Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 89 of 203
Found at i:28311133 original size:50 final size:50
Alignment explanation
Indices: 28311054--28311199 Score: 170
Period size: 50 Copynumber: 2.9 Consensus size: 50
28311044 TTTCCTGTAC
* * **
28311054 TGCCAATGCCATATCCCAGATAT-GATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATAG-TCTTACATGGGACCTCTCATATCGG
* * * *
28311104 TGCCCATGCAATGTCCCAGACATAGTCTTACGA-GGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATAGTCTTAC-ATGGGACCTCTCATATCGG
* *
28311154 TGCCAATGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATA
28311200 ACCTCAATAA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 77 0.96
51 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATATCGG
Found at i:28315377 original size:24 final size:23
Alignment explanation
Indices: 28315344--28315390 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
28315334 CATGGTTTCC
28315344 TCTTTACCTTTCTTTTTTATGCT
1 TCTTTACCTTTCTTTTTTATGCT
*
28315367 NTCTTTCCCTTTCTTTTTTATGCT
1 -TCTTTACCTTTCTTTTTTATGCT
28315391 AAAAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.06, C:0.23, G:0.04, T:0.64
Consensus pattern (23 bp):
TCTTTACCTTTCTTTTTTATGCT
Found at i:28321801 original size:21 final size:21
Alignment explanation
Indices: 28321759--28321802 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28321749 ACATTTGCTT
**
28321759 CAGGTAACAACTCTGTCGCTC
1 CAGGTAACAACTCTGTAACTC
28321780 CAGGTAACAACTCTGTAACTC
1 CAGGTAACAACTCTGTAACTC
28321801 CA
1 CA
28321803 CCAGAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (21 bp):
CAGGTAACAACTCTGTAACTC
Found at i:28322654 original size:85 final size:85
Alignment explanation
Indices: 28322511--28322684 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 85
28322501 AAAAAATAAT
*
28322511 AATAACATAAACGCAACACGAATATACAAATGTCTCCAAACCTATTTAATACAAATTAAATGTGT
1 AATAACATAAACACAACACGAATATACAAATGTCTCCAAACCTATTTAATACAAATTAAATGTGT
28322576 TAAATTTTATATAAATAAAA
66 TAAATTTTATATAAATAAAA
*
28322596 AATAACATAAACACAACACGAATATACAGATGTCTCCAAACCTATTTAATACAAATTAAATGTGT
1 AATAACATAAACACAACACGAATATACAAATGTCTCCAAACCTATTTAATACAAATTAAATGTGT
28322661 TAAATTTTATATAAATAAAA
66 TAAATTTTATATAAATAAAA
28322681 AATA
1 AATA
28322685 CCTTAACCAC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (85 bp):
AATAACATAAACACAACACGAATATACAAATGTCTCCAAACCTATTTAATACAAATTAAATGTGT
TAAATTTTATATAAATAAAA
Found at i:28328194 original size:31 final size:32
Alignment explanation
Indices: 28328131--28328199 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
28328121 TATCATAATT
*
28328131 TAAATTTATTCAAAAAGTACAAAAAATTAAAA
1 TAAATTAATTCAAAAAGTACAAAAAATTAAAA
* *
28328163 TTAATTAATTTAAAAA-TAC-AAAAATTAAAAA
1 TAAATTAATTCAAAAAGTACAAAAAATT-AAAA
28328194 TAAATT
1 TAAATT
28328200 TTAATTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.22
31 12 0.38
32 13 0.41
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (32 bp):
TAAATTAATTCAAAAAGTACAAAAAATTAAAA
Found at i:28328303 original size:22 final size:22
Alignment explanation
Indices: 28328278--28328329 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
28328268 AATAAATTAT
*
28328278 AAATTAAAAATGCTATAA-CTTG
1 AAATTAAAAAAGCT-TAATCTTG
28328300 AAATTTAAAAAAGCTTAATCTTG
1 AAA-TTAAAAAAGCTTAATCTTG
*
28328323 GAATTAA
1 AAATTAA
28328330 GCCAAAGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTAAAAAAGCTTAATCTTG
Found at i:28330895 original size:50 final size:50
Alignment explanation
Indices: 28330837--28330999 Score: 227
Period size: 50 Copynumber: 3.3 Consensus size: 50
28330827 TATCACAGAT
** * * * *
28330837 ATGGTCTTACATGGGAGTTCTCATATAAGTGCCCATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAAC
** * *
28330887 ATGGTCTTACGGGGGACCTCTTATCTCAGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAAC
*
28330937 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAAC
28330987 ATGGTCTTACATG
1 ATGGTCTTACATG
28331000 ACATGGTCTT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 98 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAAC
Found at i:28331005 original size:15 final size:15
Alignment explanation
Indices: 28330985--28331015 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28330975 CATGTCCCAA
28330985 ACATGGTCTTACATG
1 ACATGGTCTTACATG
28331000 ACATGGTCTTACATG
1 ACATGGTCTTACATG
28331015 A
1 A
28331016 GACCTCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (15 bp):
ACATGGTCTTACATG
Found at i:28339859 original size:27 final size:27
Alignment explanation
Indices: 28339828--28339954 Score: 168
Period size: 27 Copynumber: 4.7 Consensus size: 27
28339818 CCTAATATTT
*
28339828 GTAAAATGA-CTGTAATACCCTTGTAGG
1 GTAAAATGATC-GTAATACCCCTGTAGG
* *
28339855 GTAAAATAATCGTAATGCCCCTGTAGG
1 GTAAAATGATCGTAATACCCCTGTAGG
* *
28339882 GTAAACTGATCGTAAT-GCCCTGTAGG
1 GTAAAATGATCGTAATACCCCTGTAGG
* *
28339908 GTAAAATGACCGTAATACCCCTATAGG
1 GTAAAATGATCGTAATACCCCTGTAGG
28339935 GTAAAATGATCGTAATACCC
1 GTAAAATGATCGTAATACCC
28339955 GTAGAGGGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 23 0.26
27 63 0.72
28 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAAAATGATCGTAATACCCCTGTAGG
Found at i:28339906 original size:53 final size:53
Alignment explanation
Indices: 28339828--28339958 Score: 176
Period size: 53 Copynumber: 2.5 Consensus size: 53
28339818 CCTAATATTT
* * *
28339828 GTAAAATGA-CTGTAATACCCTTGTAGGGTAAAATAATCGTAATGCCCCTGTAGG
1 GTAAAATGATC-GTAATACCC-TGTAGGGTAAAATAACCGTAATACCCCTATAGG
* * *
28339882 GTAAACTGATCGTAATGCCCTGTAGGGTAAAATGACCGTAATACCCCTATAGG
1 GTAAAATGATCGTAATACCCTGTAGGGTAAAATAACCGTAATACCCCTATAGG
28339935 GTAAAATGATCGTAATACCC-GTAG
1 GTAAAATGATCGTAATACCCTGTAG
28339959 AGGGTAAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 4 0.06
53 47 0.69
54 16 0.24
55 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (53 bp):
GTAAAATGATCGTAATACCCTGTAGGGTAAAATAACCGTAATACCCCTATAGG
Found at i:28340016 original size:23 final size:23
Alignment explanation
Indices: 28339986--28340029 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28339976 TGCCCCTCGA
28339986 GGTTAAATGATTGATTTGTCTAT
1 GGTTAAATGATTGATTTGTCTAT
*
28340009 GGTTAAATGGTTGATTTGTCT
1 GGTTAAATGATTGATTTGTCT
28340030 GTGTTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.48
Consensus pattern (23 bp):
GGTTAAATGATTGATTTGTCTAT
Found at i:28340066 original size:24 final size:24
Alignment explanation
Indices: 28340020--28340072 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
28340010 GTTAAATGGT
*
28340020 TGATTTGTCTGTGTTTGGTATGAC
1 TGATTTGTCTGTGTTTGGAATGAC
28340044 TGATTTGTCTGTGATTT-GAATGAC
1 TGATTTGTCTGTG-TTTGGAATGAC
*
28340068 CGATT
1 TGATT
28340073 CTGAGCATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.47
Consensus pattern (24 bp):
TGATTTGTCTGTGTTTGGAATGAC
Found at i:28340285 original size:32 final size:31
Alignment explanation
Indices: 28340244--28340416 Score: 179
Period size: 32 Copynumber: 5.5 Consensus size: 31
28340234 GCTGCGATGC
28340244 TACTGATGGCTTTGTGCCGATCATATTAGCGT
1 TACTGATGGCTTTGTGCCGATCATATTA-CGT
*
28340276 TACTGATGGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTA-CGT
* *
28340308 TACTGATGACTTTGTGCCGATCATATTATCAT
1 TACTGATGGCTTTGTGCCGATCATATTA-CGT
* ** * * *
28340340 TACTGATGTCTGCGTGCCTATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTAC-GT
* *
28340372 TATTGATGGCTTTGTGCCAATCATATTAC-T
1 TACTGATGGCTTTGTGCCGATCATATTACGT
*
28340402 GTACTTATGG-TTTGT
1 -TACTGATGGCTTTGT
28340417 AGCCATTCTT
Statistics
Matches: 117, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
30 5 0.04
31 8 0.07
32 104 0.89
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (31 bp):
TACTGATGGCTTTGTGCCGATCATATTACGT
Found at i:28340324 original size:64 final size:64
Alignment explanation
Indices: 28340242--28340399 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 64
28340232 TTGCTGCGAT
* ** *
28340242 GCTACTGATGGCTTTGTGCCGATCATATTAGCGTTACTGATGGCTTTGTACCGATCATATTACC
1 GCTACTGATGGCTTTGTGCCGATCATATTAGCATTACTGATGGCTGCGTACCGATCATATCACC
* * * * * * *
28340306 GTTACTGATGACTTTGTGCCGATCATATTATCATTACTGATGTCTGCGTGCCTATCATATCACT
1 GCTACTGATGGCTTTGTGCCGATCATATTAGCATTACTGATGGCTGCGTACCGATCATATCACC
* *
28340370 GCTATTGATGGCTTTGTGCCAATCATATTA
1 GCTACTGATGGCTTTGTGCCGATCATATTA
28340400 CTGTACTTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (64 bp):
GCTACTGATGGCTTTGTGCCGATCATATTAGCATTACTGATGGCTGCGTACCGATCATATCACC
Found at i:28342902 original size:21 final size:21
Alignment explanation
Indices: 28342856--28342910 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
28342846 TACTGTCTCA
* *
28342856 AATGTTGTGACTTCTAATGTTG
1 AATGTTGCGAC-TCTAAGGTTG
28342878 AATGTTGCGACTCTAAGGTCT-
1 AATGTTGCGACTCTAAGGT-TG
*
28342899 AATGTTACGACT
1 AATGTTGCGACT
28342911 TCTTGCTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (21 bp):
AATGTTGCGACTCTAAGGTTG
Found at i:28350242 original size:19 final size:19
Alignment explanation
Indices: 28350220--28350291 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
28350210 AAAAATACAA
28350220 AAAAATTCAAAATCATTTT
1 AAAAATTCAAAATCATTTT
*
28350239 AAAAAATTCAAAATAAATTTT
1 -AAAAATTCAAAAT-CATTTT
28350260 -AAAATTCAAAA-CATTTAT
1 AAAAATTCAAAATCATTT-T
28350278 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
28350292 TTATATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 17 0.38
20 18 0.40
21 5 0.11
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTCAAAATCATTTT
Found at i:28350293 original size:18 final size:19
Alignment explanation
Indices: 28350220--28350296 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
28350210 AAAAATACAA
28350220 AAAAATTCAAAATCATTT-T
1 AAAAATTCAAAA-CATTTAT
*
28350239 AAAAAATTCAAAATAAATTT-T
1 -AAAAATTC-AAA-ACATTTAT
28350260 -AAAATTCAAAACATTTAT
1 AAAAATTCAAAACATTTAT
*
28350278 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAACATTTAT
28350296 A
1 A
28350297 TTTTTAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
17 5 0.10
18 11 0.22
19 17 0.34
20 8 0.16
21 8 0.16
22 1 0.02
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAACATTTAT
Found at i:28350325 original size:19 final size:21
Alignment explanation
Indices: 28350301--28350344 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
28350291 TTTATATTTT
*
28350301 TAAAAATTTATAAA-AAT-TA
1 TAAAAAATTATAAAGAATATA
*
28350320 TAAAAAATTCTAAAGAATATA
1 TAAAAAATTATAAAGAATATA
28350341 TAAA
1 TAAA
28350345 GAAAGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 3 0.14
21 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAAAATTATAAAGAATATA
Found at i:28351766 original size:18 final size:19
Alignment explanation
Indices: 28351732--28351780 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
28351722 AATTTTTTAT
*
28351732 TAAATTATTTATGTAA-TA
1 TAAATTATTTATATAATTA
*
28351750 TAAATTATTTTTATAATTA
1 TAAATTATTTATATAATTA
28351769 TATTAATTATTT
1 TA--AATTATTT
28351781 GGATTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 14 0.54
19 4 0.15
21 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TAAATTATTTATATAATTA
Found at i:28352250 original size:13 final size:13
Alignment explanation
Indices: 28352232--28352264 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28352222 TGACAAATTT
28352232 TAATATTTTTAAA
1 TAATATTTTTAAA
*
28352245 TAATATATTTAAA
1 TAATATTTTTAAA
28352258 TAA-ATTT
1 TAATATTT
28352265 AAATGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 3 0.17
13 15 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATATTTTTAAA
Found at i:28352282 original size:28 final size:28
Alignment explanation
Indices: 28352252--28352321 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
28352242 AAATAATATA
28352252 TTTAAATAAATTTA-AATGATTTTTACTAT
1 TTTAAATAAATTTACAAT--TTTTTACTAT
**
28352281 TTTTTATAAATTTACAATTTTTTAC-AT
1 TTTAAATAAATTTACAATTTTTTACTAT
28352308 TTTAAAATAAATTT
1 TTT-AAATAAATTT
28352322 TTTAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.14
28 15 0.43
29 12 0.34
30 3 0.09
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (28 bp):
TTTAAATAAATTTACAATTTTTTACTAT
Found at i:28352322 original size:21 final size:18
Alignment explanation
Indices: 28352296--28352336 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
28352286 ATAAATTTAC
28352296 AATTTTTTACATTTTAAAATA
1 AATTTTTTA-A-TTT-AAATA
28352317 AATTTTTTAATTTAAATA
1 AATTTTTTAATTTAAATA
28352335 AA
1 AA
28352337 AAACATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 1 0.05
21 9 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTTTTAATTTAAATA
Found at i:28352826 original size:11 final size:11
Alignment explanation
Indices: 28352810--28352841 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28352800 CACTATTCAC
28352810 CTAAACCCAAT
1 CTAAACCCAAT
*
28352821 CTAAACCAAAT
1 CTAAACCCAAT
28352832 CTAAACCCAA
1 CTAAACCCAA
28352842 GTATTCAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (11 bp):
CTAAACCCAAT
Found at i:28352858 original size:18 final size:18
Alignment explanation
Indices: 28352835--28352877 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28352825 ACCAAATCTA
**
28352835 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
28352853 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
28352871 AACCCAA
1 AACCCAA
28352878 TCATAAAAAT
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:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:28352995 original size:9 final size:9
Alignment explanation
Indices: 28352981--28353047 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
28352971 ATAGTGATTC
28352981 AATTCGGTT
1 AATTCGGTT
28352990 AATTCGGTT
1 AATTCGGTT
28352999 AATTCGAG-T
1 AATTCG-GTT
*
28353008 AATTCGGGT
1 AATTCGGTT
*
28353017 AAGTT-GGCT
1 AA-TTCGGTT
28353026 AATTCGGTT
1 AATTCGGTT
28353035 AATTCGGTT
1 AATTCGGTT
28353044 AATT
1 AATT
28353048 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 3 0.06
9 46 0.88
10 3 0.06
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28357024 original size:14 final size:14
Alignment explanation
Indices: 28357005--28357032 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28356995 GCCTTTTAAG
28357005 GAACTATAGGGACA
1 GAACTATAGGGACA
28357019 GAACTATAGGGACA
1 GAACTATAGGGACA
28357033 TGTGACTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
GAACTATAGGGACA
Found at i:28357165 original size:29 final size:29
Alignment explanation
Indices: 28357123--28357181 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28357113 CAAAGTTGGA
28357123 AGCTTTAATGGAACAAATGGTTACAAGGC
1 AGCTTTAATGGAACAAATGGTTACAAGGC
28357152 AGCTTTAATGGAACAAATGGTTACAAGGC
1 AGCTTTAATGGAACAAATGGTTACAAGGC
28357181 A
1 A
28357182 ACAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCTTTAATGGAACAAATGGTTACAAGGC
Found at i:28359450 original size:37 final size:37
Alignment explanation
Indices: 28359400--28359474 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
28359390 GGAGGAAAAT
* *
28359400 GAGAGGATGGGAATTTAGTTGATGGCTATGGTGACTA
1 GAGAGGATGGGAATTTAGTTGATGGCTACGGAGACTA
28359437 GAGAGGATGGGAATTTAGTTGATGGCTACGGAGACTA
1 GAGAGGATGGGAATTTAGTTGATGGCTACGGAGACTA
28359474 G
1 G
28359475 CCTATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.28, C:0.07, G:0.39, T:0.27
Consensus pattern (37 bp):
GAGAGGATGGGAATTTAGTTGATGGCTACGGAGACTA
Found at i:28360952 original size:28 final size:28
Alignment explanation
Indices: 28360912--28360966 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
28360902 TTTCTTACGT
*
28360912 CCCGACGGACTT-ACCCTGTGTTTATTGC
1 CCCGACGGACTTAACCC-GTATTTATTGC
*
28360940 CCCGGCGGACTTAACCCGTATTTATTG
1 CCCGACGGACTTAACCCGTATTTATTG
28360967 TCTCAACGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (28 bp):
CCCGACGGACTTAACCCGTATTTATTGC
Found at i:28361053 original size:66 final size:66
Alignment explanation
Indices: 28360967--28361118 Score: 169
Period size: 66 Copynumber: 2.3 Consensus size: 66
28360957 GTATTTATTG
* * * * *
28360967 TCTCAACGGAATATCTCTATTTTGTGTTTGCTATCCCAGAAAACTATCTCTATTATGTGTTTACT
1 TCTCAACGGACTATCTCTATTATATGTTTACTATCCCAGAAAACTATCTCTATTATATGTTTACT
28361032 A
66 A
* * * *** * * *
28361033 TCTCAGCGGACTATCTCTATTATATGTTTATTGTCCCAGTGGACTATCTTTGTTTTATGTTTACT
1 TCTCAACGGACTATCTCTATTATATGTTTACTATCCCAGAAAACTATCTCTATTATATGTTTACT
28361098 A
66 A
*
28361099 TCCCAACGGACTATCTCTAT
1 TCTCAACGGACTATCTCTAT
28361119 GGATGTAGTG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (66 bp):
TCTCAACGGACTATCTCTATTATATGTTTACTATCCCAGAAAACTATCTCTATTATATGTTTACT
A
Found at i:28361110 original size:33 final size:33
Alignment explanation
Indices: 28360973--28361118 Score: 148
Period size: 33 Copynumber: 4.4 Consensus size: 33
28360963 ATTGTCTCAA
* * * *
28360973 CGGAATATCTCTATTTTGTGTTTGCTATCCCAG
1 CGGACTATCTCTATTATATGTTTACTATCCCAG
*** * *
28361006 AAAACTATCTCTATTATGTGTTTACTATCTCAG
1 CGGACTATCTCTATTATATGTTTACTATCCCAG
* *
28361039 CGGACTATCTCTATTATATGTTTATTGTCCCAG
1 CGGACTATCTCTATTATATGTTTACTATCCCAG
* * * * *
28361072 TGGACTATCTTTGTTTTATGTTTACTATCCCAA
1 CGGACTATCTCTATTATATGTTTACTATCCCAG
28361105 CGGACTATCTCTAT
1 CGGACTATCTCTAT
28361119 GGATGTAGTG
Statistics
Matches: 89, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (33 bp):
CGGACTATCTCTATTATATGTTTACTATCCCAG
Found at i:28365638 original size:13 final size:13
Alignment explanation
Indices: 28365581--28365692 Score: 91
Period size: 13 Copynumber: 8.3 Consensus size: 13
28365571 TGATATACAA
*
28365581 AAATGATTATGTG
1 AAATGATTATATG
28365594 TTAAATG-TGTATATG
1 --AAATGAT-TATATG
* *
28365609 AAATGATAAAAATG
1 AAATGAT-TATATG
* *
28365623 AAATGTTTAGATG
1 AAATGATTATATG
* *
28365636 AAATGGTTATACG
1 AAATGATTATATG
28365649 AAATGATTATATG
1 AAATGATTATATG
*
28365662 AAATGCTTATATG
1 AAATGATTATATG
*
28365675 AAATGGTTATATAG
1 AAATGATTATAT-G
28365689 AAAT
1 AAAT
28365693 AGATGTATAA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
13 53 0.66
14 17 0.21
15 10 0.12
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.36
Consensus pattern (13 bp):
AAATGATTATATG
Found at i:28373369 original size:22 final size:21
Alignment explanation
Indices: 28373344--28373387 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28373334 ATCATACAAC
* *
28373344 ATCATAACATTTAAGGCCCTAA
1 ATCA-AACATTCAAGACCCTAA
*
28373366 ATCAAGCATTCAAGACCCTAA
1 ATCAAACATTCAAGACCCTAA
28373387 A
1 A
28373388 AATAGCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (21 bp):
ATCAAACATTCAAGACCCTAA
Found at i:28385336 original size:5 final size:5
Alignment explanation
Indices: 28385326--28385350 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28385316 CTTTATTTGG
28385326 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
28385351 GTATGTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:28385664 original size:50 final size:49
Alignment explanation
Indices: 28385610--28385956 Score: 221
Period size: 50 Copynumber: 6.9 Consensus size: 49
28385600 TGTAATGTCG
** *
28385610 GGGAAGTAAGATTCATCGTTGTGGTTTCAATCTGTTCCACTGCACCGTCT
1 GGGAAGTAAGATTCGCCGTTGTGGTTT-AATCTGTTCAACTGCACCGTCT
* * * * * ** *
28385660 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTTTAACTGTAGTGTCG
1 GGGAAGTAAGATTCGCCGTTGT-GGTTTAATC--TGTTCAACTGCACCGTCT
* ** * * *
28385712 GGGAAGCAAGATTCGCCCATGTGGCTTCAATCTGTTCCACTGCACCGCCT
1 GGGAAGTAAGATTCGCCGTTGTGG-TTTAATCTGTTCAACTGCACCGTCT
* ** * * * ** *
28385762 AGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGT-GGTTTAATCTGTTCAACTGCACCGTCT
* * * *
28385812 GGGAAGCAAGATTCGCCATTGTGGCTTTAGTCTGTTCTACTGCACC--CT
1 GGGAAGTAAGATTCGCCGTTGTGG-TTTAATCTGTTCAACTGCACCGTCT
** * * * * ** *
28385860 GGGAAGTAAGATTCGCTATTGTAGCTTTAATCTTTTTAATTGCAATGTCA
1 GGGAAGTAAGATTCGCCGTTGT-GGTTTAATCTGTTCAACTGCACCGTCT
* * *
28385910 GGGACGTAAGATTCGCCGTTGTAGCTTTAATCTGTTCCACTGCACCG
1 GGGAAGTAAGATTCGCCGTTGT-GGTTTAATCTGTTCAACTGCACCG
28385957 CAATCTTCAA
Statistics
Matches: 215, Mismatches: 73, Indels: 18
0.70 0.24 0.06
Matches are distributed among these distances:
48 35 0.16
49 2 0.01
50 137 0.64
51 6 0.03
52 35 0.16
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCGTTGTGGTTTAATCTGTTCAACTGCACCGTCT
Found at i:28385723 original size:102 final size:98
Alignment explanation
Indices: 28385586--28385957 Score: 467
Period size: 98 Copynumber: 3.7 Consensus size: 98
28385576 ATCTGTAACA
** * * **
28385586 TTAATCTGCTTAACTGTAATGTCGGGGAAGTAAGATTCATCGTTGTGGTTTCAATCTGTTCCACT
1 TTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGGTTT-AATCTGTTCCACT
28385651 GCACCGTCTGGGAAGTAAGATTCGCTGTTGTAGCT
65 GCACCG-CTGGGAAGTAAGATTCGCTGTTGTAGCT
* * ** *
28385686 TTAATCTTTTTTTAACTGTAGTGTCGGGGAAGCAAGATTCGCCCATGTGGCTTCAATCTGTTCCA
1 TTAATC--TTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGG-TTTAATCTGTTCCA
* *
28385751 CTGCACCGCCTAGGAAGTAAGATTCGTTGTTGTAGCT
63 CTGCACCG-CTGGGAAGTAAGATTCGCTGTTGTAGCT
* * *
28385788 TTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAGTCTGTTCTACT
1 TTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGG-TTTAATCTGTTCCACT
*
28385853 GCACC-CTGGGAAGTAAGATTCGCTATTGTAGCT
65 GCACCGCTGGGAAGTAAGATTCGCTGTTGTAGCT
* * * * *
28385886 TTAATCTTTTTAATTGCAATGTCAGGGACGTAAGATTCGCCGTTGTAGCTTTAATCTGTTCCACT
1 TTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT-GGTTTAATCTGTTCCACT
28385951 GCACCGC
65 GCACCGC
28385958 AATCTTCAAC
Statistics
Matches: 237, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
98 85 0.36
99 2 0.01
100 63 0.27
102 85 0.36
103 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (98 bp):
TTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGGTTTAATCTGTTCCACTG
CACCGCTGGGAAGTAAGATTCGCTGTTGTAGCT
Found at i:28387469 original size:48 final size:48
Alignment explanation
Indices: 28387417--28387560 Score: 254
Period size: 48 Copynumber: 3.0 Consensus size: 48
28387407 TTACTTATTA
* *
28387417 TTTTTTT-GGACTCAAAGCGCCTTTTGCGGGTTTTCACCTTGGCCCTT
1 TTTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCCTT
28387464 TTTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCCTT
1 TTTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCCTT
28387512 TTTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTCCCTT
1 TTTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGG-CCCTT
28387561 CTCCTCCTTC
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
47 7 0.08
48 81 0.87
49 5 0.05
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (48 bp):
TTTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCCTT
Found at i:28388422 original size:19 final size:18
Alignment explanation
Indices: 28388400--28388456 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
28388390 TTGATTTTGA
*
28388400 TTTTGATTTTTTCTTTTTT
1 TTTTG-TTTTTTCTTTATT
*
28388419 TTTTCTTTTTTTCTTTATT
1 TTTT-GTTTTTTCTTTATT
28388438 TTTTGTTTTTT-TTTATT
1 TTTTGTTTTTTCTTTATT
28388455 TT
1 TT
28388457 CATTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 20 0.59
ACGTcount: A:0.05, C:0.05, G:0.04, T:0.86
Consensus pattern (18 bp):
TTTTGTTTTTTCTTTATT
Found at i:28388476 original size:48 final size:47
Alignment explanation
Indices: 28388408--28388519 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
28388398 GATTTTGATT
* * *
28388408 TTTTCTTTTTTT-TTTCT-TTTTTTCTTTATTTTTTGT-TTT-TTTTTA
1 TTTTCTTTTTTTATTT-TGTTTTTTATTGATTTTTT-TATTTAATTTTA
*
28388453 TTTTCATTTTTTTATTTTGTTTTTTATTGATTTTTTTATTTCAATTTTC
1 TTTTC-TTTTTTTATTTTGTTTTTTATTGATTTTTTTATTT-AATTTTA
28388502 TTTTCTTTTTTTATTTTG
1 TTTTCTTTTTTTATTTTG
28388520 ATTGTGATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
45 5 0.09
46 9 0.16
47 21 0.37
48 13 0.23
49 9 0.16
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (47 bp):
TTTTCTTTTTTTATTTTGTTTTTTATTGATTTTTTTATTTAATTTTA
Found at i:28388477 original size:30 final size:28
Alignment explanation
Indices: 28388408--28388518 Score: 96
Period size: 30 Copynumber: 3.7 Consensus size: 28
28388398 GATTTTGATT
*
28388408 TTTTCTTTTTTTTTTCTTTTTTTCTTTA
1 TTTTCTTTTTTTTTTATTTTTTTCTTTA
* *
28388436 TTTTTTGTTTTTTTTTATTTTCATTTTTTTA
1 TTTTCT-TTTTTTTTTATTTT--TTTCTTTA
* * * *
28388467 TTTTGTTTTTTATTGATTTTTTTATTTCAA
1 TTTTCTTTTTTTTTTATTTTTTTCTTT--A
28388497 TTTTCTTTTCTTTTTTTATTTT
1 TTTTC-TTT-TTTTTTTATTTT
28388519 GATTGTGATT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
28 11 0.17
29 13 0.20
30 17 0.26
31 15 0.23
32 10 0.15
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (28 bp):
TTTTCTTTTTTTTTTATTTTTTTCTTTA
Found at i:28388489 original size:1 final size:1
Alignment explanation
Indices: 28388406--28388477 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
28388396 TTGATTTTGA
* * * * * * ** *
28388406 TTTTTTCTTTTTTTTTTCTTTTTTTCTTTATTTTTTGTTTTTTTTTATTTTCATTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
28388471 GTTTTTT
1 TTTTTTT
28388478 ATTGATTTTT
Statistics
Matches: 52, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.86
Consensus pattern (1 bp):
T
Found at i:28388499 original size:14 final size:12
Alignment explanation
Indices: 28388413--28388517 Score: 69
Period size: 12 Copynumber: 8.9 Consensus size: 12
28388403 TGATTTTTTC
*
28388413 TTTTTTT-TTTC
1 TTTTTTTATTTA
*
28388424 TTTTTTTCTTTA
1 TTTTTTTATTTA
28388436 TTTTTTGT-TTT-
1 TTTTTT-TATTTA
*
28388447 TTTTTATT-TTCA
1 TTTTT-TTATTTA
28388459 TTTTTTTATTT-
1 TTTTTTTATTTA
*
28388470 TGTTTTTTATTGA
1 T-TTTTTTATTTA
28388483 TTTTTTTATTTCA
1 TTTTTTTATTT-A
* * *
28388496 ATTTTCT-TTTC
1 TTTTTTTATTTA
28388507 TTTTTTTATTT
1 TTTTTTTATTT
28388518 TGATTGTGAT
Statistics
Matches: 75, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
11 23 0.31
12 44 0.59
13 8 0.11
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:28388512 original size:36 final size:37
Alignment explanation
Indices: 28388413--28388516 Score: 96
Period size: 38 Copynumber: 2.9 Consensus size: 37
28388403 TGATTTTTTC
*
28388413 TTTTTT-TTTTC--TTT-TTTTCTTTATTTT-TTGTTT
1 TTTTTTATTTTCATTTTCTTTTCTTT-TTTTATTGTAT
* *
28388446 TTTTTTATTTTCATTTTTTTATTTTGTTTTTTATTG-AT
1 TTTTTTATTTTCATTTTCTT-TTCT-TTTTTTATTGTAT
28388484 TTTTTTA-TTTCAATTTTCTTTTCTTTTTTTATT
1 TTTTTTATTTTC-ATTTTCTTTTCTTTTTTTATT
28388517 TTGATTGTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
33 6 0.10
34 5 0.08
36 12 0.20
37 9 0.15
38 22 0.37
39 5 0.08
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.82
Consensus pattern (37 bp):
TTTTTTATTTTCATTTTCTTTTCTTTTTTTATTGTAT
Found at i:28396293 original size:42 final size:42
Alignment explanation
Indices: 28396247--28396329 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
28396237 GTTTCAGCTT
* *
28396247 AGCTCTT-TCGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTC
1 AGCTCTTAT-GAGCTTCAGTTCAACCCTTATGGGTTTCCGTTC
*
28396289 AGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCCGTT
1 AGCTCTTATGAGCTTCAGTTCAACCCTTATGGGTTTCCGTT
28396330 TAGCACTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.41
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCAGTTCAACCCTTATGGGTTTCCGTTC
Found at i:28396298 original size:21 final size:21
Alignment explanation
Indices: 28396268--28396329 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
28396258 GCTTCAGTTT
*
28396268 AACCCTTATGGGTTTTCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * * *
28396289 AGCTCTTATGAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
28396310 AACCCTTATGGGTTTCCGTT
1 AACCCTTATGGGTTTCCGTT
28396330 TAGCACTTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:28398636 original size:59 final size:59
Alignment explanation
Indices: 28398529--28398686 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 59
28398519 GAAGGAGAAA
* *
28398529 CCCATAACA-CTTACTGTGAAAGTCCGTCGGGACTGTAAACACACGATTCTGTGTGTTGC
1 CCCATGACACCTT-CTGTGAAAGTCCGTCGGGACAGTAAACACACGATTCTGTGTGTTGC
* * * *
28398588 CTCAT-AGCACCTTCTGTGAAAGTCTG-CTGGGACAGTAAACATATGATTCTGTGTGTTGC
1 CCCATGA-CACCTTCTGTGAAAGTCCGTC-GGGACAGTAAACACACGATTCTGTGTGTTGC
*
28398647 CCCATGACACCTTCTGTGAAAGTCCGTCGGGACAATAAAC
1 CCCATGACACCTTCTGTGAAAGTCCGTCGGGACAGTAAAC
28398687 TCGTAATTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
58 2 0.02
59 79 0.92
60 5 0.06
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (59 bp):
CCCATGACACCTTCTGTGAAAGTCCGTCGGGACAGTAAACACACGATTCTGTGTGTTGC
Found at i:28398700 original size:59 final size:58
Alignment explanation
Indices: 28398529--28398706 Score: 191
Period size: 59 Copynumber: 3.0 Consensus size: 58
28398519 GAAGGAGAAA
* * *
28398529 CCCATA-ACACTTACTGTGAAAGTCCGTCGGGACTGTAAACACACGATTCTGTGTGTTGC
1 CCCATACAC-CTT-CTGTGAAAGTCCGTCGGGACAGTAAACTCATGATTCTGTGTGTTGC
* *
28398588 CTCATAGCACCTTCTGTGAAAGTCTG-CTGGGACAGTAAACAT-ATGATTCTGTGTGTTGC
1 CCCATA-CACCTTCTGTGAAAGTCCGTC-GGGACAGTAAAC-TCATGATTCTGTGTGTTGC
* * * * *
28398647 CCCATGACACCTTCTGTGAAAGTCCGTCGGGACAATAAACTCGTAATTTTGTGTATTGC
1 CCCAT-ACACCTTCTGTGAAAGTCCGTCGGGACAGTAAACTCATGATTCTGTGTGTTGC
28398706 C
1 C
28398707 TATGTGTCGT
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
58 2 0.02
59 91 0.91
60 5 0.05
61 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (58 bp):
CCCATACACCTTCTGTGAAAGTCCGTCGGGACAGTAAACTCATGATTCTGTGTGTTGC
Found at i:28403574 original size:13 final size:15
Alignment explanation
Indices: 28403556--28403597 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
28403546 TATTGTTTGA
28403556 TAAAATT-ATTTT-T
1 TAAAATTAATTTTAT
28403569 TAAAATTTAATTTTAT
1 TAAAA-TTAATTTTAT
28403585 TAAAATTTAATTT
1 TAAAA-TTAATTT
28403598 AATTTTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.19
14 2 0.08
15 5 0.19
16 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAATTAATTTTAT
Found at i:28403589 original size:16 final size:15
Alignment explanation
Indices: 28403563--28403597 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
28403553 TGATAAAATT
28403563 ATTTTTTAAAATTTA
1 ATTTTTTAAAATTTA
28403578 ATTTTATTAAAATTTA
1 ATTTT-TTAAAATTTA
28403594 ATTT
1 ATTT
28403598 AATTTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTAAAATTTA
Found at i:28404189 original size:31 final size:31
Alignment explanation
Indices: 28404155--28404215 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
28404145 AAAAATTATA
* *
28404155 AAATAATTCAAAATAATTTTAAAATAATTCA
1 AAATAATTCAAAATAATTTCAAAATAATTTA
*
28404186 AAATAATTTTAAAATAATTT-AAAATAATTT
1 AAATAA-TTCAAAATAATTTCAAAATAATTT
28404216 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAATTCAAAATAATTTCAAAATAATTTA
Found at i:28404243 original size:29 final size:29
Alignment explanation
Indices: 28404146--28404265 Score: 57
Period size: 32 Copynumber: 3.9 Consensus size: 29
28404136 TCTCTCAACA
* *
28404146 AAAATTATAAAATAATTCAAAATAATTTTAA
1 AAAATT-TAAAATAATTTAAAAAAATTTT-A
* * *
28404177 AATAATTCAAAATAATTTTAAAATAATTTAA
1 AA-AATTTAAAATAA-TTTAAAAAAATTTTA
** *
28404208 AATAATTTTTAA-AATTT-AAAATATTTATAA
1 AA-AATTTAAAATAATTTAAAAAAATTT-T-A
*
28404238 AAAATTTTAAAA-AATATATAAAAAATTT
1 AAAA-TTTAAAATAATTTA-AAAAAATTT
28404266 AAGATTTAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
28 7 0.10
29 5 0.07
30 14 0.20
31 19 0.28
32 24 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAATTTAAAATAATTTAAAAAAATTTTA
Found at i:28404248 original size:21 final size:21
Alignment explanation
Indices: 28404148--28404267 Score: 126
Period size: 21 Copynumber: 5.9 Consensus size: 21
28404138 TCTCAACAAA
* *
28404148 AATTATAAAATAATTCAAAAT
1 AATTTTAAAATAATTTAAAAT
*
28404169 AATTTTAAAATAATTCAAAAT
1 AATTTTAAAATAATTTAAAAT
28404190 AATTTTAAAATAATTTAAAAT
1 AATTTTAAAATAATTTAAAAT
*
28404211 AATTTT-TAA-AATTTAAAAT
1 AATTTTAAAATAATTTAAAAT
28404230 -ATTTATAAAA-AATTTTAAAA-
1 AATTT-TAAAATAA-TTTAAAAT
*
28404250 AATATATAAAA-AATTTAA
1 AAT-TTTAAAATAATTTAA
28404268 GATTTAAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.04
19 11 0.12
20 11 0.12
21 62 0.70
22 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTTAAAATAATTTAAAAT
Found at i:28404250 original size:11 final size:10
Alignment explanation
Indices: 28404148--28404267 Score: 104
Period size: 10 Copynumber: 11.7 Consensus size: 10
28404138 TCTCAACAAA
28404148 AATTATAAAAT
1 AATT-TAAAAT
*
28404159 AATTCAAAAT
1 AATTTAAAAT
28404169 AATTTTAAAAT
1 AA-TTTAAAAT
*
28404180 AATTCAAAAT
1 AATTTAAAAT
28404190 AATTTTAAAAT
1 AA-TTTAAAAT
28404201 AATTTAAAAT
1 AATTTAAAAT
**
28404211 AATTTTTAA-
1 AATTTAAAAT
28404220 AATTTAAAAT
1 AATTTAAAAT
*
28404230 -ATTTATAAAA
1 AATTTA-AAAT
28404240 AATTTTAAAA-
1 AA-TTTAAAAT
28404250 AATATATAAAA-
1 AAT-T-TAAAAT
28404261 AATTTAA
1 AATTTAA
28404268 GATTTAAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
9 16 0.17
10 38 0.41
11 34 0.37
12 4 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:28408070 original size:40 final size:40
Alignment explanation
Indices: 28407987--28408249 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
28407977 TTGAATGCTG
* * * * * *
28407987 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28408027 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28408067 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28408107 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
28408147 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28408187 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28408226 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28408250 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:28408269 original size:79 final size:80
Alignment explanation
Indices: 28408026--28408284 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
28408016 AAGTGAATAT
* * * * * *
28408026 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
28408090 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
28408106 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
28408171 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
28408186 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
28408250 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
28408265 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
28408285 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:28414738 original size:7 final size:8
Alignment explanation
Indices: 28414715--28414739 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28414705 AAAAAGAGAG
28414715 AAGGAAAA
1 AAGGAAAA
28414723 AAGGAAAA
1 AAGGAAAA
28414731 AAGGAAAA
1 AAGGAAAA
28414739 A
1 A
28414740 TAAAAGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:28415609 original size:7 final size:7
Alignment explanation
Indices: 28415593--28415636 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
28415583 TTGAGTAAAA
28415593 AAAAAGTG
1 AAAAA-TG
28415601 AAAAATG
1 AAAAATG
28415608 AAAAAGTG
1 AAAAA-TG
28415616 -AAAATG
1 AAAAATG
*
28415622 AAAAATA
1 AAAAATG
28415629 AAAAATG
1 AAAAATG
28415636 A
1 A
28415637 TGAAAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 23 0.72
8 7 0.22
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:28415619 original size:14 final size:15
Alignment explanation
Indices: 28415593--28415654 Score: 67
Period size: 14 Copynumber: 4.1 Consensus size: 15
28415583 TTGAGTAAAA
28415593 AAAAAGTGAAAAATG
1 AAAAAGTGAAAAATG
28415608 AAAAAGTG-AAAATG
1 AAAAAGTGAAAAATG
*
28415622 AAAAA-TAAAAAATGATG
1 AAAAAGT-GAAAA--ATG
28415639 AAAAAGT-AAAAATG
1 AAAAAGTGAAAAATG
28415653 AA
1 AA
28415655 GAGGCTAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 1 0.02
14 16 0.39
15 11 0.27
16 4 0.10
17 8 0.20
18 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.15
Consensus pattern (15 bp):
AAAAAGTGAAAAATG
Found at i:28416992 original size:44 final size:44
Alignment explanation
Indices: 28416888--28416978 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
28416878 TGGTGAAATC
* *
28416888 ACAAGTTCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
1 ACAAGTCCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
*
28416932 GCAAGTCCTAACTCCCTGACCAGCAGTGGAATAGGTTGGAA-ATT
1 ACAAGTCCTAACTCCCTGACCAGCAGTGGAATAGGTT-GAAGATT
28416976 ACA
1 ACA
28416979 GATCTTATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 39 0.93
45 3 0.07
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (44 bp):
ACAAGTCCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
Found at i:28417302 original size:129 final size:129
Alignment explanation
Indices: 28416933--28417327 Score: 598
Period size: 128 Copynumber: 3.1 Consensus size: 129
28416923 TTGAAGATTG
** *
28416933 CAAGTCCTA-ACTCCCTGACCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTATCTCCCTAAG
1 CAAGTCCTATA-TCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAG
** * * *
28416996 CAGTAGTAGAGCAGATCGAAGACGGTAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCT
65 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCA
* * *
28417061 CAAGTCTTATTTCTCTGGTCAGCAGTGGAATAGGTTGGG-AATTACAGATCTTGTCTCCCTAAGC
1 CAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGC
*
28417125 AGTAGCGGAGCAGATCGAAAACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCA
66 AGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCA
28417189 CAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGC
1 CAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGC
* * ** *
28417254 AGTAGCGGAGCAGATCGAAGACTGCGAATCTTATCTTCAACTGTAAGGAAGTAGATTTAAGCCA
66 AGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCA
*
28417318 CAAATCCTAT
1 CAAGTCCTAT
28417328 CTCCTTGAAG
Statistics
Matches: 242, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
128 148 0.61
129 94 0.39
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (129 bp):
CAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGC
AGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCA
Found at i:28417515 original size:45 final size:44
Alignment explanation
Indices: 28417453--28417565 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 44
28417443 TAAGCAGGTG
* * *
28417453 TTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGA-AAATC
* * * * *
28417498 TTATCTCCCTGAGGTTGCAGTGAAACAGATTGAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGAAAATC
*
28417542 CTATCTCCCTGAAGTTGCAGTGGA
1 TTATCTCCCTGAAGTTGCAGTGGA
28417566 GCGGATTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 25 0.44
45 32 0.56
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGAAAATC
Found at i:28417591 original size:44 final size:44
Alignment explanation
Indices: 28417453--28417832 Score: 136
Period size: 44 Copynumber: 8.7 Consensus size: 44
28417443 TAAGCAGGTG
* * * * * *
28417453 TTATCCCCCTGAAGTTGCAGTGG-GACAGATCGAAGATGACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAG-CAGAT-TAAAATAATAGATC
* * * ****
28417498 TTATCTCCCTGAGGTTGCAGTGAAACAGATTGAAGCCGATA-ATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAATAGATC
* *
28417542 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAATAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATC
** * ** *** * *
28417586 TTATCTTTCTGAAGTTGCAGTAGAGTGGA-TGGCAT--CAGGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATC
* *
28417627 TTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAA-ACA-AG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAATA-ATAGATC
* * ** * *** * *
28417671 TTCT-TCCCCTAAAGTCACAGTGGGGCAGA-CCGAATAAGCAAATC
1 TTATCT-CCCTGAAGTTGCAGTGGAGCAGATTAAAATAA-TAGATC
* * * * *
28417715 TTATCTCCCTG-AGATTACAGTGGAGTAGATTGAAGTCGATA-ATC
1 TTATCTCCCTGAAG-TTGCAGTGGAGCAGATTAAAAT-AATAGATC
* * * * * *
28417759 CTATCTCCCTAAAGTTGTAGTGGAGCGGGTTAAAGTAATAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATC
* *
28417803 TTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGAT
28417833 CGCATCAAGT
Statistics
Matches: 241, Mismatches: 74, Indels: 41
0.68 0.21 0.12
Matches are distributed among these distances:
41 30 0.12
42 1 0.00
43 15 0.06
44 155 0.64
45 39 0.16
46 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATC
Found at i:28417802 original size:217 final size:218
Alignment explanation
Indices: 28417320--28417845 Score: 712
Period size: 218 Copynumber: 2.4 Consensus size: 218
28417310 TTAAGCCACA
* * * *
28417320 AATCCTATCTCCTTGAAGTTGTAGTGAAGCGGATTAAAGTAATAAATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
* * * * *
28417385 CAGTAGAGTGGATCGCATTAGGTCTTATCTCTCTAAGGTTGCAGCGGAACAGACTGAGTAAGCAG
66 CAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGCGGAACAGACTGAGAAAACAA
* * ** * * * *
28417450 GTGTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGACAAATCTTATCTCCCTGAGGTTG
131 GTCTTATCCCCCTAAAGTCACAGTGGGACAGACCGAAGAAGACAAATCTTATCTCCCTGAGATTA
28417515 CAGTGAAACAGATTGAAGCCGAT
196 CAGTGAAACAGATTGAAGCCGAT
* * *
28417538 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAATAGATCTTATCTTTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
* * * *
28417603 CAGTAGAGTGGATGGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAAACAA
66 CAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGCGGAACAGACTGAGAAAACAA
* * * *
28417668 GTCTTCTTCCCCTAAAGTCACAGTGGGGCAGACCGAATAAG-CAAATCTTATCTCCCTGAGATTA
131 GTCTTATCCCCCTAAAGTCACAGTGGGACAGACCGAAGAAGACAAATCTTATCTCCCTGAGATTA
* ** *
28417732 CAGTGGAGTAGATTGAAGTCGAT
196 CAGTGAAACAGATTGAAGCCGAT
* *
28417755 AATCCTATCTCCCTAAAGTTGTAGTGGAGCGGGTTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
** *
28417820 CAGTAGAGCAGATCGCATCAAGTCTT
66 CAGTAGAGTGGATCGCATCAGGTCTT
28417846 GCCGACTAGA
Statistics
Matches: 267, Mismatches: 41, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
217 122 0.46
218 145 0.54
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (218 bp):
AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
CAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGCGGAACAGACTGAGAAAACAA
GTCTTATCCCCCTAAAGTCACAGTGGGACAGACCGAAGAAGACAAATCTTATCTCCCTGAGATTA
CAGTGAAACAGATTGAAGCCGAT
Found at i:28422761 original size:285 final size:290
Alignment explanation
Indices: 28422310--28422932 Score: 687
Period size: 291 Copynumber: 2.2 Consensus size: 290
28422300 TTTTTAATTT
* * * ** * * ** *
28422310 AAAAGACTAAAATATCTTCGAATAATATAAGTTATTTTAAATATGGAATGACATTTTTTTAATTT
1 AAAAGACTAAAATACCTTCGAATAATATAACTCATTTTAAATACAGAAGGACATCTTCGTAATTC
* *
28422375 CCTAAACAAGTTGGTGCCTAGTTGACTCATGATACCAACTCAGCCAAGAATTTTATTAATAGTTT
66 CCTAAACAAGTTGGTGCCTAGTTGACTCATGATACCAACTCAGCCAAGAATCTTA-TAATAG-AT
* * *
28422440 AGATACAATTGATGGAATTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAGTAT-TAAAA
129 AGATACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATCAAAAA
* * * *
28422504 AA-ACTTT-T-AGTGGTAAATTAAATATTTTACTAATGCAATTGACTTATGTGGGTTCAAATCTC
194 AAGACTTTGTAAGCGGTAAATTAAAGATTTTACTAATACAATTG----ATGTAGGTTCAAATCTC
** *
28422566 ACCATGTGCATATTTTTATT-G-GTGTTTTAAAGTA
255 ACCATACGCATATTTTTATTAGTGTGTTTTAAAATA
*
28422600 AAAAGATTAAAATACCTTCGAATAATATAACTCATTTTAAATACAGAAGGACATCTTCGTAATTC
1 AAAAGACTAAAATACCTTCGAATAATATAACTCATTTTAAATACAGAAGGACATCTTCGTAATT-
* * * * * *
28422665 CCCTAATCGAGTTGGTGTCTGGTTTACTCAT-ATCACCAACTCAGTCAAGAA-CTTA-AATA-AT
65 CCCTAAACAAGTTGGTGCCTAGTTGACTCATGAT-ACCAACTCAGCCAAGAATCTTATAATAGAT
* * * *
28422726 AG-TACAATTGATGGAGGTAATAAAGTGTGCATAATAAATTTAGAATGTATAAAAATGTCAAAAA
129 AGATACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATCAAAAA
* * *
28422790 AAGAGTTTAGGTAAGCGGTAAATTAAAGGTTTTTCTAATACAATTGATGTAGGTTCAAATCTCAC
194 AAGACTTT--GTAAGCGGTAAATTAAAGATTTTACTAATACAATTGATGTAGGTTCAAATCTCAC
* *
28422855 CATACGCATATTTTTATTAGTTTTTTTTAAAATA
257 CATACGCATATTTTTATTAGTGTGTTTTAAAATA
* *
28422889 AAACA-ACTAAAATACCCTT-GAATAATATTACCCATTTTAAATAC
1 AAA-AGACTAAAATA-CCTTCGAATAATATAACTCATTTTAAATAC
28422933 GAAAATACAT
Statistics
Matches: 280, Mismatches: 41, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
285 50 0.18
286 9 0.03
287 38 0.14
288 5 0.02
289 44 0.16
290 65 0.23
291 69 0.25
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (290 bp):
AAAAGACTAAAATACCTTCGAATAATATAACTCATTTTAAATACAGAAGGACATCTTCGTAATTC
CCTAAACAAGTTGGTGCCTAGTTGACTCATGATACCAACTCAGCCAAGAATCTTATAATAGATAG
ATACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATCAAAAAAA
GACTTTGTAAGCGGTAAATTAAAGATTTTACTAATACAATTGATGTAGGTTCAAATCTCACCATA
CGCATATTTTTATTAGTGTGTTTTAAAATA
Found at i:28423013 original size:289 final size:282
Alignment explanation
Indices: 28422443--28423015 Score: 616
Period size: 289 Copynumber: 2.0 Consensus size: 282
28422433 ATAGTTTAGA
* * *
28422443 TACAATTGATGGAATTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAGTATTAAAAAAAC
1 TACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATAAAAAAAAC
* * * * **
28422508 TTTTAGTGGTAAATTAAATATTTTACTAATGCAATTGACTTATGTGGGTTCAAATCTCACCATGT
66 TTTTAGCGGTAAATTAAAGATTTTACTAATACAATTG---TATGTAGGTTCAAATCTCACCATAC
* * *
28422573 GCATATTTTTATTGGTGTTTTAAAGTAAAAAGATTAAAATACCTTCGAATAATATAACTCATTTT
128 GCATATTTTTATTGGTGTTTTAAAATAAAAAGACTAAAATACCTTCGAATAATATAACCCATTTT
* * **** * *
28422638 AAATACAGAAGGACATCTTCGTAATTCCCCTAATCGAGTTGGTGTCTGGTTTACTCATATCACCA
193 AAATACAGAAAGACATCTTCGTAATTCCCCTAATCAAGTTGACACCCGATTTACTCATATCACCA
* *
28422703 ACTCAGTCAAGAACTTAAATAATAG
258 ACTCAATCAAGAACATAAATAATAG
* * * *
28422728 TACAATTGATGGAGGTAATAAAGTGTGCATAATAAATTTAGAATGTATAAAAATGTCAAAAAAAG
1 TACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATAT-AAAAAAA-
* * *
28422793 AGTTTAGGTAAGCGGTAAATTAAAGGTTTTTCTAATACAATTG-ATGTAGGTTCAAATCTCACCA
64 ACTTT---T-AGCGGTAAATTAAAGATTTTACTAATACAATTGTATGTAGGTTCAAATCTCACCA
* * *
28422857 TACGCATATTTTTATTAGTTTTTTTTAAAATAAAACA-ACTAAAATACCCTT-GAATAATATTAC
125 TACGCATATTTTTATT-G-GTGTTTTAAAATAAAA-AGACTAAAATA-CCTTCGAATAATATAAC
* * * * *
28422920 CCATTTTAAATAC-GAAAATACATTTTTGTAATTTCTCTAATCAAGTTGACACCCGATTTACTCA
186 CCATTTTAAATACAG-AAAGACATCTTCGTAATTCCCCTAATCAAGTTGACACCCGATTTACTCA
* * *
28422984 TGAT-ACCAATTCAATCAATAGCATAAATAATA
250 T-ATCACCAACTCAATCAAGAACATAAATAATA
28423016 TATAGATGTT
Statistics
Matches: 236, Mismatches: 40, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
285 50 0.21
286 6 0.03
287 38 0.16
288 2 0.01
289 104 0.44
290 8 0.03
291 28 0.12
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (282 bp):
TACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATAAAAAAAAC
TTTTAGCGGTAAATTAAAGATTTTACTAATACAATTGTATGTAGGTTCAAATCTCACCATACGCA
TATTTTTATTGGTGTTTTAAAATAAAAAGACTAAAATACCTTCGAATAATATAACCCATTTTAAA
TACAGAAAGACATCTTCGTAATTCCCCTAATCAAGTTGACACCCGATTTACTCATATCACCAACT
CAATCAAGAACATAAATAATAG
Found at i:28425726 original size:17 final size:17
Alignment explanation
Indices: 28425700--28425733 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28425690 TCAAAACAAC
*
28425700 ATAATGAACATTCAAAT
1 ATAATGAACATTAAAAT
*
28425717 ATAATTAACATTAAAAT
1 ATAATGAACATTAAAAT
28425734 GATTACGGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAATGAACATTAAAAT
Found at i:28426222 original size:19 final size:18
Alignment explanation
Indices: 28426194--28426241 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 18
28426184 TAACAGCCCG
28426194 TATTTATCATC-AATTTGTAA
1 TATTT-TCATCTAATTT-T-A
28426214 TATTTTCATCTAATTTTA
1 TATTTTCATCTAATTTTA
28426232 TCATTTTCAT
1 T-ATTTTCAT
28426242 AAATAAGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTTTCATCTAATTTTA
Found at i:28437855 original size:13 final size:13
Alignment explanation
Indices: 28437837--28437878 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
28437827 AGATTTTTCG
28437837 TAAATATTATCAC
1 TAAATATTATCAC
28437850 TAAATA--ATC-C
1 TAAATATTATCAC
28437860 TAAATATTATCAC
1 TAAATATTATCAC
28437873 TAAATA
1 TAAATA
28437879 AATCAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:28437887 original size:23 final size:23
Alignment explanation
Indices: 28437838--28437887 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
28437828 GATTTTTCGT
*
28437838 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCCA
28437861 AAATATTATCACTAAATAAAT-CA
1 AAATATTATCACTAAAT-AATCCA
28437884 AAAT
1 AAAT
28437888 TTAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:28441647 original size:13 final size:13
Alignment explanation
Indices: 28441629--28441661 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
28441619 AATTTTGATT
28441629 TATTTAGTGATAA
1 TATTTAGTGATAA
28441642 TATTTAGTGATAA
1 TATTTAGTGATAA
28441655 TATTTAG
1 TATTTAG
28441662 GGAAAATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:28444312 original size:21 final size:21
Alignment explanation
Indices: 28444288--28444328 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28444278 ATATGGAATC
*
28444288 AGATTTTGTTTAAAGGCTTTA
1 AGATTCTGTTTAAAGGCTTTA
28444309 AGATTCTGTTTAAAGGCTTT
1 AGATTCTGTTTAAAGGCTTT
28444329 CTTTTGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (21 bp):
AGATTCTGTTTAAAGGCTTTA
Found at i:28446088 original size:22 final size:23
Alignment explanation
Indices: 28446039--28446082 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
28446029 TTTCGATGCC
*
28446039 TGTAATAGCCCGAAAATTACTAA
1 TGTAATAGCCCAAAAATTACTAA
28446062 TGTAATA-CCCAAAAATTACTA
1 TGTAATAGCCCAAAAATTACTA
28446083 CAGTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (23 bp):
TGTAATAGCCCAAAAATTACTAA
Found at i:28463487 original size:15 final size:14
Alignment explanation
Indices: 28463469--28463498 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28463459 AATGACTATT
28463469 ACATTAATAATGAAA
1 ACATTAATAAT-AAA
28463484 ACATTAATAATAAA
1 ACATTAATAATAAA
28463498 A
1 A
28463499 TAAGTATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (14 bp):
ACATTAATAATAAA
Found at i:28463976 original size:22 final size:21
Alignment explanation
Indices: 28463946--28463990 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
28463936 AATTATTATC
* *
28463946 ATATTTAAAATAATTCATACTT
1 ATATATAAAAAAATT-ATACTT
*
28463968 ATATATAAAAAAATTATATTT
1 ATATATAAAAAAATTATACTT
28463989 AT
1 AT
28463991 TTAATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATAAAAAAATTATACTT
Found at i:28467349 original size:39 final size:38
Alignment explanation
Indices: 28467302--28467416 Score: 106
Period size: 39 Copynumber: 3.0 Consensus size: 38
28467292 ATAAAGATGC
28467302 TTTAGAGTATTGTGGTATATGCTTGAATGTTATGTGAT
1 TTTAGAGTATTGTGGTATATGCTTGAATGTTATGTGAT
* * * * *
28467340 TTTACGAGTATTATGAG-ATATGCTTAAACGTCATGAGAT
1 TTTA-GAGTATTGTG-GTATATGCTTGAATGTTATGTGAT
* * * * *
28467379 TATATGAGTATGGTGATATATGCTTGTATGTTAAGTGA
1 TTTA-GAGTATTGTGGTATATGCTTGAATGTTATGTGA
28467417 CCTAAAACCT
Statistics
Matches: 58, Mismatches: 16, Indels: 5
0.73 0.20 0.06
Matches are distributed among these distances:
38 4 0.07
39 53 0.91
40 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (38 bp):
TTTAGAGTATTGTGGTATATGCTTGAATGTTATGTGAT
Found at i:28474909 original size:108 final size:108
Alignment explanation
Indices: 28474782--28475416 Score: 509
Period size: 108 Copynumber: 5.9 Consensus size: 108
28474772 TGGAGTTTGC
** * * * *
28474782 TGATTTACGATCACAACCTTCTCCTTACAGGATTTTACGGATCTCACAGTCTGCCGATTTACGAT
1 TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTGCTGATTTACGAT
* * * **
28474847 CACAACTTTCTACTTTA-GGGATTTTACAAATCTTGCGATTCGT
66 CACGACCTTCTAC-TTACGGGATTTTACGAATCTCACGATTCGT
* * * * **
28474890 TGATTTACGATCATGACCTTTTACTGACGGGACTTTACAAATCTCGTAGTCTGCTGATTTACGAT
1 TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTGCTGATTTACGAT
* ** * *
28474955 TACGA-C--CTACTTACAAGATTTTATGACTCTCACGATCTAC-T
66 CACGACCTTCTACTTACGGGATTTTACGAATCTCACGAT-T-CGT
* * * * * * **
28474996 T-ATTTACGATGATAACCTTTTACATATGGGATTTTACAAATCTCATGGTCTGCTGATTTACGAT
1 TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTGCTGATTTACGAT
* * * * ** * * *
28475060 AATGACCTTTTACTTATGAAATTTTATGAATCTCACGATTAGC
66 CACGACCTTCTACTTACGGGATTTTACGAATCTCACGATTCGT
* * * * * ** *
28475103 TAATTTACGATCAAGACCTTCTACTTATGAGATTTTACGAATCTTACAGTCCACTGATTTATGAT
1 TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTGCTGATTTACGAT
* * * *
28475168 CATGACCTTCTACTTACGGGATTTTACAAATCTCAC-AGTCCTT
66 CACGACCTTCTACTTACGGGATTTTACGAATCTCACGA-TTCGT
* * * *
28475211 TGATTTACGATCATGATCTTCTACTTACGGGATTTTACGAATCTCACGGT-TCGTTGATTTATGA
1 TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCT-GCTGATTTACGA
* * *
28475275 TCATGACCTCCTACTTATGGGATTTTACGAATCT-AGCGATAT-GT
65 TCACGACCTTCTACTTACGGGATTTTACGAATCTCA-CGAT-TCGT
* * * * * *
28475319 TAATTTACGTTCATGACCTTCTACTTACGGGATTTTACGAATCTCACGGTCCT-CTAATTTATGT
1 TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGT-CTGCTGATTTACGA
** * *
28475383 TCATAACCTTCTAATTACGTGATTTTACGAATCT
65 TCACGACCTTCTACTTACGGGATTTTACGAATCT
28475417 AGGTGTGTTT
Statistics
Matches: 423, Mismatches: 89, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
104 3 0.01
105 77 0.18
106 4 0.01
107 5 0.01
108 332 0.78
109 1 0.00
110 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (108 bp):
TGATTTACGATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTGCTGATTTACGAT
CACGACCTTCTACTTACGGGATTTTACGAATCTCACGATTCGT
Found at i:28475017 original size:105 final size:106
Alignment explanation
Indices: 28474892--28475115 Score: 276
Period size: 105 Copynumber: 2.1 Consensus size: 106
28474882 CGATTCGTTG
* * *
28474892 ATTTACGATCATGACCTTTTAC-TGACGGGACTTTACAAATCTCGTAGTCTGCTGATTTACGATT
1 ATTTACGATCATAACCTTTTACAT-ACGGGACTTTACAAATCTCATAGTCTGCTGATTTACGATA
* *
28474956 ACGACC-TACTTA-CAAGATTTTATGACTCTCACGATCTA-CTT
65 ACGACCTTACTTATCAA-ATTTTATGAATCTCACGAT-TAGCTA
* * * *
28474997 ATTTACGATGATAACCTTTTACATATGGGATTTTACAAATCTCATGGTCTGCTGATTTACGATAA
1 ATTTACGATCATAACCTTTTACATACGGGACTTTACAAATCTCATAGTCTGCTGATTTACGATAA
* *
28475062 TGACCTTTTACTTATGAAATTTTATGAATCTCACGATTAGCTA
66 CGACC--TTACTTATCAAATTTTATGAATCTCACGATTAGCTA
28475105 ATTTACGATCA
1 ATTTACGATCA
28475116 AGACCTTCTA
Statistics
Matches: 101, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
105 60 0.59
106 1 0.01
107 2 0.02
108 36 0.36
109 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (106 bp):
ATTTACGATCATAACCTTTTACATACGGGACTTTACAAATCTCATAGTCTGCTGATTTACGATAA
CGACCTTACTTATCAAATTTTATGAATCTCACGATTAGCTA
Found at i:28475256 original size:54 final size:53
Alignment explanation
Indices: 28474629--28475416 Score: 455
Period size: 54 Copynumber: 14.7 Consensus size: 53
28474619 TTTAATTAAA
* * * * * ** * *
28474629 ATCACGACTTTCTACTTACAGAATTTTATGAATCTTGCGGTCCTCTGATTTAAG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGT-CTCTGATTTACG
* * * ** * * * * * *
28474683 ATCATGACATTTTACATATAGGATTTTACGAATCTCATGAGCCACTCATTTTCA
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCA-CAGTCTCTGATTTACG
* * *** *
28474737 ATCA-GAACCTT-TAACTTACGAGATTTTACGAACCTTGGAGTTTGCTGATTTACG
1 ATCATG-ACCTTCT-ACTTACGGGATTTTACGAATCTCACAGTCT-CTGATTTACG
** * * * *
28474791 ATCACAACCTTCTCCTTACAGGATTTTACGGATCTCACAGTCTGCCGATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCT-CTGATTTACG
** * * ** *
28474845 ATCACAACTTTCTACTTTA-GGGATTTTACAAATCTTGCGATTCGT-TGATTTACG
1 ATCATGACCTTCTAC-TTACGGGATTTTACGAATCTCAC-AGTC-TCTGATTTACG
* * * * **
28474899 ATCATGACCTTTTACTGACGGGACTTTACAAATCTCGTAGTCTGCTGATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCT-CTGATTTACG
* * ** * * *
28474953 ATTACGA-C--CTACTTACAAGATTTTATGACTCTCAC-GATCTACTTATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAG-TCT-CTGATTTACG
* * * * * * **
28475004 ATGATAACCTTTTACATATGGGATTTTACAAATCTCATGGTCTGCTGATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCT-CTGATTTACG
* * * ** * * ** *
28475058 ATAATGACCTTTTACTTATGAAATTTTATGAATCTCACGATTAGCTAATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCAC-AGTCTCTGATTTACG
* * * * * *
28475112 ATCAAGACCTTCTACTTATGAGATTTTACGAATCTTACAGTCCACTGATTTATG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGT-CTCTGATTTACG
* *
28475166 ATCATGACCTTCTACTTACGGGATTTTACAAATCTCACAGTCCTTTGATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGT-CTCTGATTTACG
* * *
28475220 ATCATGATCTTCTACTTACGGGATTTTACGAATCTCACGGT-TCGTTGATTTATG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTC--TGATTTACG
* * * * *
28475274 ATCATGACCTCCTACTTATGGGATTTTACGAATCT-AGC-GATATGTTAATTTACG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCA-CAG-TCT-CTGATTTACG
* * * *
28475328 TTCATGACCTTCTACTTACGGGATTTTACGAATCTCACGGTCCTCTAATTTATG
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGT-CTCTGATTTACG
* * * *
28475382 TTCATAACCTTCTAATTACGTGATTTTACGAATCT
1 ATCATGACCTTCTACTTACGGGATTTTACGAATCT
28475417 AGGTGTGTTT
Statistics
Matches: 566, Mismatches: 140, Indels: 56
0.74 0.18 0.07
Matches are distributed among these distances:
50 1 0.00
51 33 0.06
52 3 0.01
53 15 0.03
54 499 0.88
55 14 0.02
56 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (53 bp):
ATCATGACCTTCTACTTACGGGATTTTACGAATCTCACAGTCTCTGATTTACG
Found at i:28475860 original size:54 final size:54
Alignment explanation
Indices: 28475748--28475925 Score: 144
Period size: 54 Copynumber: 3.3 Consensus size: 54
28475738 TGGTCTATTG
* * * * * * * **** *
28475748 ATTTACGATAATGACCTTTTACTTACGGGATTTTATGAATCTCACAGTTTGTTG
1 ATTTACGATCATGACCTTCTACATACAGGATTTTAAGAATCCCACGGTCCACTA
* *
28475802 ATTTACGATCATGACCTTCTACTTA-TGAGATTTTACA-AATCCCACGGTCCACTA
1 ATTTACGATCATGACCTTCTACATACAG-GATTTTA-AGAATCCCACGGTCCACTA
** **
28475856 ATTTACGATCATGATTTTCTACATACAGGATTTTAAGAATCTTACGGTCCACTA
1 ATTTACGATCATGACCTTCTACATACAGGATTTTAAGAATCCCACGGTCCACTA
* *
28475910 ATTTATGATCACGACC
1 ATTTACGATCATGACC
28475926 ACCTATTTAC
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
53 2 0.02
54 96 0.97
55 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (54 bp):
ATTTACGATCATGACCTTCTACATACAGGATTTTAAGAATCCCACGGTCCACTA
Found at i:28477094 original size:13 final size:13
Alignment explanation
Indices: 28477076--28477101 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28477066 GAAACAAAGA
28477076 AACCCTAGCCTCT
1 AACCCTAGCCTCT
28477089 AACCCTAGCCTCT
1 AACCCTAGCCTCT
28477102 GTCGCCGCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
AACCCTAGCCTCT
Found at i:28477999 original size:3 final size:3
Alignment explanation
Indices: 28477991--28478076 Score: 57
Period size: 3 Copynumber: 27.7 Consensus size: 3
28477981 TGTAATCCTT
*** * * *
28477991 TTA TTA TTA TTA TTA TTA TTA AGC TTA TTA TGA TTA TTA TTC TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
28478039 TTGCA TTTA TTA TTA TTA CTT- TCC TTA TTA TTA TTA TT
1 TT--A -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
28478077 TACCCACTTA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 1 0.02
3 57 0.89
4 3 0.05
5 1 0.02
6 2 0.03
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28478335 original size:25 final size:27
Alignment explanation
Indices: 28478284--28478344 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28478274 AGGCTTTATA
*
28478284 ATTTATATATATACATAGATATGCATAT
1 ATTT-TATATATACATACATATGCATAT
* *
28478312 TTTTTATATGTACATACAT-T-CATAT
1 ATTTTATATATACATACATATGCATAT
28478337 ATTTTATA
1 ATTTTATA
28478345 ATTTATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 12 0.41
26 1 0.03
27 13 0.45
28 3 0.10
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (27 bp):
ATTTTATATATACATACATATGCATAT
Found at i:28478514 original size:33 final size:33
Alignment explanation
Indices: 28478473--28478545 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
28478463 GCTTTAGTTC
28478473 TTTTTATTTACTCATTGCTTCATGTATAATTGT
1 TTTTTATTTACTCATTGCTTCATGTATAATTGT
28478506 TTTTTATTTACTCATTGCTTCATGTATAATTGT
1 TTTTTATTTACTCATTGCTTCATGTATAATTGT
28478539 TTTTTAT
1 TTTTTAT
28478546 GTGTCCTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (33 bp):
TTTTTATTTACTCATTGCTTCATGTATAATTGT
Found at i:28479066 original size:107 final size:108
Alignment explanation
Indices: 28478862--28479066 Score: 324
Period size: 107 Copynumber: 1.9 Consensus size: 108
28478852 AAAAATAACG
* * *
28478862 AAGGTAAATATTTTGCTTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTTCGATTTTT
1 AAGGTAAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTC
*
28478927 TCATTTGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAAT
66 TCATTTGACCAAATAGCCAAATATCCTCTTAAAATTTCAAAAT
*
28478970 AAGG-AAATATTTTGCGTTTGAGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGA-TTT
1 AAGGTAAATATTTTGCGTTTG-GAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTT
* *
28479033 CTCATTTGACCAAATAGTCAAATATTCTCTTAAA
65 CTCATTTGACCAAATAGCCAAATATCCTCTTAAA
28479067 TCTTAATCCA
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 48 0.54
108 41 0.46
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (108 bp):
AAGGTAAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTC
TCATTTGACCAAATAGCCAAATATCCTCTTAAAATTTCAAAAT
Found at i:28482763 original size:17 final size:17
Alignment explanation
Indices: 28482743--28482785 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
28482733 AATCAAAGTC
*
28482743 AAAAATAAGAGAAAAAG
1 AAAAAAAAGAGAAAAAG
*
28482760 AAAAAAAATAGAAAAAG
1 AAAAAAAAGAGAAAAAG
28482777 AAAAGAAAA
1 AAAA-AAAA
28482786 AGGAGAGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAAG
Found at i:28482787 original size:11 final size:11
Alignment explanation
Indices: 28482755--28482787 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28482745 AAATAAGAGA
28482755 AAAAGAAAAA-
1 AAAAGAAAAAG
28482765 AAATAGAAAAAG
1 AAA-AGAAAAAG
28482777 AAAAGAAAAAG
1 AAAAGAAAAAG
28482788 GAGAGGTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:28485022 original size:88 final size:88
Alignment explanation
Indices: 28484873--28485538 Score: 1035
Period size: 88 Copynumber: 7.6 Consensus size: 88
28484863 AACAGATCAA
*
28484873 TGAAGACAACAAATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
* *
28484938 CTCTCAGTTGTAGCGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * *
28484961 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGTGAAGCAAATCGAAGACAAAAACCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
* * *
28485026 CTCTCGGTTGTCGCGGAGCTAGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* *
28485049 TGAAGACAATAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
28485114 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * * *
28485137 TGATGACAACAGATCTTGCCTTCCTGAATCGACAACGAAGCAAATCGAAGACACAAACCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
*
28485202 CTCTCAGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * *
28485225 TGATGACAACAGATCTTGCCTTCCTGCATTGATAGCAAAGCAGATCGAAGACACAAACCTTGTCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
**
28485290 CTCTCGGTTGTAGCAGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
28485313 TGAAGACAACAGATCTTGCCTTCCTGCATTGATAGCAAAGCAGATCGAAGACACAAACTTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
28485378 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* *
28485401 TGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGATCGAAGACATAAACCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
28485466 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * *
28485489 TGAAAACAACAGATCTTGCCTTCCTGCATTAACGGTGAAGCAGATCGAAG
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAG
28485539 TTACAAATCC
Statistics
Matches: 530, Mismatches: 48, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 530 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (88 bp):
TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
CTCTCGGTTGTAGTGGAGCTGGT
Found at i:28485507 original size:44 final size:44
Alignment explanation
Indices: 28484931--28485509 Score: 251
Period size: 44 Copynumber: 13.2 Consensus size: 44
28484921 AGACACAAAC
* *
28484931 CTTGCCTCTCTCAGTTGTAGCGGAGCTGGTTGAAGACAATAGAT
1 CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
* * * * *** * * *
28484975 CTTGCCT-TC-CTGCATTGACAGTGAAGCAAATCGAAGACAA-AAAC
1 CTTGCCTCTCTC-G-GTTG-TAGCGGAGCTGGTTGAAGACAACAGAT
* * *
28485019 CTTGCCTCTCTCGGTTGTCGCGGAGCTAGTTGAAGACAATAGAT
1 CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
* * * * * * * *
28485063 CTTGCCT-TCCTAC-ATTGACAGCGAAGCAGATCGAAGAC-ACAAAC
1 CTTGCCTCT-CT-CGGTTG-TAGCGGAGCTGGTTGAAGACAACAGAT
* *
28485107 CTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGATGACAACAGAT
1 CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
* * * * * *** * * *
28485151 CTTGCCT-TC-CTGAATCGACAACGAAGCAAATCGAAGAC-ACAAAC
1 CTTGCCTCTCTC-G-GTTG-TAGCGGAGCTGGTTGAAGACAACAGAT
* * *
28485195 CTTGCCTCTCTCAGTTGTAGTGGAGCTGGTTGATGACAACAGAT
1 CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
* ** * * * * *
28485239 CTTGCCT-TC-CTGCATTGATAGCAAAGCAGATCGAAGAC-ACAAAC
1 CTTGCCTCTCTC-G-GTTG-TAGCGGAGCTGGTTGAAGACAACAGAT
* *
28485283 CTTGTCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGACAACAGAT
1 CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
* ** * * * *
28485327 CTTGCCT-TC-CTGCATTGATAGCAAAGCAGATCGAAGAC-ACA-AA
1 CTTGCCTCTCTC-G-GTTG-TAGCGGAGCTGGTTGAAGACAACAGAT
*
28485370 CTTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAGAT
1 C-TTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
* * * * * * * *
28485415 CTTGCCT-TCTTGCATTGACAGCGAAGCAGATCGAAGACATA-A-AC
1 CTTGCCTCTCTCG-GTTG-TAGCGGAGCTGGTTGAAGACA-ACAGAT
* *
28485459 CTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAAACAACAGAT
1 CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
28485503 CTTGCCT
1 CTTGCCT
28485510 TCCTGCATTA
Statistics
Matches: 375, Mismatches: 122, Indels: 76
0.65 0.21 0.13
Matches are distributed among these distances:
42 5 0.01
43 102 0.27
44 160 0.43
45 103 0.27
46 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTGTAGCGGAGCTGGTTGAAGACAACAGAT
Found at i:28485753 original size:128 final size:128
Alignment explanation
Indices: 28485541--28485942 Score: 626
Period size: 128 Copynumber: 3.1 Consensus size: 128
28485531 GATCGAAGTT
* * *
28485541 ACAAATCCTATCTCCTTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCTTAAGC
1 ACAAATCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* *
28485606 AGTAGCGGAGCAGATCGAAGATGGCAAATATTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
* *
28485669 ACAAATCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
1 ACAAATCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * * * *
28485734 AGTAACGGAACATATCGAAGACGGCAAATCTTATCTTCAAGAGTAATGAAGTAGATTTAAGCC
66 AGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
* * *
28485797 ACAAGTCCTATTTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAATCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* *
28485862 AGTAGCAGAGCAGATC-AATGACGACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATCGAA-GACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
*
28485925 ACAAATCCTATTTCCCTG
1 ACAAATCCTATCTCCCTG
28485943 AAGTTGCAGT
Statistics
Matches: 248, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
127 2 0.01
128 246 0.99
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (128 bp):
ACAAATCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
AGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
Found at i:28486101 original size:105 final size:110
Alignment explanation
Indices: 28485969--28486172 Score: 283
Period size: 113 Copynumber: 1.9 Consensus size: 110
28485959 AGTTGAAGCT
* * * *
28485969 ACAAGTCTTATCTCACTGAGGTTGCAGTGTAGC-GA-T-AG-T-AAATGTTTTCTCGAAGAGCCA
1 ACAAGTCTTATCTCACTAAAGTTGCAGTATAGCAGACTAAGATAAAATGTTTCCTCGAAGAGCCA
* *
28486029 CAGATCTTATCTCTCTGAAGTTTCAGTAGAGTGGATTACACCATA
66 CAGATCTTATCTCTCTGAAGTTGCAATAGAGTGGATTACACCATA
28486074 ACAAGTCTTATCTCACTAAAGTTGCAGTATAGCAGACTAAAGATAGCAAATGTTTCCTCGAAGAG
1 ACAAGTCTTATCTCACTAAAGTTGCAGTATAGCAGACT-AAGATA--AAATGTTTCCTCGAAGAG
*
28486139 CCACAGATCTTATCTTTCTGAAGTTGCAATAGAG
63 CCACAGATCTTATCTCTCTGAAGTTGCAATAGAG
28486173 CAGACTGAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
105 30 0.36
106 2 0.02
107 1 0.01
109 2 0.02
110 1 0.01
113 48 0.57
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (110 bp):
ACAAGTCTTATCTCACTAAAGTTGCAGTATAGCAGACTAAGATAAAATGTTTCCTCGAAGAGCCA
CAGATCTTATCTCTCTGAAGTTGCAATAGAGTGGATTACACCATA
Found at i:28487649 original size:3 final size:3
Alignment explanation
Indices: 28487641--28487738 Score: 72
Period size: 3 Copynumber: 31.7 Consensus size: 3
28487631 TCTAATCCTT
*** * *
28487641 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA AGC TTA TTA TGA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
28487689 TTA TTC TTG TTA TTGCA TTTA TTA TTA TTA CTT- TCC TTA TTA TTA TTA
1 TTA TTA TTA TTA TT--A -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
28487737 TT
1 TT
28487739 TACCCACTTA
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
2 1 0.01
3 67 0.91
4 3 0.04
5 1 0.01
6 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28487995 original size:25 final size:27
Alignment explanation
Indices: 28487944--28488004 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28487934 AGGCTTTATA
*
28487944 ATTTATATATATACATAGATATGCATAT
1 ATTT-TATATATACATACATATGCATAT
* *
28487972 TTTTTATATGTACATACAT-T-CATAT
1 ATTTTATATATACATACATATGCATAT
28487997 ATTTTATA
1 ATTTTATA
28488005 ATTTATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 12 0.41
26 1 0.03
27 13 0.45
28 3 0.10
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (27 bp):
ATTTTATATATACATACATATGCATAT
Found at i:28489483 original size:54 final size:54
Alignment explanation
Indices: 28489425--28489591 Score: 153
Period size: 54 Copynumber: 3.1 Consensus size: 54
28489415 ACAACCTTTT
*
28489425 ACTTATGGGACTTTACGAATCTCATGGTCT-ATCGATTT-TCGATGACGACCTTCA
1 ACTTATGGGACTTTACGAATCTCATGGTCTGAT-GATTTAT-GATAACGACCTTCA
* * * * **
28489479 ACTTACGAGACTTTACGAATCTCGTGGTCTGATGATTTATGATAATGACCTTTT
1 ACTTATGGGACTTTACGAATCTCATGGTCTGATGATTTATGATAACGACCTTCA
* * * * * *
28489533 ACTTATGGGATTTTACGAATGC-CACGGT-TCATTGATTTGTGATCACGACCTTCT
1 ACTTATGGGACTTTACGAAT-CTCATGGTCTGA-TGATTTATGATAACGACCTTCA
28489587 ACTTA
1 ACTTA
28489592 CGTGATTTTA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
53 2 0.02
54 86 0.93
55 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (54 bp):
ACTTATGGGACTTTACGAATCTCATGGTCTGATGATTTATGATAACGACCTTCA
Found at i:28490032 original size:452 final size:447
Alignment explanation
Indices: 28489120--28490036 Score: 1078
Period size: 452 Copynumber: 2.0 Consensus size: 447
28489110 TAGTCTAATA
* * *
28489120 ATTTACGATCACGACCTTCCAGTTATGTGATTTTACGAATCTAGGTGTGTTGAGGAATAACTCAA
1 ATTTACGATCACGACCTTCCACTTACGTGATTTTACAAATCTAGGTGTGTTGAGGAATAACTCAA
* * * * *
28489185 AACTGACCTTTTTGCCTTTCAGAGCAAGTTAGATGCTAGAGATGATGAATATAAGCGTGTTGAGG
66 AACTGACCTATTTGCCCTTCAGAGCAAGTGAAATGCTAGAAATGATGAATATAAGCGTGTTGAGG
*
28489250 AATAACTGACATTAAAAGGAGAATAAAGGAATCAATTTTGTTATATTGCCTTAGGAAGGCTGAAG
131 AATAACTGACATTAAAAGGAGAATAAAGGAATCAATTTTGTCATATTGCCTTAGGAAGGCTGAAG
* * * * **
28489315 TTAGTTCTATTCACCATGTGTCTGAAATAAGGCTTGAAATAGATCGATTTCCTCACAAAAAACAA
196 CTAGTTCTATACACCATATGTATGAAATAAGGCTTGAAATAGATCGAGCTCCTCACAAAAAACAA
* * * *
28489380 GGAACTTTTTGAAAAACTTTAGTTGATTTACAATCACAACCTTTTACTTATGGGACTTTACGAAT
261 GGAACTTTCTGAAAAAATTTAGTTGATTTACAATCACAACCTTTTACTTATGAGACTTTACAAAT
* * * * ** * * * *
28489445 CTCATGGTCTATCGATTTTCGATGACGACCTTCAACTTACGAGACTTTACGAATCTCGTGGTCTG
326 CTCACGGTCGATCAATTTTCAACAACAACATTCAACTTACGAGACTTTACAAATCTCGTAGTCTG
* * * * *
28489510 ATGATTTATGATAATGACCTTTTACTTATGGGATTTTACGAATGCCACGGTTCATTG
391 ATGATTTACGATAATCACCTTTTACTTATAGGATTTTACGAATGCCACGGTACACTG
** *
28489567 ATTTGTGATCACGACCTTCTACTTACGTGATTTTACAAATCTAGGTGTGTTGAGGAATAACTCAA
1 ATTTACGATCACGACCTTCCACTTACGTGATTTTACAAATCTAGGTGTGTTGAGGAATAACTCAA
* *
28489632 AATTGACCTATTTGCCCTTCAGAGCAAGTGAAATGCTAGAAATGATGAATATAGGCGTGTTGAGG
66 AACTGACCTATTTGCCCTTCAGAGCAAGTGAAATGCTAGAAATGATGAATATAAGCGTGTTGA-G
* * * * *
28489697 AAGAACTCAAACTGA-ACTTGAAAGGAGGATAGCA-GTATCAATTTTGTCCTATTGCCATT-GTG
130 --GAA-T--AACTGACA-TTAAAAGGAGAATA-AAGGAATCAATTTTGTCATATTGCC-TTAG-G
* * * *
28489759 -AGGCTGAAGCTAGTTCTCTACACCATATGTATGAAATGAGGCTTGAAATGGATCGAGCTGCTCA
186 AAGGCTGAAGCTAGTTCTATACACCATATGTATGAAATAAGGCTTGAAATAGATCGAGCTCCTCA
* * * * *
28489823 -GAAAAATAAGGAACTTTCTGAAAAAATTTAGTTGATTTACAATCACGATCTTTTACTTCTGAGA
251 CAAAAAACAAGGAACTTTCTGAAAAAATTTAGTTGATTTACAATCACAACCTTTTACTTATGAGA
* * * * *
28489887 CTTTATAAATTTCACGGTTCGCT-AATTTTCAACAACAACATTCTACTTACGAGATTTTACAAAT
316 CTTTACAAATCTCACGG-TCGATCAATTTTCAACAACAACATTCAACTTACGAGACTTTACAAAT
** **
28489951 CTCGTAGTCT-ATTGATTTACGATAA-CATTTTTTTACTTATAGGATTTTATTAAT-CTCACGGT
380 CTCGTAGTCTGA-TGATTTACGATAATCA-CCTTTTACTTATAGGATTTTACGAATGC-CACGGT
28490013 ACACTG
442 ACACTG
*
28490019 ATTTACAATCACGACCTT
1 ATTTACGATCACGACCTT
28490037 TTATTTATTA
Statistics
Matches: 391, Mismatches: 65, Indels: 23
0.82 0.14 0.05
Matches are distributed among these distances:
447 115 0.29
448 1 0.00
450 3 0.01
451 4 0.01
452 169 0.43
453 95 0.24
454 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (447 bp):
ATTTACGATCACGACCTTCCACTTACGTGATTTTACAAATCTAGGTGTGTTGAGGAATAACTCAA
AACTGACCTATTTGCCCTTCAGAGCAAGTGAAATGCTAGAAATGATGAATATAAGCGTGTTGAGG
AATAACTGACATTAAAAGGAGAATAAAGGAATCAATTTTGTCATATTGCCTTAGGAAGGCTGAAG
CTAGTTCTATACACCATATGTATGAAATAAGGCTTGAAATAGATCGAGCTCCTCACAAAAAACAA
GGAACTTTCTGAAAAAATTTAGTTGATTTACAATCACAACCTTTTACTTATGAGACTTTACAAAT
CTCACGGTCGATCAATTTTCAACAACAACATTCAACTTACGAGACTTTACAAATCTCGTAGTCTG
ATGATTTACGATAATCACCTTTTACTTATAGGATTTTACGAATGCCACGGTACACTG
Found at i:28490039 original size:54 final size:54
Alignment explanation
Indices: 28489981--28490114 Score: 157
Period size: 53 Copynumber: 2.5 Consensus size: 54
28489971 GATAACATTT
*
28489981 TTTTACTTATAGGATTTTATTAATCTCACGGTAC-ACTGATTTACAATCACGACC
1 TTTTACTTATAGGATTTTATGAATCTCACGGT-CTACTGATTTACAATCACGACC
* * *
28490035 TTTTATTTATTA-GA-TTTATGAATCTCACGGTCTATTGATTTACAATTACGACC
1 TTTTACTTA-TAGGATTTTATGAATCTCACGGTCTACTGATTTACAATCACGACC
* * **
28490088 CTCTACTTACGGGATTTTATGAATCTC
1 TTTTACTTATAGGATTTTATGAATCTC
28490115 GTGATCCTCT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
52 1 0.01
53 42 0.63
54 22 0.33
55 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (54 bp):
TTTTACTTATAGGATTTTATGAATCTCACGGTCTACTGATTTACAATCACGACC
Found at i:28490147 original size:54 final size:54
Alignment explanation
Indices: 28490089--28490221 Score: 171
Period size: 54 Copynumber: 2.5 Consensus size: 54
28490079 ATTACGACCC
* *
28490089 TCTACTTACGGGATTTTATGAATCTCGTGATCCTCTAATTTAAGATAAT-GAACT
1 TCTACTTACGGGATTTTATGAATCTCGTGATCCGCTAATTTAAGAT-ATCGAACA
* * *
28490143 TCTACTTACAGGGATTTT-TGAATCTCGTGATCCGCTAATTTATGATCTCGACCA
1 TCTACTTAC-GGGATTTTATGAATCTCGTGATCCGCTAATTTAAGATATCGAACA
* *
28490197 TCTAATTACGTGATTTTATGAATCT
1 TCTACTTACGGGATTTTATGAATCT
28490222 AAGTGTGTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
53 8 0.12
54 53 0.77
55 8 0.12
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (54 bp):
TCTACTTACGGGATTTTATGAATCTCGTGATCCGCTAATTTAAGATATCGAACA
Found at i:28490609 original size:54 final size:54
Alignment explanation
Indices: 28490467--28490664 Score: 170
Period size: 54 Copynumber: 3.7 Consensus size: 54
28490457 AAACTTCATT
* * * * * * *
28490467 TGATTTACAATCACGACCTTTAACTT-CTGGGACTTTATGAATCTCA-CAGTCCAC
1 TGATTTACGATAACGACCTTTTACTTAC-AGGATTTTACGAATCTCATGA-TCCAC
* * * * * * * *
28490521 TGATTTTCGATGACGACCTTCTAATTA-TGAGATTTTACGAATCTCGTGGTCTAC
1 TGATTTACGATAACGACCTTTTACTTACAG-GATTTTACGAATCTCATGATCCAC
* *
28490575 TGATTTACGATAATGACCTTTTA-TATACAGGATTTTACTAATCTCATGATCCAC
1 TGATTTACGATAACGACCTTTTACT-TACAGGATTTTACGAATCTCATGATCCAC
*
28490629 TGATTTATGATAACGACCTTTTACTTACAGGATTTT
1 TGATTTACGATAACGACCTTTTACTTACAGGATTTT
28490665 GCAAATCCCA
Statistics
Matches: 114, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
53 2 0.02
54 110 0.96
55 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (54 bp):
TGATTTACGATAACGACCTTTTACTTACAGGATTTTACGAATCTCATGATCCAC
Found at i:28490609 original size:612 final size:612
Alignment explanation
Indices: 28489403--28490655 Score: 1489
Period size: 612 Copynumber: 2.0 Consensus size: 612
28489393 AAACTTTAGT
* * * * *
28489403 TGATTTACAATCACAACCTTTTACTTATGGGACTTTACGAATCTCATGGTCTATCGATTTTCGAT
1 TGATTTACAATCACGACCTTTTACTTATGAGACTTTACGAATCTCACGGTCTATCGATTTACAAT
* * * * * *
28489468 GACGACCTTCAACTTACGAGACTTTACGAATCTCGTGGTCTGATGATTTATGATAATGACCTTTT
66 GACGACCCTCAACTTACGAGACTTTACGAATCTCGTGATCTGATAATTTAAGATAATGAACTTCT
* * * * * * *
28489533 ACTTATGGGATTTTACGAATGCCACGGTTCATTGATTTGTGATCACGACCTTCTACTTACGTGAT
131 ACTTAAGGGATTTTACGAAT-CCACGGTCCACTAATTTATGATCACGACCATCTAATTACGTGAT
* * * * * *
28489598 TTTACAAATCTAGGTGTGTTGAGGAATAACTCAAAATTGACCTATTTGCCCTTCAGAGCAAGTGA
195 TTTACAAATCTAAGTGTGTTGAGGAAGAACTCAAAACTGACCTATCTACCCTTCAGAACAAGTGA
28489663 AATGCTAGAAATGATGAATATAGGCGTGTTGAGGAAGAACTCAAACTGAACTTGAAAGGAGGATA
260 AATGCTAGAAATGATGAATATAGGCGTGTTGAGGAAGAACTCAAACTGAACTTGAAAGGAGGATA
* * * *
28489728 GCAGTATCAATTTTGTCCTATTGCCATTGTGAGGCTGAAGCTAGTTCTCTACACCATATGTATGA
325 GCAGTATCAATTTTGTCATATTGACATTGTGAAGCTGAAGCTAGTGCTCTACACCATATGTATGA
* * * * *
28489793 AATGAGGCTTGAAATGGATCGAGCTGCTCAGAAAAATAAGGAACTTTCTGAAAAAATTTAGTTGA
390 AATGAGGCTTGAAATAGAGCGAGCTGCTCAGAAAAATAAGAAAATTTCTGAAAAAATTCAGTTGA
* * * * * *
28489858 TTTACAATCACGATCTTTTACTTCTGAGACTTTATAAATTTCACGGTTCGCTAATTTTCAACAAC
455 TTTACAATCACGACCTTTAACTTCTGAGACTTTATAAATCTCACAGTCCACTAATTTTCAACAAC
* * * *
28489923 AACATTCTACTTACGAGATTTTACAAATCTCGTAGTCTATTGATTTACGATAACATTTTTTTACT
520 AACATTCTAATTACGAGATTTTACAAATCTCGTAGTCTACTGATTTACGATAACACTTTTATAC-
* * *
28489988 TATAGGATTTTATTAATCTCACGGTACAC
584 TACAGGATTTTACTAATCTCACGATACAC
* * * *
28490017 TGATTTACAATCACGACCTTTTATTTATTAGA-TTTATGAATCTCACGGTCTATTGATTTACAAT
1 TGATTTACAATCACGACCTTTTACTTATGAGACTTTACGAATCTCACGGTCTATCGATTTACAAT
* * * * * *
28490081 TACGACCCTCTACTTACGGGATTTTATGAATCTCGTGATCCT-CTAATTTAAGATAATGAACTTC
66 GACGACCCTCAACTTACGAGACTTTACGAATCTCGTGAT-CTGATAATTTAAGATAATGAACTTC
* * * *
28490145 TACTTACAGGGATTTT-TGAAT-CTCGTGATCCGCTAATTTATGATCTCGACCATCTAATTACGT
130 TACTTA-AGGGATTTTACGAATCCACG-G-TCCACTAATTTATGATCACGACCATCTAATTACGT
** * * *
28490208 GATTTTATGAATCTAAGTGTGTTGATGAAGAACT-TAAACTGACCTCTCTACCCTTCAGAACAAG
192 GATTTTACAAATCTAAGTGTGTTGAGGAAGAACTCAAAACTGACCTATCTACCCTTCAGAACAAG
** * * *
28490272 TTTAATGCTAGAGATGATGAATTTAGGCGTGTTGAGGAAGAACTCAAAACTGATCTTGAAAGGAG
257 TGAAATGCTAGAAATGATGAATATAGGCGTGTTGAGGAAGAACTC-AAACTGAACTTGAAAGGAG
* * * *
28490337 GATAG-AGGTATCAATTTTTTTATATTGACTTTGTGAAGCTGAAGCTAGTGCTCTTCACCATATG
321 GATAGCA-GTATCAATTTTGTCATATTGACATTGTGAAGCTGAAGCTAGTGCTCTACACCATATG
* * *
28490401 TCTGAAATGAGGCTTGAAA-AGAGCGATCTGCTCAGAAAAATAAGAAAATCTT-TGAAAAACTTC
385 TATGAAATGAGGCTTGAAATAGAGCGAGCTGCTCAGAAAAATAAGAAAAT-TTCTGAAAAAATTC
* * * *
28490464 ATTTGATTTACAATCACGACCTTTAACTTCTGGGACTTTATGAATCTCACAGTCCACTGATTTTC
449 AGTTGATTTACAATCACGACCTTTAACTTCTGAGACTTTATAAATCTCACAGTCCACTAATTTTC
* ** * * * * * *
28490529 GATGACGACCTTCTAATTATGAGATTTTACGAATCTCGTGGTCTACTGATTTACGATAATGACCT
514 AACAACAACATTCTAATTACGAGATTTTACAAATCTCGTAGTCTACTGATTTACGATAA-CA-CT
* *
28490594 TTTATA-TACAGGATTTTACTAATCTCATGATCCAC
577 TTTATACTACAGGATTTTACTAATCTCACGATACAC
** *
28490629 TGATTTATGATAACGACCTTTTACTTA
1 TGATTTACAATCACGACCTTTTACTTA
28490656 CAGGATTTTG
Statistics
Matches: 534, Mismatches: 96, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
611 3 0.01
612 252 0.47
613 235 0.44
614 44 0.08
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (612 bp):
TGATTTACAATCACGACCTTTTACTTATGAGACTTTACGAATCTCACGGTCTATCGATTTACAAT
GACGACCCTCAACTTACGAGACTTTACGAATCTCGTGATCTGATAATTTAAGATAATGAACTTCT
ACTTAAGGGATTTTACGAATCCACGGTCCACTAATTTATGATCACGACCATCTAATTACGTGATT
TTACAAATCTAAGTGTGTTGAGGAAGAACTCAAAACTGACCTATCTACCCTTCAGAACAAGTGAA
ATGCTAGAAATGATGAATATAGGCGTGTTGAGGAAGAACTCAAACTGAACTTGAAAGGAGGATAG
CAGTATCAATTTTGTCATATTGACATTGTGAAGCTGAAGCTAGTGCTCTACACCATATGTATGAA
ATGAGGCTTGAAATAGAGCGAGCTGCTCAGAAAAATAAGAAAATTTCTGAAAAAATTCAGTTGAT
TTACAATCACGACCTTTAACTTCTGAGACTTTATAAATCTCACAGTCCACTAATTTTCAACAACA
ACATTCTAATTACGAGATTTTACAAATCTCGTAGTCTACTGATTTACGATAACACTTTTATACTA
CAGGATTTTACTAATCTCACGATACAC
Found at i:28490689 original size:54 final size:54
Alignment explanation
Indices: 28490577--28490693 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 54
28490567 TGGTCTACTG
* * * ** * *
28490577 ATTTACGATAATGACCTTTTATATACAGGATTTTACTAATCTCATGATCCACTG
1 ATTTACGATAACGACCTTTTATATACAGGATTTTACAAATCCCACAATACACTA
* * *
28490631 ATTTATGATAACGACCTTTTACT-TACAGGATTTTGCAAATCCCACAATACGCTA
1 ATTTACGATAACGACCTTTTA-TATACAGGATTTTACAAATCCCACAATACACTA
28490685 ATTTACGAT
1 ATTTACGAT
28490694 CGCAACCTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (54 bp):
ATTTACGATAACGACCTTTTATATACAGGATTTTACAAATCCCACAATACACTA
Found at i:28490780 original size:54 final size:55
Alignment explanation
Indices: 28490735--28490865 Score: 176
Period size: 54 Copynumber: 2.4 Consensus size: 55
28490725 CTTGCAGTCC
* * * *
28490735 GCTGATTTATGATCAAGACCTTCCT-TTTACAAGATCTTACGAATCTCGTGGTCT
1 GCTGATTTAAGATCACGACCTTCCTATTTACAAGATATTACGAATCTCGCGGTCT
* * * *
28490789 GCTAATTTACGATCACGA-CTTCCTATTTACAGGATATTATGAATCTCGCGGTCT
1 GCTGATTTAAGATCACGACCTTCCTATTTACAAGATATTACGAATCTCGCGGTCT
28490843 GCTGATTTAAGATCACGACCTTC
1 GCTGATTTAAGATCACGACCTTC
28490866 TACTTACGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
53 6 0.09
54 56 0.85
55 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (55 bp):
GCTGATTTAAGATCACGACCTTCCTATTTACAAGATATTACGAATCTCGCGGTCT
Found at i:28490888 original size:54 final size:54
Alignment explanation
Indices: 28490713--28490888 Score: 153
Period size: 54 Copynumber: 3.3 Consensus size: 54
28490703 TTATTTATAG
* * * * *
28490713 GGATA-TACAAATCTTGCAGTCCGCTGATTTATGATCAAGACCTTCCT-TTTAC
1 GGATATTACAAATCTCGCGGTCTGCTGATTTAAGATCACGACCTTCCTATTTAC
* * * * * *
28490765 AAGATCTTACGAATCTCGTGGTCTGCTAATTTACGATCACGA-CTTCCTATTTAC
1 -GGATATTACAAATCTCGCGGTCTGCTGATTTAAGATCACGACCTTCCTATTTAC
** *
28490819 AGGATATTATGAATCTCGCGGTCTGCTGATTTAAGATCACGACCTT-CTACTTAC
1 -GGATATTACAAATCTCGCGGTCTGCTGATTTAAGATCACGACCTTCCTATTTAC
* *
28490873 GTTATTTTACAAATCT
1 G-GATATTACAAATCT
28490889 AGGTGTGTTA
Statistics
Matches: 98, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
53 10 0.10
54 85 0.87
55 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (54 bp):
GGATATTACAAATCTCGCGGTCTGCTGATTTAAGATCACGACCTTCCTATTTAC
Found at i:28491615 original size:54 final size:53
Alignment explanation
Indices: 28491548--28491722 Score: 199
Period size: 54 Copynumber: 3.3 Consensus size: 53
28491538 TTGCTTTTTG
* *
28491548 GATTTTACGAATCTTATGGTCCGTTAATTTACGATCATGACCTTCTACTTATGA
1 GATTTTACGAATCTCACGGTCCGTTAATTTACGATCA-GACCTTCTACTTATGA
* * * * * *
28491602 GATTTTACAAATCTCGCGGTCCGTTGATTTACAATC-GCACCTTCTACCTACGA
1 GATTTTACGAATCTCACGGTCCGTTAATTTACGATCAG-ACCTTCTACTTATGA
* * * * *
28491655 GATTTTACGAATCTCACGGTCCGCTAATTTACGGTTACGACCTTTTACTTATGT
1 GATTTTACGAATCTCACGGTCCGTTAATTTACGATCA-GACCTTCTACTTATGA
28491709 GATTTTACGAATCT
1 GATTTTACGAATCT
28491723 AGATGTGTTG
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
52 1 0.01
53 42 0.42
54 55 0.56
55 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (53 bp):
GATTTTACGAATCTCACGGTCCGTTAATTTACGATCAGACCTTCTACTTATGA
Found at i:28491713 original size:380 final size:378
Alignment explanation
Indices: 28490955--28491751 Score: 868
Period size: 380 Copynumber: 2.1 Consensus size: 378
28490945 GCTAGAGATG
* * * * * * *
28490955 ATGAATGTAGATGTGTTGAGGAAGAACTTAAAACTGTCCTTTAAATAAGGAGGATAGAGGAATCA
1 ATGAATCTAGATGTGTTGAGGAAGAACTCAAAACTGACCTTGAAAGAAGAAGGATAGAAGAATCA
* * * *
28491020 ATTTTGTTATATTGCCTTTGTGAAGCTGAAGCTAGTTCTCTTACCATAAATCTGAAATGAGGCTT
66 ATTTTGTTACATTGCCTCTGTGAAGCTGAAGCTAGTTCTCTCACCACAAATCTGAAATGAGGCTT
* * * * **
28491085 AAAATATATCAATCTGCTCAGACAAACAAGAAACTTTTTGAAAAGCTTCAGTTGATTTACAATCA
131 AAAATATATAAATCTACTCAGAAAAACAAGAAACTTTTTAAAAAAATTCAGTTGATTTACAATCA
* * * * *
28491150 TGACTTTTTACTTACATGATTTTATGAATCTCACGATCTACAAATTTACGATGAGAACCTTCTCC
196 CGACTTTTTACTTACATGATTTTACGAATCTCACGATCCACAAATTTACGATCAGAACCTTCTAC
* * * *
28491215 TTATGGGATTTTACAAATCTCATGATTCGCTGATTTACTATAATGACCTTCTACTAACGGGACTT
261 TTATGAGATTTTACAAATCTCACGATCCGCTGATTTAC--TAATGACCTTCTACTAACGAGACTT
* * * * *
28491280 TATGAATATCACAGTCTACTGATTTACAATCATGACCTTCTACTTCCGTGATTTT
324 TACGAATATCACAGTCCACTAATTTACAATCACGACCTTCTACTTACGTGATTTT
28491335 ATGAATCTAGATGTGTTGAGGAAGAACTCAAAACTGACCTTGAAAGAAGAAGGATAGAAGAATCA
1 ATGAATCTAGATGTGTTGAGGAAGAACTCAAAACTGACCTTGAAAGAAGAAGGATAGAAGAATCA
* * * * *
28491400 ATTTTGTTACATTGCCTCTGTGAGGCTGAAGCTAGTTCTCATCATCACACATTTTAAATGAGGCT
66 ATTTTGTTACATTGCCTCTGTGAAGCTGAAGCTAGTTCTC-TCACCACAAATCTGAAATGAGGCT
* * * * *
28491465 TCAAAT-TGA-AAGATCTACTCAGAAAAATAAGGAATTTTTTAAAAAAATTTAGTTGATTTACAA
130 TAAAATAT-ATAA-ATCTACTCAGAAAAACAAGAAACTTTTTAAAAAAATTCAGTTGATTTACAA
* * ** * * * ***
28491528 TCACGATTTTTTGCTT-TTTGGATTTTACGAATCTTATGGTCCGTTAATTTACGATCATG-ACCT
193 TCACGACTTTTTACTTACAT-GATTTTACGAATCTCACGATCCACAAATTTACGATCA-GAACCT
* * *
28491591 TCTACTTATGAGATTTTACAAATCTCGCGGTCCGTTGATTTAC-AATCGCACCTTCTACCT-ACG
256 TCTACTTATGAGATTTTACAAATCTCACGATCCGCTGATTTACTAAT-G-ACCTTCTA-CTAACG
* * * * ** * * *
28491654 AGATTTTACGAATCTCACGGTCCGCTAATTTACGGTTACGACCTTTTACTTATGTGATTTT
318 AGACTTTACGAATATCACAGTCCACTAATTTACAATCACGACCTTCTACTTACGTGATTTT
* * *
28491715 ACGAATCTAGATGTGTTGAGAAATAACTCAAAACTGA
1 ATGAATCTAGATGTGTTGAGGAAGAACTCAAAACTGA
28491752 TATCTTTTTC
Statistics
Matches: 343, Mismatches: 66, Indels: 16
0.81 0.16 0.04
Matches are distributed among these distances:
378 3 0.01
379 1 0.00
380 189 0.55
381 149 0.43
382 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (378 bp):
ATGAATCTAGATGTGTTGAGGAAGAACTCAAAACTGACCTTGAAAGAAGAAGGATAGAAGAATCA
ATTTTGTTACATTGCCTCTGTGAAGCTGAAGCTAGTTCTCTCACCACAAATCTGAAATGAGGCTT
AAAATATATAAATCTACTCAGAAAAACAAGAAACTTTTTAAAAAAATTCAGTTGATTTACAATCA
CGACTTTTTACTTACATGATTTTACGAATCTCACGATCCACAAATTTACGATCAGAACCTTCTAC
TTATGAGATTTTACAAATCTCACGATCCGCTGATTTACTAATGACCTTCTACTAACGAGACTTTA
CGAATATCACAGTCCACTAATTTACAATCACGACCTTCTACTTACGTGATTTT
Found at i:28492067 original size:54 final size:54
Alignment explanation
Indices: 28491969--28492226 Score: 198
Period size: 54 Copynumber: 4.8 Consensus size: 54
28491959 AAAACTTCAA
* * ** *
28491969 TTGATTTAC-AGTCACGACCTTTTACTT-CTGAGACATTACGAATCTCACGGTCCG
1 TTGATTTACTA-TAACGACCTTCTACTTAC-GAGATTTTACGAATCTCACGGTCTG
* * * * *
28492023 TTGATTTTCTATGACGACCTTCTACTTACGAGATTTTACAAATCTCATGGTCTA
1 TTGATTTACTATAACGACCTTCTACTTACGAGATTTTACGAATCTCACGGTCTG
* * * * * *
28492077 CTGATTTACAATAACGACCTTTTAATTATGAGATTTTACGAACCTCACGGTCTG
1 TTGATTTACTATAACGACCTTCTACTTACGAGATTTTACGAATCTCACGGTCTG
* * ** * * * * * *
28492131 TTGATTTACTATCATGACCTTCTACAAATGGGATTTTTCGAATCTTATGGTCTA
1 TTGATTTACTATAACGACCTTCTACTTACGAGATTTTACGAATCTCACGGTCTG
* * * *
28492185 CTGATTTACGATCACGACCTTCTCCTTAC-ATGATTTTACGAA
1 TTGATTTACTATAACGACCTTCTACTTACGA-GATTTTACGAA
28492227 AGTAGGCGTG
Statistics
Matches: 158, Mismatches: 43, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
54 156 0.99
55 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (54 bp):
TTGATTTACTATAACGACCTTCTACTTACGAGATTTTACGAATCTCACGGTCTG
Found at i:28492166 original size:108 final size:108
Alignment explanation
Indices: 28491970--28492205 Score: 301
Period size: 108 Copynumber: 2.2 Consensus size: 108
28491960 AAACTTCAAT
* * * * *
28491970 TGATTTACAGTCACGACCTTTTACTTCTGAGACATTACGAATCTCACGGTCCGTTGATTTTCTAT
1 TGATTTACAATCACGACCTTTTAATTATGAGACATTACGAACCTCACGGTCCGTTGATTTACTAT
* **
28492035 GACGACCTTCTACTTACGAGATTTTACAAATCTCATGGTCTAC
66 CACGACCTTCTACAAACGAGATTTTACAAATCTCATGGTCTAC
* ** *
28492078 TGATTTACAATAACGACCTTTTAATTATGAGATTTTACGAACCTCACGGTCTGTTGATTTACTAT
1 TGATTTACAATCACGACCTTTTAATTATGAGACATTACGAACCTCACGGTCCGTTGATTTACTAT
* * * * * *
28492143 CATGACCTTCTACAAATGGGATTTTTCGAATCTTATGGTCTAC
66 CACGACCTTCTACAAACGAGATTTTACAAATCTCATGGTCTAC
*
28492186 TGATTTACGATCACGACCTT
1 TGATTTACAATCACGACCTT
28492206 CTCCTTACAT
Statistics
Matches: 108, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (108 bp):
TGATTTACAATCACGACCTTTTAATTATGAGACATTACGAACCTCACGGTCCGTTGATTTACTAT
CACGACCTTCTACAAACGAGATTTTACAAATCTCATGGTCTAC
Found at i:28493169 original size:54 final size:54
Alignment explanation
Indices: 28493066--28493187 Score: 147
Period size: 54 Copynumber: 2.3 Consensus size: 54
28493056 CTAAATATGA
* ** * *
28493066 GATTTTACGAACCTCGTGGTCTGTTGATTTACGATAATGACATTTTACTTACGG
1 GATTTTACGAATCTCGTGGTCTAATGATTTACGATAATGACATTCTACTTACAG
* * *
28493120 GATTTTACGAATCTCTTGGTCTAATGATTTACGATCATGACCA-TCTACTTATAG
1 GATTTTACGAATCTCGTGGTCTAATGATTTACGATAATGA-CATTCTACTTACAG
*
28493174 GATTTTATGAATCT
1 GATTTTACGAATCT
28493188 TCTGTTCCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 56 0.97
55 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (54 bp):
GATTTTACGAATCTCGTGGTCTAATGATTTACGATAATGACATTCTACTTACAG
Found at i:28493684 original size:54 final size:54
Alignment explanation
Indices: 28493524--28493698 Score: 165
Period size: 54 Copynumber: 3.2 Consensus size: 54
28493514 ACTTTCTAGA
* * * *
28493524 TTTACGAATCTCACGGTCCATTAATTTACGATCATGACCTTCTACTTACGAGAT
1 TTTACGAATCTCACAGTCCATTAATTTACGATCATGACCTTCTACCTATGGGAT
* ** * ** ** *
28493578 TTTATGAATCTCTTGATTTGA-TAATTTTAAAATCATGATCTTCTA-CTAATGGGAT
1 TTTACGAATCTC-ACAGTCCATTAA-TTTACGATCATGACCTTCTACCT-ATGGGAT
* *
28493633 TTTACAAATCTCACAGTCCATTGATTTACGATCATGACCTTCTACCTATGGGAT
1 TTTACGAATCTCACAGTCCATTAATTTACGATCATGACCTTCTACCTATGGGAT
*
28493687 TTTATGAATCTC
1 TTTACGAATCTC
28493699 GTGGTCTGCT
Statistics
Matches: 90, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
54 52 0.58
55 38 0.42
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (54 bp):
TTTACGAATCTCACAGTCCATTAATTTACGATCATGACCTTCTACCTATGGGAT
Found at i:28493714 original size:54 final size:54
Alignment explanation
Indices: 28493545--28493717 Score: 152
Period size: 54 Copynumber: 3.2 Consensus size: 54
28493535 CACGGTCCAT
* * * * * *
28493545 TAATTTACGATCATGACCTTCTACTTACGAGATTTTATGAATCTCTTGATTTGA
1 TAATTTACGATCATGACCTTCTACCTATGGGATTTTATGAATCTCATGGTCTGA
** * ** ** *
28493599 TAATTTTAAAATCATGATCTTCTA-CTAATGGGATTTTACAAATCTCACAGTC-CA
1 TAA-TTTACGATCATGACCTTCTACCT-ATGGGATTTTATGAATCTCATGGTCTGA
* * *
28493653 TTGATTTACGATCATGACCTTCTACCTATGGGATTTTATGAATCTCGTGGTCTGC
1 -TAATTTACGATCATGACCTTCTACCTATGGGATTTTATGAATCTCATGGTCTGA
28493708 TAATTTACGA
1 TAATTTACGA
28493718 CCGCGACCTT
Statistics
Matches: 88, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
54 51 0.58
55 37 0.42
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (54 bp):
TAATTTACGATCATGACCTTCTACCTATGGGATTTTATGAATCTCATGGTCTGA
Found at i:28494095 original size:54 final size:54
Alignment explanation
Indices: 28494031--28494170 Score: 145
Period size: 54 Copynumber: 2.6 Consensus size: 54
28494021 CTTTTGGGTC
* * *** * *
28494031 TTTACGAATCTCATTGTCTGCTGATTTTTTATGACAACCTTCTAAATATGAGAT
1 TTTACAAATCTCATGGTCTGCTGATTTACGATAACAACCTTCTAAATACGAGAT
* * * **
28494085 TTTACAAATCTCGTGGTCTGTTGATTTACGATAACAACCTTTTACTTACGAGAT
1 TTTACAAATCTCATGGTCTGCTGATTTACGATAACAACCTTCTAAATACGAGAT
* **
28494139 TTTACAAATCTCCTGGTCCACTGATTTACGAT
1 TTTACAAATCTCATGGTCTGCTGATTTACGAT
28494171 CACGACCATC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (54 bp):
TTTACAAATCTCATGGTCTGCTGATTTACGATAACAACCTTCTAAATACGAGAT
Found at i:28494147 original size:506 final size:506
Alignment explanation
Indices: 28491548--28495194 Score: 3209
Period size: 506 Copynumber: 7.2 Consensus size: 506
28491538 TTGCTTTTTG
** * * * * *
28491548 GATTTTACGAATCTTATGGTCCGTTAATTTACGATCATGACCTTCTACTTATGAGATTTTACAAA
1 GATTTTACGAATCTCGTGGTCTGCTAATTTACGATAACGACCTTCTACTTACGAGATTTTACAAA
* * * * * *
28491613 TCTCGCGGTCCGTTGATTTACAATC--GCACCTTCTACCTA-CGAGATTTTACGAATCTCACGGT
66 TCTCACGGTCCATTGATTTACGATCATG-ACCTTCTACCTATAG-GATTTTATGAATCTCATGGT
* * * * * ** *
28491675 CCGCTAATTTACGGTTACGACCTTTTACTTATGTGATTTTACGAATCTAGATGTGTTGAGAAATA
129 CTGCTTATTTACGATCACGACCTTCTACTTATGTGATTTTACGAATCTAGGCGTGTTGAGGAATA
** ** * * * * * *
28491740 ACTCAAAACTGATATCTTTTTCCTTTA-ATGCAAGATAGATGCTAAAGATCATGAATATAGGTGT
194 ACTCAAAACTGACCTCTTTACCCTTCAGA-GCAAGCTAAATGCTAGAGATGATGAATATAGGCGT
* *
28491804 GCTT-AGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATTAATTTTTTTATATTGCC
258 G-TTGAGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATCAATTTTGTTATATTGCC
* ** * * * *
28491868 TTTGTGAGGCTAAAGCTAGTTCTCTTCACCGTACGTTTGAAATGAGGCTTGAAATGGGTCAATCT
322 TTTGTGA-GCTGAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGATCT
* * * * * * * *
28491933 GTTCATAAGAAA-AAGGAACTTTCTGAAAAACTTCAATTGATTTACAGTCACGACCTTTTACTTC
386 GCTCAGAA-AAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACTTT
* * * * *
28491997 T-GAGACATTACGAATCTCACGGTCCGTTGATTTTCTATGACGACCTTCTACTTACGA
450 TAG-GTCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * * * * * *
28492054 GATTTTACAAATCTCATGGTCTACTGATTTACAATAACGACCTTTTAATTATGAGATTTTACGAA
1 GATTTTACGAATCTCGTGGTCTGCTAATTTACGATAACGACCTTCTACTTACGAGATTTTACAAA
* ** * ** * *
28492119 CCTCACGGTCTGTTGATTTACTATCATGACCTTCTACAAATGGGATTTT-TCGAATCTTATGGTC
66 TCTCACGGTCCATTGATTTACGATCATGACCTTCTACCTATAGGATTTTAT-GAATCTCATGGTC
* * * ** ** *
28492183 TACTGATTTACGATCACGACCTTCTCCTTACATGATTTTACGAAAGTAGGCGTGTTGAAGAATAA
130 TGCTTATTTACGATCACGACCTTCTACTTATGTGATTTTACGAATCTAGGCGTGTTGAGGAATAA
* * * *
28492248 CTCAAAACTGACCT-TTCTACCCTTCAAAGCAAGTTAGAA-GATAGAGATGATGAATATAGGTGT
195 CTCAAAACTGACCTCTT-TACCCTTCAGAGCAAGCTA-AATGCTAGAGATGATGAATATAGGCGT
* * * * * * * *
28492311 GTTTAGGAAGAACGCAAAAGTGACCTTGAAAGAAGGAGGATAAATGAATCAATTTTGTTAGATTT
258 GTTGAGGAAGAACTCAAAACTGACCTTG--A-AAGGAGGATAGAGGTATCAATTTTGTTATATTG
* * ** * *
28492376 TCTTTGTGAAGCTGAAGCTAGTTCTCAAAATGATACATTTGAAATGAGGTTTGTAATGGATCGAT
320 CCTTTGTG-AGCTGAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGAT
* * * ** * * * *
28492441 TTGCTCAGAAAAACAATGAAATTTCTTTAAAGTTTCAATTGATTTACAATCATAACCTTTTACTT
384 CTGCTCAGAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACTT
* * * * * *
28492506 TCTAGAT-TTTACGAATATCACGGTCCGCTGATTTATGATCACGACCTTCTACTTACGA
449 T-TAGGTCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * * * * * * * * * *
28492564 GATTTTACGAATCTAGCGATTTGCCAATTTTAAGGTCATGATCTTCTACTAATGGGATTTTACAA
1 GATTTTACGAATCTCGTGGTCTGCTAA-TTTACGATAACGACCTTCTACTTACGAGATTTTACAA
** * * *
28492629 GCCTCGCGGTCCATTGATTTATGATCATGA-C--CTACCTACT-GGATTTTATGAATCTTATGGT
65 ATCTCACGGTCCATTGATTTACGATCATGACCTTCTACCTA-TAGGATTTTATGAATCTCATGGT
* * ** * * *
28492690 CTACTTATTTACAATCACGACCTTCTACTTACATGCTTCTACGAATCTAGGCATGTTGAGGAATA
129 CTGCTTATTTACGATCACGACCTTCTACTTATGTGATTTTACGAATCTAGGCGTGTTGAGGAATA
* * *
28492755 ACTCAAAACTGACCTCTTTGCCCTTCAGAGCAAGCTAGATGCTAGAGATGATGAATATAGGCATG
194 ACTCAAAACTGACCTCTTTACCCTTCAGAGCAAGCTAAATGCTAGAGATGATGAATATAGGCGTG
* * * ** * *
28492820 TTGAGAAAGAACTC-AAACTAAACTTGAAAAAAAGATAGAGGTATCAATTTTGTTATATTACCTT
259 TTGAGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATCAATTTTGTTATATTGCCTT
* * ** * * * * *
28492884 TGTAAGGTAGAAGCTAGTTCTCTTCACCAAACGTCTGAAATGAGGCTTGAAATGCATCAATCTGC
324 TGTGAGCT-GAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGATCTGC
* * **
28492949 T-A-AAAAACAAGGAACTTTCTGAAAAACTTTAGTTGATTTACAGTCATGACCTTTTACTTCCAG
388 TCAGAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACTTTTAG
* * * ** *
28493012 GTTTTTACGAATCTCATGGTCCACTGATTTTTTATGACAACCTTCTAAATATGA
453 GTCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * * * * *
28493066 GATTTTACGAACCTCGTGGTCTGTTGATTTACGATAATGACATTTTACTTACGGGATTTTACGAA
1 GATTTTACGAATCTCGTGGTCTGCTAATTTACGATAACGACCTTCTACTTACGAGATTTTACAAA
** * * * * *
28493131 TCTCTTGGTCTAATGATTTACGATCATGACCATCTACTTATAGGATTTTATGAATCTTC-TGTTC
66 TCTCACGGTCCATTGATTTACGATCATGACCTTCTACCTATAGGATTTTATGAATC-TCATGGTC
* * * * * *
28493195 CGTTTATTTACAACCACGACCTTCAACTTACT-TGATTTTACGAATCTAGGCATGTTGAGGAATA
130 TGCTTATTTACGATCACGACCTTCTACTTA-TGTGATTTTACGAATCTAGGCGTGTTGAGGAATA
* * * * * *
28493259 ACTCAAAATTGACCT-TTCTACCTTTTAGAGCAAGTTAGAA-GCTAGAGATGATGAATATAGACA
194 ACTCAAAACTGACCTCTT-TACCCTTCAGAGCAAGCTA-AATGCTAGAGATGATGAATATAGGCG
* * * * *
28493322 TGCTGAGAAAGAACTCAAAATTGACCTTGAAAGAAGGAGGATAGAGGAATCAATTTTGTTACATT
257 TGTTGAGGAAGAACTCAAAACTGACCTTG--A-AAGGAGGATAGAGGTATCAATTTTGTTATATT
** * * *
28493387 TTCTTTGTGAGGCTGGAGCTAGTTTTCAACACCATACATTTGAAATGAGGCTTCAAATGGATCGA
319 GCCTTTGTGA-GCTGAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGA
* ** * * ** *
28493452 TCTACTCAGAAAAACAAGGAACTTAATTAAAAGTTTTAGTTTTTTTATAATCATGACCTTTTACT
383 TCTGCTCAGAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACT
* ** * *** * **
28493517 TTCTA-G-ATTTACGAATCTCACGGTCCATTAATTTACGATCATGACCTTCTACTTACGA
448 TT-TAGGTCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * * ** * * * * * *
28493575 GATTTTATGAATCTCTTGATTTGATAATTTTAAAATCATGATCTTCTACTAATGGGATTTTACAA
1 GATTTTACGAATCTCGTGGTCTGCTAA-TTTACGATAACGACCTTCTACTTACGAGATTTTACAA
* * *
28493640 ATCTCACAGTCCATTGATTTACGATCATGACCTTCTACCTATGGGATTTTATGAATCTCGTGGTC
65 ATCTCACGGTCCATTGATTTACGATCATGACCTTCTACCTATAGGATTTTATGAATCTCATGGTC
* * * * ** *
28493705 TGCTAATTTACGACCGCGACCTTTTACTTATGTTCTTTTAGGAATCTAGGCGTGTTGAGGAATAA
130 TGCTTATTTACGATCACGACCTTCTACTTATGTGATTTTACGAATCTAGGCGTGTTGAGGAATAA
* * * * * *
28493770 CTCAAAACTGACCTCTTTGCCCTTTAGAGAAAGCTAAATGCTAAAGATGATGACTATAAGCGTGT
195 CTCAAAACTGACCTCTTTACCCTTCAGAGCAAGCTAAATGCTAGAGATGATGAATATAGGCGTGT
* * *
28493835 TGAGGAAGAACTC-AAACTAACCTTGAAAGGAGGATAGGGGTATCAATTTTTTTATATTGCCTTT
260 TGAGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATCAATTTTGTTATATTGCCTTT
* ** * * * * * * * *
28493899 GTAATGCTGAAGCTAGTTCTCTTCGCAAAACGTCTGAAATGAGGCTTGAAATGCATTGATCTGTT
325 GTGA-GCTGAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGATCTGCT
* * * *
28493964 CAGAAAAATAAGGAACTTTATGAAAAATTTTAGTTAATTTACAATCATGACCTTTTACTTTTGGG
389 CAGAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACTTTTAGG
** * ** *
28494029 TCTTTACGAATCTCATTGTCTGCTGATTTTTTATGACAACCTTCTAAATATGA
454 TCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * *
28494082 GATTTTACAAATCTCGTGGTCTGTTGATTTACGATAACAACCTTTTACTTACGAGATTTTACAAA
1 GATTTTACGAATCTCGTGGTCTGCTAATTTACGATAACGACCTTCTACTTACGAGATTTTACAAA
* * * * *
28494147 TCTC-CTGGTCCACTGATTTACGATCACGACCATCTACTTATAGGATTTTACGAATCTTCTAT--
66 TCTCAC-GGTCCATTGATTTACGATCATGACCTTCTACCTATAGGATTTTATGAATC-TC-ATGG
* * * * *
28494209 TCCG-TTGATTTACAATCACGACCCTCAACTTACT-TGATTTTACGAATCTAGGCATGTTGAGGA
128 TCTGCTT-ATTTACGATCACGACCTTCTACTTA-TGTGATTTTACGAATCTAGGCGTGTTGAGGA
* *
28494272 ATAACTCAAAACTGACCT-TTCTACCCTTCAGAGCAAGTTAGAA-GCTAGAGATGATGGATATAG
191 ATAACTCAAAACTGACCTCTT-TACCCTTCAGAGCAAGCTA-AATGCTAGAGATGATGAATATAG
* * * * * *
28494335 GTGTGTTGAGGAAGAACTCAAAATTGACATTAAAAGGAGGATAGAGGAATCAATTTTGTTACATT
254 GCGTGTTGAGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATCAATTTTGTTATATT
* * * * * *
28494400 GTCTTTGTGAGGTTAGAGCTAGTTCTCAACACCATACATTTGAAATGAGGTTTGTAATGGATAGA
319 GCCTTTGTGAGCTGA-AGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGA
* * * * * * *
28494465 TCTGCTCAGAAAAACAATGAAATTTCTTAAAAGTTTCAATTGATTTACAATCATGAACTTTTA-T
383 TCTGCTCAGAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACT
* * * * * * *
28494529 TTTTGGAT-TTTACGAATCTCACAGTCCGTTGATTTATGATCACGACCTTCTACTTACGA
448 TTTAGG-TCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * * * *
28494588 GATTTTATGAATCTCGTGATTTGCTAATTTTAAGATCACGATCTTCTACTAACGAGATTTTACAA
1 GATTTTACGAATCTCGTGGTCTGCTAA-TTTACGATAACGACCTTCTACTTACGAGATTTTACAA
* * * * *
28494653 ATCTCGCGGTTCC-CTAATTTACGATCATGACCTTCTACCCATAGGATTTTATGAA-C-CTTGCA
65 ATCTCACGG-TCCATTGATTTACGATCATGACCTTCTACCTATAGGATTTTATGAATCTCATG--
** * * * * * *
28494715 GTCTATTTATTTACGATGACAACTTTTTACTTACGT-ACTTTTATGAATCTAGGCGTGTTGAGGA
127 GTCTGCTTATTTACGATCACGACCTTCTACTTATGTGA-TTTTACGAATCTAGGCGTGTTGAGGA
* * * *
28494779 ATAACTCAAAACTGACCTCTTTGCCCTTCAGAGCAAGCTGATTGCTAGAGATGATGAATATAAGC
191 ATAACTCAAAACTGACCTCTTTACCCTTCAGAGCAAGCTAAATGCTAGAGATGATGAATATAGGC
* * *
28494844 GTGTTGAGGAAGAACTC-AAACTAAGCTTGAAAGAAGGATAGAGGTATCAATTTTGTTATATTGC
256 GTGTTGAGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATCAATTTTGTTATATTGC
* * * * * * *
28494908 CTTTGTGAGTATGAAACTAGTTCTCAACACCATACATATGAAATGAGACTTAAAATGTATCGAAC
321 CTTTGTGAG-CTGAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGATC
* * * * * * * * *
28494973 TACTTAAAAAAATAAGGAACTTTGTGAAAAA-TTTAGTTGATTTACGATCACGACATTTTACTTC
385 TGCTCAGAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACTTT
* * * * * * *
28495037 CAGGACTATACGAATTTCATGGTCCGTTGATTTTTAATGACAACCTTCTACTTACGA
450 TAGGTCTTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
* * * * * **
28495094 GATTTTACGAATCTCATGGTCTACTGA-TTACCGATAACAACCTTTTACTTACGAGATTTTATGA
1 GATTTTACGAATCTCGTGGTCTGCTAATTTA-CGATAACGACCTTCTACTTACGAGATTTTACAA
* * * *
28495158 ATCTCATGGTCTACTGATTTTCGATCATGACCTTCTA
65 ATCTCACGGTCCATTGATTTACGATCATGACCTTCTA
28495195 TTTATGTGAT
Statistics
Matches: 2499, Mismatches: 570, Indels: 145
0.78 0.18 0.05
Matches are distributed among these distances:
501 54 0.02
502 108 0.04
503 8 0.00
504 226 0.09
505 94 0.04
506 655 0.26
507 546 0.22
508 237 0.09
509 85 0.03
510 430 0.17
511 55 0.02
512 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (506 bp):
GATTTTACGAATCTCGTGGTCTGCTAATTTACGATAACGACCTTCTACTTACGAGATTTTACAAA
TCTCACGGTCCATTGATTTACGATCATGACCTTCTACCTATAGGATTTTATGAATCTCATGGTCT
GCTTATTTACGATCACGACCTTCTACTTATGTGATTTTACGAATCTAGGCGTGTTGAGGAATAAC
TCAAAACTGACCTCTTTACCCTTCAGAGCAAGCTAAATGCTAGAGATGATGAATATAGGCGTGTT
GAGGAAGAACTCAAAACTGACCTTGAAAGGAGGATAGAGGTATCAATTTTGTTATATTGCCTTTG
TGAGCTGAAGCTAGTTCTCAACACCATACATTTGAAATGAGGCTTGAAATGGATCGATCTGCTCA
GAAAAACAAGGAACTTTCTGAAAAATTTTAGTTGATTTACAATCATGACCTTTTACTTTTAGGTC
TTTACGAATCTCACGGTCCGCTGATTTTTTATGACAACCTTCTACTTACGA
Found at i:28494185 original size:54 final size:54
Alignment explanation
Indices: 28494080--28494257 Score: 169
Period size: 54 Copynumber: 3.3 Consensus size: 54
28494070 TTCTAAATAT
* * * * * *
28494080 GAGATTTTACAAATCTCGTGGTCTGTTGATTTACGATAACAACCTTTTACTTAC
1 GAGATTTTACAAATCTCCTGGTCCGTTGATTTACGATCACGACCATCTACTTAC
**
28494134 GAGATTTTACAAATCTCCTGGTCCACTGATTTACGATCACGACCATCTACTTA-
1 GAGATTTTACAAATCTCCTGGTCCGTTGATTTACGATCACGACCATCTACTTAC
* * * ** * * *
28494187 TAGGATTTTACGAATCTTCTATTCCGTTGATTTACAATCACGACCCTCAACTTAC
1 GA-GATTTTACAAATCTCCTGGTCCGTTGATTTACGATCACGACCATCTACTTAC
** *
28494242 TTGATTTTACGAATCT
1 GAGATTTTACAAATCT
28494258 AGGCATGTTG
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.01
54 101 0.98
55 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (54 bp):
GAGATTTTACAAATCTCCTGGTCCGTTGATTTACGATCACGACCATCTACTTAC
Found at i:28494670 original size:55 final size:54
Alignment explanation
Indices: 28494560--28494690 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 54
28494550 CAGTCCGTTG
* * ** * **
28494560 ATTTATGATCACGACCTTCTACTTACGAGATTTTATGAATCTCGTGATTTGCTA
1 ATTTAAGATCACGACCTTCTACTAACGAGATTTTACAAATCTCGCGATTCCCTA
* *
28494614 ATTTTAAGATCACGATCTTCTACTAACGAGATTTTACAAATCTCGCGGTTCCCTA
1 A-TTTAAGATCACGACCTTCTACTAACGAGATTTTACAAATCTCGCGATTCCCTA
* *
28494669 ATTTACGATCATGACCTTCTAC
1 ATTTAAGATCACGACCTTCTAC
28494691 CCATAGGATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 19 0.30
55 45 0.70
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (54 bp):
ATTTAAGATCACGACCTTCTACTAACGAGATTTTACAAATCTCGCGATTCCCTA
Found at i:28495219 original size:29 final size:29
Alignment explanation
Indices: 28495172--28495235 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
28495162 CATGGTCTAC
* ** *
28495172 TGATTTTCGATCATGACCTTCTATTTATG
1 TGATTTACGATCACAACCTTCTACTTATG
28495201 TGATTTACGATCACAACCTTCTACTTATG
1 TGATTTACGATCACAACCTTCTACTTATG
*
28495230 GGATTT
1 TGATTT
28495236 TATGAATCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (29 bp):
TGATTTACGATCACAACCTTCTACTTATG
Found at i:28495352 original size:54 final size:54
Alignment explanation
Indices: 28495203--28495352 Score: 169
Period size: 54 Copynumber: 2.8 Consensus size: 54
28495193 TATTTATGTG
* * *
28495203 ATTTACGATCACAACCTTCTACTTATGGGATTTTATGAATCTCGCAATTCGCTA
1 ATTTACAATCACAACCTTCTACTTACGGGATTTTACGAATCTCGCAATTCGCTA
* * ** *
28495257 ATTTAAAATAATGACCTTCTACTTACGGGGA-TTTACAAATCTCGCAA-TCTGCTA
1 ATTTACAATCACAACCTTCTACTTAC-GGGATTTTACGAATCTCGCAATTC-GCTA
* * *
28495311 ATTTACAATCACAACCTTCTAATTACGTGATTTTGCGAATCT
1 ATTTACAATCACAACCTTCTACTTACGGGATTTTACGAATCT
28495353 AGGAATGTTA
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
53 5 0.06
54 68 0.88
55 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (54 bp):
ATTTACAATCACAACCTTCTACTTACGGGATTTTACGAATCTCGCAATTCGCTA
Found at i:28495710 original size:54 final size:54
Alignment explanation
Indices: 28495644--28495782 Score: 136
Period size: 54 Copynumber: 2.6 Consensus size: 54
28495634 TTCGATGACG
* * * * * *
28495644 ACCTTCTACTTACGAGATTATACAAATCTCGTTGTCTACTGATTCACAATAACA
1 ACCTTTTACTTACGAGATTATACGAATCTCATAGCCCACTGATTCACAATAACA
* * * ** *
28495698 ACCTTTTACTTAC-AGGATTTTACGAATCTCATAGCCCATTGATTTACGGTAATA
1 ACCTTTTACTTACGA-GATTATACGAATCTCATAGCCCACTGATTCACAATAACA
* *
28495752 ACCTTTTACTTATGAGATTCTACGAATCTCA
1 ACCTTTTACTTACGAGATTATACGAATCTCA
28495783 CGAAATTTTG
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.01
54 67 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (54 bp):
ACCTTTTACTTACGAGATTATACGAATCTCATAGCCCACTGATTCACAATAACA
Found at i:28495794 original size:54 final size:54
Alignment explanation
Indices: 28495736--28495838 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
28495726 TCATAGCCCA
* * * *
28495736 TTGATTTACGGTAATAACCTTTTACTTAT-GAGATTCTACGAATCTCACGAAATT
1 TTGATTTACGATAATAACCTTATACATATGGAGA-TATACGAATCTCACGAAATT
* * *
28495790 TTGATTTATGATCATAACCTTATACATATGGGGATATACGAATCTCACG
1 TTGATTTACGATAATAACCTTATACATATGGAGATATACGAATCTCACG
28495839 GTCTACTGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 38 0.93
55 3 0.07
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (54 bp):
TTGATTTACGATAATAACCTTATACATATGGAGATATACGAATCTCACGAAATT
Found at i:28495864 original size:54 final size:55
Alignment explanation
Indices: 28495791--28495911 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 55
28495781 CACGAAATTT
* **
28495791 TGATTTATGATC-ATAACCTTATACATATGGGGAT-ATACGAATCTCACGGTCTAC
1 TGATTTACGATCAATAACCTTATACATA-CAGGATCATACGAATCTCACGGTCTAC
* *** *
28495845 TGATTTACGATCAAT-ACCTTCTTTTTACAGGATCTTACGAATCTCACGGTCTAC
1 TGATTTACGATCAATAACCTTATACATACAGGATCATACGAATCTCACGGTCTAC
*
28495899 TAATTTACGATCA
1 TGATTTACGATCA
28495912 CGACCTCATA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 4 0.07
54 50 0.89
55 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (55 bp):
TGATTTACGATCAATAACCTTATACATACAGGATCATACGAATCTCACGGTCTAC
Found at i:28495926 original size:54 final size:53
Alignment explanation
Indices: 28495821--28495971 Score: 178
Period size: 54 Copynumber: 2.8 Consensus size: 53
28495811 ATACATATGG
* ** *
28495821 GGATA-TACGAATCTCACGGTCTACTGATTTACGATCAATACCTTCTTTTTACA
1 GGATATTACGAATCTCACGGTCTACTAATTTACGATCACGACC-TCTATTTACA
* *
28495874 GGATCTTACGAATCTCACGGTCTACTAATTTACGATCACGACCTCATATTTACG
1 GGATATTACGAATCTCACGGTCTACTAATTTACGATCACGACCTC-TATTTACA
* *** *
28495928 GGATATTACAAATCTTGTGATCTACTAATTTACGATCACGACCT
1 GGATATTACGAATCTCACGGTCTACTAATTTACGATCACGACCT
28495972 TTTACTTACG
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 6 0.07
54 78 0.93
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (53 bp):
GGATATTACGAATCTCACGGTCTACTAATTTACGATCACGACCTCTATTTACA
Found at i:28495981 original size:54 final size:54
Alignment explanation
Indices: 28495894--28495996 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
28495884 AATCTCACGG
*
28495894 TCTACTAATTTACGATCACGACCTCATATTTACGGGATATTACAAATCTTGTGA
1 TCTACTAATTTACGATCACGACCTCATACTTACGGGATATTACAAATCTTGTGA
** * * *
28495948 TCTACTAATTTACGATCACGACCTTTTACTTACGTGATTTTACGAATCT
1 TCTACTAATTTACGATCACGACCTCATACTTACGGGATATTACAAATCT
28495997 AGGCGTGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (54 bp):
TCTACTAATTTACGATCACGACCTCATACTTACGGGATATTACAAATCTTGTGA
Found at i:28496390 original size:54 final size:54
Alignment explanation
Indices: 28496303--28496507 Score: 178
Period size: 54 Copynumber: 3.8 Consensus size: 54
28496293 ACGATCTACC
* * * *** *
28496303 AATTTATGATGACGACCTTTTACTTATACGATTTTACGAATCTCATGGTCCACT
1 AATTTACGATAACGACCTTCTACTTACGTGATTTTACGAATCTCATGGTCCGCT
* * * * * * *
28496357 AATTTACGATAACAACCTTCTACTAACGGGATTTTATGAATATCACGTTCCGCT
1 AATTTACGATAACGACCTTCTACTTACGTGATTTTACGAATCTCATGGTCCGCT
* * * * ** * *
28496411 AATTTACAATTACGACCTTCTACTTACGTGTTTTTAAGAATCTTGTGGCCCGTT
1 AATTTACGATAACGACCTTCTACTTACGTGATTTTACGAATCTCATGGTCCGCT
* *
28496465 AATTTACGATCACGACATTCTACTTACGTGATTTT-CTGAATCT
1 AATTTACGATAACGACCTTCTACTTACGTGATTTTAC-GAATCT
28496508 ATACATGTTG
Statistics
Matches: 118, Mismatches: 32, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
54 118 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (54 bp):
AATTTACGATAACGACCTTCTACTTACGTGATTTTACGAATCTCATGGTCCGCT
Done.