Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 10 of 163
Found at i:3281172 original size:187 final size:188
Alignment explanation
Indices: 3280847--3281221 Score: 743
Period size: 187 Copynumber: 2.0 Consensus size: 188
3280837 AAATTAAAAA
3280847 AATATTCATAACATTATTTTTAAAAAAATTAGAATAAAATTTAAATTTTAATAAAAGCCTACACC
1 AATATTCATAACATTATTTTTAAAAAAATTAGAATAAAATTTAAATTTTAATAAAAGCCTACACC
3280912 CATTAAGCTTTTAGAGATTTTATATTTCCACTTTTTCTTTTTATTGGCTTATTTATTAAATAATT
66 CATTAAGCTTTTAGAGATTTTATATTTCCACTTTTTCTTTTTATTGGCTTATTTATTAAATAATT
3280977 TTGTTTTCTACTTAAAATATTAAAGTTTGTACTTTAATTTTCTTAAAAGTTTAAAGTT
131 TTGTTTTCTACTTAAAATATTAAAGTTTGTACTTTAATTTTCTTAAAAGTTTAAAGTT
3281035 AATATTCAT-ACATTATTTTTAAAAAAATTAGAATAAAATTTAAATTTTAATAAAAGCCTACACC
1 AATATTCATAACATTATTTTTAAAAAAATTAGAATAAAATTTAAATTTTAATAAAAGCCTACACC
3281099 CATTAAGCTTTTAGAGATTTTATATTTCCACTTTTTCTTTTTATTGGCTTATTTATTAAATAATT
66 CATTAAGCTTTTAGAGATTTTATATTTCCACTTTTTCTTTTTATTGGCTTATTTATTAAATAATT
3281164 TTGTTTTCTACTTAAAATATTAAAGTTTGTACTTTAATTTTCTTAAAAGTTTAAAGTT
131 TTGTTTTCTACTTAAAATATTAAAGTTTGTACTTTAATTTTCTTAAAAGTTTAAAGTT
3281222 GGTAAAAGAA
Statistics
Matches: 187, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 178 0.95
188 9 0.05
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (188 bp):
AATATTCATAACATTATTTTTAAAAAAATTAGAATAAAATTTAAATTTTAATAAAAGCCTACACC
CATTAAGCTTTTAGAGATTTTATATTTCCACTTTTTCTTTTTATTGGCTTATTTATTAAATAATT
TTGTTTTCTACTTAAAATATTAAAGTTTGTACTTTAATTTTCTTAAAAGTTTAAAGTT
Found at i:3285981 original size:19 final size:19
Alignment explanation
Indices: 3285954--3285996 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3285944 TAAATAAGTT
*
3285954 TCAAATATA-AAAGTATTAA
1 TCAATTATATAAA-TATTAA
*
3285973 TCAATTATATAAATATTCA
1 TCAATTATATAAATATTAA
3285992 TCAAT
1 TCAAT
3285997 AAACTTCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (19 bp):
TCAATTATATAAATATTAA
Found at i:3286965 original size:26 final size:25
Alignment explanation
Indices: 3286934--3286985 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3286924 CCCATTTTTT
* * *
3286934 AATAAACATTAAAAAATTGTTTTAAA
1 AATAAAAAATAAAAAA-TATTTTAAA
3286960 AATAAAAAATAAAAAATATTTTAAA
1 AATAAAAAATAAAAAATATTTTAAA
3286985 A
1 A
3286986 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AATAAAAAATAAAAAATATTTTAAA
Found at i:3287436 original size:29 final size:30
Alignment explanation
Indices: 3287393--3287452 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
3287383 TATTATAGAG
* *
3287393 ATATAATCAAATTAGTTCATTTACTATTAA
1 ATATAATCAAATTAGTCCATATACTATTAA
* *
3287423 ATAT-ATCAATTTAGTCCCTATACTATTAA
1 ATATAATCAAATTAGTCCATATACTATTAA
3287452 A
1 A
3287453 AAAAACAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (30 bp):
ATATAATCAAATTAGTCCATATACTATTAA
Found at i:3293753 original size:13 final size:13
Alignment explanation
Indices: 3293735--3293759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3293725 CATTAAAAAA
3293735 AATTAGTGTGTTT
1 AATTAGTGTGTTT
3293748 AATTAGTGTGTT
1 AATTAGTGTGTT
3293760 AATCGATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
AATTAGTGTGTTT
Found at i:3303769 original size:60 final size:57
Alignment explanation
Indices: 3303705--3303843 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 57
3303695 TGAACTTAAT
* * * *
3303705 AATTGTTCCCACATTGGTGCTTGAATTTTTTTTTTGTCTAAGTTAGTCA-TTGAACTTGGC
1 AATTGTTCCCACATTGGGGCCTGAA---CTTTTTTGTCCAAGTTAG-CACTTGAACTTGGC
* * * *
3303765 AATTGTTCGCAAATTGGGGCCTGGACTTTTTTGTCCAAGTTAGCACTTGCACTTGGC
1 AATTGTTCCCACATTGGGGCCTGAACTTTTTTGTCCAAGTTAGCACTTGAACTTGGC
* *
3303822 AATTGTTACCACATTTGGGCCT
1 AATTGTTCCCACATTGGGGCCT
3303844 AAATATTTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 2 0.03
57 44 0.67
60 20 0.30
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (57 bp):
AATTGTTCCCACATTGGGGCCTGAACTTTTTTGTCCAAGTTAGCACTTGAACTTGGC
Found at i:3320308 original size:214 final size:213
Alignment explanation
Indices: 3319549--3320353 Score: 714
Period size: 218 Copynumber: 3.7 Consensus size: 213
3319539 GGCTGGTCCG
* * * * *
3319549 AGTTTTAAGTTACAACCAGCAACTTTAGGCCTCAGATTTGTAACTTTTAATT-TCATCAGACTGA
1 AGTTTTAAGTTACGACCGGCAGCTTTAGGCCTCAGATTTGT-AGTTTTTATTCTCATCAGACTGA
* * * * * *
3319613 AGGTCTGACAATGTAGGCAATTCTTAATCATCATGAGCCTCTTAAATCTGTAGATTCATTAATAG
65 AGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGC-ATAGATTC-TTACTAA
* * * * *
3319678 TTACATCACTCAAAACAAAGCCAA-ATACAGACTACACGCATGTTTTAACATAGGGAGAAAACG-
128 TTACATCACTCAAAACAAAG-CAATACACAGACTACAAGCATG---T-ATATAAGGAGAAAATGA
* * * * *
3319741 GA-TGGTCCATGCCCAACAAGCATGACCACCACCATC
188 AATTGGTTC--GTCC-ACCAGCA--A--A--A--ATA
**** * *** * *
3319777 ACAAATAACTT--GACCAAAAACTTTAGGCCTCAGATTTGTAAG-TTTTAATCTCATCAGACTGA
1 AGTTTTAAGTTACGACCGGCAGCTTTAGGCCTCAGATTTGT-AGTTTTTATTCTCATCAGACTGA
* * *
3319839 AGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCGTAGATTAATTAATAAT
65 AGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCATAGATT-CTTACTAAT
* * * * *
3319904 TACATCACTCAAAACAAAGCTATATACAGACTACATGCATGCTTTAATGTAGGGAGAAAATGAAA
129 TACATCACTCAAAACAAAGCAATACACAGACTACAAGCATG---T-ATATAAGGAGAAAATGAAA
* * *
3319969 TTGGTTCGTTCACCATCACAAATA
190 TTGGTTCGTCCACCAGCAAAAATA
* * * * * * *
3319993 AGTTTTATGTTATGACCGGCAGCTTTAGGCCTCAGATTTGCAATTTCTATTTTCATCAGACTAAA
1 AGTTTTAAGTTACGACCGGCAGCTTTAGGCCTCAGATTTGTAGTTTTTATTCTCATCAGACTGAA
* **
3320058 GGTCCGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCATAGGCTCTTCACTAATT
66 GGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCATAGATTCTT-ACTAATT
*
3320123 ACATCACTCAAAACAAAGCAATACACAGAGTACAAGCATG-ATATAAGGAGAAAATGAAATTGGT
130 ACATCACTCAAAACAAAGCAATACACAGACTACAAGCATGTATATAAGGAGAAAATGAAATTGGT
*
3320187 TGGTCCACCAGCAAAAAATA
195 TCGTCCACCAGC-AAAAATA
* * * *
3320207 AGTTTTTAAGTTACGACCATTG-A-C-TTGGGCCTCAGATTTGTAGTTTTTGTTGTCATCAGACT
1 AG-TTTTAAGTTACGACC--GGCAGCTTTAGGCCTCAGATTTGTAGTTTTTATTCTCATCAGACT
*
3320269 GAAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAAGCATAGATTCTTTACA
63 GAAGGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCT-AAAAGCATAGATTC-TTACT
3320334 AATTACATCACTCAAAACAA
126 AATTACATCACTCAAAACAA
3320354 TGATATATAT
Statistics
Matches: 486, Mismatches: 76, Indels: 43
0.80 0.13 0.07
Matches are distributed among these distances:
213 31 0.06
214 82 0.17
215 48 0.10
216 10 0.02
217 4 0.01
218 133 0.27
220 1 0.00
224 7 0.01
225 74 0.15
226 85 0.17
227 5 0.01
228 6 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (213 bp):
AGTTTTAAGTTACGACCGGCAGCTTTAGGCCTCAGATTTGTAGTTTTTATTCTCATCAGACTGAA
GGTCTGACAATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAGCATAGATTCTTACTAATTA
CATCACTCAAAACAAAGCAATACACAGACTACAAGCATGTATATAAGGAGAAAATGAAATTGGTT
CGTCCACCAGCAAAAATA
Found at i:3322927 original size:14 final size:15
Alignment explanation
Indices: 3322899--3322936 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
3322889 CATAAGGGGC
3322899 ATTTTTTAATTAAATT
1 ATTTTTTAA-TAAATT
3322915 ATTTTTTAA-AAATT
1 ATTTTTTAATAAATT
3322929 ATTTTTTA
1 ATTTTTTA
3322937 CCAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTTAATAAATT
Found at i:3323548 original size:30 final size:29
Alignment explanation
Indices: 3323505--3323584 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
3323495 ATTCTCAAAA
*
3323505 TTATATATGAA-TTTAATTTTAGATATAATT
1 TTATATATAAATTTTAATTTT-GA-ATAATT
*
3323535 TTATATCTAAATTTTAATTTTGAATAATT
1 TTATATATAAATTTTAATTTTGAATAATT
*
3323564 TTA-AAAGTGAAATTTTAATTT
1 TTATATA-T-AAATTTTAATTT
3323585 GATTTAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.02
29 10 0.23
30 23 0.53
31 9 0.21
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (29 bp):
TTATATATAAATTTTAATTTTGAATAATT
Found at i:3323554 original size:31 final size:30
Alignment explanation
Indices: 3323516--3323584 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3323506 TATATATGAA
* *
3323516 TTTAATTTTAGATATAATTTTATATCT-AAAT
1 TTTAATTTT-GA-ATAATTTTAAAACTGAAAT
*
3323547 TTTAATTTTGAATAATTTTAAAAGTGAAAT
1 TTTAATTTTGAATAATTTTAAAACTGAAAT
3323577 TTTAATTT
1 TTTAATTT
3323585 GATTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 11 0.32
30 14 0.41
31 9 0.26
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTAATTTTGAATAATTTTAAAACTGAAAT
Found at i:3324135 original size:15 final size:16
Alignment explanation
Indices: 3324105--3324139 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3324095 AAAATTTGTC
*
3324105 ATATATTTTCTTTTAA
1 ATATATATTCTTTTAA
3324121 ATATATATT-TTTTAA
1 ATATATATTCTTTTAA
3324136 ATAT
1 ATAT
3324140 TTTAATACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATATTCTTTTAA
Found at i:3328837 original size:11 final size:11
Alignment explanation
Indices: 3328823--3328880 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
3328813 TTTTTTTTAA
3328823 TTTTAAAATAC
1 TTTTAAAATAC
3328834 TTTTAAAATAC
1 TTTTAAAATAC
**
3328845 TTTTTTTAA-A-
1 -TTTTAAAATAC
**
3328855 TTTTAAAATTT
1 TTTTAAAATAC
3328866 TTTTAAAATAC
1 TTTTAAAATAC
3328877 TTTT
1 TTTT
3328881 TAATTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
9 6 0.16
11 25 0.68
12 6 0.16
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:3328857 original size:32 final size:32
Alignment explanation
Indices: 3328813--3328881 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
3328803 TATTTTTTTA
*
3328813 TTTTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATACTTTTAAAATAC
**
3328845 TTTTTTTAAATTTTAAAATTTTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATACTTTTAAAATAC
3328877 TTTTT
1 TTTTT
3328882 AATTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTTTAAATTTTAAAATACTTTTAAAATAC
Found at i:3328860 original size:21 final size:19
Alignment explanation
Indices: 3328834--3328913 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 19
3328824 TTTAAAATAC
3328834 TTTTAAAATACTTTTTTTAAA
1 TTTTAAAAT--TTTTTTTAAA
*
3328855 TTTTAAAATTTTTTTAAAA
1 TTTTAAAATTTTTTTTAAA
**
3328874 TACTTTTTAATTTTTTTT-AA
1 T--TTTAAAATTTTTTTTAAA
* *
3328894 TTTTAAAATATTTTTAAAA
1 TTTTAAAATTTTTTTTAAA
3328913 T
1 T
3328914 ACTTTTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 11 0.23
19 13 0.27
20 3 0.06
21 21 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAAATTTTTTTTAAA
Found at i:3328908 original size:11 final size:11
Alignment explanation
Indices: 3328894--3328942 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
3328884 TTTTTTTTAA
3328894 TTTTAAAATAT
1 TTTTAAAATAT
3328905 TTTTAAAATACT
1 TTTTAAAATA-T
**
3328917 TTTTTTAA-AT
1 TTTTAAAATAT
3328927 TTTTAAAATAAT
1 TTTTAAAAT-AT
3328939 TTTT
1 TTTT
3328943 TGGTATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 7 0.23
11 11 0.35
12 13 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3328932 original size:39 final size:38
Alignment explanation
Indices: 3328823--3328920 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 38
3328813 TTTTTTTTAA
* *
3328823 TTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTAAAATTT
1 TTTTAAAATACTTTT-TAATA---TTTTT-AATTTTAAAATAT
*
3328866 TTTTAAAATACTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAA-TATTTTTAATTTTAAAATAT
3328905 TTTTAAAATACTTTTT
1 TTTTAAAATACTTTTT
3328921 TTAAATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
39 28 0.55
40 5 0.10
42 2 0.04
43 16 0.31
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (38 bp):
TTTTAAAATACTTTTTAATATTTTTAATTTTAAAATAT
Found at i:3328950 original size:22 final size:22
Alignment explanation
Indices: 3328901--3328950 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3328891 TAATTTTAAA
* *
3328901 ATATTTTTAAAATACTTTTTTT
1 ATATTTTTAAAATAATTTTTTG
*
3328923 AAATTTTTAAAATAATTTTTTG
1 ATATTTTTAAAATAATTTTTTG
*
3328945 GTATTT
1 ATATTT
3328951 ATTTAAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATTTTTAAAATAATTTTTTG
Found at i:3332467 original size:35 final size:35
Alignment explanation
Indices: 3332403--3332470 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
3332393 GGTAAAGTTA
* *
3332403 GTATATTCTCTTATTTTGTGCACTGTGATCCTACT
1 GTATATTCTCTTATTCTGTGCACTCTGATCCTACT
* * *
3332438 GTATATTGTCTTCTTCTGTTCACTCTGATCCTA
1 GTATATTCTCTTATTCTGTGCACTCTGATCCTA
3332471 GCGCTATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (35 bp):
GTATATTCTCTTATTCTGTGCACTCTGATCCTACT
Found at i:3343087 original size:230 final size:230
Alignment explanation
Indices: 3342822--3343304 Score: 602
Period size: 230 Copynumber: 2.1 Consensus size: 230
3342812 AAAAAAATTT
* * * *
3342822 AACTTGGCAGACAAGAACTTGATTATATGATCATGCAAACAGATGATT-AGATTAAAACAAGAGA
1 AACTTGACAAACAA-AACTTGATTATATGATCATGCAAACACAAGATTCAG-TTAAAACAAGAGA
** * * **
3342886 TGT-AATTGCCTCGAAGTTA-TCTAATTTCATCTAACACTACCAAGTTTAAAGCAGTGA-CCAAC
64 T-TAAATCACCTCAAAGTCACT-TAATTTCATAAAACACTA-CAAGTTTAAAGCAGTGATCC-AC
* * * *
3342948 ATGAAACAATATAAC-AAAGAATTCTCAACAACTATTAATCTTTTCTTTTTCCTGATCAAA-TTT
125 ATGAAACAACATAACAAAAAAATT-TCAACAACTATTAATCTTCTCTTTTTACTGAT-AAATTTT
* *
3343011 TCATCAATAATTTAACATCAAAATTATCAAGCAA-AAAAAAAA
188 TCATCAATAATTTAACAGCAAAATTATCAAACAAGAAAAAAAA
* * *
3343053 AACTTTACAAACAAAACTTGATTATTTGATCATGCAAACACAAGATTCAGTTAAAACAATAGATT
1 AACTTGACAAACAAAACTTGATTATATGATCATGCAAACACAAGATTCAGTTAAAACAAGAGATT
*
3343118 AAATCACCTCAAAGTCACTTAATTTCATAAAACACTACGAGTTTAAAGCAGTGATCCACATGAAA
66 AAATCACCTCAAAGTCACTTAATTTCATAAAACACTACAAGTTTAAAGCAGTGATCCACATGAAA
* *
3343183 CAACATAACTAAAAAAATTTCAACAATTATTCATCTTCTCTTTTTACTGATAAATTTTTCATCAA
131 CAACATAAC-AAAAAAATTTCAACAACTATTAATCTTCTCTTTTTACTGATAAATTTTTCATCAA
* * *
3343248 TAATTTAACAGCAAAATTATTAAATAAGGAAAAAAAT
195 TAATTTAACAGCAAAATTATCAAACAA-GAAAAAAAA
3343285 AACTTGACAAACAAAACTTG
1 AACTTGACAAACAAAACTTG
3343305 GGTTCAATTA
Statistics
Matches: 217, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
229 36 0.17
230 134 0.62
231 21 0.10
232 26 0.12
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (230 bp):
AACTTGACAAACAAAACTTGATTATATGATCATGCAAACACAAGATTCAGTTAAAACAAGAGATT
AAATCACCTCAAAGTCACTTAATTTCATAAAACACTACAAGTTTAAAGCAGTGATCCACATGAAA
CAACATAACAAAAAAATTTCAACAACTATTAATCTTCTCTTTTTACTGATAAATTTTTCATCAAT
AATTTAACAGCAAAATTATCAAACAAGAAAAAAAA
Found at i:3344211 original size:11 final size:11
Alignment explanation
Indices: 3344197--3344230 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3344187 TAAAAGGCAA
3344197 AAAAAAAGAAG
1 AAAAAAAGAAG
3344208 AAAAAAAG-AG
1 AAAAAAAGAAG
3344218 AAAATAAAGAAG
1 AAAA-AAAGAAG
3344230 A
1 A
3344231 TCAGAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 12 0.57
12 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:3346231 original size:13 final size:12
Alignment explanation
Indices: 3346209--3346242 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3346199 NNNTAAATTA
3346209 TTATAATAATAT
1 TTATAATAATAT
3346221 TTATAAATAATAT
1 TTAT-AATAATAT
3346234 TTA-AATAAT
1 TTATAATAAT
3346243 TTAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 4 0.19
13 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATAATAATAT
Found at i:3346895 original size:2 final size:2
Alignment explanation
Indices: 3346878--3346910 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3346868 GTGTATATGC
*
3346878 AT AT AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3346911 TTTATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3347523 original size:6 final size:6
Alignment explanation
Indices: 3347514--3347541 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3347504 CTCCACCCCT
3347514 GCCTCG GCCTCG GCCTCG GCCTCG GCCT
1 GCCTCG GCCTCG GCCTCG GCCTCG GCCT
3347542 GTGAACGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.32, T:0.18
Consensus pattern (6 bp):
GCCTCG
Found at i:3358253 original size:9 final size:9
Alignment explanation
Indices: 3358235--3358263 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3358225 AGCTTCTTCC
3358235 TTTT-TTTT
1 TTTTCTTTT
3358243 TTTTCTTTT
1 TTTTCTTTT
3358252 TTTTCTTTT
1 TTTTCTTTT
3358261 TTT
1 TTT
3358264 ATCTCTGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:3360642 original size:16 final size:18
Alignment explanation
Indices: 3360610--3360642 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3360600 ACTAATTTAA
3360610 AAATCAAAATAATTATTC
1 AAATCAAAATAATTATTC
3360628 AAAT-AAAAT-ATTATT
1 AAATCAAAATAATTATT
3360643 ATACTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATCAAAATAATTATTC
Found at i:3363416 original size:21 final size:23
Alignment explanation
Indices: 3363372--3363418 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
3363362 TTAAATCTAA
*
3363372 AAAATAAAATAATTAAATTCATT
1 AAAATAAAATAATTAAAGTCATT
*
3363395 AAAATAAAA-AA-TAAAGTGATT
1 AAAATAAAATAATTAAAGTCATT
3363416 AAA
1 AAA
3363419 TTCTAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
23 9 0.41
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATAAAATAATTAAAGTCATT
Found at i:3364188 original size:16 final size:18
Alignment explanation
Indices: 3364152--3364188 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3364142 TATTTAATGA
3364152 GAAGAACTAAAGTTCAAT
1 GAAGAACTAAAGTTCAAT
*
3364170 GAAGAA-TAAA-TTTAAT
1 GAAGAACTAAAGTTCAAT
3364186 GAA
1 GAA
3364189 CTCTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.24
Consensus pattern (18 bp):
GAAGAACTAAAGTTCAAT
Found at i:3364808 original size:56 final size:56
Alignment explanation
Indices: 3364743--3364853 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
3364733 ACTTATTAAC
3364743 TTATAAATCTATACAATTTAGGGGTAAGGCCCTGCCTACCCCTCTCTCCTATTGCT
1 TTATAAATCTATACAATTTAGGGGTAAGGCCCTGCCTACCCCTCTCTCCTATTGCT
*
3364799 TTATAAATCTATACAATTTAGGGGTAAGGCCCTGCCTACCTCTCTCTCCTATTGC
1 TTATAAATCTATACAATTTAGGGGTAAGGCCCTGCCTACCCCTCTCTCCTATTGC
3364854 CCGTGCAAGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.34
Consensus pattern (56 bp):
TTATAAATCTATACAATTTAGGGGTAAGGCCCTGCCTACCCCTCTCTCCTATTGCT
Found at i:3365720 original size:25 final size:26
Alignment explanation
Indices: 3365692--3365742 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3365682 CATTTAAAGA
3365692 ATTAAATACAT-TAATTTATTT-TTAT
1 ATTAAATACATATAA-TTATTTATTAT
*
3365717 ATTAGATACATATAATTATTTATTAT
1 ATTAAATACATATAATTATTTATTAT
3365743 GCAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTAAATACATATAATTATTTATTAT
Found at i:3370114 original size:50 final size:49
Alignment explanation
Indices: 3370012--3370115 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 49
3370002 AGATAATTTT
* * *
3370012 ATTTCGGGTTTAGGTTAATTCAGATCGTTTGGATATGTCAGTTGGGTATC
1 ATTTCGGGTTTAGGTCAATTCAGATCATTTGGATATCTCAGTTGGG-ATC
* *
3370062 ATTTCGGGTTTAGGTCCATTCAAGATCATTTTGAGTATCTCAGTTGGG-TC
1 ATTTCGGGTTTAGGTCAATTC-AGATCATTTGGA-TATCTCAGTTGGGATC
3370112 ATTT
1 ATTT
3370116 AAGGTTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 25 0.53
51 10 0.21
52 12 0.26
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (49 bp):
ATTTCGGGTTTAGGTCAATTCAGATCATTTGGATATCTCAGTTGGGATC
Found at i:3371443 original size:22 final size:22
Alignment explanation
Indices: 3371412--3371453 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3371402 TCTTGCTGCA
* * *
3371412 TATATGTATGTATGTATGTATG
1 TATATATATGCATGCATGTATG
3371434 TATATATATGCATGCATGTA
1 TATATATATGCATGCATGTA
3371454 CACTGTACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (22 bp):
TATATATATGCATGCATGTATG
Found at i:3372042 original size:26 final size:25
Alignment explanation
Indices: 3372013--3372062 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
3372003 TAATGACCTT
3372013 CATAATATTTGTAGCACTTTGAATTC
1 CATAATATTTGTAGCAC-TTGAATTC
*
3372039 CATAATATTTTTAGCACTTGAATT
1 CATAATATTTGTAGCACTTGAATT
3372063 GTGAAAATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (25 bp):
CATAATATTTGTAGCACTTGAATTC
Found at i:3374713 original size:5 final size:5
Alignment explanation
Indices: 3374693--3374738 Score: 74
Period size: 5 Copynumber: 8.8 Consensus size: 5
3374683 TCAATTAGGT
3374693 AAAAG AAAAAG CAAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
3374739 AAGTGCTGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 29 0.74
6 10 0.26
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3376182 original size:30 final size:30
Alignment explanation
Indices: 3376123--3376182 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3376113 TAATTGCTTA
* *
3376123 AAAAATATTTAAATTTTATATTTCATATAT
1 AAAAATATTAAAATATTATATTTCATATAT
*
3376153 AAAAATATTAATAATATTAT-TTTCTTATAT
1 AAAAATATTAA-AATATTATATTTCATATAT
3376183 TTTTATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
AAAAATATTAAAATATTATATTTCATATAT
Found at i:3396588 original size:33 final size:34
Alignment explanation
Indices: 3396522--3396588 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
3396512 ATAATCTTCA
* * *
3396522 AATAAAATAAGTGAAAAATATCATTTGAAAATTG
1 AATAAAAAAAGTGAAAAATATCATATAAAAATTG
3396556 AATAAAAAAAGT-AATAAAT-TCATATAAAAATTG
1 AATAAAAAAAGTGAA-AAATATCATATAAAAATTG
3396589 GTGCCATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (34 bp):
AATAAAAAAAGTGAAAAATATCATATAAAAATTG
Found at i:3399569 original size:77 final size:78
Alignment explanation
Indices: 3399470--3399624 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
3399460 AATTTTGTAA
3399470 GATCTAATTAAAAATTTTAAAACTTTTGGAAGGCTTAACTAAAATTTCTAAAAATCTAAGGGTAT
1 GATCTAATTAAAAATTTTAAAACTTTTGGAAGGCTTAACTAAAATTTCTAAAAATCTAAGGGTAT
3399535 CTAATTAAAACTT
66 CTAATTAAAACTT
3399548 GATCTAATT-AAAATTTTAAAACTTTTGGAAGGCTTAACTAAAATTTCTAAAAATCTAAGGGTAT
1 GATCTAATTAAAAATTTTAAAACTTTTGGAAGGCTTAACTAAAATTTCTAAAAATCTAAGGGTAT
3399612 CTAATTAAAACTT
66 CTAATTAAAACTT
3399625 TTTAAAATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 68 0.88
78 9 0.12
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (78 bp):
GATCTAATTAAAAATTTTAAAACTTTTGGAAGGCTTAACTAAAATTTCTAAAAATCTAAGGGTAT
CTAATTAAAACTT
Found at i:3402584 original size:15 final size:15
Alignment explanation
Indices: 3402564--3402602 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3402554 GGTTAAAATA
3402564 TAATTTTATTTTTAT
1 TAATTTTATTTTTAT
*
3402579 TAATTTAAATTTTTAT
1 TAATTT-TATTTTTAT
*
3402595 AAATTTTA
1 TAATTTTA
3402603 AAGAAACTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTTAT
Found at i:3403499 original size:2 final size:2
Alignment explanation
Indices: 3403492--3403527 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3403482 TCACTTTCTT
3403492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3403528 AAGATGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3411058 original size:23 final size:25
Alignment explanation
Indices: 3411020--3411066 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3411010 AATTTAAAAT
*
3411020 TAATTTATTTACTTTTA-TTTTCAG
1 TAATTTATATACTTTTACTTTTCAG
3411044 TAATTTA-ATACTTTTACTTTTCA
1 TAATTTATATACTTTTACTTTTCA
3411067 AAGTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.60
Consensus pattern (25 bp):
TAATTTATATACTTTTACTTTTCAG
Found at i:3420002 original size:220 final size:220
Alignment explanation
Indices: 3419620--3420060 Score: 882
Period size: 220 Copynumber: 2.0 Consensus size: 220
3419610 GTCTTAAAAT
3419620 ACTTTTTTAATGTTTATTAAAAAATGGGCCGGGCCCGGGCTTATCATATTTTTCCTGGGCCGGGC
1 ACTTTTTTAATGTTTATTAAAAAATGGGCCGGGCCCGGGCTTATCATATTTTTCCTGGGCCGGGC
3419685 CTGGGAAAAATTTTAGGCCCATATTTCGGGCCGTGCCCGGGCCTAGGAGGCGGGCCGAAAAATTT
66 CTGGGAAAAATTTTAGGCCCATATTTCGGGCCGTGCCCGGGCCTAGGAGGCGGGCCGAAAAATTT
3419750 TTTTGGGCTTAGCCCGAACCCGGCCCGGCCCATGGACAGGTCTAGTTTGCCCCTATTTTACCCAA
131 TTTTGGGCTTAGCCCGAACCCGGCCCGGCCCATGGACAGGTCTAGTTTGCCCCTATTTTACCCAA
3419815 AAAGCGTATGACGTGGCATCCGATA
196 AAAGCGTATGACGTGGCATCCGATA
3419840 ACTTTTTTAATGTTTATTAAAAAATGGGCCGGGCCCGGGCTTATCATATTTTTCCTGGGCCGGGC
1 ACTTTTTTAATGTTTATTAAAAAATGGGCCGGGCCCGGGCTTATCATATTTTTCCTGGGCCGGGC
3419905 CTGGGAAAAATTTTAGGCCCATATTTCGGGCCGTGCCCGGGCCTAGGAGGCGGGCCGAAAAATTT
66 CTGGGAAAAATTTTAGGCCCATATTTCGGGCCGTGCCCGGGCCTAGGAGGCGGGCCGAAAAATTT
3419970 TTTTGGGCTTAGCCCGAACCCGGCCCGGCCCATGGACAGGTCTAGTTTGCCCCTATTTTACCCAA
131 TTTTGGGCTTAGCCCGAACCCGGCCCGGCCCATGGACAGGTCTAGTTTGCCCCTATTTTACCCAA
3420035 AAAGCGTATGACGTGGCATCCGATA
196 AAAGCGTATGACGTGGCATCCGATA
3420060 A
1 A
3420061 GAATATACCA
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 221 1.00
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (220 bp):
ACTTTTTTAATGTTTATTAAAAAATGGGCCGGGCCCGGGCTTATCATATTTTTCCTGGGCCGGGC
CTGGGAAAAATTTTAGGCCCATATTTCGGGCCGTGCCCGGGCCTAGGAGGCGGGCCGAAAAATTT
TTTTGGGCTTAGCCCGAACCCGGCCCGGCCCATGGACAGGTCTAGTTTGCCCCTATTTTACCCAA
AAAGCGTATGACGTGGCATCCGATA
Found at i:3421408 original size:31 final size:32
Alignment explanation
Indices: 3421373--3421451 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 32
3421363 ACATTTCAAT
**
3421373 TTTAATTCAAATTTAAAAAATTTTAAATT-AA
1 TTTAATTCAAATTTAAAAAATTGAAAATTAAA
*
3421404 TTTAATTCAAATTTAAAAACTTGAAAATTAAA
1 TTTAATTCAAATTTAAAAAATTGAAAATTAAA
3421436 TTTAATTC-AATTTAAA
1 TTTAATTCAAATTTAAA
3421452 TCGATGACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 34 0.77
32 10 0.23
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (32 bp):
TTTAATTCAAATTTAAAAAATTGAAAATTAAA
Found at i:3422458 original size:32 final size:32
Alignment explanation
Indices: 3422422--3422483 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
3422412 GAAAATTTTG
3422422 AAAT-AACTCAAAACAGAAATAATTTAAACTAA
1 AAATAAACT-AAAACAGAAATAATTTAAACTAA
* * *
3422454 AAATAAACTAAACCCGAAATAATTTTAACT
1 AAATAAACTAAAACAGAAATAATTTAAACT
3422484 TGAATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (32 bp):
AAATAAACTAAAACAGAAATAATTTAAACTAA
Found at i:3422828 original size:26 final size:26
Alignment explanation
Indices: 3422797--3422853 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3422787 AGTTGAGTTT
3422797 AGTTTTAATGTTCAAGTTGATATTTG
1 AGTTTTAATGTTCAAGTTGATATTTG
** * *
3422823 AGTTTTTTTTTTCAATTTGATATTTG
1 AGTTTTAATGTTCAAGTTGATATTTG
3422849 AGTTT
1 AGTTT
3422854 GACTTTGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.04, G:0.16, T:0.58
Consensus pattern (26 bp):
AGTTTTAATGTTCAAGTTGATATTTG
Found at i:3427463 original size:19 final size:18
Alignment explanation
Indices: 3427423--3427463 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3427413 AATATTACAC
*
3427423 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
3427441 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
3427460 ATTT
1 ATTT
3427464 TGCCTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:3427899 original size:24 final size:22
Alignment explanation
Indices: 3427872--3427916 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
3427862 TGGTCGTGCG
3427872 TTTCTCTCTTTTTTCTTCGTTCTT
1 TTTCTCTCTTTTTT-TTC-TTCTT
*
3427896 TTTCTTTCTTTTTTTTCTTCT
1 TTTCTCTCTTTTTTTTCTTCT
3427917 ATTCATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTCTCTCTTTTTTTTCTTCTT
Found at i:3429551 original size:14 final size:14
Alignment explanation
Indices: 3429534--3429563 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3429524 AGGTGAACTA
3429534 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
3429548 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
3429562 GC
1 GC
3429564 TGCAATCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:3429611 original size:33 final size:33
Alignment explanation
Indices: 3429574--3429640 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3429564 TGCAATCGTT
3429574 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
* *
3429607 AGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
3429640 A
1 A
3429641 ATGTCTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.45, T:0.13
Consensus pattern (33 bp):
AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
Found at i:3429861 original size:13 final size:12
Alignment explanation
Indices: 3429842--3429875 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3429832 CATTTCTCTC
*
3429842 TTTTTTCTTTGT
1 TTTTTTCTTTCT
3429854 TCTTTTTCTTTCT
1 T-TTTTTCTTTCT
3429867 TTTTTTCTT
1 TTTTTTCTT
3429876 CTATTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:3434204 original size:28 final size:28
Alignment explanation
Indices: 3434151--3434215 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
3434141 TTTATTGTAA
*
3434151 TTTATTTATATTTTTATAACTCTTTAAT
1 TTTATTTATATTTTTATAAATCTTTAAT
3434179 TTTATTTATATTTTTATATAAT-TTTAAT
1 TTTATTTATATTTTTATA-AATCTTTAAT
*
3434207 ATT-TTTATA
1 TTTATTTATA
3434216 AATTTGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 6 0.18
28 26 0.76
29 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTATTTATATTTTTATAAATCTTTAAT
Found at i:3434210 original size:19 final size:18
Alignment explanation
Indices: 3434186--3434225 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
3434176 AATTTTATTT
*
3434186 ATATTTTTATATAATTTTA
1 ATATTTTTATA-AATTTGA
3434205 ATATTTTTATAAATTTGA
1 ATATTTTTATAAATTTGA
3434223 ATA
1 ATA
3434226 ATTGTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATTTTTATAAATTTGA
Found at i:3435836 original size:2 final size:2
Alignment explanation
Indices: 3435825--3435855 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3435815 TTGGTGATGG
3435825 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3435856 GTTCTATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3436696 original size:41 final size:38
Alignment explanation
Indices: 3436651--3436783 Score: 124
Period size: 40 Copynumber: 3.4 Consensus size: 38
3436641 ATTTGAGTCA
*
3436651 ATGAGACACTGGGTGTCAATTACCTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGTCAATTA--TACTTCGGATT-ATCCG
* * * *
3436692 ATGAGGCACTGGGTGCCAATT-TACTTCGGTTTAGCCG
1 ATGAGACACTGGGTGTCAATTATACTTCGGATTATCCG
* * *
3436729 ATGAGACACCGGGTATCAAATTATTACTTCGAATTATCCG
1 ATGAGACACTGGGTGTC-AATTA-TACTTCGGATTATCCG
* *
3436769 ATGAGGCACTAGGTG
1 ATGAGACACTGGGTG
3436784 CCAAACTGGT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 16 0.22
38 14 0.19
40 24 0.33
41 19 0.26
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (38 bp):
ATGAGACACTGGGTGTCAATTATACTTCGGATTATCCG
Found at i:3437202 original size:15 final size:15
Alignment explanation
Indices: 3437182--3437210 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3437172 TAGTTAATTG
3437182 ATGTTGTTATTTAAA
1 ATGTTGTTATTTAAA
3437197 ATGTTGTTATTTAA
1 ATGTTGTTATTTAA
3437211 GTTTATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (15 bp):
ATGTTGTTATTTAAA
Found at i:3446491 original size:125 final size:124
Alignment explanation
Indices: 3446362--3446617 Score: 379
Period size: 125 Copynumber: 2.1 Consensus size: 124
3446352 AAATAGTGGG
** * * * *
3446362 AAATCGCTTCTACCAGGATGCTATTTGAGAAAAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
*
3446427 TCGCTACAG-TGGTCATGTAAGAAATAATTTTTTTTTGACTTTTACTGAGCAAATAGTATA
66 TCGCTACAGTTGGTCATGTAAGAAATAA-TTTTTTTTGACGTTT-CTGAGCAAATAGTATA
* *
3446487 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATA
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
* * *
3446552 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
3446611 AAATCGC
1 AAATCGC
3446618 GCCCTCGTGG
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 21 0.18
125 80 0.68
126 17 0.14
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
TCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:3449917 original size:22 final size:23
Alignment explanation
Indices: 3449889--3449941 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
3449879 TTTTATAACA
*
3449889 AAAAATAAATTAAT-AAATATCT
1 AAAAATAAATAAATAAAATATCT
*
3449911 AAAAATACATAAATAAAATATCT
1 AAAAATAAATAAATAAAATATCT
*
3449934 -TAAATAAA
1 AAAAATAAA
3449942 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAATAAATAAATAAAATATCT
Found at i:3451046 original size:27 final size:28
Alignment explanation
Indices: 3451014--3451072 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
3451004 CCCATTTTTT
* *
3451014 AATAAAACACT-AAAAATTTATTTTAAA
1 AATAAAAAACTAAAAAATATATTTTAAA
*
3451041 AATAAAAAATTAAAAAATATATTTTAAA
1 AATAAAAAACTAAAAAATATATTTTAAA
3451069 AATA
1 AATA
3451073 TTTTAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (28 bp):
AATAAAAAACTAAAAAATATATTTTAAA
Found at i:3454397 original size:14 final size:14
Alignment explanation
Indices: 3454378--3454405 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3454368 CATGTTTCAT
3454378 TGTTTATATTTTTG
1 TGTTTATATTTTTG
3454392 TGTTTATATTTTTG
1 TGTTTATATTTTTG
3454406 GAGTTAATTA
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:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (14 bp):
TGTTTATATTTTTG
Found at i:3457299 original size:21 final size:21
Alignment explanation
Indices: 3457275--3457314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3457265 TATAGCAATA
*
3457275 TATTTAAAATATATATATATT
1 TATTTAAAAAATATATATATT
*
3457296 TATTTAAAAAATATTTATA
1 TATTTAAAAAATATATATA
3457315 AATGGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTAAAAAATATATATATT
Found at i:3459666 original size:16 final size:16
Alignment explanation
Indices: 3459645--3459675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3459635 CATGTTGAGG
3459645 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
3459661 CATATATATTTGAAA
1 CATATAAATTTGAAA
3459676 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:3462543 original size:18 final size:18
Alignment explanation
Indices: 3462520--3462554 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3462510 CATCAACAAT
*
3462520 TAAAATTTATTAAAATTG
1 TAAAATATATTAAAATTG
3462538 TAAAATATATTAAAATT
1 TAAAATATATTAAAATT
3462555 ATTATTTATT
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:0.03, T:0.43
Consensus pattern (18 bp):
TAAAATATATTAAAATTG
Found at i:3466058 original size:16 final size:17
Alignment explanation
Indices: 3466025--3466058 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3466015 TAAGTATTAT
3466025 ATAAAAATATATATATG
1 ATAAAAATATATATATG
*
3466042 ATAAAAATTTATA-ATG
1 ATAAAAATATATATATG
3466058 A
1 A
3466059 GATTTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
ATAAAAATATATATATG
Found at i:3466482 original size:20 final size:20
Alignment explanation
Indices: 3466444--3466481 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3466434 CATATTATTT
3466444 TTTAATATATGTTATTTTTA
1 TTTAATATATGTTATTTTTA
*
3466464 TTTAATAT-TTTTATTTTT
1 TTTAATATATGTTATTTTT
3466482 TTTGTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTAATATATGTTATTTTTA
Found at i:3469941 original size:14 final size:14
Alignment explanation
Indices: 3469922--3469949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3469912 TATTTTTATG
3469922 AAATATTTTAAAAT
1 AAATATTTTAAAAT
3469936 AAATATTTTAAAAT
1 AAATATTTTAAAAT
3469950 GCGAGGATGA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATTTTAAAAT
Found at i:3471277 original size:54 final size:54
Alignment explanation
Indices: 3471199--3471483 Score: 570
Period size: 54 Copynumber: 5.3 Consensus size: 54
3471189 AAAATTATAT
3471199 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
1 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
3471253 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
1 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
3471307 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
1 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
3471361 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
1 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
3471415 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
1 AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
3471469 AAAATCTTATTTAAA
1 AAAATCTTATTTAAA
3471484 ACCAGAAGAA
Statistics
Matches: 231, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 231 1.00
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (54 bp):
AAAATCTTATTTAAATTACCCAAATATATCCCTCAAGAATTTTTCTCAAGTAAA
Found at i:3472587 original size:27 final size:27
Alignment explanation
Indices: 3472546--3472597 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3472536 TAGTATTGGC
3472546 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
3472573 GCCTATTTGGGAGGCGCCAATGGTG
1 GCCTATCTGGAAGGCGCCAATGGTG
3472598 AACAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGAAGGCGCCAATGGTGGT
Found at i:3472681 original size:27 final size:23
Alignment explanation
Indices: 3472644--3472718 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 23
3472634 AATTAATTAT
*
3472644 AAAATAATTACAATATTCATACA
1 AAAAAAATTACAATATTCATACA
3472667 AAATTACAATATTACAATATTCATAC-
1 AAA--A-AA-ATTACAATATTCATACA
*
3472693 AAAAAAATTGCAATATTCATACA
1 AAAAAAATTACAATATTCATACA
3472716 AAA
1 AAA
3472719 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 15 0.33
23 8 0.18
24 1 0.02
25 1 0.02
26 4 0.09
27 16 0.36
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.29
Consensus pattern (23 bp):
AAAAAAATTACAATATTCATACA
Found at i:3473839 original size:16 final size:17
Alignment explanation
Indices: 3473812--3473843 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3473802 GCCCAGCCCG
3473812 TTTTTAATTAAAATTAT
1 TTTTTAATTAAAATTAT
3473829 TTTTTAA-TAAAATTA
1 TTTTTAATTAAAATTA
3473844 AAACTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATTAAAATTAT
Found at i:3473845 original size:22 final size:22
Alignment explanation
Indices: 3473817--3473866 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
3473807 GCCCGTTTTT
* *
3473817 AATTAAAATTATTTTTTAATAA
1 AATTAAAACTATTTGTTAATAA
*
3473839 AATTAAAACTATTTGTTATTAA
1 AATTAAAACTATTTGTTAATAA
3473861 AATTAA
1 AATTAA
3473867 TTGTTAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTAAAACTATTTGTTAATAA
Found at i:3473859 original size:16 final size:16
Alignment explanation
Indices: 3473840--3473883 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3473830 TTTTAATAAA
*
3473840 ATTAAAACTATTTGTT
1 ATTAAAATTATTTGTT
*
3473856 ATTAAAATTAATTGTT
1 ATTAAAATTATTTGTT
*
3473872 AGTAAAATTATT
1 ATTAAAATTATT
3473884 AAATTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (16 bp):
ATTAAAATTATTTGTT
Found at i:3473966 original size:9 final size:9
Alignment explanation
Indices: 3473954--3473981 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3473944 TTTATGAAAT
3473954 TATTAATTG
1 TATTAATTG
3473963 TATTAATTG
1 TATTAATTG
3473972 TATTAATTG
1 TATTAATTG
3473981 T
1 T
3473982 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3473986 original size:68 final size:66
Alignment explanation
Indices: 3473870--3474012 Score: 241
Period size: 68 Copynumber: 2.1 Consensus size: 66
3473860 AAATTAATTG
* *
3473870 TTAGTAAAATTATTAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 TTAGTAAAATTATGAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
3473935 A
66 A
*
3473936 TTAGTAAATTTATGAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATGAAATTATTAATTG--TTAATTGTATTAATTGTTGTAACAAAATCTAACATT
3474001 TGA
64 TGA
3474004 TTAGTAAAA
1 TTAGTAAAA
3474013 CAAACTTGCT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 25 0.35
68 46 0.65
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (66 bp):
TTAGTAAAATTATGAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
A
Found at i:3474030 original size:3 final size:3
Alignment explanation
Indices: 3474022--3474056 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3474012 ACAAACTTGC
3474022 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3474057 ACACTAGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3477903 original size:239 final size:237
Alignment explanation
Indices: 3477331--3478084 Score: 805
Period size: 239 Copynumber: 3.1 Consensus size: 237
3477321 TGTCATCCAA
* * * *
3477331 GGAAAGAATGGTATTATATTGACTGAAAGATTTGCATCGTGATATAGAACCATTAATTTTCTCCT
1 GGAAAGAATGGTA-TATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATTCATTTTCTCCT
* * * *
3477396 CTGTAGGTGTTAAGGTTGTATGGATATGTTCAATAGTTACCTGTCTCTGAGTGCACTTCGAGTTT
65 TTGTAGGTGTTAAGGTTGTAT---TATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTT
* * *
3477461 GCCATTCTAAGATGGGCGAAGGAGAATTCATGGGT-TTTTTATGTTCA-TTATAAGTATAGGAGG
127 GCCATTCTAAGATAGGC-AAGGAGAATT--T-GTTCTTTTTATGTT-AGTTATAAGTATAGGAAG
* * * * * **
3477524 GGGACAAGTCTGGGAGTTAATGTATTGTTTCGTTATCAGCTTGTCACGTGT
187 GGGTCGAGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
** * * * * * * *
3477575 GG--A-AA--G--TATGTTGACCAAAAGGTTCTCATCATGTTATAGAGCCTTTCCTTTTTTTTGC
1 GGAAAGAATGGTATATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATT-C-ATTTTCT--
* *
3477633 CCTTTGTCGGTGTTAAGGTTGTATGATTATATTCAATAATTG-CTCATCTCTGAGTGCACTTCGA
62 CCTTTGTAGGTGTTAAGGTTG--T-ATTATATTCAATAATTGCCT-GTCTCTGAGTGCACTTCGA
* * *
3477697 GCTTGCCATTTTGAGATAGGCAAAGGAGAATTTGTTACTTTTTATGTTAGTTATAAGTATAGGAA
123 GTTTGCCATTCTAAGATAGGC-AAGGAGAATTTGTT-CTTTTTATGTTAGTTATAAGTATAGGAA
* * *
3477762 GGAGTCGAGTGTGGAAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
186 GGGGTCGAGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
* * *
3477814 GGAAAGAATCGTATATGTTGGCTGAAAGGTTCGCATCGTGATATAGAACCGTT-ATTATTCTCCT
1 GGAAAGAATGGTATATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATTCATT-TTCTCCT
*
3477878 TTGTAGGTGTTAAGGTTGTATTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTTGCA
65 TTGTAGGTGTTAAGGTTGTATTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTTGCC
* * * *
3477943 ATTCTAAGATGAGTG-AAGCAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAGGAAGGGGAT
130 ATTCTAAGAT-AG-GCAAGGAGAATTTGT-TCTTTTTATGTTAGTTATAAGTATAGGAAGGGG-T
3478007 -GAGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
191 CGAGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
*
3478053 AGAAAGAATGGTATATGTTGACTGAAAGGTTC
1 GGAAAGAATGGTATATGTTGACTGAAAGGTTC
3478085 ATGTACTTTT
Statistics
Matches: 424, Mismatches: 62, Indels: 53
0.79 0.12 0.10
Matches are distributed among these distances:
236 30 0.07
237 2 0.00
238 7 0.02
239 233 0.55
240 82 0.19
241 4 0.01
242 24 0.06
243 4 0.01
244 6 0.01
246 32 0.08
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (237 bp):
GGAAAGAATGGTATATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATTCATTTTCTCCTT
TGTAGGTGTTAAGGTTGTATTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTTGCCA
TTCTAAGATAGGCAAGGAGAATTTGTTCTTTTTATGTTAGTTATAAGTATAGGAAGGGGTCGAGT
CTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
Found at i:3486041 original size:26 final size:26
Alignment explanation
Indices: 3486009--3486062 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
3485999 TATCAGCTCA
* * *
3486009 ATTAAAATTTTTATCGTGTAAAAATT
1 ATTAAAATATTAATCGTATAAAAATT
3486035 ATTAAAATATTAATCGTATAAAAATT
1 ATTAAAATATTAATCGTATAAAAATT
3486061 AT
1 AT
3486063 GAAAGTGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
ATTAAAATATTAATCGTATAAAAATT
Found at i:3489535 original size:5 final size:5
Alignment explanation
Indices: 3489519--3489550 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
3489509 TTTATAAATA
3489519 TTAAT ATTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT -TTAAT TTAAT TTAAT TTAAT TTAAT T
3489551 ACCCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:3493439 original size:86 final size:87
Alignment explanation
Indices: 3493330--3493503 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 87
3493320 ATTAAAAATT
3493330 TGGGGTGTTTTAATTATTATATTAGTTTATAATTTTATAATTTTTAAAAGATTTTAGAGGCAATT
1 TGGGGTGTTTTAATTATTATATTAGTTTATAATTTTATAATTTTTAAAAGATTTTAGAGGCAATT
3493395 TTACCATTTTGAGACTCCATAC
66 TTACCATTTTGAGACTCCATAC
3493417 TGGGGTGTTTT-ATTATTATATTAGTTTATAATTTTATAATTTTTAAAAGATTTTAGAGGCAATT
1 TGGGGTGTTTTAATTATTATATTAGTTTATAATTTTATAATTTTTAAAAGATTTTAGAGGCAATT
3493481 TTACCATTTTGAGACTCCATAC
66 TTACCATTTTGAGACTCCATAC
3493503 T
1 T
3493504 CTTTTTTAAG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 76 0.87
87 11 0.13
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (87 bp):
TGGGGTGTTTTAATTATTATATTAGTTTATAATTTTATAATTTTTAAAAGATTTTAGAGGCAATT
TTACCATTTTGAGACTCCATAC
Found at i:3495281 original size:2 final size:2
Alignment explanation
Indices: 3495274--3495315 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3495264 NNNNNNNNNN
*
3495274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3495316 CTGATTAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3496596 original size:14 final size:14
Alignment explanation
Indices: 3496552--3496601 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
3496542 AACTTGACAA
* *
3496552 ATTAAAATTAAACA
1 ATTAAAATTTAACT
* *
3496566 ATTAAAATTTGATT
1 ATTAAAATTTAACT
*
3496580 ATTCAAATTTAACT
1 ATTAAAATTTAACT
3496594 ATTAAAAT
1 ATTAAAAT
3496602 ATAAAGAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (14 bp):
ATTAAAATTTAACT
Found at i:3500740 original size:159 final size:157
Alignment explanation
Indices: 3500480--3500799 Score: 453
Period size: 159 Copynumber: 2.0 Consensus size: 157
3500470 CTAACTATTC
* ** *
3500480 CATTTTTAACATTCAAAACCACTGAAAACAAAACACTACCCTTTACTGAACTCAGATGACAAAAG
1 CATTTGTAACATTCAAAACCAAAGAAAACAAAACACTACCCTTTACTGAACTCAGATGACAAAAC
3500545 CAGGTTCATTTTCACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTACTT
66 CAGGTTCATTTTCACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTACTT
*
3500610 TCTCAGTAACCAAACAGGAAGTGAACT
131 TCTCAGTAACAAAACAGGAAGTGAACT
* ** * * *
3500637 CATTTGTAACATTTAAAACCAAAGAAAACATGATACTACCCTTTAGTGAACACTCGGATGACAAA
1 CATTTGTAACATTCAAAACCAAAGAAAACAAAACACTACCCTTTACTG-A-ACTCAGATGACAAA
** * *
3500702 ACCAGGTTC-TTTTGCACAGTGAAATGATCGTTTCAACTTTCCCTTTTCCTCCAATTTTCCTTTA
64 ACCAGGTTCATTTT-CACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTA
**
3500766 CTTTCTTGGTAACAAAACAGGAAGTGAACT
128 CTTTCTCAGTAACAAAACAGGAAGTGAACT
3500796 CATT
1 CATT
3500800 GCAGTAAAAA
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
157 40 0.28
158 5 0.03
159 98 0.69
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (157 bp):
CATTTGTAACATTCAAAACCAAAGAAAACAAAACACTACCCTTTACTGAACTCAGATGACAAAAC
CAGGTTCATTTTCACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTACTT
TCTCAGTAACAAAACAGGAAGTGAACT
Found at i:3501848 original size:300 final size:291
Alignment explanation
Indices: 3501195--3501870 Score: 946
Period size: 300 Copynumber: 2.3 Consensus size: 291
3501185 AATAAAACTT
* * *
3501195 ATCTCCAAATTGAGAAACCAAATGCATTGAGAATTACTTATCATTTACCAAACAACACCTAACCG
1 ATCTCCAAAATGAGAAACCAAACGCATTGAGAATTACTTATCATTTACCAAACAACACCTAACTG
* * *
3501260 TTCCATTTTTAACATTCAAAACCAATGAAAATAAAATACTAACCTTAAGTCAGATAACAAAAGCA
66 TTCCATTTTTAACATTCAAAAACAATGAAAATAAAATACTAACCTTAACTCAGATAACAAAACCA
*
3501325 GGTTCTTGTGAACAGTAAAACAATCATTTCAACTTTCCATTTTCCTTCACTTTCTCGGTAACCAA
131 GGTTCTTGTGAACAGTAAAACAATCATTTCAACTTTCCATGTTCCTTCACTTTCTCGGTAACCAA
3501390 ACAGGAAGTGAACTCATAGCAGTCAAATGATGAAAAGAAAACATTGCCGTAACACATTAAGTAGT
196 ACAGGAAGTGAACTCATAGCAGTCAAATGATGAAAAGAAAACATTGCCGTAACACATTAAGTAGT
* *
3501455 ATATATTATTGAAAATAATTCATTAAGCTTA
261 ATATATTATTGAAAACAATTCATCAAGCTTA
* * * * *
3501486 ATCTCCAGAATAAGAAACCAAACGCATTGAGAGTTACTTATCGTTCACCAAACAACACCTAACTG
1 ATCTCCAAAATGAGAAACCAAACGCATTGAGAATTACTTATCATTTACCAAACAACACCTAACTG
* * *
3501551 TTCCATTTTTAACATTCAAAAACAATGGAAATAAAAATACTACCCTTTACTGAACACTCAGATGA
66 TTCCATTTTTAACATTCAAAAACAATGAAAAT-AAAATACTAACC--T--T--A-ACTCAGATAA
* * * *
3501616 CAAAACCAGGTTCTTTTGCACAGTGAAACAAT-GTTTCAACTTTCCATGTTCCTTCACTTTCTCG
123 CAAAACCAGGTTCTTGTGAACAGTAAAACAATCATTTCAACTTTCCATGTTCCTTCACTTTCTCG
** **
3501680 GTAACCAAACAGGAAGTGAACTCATAGTGGTCAAATGATGGGAAAA-AAATAGCATTGCTTTAAC
188 GTAACCAAACAGGAAGTGAACTCATAGCAGTCAAATGAT--GAAAAGAAA-A-CATTGCCGTAAC
*
3501744 TCA-TAAGTAGTATATATTATTGAAAACAA-TCAATCAAGCTTA
249 ACATTAAGTAGTATATATTATTGAAAACAATTC-ATCAAGCTTA
** *
3501786 ATCTCCAAAATGAGAAACCAAACGCATTGAGAATCGCTTATCATTTACCAAACAATACCTAACTG
1 ATCTCCAAAATGAGAAACCAAACGCATTGAGAATTACTTATCATTTACCAAACAACACCTAACTG
3501851 TTCCATTTTTAACATTCAAA
66 TTCCATTTTTAACATTCAAA
3501871 CTGAACACTC
Statistics
Matches: 338, Mismatches: 34, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
291 87 0.26
292 11 0.03
294 1 0.00
296 1 0.00
298 68 0.20
299 41 0.12
300 117 0.35
301 12 0.04
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (291 bp):
ATCTCCAAAATGAGAAACCAAACGCATTGAGAATTACTTATCATTTACCAAACAACACCTAACTG
TTCCATTTTTAACATTCAAAAACAATGAAAATAAAATACTAACCTTAACTCAGATAACAAAACCA
GGTTCTTGTGAACAGTAAAACAATCATTTCAACTTTCCATGTTCCTTCACTTTCTCGGTAACCAA
ACAGGAAGTGAACTCATAGCAGTCAAATGATGAAAAGAAAACATTGCCGTAACACATTAAGTAGT
ATATATTATTGAAAACAATTCATCAAGCTTA
Found at i:3503868 original size:2 final size:2
Alignment explanation
Indices: 3503861--3503893 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3503851 ATGGAAGAGT
*
3503861 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3503894 GAGATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3504319 original size:248 final size:249
Alignment explanation
Indices: 3503870--3504366 Score: 987
Period size: 248 Copynumber: 2.0 Consensus size: 249
3503860 TTATATATAT
3503870 GTATATATATATATATATATATATGAGATTAAAATGATTTTGTACCTAATGCAATTCATCATGTA
1 GTATATATATATATATATATATATGAGATTAAAATGATTTTGTACCTAATGCAATTCATCATGTA
3503935 CAATCTTTTTTTATTTTAAATGGCAGGGGAGATTGTAACCATTTCAATTTTTATATTTATAACTA
66 CAATCTTTTTTTATTTTAAATGGCAGGGGAGATTGTAACCATTTCAATTTTTATATTTATAACTA
3504000 AGGGTAAGTTTGGATGGGCGATTGGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGT
131 AGGGTAAGTTTGGATGGGCGATTGGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGT
3504065 ATGCTACAGTATCTAATCTCACCGCTACCGTTGTTTTTACACTAACCGCAGGTA
196 ATGCTACAGTATCTAATCTCACCGCTACCGTTGTTTTTACACTAACCGCAGGTA
3504119 GTATATATAT-TATATATATATATGAGATTAAAATGATTTTGTACCTAATGCAATTCATCATGTA
1 GTATATATATATATATATATATATGAGATTAAAATGATTTTGTACCTAATGCAATTCATCATGTA
3504183 CAATCTTTTTTTATTTTAAATGGCAGGGGAGATTGTAACCATTTCAATTTTTATATTTATAACTA
66 CAATCTTTTTTTATTTTAAATGGCAGGGGAGATTGTAACCATTTCAATTTTTATATTTATAACTA
3504248 AGGGTAAGTTTGGATGGGCGATTGGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGT
131 AGGGTAAGTTTGGATGGGCGATTGGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGT
3504313 ATGCTACAGTATCTAATCTCACCGCTACCGTTGTTTTTACACTAACCGCAGGTA
196 ATGCTACAGTATCTAATCTCACCGCTACCGTTGTTTTTACACTAACCGCAGGTA
3504367 AACGCATCGT
Statistics
Matches: 248, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
248 238 0.96
249 10 0.04
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (249 bp):
GTATATATATATATATATATATATGAGATTAAAATGATTTTGTACCTAATGCAATTCATCATGTA
CAATCTTTTTTTATTTTAAATGGCAGGGGAGATTGTAACCATTTCAATTTTTATATTTATAACTA
AGGGTAAGTTTGGATGGGCGATTGGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGT
ATGCTACAGTATCTAATCTCACCGCTACCGTTGTTTTTACACTAACCGCAGGTA
Found at i:3505145 original size:35 final size:35
Alignment explanation
Indices: 3505106--3505215 Score: 91
Period size: 35 Copynumber: 3.1 Consensus size: 35
3505096 TAATTTTGTA
3505106 TATTTAATACACATATATAATGATTGTATAAAATT
1 TATTTAATACACATATATAATGATTGTATAAAATT
* ** * * * ** *
3505141 TATTTTATATTCATATTTACTTTTATTGCTA-ATGA-G
1 TATTTAATACACATATATA--ATGATTG-TATAAAATT
3505177 TATTTAATACA-ATATATAATGATTGTATAAAATT
1 TATTTAATACACATATATAATGATTGTATAAAATT
3505211 TATTT
1 TATTT
3505216 TATATTCATA
Statistics
Matches: 52, Mismatches: 18, Indels: 11
0.64 0.22 0.14
Matches are distributed among these distances:
32 2 0.04
33 7 0.13
34 5 0.10
35 21 0.40
36 8 0.15
37 7 0.13
38 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (35 bp):
TATTTAATACACATATATAATGATTGTATAAAATT
Found at i:3505203 original size:70 final size:71
Alignment explanation
Indices: 3505106--3505255 Score: 284
Period size: 70 Copynumber: 2.1 Consensus size: 71
3505096 TAATTTTGTA
3505106 TATTTAATACACATATATAATGATTGTATAAAATTTATTTTATATTCATATTTACTTTTATTGCT
1 TATTTAATACACATATATAATGATTGTATAAAATTTATTTTATATTCATATTTACTTTTATTGCT
3505171 AATGAG
66 AATGAG
3505177 TATTTAATACA-ATATATAATGATTGTATAAAATTTATTTTATATTCATATTTACTTTTATTGCT
1 TATTTAATACACATATATAATGATTGTATAAAATTTATTTTATATTCATATTTACTTTTATTGCT
3505241 AATGAG
66 AATGAG
*
3505247 TTTTTAATA
1 TATTTAATA
3505256 TAATTTACAA
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 67 0.86
71 11 0.14
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.51
Consensus pattern (71 bp):
TATTTAATACACATATATAATGATTGTATAAAATTTATTTTATATTCATATTTACTTTTATTGCT
AATGAG
Found at i:3507084 original size:23 final size:25
Alignment explanation
Indices: 3507058--3507108 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
3507048 CATAAACTAA
*
3507058 AATTATAATTACAATTAAC-A-TAT
1 AATTATAATAACAATTAACTATTAT
*
3507081 AATTATGATAACAATTAACTATTAT
1 AATTATAATAACAATTAACTATTAT
3507106 AAT
1 AAT
3507109 GCACAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 1 0.04
25 6 0.25
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (25 bp):
AATTATAATAACAATTAACTATTAT
Found at i:3508311 original size:81 final size:82
Alignment explanation
Indices: 3508204--3508381 Score: 324
Period size: 81 Copynumber: 2.2 Consensus size: 82
3508194 ATTTAGGTCA
*
3508204 TTTATAATTTATAAAATTTTAAATTAATAATGGTAAAATTATACTTTGGCCCTCTAAAAACTATG
1 TTTAAAATTTATAAAATTTTAAATTAATAATGGTAAAATTATACTTTGGCCCTCTAAAAACTATG
3508269 AAAATTTGATTTAACAT
66 AAAATTTGATTTAACAT
3508286 TTTAAAATTTAT-AAATTTTAAATTAATAATGGTAAAATTATACTTTGGCCCTCTAAAAACTATG
1 TTTAAAATTTATAAAATTTTAAATTAATAATGGTAAAATTATACTTTGGCCCTCTAAAAACTATG
3508350 AAAATTTGATTTAACAT
66 AAAATTTGATTTAACAT
*
3508367 TTTAAAA-ATATAAAA
1 TTTAAAATTTATAAAA
3508382 ATATAGACTA
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
80 3 0.03
81 79 0.85
82 11 0.12
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (82 bp):
TTTAAAATTTATAAAATTTTAAATTAATAATGGTAAAATTATACTTTGGCCCTCTAAAAACTATG
AAAATTTGATTTAACAT
Found at i:3508600 original size:7 final size:7
Alignment explanation
Indices: 3508588--3508613 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3508578 TTTTAATTTT
3508588 ATAATAC
1 ATAATAC
3508595 ATAATAC
1 ATAATAC
3508602 ATAATAC
1 ATAATAC
3508609 ATAAT
1 ATAAT
3508614 CATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (7 bp):
ATAATAC
Found at i:3512945 original size:159 final size:162
Alignment explanation
Indices: 3512651--3512953 Score: 362
Period size: 160 Copynumber: 1.9 Consensus size: 162
3512641 TCTTTAGGGT
* * * *
3512651 TTTAAAATATATATAATGATCTCTTAGGAAAAAAAAAAGTACTTCTTTTTAAGTATTGAATATTC
1 TTTAAAATATACATAATGATCTCCTAGGAAAAAAAAAAGTA-TTCTTTTTAAGTATTCAATAATC
** * * * * * * ** *
3512716 GTATTAGATTCCGATTAAATTTAGAGTCGAACTTTTAAATTGAGGTAAAATTCTTCCGACTCTTT
65 ACATTAGATCCCGATCAAATCTAGACTCAAACTTTTAAATGGAGACAAAACTCTTCCGACTCTTT
*
3512781 TATTTTTCCTCCATATTCGACTTTAAATGGAAA
130 CATTTTTCCTCCATATTCGACTTTAAATGGAAA
*
3512814 TTTAAAATATACATAATGATCTCCTA-GAAAAAAAAATAGT-TT-TTTTTATGTATTCAATAATC
1 TTTAAAATATACATAATGATCTCCTAGGAAAAAAAAA-AGTATTCTTTTTAAGTATTCAATAATC
* * * *
3512876 ACGTTAGATCCCGATCAAATCTAGACTCAAACTTTTAAATGGAGACAAAGCTGTT-CTACTCTTT
65 ACATTAGATCCCGATCAAATCTAGACTCAAACTTTTAAATGGAGACAAAACTCTTCCGACTCTTT
*
3512940 CATTTTTCTTCCAT
130 CATTTTTCCTCCAT
3512954 CATATTCGAA
Statistics
Matches: 117, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
159 20 0.17
160 58 0.50
161 2 0.02
162 10 0.09
163 27 0.23
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (162 bp):
TTTAAAATATACATAATGATCTCCTAGGAAAAAAAAAAGTATTCTTTTTAAGTATTCAATAATCA
CATTAGATCCCGATCAAATCTAGACTCAAACTTTTAAATGGAGACAAAACTCTTCCGACTCTTTC
ATTTTTCCTCCATATTCGACTTTAAATGGAAA
Found at i:3518465 original size:13 final size:14
Alignment explanation
Indices: 3518442--3518470 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3518432 TTTTTCAACA
3518442 AAAACAAATAATAC
1 AAAACAAATAATAC
3518456 AAAA-AAATAATAC
1 AAAACAAATAATAC
3518469 AA
1 AA
3518471 CAATAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAACAAATAATAC
Found at i:3524006 original size:22 final size:22
Alignment explanation
Indices: 3523978--3524019 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3523968 AATTACCCTA
*
3523978 ACAAAAAGA-ACAATCCAAAAAG
1 ACAAAAAAACACAAT-CAAAAAG
3524000 ACAAAAAAACACAATCAAAA
1 ACAAAAAAACACAATCAAAA
3524020 CATGTAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.71, C:0.19, G:0.05, T:0.05
Consensus pattern (22 bp):
ACAAAAAAACACAATCAAAAAG
Found at i:3526261 original size:91 final size:91
Alignment explanation
Indices: 3526161--3526343 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
3526151 ATTTATGTTG
* * * * * *
3526161 ATTTATAATTTATAATTGGATTAGTAATGGTAAAATTGCACTGTGACCTCTAAAAATTATAAAAA
1 ATTTATAATTTATAATTGAATTAATAATGGTAAAATTGCACTCTGACATCCAAAAATGATAAAAA
* *
3526226 TTTGATTTAATCTTTTAAAAATTATA
66 ATTGATTTAATCTTTTAAAAATAATA
* *
3526252 ATTTATAATTTATAATTGAATTAATAATGTTAAAATTGCACTCTGGCATCCAAAAATGATAAAAA
1 ATTTATAATTTATAATTGAATTAATAATGGTAAAATTGCACTCTGACATCCAAAAATGATAAAAA
3526317 ATTGATTTAATCTTTTAAAAATAATA
66 ATTGATTTAATCTTTTAAAAATAATA
3526343 A
1 A
3526344 AGAATTGCAC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (91 bp):
ATTTATAATTTATAATTGAATTAATAATGGTAAAATTGCACTCTGACATCCAAAAATGATAAAAA
ATTGATTTAATCTTTTAAAAATAATA
Found at i:3526278 original size:19 final size:20
Alignment explanation
Indices: 3526251--3526289 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3526241 TAAAAATTAT
* *
3526251 AATTTATAAT-TTATAATTG
1 AATTAATAATGTTAAAATTG
3526270 AATTAATAATGTTAAAATTG
1 AATTAATAATGTTAAAATTG
3526290 CACTCTGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
AATTAATAATGTTAAAATTG
Found at i:3526344 original size:30 final size:30
Alignment explanation
Indices: 3526303--3526403 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
3526293 TCTGGCATCC
*
3526303 AAAAATGATAAAAAATTGATTTAATCTTTT
1 AAAAATTATAAAAAATTGATTTAATCTTTT
* * * * *
3526333 AAAAATAATAAAGAATTGCACTGT-A-CCTCT
1 AAAAATTATAAAAAATTG-A-TTTAATCTTTT
*
3526363 AAAAATTATAAAAATTTGATTTAATCTTTT
1 AAAAATTATAAAAAATTGATTTAATCTTTT
3526393 AAAAATTATAA
1 AAAAATTATAA
3526404 TTTATAATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 48 0.86
31 2 0.04
32 2 0.04
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (30 bp):
AAAAATTATAAAAAATTGATTTAATCTTTT
Found at i:3526350 original size:61 final size:60
Alignment explanation
Indices: 3526285--3526403 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
3526275 ATAATGTTAA
*
3526285 AATTGCACTCTGGCATCCAAAAATGATAAAAAATTGATTTAATCTTTTAAAAATAATAAAG
1 AATTGCACTCT-ACATCCAAAAATGATAAAAAATTGATTTAATCTTTTAAAAATAATAAAG
* * * * * *
3526346 AATTGCACTGTACCTCTAAAAATTATAAAAATTTGATTTAATCTTTTAAAAATTATAA
1 AATTGCACTCTACATCCAAAAATGATAAAAAATTGATTTAATCTTTTAAAAATAATAA
3526404 TTTATAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 41 0.80
61 10 0.20
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (60 bp):
AATTGCACTCTACATCCAAAAATGATAAAAAATTGATTTAATCTTTTAAAAATAATAAAG
Found at i:3526372 original size:151 final size:152
Alignment explanation
Indices: 3526194--3526497 Score: 601
Period size: 151 Copynumber: 2.0 Consensus size: 152
3526184 GTAATGGTAA
3526194 AATTGCACTGTGACCTCTAAAAATTATAAAAATTTGATTTAATCTTTTAAAAATTATAATTTATA
1 AATTGCACTGTGACCTCTAAAAATTATAAAAATTTGATTTAATCTTTTAAAAATTATAATTTATA
3526259 ATTTATAATTGAATTAATAATGTTAAAATTGCACTCTGGCATCCAAAAATGATAAAAAATTGATT
66 ATTTATAATTGAATTAATAATGTTAAAATTGCACTCTGGCATCCAAAAATGATAAAAAATTGATT
3526324 TAATCTTTTAAAAATAATAAAG
131 TAATCTTTTAAAAATAATAAAG
3526346 AATTGCACTGT-ACCTCTAAAAATTATAAAAATTTGATTTAATCTTTTAAAAATTATAATTTATA
1 AATTGCACTGTGACCTCTAAAAATTATAAAAATTTGATTTAATCTTTTAAAAATTATAATTTATA
3526410 ATTTATAATTGAATTAATAATGTTAAAATTGCACTCTGGCATCCAAAAATGATAAAAAATTGATT
66 ATTTATAATTGAATTAATAATGTTAAAATTGCACTCTGGCATCCAAAAATGATAAAAAATTGATT
3526475 TAATCTTTTAAAAATAATAAAG
131 TAATCTTTTAAAAATAATAAAG
3526497 A
1 A
3526498 TATAGACTAT
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
151 141 0.93
152 11 0.07
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.38
Consensus pattern (152 bp):
AATTGCACTGTGACCTCTAAAAATTATAAAAATTTGATTTAATCTTTTAAAAATTATAATTTATA
ATTTATAATTGAATTAATAATGTTAAAATTGCACTCTGGCATCCAAAAATGATAAAAAATTGATT
TAATCTTTTAAAAATAATAAAG
Found at i:3526429 original size:19 final size:20
Alignment explanation
Indices: 3526402--3526440 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3526392 TAAAAATTAT
* *
3526402 AATTTATAAT-TTATAATTG
1 AATTAATAATGTTAAAATTG
3526421 AATTAATAATGTTAAAATTG
1 AATTAATAATGTTAAAATTG
3526441 CACTCTGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
AATTAATAATGTTAAAATTG
Found at i:3529351 original size:6 final size:6
Alignment explanation
Indices: 3529335--3529401 Score: 73
Period size: 6 Copynumber: 11.0 Consensus size: 6
3529325 ATAAATATAT
*** *
3529335 TTTTTA TTTTTTA TTTTTA -AAATA TTTTTA TTTTTA TTTTTGT TTTTTA
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTTTTA
3529384 TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA
3529402 AAATAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
5 2 0.04
6 37 0.74
7 11 0.22
ACGTcount: A:0.19, C:0.00, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:3529361 original size:25 final size:24
Alignment explanation
Indices: 3529326--3529423 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
3529316 CCGAATATAA
3529326 TAAATATATTTTTTATTTTTTATTTT
1 TAAA-ATATTTTTTA-TTTTTATTTT
3529352 TAAAATA-TTTTTATTTTTATTTT
1 TAAAATATTTTTTATTTTTATTTT
**** *
3529375 TGTTTTTTATTTTTATTTTTATTTT
1 TAAAATAT-TTTTTATTTTTATTTT
*
3529400 TAAAATAATTTTTTAATGTTTATT
1 TAAAAT-ATTTTTT-ATTTTTATT
3529424 AAAAATGGCC
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
23 12 0.21
24 6 0.11
25 26 0.46
26 13 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (24 bp):
TAAAATATTTTTTATTTTTATTTT
Found at i:3529381 original size:19 final size:19
Alignment explanation
Indices: 3529332--3529400 Score: 84
Period size: 19 Copynumber: 3.4 Consensus size: 19
3529322 ATAATAAATA
3529332 TATTTTTTATTTTTTATTTT
1 TATTTTTTA-TTTTTATTTT
3529352 TAAAATATTTTTATTTTTATTTT
1 T---AT-TTTTTATTTTTATTTT
*
3529375 TGTTTTTTATTTTTATTTT
1 TATTTTTTATTTTTATTTT
3529394 TATTTTT
1 TATTTTT
3529401 AAAATAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
19 22 0.51
20 2 0.05
23 13 0.30
24 6 0.14
ACGTcount: A:0.19, C:0.00, G:0.01, T:0.80
Consensus pattern (19 bp):
TATTTTTTATTTTTATTTT
Found at i:3548869 original size:95 final size:96
Alignment explanation
Indices: 3548557--3548843 Score: 425
Period size: 96 Copynumber: 3.0 Consensus size: 96
3548547 TATTCGGAGT
* * * ** * * * *
3548557 TGAATATCGGTTTTTAACTTATTGGGTGATAGATTTTGATTTATAGTTTCTTTGGAGGATTCTTT
1 TGAATATCAGTTTTAAACATATTGCATGATAGGTTTT-CTTGATAGTTTCTTTGTAGGATTCTTT
* *
3548622 TAACT-GAATTATTCGGATTCGAGTGTGAGCGA
65 TAACTAG-GTTATTTGGATTCGAGTGTGAGCGA
*
3548654 TGAATATCAGTTTTAAACATATTGCATGATAGTTTTTCTTGATAGTTTCTTTGTAGGATTCTTTT
1 TGAATATCAGTTTTAAACATATTGCATGATAGGTTTTCTTGATAGTTTCTTTGTAGGATTCTTTT
*
3548719 AACTAGGTTATTTGGGTTCGAGTGTGAGCGA
66 AACTAGGTTATTTGGATTCGAGTGTGAGCGA
3548750 TGAATATCAGTTTTAAACATATTGCATGATAGGTTTT-TTGATAGTTTCTTTGTAGGATTCTTTT
1 TGAATATCAGTTTTAAACATATTGCATGATAGGTTTTCTTGATAGTTTCTTTGTAGGATTCTTTT
3548814 AACTAGGTTATTTGGATTCGAGTGTGAGCG
66 AACTAGGTTATTTGGATTCGAGTGTGAGCG
3548844 TTAAATACCG
Statistics
Matches: 175, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
95 56 0.32
96 87 0.50
97 32 0.18
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (96 bp):
TGAATATCAGTTTTAAACATATTGCATGATAGGTTTTCTTGATAGTTTCTTTGTAGGATTCTTTT
AACTAGGTTATTTGGATTCGAGTGTGAGCGA
Found at i:3548879 original size:14 final size:14
Alignment explanation
Indices: 3548862--3548891 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3548852 CGGTATTTAA
3548862 CGAATTGCCTCTTT
1 CGAATTGCCTCTTT
3548876 CGAATTGCCTCTTT
1 CGAATTGCCTCTTT
3548890 CG
1 CG
3548892 GGTTTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (14 bp):
CGAATTGCCTCTTT
Found at i:3548996 original size:88 final size:92
Alignment explanation
Indices: 3548876--3549114 Score: 218
Period size: 98 Copynumber: 2.5 Consensus size: 92
3548866 TTGCCTCTTT
* * * *
3548876 CGAATTGCCTCTTTCGGGTTTTGTTT-ACATGATAGTTTGTCTGGGGGATTC-A-T-TT-GGATT
1 CGAATTG-C-CTTTCGGGGTTTGTTTCA-ATGATAGTTTCTCTGGAGGATTCAAGTATTCAGATT
* *
3548936 CGAGTGTGAGCGTTAAATACCGGTTTTTAA
63 CGAATATGAGCGTTAAATACCGGTTTTTAA
* *
3548966 CGAATTGCCTTTGGGGGTTTGTTTCAATGATAGTTTCTTTGGAGGATTCTAAAAAATGTATTCAG
1 CGAATTGCCTTTCGGGGTTTGTTTCAATGATAGTTTCTCTGGAGGATTC-----AA-GTATTCAG
* * *
3549031 ATTCGAATATGAGTGTTGAATACTGGTTTTTAA
60 ATTCGAATATGAGCGTTAAATACCGGTTTTTAA
* * *
3549064 CGAATTGCCTTTTTGGGGTTTGTTTCAATGATAGTTCTTTTTGGAGGATTC
1 CGAATTGCC-TTTCGGGGTTTGTTTCAATGATAGTT-TCTCTGGAGGATTC
3549115 TTAACTACGT
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
88 34 0.28
89 2 0.02
90 7 0.06
94 1 0.01
96 1 0.01
97 2 0.02
98 38 0.31
99 25 0.20
100 13 0.11
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.42
Consensus pattern (92 bp):
CGAATTGCCTTTCGGGGTTTGTTTCAATGATAGTTTCTCTGGAGGATTCAAGTATTCAGATTCGA
ATATGAGCGTTAAATACCGGTTTTTAA
Found at i:3549063 original size:98 final size:100
Alignment explanation
Indices: 3548932--3549151 Score: 291
Period size: 98 Copynumber: 2.2 Consensus size: 100
3548922 GATTCATTTG
* *
3548932 GATTCGAGTGTGAGCGTTAAATACCGGTTTTTAACGAATTGCC-TTTGGGGGTTTGTTTCAATGA
1 GATTCGAATATGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTTGGGGGTTTGTTTCAATGA
3548996 TAGTT-TCTTTGGAGGATTCTAAAAAATGTATTCA
66 TAGTTCTCTTTGGAGGATTCTAAAAAATGTATTCA
* * * *
3549030 GATTCGAATATGAGTGTTGAATACTGGTTTTTAACGAATTGCCTTTTTGGGGTTTGTTTCAATGA
1 GATTCGAATATGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTTGGGGGTTTGTTTCAATGA
* * ** * *
3549095 TAGTTCTTTTTGGAGGATTCTTAACTACGTTATTCG
66 TAGTTCTCTTTGGAGGATTCTAAAAAATG-TATTCA
* *
3549131 GATTCGAGTATGAGCGCTAAA
1 GATTCGAATATGAGCGTTAAA
3549152 ATGGTTTTTT
Statistics
Matches: 103, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
98 38 0.37
99 25 0.24
100 18 0.17
101 22 0.21
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (100 bp):
GATTCGAATATGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTTGGGGGTTTGTTTCAATGA
TAGTTCTCTTTGGAGGATTCTAAAAAATGTATTCA
Found at i:3549157 original size:99 final size:96
Alignment explanation
Indices: 3548931--3549160 Score: 280
Period size: 99 Copynumber: 2.3 Consensus size: 96
3548921 GGATTCATTT
* *
3548931 GGATTCGAGTGTGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTGGGGGTTTGTTTCAATGA
1 GGATTCGAGTATGAGCGTTAAA-A-TGGTTTTTAACGAATTGCCTTTGGGGGTTTGTTTCAATGA
*
3548996 TAGTTTCTTTGGAGGATTCTAAAAAATGTATTC
64 TAGTTTCTTTGGAGGATTCTAAAAAACGTATTC
* * * * *
3549029 AGATTCGAATATGAGTGTTGAATACTGGTTTTTAACGAATTGCCTTTTTGGGGTTTGTTTCAATG
1 GGATTCGAGTATGAGCGTT-AA-AATGGTTTTTAACGAATTGCC-TTTGGGGGTTTGTTTCAATG
* * **
3549094 ATAGTTCTTTTTGGAGGATTCTTAACTACGTTATTC
63 ATAGTT-TCTTTGGAGGATTCTAAAAAACG-TATTC
*
3549130 GGATTCGAGTATGAGCGCTAAAATGGTTTTT
1 GGATTCGAGTATGAGCGTTAAAATGGTTTTT
3549161 TAACTACTTT
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
98 33 0.30
99 36 0.33
100 21 0.19
101 20 0.18
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (96 bp):
GGATTCGAGTATGAGCGTTAAAATGGTTTTTAACGAATTGCCTTTGGGGGTTTGTTTCAATGATA
GTTTCTTTGGAGGATTCTAAAAAACGTATTC
Found at i:3549189 original size:54 final size:54
Alignment explanation
Indices: 3549115--3549218 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
3549105 TGGAGGATTC
** * *
3549115 TTAACTACGTTATTCGGATTCGAGTATGAGCGCTAAAAT-GGTTTTTTAACTACT
1 TTAACTACCCTATTCAGATTCGAGTATGAGCG-TAAAATCAGTTTTTTAACTACT
* *
3549169 TTAACTACCCTATTCAGATTCGAGTGTGAGCGTTAAATCAGTTTTTTAAC
1 TTAACTACCCTATTCAGATTCGAGTATGAGCGTAAAATCAGTTTTTTAAC
3549219 ATATTGCCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.12
54 38 0.88
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (54 bp):
TTAACTACCCTATTCAGATTCGAGTATGAGCGTAAAATCAGTTTTTTAACTACT
Found at i:3554037 original size:29 final size:28
Alignment explanation
Indices: 3553987--3554041 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
3553977 CTGATTTAAA
**
3553987 TTATTTAAATTCCTTTTTTAAAGAAAAAT
1 TTATTTAAATTCCTTTAATAAA-AAAAAT
3554016 TTATTTCAAATT-CTTTAATAAAAAAA
1 TTATTT-AAATTCCTTTAATAAAAAAA
3554042 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 14 0.61
30 5 0.22
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (28 bp):
TTATTTAAATTCCTTTAATAAAAAAAAT
Found at i:3556340 original size:9 final size:9
Alignment explanation
Indices: 3556326--3556350 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3556316 AGCAAAAAAT
3556326 AAATAAAGG
1 AAATAAAGG
3556335 AAATAAAGG
1 AAATAAAGG
3556344 AAATAAA
1 AAATAAA
3556351 AGTAAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (9 bp):
AAATAAAGG
Found at i:3563728 original size:170 final size:174
Alignment explanation
Indices: 3563424--3563756 Score: 451
Period size: 176 Copynumber: 1.9 Consensus size: 174
3563414 AAAAAAGTAA
* * * *
3563424 AGTGAAAATGCAATGATTCAGATCTAAATACTAAATATATACAGAGATTTGCGATCTAATATCCA
1 AGTGAAAATGCAATGATTCAGATCGAAATACTAAACATATACACAGATTTGCGATCTAATATACA
* *
3563489 AGGCATTCAAATTTAACAGAGGCAATGCAGAATTGTAGATTTCAACAAAACTTAATTTTCGAAAG
66 AGGCATTCAAATTTAACAGAGG-AATGCA-AATTGCAGATTTCAACAAAACTTAATTTCCGAAAG
*
3563554 CTACCAAAAGAAATCCAACAAAAAGTTGATGATAAAGAAAATATCG
129 CTACCAAAAGAAATCCAACAAAAAGATGATGATAAAGAAAATATCG
* * * * * *
3563600 AGTGAATATGCGATGCTTCAGATCGAAATACTGAACATATCCACAGATTTGCGATCTACTATACA
1 AGTGAAAATGCAATGATTCAGATCGAAATACTAAACATATACACAGATTTGCGATCTAATATACA
* * *
3563665 AGGTATTCAACTATTAACAGA-G-A-GC-AA-TGCAGATTTCAACAGAACTTAATTTCCGAAAGC
66 AGGCATTCAAAT-TTAACAGAGGAATGCAAATTGCAGATTTCAACAAAACTTAATTTCCGAAAGC
*
3563725 TACCGAAAGAAATCCAACAAAAAGATGATGAT
130 TACCAAAAGAAATCCAACAAAAAGATGATGAT
3563757 GTTGATGATG
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
170 60 0.43
171 2 0.01
173 2 0.01
174 1 0.01
176 66 0.47
177 8 0.06
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (174 bp):
AGTGAAAATGCAATGATTCAGATCGAAATACTAAACATATACACAGATTTGCGATCTAATATACA
AGGCATTCAAATTTAACAGAGGAATGCAAATTGCAGATTTCAACAAAACTTAATTTCCGAAAGCT
ACCAAAAGAAATCCAACAAAAAGATGATGATAAAGAAAATATCG
Found at i:3563756 original size:3 final size:3
Alignment explanation
Indices: 3563748--3563782 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3563738 CCAACAAAAA
* *
3563748 GAT GAT GAT GTT GAT GAT GAT GAT GAT GAC GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3563783 CGATAAAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3564464 original size:4 final size:4
Alignment explanation
Indices: 3564446--3564486 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
3564436 TATCAATGGA
* *
3564446 AGTG AGCG AGCG AGTG AGTG AGTG AGTG AGTG AGTTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AG-TG AGTG
3564487 GTTGTTTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.24, C:0.05, G:0.49, T:0.22
Consensus pattern (4 bp):
AGTG
Found at i:3567582 original size:3 final size:3
Alignment explanation
Indices: 3567576--3567606 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3567566 TTTTAAGCAA
3567576 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3567607 TATTTTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3571556 original size:14 final size:14
Alignment explanation
Indices: 3571523--3571573 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
3571513 AAAAATAACT
*
3571523 TAAAAAT-TCTATA
1 TAAAAATATATATA
*
3571536 TACAAAATATATATT
1 TA-AAAATATATATA
3571551 TAAAAATAT-TATA
1 TAAAAATATATATA
3571564 TAAAAA-ATAT
1 TAAAAATATAT
3571574 TGATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 2 0.06
13 12 0.38
14 12 0.38
15 6 0.19
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAAATATATATA
Found at i:3571574 original size:14 final size:14
Alignment explanation
Indices: 3571532--3571574 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3571522 TTAAAAATTC
*
3571532 TATATACAAAATA-
1 TATATAAAAAATAT
*
3571545 TATATTTAAAAATAT
1 TATA-TAAAAAATAT
3571560 TATATAAAAAATAT
1 TATATAAAAAATAT
3571574 T
1 T
3571575 GATTATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATAAAAAATAT
Found at i:3583790 original size:85 final size:84
Alignment explanation
Indices: 3583604--3583825 Score: 275
Period size: 85 Copynumber: 2.6 Consensus size: 84
3583594 AATAGTTGAG
* * * * *
3583604 TAACTATCAATATAATTTACCCTTATTAATTAAACTCGTCTCGACTCGATTTTTGTATCTTTTGT
1 TAACTATCAGTATAATTTACCATTATTAATTAAATTCGGCTCGACTCGATTTTTGTATCTTCTGT
*
3583669 GACAATCATCGATAACCGAA
66 GACAAT-ATCAATAACCGAA
* * *
3583689 TAACTATCGGTATAATTTACCTATTATTAATTAAATTTGGCTTGACTCGATTTTTGTATCTTCTG
1 TAACTATCAGTATAATTTACC-ATTATTAATTAAATTCGGCTCGACTCGATTTTTGTATCTTCTG
* *
3583754 TGTCAA-ATTCAATAATCGAA
65 TGACAATA-TCAATAACCGAA
* * *
3583774 TAACTATCTGTATAATTTACCCGTTATTAATTAAATTCGGCTCGATTCGATT
1 TAACTATCAGTATAATTTA-CCATTATTAATTAAATTCGGCTCGACTCGATT
3583826 ATAGCACCAG
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 73 0.62
86 44 0.37
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (84 bp):
TAACTATCAGTATAATTTACCATTATTAATTAAATTCGGCTCGACTCGATTTTTGTATCTTCTGT
GACAATATCAATAACCGAA
Found at i:3589378 original size:35 final size:35
Alignment explanation
Indices: 3589332--3589401 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3589322 ATTCTTCAGT
3589332 TAGTTACTTCTGCTCTTTGCCTTCCTACTGAACAG
1 TAGTTACTTCTGCTCTTTGCCTTCCTACTGAACAG
3589367 TAGTTACTTCTGCTCTTTGCCTTCCTACTGAACAG
1 TAGTTACTTCTGCTCTTTGCCTTCCTACTGAACAG
3589402 GGACGAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.14, T:0.40
Consensus pattern (35 bp):
TAGTTACTTCTGCTCTTTGCCTTCCTACTGAACAG
Found at i:3603195 original size:19 final size:19
Alignment explanation
Indices: 3603168--3603204 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3603158 AGACTGTAAC
3603168 AATGATGTTTGAAAACTTT
1 AATGATGTTTGAAAACTTT
*
3603187 AATGTTGTTTGAAAACTT
1 AATGATGTTTGAAAACTT
3603205 AGTTATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.43
Consensus pattern (19 bp):
AATGATGTTTGAAAACTTT
Found at i:3603822 original size:22 final size:23
Alignment explanation
Indices: 3603788--3603830 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3603778 GTATTTGTGT
* *
3603788 TTTTTTAATAAATAATATAATGA
1 TTTTATAATAAATAAGATAATGA
3603811 TTTTATAA-AAATAAGATAAT
1 TTTTATAATAAATAAGATAAT
3603831 TCCAAAGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
TTTTATAATAAATAAGATAATGA
Found at i:3604440 original size:30 final size:30
Alignment explanation
Indices: 3604406--3604469 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
3604396 CTATAGCTAA
*
3604406 ATTATCACTTTGA-TACTTGTA-TTTTTTATT
1 ATTATCAATTTGACTA-TTGTACTTTTTT-TT
3604436 ATTATCAATTTGACTATTGTACTTTTTTTT
1 ATTATCAATTTGACTATTGTACTTTTTTTT
3604466 ATTA
1 ATTA
3604470 GTTTGGCCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.59
Consensus pattern (30 bp):
ATTATCAATTTGACTATTGTACTTTTTTTT
Found at i:3622875 original size:28 final size:28
Alignment explanation
Indices: 3622815--3622876 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
3622805 GCGATTTCGC
3622815 GAAAAATGACCCATTCCGGTAAATAATT
1 GAAAAATGACCCATTCCGGTAAATAATT
* * *
3622843 AAAAAATCGACCCATTTCGGTAAAT-TTT
1 GAAAAAT-GACCCATTCCGGTAAATAATT
3622871 GAAAAA
1 GAAAAA
3622877 AAACGGCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (28 bp):
GAAAAATGACCCATTCCGGTAAATAATT
Found at i:3624556 original size:9 final size:9
Alignment explanation
Indices: 3624542--3624595 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
3624532 GATCAGCACT
3624542 ATGGTGATG
1 ATGGTGATG
3624551 ATGGTGATG
1 ATGGTGATG
* *
3624560 GTGGTGGTG
1 ATGGTGATG
3624569 ATGGTG--G
1 ATGGTGATG
*
3624576 -TGGTGGTG
1 ATGGTGATG
*
3624584 GTGGTGATG
1 ATGGTGATG
3624593 ATG
1 ATG
3624596 ATTACTGTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
6 5 0.14
7 1 0.03
8 1 0.03
9 30 0.81
ACGTcount: A:0.13, C:0.00, G:0.54, T:0.33
Consensus pattern (9 bp):
ATGGTGATG
Done.