Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 161 of 173
Found at i:48323045 original size:99 final size:98
Alignment explanation
Indices: 48322822--48323024 Score: 246
Period size: 99 Copynumber: 2.1 Consensus size: 98
48322812 TAATTCAGGC
* * * *
48322822 TTGGGCAATTCTGGCTTAGGTAAC-TCGGGAACTTTAGGCAATTCTGGCTTTGGTAACTCAGGAA
1 TTGGGTAATTCAGGCTT-GG-AACTTCAGGAACTTTAGGAAATTCTGGCTTTGGTAACTCAGGAA
* * * *
48322886 CTTTTGGTAATTCAGGTTTTGGCAACTCGGGAGCT
64 CTTTTGGTAATTCAGATTTTGACAACTCAGGAGCA
* *
48322921 TTGGGTAATTCAGGCTTGGGCACTTCAGGAACTTTAGGAAATTCTGGCTTTGGTAACTCCGGAAC
1 TTGGGTAATTCAGGCTT-GGAACTTCAGGAACTTTAGGAAATTCTGGCTTTGGTAACTCAGGAAC
** * *
48322986 TTTTGGTGCTTCAGATTTTGACAATTTAGGAGCA
65 TTTTGGTAATTCAGATTTTGACAACTCAGGAGCA
48323020 TTGGG
1 TTGGG
48323025 AATCTCTGGA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 2 0.02
99 86 0.98
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (98 bp):
TTGGGTAATTCAGGCTTGGAACTTCAGGAACTTTAGGAAATTCTGGCTTTGGTAACTCAGGAACT
TTTGGTAATTCAGATTTTGACAACTCAGGAGCA
Found at i:48323141 original size:51 final size:51
Alignment explanation
Indices: 48323059--48323207 Score: 154
Period size: 51 Copynumber: 2.9 Consensus size: 51
48323049 GGATTTTTTC
* * * * ** *
48323059 AACTCGGGAATCTTAGGAAATTCAGGCTTTGGCAACTCTGGCACTTTCGGA
1 AACTCAGGAACCTTAGGCAATTCTGATTTTGGCAACTCTGGAACTTTCGGA
* *
48323110 AACTCAGGAACCTTGGGTAATTCTGATTTTGGCAACTCTGGAACTTTCGGA
1 AACTCAGGAACCTTAGGCAATTCTGATTTTGGCAACTCTGGAACTTTCGGA
* * * *** *
48323161 AACTCGGGGACCTTAGGCAATTCGGGCCTTGGCAACTCCGGAACTTT
1 AACTCAGGAACCTTAGGCAATTCTGATTTTGGCAACTCTGGAACTTT
48323208 AGGCAATTCA
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (51 bp):
AACTCAGGAACCTTAGGCAATTCTGATTTTGGCAACTCTGGAACTTTCGGA
Found at i:48323198 original size:33 final size:33
Alignment explanation
Indices: 48323161--48323234 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
48323151 AACTTTCGGA
* *
48323161 AACTCGGGGACCTTAGGCAATTCGGGCCTTGGC
1 AACTCGGGAACCTTAGGCAATTCAGGCCTTGGC
* * **
48323194 AACTCCGGAACTTTAGGCAATTCAGGTTTTGGC
1 AACTCGGGAACCTTAGGCAATTCAGGCCTTGGC
48323227 AACTCGGG
1 AACTCGGG
48323235 CATTTTAGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (33 bp):
AACTCGGGAACCTTAGGCAATTCAGGCCTTGGC
Found at i:48323242 original size:33 final size:33
Alignment explanation
Indices: 48323173--48323255 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
48323163 CTCGGGGACC
* **
48323173 TTAGGCAATTCGGGCCTTGGCAACTCCGGAACT
1 TTAGGCAATTCAGGTTTTGGCAACTCCGGAACT
* * *
48323206 TTAGGCAATTCAGGTTTTGGCAACTCGGGCATT
1 TTAGGCAATTCAGGTTTTGGCAACTCCGGAACT
* *
48323239 TTAGGTAGTTCAGGTTT
1 TTAGGCAATTCAGGTTT
48323256 CGGGATTTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (33 bp):
TTAGGCAATTCAGGTTTTGGCAACTCCGGAACT
Found at i:48328423 original size:33 final size:33
Alignment explanation
Indices: 48328333--48328433 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 33
48328323 ACTCCTATCT
* * * * *
48328333 GATTAACCTGGCTGGTCCGGGTTGGCTCGGGCT
1 GATTAACCTGGCTCGTCCGCGTAGGCTCCGGCC
*
48328366 GATTAACCTGGCTCGAT-TGCGTAGGCTCCGGCC
1 GATTAACCTGGCTCG-TCCGCGTAGGCTCCGGCC
* * *
48328399 GATTAACCTGGCTTGTCCGTGTAGGCTCTGGCC
1 GATTAACCTGGCTCGTCCGCGTAGGCTCCGGCC
48328432 GA
1 GA
48328434 CTAATGTGGC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
32 1 0.02
33 54 0.96
34 1 0.02
ACGTcount: A:0.13, C:0.27, G:0.34, T:0.27
Consensus pattern (33 bp):
GATTAACCTGGCTCGTCCGCGTAGGCTCCGGCC
Found at i:48328745 original size:48 final size:48
Alignment explanation
Indices: 48328693--48328968 Score: 302
Period size: 48 Copynumber: 5.6 Consensus size: 48
48328683 AACAGCGTTT
48328693 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
*
48328741 GCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGTGCCGGTGGTTGCATAAACA
1 ------GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
* * * * *
48328795 GCGTTTGCGTTTCCTTCGGAGGCGAAGGAGCCGGCGGCTGCATAAACA
1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
* * * * * *
48328843 ACGTCTGCGTTTCCTTAGGAGGCGGAGGAGCCGGCGGTTGCATAAACA
1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
* * * **
48328891 GCGTTTGCGTCTCTTTCGGAGGCGCAGACGGTGGCT-GTTGCATAAACA
1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGG-TGGTTGCATAAACA
* * *
48328939 GCGTCTGCGTCTCTTTCGGAGGCGGCGGCG
1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCG
48328969 GTTGCATAAA
Statistics
Matches: 195, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
48 148 0.76
54 47 0.24
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (48 bp):
GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
Found at i:48328758 original size:54 final size:54
Alignment explanation
Indices: 48328670--48328900 Score: 288
Period size: 54 Copynumber: 4.5 Consensus size: 54
48328660 TTTCTTTCGG
* *
48328670 CGGCGATTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGCGC
1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC
* *
48328724 CGGTGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGTGC
1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC
* *
48328778 CGGTGGTTGCATAAACAGCGTTTGCGTTT-C----C-TTCGGAGGCGAAGGAGC
1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC
* * * *
48328826 CGGCGGCTGCATAAACAACG--T-C---TGCGTTTCCTTAGGAGGCGGAGGAGC
1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC
48328874 CGGCGGTTGCATAAACAGCGTTTGCGT
1 CGGCGGTTGCATAAACAGCGTTTGCGT
48328901 CTCTTTCGGA
Statistics
Matches: 154, Mismatches: 12, Indels: 23
0.81 0.06 0.12
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 65 0.42
49 1 0.01
50 1 0.01
51 1 0.01
53 1 0.01
54 80 0.52
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.26
Consensus pattern (54 bp):
CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC
Found at i:48329028 original size:3 final size:3
Alignment explanation
Indices: 48329016--48329047 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
48329006 TTGCGGTTGT
*
48329016 TGC TGA TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
48329048 ATGGTGGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.28, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:48330694 original size:22 final size:22
Alignment explanation
Indices: 48330669--48330725 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
48330659 GGTTGTTGTT
* * *
48330669 ATTTTATTGTTGTTTTGCTACC
1 ATTTTATTGTTATATTACTACC
* * *
48330691 ATTTTACTATTATATTACTACT
1 ATTTTATTGTTATATTACTACC
48330713 ATTTTATTGTTAT
1 ATTTTATTGTTAT
48330726 TATTTGGATA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (22 bp):
ATTTTATTGTTATATTACTACC
Found at i:48337129 original size:21 final size:20
Alignment explanation
Indices: 48337092--48337138 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
48337082 TTTTATTTAA
** *
48337092 TTTATAAATAATTTAAATTT
1 TTTATAAATAAAATAAATAT
48337112 TTTATAATATAAAATAAATAT
1 TTTATAA-ATAAAATAAATAT
48337133 TTTATA
1 TTTATA
48337139 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATAAATAAAATAAATAT
Found at i:48343354 original size:22 final size:22
Alignment explanation
Indices: 48343326--48343372 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
48343316 TTTTGTACTT
48343326 GCTTTCTTGTTTAATATTTATA
1 GCTTTCTTGTTTAATATTTATA
48343348 GCTTTCTTGTTTAATATTTATA
1 GCTTTCTTGTTTAATATTTATA
48343370 GCT
1 GCT
48343373 GTTCAATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (22 bp):
GCTTTCTTGTTTAATATTTATA
Found at i:48343683 original size:18 final size:19
Alignment explanation
Indices: 48343655--48343691 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
48343645 TAATGGCAAC
48343655 TTTCATTGCTTTTGGTGTT
1 TTTCATTGCTTTTGGTGTT
*
48343674 TTTC-TTGCTTTTTGTGTT
1 TTTCATTGCTTTTGGTGTT
48343692 GGGCACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.11, G:0.19, T:0.68
Consensus pattern (19 bp):
TTTCATTGCTTTTGGTGTT
Found at i:48358240 original size:6 final size:6
Alignment explanation
Indices: 48358229--48358269 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
48358219 CAAGAGTTGG
48358229 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
48358270 AATTTGAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:48372425 original size:13 final size:12
Alignment explanation
Indices: 48372403--48372450 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
48372393 AAAATAAAAT
48372403 CAATAATAATAA
1 CAATAATAATAA
48372415 CAATGAATAATAA
1 CAAT-AATAATAA
* *
48372428 CAACAATAACAA
1 CAATAATAATAA
*
48372440 TAATAA-AATAA
1 CAATAATAATAA
48372451 ACACATAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 4 0.13
12 15 0.50
13 11 0.37
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:48372458 original size:22 final size:22
Alignment explanation
Indices: 48372410--48372461 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
48372400 AATCAATAAT
*
48372410 AATAACAATGAATAATAACAAC
1 AATAACAATGAATAATAAAAAC
48372432 AATAACAAT-AATAA-AATAAAC
1 AATAACAATGAATAATAA-AAAC
48372453 ACATAACAA
1 A-ATAACAA
48372462 GGCTGTAGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 9 0.33
22 16 0.59
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.17
Consensus pattern (22 bp):
AATAACAATGAATAATAAAAAC
Found at i:48372880 original size:18 final size:20
Alignment explanation
Indices: 48372825--48372900 Score: 83
Period size: 19 Copynumber: 4.1 Consensus size: 20
48372815 GAATCTCTTG
48372825 TTTTGAAAACACGAGAA---
1 TTTTGAAAACACGAGAATTT
* * *
48372842 TTTTG-AAACACAATATTTT
1 TTTTGAAAACACGAGAATTT
48372861 TTTTGAAAACACG-GAATTT
1 TTTTGAAAACACGAGAATTT
48372880 TTTTG-AAACACGAGAATTT
1 TTTTGAAAACACGAGAATTT
48372899 TT
1 TT
48372901 GAAAACCTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.17
17 5 0.10
18 7 0.15
19 22 0.46
20 6 0.12
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTTGAAAACACGAGAATTT
Found at i:48373212 original size:38 final size:37
Alignment explanation
Indices: 48372983--48373230 Score: 167
Period size: 35 Copynumber: 6.9 Consensus size: 37
48372973 GAACACGAAA
** *
48372983 TAAAACACGGAAATTCGTGAAGCACGAGAATTTTTTT
1 TAAAACACGGAAATTTTTGAAACACGAGAATTTTTTT
* ** *
48373020 TTAAACACGGAAGCTTTTGAAATACGAGAA---TTTT
1 TAAAACACGGAAATTTTTGAAACACGAGAATTTTTTT
* * * ** * *
48373054 AAAAACACGAAAATTTTTTAAA-ACCTGAA-ATATTT
1 TAAAACACGGAAATTTTTGAAACACGAGAATTTTTTT
* ** * *
48373089 TAAAACACGAAAATTTGCGAGACACGACAA--TTTTT
1 TAAAACACGGAAATTTTTGAAACACGAGAATTTTTTT
* * *
48373124 TGAAACACGAGAAATTTTTGAGAACGCGA-AA---ATTT
1 TAAAACACG-GAAATTTTTGA-AACACGAGAATTTTTTT
* *
48373159 TAAAACGCGGAAATTTTTGAAACACGAGGATTTTTTT
1 TAAAACACGGAAATTTTTGAAACACGAGAATTTTTTT
*
48373196 TAAAAGCACGGAAATTTTTGAAATACGAGAATTTT
1 TAAAA-CACGGAAATTTTTGAAACACGAGAATTTT
48373231 AAAAACATGA
Statistics
Matches: 161, Mismatches: 40, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
33 11 0.07
34 32 0.20
35 42 0.26
36 14 0.09
37 36 0.22
38 26 0.16
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (37 bp):
TAAAACACGGAAATTTTTGAAACACGAGAATTTTTTT
Found at i:48373289 original size:17 final size:17
Alignment explanation
Indices: 48372860--48373283 Score: 164
Period size: 17 Copynumber: 24.3 Consensus size: 17
48372850 CACAATATTT
**
48372860 TTTTTGAAAACACGGAATT
1 TTTTT-AAAACAC-GAAAA
* *
48372879 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAAAA
48372896 TTTTTGAAAAC-CTGAAAA
1 TTTTT-AAAACAC-GAAAA
*
48372914 TTTTTACAACACGAAAA
1 TTTTTAAAACACGAAAA
** * *
48372931 TTTGCAAAACATGACAA
1 TTTTTAAAACACGAAAA
* *
48372948 TTTTTGAAACACGATAAT
1 TTTTTAAAACACGA-AAA
*
48372966 TTTTTGAGAACACG-AAA
1 TTTTT-AAAACACGAAAA
*
48372983 ----TAAAACACGGAAA
1 TTTTTAAAACACGAAAA
** * * *
48372996 TTCGTGAAGCACGAGAATTT
1 TTTTTAAAACACGA-AA--A
* * *
48373016 TTTTTTAAACACGGAAG
1 TTTTTAAAACACGAAAA
* * * *
48373033 CTTTTGAAATACGAGAA
1 TTTTTAAAACACGAAAA
*
48373050 TTTTAAAAACACGAAAA
1 TTTTTAAAACACGAAAA
48373067 TTTTTTAAAAC-CTG-AAA
1 -TTTTTAAAACAC-GAAAA
48373084 TATTTTAAAACACGAAAA
1 T-TTTTAAAACACGAAAA
*** * *
48373102 TTTGCGAGACACGACAAT
1 TTTTTAAAACACGA-AAA
*
48373120 TTTTTGAAACACGAGAAA
1 TTTTTAAAACACGA-AAA
* *
48373138 TTTTTGAGAACGCGAAAA
1 TTTTT-AAAACACGAAAA
* *
48373156 -TTTTAAAACGCGGAAA
1 TTTTTAAAACACGAAAA
* **
48373172 TTTTTGAAACACGAGGATTT
1 TTTTTAAAACACGA--A-AA
*
48373192 TTTTTAAAAGCACGGAAA
1 TTTTTAAAA-CACGAAAA
* * *
48373210 TTTTTGAAATACGAGAA
1 TTTTTAAAACACGAAAA
* *
48373227 TTTTAAAAACATGAAAA
1 TTTTTAAAACACGAAAA
** *
48373244 TTTACAAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
48373261 TTTTTAAAAATACGAAAA
1 TTTTT-AAAACACGAAAA
48373279 TTTTT
1 TTTTT
48373284 GAAATAATAG
Statistics
Matches: 294, Mismatches: 85, Indels: 53
0.68 0.20 0.12
Matches are distributed among these distances:
12 7 0.02
13 4 0.01
16 11 0.04
17 141 0.48
18 89 0.30
19 21 0.07
20 17 0.06
21 4 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:48373420 original size:18 final size:18
Alignment explanation
Indices: 48373399--48373509 Score: 82
Period size: 18 Copynumber: 6.2 Consensus size: 18
48373389 GAAAATTTAC
48373399 AAAACATGAAAATTTTTG
1 AAAACATGAAAATTTTTG
* * *
48373417 AAAATACGATAATTTTTG
1 AAAACATGAAAATTTTTG
* **
48373435 AAAACTTGGGAATTTTT-
1 AAAACATGAAAATTTTTG
* * *
48373452 AAAACACGGGAATTTTTTG
1 AAAACA-TGAAAATTTTTG
*
48373471 -AAACATCGAAATTTTTTG
1 AAAACAT-GAAAATTTTTG
* *
48373489 GAAACACGAAAATTTTTG
1 AAAACATGAAAATTTTTG
48373507 AAA
1 AAA
48373510 TACAAATTTT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
17 5 0.07
18 62 0.86
19 5 0.07
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (18 bp):
AAAACATGAAAATTTTTG
Found at i:48373449 original size:36 final size:36
Alignment explanation
Indices: 48373382--48373509 Score: 102
Period size: 36 Copynumber: 3.6 Consensus size: 36
48373372 AGAATTCAAA
* **
48373382 AAAATACGAAAA-TTTACAAAACAT-GAAAATTTTTG
1 AAAACACGAAAATTTTTGAAAACATCG-AAATTTTTG
* * * * *
48373417 AAAATACGATAATTTTTGAAAACTTGGGAATTTTT-
1 AAAACACGAAAATTTTTGAAAACATCGAAATTTTTG
* *
48373452 AAAACACGGGAATTTTTTG-AAACATCGAAATTTTTTG
1 AAAACAC-GAAAATTTTTGAAAACATCGAAA-TTTTTG
*
48373489 GAAACACGAAAATTTTTGAAA
1 AAAACACGAAAATTTTTGAAA
48373510 TACAAATTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
35 25 0.35
36 38 0.53
37 9 0.12
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (36 bp):
AAAACACGAAAATTTTTGAAAACATCGAAATTTTTG
Found at i:48373486 original size:19 final size:18
Alignment explanation
Indices: 48373464--48373521 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
48373454 AACACGGGAA
48373464 TTTTTTGAAACATCGAAAT
1 TTTTTTGAAACA-CGAAAT
*
48373483 TTTTTGGAAACACGAAA-
1 TTTTTTGAAACACGAAAT
* *
48373500 ATTTTTGAAATAC-AAAT
1 TTTTTTGAAACACGAAAT
48373517 TTTTT
1 TTTTT
48373522 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 3 0.09
17 14 0.42
18 5 0.15
19 11 0.33
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTTTTGAAACACGAAAT
Found at i:48373961 original size:19 final size:18
Alignment explanation
Indices: 48373933--48373968 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48373923 AACACCATTT
48373933 AAATACATTAAATAAAATA
1 AAATACATTAAA-AAAATA
*
48373952 AAATAGATTAAAAAAAT
1 AAATACATTAAAAAAAT
48373969 TTACCAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (18 bp):
AAATACATTAAAAAAATA
Found at i:48374280 original size:10 final size:10
Alignment explanation
Indices: 48374267--48374333 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
48374257 TTTTATTTTA
48374267 TTTTTCTTTC
1 TTTTTCTTTC
*
48374277 TTTTTCTCTC
1 TTTTTCTTTC
48374287 TTTTTCTTTC
1 TTTTTCTTTC
*
48374297 TCCTTTC-TTC
1 T-TTTTCTTTC
*
48374307 TTCTTCCCTTTTC
1 TT-TT-TC-TTTC
48374320 TTTTTTCTTTC
1 -TTTTTCTTTC
48374331 TTT
1 TTT
48374334 CAAGCCCCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 28 0.62
11 9 0.20
12 1 0.02
13 5 0.11
14 2 0.04
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:48374296 original size:14 final size:14
Alignment explanation
Indices: 48374272--48374308 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
48374262 TTTTATTTTT
48374272 CTTTCTT-TTTCTC
1 CTTTCTTCTTTCTC
48374285 TCTTT-TTCTTTCTC
1 -CTTTCTTCTTTCTC
48374299 CTTTCTTCTT
1 CTTTCTTCTT
48374309 CTTCCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTCTTCTTTCTC
Found at i:48374303 original size:27 final size:27
Alignment explanation
Indices: 48374272--48374333 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
48374262 TTTTATTTTT
*
48374272 CTTTCTTTTTC-TCTCTTTTTCTTTCTC
1 CTTTCTTTTTCTTC-CCTTTTCTTTCTC
* * *
48374299 CTTTCTTCTTCTTCCCTTTTCTTTTTT
1 CTTTCTTTTTCTTCCCTTTTCTTTCTC
48374326 CTTTCTTT
1 CTTTCTTT
48374334 CAAGCCCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (27 bp):
CTTTCTTTTTCTTCCCTTTTCTTTCTC
Found at i:48375783 original size:31 final size:31
Alignment explanation
Indices: 48375745--48375807 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
48375735 ACTAAAAGAG
*
48375745 ATGAAATTATCTGCATTCAGATTATTTTCCC
1 ATGAAATTATCTGCATTCAGATTATTTGCCC
48375776 ATGAAATTATCTGCATTCAGATTATTTGCCC
1 ATGAAATTATCTGCATTCAGATTATTTGCCC
48375807 A
1 A
48375808 CCTATCAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (31 bp):
ATGAAATTATCTGCATTCAGATTATTTGCCC
Found at i:48377594 original size:37 final size:37
Alignment explanation
Indices: 48377411--48377595 Score: 300
Period size: 37 Copynumber: 5.0 Consensus size: 37
48377401 GCTAAAGCCA
*
48377411 CCACTTATCACTTTGTCTCTTGATCAGATAAGTTTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
48377448 -CACTTATCACTTTGTCACTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
48377484 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
48377521 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
48377558 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
48377595 C
1 C
48377596 TAAAACTACC
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
36 33 0.24
37 106 0.76
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:48384594 original size:7 final size:7
Alignment explanation
Indices: 48384584--48384616 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
48384574 ACTAAAACAA
48384584 AAAACGT
1 AAAACGT
48384591 AAAACGT
1 AAAACGT
48384598 AAAACGT
1 AAAACGT
*
48384605 AAAACAT
1 AAAACGT
48384612 AAAAC
1 AAAAC
48384617 TTAGAGCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.64, C:0.15, G:0.09, T:0.12
Consensus pattern (7 bp):
AAAACGT
Found at i:48384595 original size:14 final size:14
Alignment explanation
Indices: 48384576--48384616 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
48384566 TTTTATTTAC
*
48384576 TAAAACAAAAAACG
1 TAAAACATAAAACG
*
48384590 TAAAACGTAAAACG
1 TAAAACATAAAACG
48384604 TAAAACATAAAAC
1 TAAAACATAAAAC
48384617 TTAGAGCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12
Consensus pattern (14 bp):
TAAAACATAAAACG
Found at i:48384600 original size:21 final size:21
Alignment explanation
Indices: 48384576--48384616 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48384566 TTTTATTTAC
*
48384576 TAAAACAAAAAACGTAAAACG
1 TAAAACAAAAAACATAAAACG
**
48384597 TAAAACGTAAAACATAAAAC
1 TAAAACAAAAAACATAAAAC
48384617 TTAGAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12
Consensus pattern (21 bp):
TAAAACAAAAAACATAAAACG
Found at i:48385200 original size:17 final size:17
Alignment explanation
Indices: 48385178--48385350 Score: 56
Period size: 17 Copynumber: 9.8 Consensus size: 17
48385168 GAATCTCTTG
48385178 TTTTGAAAACACGAGAA
1 TTTTGAAAACACGAGAA
* * *
48385195 TTTTG-AAACACAATATTTT
1 TTTTGAAAACACGAGA---A
48385214 TTTTGAAAACACG-GAA
1 TTTTGAAAACACGAGAA
48385230 TTTTTTTG-AAACACGAGAA
1 ---TTTTGAAAACACGAGAA
*
48385249 TTTT-AGAAACAC-AAAA
1 TTTTGA-AAACACGAGAA
** *
48385265 CTTTTTGAAAACTTGAAAA
1 --TTTTGAAAACACGAGAA
*
48385284 TTCTT-ACAACACGA-AA
1 TT-TTGAAAACACGAGAA
* * *
48385300 ATTTGCAAAACATGACAA
1 TTTTG-AAAACACGAGAA
*
48385318 TTTTTG-AAACATGAGAA
1 -TTTTGAAAACACGAGAA
48385335 TTTTTTGAAAACACGA
1 --TTTTGAAAACACGA
48385351 AATAAAACAC
Statistics
Matches: 117, Mismatches: 18, Indels: 40
0.67 0.10 0.23
Matches are distributed among these distances:
15 2 0.02
16 18 0.15
17 36 0.31
18 25 0.21
19 30 0.26
20 6 0.05
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTTGAAAACACGAGAA
Found at i:48385233 original size:18 final size:19
Alignment explanation
Indices: 48385157--48385252 Score: 83
Period size: 19 Copynumber: 4.9 Consensus size: 19
48385147 CGTGATTCAA
48385157 TTGAAACACGAGAATCTCTTGTT
1 TTGAAACACGAGAA--T-TT-TT
48385180 TTGAAAACACGAGAA---TT
1 TTG-AAACACGAGAATTTTT
* * *
48385197 TTGAAACACAATATTTTTT
1 TTGAAACACGAGAATTTTT
48385216 TTGAAAACACG-GAATTTTT
1 TTG-AAACACGAGAATTTTT
48385235 TTGAAACACGAGAATTTT
1 TTGAAACACGAGAATTTT
48385253 AGAAACACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
16 8 0.13
17 5 0.08
18 7 0.11
19 21 0.34
20 6 0.10
23 3 0.05
24 11 0.18
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (19 bp):
TTGAAACACGAGAATTTTT
Found at i:48385346 original size:19 final size:18
Alignment explanation
Indices: 48385301--48385347 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
48385291 AACACGAAAA
48385301 TTTGCAAAACATGACAATT
1 TTTG-AAAACATGACAATT
*
48385320 TTTG-AAACATGAGAATTT
1 TTTGAAAACATGACAA-TT
48385338 TTTGAAAACA
1 TTTGAAAACA
48385348 CGAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 9 0.36
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (18 bp):
TTTGAAAACATGACAATT
Found at i:48385427 original size:18 final size:18
Alignment explanation
Indices: 48385400--48385627 Score: 116
Period size: 17 Copynumber: 12.9 Consensus size: 18
48385390 TTAAACACGG
*
48385400 AAACGCGAAAATTTTTTA
1 AAACACGAAAATTTTTTA
*
48385418 AAAC-CTG-AAATATTTTA
1 AAACAC-GAAAATTTTTTA
***
48385435 AAACACGAAAA-TTTGCG
1 AAACACGAAAATTTTTTA
* * *
48385452 AGACACGACAATTTTTTG
1 AAACACGAAAATTTTTTA
*
48385470 AAACACGAGAAATTTTTGA
1 AAACACGA-AAATTTTTTA
* *
48385489 GAACGCGAAAA--TTTTA
1 AAACACGAAAATTTTTTA
* *
48385505 AAACGCGAAAA-TTTTTG
1 AAACACGAAAATTTTTTA
* *
48385522 AAACACGAGGATTTTGTTTA
1 AAACACGA-AAATTT-TTTA
*
48385542 AAAGCACGAAAA-TTTTTG
1 AAA-CACGAAAATTTTTTA
* * *
48385560 AAATACGAGAA-TTTTAA
1 AAACACGAAAATTTTTTA
* **
48385577 AAACATGAAAA-TTTACA
1 AAACACGAAAATTTTTTA
*
48385594 AAACAC-AAGAATTTTTAA
1 AAACACGAA-AATTTTTTA
*
48385612 AAATACGAAAATTTTT
1 AAACACGAAAATTTTT
48385628 GAAACAATAG
Statistics
Matches: 159, Mismatches: 38, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
16 16 0.10
17 66 0.42
18 46 0.29
19 19 0.12
20 7 0.04
21 5 0.03
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (18 bp):
AAACACGAAAATTTTTTA
Found at i:48385503 original size:70 final size:69
Alignment explanation
Indices: 48385399--48385632 Score: 197
Period size: 70 Copynumber: 3.3 Consensus size: 69
48385389 TTTAAACACG
* * *
48385399 GAAACGCGAAAATTTTTTAAAACCTGAAATATTTTAAAACACGAAAATTTGCGAGACACGA-CAA
1 GAAACACGAAAA-TTTTTGAAACC-GAAA-ATTTTAAAACACGAAAATTTGCGAAACACGAGCAA
48385463 TTT-TTT
63 TTTGTTT
* ** * *
48385469 GAAACACGAGAAATTTTTGAGAACGCGAAAATTTTAAAACGCGAAAATTTTTGAAACACGAGGAT
1 GAAACACGA-AAATTTTTGA-AAC-CGAAAATTTTAAAACACGAAAATTTGCGAAACACGAGCAA
48385534 TTTGTTT
63 TTTGTTT
* * * * * * *
48385541 AAAAGCACGAAAATTTTTGAAATACGAGAATTTTAAAAACATGAAAATTTACAAAACACAAG-AA
1 GAAA-CACGAAAATTTTTGAAA-CCGAAAATTTT-AAAACACGAAAATTTGCGAAACACGAGCAA
*
48385605 TTT-TTA
63 TTTGTTT
* *
48385611 AAAATACGAAAATTTTTGAAAC
1 GAAACACGAAAATTTTTGAAAC
48385633 AATAGATTTT
Statistics
Matches: 135, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
69 16 0.12
70 47 0.35
71 29 0.21
72 38 0.28
73 5 0.04
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (69 bp):
GAAACACGAAAATTTTTGAAACCGAAAATTTTAAAACACGAAAATTTGCGAAACACGAGCAATTT
GTTT
Found at i:48385556 original size:38 final size:37
Alignment explanation
Indices: 48385431--48385633 Score: 140
Period size: 35 Copynumber: 5.7 Consensus size: 37
48385421 CCTGAAATAT
** * *
48385431 TTTAAAACACGAAAATTTGCGAGACACGACAA-TTT-
1 TTTAAAACACGAAAATTTTTGAAACACGAGAATTTTG
* * *
48385466 TTTGAAACACGAGAAATTTTTGAGAACGCGA-AA--AT-
1 TTTAAAACACGA-AAATTTTTGA-AACACGAGAATTTTG
* *
48385501 TTTAAAACGCGAAAATTTTTGAAACACGAGGATTTTG
1 TTTAAAACACGAAAATTTTTGAAACACGAGAATTTTG
*
48385538 TTTAAAAGCACGAAAATTTTTGAAATACGAGAA--TT-
1 TTTAAAA-CACGAAAATTTTTGAAACACGAGAATTTTG
* * *** *
48385573 TTAAAAACATGAAAATTTACAAAACACAAGAA-TTT-
1 TTTAAAACACGAAAATTTTTGAAACACGAGAATTTTG
* *
48385608 TTAAAAATACGAAAATTTTTGAAACA
1 TTTAAAACACGAAAATTTTTGAAACA
48385634 ATAGATTTTC
Statistics
Matches: 134, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
33 6 0.04
34 30 0.22
35 51 0.38
36 13 0.10
37 12 0.09
38 22 0.16
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (37 bp):
TTTAAAACACGAAAATTTTTGAAACACGAGAATTTTG
Found at i:48385587 original size:34 final size:34
Alignment explanation
Indices: 48385429--48385633 Score: 162
Period size: 34 Copynumber: 5.9 Consensus size: 34
48385419 AACCTGAAAT
** * *
48385429 ATTTT-AAAACACGAAAATTTGCGAGACACGACA
1 ATTTTAAAAACACGAAAATTTTTGAAACACGAGA
** * *
48385462 ATTTTTTGAAACACGAGAAATTTTTGAGAACGCGAAA
1 A-TTTTAAAAACACGA-AAATTTTTGA-AACACGAGA
*
48385499 ATTTT-AAAACGCGAAAATTTTTGAAACACGAGGA
1 ATTTTAAAAACACGAAAATTTTTGAAACACGA-GA
* * *
48385533 TTTTGTTTAAAAGCACGAAAATTTTTGAAATACGAGA
1 --AT-TTTAAAAACACGAAAATTTTTGAAACACGAGA
* *** *
48385570 ATTTTAAAAACATGAAAATTTACAAAACACAAGA
1 ATTTTAAAAACACGAAAATTTTTGAAACACGAGA
*
48385604 ATTTTTAAAAATACGAAAATTTTTGAAACA
1 A-TTTTAAAAACACGAAAATTTTTGAAACA
48385634 ATAGATTTTC
Statistics
Matches: 135, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
33 7 0.05
34 41 0.30
35 39 0.29
36 13 0.10
37 12 0.09
38 23 0.17
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (34 bp):
ATTTTAAAAACACGAAAATTTTTGAAACACGAGA
Found at i:48385793 original size:35 final size:34
Alignment explanation
Indices: 48385753--48385888 Score: 139
Period size: 35 Copynumber: 3.9 Consensus size: 34
48385743 CAAAACATGA
*
48385753 AAATTTTTGAAAACACGATAATTTTTGAAACTCGG
1 AAATTTTTGAAAACACGA-AATTTTTGAAACACGG
* * *
48385788 GAATTTTT-AAAACACGGGAATTTTTTGAAACACCG
1 AAATTTTTGAAAACAC--GAAATTTTTGAAACACGG
* *
48385823 AAATTTTTTGAAAACACGAAGATTTTTAAAACACGC
1 AAA-TTTTTGAAAACACGAA-ATTTTTGAAACACGG
* *
48385859 AAAATTTTGGAAACACGAAAATTTTTGAAA
1 AAATTTTTGAAAACACG-AAATTTTTGAAA
48385889 TACGAATTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
34 7 0.08
35 46 0.55
36 23 0.28
37 7 0.08
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (34 bp):
AAATTTTTGAAAACACGAAATTTTTGAAACACGG
Found at i:48385893 original size:17 final size:17
Alignment explanation
Indices: 48385745--48385894 Score: 138
Period size: 18 Copynumber: 8.5 Consensus size: 17
48385735 AAAATTTACA
*
48385745 AAACATGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
48385762 AAAACACGATAATTTTTG
1 -AAACACGAAAATTTTTG
* ** *
48385780 AAACTCGGGAATTTTTA
1 AAACACGAAAATTTTTG
* *
48385797 AAACACGGGAATTTTTTG
1 AAACAC-GAAAATTTTTG
*
48385815 AAACACCGAAATTTTTTG
1 AAACA-CGAAAATTTTTG
* *
48385833 AAAACACGAAGATTTTTA
1 -AAACACGAAAATTTTTG
*
48385851 AAACACGCAAAATTTTGG
1 AAACACG-AAAATTTTTG
48385869 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
48385886 AAATACGAA
1 AAACACGAA
48385895 TTTTTTATTT
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
17 42 0.39
18 61 0.56
19 6 0.06
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:48386338 original size:19 final size:18
Alignment explanation
Indices: 48386310--48386345 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48386300 AACACCATTT
48386310 AAATACATTAAATAAAATA
1 AAATACATTAAA-AAAATA
*
48386329 AAATAGATTAAAAAAAT
1 AAATACATTAAAAAAAT
48386346 TACCAAAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (18 bp):
AAATACATTAAAAAAATA
Found at i:48386654 original size:10 final size:10
Alignment explanation
Indices: 48386641--48386711 Score: 63
Period size: 10 Copynumber: 6.7 Consensus size: 10
48386631 ACCTTTTTAT
48386641 TTTCTTTTTC
1 TTTCTTTTTC
48386651 TTTCTTTTTC
1 TTTCTTTTTC
*
48386661 TCTCTTTTTC
1 TTTCTTTTTC
**
48386671 TTTCTCCCTTC
1 TTTCT-TTTTC
48386682 -TTCTTCTTTCC
1 TTTCTT-TTT-C
48386693 TTTTCTTTTTTC
1 -TTTC-TTTTTC
48386705 TTTCTTT
1 TTTCTTT
48386712 CAAGCCCCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 32 0.65
11 8 0.16
12 1 0.02
13 6 0.12
14 2 0.04
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:48386709 original size:27 final size:27
Alignment explanation
Indices: 48386640--48386710 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
48386630 TACCTTTTTA
* *
48386640 TTTTC-TTTTTCTTTCTTTTTCTCTCT
1 TTTTCTTTTTTCTTTCTTCTTCTCTCC
* * * *
48386666 TTTTCTTTCTCCCTTCTTCTTCTTTCC
1 TTTTCTTTTTTCTTTCTTCTTCTCTCC
48386693 TTTTCTTTTTTCTTTCTT
1 TTTTCTTTTTTCTTTCTT
48386711 TCAAGCCCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 5 0.14
27 30 0.86
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTCTTTTTTCTTTCTTCTTCTCTCC
Found at i:48387452 original size:30 final size:31
Alignment explanation
Indices: 48387418--48387539 Score: 139
Period size: 30 Copynumber: 4.1 Consensus size: 31
48387408 ATTTCTTGAG
* *
48387418 AGTTTAGGGGTTAAAGTG-AAATTTT-GAGAA
1 AGTTTAGGGGTCAAAATGTAAATTTTAGA-AA
**
48387448 AGTTTAGGGGTTGAAATGT-AATTTTAGAAA
1 AGTTTAGGGGTCAAAATGTAAATTTTAGAAA
*
48387478 AGTTTA-AGGTCAAAATGTAAATTTTAGAAA
1 AGTTTAGGGGTCAAAATGTAAATTTTAGAAA
*
48387508 AGTTT-GGGGTCAAAATGTAAATTTCA-AAA
1 AGTTTAGGGGTCAAAATGTAAATTTTAGAAA
48387537 AGT
1 AGT
48387540 ACAAGGGTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
29 15 0.19
30 64 0.79
31 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (31 bp):
AGTTTAGGGGTCAAAATGTAAATTTTAGAAA
Found at i:48387482 original size:60 final size:59
Alignment explanation
Indices: 48387370--48387532 Score: 140
Period size: 60 Copynumber: 2.7 Consensus size: 59
48387360 GCTCCTGGGG
* * * * *
48387370 CAAAAGTGT-AATTTTAGCAAAA-TAT-GGGCCAAAATGTAATTTCTTGAGAGTTTAGGGGT
1 CAAAA-TGTAAATTTTAG-AAAAGTTTGGGGTCAAAATGTAATTTCTAGAAAGTTTA-AGGT
* * **
48387429 TAAAGTG-AAATTTT-GAGAAAGTTTAGGGGTTGAAATGTAATTT-TAGAAAAGTTTAAGGT
1 CAAAATGTAAATTTTAGA-AAAGTTT-GGGGTCAAAATGTAATTTCTAG-AAAGTTTAAGGT
48387488 CAAAATGTAAATTTTAGAAAAGTTTGGGGTCAAAATGTAAATTTC
1 CAAAATGTAAATTTTAGAAAAGTTTGGGGTCAAAATGT-AATTTC
48387533 AAAAAGTACA
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
56 1 0.01
57 4 0.05
58 10 0.12
59 24 0.30
60 40 0.49
61 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (59 bp):
CAAAATGTAAATTTTAGAAAAGTTTGGGGTCAAAATGTAATTTCTAGAAAGTTTAAGGT
Found at i:48387876 original size:12 final size:12
Alignment explanation
Indices: 48387858--48387892 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
48387848 AGTTGTAGTA
48387858 ATAATAATAATG
1 ATAATAATAATG
*
48387870 GTAATAATAATG
1 ATAATAATAATG
48387882 ATAATAATAAT
1 ATAATAATAAT
48387893 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:48387915 original size:3 final size:3
Alignment explanation
Indices: 48387856--48387898 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
48387846 AAAGTTGTAG
** *
48387856 TAA TAA TAA TAA TGG TAA TAA TAA TGA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
48387899 AAAAACGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:48390411 original size:43 final size:43
Alignment explanation
Indices: 48390321--48390675 Score: 393
Period size: 43 Copynumber: 8.3 Consensus size: 43
48390311 ACGTCGCTAA
* *
48390321 CTTTTGCGGCGCTTACA-GAAA-AAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGC-TA-AGGAAATAAACGCCGCTAAAGATCATGTT
* *
48390364 CTTTAGCGGTGCTAAGGAAATAAACGCCTCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
* * * * *
48390407 CTTTAGCGGCTCTTATGAAAAAAACGCCGCTAAAGATCCTGTT
1 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
*
48390450 CTTTAGCGGCGCTACGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
* * *
48390493 CTTTAGCGGCACTAAGTAAATAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
* * *
48390536 CTTTAGCGACGCTTAGGAAA-AAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
* * * *
48390578 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTGAAAG-TAATGTT
1 CTTTAGCGGCGCTAAGGAAATAAACGCCGCT-AAAGATCATGTT
* * *
48390621 CTATAGCGGCGCT-TGGTCAA-AAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTAAGG-AAATAAACGCCGCTAAAGA-TCA-TGTT
48390663 CTTTAGCGGCGCT
1 CTTTAGCGGCGCT
48390676 TATTTCACAA
Statistics
Matches: 268, Mismatches: 36, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
41 5 0.02
42 72 0.27
43 187 0.70
44 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
Found at i:48390607 original size:85 final size:86
Alignment explanation
Indices: 48390321--48390677 Score: 433
Period size: 86 Copynumber: 4.2 Consensus size: 86
48390311 ACGTCGCTAA
* * * * * *
48390321 CTTTTGCGGCGCTTACAGAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGTGCTAAGGAAATA
1 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAATA
*
48390386 AACGCCTCTAAAGATCATGTT
66 AACGCCGCTAAAGATCATGTT
* *
48390407 CTTTAGCGGCTCTTATG-AAAAAAACGCCGCTAAAGATCCTGTTCTTTAGCGGCGC-TACGGAAA
1 CTTTAGCGGCGCTTA-GAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-GGAAA
48390470 TAAACGCCGCTAAAGATCATGTT
64 TAAACGCCGCTAAAGATCATGTT
* * * * * *
48390493 CTTTAGCGGCACTAAGTAAATAAATGCCGCTAAAGATCATGTTCTTTAGCGACGCTTAGGAAA-A
1 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAATA
*
48390557 AACGCCACTAAAGATCATGTT
66 AACGCCGCTAAAGATCATGTT
* * *
48390578 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTGAAAG-TAATGTTCTATAGCGGCGCTT-GGTCAA
1 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTAGG-AAA
48390641 -AAACGCCGCTAAA-AGT-AGTGTT
64 TAAACGCCGCTAAAGA-TCA-TGTT
48390663 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
48390678 TTTCACAAAC
Statistics
Matches: 237, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
84 4 0.02
85 101 0.43
86 130 0.55
87 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAATA
AACGCCGCTAAAGATCATGTT
Found at i:48391148 original size:21 final size:21
Alignment explanation
Indices: 48391124--48391192 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
48391114 GCTTCTATCG
*
48391124 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
48391145 CTGCTTCTCTTGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
48391166 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
48391187 CTGCTT
1 CTGCTT
48391193 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.01, C:0.42, G:0.20, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:48396742 original size:9 final size:9
Alignment explanation
Indices: 48396702--48396966 Score: 210
Period size: 9 Copynumber: 29.8 Consensus size: 9
48396692 ATAAAGAAAA
48396702 TTATGTAAG
1 TTATGTAAG
* *
48396711 TTATTTACG
1 TTATGTAAG
48396720 TGTATGT-A-
1 T-TATGTAAG
48396728 TTATGTAAG
1 TTATGTAAG
48396737 TTATGT-A-
1 TTATGTAAG
**
48396744 TTAAATAAG
1 TTATGTAAG
*
48396753 CTATGTAAG
1 TTATGTAAG
*
48396762 TTGTGTATTATG
1 TTATGTA--A-G
*
48396774 TCAT-TAAG
1 TTATGTAAG
48396782 TTATGTAAG
1 TTATGTAAG
**
48396791 TTATCAAAG
1 TTATGTAAG
* * *
48396800 TAATGCATG
1 TTATGTAAG
48396809 TTATGTAAG
1 TTATGTAAG
48396818 TTATGTAAG
1 TTATGTAAG
*
48396827 TTTTGT-A-
1 TTATGTAAG
48396834 TTATGTAAG
1 TTATGTAAG
48396843 TTATGTAAG
1 TTATGTAAG
*
48396852 TTA--AAAG
1 TTATGTAAG
*
48396859 TATTATGTAGG
1 --TTATGTAAG
48396870 TTATGTAAG
1 TTATGTAAG
*
48396879 TTGTGTAAG
1 TTATGTAAG
48396888 TTATGTAAG
1 TTATGTAAG
48396897 TTATGTAAG
1 TTATGTAAG
48396906 TTAAATGT-A-
1 TT--ATGTAAG
*
48396915 TTATGTAGG
1 TTATGTAAG
48396924 TTATGTAAG
1 TTATGTAAG
*
48396933 TTGTGTAAG
1 TTATGTAAG
48396942 TTATGTAAG
1 TTATGTAAG
*
48396951 TTATGTGAG
1 TTATGTAAG
48396960 TTATGTA
1 TTATGTA
48396967 TGCTAAGTAT
Statistics
Matches: 200, Mismatches: 37, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
7 21 0.10
8 10 0.05
9 152 0.76
10 5 0.03
11 9 0.05
12 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:48396906 original size:54 final size:54
Alignment explanation
Indices: 48396809--48396962 Score: 258
Period size: 54 Copynumber: 2.9 Consensus size: 54
48396799 GTAATGCATG
* *
48396809 TTATGTAAGTTATGTAAGTTTTGT-A-TTATGTAAGTTATGTAAGTTAAAAGTA
1 TTATGTAGGTTATGTAAGTTGTGTAAGTTATGTAAGTTATGTAAGTTAAAAGTA
*
48396861 TTATGTAGGTTATGTAAGTTGTGTAAGTTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAGGTTATGTAAGTTGTGTAAGTTATGTAAGTTATGTAAGTTAAAAGTA
*
48396915 TTATGTAGGTTATGTAAGTTGTGTAAGTTATGTAAGTTATGTGAGTTA
1 TTATGTAGGTTATGTAAGTTGTGTAAGTTATGTAAGTTATGTAAGTTA
48396963 TGTATGCTAA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 22 0.23
53 1 0.01
54 73 0.76
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.45
Consensus pattern (54 bp):
TTATGTAGGTTATGTAAGTTGTGTAAGTTATGTAAGTTATGTAAGTTAAAAGTA
Found at i:48396961 original size:27 final size:25
Alignment explanation
Indices: 48396861--48396986 Score: 94
Period size: 27 Copynumber: 4.7 Consensus size: 25
48396851 GTTAAAAGTA
*
48396861 TTATGTAGGTTATGTAAGTTGTGTAAG
1 TTATGTA--TTATGTAAGTTATGTAAG
48396888 TTATGTAAGTTATGTAAGTTAAATGT-A-
1 TTATGT-A-TTATGTAAGTT--ATGTAAG
*
48396915 TTATGTAGGTTATGTAAGTTGTGTAAG
1 TTATGTA--TTATGTAAGTTATGTAAG
* *
48396942 TTATGTAAGTTATGTGAGTTATGTATG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
48396969 CTAAGTATTATGTAAGTT
1 TTATGTATTATGTAAGTT
48396987 GTTATGTTAC
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
25 13 0.15
26 3 0.04
27 62 0.74
28 3 0.04
29 3 0.04
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:48397106 original size:39 final size:39
Alignment explanation
Indices: 48397052--48397151 Score: 173
Period size: 39 Copynumber: 2.6 Consensus size: 39
48397042 AGTTAATATG
*
48397052 TAAGTAATGTATTATGTAAGTTTATATAAAAAAAAATTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAATTA
* *
48397091 TAAGTTATGAATTATGTAAGTTTATATAAAAAAAATTTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAATTA
48397130 TAAGTTATGTATTATGTAAGTT
1 TAAGTTATGTATTATGTAAGTT
48397152 AAAAGTAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (39 bp):
TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAATTA
Found at i:48397157 original size:23 final size:23
Alignment explanation
Indices: 48397131--48397174 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
48397121 AAAAATTTAT
*
48397131 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
48397154 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
48397175 TACATATAAG
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:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:48397209 original size:36 final size:36
Alignment explanation
Indices: 48397168--48397272 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 36
48397158 AATGTATTAT
48397168 GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
1 GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
* ** * *
48397204 GTAAGTAATGTATTTAAGT-AACATACTT-AA----A
1 GTAAGT-TTACATATAAGTAAACTTACTTAAATTTTA
48397235 -T---TTTACATATAAGTAAACTTACTTAAATTTTA
1 GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
48397267 GTAAGT
1 GTAAGT
48397273 AATGTATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 22
0.60 0.12 0.28
Matches are distributed among these distances:
26 8 0.17
27 9 0.19
28 2 0.04
30 1 0.02
31 1 0.02
32 1 0.02
33 1 0.02
35 2 0.04
36 15 0.31
37 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (36 bp):
GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
Found at i:48397241 original size:63 final size:63
Alignment explanation
Indices: 48397173--48397291 Score: 238
Period size: 63 Copynumber: 1.9 Consensus size: 63
48397163 ATTATGTAAG
48397173 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAAT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAAT
48397236 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATA
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATA
48397292 TTCAAGTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (63 bp):
TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAAT
Found at i:48397286 original size:13 final size:13
Alignment explanation
Indices: 48397268--48397319 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
48397258 TAAATTTTAG
*
48397268 TAAGTAATGTATT
1 TAAGTAATATATT
*
48397281 TAAGTAACATATT
1 TAAGTAATATATT
* *
48397294 CAAGTAATAAATT
1 TAAGTAATATATT
48397307 TAA-TATATATATT
1 TAAGTA-ATATATT
48397320 AGTAATAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 2 0.06
13 29 0.94
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:48400045 original size:365 final size:363
Alignment explanation
Indices: 48399369--48400081 Score: 995
Period size: 365 Copynumber: 2.0 Consensus size: 363
48399359 TAAGTCAGAG
*
48399369 TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCGTTTTAT
1 TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTAT
* * * *
48399434 AAAAATACAAGAAAACCTGGCGTTTTCCCAAACACGCCACAATCAATATATTATCGAACCGGCGT
66 AAAAATACAAGAAAACCTGCCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGACGC
** *
48399499 CGTTTTCAGTAAATTTTATACATCTTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCCATC
131 CGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAAGATTCCATC
* * * *
48399564 CTTCAACTAAAACAGCGTCGTTTTCGCAGAGTTCAAATATTATTTACGGCTCTTTAAGGAAAAAC
196 CTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCGCTTTAAGGAAAAAC
* *
48399629 GCCACAAGATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAAT-AAATATTC
261 GCCACAAGATAAACTTATCCCCTCAATCGAAACGACGACGTATCGGTAAATGCAATAAAAT-TTC
*
48399693 GTGGCGCTTTTTATAAAAACGCCGGTAATGTCAGACTTT
325 GTGGCGCTTTTTAGAAAAACGCCGGTAATGTCAGACTTT
** * *
48399732 TTGCGGCG-TTTAATTGGAAACGCCACTAAAATTTCAAGTACAGAAATAAACGGCGCCATTTTAT
1 TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTAT
* * * *
48399796 AAAAATATAAGGAAACGTTCTGCCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAATCGA
66 AAAAATACAAGAAAAC---CTGCCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGA
*
48399861 CGCCGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAATATTCC
128 CGCCGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAAGATTCC
* * * * ** *
48399926 ATCCTTCAACTTAAACGGCGCCGTTTTGGCAAAGTTTAAA-AGTTATTTACAGCGCTTTTCGGTA
193 ATCCTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATA-TTATTTACAGCGCTTTAAGGAA
* * *
48399990 AAACGCCACAA-CTGAAACTTATTCCCT-AATCCGAAACGACGCCGTATCGGTAAATGCAATAAA
257 AAACGCCACAAGAT-AAACTTATCCCCTCAAT-CGAAACGACGACGTATCGGTAAATGCAATAAA
* * *
48400053 ATTTTGTGGCGTTTTTTAGCAAAACGCCG
320 ATTTCGTGGCGCTTTTTAGAAAAACGCCG
48400082 CTAAATCTTA
Statistics
Matches: 306, Mismatches: 37, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
362 65 0.21
363 8 0.03
364 4 0.01
365 225 0.74
366 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (363 bp):
TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTAT
AAAAATACAAGAAAACCTGCCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGACGC
CGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAAGATTCCATC
CTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCGCTTTAAGGAAAAAC
GCCACAAGATAAACTTATCCCCTCAATCGAAACGACGACGTATCGGTAAATGCAATAAAATTTCG
TGGCGCTTTTTAGAAAAACGCCGGTAATGTCAGACTTT
Found at i:48400151 original size:24 final size:24
Alignment explanation
Indices: 48400124--48400204 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 24
48400114 TGTATCATTC
48400124 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTATCT
*
48400148 ATTTAAACAATTAATTACCTA-CAAATT
1 ATTTAAATAATTAATTACCTATC----T
*
48400175 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTATCT
48400200 ATTTA
1 ATTTA
48400205 TTTATTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.02
24 25 0.52
25 1 0.02
27 1 0.02
28 20 0.42
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATCT
Found at i:48400202 original size:4 final size:4
Alignment explanation
Indices: 48400195--48400219 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
48400185 ATTAATTACC
48400195 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
48400220 TTTCTTCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:48400207 original size:28 final size:26
Alignment explanation
Indices: 48400124--48400208 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 26
48400114 TGTATCATTC
*
48400124 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
48400148 ATTTAAACAATTAATTACCTACAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
48400176 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
48400204 ATTTA
1 ATTTA
48400209 TTTATTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 18 0.38
26 1 0.02
28 29 0.60
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:48400586 original size:7 final size:7
Alignment explanation
Indices: 48400574--48400615 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
48400564 ATGACCGTTG
48400574 AAACCCT
1 AAACCCT
48400581 AAACCCT
1 AAACCCT
*
48400588 AAACCCC
1 AAACCCT
48400595 AAATCCCT
1 AAA-CCCT
*
48400603 AACCCCT
1 AAACCCT
48400610 AAACCC
1 AAACCC
48400616 GATCTTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:48400761 original size:12 final size:12
Alignment explanation
Indices: 48400744--48400768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48400734 CTCTTAACAT
48400744 CTAACCCCTAAC
1 CTAACCCCTAAC
48400756 CTAACCCCTAAC
1 CTAACCCCTAAC
48400768 C
1 C
48400769 CCTGACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:48400840 original size:14 final size:14
Alignment explanation
Indices: 48400775--48400849 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
48400765 AACCCCTGAC
* *
48400775 CCTTAACCCATAAA
1 CCTTAATCCATAAT
*
48400789 CCTTAAATCACATTAAC
1 CCTT-AATC-CA-TAAT
* *
48400806 CCTTAAACCAGAAT
1 CCTTAATCCATAAT
*
48400820 CCCTAATCCATAAT
1 CCTTAATCCATAAT
48400834 CCTTAATTCCATAAT
1 CCTTAA-TCCATAAT
48400849 C
1 C
48400850 TATAAAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 22 0.46
15 14 0.29
16 5 0.10
17 7 0.15
ACGTcount: A:0.39, C:0.32, G:0.01, T:0.28
Consensus pattern (14 bp):
CCTTAATCCATAAT
Found at i:48401545 original size:114 final size:112
Alignment explanation
Indices: 48401408--48402043 Score: 740
Period size: 113 Copynumber: 5.6 Consensus size: 112
48401398 GCGCTTTACA
* * * *
48401408 AAAAATGCCACTAAAT-CCCGAAAGCTCAGAAAACGGCGTCGTTGTGCTTAGGTTATTTGTGGCG
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
**** * * * *
48401472 CTTTATCTAAAATGCCGCTAATGCCCTGGATATTAGCAG-CGCTTACTTG
66 CTTTGGAAAAAACGCCGCTAAAGCCCTGGGTATTAGC-GTCGCTT-C-CG
* * *
48401521 AAAAACGCCGCTAAATCTCCGAAAGCTCATAAAACGGCATCGTTGGGCTTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTGTGGC
* * *
48401586 GCTTTGGAAAAAACGCCGCTAAAGCCATGGGTGTTAGCGTCACTTTCCG
65 GCTTTGGAAAAAACGCCGCTAAAGCCCTGGGTATTAGCGTCGC-TTCCG
*
48401635 AAAAACGCCGCTAAGTCCCCGAAAGCTCA-AGAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGA-AAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGC
* * * *
48401699 ACTTTGGAAAAAACGTCGCTAAAGCCATGGGTATTAGCGTCGCTTTCCA
65 GCTTTGGAAAAAACGCCGCTAAAGCCCTGGGTATTAGCGTCGC-TTCCG
* * *
48401748 AAAAACGCCGTTAAGTCCCCGAAAGCTCAGGAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
*
48401813 CTTTGGAAAAAATCGCCGCTAAAGCCCTGGGTATTAGCTTCGCTTCCTG
66 CTTTGGAAAAAA-CGCCGCTAAAGCCCTGGGTATTAGCGTCGCTTCC-G
* * * * *
48401862 AAAAACGCTGCTAGATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGGCTCAGTTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG-GTTTTTTGTGGC
*** * * **
48401927 GCTTTGTTGAAAACGCTGCTAAAG-CCTGGGTTTTAGCGTCGCTTCAAA
65 GCTTTGGAAAAAACGCCGCTAAAGCCCTGGGTATTAGCGTCGCTTC-CG
* * * * * *
48401975 AAAAACGCCGCTAATTCCCCTAAAGCTCAGAAAACAGCATCGTTGGGATTAGGTATTTTGTGGCG
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
48402040 CTTT
66 CTTT
48402044 TTCGAAAACG
Statistics
Matches: 455, Mismatches: 58, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
112 15 0.03
113 209 0.46
114 166 0.36
115 63 0.14
116 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (112 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
CTTTGGAAAAAACGCCGCTAAAGCCCTGGGTATTAGCGTCGCTTCCG
Found at i:48401832 original size:227 final size:225
Alignment explanation
Indices: 48401424--48402043 Score: 757
Period size: 227 Copynumber: 2.7 Consensus size: 225
48401414 GCCACTAAAT
* * * ** *
48401424 CCCGAAAGCTC-AGAAAACGGCGTCGTTGTGCTTAGGTTATTTGTGGCGCTTTATCTAAAATGCC
1 CCCGAAAGCTCAAG-AAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGTAAAAAACG-C
* * * *** * *
48401488 GCTAATGCCCTGGATATTAGCAG-CGCTTACTTGAAAAACGCCGCTAAATCTCCGAAAGCTCATA
64 GCTAAAG-CCTGGGTATTAGC-GTCGCTTTCAAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGA
48401552 AAACGGCATCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCATGGG
127 AAACGGCATCGTTGGGCTTAGG-TTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCATGGG
*
48401617 TGTTAGCGTCACTTTCC-GAAAAACGCCGCTA-AGTC
191 TATTAGCGTCAC-TTCCTGAAAAACGCCGCTAGA-TC
* *
48401652 CCCGAAAGCTCAAGAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCACTTTGGAAAAAACGTCG
1 CCCGAAAGCTCAAGAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGTAAAAAACG-CG
* * * *
48401717 CTAAAGCCATGGGTATTAGCGTCGCTTTC-CAAAAAACGCCGTTAAGTCCCCGAAAGCTCAGGAA
65 CTAAAGCC-TGGGTATTAGCGTCGCTTTCAAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAA
* *
48401781 ACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGGAAAAAATCGCCGCTAAAGCCCTGGGTA
129 ACGGCATCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGGAAAAAA-CGCCGCTAAAGCCATGGGTA
* * *
48401846 TTAGCTTCGCTTCCTGAAAAACGCTGCTAGATC
193 TTAGCGTCACTTCCTGAAAAACGCCGCTAGATC
* * * **
48401879 CCCGAAAGCTCAGGAAACGGCGTCGTTGGGCTCAGTTTTTTTTGTGGCGCTTTGTTGAAAACGCT
1 CCCGAAAGCTCAAGAAACGGCGTCGTTGGGCTTAG-GTTTTTTGTGGCGCTTTGTAAAAAACGC-
* * *
48401944 GCTAAAGCCTGGGTTTTAGCGTCGC-TTCAAAAAAAACGCCGCTAATTCCCCTAAAGCTCAGAAA
64 GCTAAAGCCTGGGTATTAGCGTCGCTTTCAAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAA
* * *
48402008 ACAGCATCGTTGGGATTAGGTATTTTGTGGCGCTTT
129 ACGGCATCGTTGGGCTTAGGTTTTTTGTGGCGCTTT
48402044 TTCGAAAACG
Statistics
Matches: 341, Mismatches: 42, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
226 31 0.09
227 202 0.59
228 106 0.31
229 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (225 bp):
CCCGAAAGCTCAAGAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGTAAAAAACGCGC
TAAAGCCTGGGTATTAGCGTCGCTTTCAAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCATCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCATGGGTATTA
GCGTCACTTCCTGAAAAACGCCGCTAGATC
Found at i:48421068 original size:13 final size:12
Alignment explanation
Indices: 48421046--48421104 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
48421036 AAAATAAAAT
48421046 CAATAATAATAA
1 CAATAATAATAA
48421058 CAATGAATAATAA
1 CAAT-AATAATAA
* *
48421071 CAACAATAACAA
1 CAATAATAATAA
*
48421083 TAATAA-AATAAA
1 CAATAATAAT-AA
48421095 CACATAATAA
1 CA-ATAATAA
48421105 GACAATATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.05
12 18 0.49
13 15 0.41
14 2 0.05
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.20
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:48421101 original size:22 final size:22
Alignment explanation
Indices: 48421053--48421101 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
48421043 AATCAATAAT
*
48421053 AATAACAATGAATAATAACAAC
1 AATAACAATGAATAATAAAAAC
48421075 AATAACAAT-AATAA-AATAAAC
1 AATAACAATGAATAATAA-AAAC
48421096 ACATAA
1 A-ATAA
48421102 TAAGACAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 13 0.54
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.18
Consensus pattern (22 bp):
AATAACAATGAATAATAAAAAC
Found at i:48421244 original size:9 final size:9
Alignment explanation
Indices: 48421230--48421263 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
48421220 GTACTAACAA
48421230 TAATAATGG
1 TAATAATGG
*
48421239 TAATAATAG
1 TAATAATGG
*
48421248 TAATAATGA
1 TAATAATGG
48421257 TAATAAT
1 TAATAAT
48421264 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (9 bp):
TAATAATGG
Found at i:48421253 original size:18 final size:18
Alignment explanation
Indices: 48421230--48421264 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48421220 GTACTAACAA
*
48421230 TAATAATGGTAATAATAG
1 TAATAATGATAATAATAG
48421248 TAATAATGATAATAATA
1 TAATAATGATAATAATA
48421265 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (18 bp):
TAATAATGATAATAATAG
Found at i:48423458 original size:20 final size:21
Alignment explanation
Indices: 48423422--48423465 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
48423412 TAGTCGACAC
48423422 TTTTTTAATTTTGATTTTA-A
1 TTTTTTAATTTTGATTTTATA
*
48423442 TTTTTT-ATTATTTATTTTATA
1 TTTTTTAATT-TTGATTTTATA
48423463 TTT
1 TTT
48423466 GTTGATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTTAATTTTGATTTTATA
Found at i:48423625 original size:22 final size:22
Alignment explanation
Indices: 48423568--48423625 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
48423558 ATGATGGATT
* *
48423568 ATATTTGTAAATTTAATTGAAGA
1 ATATTT-TATATTTAATTGAAAA
48423591 ATA-TTT-TATTTAATT-AATAA
1 ATATTTTATATTTAATTGAA-AA
48423611 ATATTTTATATTTAA
1 ATATTTTATATTTAA
48423626 AATTAATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 4 0.13
22 9 0.30
23 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTATATTTAATTGAAAA
Found at i:48423629 original size:24 final size:24
Alignment explanation
Indices: 48423602--48423670 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
48423592 TATTTTATTT
48423602 AATTAATAAATATTTTATATTTAA
1 AATTAATAAATATTTTATATTTAA
**
48423626 AATTAATCTA-ATTTTATTATTTAA
1 AATTAATAAATATTTTA-TATTTAA
* **
48423650 TATTTGTAAATATTTCTATAT
1 AATTAATAAATATTT-TATAT
48423671 ATATATATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.17
24 20 0.57
25 7 0.20
26 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTAATAAATATTTTATATTTAA
Found at i:48425350 original size:16 final size:16
Alignment explanation
Indices: 48425329--48425380 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
48425319 TGATTCACTA
48425329 TAATGGAATAGAGGCG
1 TAATGGAATAGAGGCG
*
48425345 TAATGGAATAGATGCG
1 TAATGGAATAGAGGCG
*
48425361 TAATAGAATAGAGGCG
1 TAATGGAATAGAGGCG
48425377 TAAT
1 TAAT
48425381 AGGTAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.31, T:0.23
Consensus pattern (16 bp):
TAATGGAATAGAGGCG
Found at i:48425450 original size:39 final size:44
Alignment explanation
Indices: 48425366--48425466 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 44
48425356 ATGCGTAATA
* *
48425366 GAATAGAGGCGTAATAGGTAATTTTTTTGTTTGGTTGAATGGAATG
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGGAATG
48425412 GAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-GAATG
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGGAATG
* *
48425451 TAATAGAGGTGTAATA
1 GAATAGAGGCGTAATA
48425467 ACATAAGGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
39 18 0.36
40 1 0.02
43 1 0.02
44 12 0.24
45 3 0.06
46 15 0.30
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.38
Consensus pattern (44 bp):
GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGGAATG
Found at i:48425642 original size:15 final size:16
Alignment explanation
Indices: 48425624--48425653 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48425614 AAATATAATT
48425624 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
48425639 TAATAAATATTCTTA
1 TAATAAATATTCTTA
48425654 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:48425745 original size:15 final size:16
Alignment explanation
Indices: 48425725--48425754 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48425715 AAACATAATT
48425725 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
48425740 TAATAAATATTCTTA
1 TAATAAATATTCTTA
48425755 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:48425782 original size:101 final size:101
Alignment explanation
Indices: 48425603--48425833 Score: 399
Period size: 101 Copynumber: 2.3 Consensus size: 101
48425593 TATTTTAACA
*
48425603 TAATTATTATTAAATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAA
1 TAATTTTTATTAAATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAA
*
48425668 AATCATAATATATAATACTATAAAATATAATTTAAT
66 AATCATAAAATATAATACTATAAAATATAATTTAAT
* *
48425704 TAATTTTTATTAAACATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTATTAA
1 TAATTTTTATTAAATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAA
48425769 AATCATAAAATATAATACTATAAAATATAATTTAAT
66 AATCATAAAATATAATACTATAAAATATAATTTAAT
** *
48425805 TAGCTTTTATTAAATATAATTTCATAAAA
1 TAATTTTTATTAAATATAATTTAATAAAA
48425834 ATATATAATT
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 122 1.00
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (101 bp):
TAATTTTTATTAAATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAA
AATCATAAAATATAATACTATAAAATATAATTTAAT
Found at i:48427571 original size:24 final size:27
Alignment explanation
Indices: 48427520--48427572 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
48427510 TATGTGTAAT
*
48427520 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
48427547 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
48427571 AT
1 AT
48427573 GTGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:48437417 original size:3 final size:3
Alignment explanation
Indices: 48437409--48437468 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
48437399 TAATATATGT
* *
48437409 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATAA ATG CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
*
48437454 ATA AT- ATA GTA ATA A
1 ATA ATA ATA ATA ATA A
48437469 ACAATTTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48437423 original size:20 final size:19
Alignment explanation
Indices: 48437398--48437459 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
48437388 TAATGCGCAT
48437398 ATAATATATGTATAATAATA
1 ATAATA-ATGTATAATAATA
*
48437418 ATAATAATAATATAATAATA
1 ATAATAAT-GTATAATAATA
*
48437438 ATAATAAATG-CTAATAATA
1 ATAAT-AATGTATAATAATA
48437457 ATA
1 ATA
48437460 TAGTAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.35
20 21 0.57
21 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (19 bp):
ATAATAATGTATAATAATA
Found at i:48437468 original size:14 final size:14
Alignment explanation
Indices: 48437398--48437468 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
48437388 TAATGCGCAT
48437398 ATAATATATGT-ATA
1 ATAATATA-GTAATA
48437412 ATAATA-A-TAATA
1 ATAATATAGTAATA
*
48437424 ATAATATAATAATA
1 ATAATATAGTAATA
*
48437438 ATAATAAATGCTAATA
1 ATAATATA-G-TAATA
48437454 ATAATATAGTAATA
1 ATAATATAGTAATA
48437468 A
1 A
48437469 ACAATTTAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 1 0.02
12 9 0.18
13 2 0.04
14 24 0.49
15 1 0.02
16 12 0.24
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (14 bp):
ATAATATAGTAATA
Found at i:48438972 original size:7 final size:7
Alignment explanation
Indices: 48438962--48438992 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
48438952 ATCATTACTT
48438962 AATATTC
1 AATATTC
48438969 AATATTC
1 AATATTC
48438976 AATATTC
1 AATATTC
*
48438983 AATGTTC
1 AATATTC
48438990 AAT
1 AAT
48438993 TGATCATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:48442123 original size:6 final size:6
Alignment explanation
Indices: 48442113--48442148 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
48442103 TACCCTTCTT
* *
48442113 CTTCCC TTTCCC CTTCCC CTTCCC TTTCCC CTTCCC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC
48442149 TTTGGGTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
CTTCCC
Found at i:48442128 original size:18 final size:18
Alignment explanation
Indices: 48442113--48442148 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
48442103 TACCCTTCTT
48442113 CTTCCCTTTCCCCTTCCC
1 CTTCCCTTTCCCCTTCCC
48442131 CTTCCCTTTCCCCTTCCC
1 CTTCCCTTTCCCCTTCCC
48442149 TTTGGGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (18 bp):
CTTCCCTTTCCCCTTCCC
Found at i:48445557 original size:12 final size:12
Alignment explanation
Indices: 48445527--48445559 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
48445517 ATGCAATAGG
48445527 AAACCAGCA-GC
1 AAACCAGCATGC
48445538 AAACCAGCATGC
1 AAACCAGCATGC
*
48445550 AGACCAGCAT
1 AAACCAGCAT
48445560 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:48446544 original size:21 final size:21
Alignment explanation
Indices: 48446520--48446572 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
48446510 CGCTGTTTTT
*
48446520 AATCTCACTGCTACAATATCG
1 AATCTCACTGCTACAATAACG
* * * *
48446541 AATCTTACCGCTACAGTAACT
1 AATCTCACTGCTACAATAACG
48446562 AATCTCACTGC
1 AATCTCACTGC
48446573 CACCGCTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.28
Consensus pattern (21 bp):
AATCTCACTGCTACAATAACG
Found at i:48451942 original size:3 final size:3
Alignment explanation
Indices: 48451934--48451970 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
48451924 TCGTTTACTC
48451934 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48451971 ACAAGTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48452962 original size:109 final size:108
Alignment explanation
Indices: 48452748--48453176 Score: 513
Period size: 111 Copynumber: 3.9 Consensus size: 108
48452738 AAAATTCAAG
* * *
48452748 AGGATATTTGGCTATTTGGTTAAACGAG-AAATCGAAACTCAGCACATTAGGGCATG-TTCCTCG
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
* *
48452811 AATTTCCAAACGCAAAATATAGTCTTACTTT-GAAAATTTTTTTGAA
66 AATTTCCAAACGCAAAATATTGCCTTA-TTTAG-AAA--TTTTTGAA
48452857 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* *
48452922 GAATTTCTAAACGCAAAATATTGCCTTATTTTGAAATTTTTGAA
65 GAATTTCCAAACGCAAAATATTGCCTTATTTAGAAATTTTTGAA
* * * * * * *
48452966 AGTATATTTGGCTATTTAGTTGAACGAGAAAGTCGAAACCTAGCACATTAGGCCACATTTTCTCG
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
* *
48453031 AATTTCCAAACGCAAAATATTACCTTACTTTGAGAAATTTTTAAA
66 AATTTCCAAACGCAAAATATTGCCTTA-TTT-AGAAATTTTTGAA
* ** * * ** **
48453076 AGGATACTCAGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGTACATTACAGCACGTTTTTTC
1 AGGATATTTGGCTATTTGGTTGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * *
48453141 AAATTTCCAAACGCTAAATATTGCCTCATTTAGAAA
65 GAATTTCCAAACGCAAAATATTGCCTTATTTAGAAA
48453177 AACTTTCCTT
Statistics
Matches: 278, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
108 57 0.21
109 69 0.25
110 36 0.13
111 84 0.30
112 32 0.12
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (108 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
AATTTCCAAACGCAAAATATTGCCTTATTTAGAAATTTTTGAA
Found at i:48453135 original size:219 final size:217
Alignment explanation
Indices: 48452751--48453176 Score: 581
Period size: 219 Copynumber: 1.9 Consensus size: 217
48452741 ATTCAAGAGG
* *
48452751 ATATTTGGCTATTTGGTTAAACGAGAAATCGAAACTCAGCACATTAGGGCATGTTCCTCGAATTT
1 ATATTTGGCTATTTAGTTAAACGAGAAATCGAAACTCAGCACATTAGGACATGTTCCTCGAATTT
* * * **
48452816 CCAAACGCAAAATATAGTCTTACTTTGAAAATTTTTTTGAAAGGATATTTGGCTATTTGGTTGAA
66 CCAAACGCAAAATATAGCCTTACTTTGAAAA-TTTTTTAAAAGGATACTCAGCTATTTGGTTGAA
** * *
48452881 CGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCTAAACGCAAAATATTGC
130 CGAGAAAAATCGAAACCCAGCACATTACAGCACGTTTCCTCAAATTTCCAAACGCAAAATATTGC
* *
48452946 CTTATTTTGAAATTTTTGAAAGT
195 CTCATTTAGAAATTTTTGAAAGT
* *
48452969 ATATTTGGCTATTTAGTTGAACGAGAAAGTCGAAAC-CTAGCACATTAGGCCACAT-TTTCTCGA
1 ATATTTGGCTATTTAGTTAAACGAGAAA-TCGAAACTC-AGCACATTAGG--ACATGTTCCTCGA
*
48453032 ATTTCCAAACGCAAAATATTA-CCTTACTTTGAGAAA-TTTTTAAAAGGATACTCAGTTATTTGG
62 ATTTCCAAACGCAAAATA-TAGCCTTACTTTGA-AAATTTTTTAAAAGGATACTCAGCTATTTGG
* ** *
48453095 TTGAACGAGAAAAATCGAAACCCAGTACATTACAGCACGTTTTTTCAAATTTCCAAACGCTAAAT
125 TTGAACGAGAAAAATCGAAACCCAGCACATTACAGCACGTTTCCTCAAATTTCCAAACGCAAAAT
48453160 ATTGCCTCATTTAGAAA
190 ATTGCCTCATTTAGAAA
48453177 AACTTTCCTT
Statistics
Matches: 182, Mismatches: 20, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
218 27 0.15
219 112 0.62
220 35 0.19
221 8 0.04
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (217 bp):
ATATTTGGCTATTTAGTTAAACGAGAAATCGAAACTCAGCACATTAGGACATGTTCCTCGAATTT
CCAAACGCAAAATATAGCCTTACTTTGAAAATTTTTTAAAAGGATACTCAGCTATTTGGTTGAAC
GAGAAAAATCGAAACCCAGCACATTACAGCACGTTTCCTCAAATTTCCAAACGCAAAATATTGCC
TCATTTAGAAATTTTTGAAAGT
Found at i:48453227 original size:21 final size:20
Alignment explanation
Indices: 48453203--48453247 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
48453193 GTATGGTGTT
48453203 AATATACATAATG-GAATAATA
1 AATAT-CATAATGTGAATAA-A
*
48453224 AATATGATAATGTGAATAAA
1 AATATCATAATGTGAATAAA
48453244 AATA
1 AATA
48453248 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (20 bp):
AATATCATAATGTGAATAAA
Found at i:48453235 original size:20 final size:20
Alignment explanation
Indices: 48453210--48453247 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48453200 GTTAATATAC
48453210 ATAATG-GAATAATAAATATG
1 ATAATGTGAATAA-AAATATG
48453230 ATAATGTGAATAAAAATA
1 ATAATGTGAATAAAAATA
48453248 ATATGAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
ATAATGTGAATAAAAATATG
Found at i:48453367 original size:12 final size:12
Alignment explanation
Indices: 48453321--48453367 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
48453311 AATAAACTAA
48453321 AACATAAAAATG
1 AACATAAAAATG
*
48453333 AACATATAAAT-
1 AACATAAAAATG
48453344 AA-ATACATAAATG
1 AACATA-A-AAATG
48453357 AACATAAAAAT
1 AACATAAAAAT
48453368 ACAATAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.10
11 2 0.07
12 18 0.62
13 3 0.10
14 3 0.10
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (12 bp):
AACATAAAAATG
Found at i:48453862 original size:3 final size:3
Alignment explanation
Indices: 48453847--48453922 Score: 52
Period size: 3 Copynumber: 26.7 Consensus size: 3
48453837 AAAAGGTATT
* * ** * **
48453847 TAA TAA TAT TAA TAA TGA TGC TAA TAA TAA TAA TAA TAA TAG TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48453895 TAA TAA T-A TGA -AA TAA TAA -AA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
48453923 GCATATATTA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 7 0.12
3 51 0.88
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:48453878 original size:24 final size:24
Alignment explanation
Indices: 48453847--48453912 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
48453837 AAAAGGTATT
48453847 TAATAATATTAATAAT-GATGCTAA
1 TAATAATATTAATAATAG-TGCTAA
* **
48453871 TAATAATAATAATAATAGTTTTAA
1 TAATAATATTAATAATAGTGCTAA
*
48453895 TAATAATATGAAATAATA
1 TAATAATAT-TAATAATA
48453913 AAAAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 27 0.77
25 8 0.23
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (24 bp):
TAATAATATTAATAATAGTGCTAA
Found at i:48454008 original size:6 final size:5
Alignment explanation
Indices: 48453962--48454007 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
48453952 ATATAAAGAT
*
48453962 AAATGA AAATA TAAATA AAACAA AAATA AAATA AAATA AAATA AAA
1 AAAT-A AAATA -AAATA AAA-TA AAATA AAATA AAATA AAATA AAA
48454008 ACGCAAGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 23 0.64
6 13 0.36
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:48455007 original size:13 final size:11
Alignment explanation
Indices: 48454975--48454999 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48454965 GAAAATTTTG
48454975 TTGTTTCTGAT
1 TTGTTTCTGAT
48454986 TTGTTTCTGAT
1 TTGTTTCTGAT
48454997 TTG
1 TTG
48455000 AGTTTCTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (11 bp):
TTGTTTCTGAT
Found at i:48455658 original size:13 final size:12
Alignment explanation
Indices: 48455636--48455683 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
48455626 AAAATAAAAT
48455636 CAATAATAATAA
1 CAATAATAATAA
48455648 CAATGAATAATAA
1 CAAT-AATAATAA
* *
48455661 CAACAATAAAAA
1 CAATAATAATAA
*
48455673 TAATAA-AATAA
1 CAATAATAATAA
48455684 ACACATAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 4 0.13
12 15 0.50
13 11 0.37
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:48455835 original size:12 final size:12
Alignment explanation
Indices: 48455817--48455851 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
48455807 AGTTGTAGTA
48455817 ATAATAATAATG
1 ATAATAATAATG
*
48455829 GTAATAATAATG
1 ATAATAATAATG
48455841 ATAATAATAAT
1 ATAATAATAAT
48455852 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:48455874 original size:3 final size:3
Alignment explanation
Indices: 48455815--48455857 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
48455805 AAAGTTGTAG
** *
48455815 TAA TAA TAA TAA TGG TAA TAA TAA TGA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
48455858 AAAAACGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:48458270 original size:24 final size:24
Alignment explanation
Indices: 48458240--48458308 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
48458230 TATTTTATTT
48458240 AATTAATAAATATTTTATATTTAA
1 AATTAATAAATATTTTATATTTAA
**
48458264 AATTAATCTA-ATTTTATTATTTAA
1 AATTAATAAATATTTTA-TATTTAA
* **
48458288 TATTTGTAAATATTTCTATAT
1 AATTAATAAATATTT-TATAT
48458309 ACATATATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.17
24 20 0.57
25 7 0.20
26 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTAATAAATATTTTATATTTAA
Found at i:48466955 original size:40 final size:40
Alignment explanation
Indices: 48466911--48466995 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
48466901 AAAAAGTGTC
*
48466911 CTAAAGATCGAGCATTAGCGGCACTTTTTGGAAAACGCCG
1 CTAAAGATCGAGCATTAGCGGCACTTTATGGAAAACGCCG
* * *
48466951 CTAAAGATCGAGTATTAGTGGCGCTTTATGGAAAACGCCG
1 CTAAAGATCGAGCATTAGCGGCACTTTATGGAAAACGCCG
48466991 CTAAA
1 CTAAA
48466996 AATAAGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (40 bp):
CTAAAGATCGAGCATTAGCGGCACTTTATGGAAAACGCCG
Found at i:48467364 original size:22 final size:21
Alignment explanation
Indices: 48467339--48467386 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
48467329 GTGTTACCAT
*
48467339 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTATGGATTAT-GG
* *
48467361 TTTAGGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
48467382 TTTAA
1 TTTAA
48467387 AGGCTAGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATGGATTATGG
Found at i:48467381 original size:7 final size:7
Alignment explanation
Indices: 48467339--48467471 Score: 65
Period size: 7 Copynumber: 18.6 Consensus size: 7
48467329 GTGTTACCAT
*
48467339 TTTAAGG
1 TTTATGG
48467346 TTTATGG
1 TTTATGG
*
48467353 ATTATGGG
1 TTTAT-GG
*
48467361 TTTAGGG
1 TTTATGG
*
48467368 GTTATGG
1 TTTATGG
48467375 TTTATGG
1 TTTATGG
*
48467382 TTTAAAGG
1 TTT-ATGG
* *
48467390 -CTAGGG
1 TTTATGG
*
48467396 TTTAAGG
1 TTTATGG
48467403 TTTA-GAG
1 TTTATG-G
*
48467410 GTTATGTG
1 TTTATG-G
* *
48467418 TTAAGGG
1 TTTATGG
48467425 TTTATGG
1 TTTATGG
*
48467432 TTTTAGGG
1 -TTTATGG
*
48467440 TTTTAGGG
1 -TTTATGG
48467448 TTTA-GG
1 TTTATGG
48467454 TTTATGG
1 TTTATGG
*
48467461 TTTATAG
1 TTTATGG
48467468 TTTA
1 TTTA
48467472 GATTAACTAT
Statistics
Matches: 98, Mismatches: 21, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
6 10 0.10
7 61 0.62
8 27 0.28
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:48467441 original size:29 final size:31
Alignment explanation
Indices: 48467392--48467463 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 31
48467382 TTTAAAGGCT
* *
48467392 AGGGTTTAAGG-TTTAGAGGTTAT-GTGTTA
1 AGGGTTTATGGTTTTAGAGGTTATAGGGTTA
* *
48467421 AGGGTTTATGGTTTTAG-GGTTTTAGGGTTT
1 AGGGTTTATGGTTTTAGAGGTTATAGGGTTA
48467451 A-GGTTTATGGTTT
1 AGGGTTTATGGTTT
48467464 ATAGTTTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (31 bp):
AGGGTTTATGGTTTTAGAGGTTATAGGGTTA
Found at i:48468043 original size:10 final size:12
Alignment explanation
Indices: 48468015--48468047 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
48468005 CGTGATTTAA
48468015 AATTTTAAAATG
1 AATTTTAAAATG
48468027 AATTTTAAAA-G
1 AATTTTAAAATG
48468038 -ATTTTAAAAT
1 AATTTTAAAAT
48468048 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:48470936 original size:43 final size:43
Alignment explanation
Indices: 48470886--48471133 Score: 318
Period size: 43 Copynumber: 5.8 Consensus size: 43
48470876 AGATTATGTT
* ** * *
48470886 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* ** * * * *
48470929 TATAGCGGCGTTTGTGATAAAAGTGCCACTAAAGGTCGTGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
48470972 TTTAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
48471015 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTC-TGAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG-GTC
* *
48471058 TTTAACGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
48471101 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
48471134 AGCCGGTTTT
Statistics
Matches: 177, Mismatches: 26, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
42 2 0.01
43 173 0.98
44 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:48471430 original size:7 final size:7
Alignment explanation
Indices: 48471418--48471448 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
48471408 ATCATTACTT
48471418 AATATTC
1 AATATTC
48471425 AATATTC
1 AATATTC
48471432 AATATTC
1 AATATTC
48471439 AATATTC
1 AATATTC
48471446 AAT
1 AAT
48471449 TGATCATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:48475452 original size:18 final size:18
Alignment explanation
Indices: 48475431--48475492 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
48475421 ATATATGGAT
48475431 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
48475449 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
48475468 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
48475483 ATA-ATAATAA
1 ATATATAATAA
48475493 TAATAATAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:48475483 original size:35 final size:33
Alignment explanation
Indices: 48475428--48475492 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
48475418 GAGATATATG
48475428 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
48475463 GATATATATAA-ATAGTTATAATAATAATAA
1 GATATATATAATA-AGATATAATAATAATAA
48475493 TAATAATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:48476713 original size:15 final size:15
Alignment explanation
Indices: 48476693--48476744 Score: 104
Period size: 15 Copynumber: 3.5 Consensus size: 15
48476683 GGGCATGGTA
48476693 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
48476708 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
48476723 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
48476738 ATTGGGT
1 ATTGGGT
48476745 CCCTTTGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (15 bp):
ATTGGGTTTGTGGGT
Found at i:48476721 original size:8 final size:8
Alignment explanation
Indices: 48476695--48476737 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
48476685 GCATGGTAAT
48476695 TGGGTTTG
1 TGGGTTTG
*
48476703 TGGGTAT-
1 TGGGTTTG
48476710 TGGGTTTG
1 TGGGTTTG
*
48476718 TGGGTAT-
1 TGGGTTTG
48476725 TGGGTTTG
1 TGGGTTTG
48476733 TGGGT
1 TGGGT
48476738 ATTGGGTCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.47
Consensus pattern (8 bp):
TGGGTTTG
Found at i:48476995 original size:41 final size:41
Alignment explanation
Indices: 48476938--48477124 Score: 151
Period size: 44 Copynumber: 4.4 Consensus size: 41
48476928 AATCCATTGT
* *
48476938 ACTTCAGGGAAATAAGACTTGATGCGATCTGCTCTACTGCA
1 ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
*** *
48476979 ACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGCA
1 ACTTCAGAGAGATAAGA-CT-TGA-TGCGATCTGCTCTACTGCA
* * * * *
48477023 ACTTCAGAGAGATAGGA-TTGGTTTCTTCTATCTGCTCCACTGCA
1 ACTTCAGAGAGATAAGACTT-G---ATGCGATCTGCTCTACTGCA
* * * * *
48477067 ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCCGTA
1 ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
*
48477108 ACCTCAGAGAGATAAGA
1 ACTTCAGAGAGATAAGA
48477125 TCCTTTATTT
Statistics
Matches: 114, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
41 43 0.38
42 4 0.04
43 3 0.03
44 62 0.54
45 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
Found at i:48477024 original size:44 final size:43
Alignment explanation
Indices: 48476968--48477158 Score: 154
Period size: 44 Copynumber: 4.4 Consensus size: 43
48476958 GATGCGATCT
48476968 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGATCT-TGATTTTAATCC
* * * * *
48477012 GCTCTACTGCAACTTCAGAGAGATAGGAT-TGGTTTCTTCTATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATT-TT-AATCC
* * *** *
48477056 GCTCCACTGCAACTTCAGGGAGATAAGA-CTTGA-TGCGATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCC
* * * * * *
48477097 ACTCTGCCGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGAT-CTTGATTTTAATCC
* *
48477141 GCTCCACTGTAACTTCAG
1 GCTCTACTGCAACTTCAG
48477159 GGAATAGGAT
Statistics
Matches: 111, Mismatches: 30, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
41 25 0.23
42 3 0.03
43 8 0.07
44 75 0.68
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCC
Found at i:48477244 original size:44 final size:44
Alignment explanation
Indices: 48477047--48477257 Score: 155
Period size: 44 Copynumber: 4.9 Consensus size: 44
48477037 GGATTGGTTT
* * *
48477047 CTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T-G
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
* * * * ** * * **
48477088 ATGCGATCTACTCTGCCGTAACCTCAGAGAGATAAGATC-CTTTA
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTC-TGG
* * * * * ** *
48477132 TTTTAATCCGCTCCACTGTAACTTCAGGGA-ATAGGAT-AGTGT
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
* * *
48477174 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
48477218 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
48477258 GAAATTCTCC
Statistics
Matches: 123, Mismatches: 40, Indels: 11
0.71 0.23 0.06
Matches are distributed among these distances:
41 27 0.22
42 25 0.20
43 13 0.11
44 58 0.47
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
Found at i:48477301 original size:47 final size:42
Alignment explanation
Indices: 48477232--48477343 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
48477222 AATCTGCTCC
* *
48477232 ACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTACTCT
1 ACTGTAACCTCAGAGAGATAAGATC-CAAA---TCCGGTCTACTCT
*
48477278 ACTGTAATCCTCAGAGAGATAAGA-CCAAATGCGGTCTACTCT
1 ACTGTAA-CCTCAGAGAGATAAGATCCAAATCCGGTCTACTCT
* *
48477320 GCTGTAACTTCAGAGAGATAAGAT
1 ACTGTAACCTCAGAGAGATAAGAT
48477344 TTTAATTCCG
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
41 15 0.25
42 18 0.31
45 3 0.05
46 8 0.14
47 15 0.25
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
ACTGTAACCTCAGAGAGATAAGATCCAAATCCGGTCTACTCT
Found at i:48477419 original size:44 final size:46
Alignment explanation
Indices: 48477353--48477470 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
48477343 TTTTAATTCC
* * * *
48477353 GCTCCATTGTAATCTCAAGGAGATAGGAT-T--ACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTTGATCT
* *
48477397 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGATCT
*
48477443 GTTCCACTGTAATCTCAGGGAGATAAGA
1 GCTCCACTGTAATCTCAGGGAGATAAGA
48477471 CCTGTATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 25 0.40
45 1 0.02
46 35 0.56
47 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (46 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGATCT
Found at i:48489870 original size:18 final size:18
Alignment explanation
Indices: 48489849--48489910 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
48489839 ATATATGGAT
48489849 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
48489867 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
48489886 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
48489901 ATA-ATAATAA
1 ATATATAATAA
48489911 TAATAGGACA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:48489901 original size:35 final size:33
Alignment explanation
Indices: 48489846--48489910 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
48489836 GAGATATATG
48489846 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
48489881 GATATATATAA-ATAGTTATAATAATAATAA
1 GATATATATAATA-AGATATAATAATAATAA
48489911 TAATAGGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:48491126 original size:15 final size:15
Alignment explanation
Indices: 48491106--48491157 Score: 104
Period size: 15 Copynumber: 3.5 Consensus size: 15
48491096 GGGCATGGTA
48491106 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
48491121 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
48491136 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
48491151 ATTGGGT
1 ATTGGGT
48491158 CCCTTTGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (15 bp):
ATTGGGTTTGTGGGT
Done.