Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 167 of 199
Found at i:48925925 original size:19 final size:19
Alignment explanation
Indices: 48925810--48926209 Score: 154
Period size: 19 Copynumber: 21.2 Consensus size: 19
48925800 AAATTATAAT
*
48925810 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
48925829 ATTACAATATTCATAAAAAA
1 ATTACAATATTCAT-ACAAA
*
48925849 ATTATAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
48925868 ATTACAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
48925884 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
48925898 ATTGCAATATTCATACAAA
1 ATTACAATATTCATACAAA
* *
48925917 ATTATAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
48925933 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
* *
48925947 AATATAATATTCATACAAA
1 ATTACAATATTCATACAAA
* *
48925966 ATTACAA-AAT--TACAAT
1 ATTACAATATTCATACAAA
*
48925982 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
48925996 ATTGCAATATTCATACAAAACTATAA
1 ATTACAATATTCAT-----AC-A-AA
48926022 TATTACAATATTCATACAAAAA
1 -ATTACAATATTCATAC--AAA
*
48926044 ATTTA-TATATTCATACAAA
1 A-TTACAATATTCATACAAA
48926063 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
* * *
48926084 ATTACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
48926105 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
48926127 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
48926146 ATTACAATATTCATAAAAAA
1 ATTACAATATTCAT-ACAAA
*
48926166 ATTATAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
48926187 ATTTAAAATATTCATACAAA
1 A-TTACAATATTCATACAAA
48926207 ATT
1 ATT
48926210 CTAATCTAAA
Statistics
Matches: 287, Mismatches: 44, Indels: 100
0.67 0.10 0.23
Matches are distributed among these distances:
14 24 0.08
15 5 0.02
16 33 0.11
18 13 0.05
19 80 0.28
20 49 0.17
21 32 0.11
22 26 0.09
23 6 0.02
24 1 0.00
25 3 0.01
26 2 0.01
27 13 0.05
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:48925928 original size:49 final size:49
Alignment explanation
Indices: 48925687--48926073 Score: 387
Period size: 49 Copynumber: 8.1 Consensus size: 49
48925677 TTATAAAATA
* ** * *
48925687 ATTACAATATTCATAC-AAAAAATTACAATA-T--TACAATATATCCCCAC
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAA-A-ATTACAAT
*
48925734 ATTACAATATTCATACAAAATTATAATATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATAC-AAA--A-AA-ATTATAATATTCATACAAAATTACAAT
* * *
48925783 ATTGCAATATTCATAC---AAAATTATAATA-T--TACAATATTCATACAAC
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAA-AAT--TACAAT
48925829 ATTACAATATTCAT--AAAAAAATTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
** *
48925876 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
* *
48925925 ATTACAATATTCATACAAAAAAAATATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
** * *
48925974 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
*
48926023 ATTACAATATTCATACAAAAAATTTAT-ATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
48926071 ATT
1 ATT
48926074 CATACAAAAA
Statistics
Matches: 288, Mismatches: 27, Indels: 49
0.79 0.07 0.13
Matches are distributed among these distances:
38 3 0.01
39 1 0.00
40 2 0.01
41 8 0.03
42 2 0.01
43 1 0.00
44 1 0.00
45 2 0.01
46 13 0.05
47 47 0.16
48 23 0.08
49 160 0.56
50 6 0.02
51 1 0.00
52 2 0.01
53 10 0.03
54 2 0.01
55 1 0.00
56 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.33
Consensus pattern (49 bp):
ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
Found at i:48926196 original size:22 final size:21
Alignment explanation
Indices: 48926121--48926207 Score: 99
Period size: 20 Copynumber: 4.2 Consensus size: 21
48926111 ATTTAATTAT
*
48926121 AAAATAATTACAATATTCATAC
1 AAAA-AATTAAAATATTCATAC
* *
48926143 --AACATTACAATATTCATA-
1 AAAAAATTAAAATATTCATAC
*
48926161 AAAAAATTATAATATTCATAC
1 AAAAAATTAAAATATTCATAC
48926182 AAAAAATTTAAAATATTCATAC
1 AAAAAA-TTAAAATATTCATAC
48926204 AAAA
1 AAAA
48926208 TTCTAATCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
19 15 0.26
20 18 0.32
21 6 0.11
22 18 0.32
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTAAAATATTCATAC
Found at i:48926208 original size:83 final size:83
Alignment explanation
Indices: 48925968--48926208 Score: 217
Period size: 83 Copynumber: 2.8 Consensus size: 83
48925958 CATACAAAAT
** *
48925968 TACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTACAATAT
1 TACAAAATTACAATATTCAT--AAAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATAT
*
48926033 TCATACAAAA-AATTTATATATTCA
59 TCATACAAAATAATTTAAATATTCA
* * * * *
48926057 TACAAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAA
1 TACAAAATTACAATATTCATA-AAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA
*
48926117 TTATAAAATAA-TTACAATATTCA
62 -TACAAAATAATTTA-AATATTCA
*
48926140 TACAACATTACAATATTCATAAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACA
1 TACAAAATTACAATATTCATAAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACA
48926205 AAAT
66 AAAT
48926209 TCTAATCTAA
Statistics
Matches: 123, Mismatches: 17, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
81 6 0.05
82 29 0.24
83 43 0.35
84 7 0.06
85 1 0.01
87 5 0.04
88 12 0.10
89 20 0.16
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (83 bp):
TACAAAATTACAATATTCATAAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACA
AAATAATTTAAATATTCA
Found at i:48926399 original size:14 final size:15
Alignment explanation
Indices: 48926377--48926408 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
48926367 TTCTTTCTTT
48926377 CTTCTTCTTCTTCTC
1 CTTCTTCTTCTTCTC
48926392 CTTC-TCTTCTTCTC
1 CTTCTTCTTCTTCTC
48926406 CTT
1 CTT
48926409 TCTCACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTCTTCTTCTTCTC
Found at i:48936055 original size:21 final size:23
Alignment explanation
Indices: 48936012--48936058 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
48936002 AAACTATATT
*
48936012 AAATTATTAATTTTTAAGGATAA
1 AAATAATTAATTTTTAAGGATAA
*
48936035 AAATAATT-ATTTTTAA-TATAA
1 AAATAATTAATTTTTAAGGATAA
48936056 AAA
1 AAA
48936059 GTATTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATAATTAATTTTTAAGGATAA
Found at i:48940382 original size:30 final size:30
Alignment explanation
Indices: 48940326--48940382 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
48940316 AAATTTCAAA
* *
48940326 TCTTTTTAAAGGTTGATGGTTAAATTTGAC
1 TCTTTTTAAAGGTCGATGGGTAAATTTGAC
*
48940356 TCTTTTTAAAAGGTCGA-GGGTCAATTT
1 TCTTTTT-AAAGGTCGATGGGTAAATTT
48940383 AGCTATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (30 bp):
TCTTTTTAAAGGTCGATGGGTAAATTTGAC
Found at i:48942198 original size:5 final size:5
Alignment explanation
Indices: 48942188--48942223 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
48942178 TTGGATTATT
48942188 AATTA AATTA AATTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA A
48942224 TAAATAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:48945191 original size:21 final size:21
Alignment explanation
Indices: 48945167--48945226 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
48945157 TTCTTTTGAA
*
48945167 CCTCTGCTTCTCTCGCTGTGG
1 CCTCTGCTTCTCTCGCTGTAG
48945188 CCTCTGCTTCTCTCGCTGTAG
1 CCTCTGCTTCTCTCGCTGTAG
* *
48945209 CATCTGCTTCCCTCGCTG
1 CCTCTGCTTCTCTCGCTG
48945227 CCGCCTCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.03, C:0.40, G:0.20, T:0.37
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGTAG
Found at i:48948945 original size:21 final size:22
Alignment explanation
Indices: 48948919--48948973 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
48948909 TAAAGCAGTC
*
48948919 TAAACCCCAAAC-CCCAAATCT
1 TAAACCCCAAACTCCCAAACCT
*
48948940 TAAACCCCAAACTCCTAAACCT
1 TAAACCCCAAACTCCCAAACCT
*
48948962 TAAACCCAAAAC
1 TAAACCCCAAAC
48948974 ACCATAACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.45, C:0.40, G:0.00, T:0.15
Consensus pattern (22 bp):
TAAACCCCAAACTCCCAAACCT
Found at i:48948946 original size:14 final size:15
Alignment explanation
Indices: 48948927--48948960 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
48948917 TCTAAACCCC
*
48948927 AAACCCCAAA-TCTT
1 AAACCCCAAACTCCT
48948941 AAACCCCAAACTCCT
1 AAACCCCAAACTCCT
48948956 AAACC
1 AAACC
48948961 TTAAACCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (15 bp):
AAACCCCAAACTCCT
Found at i:48948966 original size:22 final size:21
Alignment explanation
Indices: 48948919--48948982 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
48948909 TAAAGCAGTC
*
48948919 TAAACCCCAAACCCCAAATCT
1 TAAACCCCAAACCCCAAACCT
*
48948940 TAAACCCCAAACTCCTAAACCT
1 TAAACCCCAAAC-CCCAAACCT
* *
48948962 TAAACCCAAAACACCATAACC
1 TAAACCCCAAACCCCA-AACC
48948983 CACATCATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.39
22 22 0.61
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (21 bp):
TAAACCCCAAACCCCAAACCT
Found at i:48949580 original size:114 final size:111
Alignment explanation
Indices: 48949420--48949872 Score: 353
Period size: 114 Copynumber: 4.0 Consensus size: 111
48949410 TTCGGTTAAT
* * *
48949420 ATATCTTGCGGCACTTCTAAGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCAATAAGC
1 ATATCTTGCGGCGCTTCT-CGAAAGCGCCGCTAATAGTATA-TTTAGCGGCGTTTTCC-GTAAGC
*
48949485 GCCACTAATTCTAATATACCTCAATACCAAACTCTACGTTTTGGTGTGC
63 GCCACTAATTCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGC
* * * **
48949534 ATATCTTGCGGCGCTTAACT-GAAAGCGCTGCTAATACTGATATTTAGCGACGTTTTATTGTAAG
1 ATATCTTGCGGCGCTT--CTCGAAAGCGCCGCTAATAGT-ATATTTAGCGGCGTTTT-CCGTAAG
* * * *
48949598 CGCCACTAATTATATTATACATGAAGACCAAAACGT-TGA-GTTTTGGT-TAAG-
62 CGCCACTAATTCTAATATACCTCAAGACC-AAAC-TCT-ACGTTTTGGTGT--GC
* * * * * * *
48949649 AAATATAGCGGCACTTCTCCAAACGCGCCGCTAATAGTACTCTTTAGTGGCGTTTTTCCGTAAGC
1 ATATCTTGCGGCGCTTCTCGAAA-GCGCCGCTAATAGTA-TATTTAGCGGCG-TTTTCCGTAAGC
* * *
48949714 GCCACTAATCCTAATATACCTTAAGACCAAACTCTGCGTTTTGGTGTGC
63 GCCACTAATTCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGC
* ** * ** *
48949763 ATATCTTGCGGCGATTCTAAAAAATCGCCGCTAATTTTATACTTTAGCGGCGTTTTTAAC-TAA-
1 ATATCTTGCGGCGCTTCT-CGAAAGCGCCGCTAATAGTATA-TTTAGCGGCG-TTTT-CCGTAAG
* * * * * *
48949826 CGCCACTAATTGTATTATACATCGAGACCAAACCGCTACGCTTTGGT
62 CGCCACTAATTCTAATATACCTCAAGACCAAA-CTCTACGTTTTGGT
48949873 TAACATTTTT
Statistics
Matches: 266, Mismatches: 52, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
113 31 0.12
114 143 0.54
115 83 0.31
116 9 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (111 bp):
ATATCTTGCGGCGCTTCTCGAAAGCGCCGCTAATAGTATATTTAGCGGCGTTTTCCGTAAGCGCC
ACTAATTCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGC
Found at i:48949811 original size:229 final size:227
Alignment explanation
Indices: 48949427--48949857 Score: 561
Period size: 229 Copynumber: 1.9 Consensus size: 227
48949417 AATATATCTT
48949427 GCGGCACTTCTAAGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTA
1 GCGGCACTTCTAAGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTA
* * *
48949492 ATTCTAATATACCTCAATACCAAACTCTACGTTTTGGTGTGCATATCTTGCGGCGCTTAACTGAA
66 ATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGCATATCTTGCGGCGCTTAAC-AAA
* **
48949557 AGCGCTGCTAATACTGATATTTAGCGACG-TTTTATTGTAAGCGCCACTAATTATATTATACAT-
130 AGCGCCGCTAATACTGATATTTAGCGACGTTTTTA-ACTAA-CGCCACTAATTATATTATACATC
48949620 GAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATA
193 G-AGACCAAAACGTTGAGTTTTGGTTAAGAAATATA
* * * *
48949656 GCGGCACTTCTCCA-AACGCGCCGCTAATAGTACT-CTTTAGTGGCGTTTTTCC-GTAAGCGCCA
1 GCGGCACTTCT-AAGAAAGCGCCGCTAATAGTA-TACTTTAGCGGCG-TTTTCCAATAAGCGCCA
* * *
48949718 CTAATCCTAATATACCTTAAGACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGATTCTAA
63 CTAATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGCATATCTTGCGGCG-CT-TAA
* * * * *
48949783 -AAAATCGCCGCTAAT-TTTATACTTTAGCGGCGTTTTTAACTAACGCCACTAATTGTATTATAC
126 CAAAAGCGCCGCTAATACTGATA-TTTAGCGACGTTTTTAACTAACGCCACTAATTATATTATAC
48949846 ATCGAGACCAAA
190 ATCGAGACCAAA
48949858 CCGCTACGCT
Statistics
Matches: 176, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
228 33 0.19
229 126 0.72
230 14 0.08
231 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (227 bp):
GCGGCACTTCTAAGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTA
ATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGCATATCTTGCGGCGCTTAACAAAA
GCGCCGCTAATACTGATATTTAGCGACGTTTTTAACTAACGCCACTAATTATATTATACATCGAG
ACCAAAACGTTGAGTTTTGGTTAAGAAATATA
Found at i:48949985 original size:75 final size:75
Alignment explanation
Indices: 48949828--48949985 Score: 172
Period size: 75 Copynumber: 2.1 Consensus size: 75
48949818 TTAACTAACG
* * * * *
48949828 CCACTAATTGTATTATACATCGAGACCAAACCGCTACGCTTTGGTTAACATTTTTTGCGGCACTT
1 CCACTAATTCTAATATACATCAAGACCAAAACGCTACGCTTTGGTTAACATATTTTGCGGCACTT
* * *
48949893 CTATTAAGCG
66 CTAGTAAACA
* * * * * *
48949903 CCACTAATTCTAATATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGCGGCGCTT
1 CCACTAATTCTAATATACATCAAGACCAAAACGCTACGCTTTGGTTAACATATTTTGCGGCACTT
*
48949968 TTAGTAAACA
66 CTAGTAAACA
*
48949978 CCGCTAAT
1 CCACTAAT
48949986 ACTTGTTTTA
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (75 bp):
CCACTAATTCTAATATACATCAAGACCAAAACGCTACGCTTTGGTTAACATATTTTGCGGCACTT
CTAGTAAACA
Found at i:48950035 original size:188 final size:186
Alignment explanation
Indices: 48949709--48950080 Score: 410
Period size: 188 Copynumber: 2.0 Consensus size: 186
48949699 CGTTTTTCCG
* * *
48949709 TAAGCGCCACTAATCCTAATATACCTTAAGACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGG
1 TAAGCGCCACTAATCCTAATATACATCAAGACAAAACTCTGCGTTTTGGTGTGCATATCTTGCGG
* * * *
48949774 CGATTCTAAAAAATCGCCGCTAATTTTATACTTTAGCGGCGTTTTTAACTAACGCCACTAATTGT
66 CGATTCTAAAAAATCACCGCTAATCTTATA-TTTAGCGGCCTTTTTAACTAACGCCACTAATTCT
* * * *
48949839 ATTATACATCGAGACCAAACCGCTACGCTTTGGTTAACATTTTTTGCGGCACTTCTAT
130 AATATACATCGAGACCAAAACGATACGCTTTCGTTAACA-TTTTTGCGGCACTTCTAT
* * *
48949897 TAAGCGCCACTAATTCTAATATACATCAAGATCAAAACTCTGCGTTTTGGT-TATCATATTTTGC
1 TAAGCGCCACTAATCCTAATATACATCAAGA-CAAAACTCTGCGTTTTGGTGT-GCATATCTTGC
* * ** * ***
48949961 GGCGCTTTTAGTAAA-CACCGCTAATACTTGT-TTTA-CTGGCCTTTTTTTGTAAGCGCCACTAA
64 GGCGATTCTAAAAAATCACCGCTAAT-CTTATATTTAGC-GGCCTTTTTAACTAA-CGCCACTAA
* * * * *
48950023 TTCTAATATACATCGATACCAAAACGATGCGTTTTCGTTAAGATTTTTGCGGCGCTTC
126 TTCTAATATACATCGAGACCAAAACGATACGCTTTCGTTAACATTTTTGCGGCACTTC
48950081 CCACAATGCG
Statistics
Matches: 152, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
186 1 0.01
187 29 0.19
188 81 0.53
189 41 0.27
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (186 bp):
TAAGCGCCACTAATCCTAATATACATCAAGACAAAACTCTGCGTTTTGGTGTGCATATCTTGCGG
CGATTCTAAAAAATCACCGCTAATCTTATATTTAGCGGCCTTTTTAACTAACGCCACTAATTCTA
ATATACATCGAGACCAAAACGATACGCTTTCGTTAACATTTTTGCGGCACTTCTAT
Found at i:48950095 original size:113 final size:113
Alignment explanation
Indices: 48949897--48950170 Score: 291
Period size: 113 Copynumber: 2.4 Consensus size: 113
48949887 GCACTTCTAT
* * ** * *
48949897 TAAGCGCCACTAATTCTAATATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGCG
1 TAAGCGCCACTAATTCTAATATACATCAATACCAAAACGATGCGTTTTCGTTAACATATTTTGCG
** * * * **
48949962 GCGCTTTTAGTAAACACCGCTAATACTTGTTTTACTGGCCTTTTTTTG
66 GCGCTTCCAGCAAACACCGCTAATACTTGCTTTACTGGCCTTTTATCA
* *
48950010 TAAGCGCCACTAATTCTAATATACATCGATACCAAAACGATGCGTTTTCGTTAAGAT-TTTTGCG
1 TAAGCGCCACTAATTCTAATATACATCAATACCAAAACGATGCGTTTTCGTTAACATATTTTGCG
* * * * *
48950074 GCGCTTCCCA-CAATGCGCCGCTATTACTTGCTTTAGTGGCGTTTTATCA
66 GCGCTT-CCAGCAA-ACACCGCTAATACTTGCTTTACTGGCCTTTTATCA
* * ** *
48950123 TAATCGCCACTAATTATTGTATACATCAATACAAAAACGATGCGTTTT
1 TAAGCGCCACTAATTCTAATATACATCAATACCAAAACGATGCGTTTT
48950171 GGTCTTGAGA
Statistics
Matches: 133, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
112 15 0.11
113 118 0.89
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (113 bp):
TAAGCGCCACTAATTCTAATATACATCAATACCAAAACGATGCGTTTTCGTTAACATATTTTGCG
GCGCTTCCAGCAAACACCGCTAATACTTGCTTTACTGGCCTTTTATCA
Found at i:48951187 original size:25 final size:24
Alignment explanation
Indices: 48951120--48951187 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
48951110 ATGAAAATGT
*
48951120 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
48951143 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
48951168 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
48951188 AAAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:48951278 original size:21 final size:21
Alignment explanation
Indices: 48951248--48951287 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48951238 TAATTGAATA
* *
48951248 AATAATAATACATGATAAAGG
1 AATAAAAATACATAATAAAGG
48951269 AATAAAAATACATAATAAA
1 AATAAAAATACATAATAAA
48951288 ATAAAATAAA
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:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (21 bp):
AATAAAAATACATAATAAAGG
Found at i:48951352 original size:12 final size:12
Alignment explanation
Indices: 48951336--48951371 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
48951326 AATAACATCT
48951336 ATAATAATAGTA
1 ATAATAATAGTA
*
48951348 GTAATAATAGTA
1 ATAATAATAGTA
48951360 ATAATAATAGTA
1 ATAATAATAGTA
48951372 TTATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:48961534 original size:36 final size:36
Alignment explanation
Indices: 48961487--48961558 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
48961477 CTTGGCTTTA
48961487 GACACCAAAACCAAGACTTAGTTTAGCTGCATTTGT
1 GACACCAAAACCAAGACTTAGTTTAGCTGCATTTGT
*
48961523 GACACCAAAACCAAGACTTAGTTTCGCTGCATTTGT
1 GACACCAAAACCAAGACTTAGTTTAGCTGCATTTGT
48961559 ACCACGACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (36 bp):
GACACCAAAACCAAGACTTAGTTTAGCTGCATTTGT
Found at i:48968004 original size:45 final size:45
Alignment explanation
Indices: 48967891--48968287 Score: 462
Period size: 45 Copynumber: 8.9 Consensus size: 45
48967881 GGATTTATTG
* * * * * *
48967891 CTTCAATCTACTTCACT-CTAACTTTAGGGAGATTAGACTTG-TAG
1 CTTCAATCTGCTCCACTGC-AACTTCAGGGAGATAAGATTTGCTAT
* *
48967935 CTTTAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* * **
48967980 CTTCAAT-TCACTCCACTACAACTTCAGGGAGATAAGATTTATTAT
1 CTTCAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* *
48968025 CTTCAATCTGCTCCACTGCCACTTCAGGGAAATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* *
48968070 CTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* *
48968115 CTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* *
48968160 CTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* * * * **
48968205 CTTCAAACTACTTCAATGCAACTTCAGGGAGATAAGATTTG-TGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
* * **
48968249 CTT-AAACTTGCTCTACTGCAACTTCAGAAAGATAAGATT
1 CTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATT
48968288 CGCCATGCTG
Statistics
Matches: 306, Mismatches: 42, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
43 4 0.01
44 62 0.20
45 239 0.78
46 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
Found at i:48974945 original size:41 final size:40
Alignment explanation
Indices: 48974888--48974976 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 40
48974878 TGTAGGCCAT
48974888 TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAA
1 TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAA
48974928 CTTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAA
1 -TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAA
*
48974969 TTAGCCCA
1 TTTGCCCA
48974977 AAACCCTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 7 0.15
41 40 0.85
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (40 bp):
TTTGCCCAGGCCCAATTACAACCCAAACCCAAACTAAAAA
Found at i:48974992 original size:40 final size:41
Alignment explanation
Indices: 48974898--48974994 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
48974888 TTTGCCCAGG
* **
48974898 CCCAATTACAACCCAAACCCAAACTAAAAACTTTGCCCAGG
1 CCCAATTACAACCCAAACCCAAACTAAAAACTTAGCCCAAA
48974939 CCCAATTACAACCCAAACCCAAACTAAAAA-TTAGCCCAAAA
1 CCCAATTACAACCCAAACCCAAACTAAAAACTTAGCCC-AAA
*
48974980 CCCTATTA-AACCCAA
1 CCCAATTACAACCCAA
48974995 GCCCGGAGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 13 0.25
41 38 0.75
ACGTcount: A:0.45, C:0.36, G:0.04, T:0.14
Consensus pattern (41 bp):
CCCAATTACAACCCAAACCCAAACTAAAAACTTAGCCCAAA
Found at i:48975360 original size:22 final size:21
Alignment explanation
Indices: 48975335--48975376 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48975325 CGGCTGGAAA
48975335 AAGAACACAAAAAAACAGTTTC
1 AAGAA-ACAAAAAAACAGTTTC
*
48975357 AAGAAATAAAAAAACAGTTT
1 AAGAAACAAAAAAACAGTTT
48975377 AAAAGGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.17
Consensus pattern (21 bp):
AAGAAACAAAAAAACAGTTTC
Found at i:48976928 original size:108 final size:108
Alignment explanation
Indices: 48976736--48977053 Score: 453
Period size: 108 Copynumber: 2.9 Consensus size: 108
48976726 TTTCTAATTG
*
48976736 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
** *
48976801 CGTTTAACCAAATACCTTAATATCCTTTTAAATTTTTAAAATA
66 CGTTTAACCAAATGGCTTAATATCCTTTTAAATTTTCAAAATA
48976844 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
48976909 CGTTCAACCAAATGGCTTAATATCCTTTCCAAAAAAATTACAAAATA
66 CGTTTAACCAAATGGCTTAATATCCTTT----TAAATTTTCAAAATA
* *
48976956 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACATGCCCTAAGGTGCTGGGTATCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
** * *
48977018 CGTTTAACCAAATGGCCAAATATCCTCTTGAATTTT
66 CGTTTAACCAAATGGCTTAATATCCTTTTAAATTTT
48977054 AATCCATGCC
Statistics
Matches: 188, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
105 4 0.02
108 89 0.47
109 29 0.15
111 26 0.14
112 40 0.21
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (108 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTTAACCAAATGGCTTAATATCCTTTTAAATTTTCAAAATA
Found at i:48987279 original size:15 final size:17
Alignment explanation
Indices: 48987259--48987294 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
48987249 CTTTGCTTCC
48987259 TAAAAAAT-AA-AAAAA
1 TAAAAAATAAATAAAAA
48987274 TAAAAAATAAATAAAAA
1 TAAAAAATAAATAAAAA
48987291 TAAA
1 TAAA
48987295 CTTTGGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
TAAAAAATAAATAAAAA
Found at i:48988748 original size:44 final size:44
Alignment explanation
Indices: 48988511--48988758 Score: 216
Period size: 44 Copynumber: 5.7 Consensus size: 44
48988501 GAAGAATTGC
* *
48988511 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA-
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTCAG
** * * * ** * *
48988554 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTCAG
* * * ** * *
48988598 GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA-TCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTCAG
* * * ***
48988641 -G-TCTTACCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAG--TCAG
* *
48988685 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTCAG
48988729 AGATCTTATCTCCCTGAGGTTACAGTGGAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAG
48988759 TGGATCACAT
Statistics
Matches: 158, Mismatches: 41, Indels: 11
0.75 0.20 0.05
Matches are distributed among these distances:
41 29 0.18
42 1 0.01
43 35 0.22
44 59 0.37
45 1 0.01
46 33 0.21
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTCAG
Found at i:48988776 original size:131 final size:128
Alignment explanation
Indices: 48988514--48988782 Score: 308
Period size: 131 Copynumber: 2.1 Consensus size: 128
48988504 GAATTGCAGA
* *
48988514 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGACACGATCCTATCTCCCTGAAGTTACAG
* ** * * *
48988579 TGGAGCGGATTAAAATGAGGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGG
66 TGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCACATCAGG
* * * * *
48988642 TCTTACCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGACA---C-GATCCTATCTCCCTGAAGTT
* * * ** *
48988706 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGGTTACAGTGGAGTGGATCACATCC
62 ACAGTGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCACAT-C
48988771 A-G
126 AGG
48988773 TCTTATCTCC
1 TCTTATCTCC
48988783 TTGACATTGC
Statistics
Matches: 116, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
127 1 0.01
128 34 0.29
130 1 0.01
131 78 0.67
132 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGACACGATCCTATCTCCCTGAAGTTACAG
TGGAGCAGATTAAAACCAGAGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCACATCAGG
Found at i:48989111 original size:41 final size:40
Alignment explanation
Indices: 48989054--48989138 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 40
48989044 GGCCATTTTG
*
48989054 CCCAGGCCCAATTACAACCCAAACCCAAACTAAAAACTTTA
1 CCCAGGCCCAATTACAACCCAAACCCAAACTAAAAA-TTAA
48989095 CCCAGGCCCAATTACAACCCAAACCCAAACTAAAAATTAA
1 CCCAGGCCCAATTACAACCCAAACCCAAACTAAAAATTAA
48989135 CCCA
1 CCCA
48989139 AAACCCTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 7 0.16
41 36 0.84
ACGTcount: A:0.45, C:0.38, G:0.05, T:0.13
Consensus pattern (40 bp):
CCCAGGCCCAATTACAACCCAAACCCAAACTAAAAATTAA
Found at i:48991096 original size:108 final size:109
Alignment explanation
Indices: 48990907--48991211 Score: 474
Period size: 108 Copynumber: 2.8 Consensus size: 109
48990897 CTAATTGAGA
*
48990907 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
* **
48990972 TTAACCAAATGGCTTAATATCCTTT-TAAAATTTTAAAATAAGG
66 TTAACCAAATGGCTTAATATCCTTTAAAAAATTACAAAATAAGG
48991015 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
*
48991080 TCAACCAAATGGCTTAATATCCTTTCCAAAAAAATTACAAAATAAGG
66 TTAACCAAATGGCTTAATATCCTTT---AAAAAATTACAAAATAAGG
* *
48991127 CAATGTTTTGCGTTTGGAAATTCGAG-GAACATGCCCTAAGGTGCTGGGTATCGA--TTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
**
48991189 TTAACCAAATGGCCAAATATCCT
66 TTAACCAAATGGCTTAATATCCT
48991212 CTTGAATTTT
Statistics
Matches: 183, Mismatches: 10, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
108 88 0.48
109 28 0.15
111 26 0.14
112 41 0.22
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
TTAACCAAATGGCTTAATATCCTTTAAAAAATTACAAAATAAGG
Found at i:48992247 original size:169 final size:169
Alignment explanation
Indices: 48991968--48992308 Score: 637
Period size: 169 Copynumber: 2.0 Consensus size: 169
48991958 TTTCGCTGCC
48991968 ACCTCTCTCCATCTTTGAACGTACTACTTAAAGCTTTCACTTGGCTTCTTTTCCATGTTTTGCAA
1 ACCTCTCTCCATCTTTGAACGTACTACTTAAAGCTTTCACTTGGCTTCTTTTCCATGTTTTGCAA
*
48992033 CGTAATTCTATCAGGTGTCATGTTGGTCACATGGCTGTATTGTTTCATTAAAGCCTGTACCAGGT
66 CGTAATTCTATCAGGTGTCATATTGGTCACATGGCTGTATTGTTTCATTAAAGCCTGTACCAGGT
*
48992098 CTTTCCATGAGTTGATTTTAGCACGGCTTAGTTAGTTGT
131 CTTTCCACGAGTTGATTTTAGCACGGCTTAGTTAGTTGT
48992137 ACCTCTCTCCATCTTTGAACGTACTACTTAAAGCTTTCACTTGGCTTCTTTTCCATGTTTTGCAA
1 ACCTCTCTCCATCTTTGAACGTACTACTTAAAGCTTTCACTTGGCTTCTTTTCCATGTTTTGCAA
* **
48992202 CGTAATTCTATCAGGTGTCATATTGGTCACATGGCTGTATTGTTTCTTTAAAGCCTGTGTCAGGT
66 CGTAATTCTATCAGGTGTCATATTGGTCACATGGCTGTATTGTTTCATTAAAGCCTGTACCAGGT
48992267 CTTTCCACGAGTTGATTTTAGCACGGCTTAGTTAGTTGT
131 CTTTCCACGAGTTGATTTTAGCACGGCTTAGTTAGTTGT
48992306 ACC
1 ACC
48992309 ACTTGGTGAC
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
169 167 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (169 bp):
ACCTCTCTCCATCTTTGAACGTACTACTTAAAGCTTTCACTTGGCTTCTTTTCCATGTTTTGCAA
CGTAATTCTATCAGGTGTCATATTGGTCACATGGCTGTATTGTTTCATTAAAGCCTGTACCAGGT
CTTTCCACGAGTTGATTTTAGCACGGCTTAGTTAGTTGT
Found at i:49000261 original size:41 final size:41
Alignment explanation
Indices: 49000216--49000323 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
49000206 AATTCGGCCA
* * *
49000216 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
49000257 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
49000298 AACATGTAGTGGCAGCATTAAATTCG
1 AACATGTAGTGGCAGCATTAAATTCG
49000324 ACATATTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
Found at i:49007293 original size:18 final size:19
Alignment explanation
Indices: 49007266--49007303 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
49007256 CTTACACGCG
49007266 GACGACGACGACAA-TGAT
1 GACGACGACGACAACTGAT
*
49007284 GACGAGGACGACAACTGAT
1 GACGACGACGACAACTGAT
49007303 G
1 G
49007304 TATATTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.37, C:0.21, G:0.32, T:0.11
Consensus pattern (19 bp):
GACGACGACGACAACTGAT
Found at i:49011026 original size:20 final size:20
Alignment explanation
Indices: 49011001--49011043 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
49010991 ATTTAGATTT
*
49011001 ATTTAAAATAAAAATATAAA
1 ATTTAAAATAAAAATAAAAA
*
49011021 ATTTAAATTAAAAATAAAAA
1 ATTTAAAATAAAAATAAAAA
49011041 ATT
1 ATT
49011044 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAAATAAAAATAAAAA
Found at i:49011515 original size:29 final size:30
Alignment explanation
Indices: 49011483--49011548 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
49011473 TTTTCTAAAA
*
49011483 TTTAAATATATTTTTTAAAATTTT-GAATT
1 TTTAAATATATATTTTAAAATTTTAGAATT
* * *
49011512 TTTATATTTATATTTTAGAATTTTAGAATT
1 TTTAAATATATATTTTAAAATTTTAGAATT
49011542 TTATAAA
1 TT-TAAA
49011549 AAATTGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 20 0.67
30 7 0.23
31 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (30 bp):
TTTAAATATATATTTTAAAATTTTAGAATT
Found at i:49011734 original size:31 final size:30
Alignment explanation
Indices: 49011668--49011738 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
49011658 CTTCTCCTAA
* **
49011668 ATTGGTACTTATAATTTTTTTTTGTCCCAG
1 ATTGGTACCTATAATTTTTTTCCGTCCCAG
49011698 ATTGGTACCTA-AATTTTTTTCCGTCCACTAG
1 ATTGGTACCTATAATTTTTTTCCGTCC-C-AG
*
49011729 TTTGGTACCT
1 ATTGGTACCT
49011739 GAGCCTAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.37
30 11 0.31
31 11 0.31
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (30 bp):
ATTGGTACCTATAATTTTTTTCCGTCCCAG
Found at i:49013684 original size:33 final size:32
Alignment explanation
Indices: 49013629--49013855 Score: 90
Period size: 33 Copynumber: 6.8 Consensus size: 32
49013619 ACGTTCATAG
* *
49013629 TGCCATAACAC-AATTATAGTCTTATCATTAGAA
1 TGCCATAAC-CTAACTATGGTCTTATCATTA-AA
*
49013662 TGCCATAACCTAGCTATGGTCTTA-CATGTATACA
1 TGCCATAACCTAACTATGGTCTTATCAT-TA-A-A
*** *
49013696 CTGCCATGGTCTAACCATGGTCTTATGTCCATT--A
1 -TGCCATAACCTAACTATGGTCTTA--T-CATTAAA
**
49013730 TGCCATAACCTAGTTATGGTCTTA-CATGTATACA
1 TGCCATAACCTAACTATGGTCTTATCAT-TA-A-A
*** *
49013764 CTGCCATGGTCTAACCATGGTCTTATGTCCATT--A
1 -TGCCATAACCTAACTATGGTCTTA--T-CATTAAA
*** *
49013798 TGCCATAACCTGGTTATGGTCTTATCATCAGAA
1 TGCCATAACCTAACTATGGTCTTATCATTA-AA
*
49013831 TGCCATAGCCTAACTATGGTCTTAT
1 TGCCATAACCTAACTATGGTCTTAT
49013856 AATTTCATAG
Statistics
Matches: 140, Mismatches: 33, Indels: 42
0.65 0.15 0.20
Matches are distributed among these distances:
29 3 0.02
30 4 0.03
31 1 0.01
32 4 0.03
33 79 0.56
34 4 0.03
35 37 0.26
38 2 0.01
39 6 0.04
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (32 bp):
TGCCATAACCTAACTATGGTCTTATCATTAAA
Found at i:49013716 original size:35 final size:35
Alignment explanation
Indices: 49013677--49013788 Score: 115
Period size: 35 Copynumber: 3.3 Consensus size: 35
49013667 TAACCTAGCT
49013677 ATGGTCTTACATGTATACACTGCCATGGTCTAACC
1 ATGGTCTTACATGTATACACTGCCATGGTCTAACC
* *** ***
49013712 ATGGTCTT--ATGTCCAT-TA-TGCCATAACCTAGTT
1 ATGGTCTTACATGT--ATACACTGCCATGGTCTAACC
49013745 ATGGTCTTACATGTATACACTGCCATGGTCTAACC
1 ATGGTCTTACATGTATACACTGCCATGGTCTAACC
49013780 ATGGTCTTA
1 ATGGTCTTA
49013789 TGTCCATTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
33 23 0.40
34 2 0.04
35 32 0.56
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (35 bp):
ATGGTCTTACATGTATACACTGCCATGGTCTAACC
Found at i:49013721 original size:68 final size:66
Alignment explanation
Indices: 49013661--49013821 Score: 259
Period size: 68 Copynumber: 2.4 Consensus size: 66
49013651 TATCATTAGA
49013661 ATGCCATAACCTAGCTATGGTCTTACATGTATACACTGCCATGGTCTAACCATGGTCTTATGTCC
1 ATGCCATAACCTAGCTATGGTCTTACATGTATACACTGCCATGGTCTAACCATGGTCTTA--TCC
49013726 ATT
64 ATT
*
49013729 ATGCCATAACCTAGTTATGGTCTTACATGTATACACTGCCATGGTCTAACCATGGTCTTATGTCC
1 ATGCCATAACCTAGCTATGGTCTTACATGTATACACTGCCATGGTCTAACCATGGTCTTA--TCC
49013794 ATT
64 ATT
* *
49013797 ATGCCATAACCTGGTTATGGTCTTA
1 ATGCCATAACCTAGCTATGGTCTTA
49013822 TCATCAGAAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 91 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (66 bp):
ATGCCATAACCTAGCTATGGTCTTACATGTATACACTGCCATGGTCTAACCATGGTCTTATCCAT
T
Found at i:49018641 original size:15 final size:15
Alignment explanation
Indices: 49018623--49018669 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
49018613 AAGTTTTTTA
49018623 ATTTTATTATTAAAC
1 ATTTTATTATTAAAC
* *
49018638 ATTTTACTCTTAAAC
1 ATTTTATTATTAAAC
*
49018653 ATTTTCCTTATTAAAC
1 ATTTT-ATTATTAAAC
49018669 A
1 A
49018670 CTTGTCCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTTATTATTAAAC
Found at i:49018668 original size:16 final size:16
Alignment explanation
Indices: 49018629--49018682 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
49018619 TTTAATTTTA
*
49018629 TTATTAAACATTTTAC
1 TTATTAAACATTTTCC
*
49018645 -TCTTAAACATTTTCC
1 TTATTAAACATTTTCC
*
49018660 TTATTAAACACTTGTCC
1 TTATTAAACA-TTTTCC
49018677 TT-TTAA
1 TTATTAA
49018683 TTTTATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 13 0.41
16 12 0.38
17 7 0.22
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (16 bp):
TTATTAAACATTTTCC
Found at i:49020469 original size:50 final size:50
Alignment explanation
Indices: 49020354--49020595 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
49020344 ACATGCCGAA
* ** * * ***
49020354 GCCATGTCCCAGACATGGTCTTACATGAGATGTTCTTATATCGGTGCCCGT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAAC
**
49020405 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
*
49020455 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* *
49020505 GCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAAC
* *
49020561 GCCATTTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
49020596 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 94 0.57
51 27 0.16
53 5 0.03
55 2 0.01
56 38 0.23
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:49022299 original size:19 final size:20
Alignment explanation
Indices: 49022270--49022308 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
49022260 TTCAAAGTTT
*
49022270 CCATAATAGGTATCGATACC
1 CCATAATAGGTACCGATACC
49022290 CCAT-ATAGGTACCGATACC
1 CCATAATAGGTACCGATACC
49022309 ATTTAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (20 bp):
CCATAATAGGTACCGATACC
Found at i:49025047 original size:27 final size:26
Alignment explanation
Indices: 49025017--49025071 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
49025007 AGAAATTTGC
*
49025017 TAAGCAACTC-AATGTTTAGTACACATA
1 TAAGCAACTCGAATGCTTA--ACACATA
*
49025044 TAAGCACCTCGAATGCTTAACACATA
1 TAAGCAACTCGAATGCTTAACACATA
49025070 TA
1 TA
49025072 CAATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 9 0.36
28 7 0.28
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (26 bp):
TAAGCAACTCGAATGCTTAACACATA
Found at i:49027729 original size:43 final size:42
Alignment explanation
Indices: 49027652--49027822 Score: 170
Period size: 43 Copynumber: 4.0 Consensus size: 42
49027642 CATAGGATTT
* *
49027652 TCGATATGTG-TTATCGTGTAAAACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACATTGGCA
* * *
49027695 TCGACTTGTGTTTACGTGTAAGACCATGTTTGGGACATTGGCA
1 TCGA-TTGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
* *
49027738 TTGTATT-TGATT-CGTGTAAGACC-CTGTCTGGGACAATGGCA
1 TCG-ATTGTGATTACGTGTAAGACCAC-GTCTGGGACATTGGCA
* * *
49027779 TCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGGCA
1 TCGAT-TGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
49027822 T
1 T
49027823 TGTACGAGTC
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
40 2 0.02
41 28 0.26
42 9 0.08
43 61 0.58
44 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
TCGATTGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:49027813 original size:84 final size:84
Alignment explanation
Indices: 49027665--49027826 Score: 211
Period size: 84 Copynumber: 1.9 Consensus size: 84
49027655 ATATGTGTTA
** * * ** *
49027665 TCGTGTAAAACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTTTGGGA
1 TCGTGTAAAACCACGTCTGGGACAATGGCATCGACTTGTGATTACATGTAAGACCACATCTGGGA
49027730 CATTGGCATTGTATTTGAT
66 CATTGGCATTGTATTTGAT
*
49027749 TCGTGTAAGACC-CTGTCTGGGACAATGGCATCGA-TATGTGATTACATGTAAGACCACATCTGG
1 TCGTGTAAAACCAC-GTCTGGGACAATGGCATCGACT-TGTGATTACATGTAAGACCACATCTGG
*
49027812 GACGTTGGCATTGTA
64 GACATTGGCATTGTA
49027827 CGAGTCTTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 2 0.03
84 65 0.97
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (84 bp):
TCGTGTAAAACCACGTCTGGGACAATGGCATCGACTTGTGATTACATGTAAGACCACATCTGGGA
CATTGGCATTGTATTTGAT
Found at i:49029687 original size:42 final size:42
Alignment explanation
Indices: 49029631--49029721 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
49029621 ACTTAAGTTC
49029631 TTTAT-CTTCACTTACCAATGTTCATGCCAAGTTTCTTTGTT
1 TTTATGCTTCACTTACCAATGTTCATGCCAAGTTTCTTTGTT
49029672 TTTATGCTTCACTTACCAATGTTCATGCCAAGTTTCTTTGTT
1 TTTATGCTTCACTTACCAATGTTCATGCCAAGTTTCTTTGTT
49029714 TTTATGCT
1 TTTATGCT
49029722 AAGTTCACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 5 0.10
42 44 0.90
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (42 bp):
TTTATGCTTCACTTACCAATGTTCATGCCAAGTTTCTTTGTT
Found at i:49033932 original size:18 final size:19
Alignment explanation
Indices: 49033879--49033935 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
49033869 ATTACAAAAA
*
49033879 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
49033898 CAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
49033917 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
49033935 A
1 A
49033936 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:49037329 original size:12 final size:12
Alignment explanation
Indices: 49037312--49037341 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
49037302 GGTATGCAGA
49037312 ATCTTGTTTTTT
1 ATCTTGTTTTTT
49037324 ATCTTG-TTTTT
1 ATCTTGTTTTTT
49037335 ATCTTGT
1 ATCTTGT
49037342 CCAAATTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.70
Consensus pattern (12 bp):
ATCTTGTTTTTT
Found at i:49040374 original size:19 final size:21
Alignment explanation
Indices: 49040337--49040375 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
49040327 TATTTTTAAT
49040337 GTTCAAATTCTTTGATAAGAG
1 GTTCAAATTCTTTGATAAGAG
*
49040358 GTTC-AATT-TTTGTTAAGA
1 GTTCAAATTCTTTGATAAGA
49040376 TGTTAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (21 bp):
GTTCAAATTCTTTGATAAGAG
Found at i:49042930 original size:7 final size:7
Alignment explanation
Indices: 49042915--49042944 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49042905 TATTTTGTCA
*
49042915 TCACACT
1 TCACCCT
49042922 TCACCCT
1 TCACCCT
49042929 TCACCCT
1 TCACCCT
49042936 TCACCCT
1 TCACCCT
49042943 TC
1 TC
49042945 GTACTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.53, G:0.00, T:0.30
Consensus pattern (7 bp):
TCACCCT
Found at i:49052793 original size:9 final size:9
Alignment explanation
Indices: 49052773--49052839 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
49052763 GTAGTGATTC
*
49052773 AATTCAGTT
1 AATTCGGTT
*
49052782 AATTCGGGT
1 AATTCGGTT
49052791 AATTCGGTT
1 AATTCGGTT
49052800 AATTCGGTT
1 AATTCGGTT
* *
49052809 AATTTGGGT
1 AATTCGGTT
*
49052818 AATTTGGTT
1 AATTCGGTT
49052827 AATTCGGTT
1 AATTCGGTT
49052836 AATT
1 AATT
49052840 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:49052840 original size:27 final size:27
Alignment explanation
Indices: 49052773--49052840 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
49052763 GTAGTGATTC
* *
49052773 AATTCAGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTTGGGTAATTCGGTT
*
49052800 AATTCGGTTAATTTGGGTAATTTGGTT
1 AATTCGGTTAATTTGGGTAATTCGGTT
49052827 AATTCGGTTAATTT
1 AATTCGGTTAATTT
49052841 TTAACCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
AATTCGGTTAATTTGGGTAATTCGGTT
Found at i:49059922 original size:16 final size:16
Alignment explanation
Indices: 49059879--49059927 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
49059869 ATAGCACGTT
*
49059879 TGGAATAGAGGCGTAA
1 TGGAATAGAGGTGTAA
49059895 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
* *
49059911 TGGATTAGAGGTATAA
1 TGGAATAGAGGTGTAA
49059927 T
1 T
49059928 AGTATTCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.35, T:0.27
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:49060145 original size:27 final size:26
Alignment explanation
Indices: 49060081--49060145 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
49060071 TCAATAATAA
*
49060081 ATAATTTAATCATATTTAAACATAATT
1 ATAATTTAAT-ATATTTAAACAAAATT
* * **
49060108 ATTATTAAATATATTATAATTAAAATT
1 ATAATTTAATATATT-TAAACAAAATT
49060135 ATAATTTAATA
1 ATAATTTAATA
49060146 AAATTCTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATTTAATATATTTAAACAAAATT
Found at i:49060233 original size:119 final size:121
Alignment explanation
Indices: 49060094--49060321 Score: 401
Period size: 121 Copynumber: 1.9 Consensus size: 121
49060084 ATTTAATCAT
49060094 ATTTAAACATAATTATTATTAAATATATTATAATTAAA-AT-TA-TAATTTAATAAAATTCTTAA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAATATATATTAA-TTAATAAAATTCTTAA
*
49060156 TAGTTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 TAATTAATATTCTTATATGAATTTACTCAAATCATAATATA-GATACTATAAAATATA
49060214 ATTT-AACATAATTATTATTAAATATATTATAATTAAATATATATTAATTAATAAAATTCTTAAT
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAATATATATTAATTAATAAAATTCTTAAT
49060278 AATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
66 AATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
49060322 ATTTAACATA
Statistics
Matches: 104, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
119 33 0.32
120 10 0.10
121 58 0.56
122 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAATATATATTAATTAATAAAATTCTTAAT
AATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATACTATAAAATATA
Found at i:49060242 original size:15 final size:15
Alignment explanation
Indices: 49060224--49060264 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
49060214 ATTTAACATA
49060224 ATTATTATTAAATAT
1 ATTATTATTAAATAT
*
49060239 ATTATAATTAAATAT
1 ATTATTATTAAATAT
49060254 A-TATTAATTAA
1 ATTATT-ATTAA
49060265 TAAAATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATTATTAAATAT
Found at i:49060712 original size:13 final size:13
Alignment explanation
Indices: 49060694--49060718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49060684 GCCTTAAAAA
49060694 GAGCAGCACTCAT
1 GAGCAGCACTCAT
49060707 GAGCAGCACTCA
1 GAGCAGCACTCA
49060719 AAACAGATTT
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:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
GAGCAGCACTCAT
Found at i:49065410 original size:16 final size:16
Alignment explanation
Indices: 49065389--49066184 Score: 483
Period size: 16 Copynumber: 51.9 Consensus size: 16
49065379 TGTATGTAAT
*
49065389 TTATGTAATTTATGTA
1 TTATGTAAGTTATGTA
*
49065405 TTATGTATGTTATG--
1 TTATGTAAGTTATGTA
*
49065419 -TAT-TAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
49065433 TTATGTAAGCTGTGTA
1 TTATGTAAGTTATGTA
49065449 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* *
49065465 ATATGTAATTTATGTA
1 TTATGTAAGTTATGTA
49065481 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* *
49065497 ATATGTAATTTATGTA
1 TTATGTAAGTTATGTA
*
49065513 TTATGTAATTTATGTAA
1 TTATGTAAGTTATGT-A
49065530 GTTATGT-A-TTATGTA
1 -TTATGTAAGTTATGTA
*
49065545 TTATGTATGTTATGTA
1 TTATGTAAGTTATGTA
*
49065561 TAATAT-TAA-TTAAG--
1 T--TATGTAAGTTATGTA
*
49065575 TTGTGT-A-TTATGTA
1 TTATGTAAGTTATGTA
*
49065589 TTATGTATGTTATGTA
1 TTATGTAAGTTATGTA
*
49065605 TTATGTTAGTTATGTA
1 TTATGTAAGTTATGTA
*
49065621 CTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
49065637 TTATGTTAGTTATGTA
1 TTATGTAAGTTATGTA
*
49065653 CTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
49065669 TTATGTATGTTATGTAA
1 TTATGTAAGTTATGT-A
49065686 GTTATGT-A-TTATGTATA
1 -TTATGTAAGTTATG--TA
*
49065703 TTATGTATTAAGTTGTGTA
1 TTATG---TAAGTTATGTA
* *
49065722 TTATGTAAGCTGTGTA
1 TTATGTAAGTTATGTA
49065738 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* *
49065754 ATATGTAATTTATGTAA
1 TTATGTAAGTTATGT-A
49065771 GTTATGT-A-TTATGTA
1 -TTATGTAAGTTATGTA
*
49065786 TTATGTATGTTATGTA
1 TTATGTAAGTTATGTA
*
49065802 TAATAT-TAA-TTAAG--
1 T--TATGTAAGTTATGTA
*
49065816 TTGTGT-A-TTATGTA
1 TTATGTAAGTTATGTA
*
49065830 TTATGTATGTTATGTA
1 TTATGTAAGTTATGTA
*
49065846 TAATAT-TAA-TTAAG--
1 T--TATGTAAGTTATGTA
*
49065860 TTGTGT-A-TTATGTA
1 TTATGTAAGTTATGTA
*
49065874 TTATGTATGTTATGTA
1 TTATGTAAGTTATGTA
*
49065890 TTATGTTAGTTATGTA
1 TTATGTAAGTTATGTA
*
49065906 CTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
49065922 TTA--T--G-TATG--
1 TTATGTAAGTTATGTA
*
49065931 TTATTTAAGTTATGTA
1 TTATGTAAGTTATGTA
* *
49065947 TAATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
49065963 TTATGT-A-TTATGTCTA
1 TTATGTAAGTTATG--TA
49065979 TTATGT-A--TAT-TA
1 TTATGTAAGTTATGTA
*
49065991 TTAAT-TAAGTTGTGTA
1 TT-ATGTAAGTTATGTA
49066007 TTATGT-A-TTATGTA
1 TTATGTAAGTTATGTA
*
49066021 TGTTATGT-A--TA-ATA
1 --TTATGTAAGTTATGTA
** *
49066035 TTAACTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
49066051 TAATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
49066067 --A-G-AA---ATGTA
1 TTATGTAAGTTATGTA
*
49066076 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
49066092 -TA---ATGTTA-G--
1 TTATGTAAGTTATGTA
**
49066101 TTATCAAAGTTATGTA
1 TTATGTAAGTTATGTA
*
49066117 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATGT-A
49066134 GTTATGTAAGTTATGTA
1 -TTATGTAAGTTATGTA
49066151 TTATGTAAGTTATCATGTTA
1 TTATGTAAG-T-T-ATG-TA
49066171 TTATGTAAGTTATG
1 TTATGTAAGTTATG
49066185 CAAGTTTATA
Statistics
Matches: 616, Mismatches: 81, Indels: 165
0.71 0.09 0.19
Matches are distributed among these distances:
9 8 0.01
10 2 0.00
11 7 0.01
12 45 0.07
13 19 0.03
14 49 0.08
15 19 0.03
16 378 0.61
17 18 0.03
18 43 0.07
19 12 0.02
20 12 0.02
21 4 0.01
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.51
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:49065972 original size:184 final size:183
Alignment explanation
Indices: 49065687--49066157 Score: 607
Period size: 184 Copynumber: 2.6 Consensus size: 183
49065677 GTTATGTAAG
* * *
49065687 TTATGTATTATGTATATTATGTATTA---AGTTGTGTATTATGTAAGCTGTGTATTATGTAAGTT
1 TTATGTATTATGTATGTTATGTATTATGTAGTTGTGTA-TATGTAAGTTATGTATTATGT-AGTT
* *
49065749 ATGTAA--TATGTAATTTATGTAAGTTATGTATTATGTATTATGTATGTTATGTATAATATTAAT
64 ATGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTATTATGTATATTATGTATAATATTAAT
*
49065812 TAAGTTGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTA
129 TAAGTTGTGTATTATGTATTATGTATGTTATGTATAATATTAACTAAGTTGTGTA
*
49065867 TTATGTATTATGTATGTTATGTATTATGTTAGTTATGTACTATGTAAGTTATGTATTATGTATGT
1 TTATGTATTATGTATGTTATGTATTATG-TAGTTGTGTA-TATGTAAGTTATGTATTATGTA-GT
* * * * *
49065932 TATTTAAGTTATGT-A-TAATGTAAGTTGTGTATTATGTATTATGTCTATTATGTATATTATTAA
63 TATGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTATTATGTATATTATGTATAATATTAA
49065995 TTAAGTTGTGTATTATGTATTATGTATGTTATGTATAATATTAACTAAGTTGTGTA
128 TTAAGTTGTGTATTATGTATTATGTATGTTATGTATAATATTAACTAAGTTGTGTA
* * ** * **
49066051 TAATGTAAGTTATGTAAGAAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGT
1 TTATGT-A-TTATGTATGTTATGTATTATGT-AGTTGTGTAT-ATGTAAGTTAT-GTA-TTATGT
*
49066116 A-TTATGTAAGTTATTTAAGTTATGTAAGTTATGTATTATGTA
60 AGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTA
49066158 AGTTATCATG
Statistics
Matches: 252, Mismatches: 24, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
180 25 0.10
183 1 0.00
184 138 0.55
185 4 0.02
186 54 0.21
187 2 0.01
188 28 0.11
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (183 bp):
TTATGTATTATGTATGTTATGTATTATGTAGTTGTGTATATGTAAGTTATGTATTATGTAGTTAT
GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTATTATGTATATTATGTATAATATTAATTA
AGTTGTGTATTATGTATTATGTATGTTATGTATAATATTAACTAAGTTGTGTA
Found at i:49066002 original size:44 final size:44
Alignment explanation
Indices: 49065734--49066066 Score: 387
Period size: 44 Copynumber: 7.2 Consensus size: 44
49065724 ATGTAAGCTG
* * * *
49065734 TGTATTATGTAAGTTATGTAATATGTAATTTATGTAAGTTATGTATTA
1 TGTATTATGTATGTTATGT-ATA-AT-ATTAAT-TAAGTTGTGTATTA
49065782 TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
1 TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
49065826 TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
1 TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
* * * * *
49065870 TGTATTATGTATGTTATGTATTATGTTAGTTATGTACTATGTAAGTTA
1 TGTATTATGTATGTTATGTATAATATTAATTAAGT--TGTGT-A-TTA
* * *
49065918 TGTATTATGTATGTTATTTAAGTTATGTATAATGTAAGTTGTGTATTA
1 TGTATTATGTATGTTATGT-A-TAATAT-TAAT-TAAGTTGTGTATTA
* * *
49065966 TGTATTATGTCTATTATGTATATTATTAATTAAGTTGTGTATTA
1 TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
* *
49066010 TGTATTATGTATGTTATGTATAATATTAACTAAGTTGTGTATAA
1 TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
49066054 TGTAAGTTATGTA
1 TGT-A-TTATGTA
49066067 AGAAATGTAT
Statistics
Matches: 251, Mismatches: 24, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
44 144 0.57
45 10 0.04
46 15 0.06
47 5 0.02
48 58 0.23
49 2 0.01
50 10 0.04
51 3 0.01
52 4 0.02
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (44 bp):
TGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
Found at i:49066053 original size:21 final size:21
Alignment explanation
Indices: 49065982--49066054 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
49065972 ATGTCTATTA
* *
49065982 TGTATATTATTAATTAAGTTG
1 TGTATAATATTAACTAAGTTG
* ** * *
49066003 TGTATTATGTATTATGTATGTTA
1 TGTA-TA-ATATTAACTAAGTTG
49066026 TGTATAATATTAACTAAGTTG
1 TGTATAATATTAACTAAGTTG
49066047 TGTATAAT
1 TGTATAAT
49066055 GTAAGTTATG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 22 0.55
22 4 0.10
23 14 0.35
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (21 bp):
TGTATAATATTAACTAAGTTG
Found at i:49066067 original size:9 final size:9
Alignment explanation
Indices: 49066053--49066190 Score: 96
Period size: 9 Copynumber: 16.0 Consensus size: 9
49066043 GTTGTGTATA
49066053 ATGTAAGTT
1 ATGTAAGTT
**
49066062 ATGTAAGAA
1 ATGTAAGTT
49066071 ATGT-A-TT
1 ATGTAAGTT
49066078 ATGTAAGTT
1 ATGTAAGTT
* *
49066087 GTGT-A-TA
1 ATGTAAGTT
*
49066094 ATGTTAGTT
1 ATGTAAGTT
**
49066103 ATCAAAGTT
1 ATGTAAGTT
49066112 ATGT-A-TT
1 ATGTAAGTT
49066119 ATGTAAGTT
1 ATGTAAGTT
*
49066128 ATTTAAGTT
1 ATGTAAGTT
49066137 ATGTAAGTT
1 ATGTAAGTT
49066146 ATGT-A-TT
1 ATGTAAGTT
49066153 ATGTAAGTTAT
1 ATGTAAG-T-T
*
49066164 CATGTTA-TT
1 -ATGTAAGTT
49066173 ATGTAAGTT
1 ATGTAAGTT
*
49066182 ATGCAAGTT
1 ATGTAAGTT
49066191 TATATATAAG
Statistics
Matches: 99, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
7 20 0.20
8 13 0.13
9 58 0.59
10 2 0.02
11 1 0.01
12 5 0.05
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:49066090 original size:41 final size:41
Alignment explanation
Indices: 49065449--49066161 Score: 275
Period size: 41 Copynumber: 17.7 Consensus size: 41
49065439 AAGCTGTGTA
* * * *
49065449 TTATGTAAGTTATGTAATATGTAATTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
* *
49065490 TTATGTAA--TATGTAATTTATGT-A-TTATGTAATTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAGTTGTGT-A-TAATGTAAG
* *
49065531 TTATGT-A-TTATGTATTATGTATGTTATGTATAA--T-A-
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
* * *
49065566 TTAAT-TAAGTTGTGTATTATGT-A-TTATGTATGTTATGT-A-
1 TT-ATGTAAGTTATGTATTATGTAAGTTGTGTA--TAATGTAAG
* * * * *
49065605 TTATGTTAGTTATGTACTATGTAAGTTATGTATTATGTTAG
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
* * *
49065646 TTATGT-A-CTATGTAAGTTATGT-A-TTATGTATGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAGTTGTGTA--TAATGTAAG
*
49065687 TTATGT-A-TTATGTATATTATGTATTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTATG--TATTATG---TAAGTTGTGTATAATGTAAG
* * * *
49065731 CTGTGT-A-TTATGTAAGTTATGTAA-TATGT-AATTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAGT-TGTGTA-TAATGTAAG
* * *
49065772 TTATGT-A-TTATGTATTATGTATGTTATGTATAATATTAA-
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAAT-GTAAG
* * *
49065811 TTAAGTTGTGTA-TTATGTATTATGTATGTTATGTATAA--T-A-
1 TT-A--TGT-AAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
* * *
49065851 TTAAT-TAAGTTGTGTATTATGT-A-TTATGTATGTTATGT-A-
1 TT-ATGTAAGTTATGTATTATGTAAGTTGTGTA--TAATGTAAG
* * * * *
49065890 TTATGTTAGTTATGTACTATGTAAGTTATGTATTATGTATG
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
* * *
49065931 TTATTTAAGTTATGTATAATGTAAGTTGTGTATTATGTATTATG
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTA--A-G
* *
49065975 TCTAT-TATGTATAT-TATTAAT-TAAGTTGTGTATTATGT-A-
1 T-TATGTAAGT-TATGTATT-ATGTAAGTTGTGTATAATGTAAG
* *
49066014 TTATGTATGTTATGTATAATATTAACTAAGTTGTGTATAATGTAAG
1 TTATGTAAGTTATGTAT--TA-T--GTAAGTTGTGTATAATGTAAG
** *
49066060 TTATGTAAGAAATGTATTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
**
49066101 TTATCAAAGTTATGTATTATGTAA---GT-TAT--T-TAAG
1 TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
49066135 TTATGTAAGTTATGTATTATGTAAGTT
1 TTATGTAAGTTATGTATTATGTAAGTT
49066162 ATCATGTTAT
Statistics
Matches: 548, Mismatches: 53, Indels: 146
0.73 0.07 0.20
Matches are distributed among these distances:
34 25 0.05
35 18 0.03
36 5 0.01
37 33 0.06
38 13 0.02
39 102 0.19
40 27 0.05
41 191 0.35
42 5 0.01
43 3 0.01
44 96 0.18
45 10 0.02
46 20 0.04
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (41 bp):
TTATGTAAGTTATGTATTATGTAAGTTGTGTATAATGTAAG
Found at i:49066159 original size:25 final size:25
Alignment explanation
Indices: 49066040--49066163 Score: 103
Period size: 25 Copynumber: 5.0 Consensus size: 25
49066030 TAATATTAAC
* *
49066040 TAAGTTGTGTATAATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
** *
49066065 TAAGAAATGTATTATGTAAGTTGTG
1 TAAGTTATGTATTATGTAAGTTATG
* **
49066090 T-A-TAATGTTAGTTATCAAAGTTATG
1 TAAGTTATG-TA-TTATGTAAGTTATG
*
49066115 T-A-TTATGTAAGTTATTTAAGTTATG
1 TAAGTTATGT-A-TTATGTAAGTTATG
49066140 TAAGTTATGTATTATGTAAGTTAT
1 TAAGTTATGTATTATGTAAGTTAT
49066164 CATGTTATTA
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
23 4 0.05
24 4 0.05
25 65 0.80
26 2 0.02
27 6 0.07
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:49066174 original size:20 final size:19
Alignment explanation
Indices: 49066111--49066183 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 19
49066101 TTATCAAAGT
49066111 TATG-TATTATGTAAGTTA
1 TATGTTATTATGTAAGTTA
*
49066129 T-T-TAAGTTATGTAAG-T-
1 TATGTTA-TTATGTAAGTTA
49066145 TATG-TATTATGTAAGTTA
1 TATGTTATTATGTAAGTTA
49066163 TCATGTTATTATGTAAGTTA
1 T-ATGTTATTATGTAAGTTA
49066183 T
1 T
49066184 GCAAGTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
16 10 0.22
17 6 0.13
18 11 0.24
19 3 0.07
20 15 0.33
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (19 bp):
TATGTTATTATGTAAGTTA
Found at i:49066201 original size:12 final size:12
Alignment explanation
Indices: 49066185--49066214 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49066175 GTAAGTTATG
49066185 CAAGTTTATATA
1 CAAGTTTATATA
*
49066197 TAAGTTTATATA
1 CAAGTTTATATA
49066209 CAAGTT
1 CAAGTT
49066215 ATGTAAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (12 bp):
CAAGTTTATATA
Found at i:49066882 original size:153 final size:151
Alignment explanation
Indices: 49066607--49067052 Score: 666
Period size: 153 Copynumber: 3.0 Consensus size: 151
49066597 CAATTGTTCG
* * * * *
49066607 TATTTTGGCCCTTTGTTCGTATTTTTTTTCGA-ATTTTATTACTTTTCAAAAATATACTATTTTT
1 TATTTCGGCCCTATGTTCGTATTTTTTTCCCAGATTTTATTACTTTTAAAAAATATACTATTTTT
*
49066671 AATTTTTTTATTTTACATTATTTTAGTACATTATATTTGAACTGTATTAATTTAGTGTGTTTTTT
66 AATTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
*
49066736 AAATAAATTTAAAAAAATCAT
131 AAATAAATTTAAAAAAACCAT
*
49066757 TATTTCGGCCCTCTGTTCGTATTTTTTTCCCTAGATTTTATTACTTTTAAAAAATATACTATTTT
1 TATTTCGGCCCTATGTTCGTATTTTTTTCCC-AGATTTTATTACTTTTAAAAAATATACTATTTT
49066822 TAAATTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTAT
65 T-AATTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTT-T
*
49066887 TTTAAATAAA-TTAAAAAAACCCT
128 TTTAAATAAATTTAAAAAAACCAT
* * * * * *
49066910 TATTTCAGCCTTATGTTCGTA-TTTTTTCCCGGATTTTAATAATTTTAAAAAATATAGTATTTTT
1 TATTTCGGCCCTATGTTCGTATTTTTTTCCCAGATTTTATTACTTTTAAAAAATATACTATTTTT
* * * *
49066974 TATTTTTTTATTTTACATTA-TTTAGTACATTATATTTGAAATTTATTAATTTAGTATATTTTTT
66 AATTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
49067038 AAATAAATTTAAAAA
131 AAATAAATTTAAAAA
49067053 TAGTGTATAG
Statistics
Matches: 272, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
148 11 0.04
149 44 0.16
150 46 0.17
151 31 0.11
152 40 0.15
153 89 0.33
154 11 0.04
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (151 bp):
TATTTCGGCCCTATGTTCGTATTTTTTTCCCAGATTTTATTACTTTTAAAAAATATACTATTTTT
AATTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTT
AAATAAATTTAAAAAAACCAT
Found at i:49067349 original size:18 final size:18
Alignment explanation
Indices: 49067326--49067414 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
49067316 ATATATAAAT
49067326 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
49067344 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
*
49067366 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
49067383 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
49067401 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
49067415 GTAAGTAATG
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.22
18 30 0.48
19 3 0.05
20 3 0.05
21 4 0.06
22 9 0.14
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:49067385 original size:39 final size:37
Alignment explanation
Indices: 49067318--49067450 Score: 146
Period size: 39 Copynumber: 3.5 Consensus size: 37
49067308 TTAAAAATAT
49067318 ATATAAATTTTAAGTAATGTAATATATTTAAGTAATGTA
1 ATATAAATTTT-AGTAA-GTAATATATTTAAGTAATGTA
49067357 AGTTATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
1 A--TATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
* ** *
49067396 ATAT--ATTTTAGTAAGTAATGTAAGTAATGTAATAT-
1 ATATAAATTTTAGTAAGTAATATATTTAA-GTAATGTA
49067431 ATACTTAAATTTTAGTAAGT
1 ATA--TAAATTTTAGTAAGT
49067451 CATGTGTTTA
Statistics
Matches: 83, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
35 23 0.28
36 6 0.07
37 4 0.05
39 35 0.42
40 5 0.06
41 10 0.12
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.44
Consensus pattern (37 bp):
ATATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
Found at i:49067414 original size:22 final size:22
Alignment explanation
Indices: 49067328--49067379 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
49067318 ATATAAATTT
*
49067328 TAAGTAATGTAATATATTTAAG
1 TAAGTAATGTAATAAATTTAAG
* *
49067350 TAATGTAA-GTTATAAATTTTAG
1 TAA-GTAATGTAATAAATTTAAG
49067372 TAAGTAAT
1 TAAGTAAT
49067380 ATATTTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 4 0.16
22 17 0.68
23 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TAAGTAATGTAATAAATTTAAG
Found at i:49074721 original size:9 final size:8
Alignment explanation
Indices: 49074692--49074726 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
49074682 CTCAAAAGTC
49074692 AAAAAAGA
1 AAAAAAGA
* *
49074700 GAAGAAGA
1 AAAAAAGA
49074708 AAAAAAGA
1 AAAAAAGA
49074716 AAAAAAGA
1 AAAAAAGA
49074724 AAA
1 AAA
49074727 CCCTTCGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:49075277 original size:21 final size:21
Alignment explanation
Indices: 49075251--49075303 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
49075241 AGTGTTTAGG
49075251 TGGGTAATGGGTTAAGTTTAT
1 TGGGTAATGGGTTAAGTTTAT
49075272 TGGGTAATGGGTTAAGTTTAT
1 TGGGTAATGGGTTAAGTTTAT
49075293 TGGGTAATGGG
1 TGGGTAATGGG
49075304 CCGGGCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.40
Consensus pattern (21 bp):
TGGGTAATGGGTTAAGTTTAT
Found at i:49075725 original size:17 final size:16
Alignment explanation
Indices: 49075705--49075760 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
49075695 CATATTTTCA
49075705 TTAAAAACATAAAAAAT
1 TTAAAAA-ATAAAAAAT
*
49075722 TT-AAAAATGAAAAAT
1 TTAAAAAATAAAAAAT
*
49075737 TATGAAAAATAAAAATAT
1 T-TAAAAAATAAAAA-AT
49075755 TTAAAA
1 TTAAAA
49075761 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.27
16 5 0.15
17 16 0.48
18 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
TTAAAAAATAAAAAAT
Found at i:49075736 original size:15 final size:15
Alignment explanation
Indices: 49075708--49075768 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 15
49075698 ATTTTCATTA
49075708 AAAACATAAAAAATTT
1 AAAA-ATAAAAAATTT
*
49075724 AAAAATGAAAAATTAT
1 AAAAATAAAAAATT-T
49075740 GAAAAATAAAAATATTT
1 -AAAAATAAAAA-ATTT
*
49075757 AAAATTAAAAAA
1 AAAAATAAAAAA
49075769 ATTGAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 10 0.26
16 15 0.38
17 11 0.28
18 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAAATAAAAAATTT
Found at i:49075775 original size:32 final size:33
Alignment explanation
Indices: 49075708--49075775 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
49075698 ATTTTCATTA
* *
49075708 AAAACATAAAAAATTTAAAAATGAAAAATTATG
1 AAAACATAAAAAATTTAAAAATAAAAAAATATG
*
49075741 AAAA-ATAAAAATATTTAAAATTAAAAAAAT-TG
1 AAAACATAAAAA-ATTTAAAAATAAAAAAATATG
49075773 AAA
1 AAA
49075776 TGATTGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (33 bp):
AAAACATAAAAAATTTAAAAATAAAAAAATATG
Found at i:49076340 original size:23 final size:24
Alignment explanation
Indices: 49076313--49076373 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
49076303 TTATTATATG
49076313 ATTAAAAATAAAT-GTTTAATAAT
1 ATTAAAAATAAATAGTTTAATAAT
*
49076336 ATTAAAAATTATAATATTTTAATAAT
1 ATTAAAAA-TA-AATAGTTTAATAAT
*
49076362 TTTAAAAATAAA
1 ATTAAAAATAAA
49076374 AATAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 8 0.24
24 4 0.12
25 5 0.15
26 16 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTAAAAATAAATAGTTTAATAAT
Found at i:49081737 original size:5 final size:6
Alignment explanation
Indices: 49081721--49081791 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
49081711 TAATTTAGCC
* * * *
49081721 ATTTTT ATTTTT ATTTTT ATTATA ATTTTT ATTTTT AGTTTA ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
49081769 ACTTTCT ATTTTT -TCTTTT ATTT
1 A-TTTTT ATTTTT AT-TTTT ATTT
49081792 GCTTCTGGCA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
5 1 0.02
6 45 0.87
7 6 0.12
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:49083870 original size:46 final size:46
Alignment explanation
Indices: 49083461--49083869 Score: 656
Period size: 46 Copynumber: 8.9 Consensus size: 46
49083451 ACAGATCAAT
*
49083461 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCAGAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
49083507 GAAGATAACAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
49083553 GAAGATAGCAGATCTTATCTTCCTGTATTTAGCAGCGAAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
* * *
49083599 AAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
*
49083645 GAAGATAGCAGATCTTATCTTCCTGTATCTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
*
49083691 GAAGATAGCAGACCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
*
49083737 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCAGAGGAGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
* * * * *
49083783 GAGGATATCAGATCTTATCTTCCTATAATTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
* *
49083829 GAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGG
1 GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGG
49083870 GTGTAACACC
Statistics
Matches: 333, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 333 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (46 bp):
GAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATC
Found at i:49084933 original size:41 final size:40
Alignment explanation
Indices: 49084888--49085131 Score: 253
Period size: 41 Copynumber: 6.0 Consensus size: 40
49084878 TTGTATAAAA
* * * *
49084888 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
* *
49084928 CCACCGGCACAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACA-TT
*
49084970 CACCGGCACT-AAGTCTGCTAGACATAAAGTCTGAAGTA-ATT
1 CACCGGCA-TAAAGCCTGCTAGACATAAAGTCTG-A-TACATT
* *
49085011 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTG--ATACATT
* *
49085052 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTG--ATACATT
* * *
49085093 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACAT
49085132 CTTATTTTCA
Statistics
Matches: 184, Mismatches: 12, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 171 0.93
42 6 0.03
43 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
Found at i:49085025 original size:82 final size:82
Alignment explanation
Indices: 49084888--49085131 Score: 307
Period size: 82 Copynumber: 3.0 Consensus size: 82
49084878 TTGTATAAAA
* * * * *
49084888 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCG--ATACATTCCACCGGCA-CAAAGCCTGCTAG
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATA-ATT-CACCGGCATC-AAGCCTGCTAG
* * *
49084950 ACATAAGGTCTGATACATTT
63 ACGTAAAGTCTGAAACATTT
* *
49084970 CACCGGCA-CTAAGTCTGCTAGACATAAAGTCTGAAGTAATTCACCGGCATCAAGCCTGCTAGAC
1 CACCGGCATC-AAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
* *
49085034 GTAAAGTCTGAAATAATT
65 GTAAAGTCTGAAACATTT
*
49085052 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
49085117 TAAAGTCTGAAACAT
66 TAAAGTCTGAAACAT
49085132 CTTATTTTCA
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
82 133 0.95
83 5 0.04
84 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (82 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
TAAAGTCTGAAACATTT
Found at i:49087113 original size:46 final size:46
Alignment explanation
Indices: 49087037--49087418 Score: 518
Period size: 46 Copynumber: 8.3 Consensus size: 46
49087027 GGTTGTTACA
* * * * *
49087037 GAGGGGATCGAAGATAGCAGATCTTGTCTTCTTATATTTGACAGTG
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
* *
49087083 GAGGAGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGTG
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
* *
49087129 GAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCA
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
* * * * *
49087175 GAGGAGATCAAAAATAGCAGATCTTATTTTCCTATATTTGGCAGCG
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
* *
49087221 AAAGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
49087267 GA-GAGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
1 GAGGA-GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
* * * *
49087313 AAGGAGATCGAGGATAGCAGATCTTGTCTTCCTGTAATTT-GTAGTG
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGT-ATTTGGCAGCG
*
49087359 GAGG-GATCGAAGATAGCAGATCATGTCTTCCTGTATTTGGCAGCG
1 GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
* *
49087404 GAGTAGATCAAAGAT
1 GAGGAGATCGAAGAT
49087419 GGTGAATCTT
Statistics
Matches: 296, Mismatches: 35, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
44 4 0.01
45 37 0.12
46 249 0.84
47 6 0.02
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (46 bp):
GAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
Found at i:49087522 original size:44 final size:43
Alignment explanation
Indices: 49087471--49087714 Score: 197
Period size: 44 Copynumber: 5.6 Consensus size: 43
49087461 GCCATTAGTC
*
49087471 CTATCACCCTAAGCAGTAGTGGATTAGGTTAAAGATTACAGATT
1 CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTA-AGATT
* * * ** * * *
49087515 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAAT
1 CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTAAGATT
* * * * * * * *
49087558 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT-AG-TT
1 C-TATC-ACCCTAA-GCAGTAGTGGAGTAGGTTAAAG--ATTAAGATT
* *
49087603 CTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATT-AAGATT
*
49087647 CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGTAGATT
1 CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATT-AAGATT
* *
49087691 CTGTCCCCCTAAGCAGTAGTGGAG
1 CTATCACCCTAAGCAGTAGTGGAG
49087715 CAGATCAACA
Statistics
Matches: 159, Mismatches: 32, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.02
43 24 0.15
44 108 0.68
45 21 0.13
46 1 0.01
47 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTAAGATT
Found at i:49087682 original size:132 final size:132
Alignment explanation
Indices: 49087403--49087682 Score: 461
Period size: 132 Copynumber: 2.1 Consensus size: 132
49087393 ATTTGGCAGC
* *
49087403 GGAGTAGATCAAAGATGGTGAATCTTATCTTCCTAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGTAGATCAAAGATGATGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* *
49087468 GTCCTATCACCCTAAGCAGTAGTGGATTAGGTTAAAGATTACAGATTCTGTCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTACAGATTCTATCACCCTAAGCAGTA
49087533 GT
131 GT
* *
49087535 GGAGCAGATCGAAGATGATGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGTAGATCAAAGATGATGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* * *
49087600 GTTCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTATCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTACAGATTCTATCACCCTAAGCAGTA
49087665 GT
131 GT
* *
49087667 GGAGTAGGTTAAAGAT
1 GGAGTAGATCAAAGAT
49087683 TGTAGATTCT
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
GGAGTAGATCAAAGATGATGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTAAAGATTACAGATTCTATCACCCTAAGCAGTA
GT
Found at i:49089479 original size:2 final size:2
Alignment explanation
Indices: 49089474--49089502 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
49089464 TACTTCCCTA
49089474 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49089503 TTTATACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:49089508 original size:14 final size:14
Alignment explanation
Indices: 49089474--49089523 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
49089464 TACTTCCCTA
49089474 ATATATATATATATAT
1 ATATATAT-TATAT-T
49089490 ATATATATTATATT
1 ATATATATTATATT
* **
49089504 TTATACCTTATATT
1 ATATATATTATATT
49089518 ATATAT
1 ATATAT
49089524 GTCCTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 16 0.55
15 5 0.17
16 8 0.28
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATATATTATATT
Found at i:49094548 original size:60 final size:60
Alignment explanation
Indices: 49094484--49094608 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 60
49094474 TATTAAGAAG
49094484 GCTAACACAGTGCTTGATGAAACTATCAAAGTAAATGATGAGTTCATTACCAAAATAGAT
1 GCTAACACAGTGCTTGATGAAACTATCAAAGTAAATGATGAGTTCATTACCAAAATAGAT
49094544 GCTAACACAGTGCTTGATGAAACTATCAAAGTAAATGATGAGTTCATTACCAAAATAGAT
1 GCTAACACAGTGCTTGATGAAACTATCAAAGTAAATGATGAGTTCATTACCAAAATAGAT
49094604 G-TAAC
1 GCTAAC
49094609 TTTGAAAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 4 0.06
60 61 0.94
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (60 bp):
GCTAACACAGTGCTTGATGAAACTATCAAAGTAAATGATGAGTTCATTACCAAAATAGAT
Found at i:49096195 original size:15 final size:15
Alignment explanation
Indices: 49096175--49096204 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49096165 AATCCAGACG
49096175 ATGGTTGAATAAAAT
1 ATGGTTGAATAAAAT
49096190 ATGGTTGAATAAAAT
1 ATGGTTGAATAAAAT
49096205 CATTCACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
ATGGTTGAATAAAAT
Found at i:49097975 original size:23 final size:22
Alignment explanation
Indices: 49097935--49097978 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
49097925 AAATTATAAA
*
49097935 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
49097957 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
49097979 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:49100452 original size:22 final size:23
Alignment explanation
Indices: 49100403--49100456 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
49100393 CCGTTTTTTA
* *
49100403 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTGTT
49100426 ATTAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
49100448 ATTAAAATT
1 ATTAAAATT
49100457 GTATCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:49101274 original size:53 final size:53
Alignment explanation
Indices: 49101198--49101378 Score: 194
Period size: 53 Copynumber: 3.7 Consensus size: 53
49101188 TTAGATTTTG
49101198 TTAC-AACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
* * *
49101250 TTACTAACAATTAATACAATTAACAATTAATAATTT--TACTAA---CAAAATG
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATA-TAATTTGATAATT
* *
49101299 TTAGTAACAA-T--T--AA-T---AATTAATAATTTGATACAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
*
49101343 TTAGTAACAATTAATACAATTAACAATTAATAATTT
1 TTACTAACAATTAATACAATTAACAATTAATAATTT
49101379 TACTAACAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 31
0.73 0.06 0.22
Matches are distributed among these distances:
40 12 0.11
41 2 0.02
42 2 0.02
43 1 0.01
44 16 0.15
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 15 0.14
50 1 0.01
51 2 0.02
52 7 0.07
53 43 0.41
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (53 bp):
TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
Found at i:49101369 original size:93 final size:93
Alignment explanation
Indices: 49101212--49101395 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
49101202 AACAATTAAT
*
49101212 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
1 ACAATTAACAATTAATAATTTGATACAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
49101277 TAATAATTTTACTAACAAAATGTTAGTA
66 TAATAATTTTACTAACAAAATGTTAGTA
* *
49101305 ACAATTAATAATTAATAATTTGATACAATTTGATAATTTTAGTAACAATTAATACAATTAACAAT
1 ACAATTAACAATTAATAATTTGATACAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
49101370 TAATAATTTTACTAACAAAATGTTAG
66 TAATAATTTTACTAACAAAATGTTAG
49101396 ATTTTACAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (93 bp):
ACAATTAACAATTAATAATTTGATACAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
TAATAATTTTACTAACAAAATGTTAGTA
Found at i:49101385 original size:19 final size:18
Alignment explanation
Indices: 49101217--49101387 Score: 63
Period size: 18 Copynumber: 9.3 Consensus size: 18
49101207 TTAATACAAT
*
49101217 TAACAATTAATAATTTGA
1 TAACAATTAATAATTTTA
* *
49101235 TATA-ATTTGATAATTTTA
1 TA-ACAATTAATAATTTTA
*
49101253 CTAACAATTAATACA--AT-
1 -TAACAATTAATA-ATTTTA
49101270 TAACAATTAATAATTTTA
1 TAACAATTAATAATTTTA
* ***
49101288 CTAACAAAATGTTAGTAACAAT-
1 -TAAC--AA--TTAATAATTTTA
* *
49101310 TAATAATTAATAATTTGA
1 TAACAATTAATAATTTTA
*
49101328 T-ACAATTTGATAATTTTA
1 TAACAA-TTAATAATTTTA
*
49101346 GTAACAATTAATACA--AT-
1 -TAACAATTAATA-ATTTTA
49101363 TAACAATTAATAATTTTA
1 TAACAATTAATAATTTTA
49101381 CTAACAA
1 -TAACAA
49101388 AATGTTAGAT
Statistics
Matches: 109, Mismatches: 23, Indels: 41
0.63 0.13 0.24
Matches are distributed among these distances:
15 2 0.02
16 24 0.22
17 11 0.10
18 27 0.25
19 27 0.25
20 6 0.06
21 5 0.05
23 7 0.06
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (18 bp):
TAACAATTAATAATTTTA
Found at i:49101465 original size:22 final size:23
Alignment explanation
Indices: 49101422--49101499 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 23
49101412 ACTAGTATAA
49101422 AAAAATATAATTTGATACAATTTTAAT
1 AAAAATATAATTT--T--AATTTTAAT
* *
49101449 AACAAT-TAGTTTTAATTTTAAT
1 AAAAATATAATTTTAATTTTAAT
49101471 AAAAATATAATTTTAATTTTAATT
1 AAAAATATAATTTTAATTTTAA-T
49101495 AAAAA
1 AAAAA
49101500 ATAGGCCGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 14 0.31
23 14 0.31
24 7 0.16
26 5 0.11
27 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (23 bp):
AAAAATATAATTTTAATTTTAAT
Found at i:49106964 original size:44 final size:44
Alignment explanation
Indices: 49106905--49106991 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
49106895 CCTTCCATTT
* * **
49106905 TTTGTCTGTTTGTTTCTGGTTAATCTGGGTAACTTCATTTTCTG
1 TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCTG
49106949 TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCT
1 TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCT
49106992 TCTTCTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.14, C:0.15, G:0.18, T:0.53
Consensus pattern (44 bp):
TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCTG
Found at i:49108704 original size:16 final size:16
Alignment explanation
Indices: 49108683--49108713 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49108673 AAAACATTTA
*
49108683 TAATATATATGTATAT
1 TAATATATATATATAT
49108699 TAATATATATATATA
1 TAATATATATATATA
49108714 GGCGCACACA
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:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATATATATATATAT
Found at i:49108741 original size:3 final size:3
Alignment explanation
Indices: 49108733--49108766 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
49108723 ATATAAATAC
*
49108733 AAT AAT AAT -AT AAT AAT AAT AAT TAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49108767 ACAATATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:49108761 original size:15 final size:14
Alignment explanation
Indices: 49108733--49108766 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
49108723 ATATAAATAC
49108733 AATAATAATATAAT
1 AATAATAATATAAT
49108747 AATAATAATTATAAT
1 AATAATAA-TATAAT
49108762 AATAA
1 AATAA
49108767 ACAATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATAATATAAT
Found at i:49109907 original size:3 final size:3
Alignment explanation
Indices: 49109899--49109928 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
49109889 TAACTACATT
49109899 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
49109929 CATTTTCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:49110835 original size:20 final size:19
Alignment explanation
Indices: 49110801--49110840 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
49110791 AGATGCTTCT
49110801 ATTTATGAATTTGGATTGG
1 ATTTATGAATTTGGATTGG
*
49110820 ATTTATGCAGTTTGGATTGG
1 ATTTATG-AATTTGGATTGG
49110840 A
1 A
49110841 AAATAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.45
Consensus pattern (19 bp):
ATTTATGAATTTGGATTGG
Found at i:49117454 original size:25 final size:25
Alignment explanation
Indices: 49117410--49117486 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
49117400 AACAAATAGC
* * *
49117410 ATCAAAGTTGTGTATAATGTTAGTT
1 ATCAAAGTTATGTACAATGTAAGTT
*
49117435 ATCAAAGTTATGTACCATGTAAGTT
1 ATCAAAGTTATGTACAATGTAAGTT
**
49117460 ATTTAAGTTATGTA-AATTGTAAGTT
1 ATCAAAGTTATGTACAA-TGTAAGTT
49117485 AT
1 AT
49117487 GCAAGTTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 1 0.02
25 43 0.98
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (25 bp):
ATCAAAGTTATGTACAATGTAAGTT
Found at i:49117492 original size:25 final size:24
Alignment explanation
Indices: 49117414--49117502 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 24
49117404 AATAGCATCA
* * *
49117414 AAGTTGTGTATAATGTTAGTTATC
1 AAGTTATGTACAATGTAAGTTATC
* *
49117438 AAAGTTATGTACCATGTAAGTTATTT
1 -AAGTTATGTACAATGTAAGTTA-TC
49117464 AAGTTATGTA-AATTGTAAGTTATGC
1 AAGTTATGTACAA-TGTAAGTTAT-C
*
49117489 AAGTTTATATACAA
1 AAG-TTATGTACAA
49117503 GTTTATATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
24 2 0.04
25 40 0.78
26 7 0.14
27 2 0.04
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (24 bp):
AAGTTATGTACAATGTAAGTTATC
Found at i:49117505 original size:12 final size:12
Alignment explanation
Indices: 49117488--49117517 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49117478 GTAAGTTATG
49117488 CAAGTTTATATA
1 CAAGTTTATATA
49117500 CAAGTTTATATA
1 CAAGTTTATATA
*
49117512 TAAGTT
1 CAAGTT
49117518 ATGCAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (12 bp):
CAAGTTTATATA
Found at i:49117674 original size:22 final size:22
Alignment explanation
Indices: 49117631--49117674 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
49117621 ATAGGGTGAT
***
49117631 ATATTAAAAAAAATAGGTTTTA
1 ATATTAAAAAAAATAACATTTA
*
49117653 ATATTTAAAAAAATAACATTTA
1 ATATTAAAAAAAATAACATTTA
49117675 CAGTTATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (22 bp):
ATATTAAAAAAAATAACATTTA
Found at i:49117795 original size:18 final size:18
Alignment explanation
Indices: 49117772--49117868 Score: 108
Period size: 18 Copynumber: 5.3 Consensus size: 18
49117762 ATATATAAAT
49117772 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
49117790 TTTAAGTAATGTAAATTATAAA
1 TTTAAGTAATGT-AA-TAT--A
*
49117812 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
49117829 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
* * *
49117847 TTTTAGTAA-GTCATGTA
1 TTTAAGTAATGTAATATA
49117864 TTTAA
1 TTTAA
49117869 CATTCTGTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
17 19 0.28
18 28 0.41
19 5 0.07
20 5 0.07
21 2 0.03
22 9 0.13
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:49117831 original size:39 final size:37
Alignment explanation
Indices: 49117764--49117868 Score: 142
Period size: 35 Copynumber: 2.8 Consensus size: 37
49117754 TTAAATATAT
49117764 ATATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAA
1 ATATAAATTTT-AGTAA-GTAATATATTTAAGTAATGT-A
49117804 ATTATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
1 A-TATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
* *
49117842 ATAT--ATTTTAGTAAGTCATGTATTTAA
1 ATATAAATTTTAGTAAGTAATATATTTAA
49117869 CATTCTGTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
35 21 0.34
37 3 0.05
38 2 0.03
39 20 0.32
40 6 0.10
41 10 0.16
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (37 bp):
ATATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
Found at i:49128655 original size:34 final size:34
Alignment explanation
Indices: 49128579--49128656 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
49128569 TAACTATAAG
*
49128579 TTTAGTTTCTTAAATTAAATTAAATTAAATTTTA
1 TTTAGTTTTTTAAATTAAATTAAATTAAATTTTA
**
49128613 TTTAGTTTTTTAAATTAAATTAAATTTTATTTTA
1 TTTAGTTTTTTAAATTAAATTAAATTAAATTTTA
49128647 TTTAGTTTTT
1 TTTAGTTTTT
49128657 CATGTAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (34 bp):
TTTAGTTTTTTAAATTAAATTAAATTAAATTTTA
Found at i:49128907 original size:33 final size:35
Alignment explanation
Indices: 49128869--49128934 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
49128859 ATTCAGGTAT
*
49128869 TACATTAGACATTTT-CAA-AATACATATATTACG
1 TACATTAAACATTTTACAAGAATACATATATTACG
*
49128902 TACATTAAACATTTTATAAGAATACATATATTA
1 TACATTAAACATTTTACAAGAATACATATATTA
49128935 AATATGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.48
34 2 0.07
35 13 0.45
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (35 bp):
TACATTAAACATTTTACAAGAATACATATATTACG
Found at i:49134211 original size:26 final size:29
Alignment explanation
Indices: 49134168--49134224 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
49134158 CATAAAACCC
49134168 AATTACAACCCAAACCC-AAGACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
* *
49134196 AATTA-AA-CCAAGCCCAAATACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
49134223 AA
1 AA
49134225 CCCAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 14 0.54
28 5 0.19
ACGTcount: A:0.53, C:0.35, G:0.04, T:0.09
Consensus pattern (29 bp):
AATTACAACCCAAACCCAAAGACCCAACA
Found at i:49135074 original size:22 final size:22
Alignment explanation
Indices: 49135049--49135105 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
49135039 TTAATTTTCA
49135049 TATATATATATATATACCTTAT
1 TATATATATATATATACCTTAT
* * * *
49135071 TATAAATATCTTTATATCTTAT
1 TATATATATATATATACCTTAT
*
49135093 TATGTATATATAT
1 TATATATATATAT
49135106 CTATATCTCT
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:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATATATATATATACCTTAT
Found at i:49135116 original size:26 final size:25
Alignment explanation
Indices: 49135067--49135116 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
49135057 TATATATACC
*
49135067 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
49135092 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
49135117 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:49151869 original size:18 final size:17
Alignment explanation
Indices: 49151836--49151874 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
49151826 TTGTATAAAT
49151836 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
49151854 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
49151871 TGTG
1 TGTG
49151875 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:49151992 original size:8 final size:8
Alignment explanation
Indices: 49151979--49152007 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
49151969 CACTAGAGAC
49151979 CAGTGTTA
1 CAGTGTTA
49151987 CAGTGTTA
1 CAGTGTTA
49151995 CAGTGTTA
1 CAGTGTTA
49152003 CAGTG
1 CAGTG
49152008 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:49173596 original size:34 final size:34
Alignment explanation
Indices: 49173553--49173621 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
49173543 AAATAATTTT
49173553 GAACAACACAAATCTACGAAGCAAAATTCAAATA
1 GAACAACACAAATCTACGAAGCAAAATTCAAATA
49173587 GAACAACACAAATCTACGAAGCAAAATTCAAATA
1 GAACAACACAAATCTACGAAGCAAAATTCAAATA
49173621 G
1 G
49173622 CTTTCTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.55, C:0.20, G:0.10, T:0.14
Consensus pattern (34 bp):
GAACAACACAAATCTACGAAGCAAAATTCAAATA
Found at i:49173618 original size:20 final size:20
Alignment explanation
Indices: 49173561--49173619 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
49173551 TTGAACAACA
49173561 CAAATCTACGAAGCAAAATT
1 CAAATCTACGAAGCAAAATT
*
49173581 CAAA--TA-GAA-CAACA--
1 CAAATCTACGAAGCAAAATT
49173595 CAAATCTACGAAGCAAAATT
1 CAAATCTACGAAGCAAAATT
49173615 CAAAT
1 CAAAT
49173620 AGCTTTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 4 0.13
16 6 0.19
17 6 0.19
18 6 0.19
20 9 0.29
ACGTcount: A:0.54, C:0.20, G:0.08, T:0.17
Consensus pattern (20 bp):
CAAATCTACGAAGCAAAATT
Found at i:49178614 original size:26 final size:26
Alignment explanation
Indices: 49178563--49178957 Score: 181
Period size: 26 Copynumber: 15.2 Consensus size: 26
49178553 TGTTATTCAT
*
49178563 TTATTTATTTTAAACCTTTTTCTTATATA
1 TTATTTATTTTAAA--TTGTT-TTATATA
*
49178592 TTATTTATTTTAAATTATTTTAT-TA
1 TTATTTATTTTAAATTGTTTTATATA
* * ** * *
49178617 TTATTTATTTCAAGTT-TTCCACATG
1 TTATTTATTTTAAATTGTTTTATATA
* * * * * *
49178642 TCATGTATTTTAAACTATTTCAAACTA
1 TTATTTATTTTAAATTGTTTTATA-TA
** *
49178669 TTATCCA-TTT---TT-TTATATATA
1 TTATTTATTTTAAATTGTTTTATATA
*
49178690 TTATTTATTTTTAAATTGTTATATATA
1 TTATTTA-TTTTAAATTGTTTTATATA
*
49178717 TTATTTATTTTGAATTGTTTTTATATACA
1 TTATTTATTTTAAATTG-TTTTATAT--A
* * * *
49178746 TCATTTATTTTTTTAAACTATTTTGTATA
1 TTATTTA---TTTTAAATTGTTTTATATA
* *
49178775 TTATTTATTTGAAACTTCTTTT-TGCATA
1 TTATTTATTTTAAA-TTGTTTTAT--ATA
* *
49178803 TTATGTATTTTAAA--CTTTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* * *
49178826 -TA-TTATTTTAAATTGTCTAATATG
1 TTATTTATTTTAAATTGTTTTATATA
* * * *
49178850 TTATTTATTTTAAATTGCTGTGTGTA
1 TTATTTATTTTAAATTGTTTTATATA
* *
49178876 TTATTTATTTTAATTTGTTTTACATA
1 TTATTTATTTTAAATTGTTTTATATA
*
49178902 TTATTTACTTTAAATTG-TTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * * *
49178926 CTATTCACTTCAAATTGTTCTATATA
1 TTATTTATTTTAAATTGTTTTATATA
49178952 TTATTT
1 TTATTT
49178958 TGTTTCATTT
Statistics
Matches: 277, Mismatches: 64, Indels: 53
0.70 0.16 0.13
Matches are distributed among these distances:
21 16 0.06
22 6 0.02
23 9 0.03
24 23 0.08
25 41 0.15
26 88 0.32
27 37 0.13
28 15 0.05
29 28 0.10
31 7 0.03
32 7 0.03
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTTATATA
Found at i:49178618 original size:25 final size:28
Alignment explanation
Indices: 49178563--49178626 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
49178553 TGTTATTCAT
*
49178563 TTATTTATTTTAAACCTTTTTCTTATATA
1 TTATTTATTTTAAA-CTTATTCTTATATA
49178592 TTATTTATTTTAAA-TTATT-TTAT-TA
1 TTATTTATTTTAAACTTATTCTTATATA
49178617 TTATTTATTT
1 TTATTTATTT
49178627 CAAGTTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.35
26 4 0.12
27 4 0.12
29 14 0.41
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATTTATTTTAAACTTATTCTTATATA
Found at i:49178740 original size:29 final size:29
Alignment explanation
Indices: 49178678--49178756 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
49178668 ATTATCCATT
49178678 TTTTTATATATATTATTTATTTTTAAATTG
1 TTTTTATATATATTATTTA-TTTTAAATTG
*
49178708 ---TTATATATATTATTTATTTTGAATTG
1 TTTTTATATATATTATTTATTTTAAATTG
* *
49178734 TTTTTATATACATCATTTATTTT
1 TTTTTATATATATTATTTATTTT
49178757 TTTAAACTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 9 0.21
27 16 0.37
29 18 0.42
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTTATATATATTATTTATTTTAAATTG
Found at i:49178803 original size:28 final size:28
Alignment explanation
Indices: 49178766--49178819 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
49178756 TTTTAAACTA
* *
49178766 TTTTGTATATTATTTATTTGAAACTTCT
1 TTTTGCATATTATGTATTTGAAACTTCT
*
49178794 TTTTGCATATTATGTATTTTAAACTT
1 TTTTGCATATTATGTATTTGAAACTT
49178820 TTTATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTGCATATTATGTATTTGAAACTTCT
Done.