at i:9830731 original size:16 final size:16
Alignment explanation
Indices: 9830710--9830741 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9830700 TGTGACTGAC
9830710 TAGACTGATAGTACAT
1 TAGACTGATAGTACAT
9830726 TAGACTGATAGTACAT
1 TAGACTGATAGTACAT
9830742 CGGATTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
TAGACTGATAGTACAT
Done.