Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 144 of 318
Found at i:44706916 original size:17 final size:17
Alignment explanation
Indices: 44706894--44706944 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
44706884 TTTGGGAAGT
*
44706894 AGAAGAACAAGAGAAAA
1 AGAAGAAAAAGAGAAAA
* **
44706911 AGAAGAATAAGA-AGATG
1 AGAAGAAAAAGAGA-AAA
44706928 AGAAGAAAAAGAGAAAA
1 AGAAGAAAAAGAGAAAA
44706945 TGGAAGGAGC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.25, T:0.04
Consensus pattern (17 bp):
AGAAGAAAAAGAGAAAA
Found at i:44712333 original size:6 final size:6
Alignment explanation
Indices: 44712322--44712346 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44712312 GATTTGAAAT
44712322 TCAGAA TCAGAA TCAGAA TCAGAA T
1 TCAGAA TCAGAA TCAGAA TCAGAA T
44712347 TACACTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (6 bp):
TCAGAA
Found at i:44716913 original size:85 final size:85
Alignment explanation
Indices: 44716770--44716932 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 85
44716760 CATAAACAAG
* * *
44716770 TACAATGCGGACGTCTCAGACGTGGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAAACA
1 TACAATGCGGACGTCCCAGACATGGTCTTACATGTAATTCAATATCGAGGCCTCTGTCCCAAACA
*
44716835 GGGTCTTACACGAAATCAGA
66 CGGTCTTACACGAAATCAGA
* * * * * *
44716855 TACAATGCTGATGTCCCAGACATGGTCTTATATGTAAATCTC-A-CTCGAGGCCTGTGTCCCAGA
1 TACAATGCGGACGTCCCAGACATGGTCTTACATGT-AAT-TCAATATCGAGGCCTCTGTCCCAAA
44716918 CACGGTCTTACACGA
64 CACGGTCTTACACGA
44716933 TGTCTCAGAC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
85 60 0.91
86 4 0.06
87 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (85 bp):
TACAATGCGGACGTCCCAGACATGGTCTTACATGTAATTCAATATCGAGGCCTCTGTCCCAAACA
CGGTCTTACACGAAATCAGA
Found at i:44718915 original size:14 final size:15
Alignment explanation
Indices: 44718889--44718922 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
44718879 TAAGTAATGT
44718889 TTAATTATATTAATA
1 TTAATTATATTAATA
*
44718904 TTAATT-TATTAATG
1 TTAATTATATTAATA
44718918 TTAAT
1 TTAAT
44718923 ACAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAATTATATTAATA
Found at i:44729979 original size:36 final size:36
Alignment explanation
Indices: 44729932--44730000 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
44729922 AGTAAACTTT
*
44729932 ATTTAGTTCAGCAACCTTTTG-GATCTATTCTGATTG
1 ATTTAGTTCAGCAACCTTTCGAG-TCTATTCTGATTG
*
44729968 ATTTAGTTCAGCAGCCTTTCGAGTCTATTCTGA
1 ATTTAGTTCAGCAACCTTTCGAGTCTATTCTGA
44730001 CTAGCATGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (36 bp):
ATTTAGTTCAGCAACCTTTCGAGTCTATTCTGATTG
Found at i:44737299 original size:55 final size:55
Alignment explanation
Indices: 44737176--44737309 Score: 146
Period size: 55 Copynumber: 2.4 Consensus size: 55
44737166 ATGGGAAATC
* * *
44737176 CTGCCAAAAC-AACACGGGCGTGCGACACGCCCGTGTCTATAAGCCATTGTTGAAA
1 CTGCC-AAACTAACACGGGCGTGCGACACGCCCGTGTCTAGAAGCCATGGTCGAAA
* * * *
44737231 CTGCCAAAATAACACGGGCGTTCGACACGCCTC-TGTCTAGAAGCCCTGGTCGATA
1 CTGCCAAACTAACACGGGCGTGCGACACGCC-CGTGTCTAGAAGCCATGGTCGAAA
* * *
44737286 CTGTCAAACTAACACAGGTGTGCG
1 CTGCCAAACTAACACGGGCGTGCG
44737310 CATATATACA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
54 3 0.05
55 61 0.94
56 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (55 bp):
CTGCCAAACTAACACGGGCGTGCGACACGCCCGTGTCTAGAAGCCATGGTCGAAA
Found at i:44737637 original size:17 final size:19
Alignment explanation
Indices: 44737615--44737652 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
44737605 CCTTCCATTT
44737615 TTCTCCCCTC-TCTC-CCC
1 TTCTCCCCTCTTCTCACCC
44737632 TTCTCCCCTCTTCTCACCC
1 TTCTCCCCTCTTCTCACCC
44737651 TT
1 TT
44737653 GCGCACCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.03, C:0.58, G:0.00, T:0.39
Consensus pattern (19 bp):
TTCTCCCCTCTTCTCACCC
Found at i:44739348 original size:16 final size:16
Alignment explanation
Indices: 44739327--44739357 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44739317 ACTACTTTTT
44739327 ATTTTATTTTTATTTA
1 ATTTTATTTTTATTTA
44739343 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
44739358 CATCCTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTATTTTTATTTA
Found at i:44742837 original size:32 final size:32
Alignment explanation
Indices: 44742796--44742861 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
44742786 CCAAGTTTAA
44742796 TACATATGACAATTTCAATACACCAAATCATT
1 TACATATGACAATTTCAATACACCAAATCATT
* * *
44742828 TACATATGACAGTTTCCATATACCAAATCATT
1 TACATATGACAATTTCAATACACCAAATCATT
44742860 TA
1 TA
44742862 AACCATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (32 bp):
TACATATGACAATTTCAATACACCAAATCATT
Found at i:44744662 original size:16 final size:18
Alignment explanation
Indices: 44744641--44744673 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44744631 GATATGATAC
44744641 TAAAAT-TAT-TAAAAAT
1 TAAAATATATATAAAAAT
44744657 TAAAATATATATAAAAA
1 TAAAATATATATAAAAA
44744674 AATTAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATATATATAAAAAT
Found at i:44744991 original size:19 final size:19
Alignment explanation
Indices: 44744966--44745056 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
44744956 AATCATATCT
44744966 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
44744985 ACTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
44745003 TCTAAGATTG--TATCGTA
1 TCTAAGATTGCATATCATA
44745020 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
44745039 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
44745057 TGAAGATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
17 15 0.23
18 15 0.23
19 35 0.54
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:44745203 original size:21 final size:20
Alignment explanation
Indices: 44745174--44745213 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
44745164 CTTGGACTTC
*
44745174 TTTTTTTTTGGGGTTTATTA
1 TTTTTTTTTGGGGCTTATTA
*
44745194 TTTTTGTTTTTGGGCTTATT
1 TTTTT-TTTTGGGGCTTATT
44745214 TCTGGGCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (20 bp):
TTTTTTTTTGGGGCTTATTA
Found at i:44745470 original size:45 final size:45
Alignment explanation
Indices: 44745406--44745724 Score: 331
Period size: 45 Copynumber: 7.1 Consensus size: 45
44745396 GGAAGCCGAT
* * *
44745406 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
44745451 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACATAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
44745496 ATCTGCT-GCTTCAATCTGCTTCCCGTCTAATACAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
44745540 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * *
44745585 ATCTGTTATCTCCGATTTTCTCCCCGTCTAATACAGATATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * * *
44745630 ATCTGTCATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAG
1 ATCTGTTATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAA
* *
44745675 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAA
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
44745722 ATC
1 ATC
44745725 ATCTTGGATC
Statistics
Matches: 225, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
43 6 0.03
44 42 0.19
45 147 0.65
46 1 0.00
47 19 0.08
48 5 0.02
49 5 0.02
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:44745571 original size:89 final size:90
Alignment explanation
Indices: 44745420--44745724 Score: 303
Period size: 89 Copynumber: 3.4 Consensus size: 90
44745410 GCTATCTTTG
* *
44745420 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCGATCTGCTCCCCGTCTAATAC
* *
44745485 ATAGACGCCAAATCTGCT-GCTTCA
66 AGAGACGCCAAATCTGCTAGCTCCA
* * *
44745509 ATCTGCTTCCCGTCTAATACAAAGATGCCAAATCTGTTATCTCCGATTTGCTCCCCGTCTAATAC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCGATCTGCTCCCCGTCTAATAC
* * * *
44745574 AGAGATGCCAAATCTGTTATCTCCG
66 AGAGACGCCAAATCTGCTAGCTCCA
* * * * ** * *
44745599 ATTTTCTCCCCGTCTAATACAGATATGCCAAATCTGTCATCTTGGATCTGCT--TCGATGTAA-A
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCGATCTGCTCCCCG-TCTAATA
* * * * * *
44745661 CACATGAAGGTCAGATCTGCTATGTCTTCG
65 CAGA-G-ACGCCAAATCTGCTA-G-CTCCA
*
44745691 ATCTGCTCCCCGTCTAATATAGAGATGCCAAATC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
44745725 ATCTTGGATC
Statistics
Matches: 177, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
88 6 0.03
89 80 0.45
90 57 0.32
92 34 0.19
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (90 bp):
ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCGATCTGCTCCCCGTCTAATAC
AGAGACGCCAAATCTGCTAGCTCCA
Found at i:44745958 original size:78 final size:78
Alignment explanation
Indices: 44745664--44745930 Score: 464
Period size: 78 Copynumber: 3.4 Consensus size: 78
44745654 ATGTAAACAC
*
44745664 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
44745729 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
44745742 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
44745806 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
44745820 ATGAAGGTCAGATCTACTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
44745885 TGGATCTGCTTCA
66 TGGATCTGCTTCA
*
44745898 ATGAAGGTCAGATCTGCTATGTCTTTGATCTGC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGC
44745931 CCTCTGTCGA
Statistics
Matches: 177, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
77 2 0.01
78 173 0.98
79 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:44760961 original size:32 final size:32
Alignment explanation
Indices: 44760922--44760986 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
44760912 TTTAATACAT
44760922 AACCAAAATTAAACATTTCAAAAGTAAAACCC
1 AACCAAAATTAAACATTTCAAAAGTAAAACCC
44760954 AACCAAAATTAAACATTTCAAAAGTAAAACCC
1 AACCAAAATTAAACATTTCAAAAGTAAAACCC
44760986 A
1 A
44760987 GCCTATACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.22, G:0.03, T:0.18
Consensus pattern (32 bp):
AACCAAAATTAAACATTTCAAAAGTAAAACCC
Found at i:44773710 original size:39 final size:39
Alignment explanation
Indices: 44773579--44773880 Score: 509
Period size: 39 Copynumber: 7.7 Consensus size: 39
44773569 TGAGCATTGG
44773579 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
44773618 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAG-T
1 -ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
44773657 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
44773696 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
44773735 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
44773774 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAG-TT
44773814 ATATATCCGGGCTAAGACCCGAAGGCAATTATGC-AGTT
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
44773852 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 -ATATATCCGGGCTAAGACCCGAAGGCAA
44773881 ATGTGTTTGC
Statistics
Matches: 249, Mismatches: 10, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
38 38 0.15
39 141 0.57
40 70 0.28
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:44782351 original size:40 final size:40
Alignment explanation
Indices: 44782296--44782603 Score: 535
Period size: 40 Copynumber: 7.7 Consensus size: 40
44782286 GAGCATTGGA
44782296 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
44782336 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
44782376 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
44782416 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
44782456 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
44782496 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
44782536 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
44782576 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
44782604 ATGTGTTTGC
Statistics
Matches: 255, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 255 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:44786526 original size:19 final size:20
Alignment explanation
Indices: 44786488--44786528 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
44786478 ATTTTAAACC
*
44786488 TACCTAGTTCAATCAACATT
1 TACCTAATTCAATCAACATT
*
44786508 TACCTAATT-AATGAACATT
1 TACCTAATTCAATCAACATT
44786527 TA
1 TA
44786529 TGCACTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (20 bp):
TACCTAATTCAATCAACATT
Found at i:44787217 original size:41 final size:39
Alignment explanation
Indices: 44787105--44787226 Score: 133
Period size: 37 Copynumber: 3.1 Consensus size: 39
44787095 CCAGTACCTT
* *
44787105 ATCGAATAATTTGAAGTAATAAGTTGACACCCAGTGTCTC
1 ATCGAATAAATCGAAGTAATAA-TTGACACCCAGTGTCTC
** *
44787145 ATCGGCTAAATCGAAGT-A-AATTGGCACCCAGTG-CATC
1 ATCGAATAAATCGAAGTAATAATTGACACCCAGTGTC-TC
*
44787182 ATCGAATTAATCCGAAGTAATAGATTGACACCCAGTGTCTC
1 ATCGAATAAAT-CGAAGTAATA-ATTGACACCCAGTGTCTC
44787223 ATCG
1 ATCG
44787227 GCTCGATGTC
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
36 1 0.01
37 22 0.33
38 8 0.12
39 2 0.03
40 14 0.21
41 19 0.28
42 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCGAATAAATCGAAGTAATAATTGACACCCAGTGTCTC
Found at i:44787359 original size:7 final size:7
Alignment explanation
Indices: 44787349--44787375 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
44787339 TTCCAATATC
44787349 CACATTT
1 CACATTT
44787356 CACATTT
1 CACATTT
44787363 CACATTT
1 CACATTT
44787370 CACATT
1 CACATT
44787376 AATTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (7 bp):
CACATTT
Found at i:44788077 original size:17 final size:16
Alignment explanation
Indices: 44788055--44788086 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
44788045 AGCTTTTCTC
44788055 CTTTTCTTTCTCTTTTT
1 CTTTTCTTTCT-TTTTT
44788072 CTTTTCTTTCTTTTT
1 CTTTTCTTTCTTTTT
44788087 CTTCTCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTCTTTCTTTTTT
Found at i:44788098 original size:21 final size:21
Alignment explanation
Indices: 44788057--44788098 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
44788047 CTTTTCTCCT
*
44788057 TTTCTTTCTCTTTTTCTTTTC
1 TTTCTTTCTCTTTCTCTTTTC
*
44788078 TTTCTTTTTC-TTCTCTGTTTC
1 TTTCTTTCTCTTTCTCT-TTTC
44788099 GTTTTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTCTTTCTCTTTTC
Found at i:44788254 original size:19 final size:21
Alignment explanation
Indices: 44788219--44788260 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
44788209 GTATTTCATA
*
44788219 TATTATTATTTTATACATATG
1 TATTATTATTTTATACACATG
44788240 TATT-TTATTTT-TACACATG
1 TATTATTATTTTATACACATG
44788259 TA
1 TA
44788261 CACACAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTATTATTTTATACACATG
Found at i:44794673 original size:41 final size:39
Alignment explanation
Indices: 44794566--44794681 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 39
44794556 CCTTATCGGA
* * *
44794566 TAATTCGAAGTAATAAGTTGACACCTAGTGTCTCATCGGC
1 TAATCCGAAGTAATAA-TTGACACCCAGTGTCTCATCGAC
* * *
44794606 TAAACCGAAGT-A-AATTGGCACCCAGTG-CATCATCGAAT
1 TAATCCGAAGTAATAATTGACACCCAGTGTC-TCATCG-AC
44794644 TAATCCGAAGTAATAGATTGACACCCAGTGTCTCATCG
1 TAATCCGAAGTAATA-ATTGACACCCAGTGTCTCATCG
44794682 GCTCGATGTC
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
36 1 0.02
37 17 0.27
38 12 0.19
39 2 0.03
40 10 0.16
41 19 0.31
42 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (39 bp):
TAATCCGAAGTAATAATTGACACCCAGTGTCTCATCGAC
Found at i:44795449 original size:17 final size:16
Alignment explanation
Indices: 44795427--44795458 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
44795417 AGCTTTTCTC
44795427 CTTTTCTTTCTCTTTTT
1 CTTTTCTTTCT-TTTTT
44795444 CTTTTCTTTCTTTTT
1 CTTTTCTTTCTTTTT
44795459 CTTCTCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTCTTTCTTTTTT
Found at i:44795470 original size:21 final size:21
Alignment explanation
Indices: 44795429--44795470 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
44795419 CTTTTCTCCT
*
44795429 TTTCTTTCTCTTTTTCTTTTC
1 TTTCTTTCTCTTTCTCTTTTC
*
44795450 TTTCTTTTTC-TTCTCTGTTTC
1 TTTCTTTCTCTTTCTCT-TTTC
44795471 GTTTTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTCTTTCTCTTTTC
Found at i:44797185 original size:26 final size:26
Alignment explanation
Indices: 44797156--44797229 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
44797146 CTCAATATAT
44797156 GGCTCTTCGTGAGCTTCCCGATAAAA
1 GGCTCTTCGTGAGCTTCCCGATAAAA
* * *
44797182 GGCTCTTCGTGAGCTTCCTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATAAAA
*
44797208 GGCTCTTC-AGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
44797230 TGGCTCCCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 11 0.26
26 31 0.74
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATAAAA
Found at i:44799946 original size:20 final size:20
Alignment explanation
Indices: 44799923--44799968 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
44799913 TAAGCTCGGT
*
44799923 TGAGCTCAAACGAGCTGAAA
1 TGAGCTCAAACAAGCTGAAA
* * *
44799943 TGAGCTTAAATAAGCTGAAT
1 TGAGCTCAAACAAGCTGAAA
44799963 TGAGCT
1 TGAGCT
44799969 GGACGGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (20 bp):
TGAGCTCAAACAAGCTGAAA
Found at i:44802090 original size:30 final size:31
Alignment explanation
Indices: 44802019--44802101 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
44802009 CTATTGTTTC
*
44802019 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATCTTCTTTTTCAATCTCA
*
44802050 AATTTC-TTTTC-GCTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATCT-TCTTTTTCAATCTCA
* *
44802079 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTCATCTTCTTTTT
44802102 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 7 0.16
30 30 0.68
31 7 0.16
ACGTcount: A:0.13, C:0.23, G:0.01, T:0.63
Consensus pattern (31 bp):
AATTTCTTTTTCATCTTCTTTTTCAATCTCA
Found at i:44802108 original size:12 final size:12
Alignment explanation
Indices: 44802077--44802101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44802067 TTTTTCAATC
44802077 TCATTTTCTTTT
1 TCATTTTCTTTT
44802089 TCATTTTCTTTT
1 TCATTTTCTTTT
44802101 T
1 T
44802102 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:44802119 original size:12 final size:12
Alignment explanation
Indices: 44802104--44802135 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
44802094 TTCTTTTTGC
44802104 TTTTCAAAGGCT
1 TTTTCAAAGGCT
44802116 TTTTCAAAGGCT
1 TTTTCAAAGGCT
44802128 TTTTCAAA
1 TTTTCAAA
44802136 TTCTCTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:44802192 original size:5 final size:5
Alignment explanation
Indices: 44802182--44802238 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
44802172 CTCTTGCCTC
* * *
44802182 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTTT TCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TC-TTT TC-TTT TCTTT
44802229 TCTTT TCTTT
1 TCTTT TCTTT
44802239 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 3 0.07
5 27 0.61
6 14 0.32
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:44802237 original size:25 final size:26
Alignment explanation
Indices: 44802186--44802234 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44802176 TGCCTCTCTT
* *
44802186 TTCTTTTT-ATTTTGTTTTCTTTTTC
1 TTCTTTTTCTTTTTCTTTTCTTTTTC
44802211 TTCTTTTTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTTCTTTTCTTTT
44802235 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (26 bp):
TTCTTTTTCTTTTTCTTTTCTTTTTC
Found at i:44804836 original size:20 final size:20
Alignment explanation
Indices: 44804813--44804858 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
44804803 TAAGCTCGGT
44804813 TGAGCTCAAACGAGCTGAAA
1 TGAGCTCAAACGAGCTGAAA
* *
44804833 TGAGCTCAAATGAGCTGAAT
1 TGAGCTCAAACGAGCTGAAA
44804853 TGAGCT
1 TGAGCT
44804859 GGACGGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (20 bp):
TGAGCTCAAACGAGCTGAAA
Found at i:44804859 original size:10 final size:10
Alignment explanation
Indices: 44804813--44804859 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
44804803 TAAGCTCGGT
*
44804813 TGAGCTCAAA
1 TGAGCTGAAA
*
44804823 CGAGCTGAAA
1 TGAGCTGAAA
*
44804833 TGAGCTCAAA
1 TGAGCTGAAA
*
44804843 TGAGCTGAAT
1 TGAGCTGAAA
44804853 TGAGCTG
1 TGAGCTG
44804860 GACGGAGCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (10 bp):
TGAGCTGAAA
Found at i:44806059 original size:79 final size:79
Alignment explanation
Indices: 44805928--44806085 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
44805918 TATCAGAGTG
44805928 TTTGCAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCT
1 TTTGCAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCT
44805993 CGAAGTCCAGTGCA
66 CGAAGTCCAGTGCA
44806007 TTTGCAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCT
1 TTTGCAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCT
44806072 CGAAGTCCAGTGCA
66 CGAAGTCCAGTGCA
44806086 CAATCCACAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.41
Consensus pattern (79 bp):
TTTGCAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCT
CGAAGTCCAGTGCA
Found at i:44813193 original size:23 final size:23
Alignment explanation
Indices: 44813146--44813188 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44813136 CATTTCAACC
44813146 TACTAAATATTAACTAAATTATA
1 TACTAAATATTAACTAAATTATA
*
44813169 TACTACATATT-A-TAAATTAT
1 TACTAAATATTAACTAAATTAT
44813189 TTATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TACTAAATATTAACTAAATTATA
Found at i:44836235 original size:20 final size:20
Alignment explanation
Indices: 44836210--44836255 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
44836200 AACGTTCGAC
44836210 ATCACTTTCTCATACACAAT
1 ATCACTTTCTCATACACAAT
44836230 ATCACTTTCTCATACACAAT
1 ATCACTTTCTCATACACAAT
44836250 ATCACT
1 ATCACT
44836256 CAATTCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (20 bp):
ATCACTTTCTCATACACAAT
Found at i:44837004 original size:11 final size:11
Alignment explanation
Indices: 44836988--44837013 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44836978 GATGATATCT
44836988 TTTTCTTTCTC
1 TTTTCTTTCTC
44836999 TTTTCTTTCTC
1 TTTTCTTTCTC
44837010 TTTT
1 TTTT
44837014 ATTCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:44843907 original size:39 final size:40
Alignment explanation
Indices: 44843806--44844029 Score: 275
Period size: 40 Copynumber: 5.7 Consensus size: 40
44843796 TTGAATGCTG
* *
44843806 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
44843845 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
44843886 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
44843925 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
44843964 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
*
44844003 AACCGGGCTAAGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
44844030 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
39 75 0.45
40 77 0.47
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:44843993 original size:79 final size:80
Alignment explanation
Indices: 44843806--44844029 Score: 296
Period size: 79 Copynumber: 2.8 Consensus size: 80
44843796 TTGAATGCTG
* * * *
44843806 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTATATCCGGGCTAAGACCCGAAGGCATT
*
44843870 TGTGCGAGATACTAAT
65 TGTGCGAGATACTAAA
44843886 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATA-TCCGGGCTAAGACCCGAAGGCAT
*
44843947 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATACTAAA
* * * *
44843964 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTATATCCGGGCTAAGACCCGAAGGCATTT
44844029 G
66 G
44844030 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
78 36 0.28
79 57 0.45
80 35 0.27
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:44844051 original size:79 final size:78
Alignment explanation
Indices: 44843806--44844062 Score: 258
Period size: 79 Copynumber: 3.3 Consensus size: 78
44843796 TTGAATGCTG
* * * * *
44843806 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATATCCGGGCTAAG-TCCCGAAGGCAT
*
44843869 TTGTGCGAGATACTAA
64 TTGTGCGAG-GACTAA
*
44843885 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATA-TCCGGGCTAAGTCCCGAAGGCA
*
44843946 TTTGTGCGAGTTACTAAA
63 TTTGTGCGAG-GACT-AA
*
44843964 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTT
**
44844029 GAACGAGGAGCTATA
66 GTGCGAGGA-CTA-A
* *
44844044 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
44844063 TACGTGATTT
Statistics
Matches: 154, Mismatches: 12, Indels: 23
0.81 0.06 0.12
Matches are distributed among these distances:
78 35 0.23
79 74 0.48
80 44 0.29
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGGACTAA
Found at i:44855821 original size:14 final size:14
Alignment explanation
Indices: 44855802--44855835 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44855792 TCCTGAAGTG
*
44855802 GATGATATGATTAT
1 GATGATATGACTAT
*
44855816 GATGATATTACTAT
1 GATGATATGACTAT
44855830 GATGAT
1 GATGAT
44855836 GAAAGTCGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (14 bp):
GATGATATGACTAT
Found at i:44856721 original size:15 final size:15
Alignment explanation
Indices: 44856697--44856740 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
44856687 TATGATATCG
44856697 TATCTTGGATTTCTC
1 TATCTTGGATTTCTC
* *
44856712 TATTTTGGATTCCTC
1 TATCTTGGATTTCTC
*
44856727 TATCTTGGTTTTCT
1 TATCTTGGATTTCT
44856741 TGTCATCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.11, C:0.18, G:0.14, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:44859893 original size:45 final size:44
Alignment explanation
Indices: 44859808--44859893 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 44
44859798 TATGTAATCT
*
44859808 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATGTGACATTC
1 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATTC
*
44859852 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATGA-ATGACA
1 GAACTCATTGAGTTGT-GTCTGAGTTCATGATAT-ATATGACA
44859894 CATCTTTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 16 0.42
45 21 0.55
46 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (44 bp):
GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATTC
Found at i:44864150 original size:90 final size:90
Alignment explanation
Indices: 44864039--44864218 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
44864029 CGGAATTCCT
44864039 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
1 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
44864104 AAGGCCTAGTAAACTTTGTGCTCTA
66 AAGGCCTAGTAAACTTTGTGCTCTA
*
44864129 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGTTTAAGATCCACGTTGAGTTGTCGA
1 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
44864194 AAGGCCTAGTAAACTTTGTGCTCTA
66 AAGGCCTAGTAAACTTTGTGCTCTA
44864219 ACTCCAAGGG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (90 bp):
CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
AAGGCCTAGTAAACTTTGTGCTCTA
Found at i:44870448 original size:44 final size:44
Alignment explanation
Indices: 44870398--44870551 Score: 160
Period size: 42 Copynumber: 3.6 Consensus size: 44
44870388 TGTGTTATTG
44870398 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
* * *
44870442 TGTAAGACCATGTCTGGGACATTGGCATCGTATATG-G-TTT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCG-ATTTGTGATTTACA
* *
44870484 TGTAAGAGCC-TGTCTGGGACAG-TGGCATTGATATT-TGA-TTATA
1 TGTAAGA-CCATGTCTGGGAC-GTTGGCATCGAT-TTGTGATTTACA
**
44870527 TGTAAGACCACATCTGGGACGTTGG
1 TGTAAGACCATGTCTGGGACGTTGG
44870552 TGTTGTACGA
Statistics
Matches: 91, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
41 2 0.02
42 32 0.35
43 23 0.25
44 30 0.33
45 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
Found at i:44870501 original size:42 final size:44
Alignment explanation
Indices: 44870397--44870551 Score: 160
Period size: 44 Copynumber: 3.6 Consensus size: 44
44870387 ATGTGTTATT
* *
44870397 GTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTAC
*
44870441 ATGTAAGACCATGTCTGGGACATTGGCATCGTATATG-G-TTT-C
1 GTGTAAGACCATGTCTGGGACATTGGCATCG-ATATGTGATTTAC
* * *
44870483 GTGTAAGAGCC-TGTCTGGGACAGTGGCATTGATATTTGATTATA-
1 GTGTAAGA-CCATGTCTGGGACATTGGCATCGATATGTGATT-TAC
** *
44870527 -TGTAAGACCACATCTGGGACGTTGG
1 GTGTAAGACCATGTCTGGGACATTGG
44870552 TGTTGTACGA
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
41 4 0.04
42 29 0.31
43 25 0.27
44 31 0.33
45 4 0.04
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (44 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTAC
Found at i:44874787 original size:12 final size:12
Alignment explanation
Indices: 44874772--44874813 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
44874762 CTCCAGTTTT
44874772 CACACGGCCTAG
1 CACACGGCCTAG
44874784 CACACGGCCTAG
1 CACACGGCCTAG
*
44874796 CACACGGCCTGG
1 CACACGGCCTAG
44874808 CACACG
1 CACACG
44874814 TGCGTGTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.24, C:0.43, G:0.26, T:0.07
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:44878632 original size:19 final size:20
Alignment explanation
Indices: 44878599--44878639 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
44878589 GGACTAAATC
*
44878599 GAAAACATTTGAAAATTTTA
1 GAAAACATTTAAAAATTTTA
44878619 GAAAA-ATTTAAAAATTTTA
1 GAAAACATTTAAAAATTTTA
44878638 GA
1 GA
44878640 CTGTAGGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (20 bp):
GAAAACATTTAAAAATTTTA
Found at i:44880822 original size:41 final size:42
Alignment explanation
Indices: 44880774--44880857 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
44880764 TTTAATTTGC
44880774 AAGTTTTGCACC-GTTACAATTTAGTCATTTTTCTTTAATTA
1 AAGTTTTGCACCTGTTACAATTTAGTCATTTTTCTTTAATTA
*
44880815 AAGTTTTGCACCTTTTACAATTTAGTCATTTTTCTTTAATTA
1 AAGTTTTGCACCTGTTACAATTTAGTCATTTTTCTTTAATTA
44880857 A
1 A
44880858 CTATCTATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 12 0.29
42 29 0.71
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.50
Consensus pattern (42 bp):
AAGTTTTGCACCTGTTACAATTTAGTCATTTTTCTTTAATTA
Found at i:44884903 original size:25 final size:25
Alignment explanation
Indices: 44884869--44884918 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
44884859 ATTTATATTC
44884869 ATCTAGCATTCATATTAGAAACCAA
1 ATCTAGCATTCATATTAGAAACCAA
44884894 ATCTAGCATTCATATTAGAAACCAA
1 ATCTAGCATTCATATTAGAAACCAA
44884919 TCAAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
ATCTAGCATTCATATTAGAAACCAA
Found at i:44890470 original size:14 final size:14
Alignment explanation
Indices: 44890447--44890476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44890437 TTGAAAATAT
44890447 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
44890461 GTTGATTTGGATTG
1 GTTGAATTGGATTG
44890475 GT
1 GT
44890477 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:44894864 original size:27 final size:27
Alignment explanation
Indices: 44894818--44894909 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
44894808 ATTACCAAAG
* * * *
44894818 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
* *
44894845 TACTCTCGATTTGCAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
44894872 TACCCTC-AGTTTACAAAATTACCATTT
1 TACCCTCGA-TTTACAAAATTACCATTT
44894899 TACCCTCGATT
1 TACCCTCGATT
44894910 GTGAAATTAC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 53 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:44894971 original size:27 final size:27
Alignment explanation
Indices: 44894941--44895091 Score: 212
Period size: 27 Copynumber: 5.6 Consensus size: 27
44894931 TGTAGAATAG
44894941 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
44894968 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
44894995 AATTACCGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
44895022 AATTACCGAAATACCCTTAATTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
44895049 AATTACCAAAATACCCCTAATTTATAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
44895076 AATTACAAAAATACCC
1 AATTACCAAAATACCC
44895092 TTGACTTTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:44894983 original size:54 final size:52
Alignment explanation
Indices: 44894908--44895094 Score: 194
Period size: 54 Copynumber: 3.5 Consensus size: 52
44894898 TTACCCTCGA
* * * *
44894908 TTGTGAAATTACTAAAATACCCTTGTAGAATAGAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCTTGTTG--TAAAATTACCAAAATACCCCTAGT
* * * *
44894962 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTAAAATTACCAAAATA-CCCTTG-TTGTAAAATTACCAAAATACCCCTAGT
* * * *
44895016 TTGTGAAATTACCGAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTAAT
1 TTGTAAAATTACCAAAATACCCTT--GTTGTAAAATTACCAAAATACCCCTAGT
* *
44895070 TTATAAAATTACAAAAATACCCTTG
1 TTGTAAAATTACCAAAATACCCTTG
44895095 ACTTTTTAAA
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
53 4 0.04
54 97 0.90
55 5 0.05
56 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (52 bp):
TTGTAAAATTACCAAAATACCCTTGTTGTAAAATTACCAAAATACCCCTAGT
Found at i:44895034 original size:81 final size:81
Alignment explanation
Indices: 44894941--44895090 Score: 237
Period size: 81 Copynumber: 1.9 Consensus size: 81
44894931 TGTAGAATAG
* * * **
44894941 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAAA
44895006 TACCACTGGTTTGTGA
66 TACCACTGGTTTGTGA
* *
44895022 AATTACCGAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAAA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAAA
44895087 TACC
66 TACC
44895091 CTTGACTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 62 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAAA
TACCACTGGTTTGTGA
Found at i:44895142 original size:27 final size:26
Alignment explanation
Indices: 44895099--44895154 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
44895089 CCCTTGACTT
44895099 TTTAAAAATTATAGAAATACCATTGG
1 TTTAAAAATTATAGAAATACCATTGG
*
44895125 TTTACAAAATTACT-GAAATACCCTTGG
1 TTTA-AAAATTA-TAGAAATACCATTGG
44895152 TTT
1 TTT
44895155 GTAGATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTATAGAAATACCATTGG
Found at i:44895186 original size:110 final size:108
Alignment explanation
Indices: 44894941--44895204 Score: 253
Period size: 110 Copynumber: 2.4 Consensus size: 108
44894931 TGTAGAATAG
* * * * * *
44894941 AATTACCAAAATACCCCTAGTTTG-TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAA
1 AATTACCAAAACACCCCTA-ATGGATAAAATTACAAAAATACCCCTACTTTGTAAAATTACAGAA
***
44895005 ATACCACTGGTTTGTGAAATTACCGAAATACCCTTAATTTGTAA
65 ATACCACTGGTTTACAAAATTACCGAAATACCCTTAATTTGTAA
* ** * * *
44895049 AATTACCAAAATACCCCTAATTTATAAAATTACAAAAATACCCTTGACTTTTTAAAAATTATAGA
1 AATTACCAAAACACCCCTAATGGATAAAATTACAAAAATACCCCT-ACTTTGT-AAAATTACAGA
* * ** *
44895114 AATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTGTAG
64 AATACCACTGGTTTACAAAATTACCGAAATACCCTTAATTTGTAA
* ** * *
44895159 ATTTACCAAAACA-CCCTTGTAGGATAAAATGACTAAAATACCCCTA
1 AATTACCAAAACACCCCTAAT-GGATAAAATTACAAAAATACCCCTA
44895205 ATAGGTAAAA
Statistics
Matches: 127, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
107 2 0.02
108 38 0.30
109 11 0.09
110 76 0.60
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (108 bp):
AATTACCAAAACACCCCTAATGGATAAAATTACAAAAATACCCCTACTTTGTAAAATTACAGAAA
TACCACTGGTTTACAAAATTACCGAAATACCCTTAATTTGTAA
Found at i:44895229 original size:27 final size:27
Alignment explanation
Indices: 44895199--44895250 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
44895189 GACTAAAATA
44895199 CCCCTAATA-GGTAAAAAGACCGTAAAG
1 CCCCT-ATAGGGTAAAAAGACCGTAAAG
**
44895226 CCCCTATAGGGTAAAGTGACCGTAA
1 CCCCTATAGGGTAAAAAGACCGTAA
44895251 TACCCTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (27 bp):
CCCCTATAGGGTAAAAAGACCGTAAAG
Found at i:44896120 original size:25 final size:24
Alignment explanation
Indices: 44896082--44896151 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
44896072 AGGAAGTGCT
*
44896082 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
44896106 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
44896131 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
44896152 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:44896164 original size:24 final size:24
Alignment explanation
Indices: 44896081--44896164 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
44896071 GAGGAAGTGC
* *
44896081 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
44896106 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
44896130 CAGAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTTTGCCCCAGTTTAT
44896154 TAAAAGAGGCT
1 TAAAAG-GGCT
44896165 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:44896358 original size:42 final size:42
Alignment explanation
Indices: 44896299--44896391 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
44896289 TAGTCTCCCC
*
44896299 AAATGGGCTTGCATACATTCATTGACATT-ACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTCA-ATGTGATATTG
44896341 AAATGGGCTTGCATACATCCATTGACATTCAATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTCAATGTGATATTG
44896383 AAATTGGGC
1 AAA-TGGGC
44896392 CTAAGGGCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 42 0.88
43 6 0.12
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTCAATGTGATATTG
Found at i:44896462 original size:31 final size:31
Alignment explanation
Indices: 44896415--44896555 Score: 246
Period size: 31 Copynumber: 4.5 Consensus size: 31
44896405 CGTTTACAGT
44896415 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
44896446 AAAAGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
44896477 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
44896508 AAAGGCTTCGACCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
44896539 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
44896556 ACATGTCAAG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:44899735 original size:10 final size:10
Alignment explanation
Indices: 44899720--44899752 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
44899710 CCAGGCCATA
44899720 TGTCTACCTG
1 TGTCTACCTG
44899730 TGTCTACCTG
1 TGTCTACCTG
44899740 TGTCTACCTG
1 TGTCTACCTG
44899750 TGT
1 TGT
44899753 GGACGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.27, G:0.21, T:0.42
Consensus pattern (10 bp):
TGTCTACCTG
Found at i:44903445 original size:24 final size:24
Alignment explanation
Indices: 44903413--44903477 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
44903403 TACTTGGGTT
*
44903413 ATTTGCCATCAATTCATCATTTTA
1 ATTTACCATCAATTCATCATTTTA
* *
44903437 ATTTACCATCAATTCATCCTTTTC
1 ATTTACCATCAATTCATCATTTTA
*
44903461 ATTTACCA-AAATTCATC
1 ATTTACCATCAATTCATC
44903478 CTTTGCCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 8 0.22
24 29 0.78
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTACCATCAATTCATCATTTTA
Found at i:44904843 original size:15 final size:15
Alignment explanation
Indices: 44904818--44904853 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
44904808 TCTTTAATTT
44904818 AATACTTTAATAAACC
1 AATA-TTTAATAAACC
44904834 AATATTTAATAAACC
1 AATATTTAATAAACC
44904849 AATAT
1 AATAT
44904854 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATTTAATAAACC
Found at i:44910677 original size:46 final size:46
Alignment explanation
Indices: 44910610--44910702 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
44910600 CGCCTTGTTT
* *
44910610 CCTAAGAGGGAGTCGTCGTATGTTAGACAAATATCAAATGACGGTA
1 CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAAATGACGGTA
* *
44910656 CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAGATGGCGGTA
1 CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAAATGACGGTA
44910702 C
1 C
44910703 ATTCTGCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (46 bp):
CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAAATGACGGTA
Found at i:44912123 original size:18 final size:18
Alignment explanation
Indices: 44912097--44912143 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
44912087 AACCGGCCAC
* * *
44912097 GTGCAGTGGTGGTTCGTA
1 GTGCGGTGGTGGTCCATA
44912115 GTGCGGTGGTGGTCCATA
1 GTGCGGTGGTGGTCCATA
*
44912133 GTGCGATGGTG
1 GTGCGGTGGTG
44912144 CTTGTAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.13, G:0.47, T:0.30
Consensus pattern (18 bp):
GTGCGGTGGTGGTCCATA
Found at i:44913256 original size:26 final size:26
Alignment explanation
Indices: 44913220--44913328 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
44913210 TGATACAAAT
44913220 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
44913246 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
44913272 TGATAATGGGTTAGGTAAA-GTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
44913297 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
44913323 TGATAA
1 TGATAA
44913329 GAATTTCATG
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
25 24 0.31
26 52 0.67
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:44913314 original size:51 final size:52
Alignment explanation
Indices: 44913220--44913328 Score: 168
Period size: 51 Copynumber: 2.1 Consensus size: 52
44913210 TGATACAAAT
44913220 TGATAATAGGTTAGGTAAATGTTCAATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCAATGATAATAGGTTAGGTAAATGTTCCA
* * *
44913272 TGATAATGGGTTAGGTAAA-GTTTC-ATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCAATGATAATAGGTTAGGTAAATGTTCCA
44913323 TGATAA
1 TGATAA
44913329 GAATTTCATG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
51 32 0.60
52 21 0.40
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCAATGATAATAGGTTAGGTAAATGTTCCA
Found at i:44914811 original size:26 final size:26
Alignment explanation
Indices: 44914748--44914822 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 26
44914738 AAAAGTAGCT
* * * *
44914748 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-GTGCA
44914776 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGGTGCA
44914802 AAATTACTGTTATA-CCCTAGG
1 AAATTACTGTTATACCCCTAGG
44914823 GTTAATTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 7 0.16
26 17 0.40
27 1 0.02
28 18 0.42
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGGTGCA
Found at i:44914988 original size:27 final size:26
Alignment explanation
Indices: 44914921--44915033 Score: 122
Period size: 27 Copynumber: 4.3 Consensus size: 26
44914911 TGGAGGAAGC
* *
44914921 GTTCTGGTGGCTATGCCACAAATAT-T
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
44914947 GAT-TGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
*
44914973 GTTCTGGTGGCCCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
44915000 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
44915027 GTTCTGG
1 GTTCTGG
44915034 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.01
25 17 0.23
26 10 0.14
27 30 0.41
28 16 0.22
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:44919001 original size:26 final size:26
Alignment explanation
Indices: 44918972--44919081 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
44918962 TGGTACAAAT
*
44918972 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATGGGTTAGGTAAATGTTTC-A
* *
44918998 TGATAATTGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
44919024 TGATAATGGGTTAGGAAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
44919050 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
44919076 TGATAA
1 TGATAA
44919082 GAATTTCATG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
26 75 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:44930925 original size:26 final size:26
Alignment explanation
Indices: 44930887--44930996 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
44930877 TGATACAAAT
*
44930887 TGATAATAAGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
44930913 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
44930939 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
44930965 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
44930991 TGATAA
1 TGATAA
44930997 GAATTTCATG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:44932476 original size:27 final size:25
Alignment explanation
Indices: 44932435--44932504 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
44932425 AAAAGTAGCT
* *
44932435 AAATTACTATAATACCCTATGTATGGA
1 AAATTACTGTTATACCCTA-G-ATGGA
* *
44932462 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATA-CCCTAGATGGA
*
44932488 AAATTACCGTTATACCC
1 AAATTACTGTTATACCC
44932505 CTAGGGTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.08
26 16 0.43
27 13 0.35
28 5 0.14
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (25 bp):
AAATTACTGTTATACCCTAGATGGA
Found at i:44932653 original size:27 final size:27
Alignment explanation
Indices: 44932612--44932724 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
44932602 GAGGAAGCGT
*
44932612 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
44932639 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * * *
44932666 TCTGGTGGCCCTGCCACGACTATCTTTA
1 TCTGGTGGCTCTGCCACAAATATC-TGA
* * * *
44932694 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
44932720 TCTGG
1 TCTGG
44932725 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
26 6 0.09
27 49 0.70
28 15 0.21
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:44932717 original size:54 final size:54
Alignment explanation
Indices: 44932610--44932733 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
44932600 TGGAGGAAGC
* *
44932610 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCCATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * * *
44932664 GTTCTGGTGGCCCTGCCACGACTATCTTTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCCATGCCACAAATATC-TGATCTGGTGACTCTGCCACATATATCT
**
44932718 GTTCTGGCAGCCATGC
1 GTTCTGGTGGCCATGC
44932734 TGCAAATTCT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 40 0.68
55 19 0.32
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.34
Consensus pattern (54 bp):
GTTCTGGTGGCCATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:44934836 original size:11 final size:11
Alignment explanation
Indices: 44934804--44934836 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
44934794 CCCTAGTTTT
*
44934804 TTTCTTTCTCT
1 TTTCTTTCTCC
44934815 TTTCTTTCTCC
1 TTTCTTTCTCC
44934826 TTTCTTTCTCC
1 TTTCTTTCTCC
44934837 CTTTTCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCTTTCTCC
Found at i:44934865 original size:18 final size:16
Alignment explanation
Indices: 44934839--44934892 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
44934829 CTTTCTCCCT
*
44934839 TTTCGTTTAAGCTTTCTG
1 TTTCTTTTAAGC-TT-TG
*
44934857 TTTCTTTTATGCTTTG
1 TTTCTTTTAAGCTTTG
*
44934873 TTTCTTTTTAACCTTTG
1 TTTC-TTTTAAGCTTTG
44934890 TTT
1 TTT
44934893 TATTTACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 6 0.19
17 15 0.48
18 10 0.32
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.65
Consensus pattern (16 bp):
TTTCTTTTAAGCTTTG
Found at i:44935172 original size:18 final size:18
Alignment explanation
Indices: 44935146--44935210 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
44935136 ATTACAAGTG
*
44935146 TATTTTCATGCACATGTT
1 TATTATCATGCACATGTT
* * *
44935164 TATTATCATTACCACAAGTG
1 TATTATCA-T-GCACATGTT
* *
44935184 TATTTTCATGCGCATGTT
1 TATTATCATGCACATGTT
44935202 TATTATCAT
1 TATTATCAT
44935211 TACCATACAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
18 20 0.57
19 2 0.06
20 13 0.37
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (18 bp):
TATTATCATGCACATGTT
Found at i:44935184 original size:38 final size:38
Alignment explanation
Indices: 44935139--44935215 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
44935129 CAAATATATT
44935139 ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
1 ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
*
44935177 ACAAGTGTATTTTCATGCGCATGTTTATTATCATTACC
1 ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
44935215 A
1 A
44935216 TACATCTACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (38 bp):
ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
Found at i:44940584 original size:23 final size:23
Alignment explanation
Indices: 44940558--44940603 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
44940548 GTACACGAAT
44940558 TCCAACCAAACACACCAGAATAA
1 TCCAACCAAACACACCAGAATAA
* *
44940581 TCCAACCAAACGCACTAGAATAA
1 TCCAACCAAACACACCAGAATAA
44940604 ATAATCCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.33, G:0.07, T:0.11
Consensus pattern (23 bp):
TCCAACCAAACACACCAGAATAA
Found at i:44940616 original size:27 final size:27
Alignment explanation
Indices: 44940558--44940627 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
44940548 GTACACGAAT
44940558 TCCAACCAAACACACCAG----AATAA
1 TCCAACCAAACACACCAGAATAAATAA
* *
44940581 TCCAACCAAACGCACTAGAATAAATAA
1 TCCAACCAAACACACCAGAATAAATAA
**
44940608 TCCTCCCAAACACACCAGAA
1 TCCAACCAAACACACCAGAA
44940628 AGGCATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 16 0.43
27 21 0.57
ACGTcount: A:0.49, C:0.34, G:0.06, T:0.11
Consensus pattern (27 bp):
TCCAACCAAACACACCAGAATAAATAA
Found at i:44941622 original size:16 final size:17
Alignment explanation
Indices: 44941601--44941640 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
44941591 GTTTGAGCTT
*
44941601 TTTGTTTC-TTTTATGC
1 TTTGTTTCTTTTTAAGC
44941617 TTTGTTTCTTTTTAAGC
1 TTTGTTTCTTTTTAAGC
44941634 TTTGTTT
1 TTTGTTT
44941641 TATTTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.70
Consensus pattern (17 bp):
TTTGTTTCTTTTTAAGC
Found at i:44945992 original size:4 final size:4
Alignment explanation
Indices: 44945983--44946106 Score: 65
Period size: 4 Copynumber: 30.8 Consensus size: 4
44945973 TTTTAATTCT
* * * *
44945983 TTTA TTTA TTCA TTTA TTTA TTTA CTTG TTTA TTTA TTCA -TTA TTCCT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA
* * * * * * * *
44946031 TTTA TTCTA ATCA TTTG TTTG TTCA TTTA CTTA TCTA TTTA TCTA -TTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
44946079 TTCA TTTA CTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTT
44946107 TAATCCTTGT
Statistics
Matches: 87, Mismatches: 26, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
3 5 0.06
4 72 0.83
5 9 0.10
6 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:44946221 original size:21 final size:21
Alignment explanation
Indices: 44946192--44946233 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
44946182 ATGCCTTCAT
*
44946192 TATTGTTACTATTTTATTATC
1 TATTATTACTATTTTATTATC
44946213 TATTATTACTATTTTATTATC
1 TATTATTACTATTTTATTATC
44946234 ATCTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTATTACTATTTTATTATC
Found at i:44946237 original size:24 final size:22
Alignment explanation
Indices: 44946187--44946230 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
44946177 TATTCATGCC
*
44946187 TTCAT-TATTGTTACTATTTTA
1 TTCATCTATTATTACTATTTTA
44946208 TT-ATCTATTATTACTATTTTA
1 TTCATCTATTATTACTATTTTA
44946229 TT
1 TT
44946231 ATCATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (22 bp):
TTCATCTATTATTACTATTTTA
Found at i:44946951 original size:26 final size:26
Alignment explanation
Indices: 44946922--44947029 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
44946912 TGGTACAAAT
44946922 TGATAATAGG-TTAGGTAAATGTTCCA
1 TGATAAT-GGATTAGGTAAATGTTCCA
*
44946948 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
44946974 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
44947000 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
44947026 TGAT
1 TGAT
44947030 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 2 0.03
26 75 0.97
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:44950539 original size:22 final size:20
Alignment explanation
Indices: 44950502--44950542 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
44950492 ATTAAAGTAA
*
44950502 TAAAATGTAAATAATTAAAT
1 TAAAATGTAAAAAATTAAAT
44950522 TAAAATGGATAAAAAATTAAA
1 TAAAAT-G-TAAAAAATTAAA
44950543 ACAAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
TAAAATGTAAAAAATTAAAT
Found at i:44956540 original size:2 final size:2
Alignment explanation
Indices: 44956533--44956566 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
44956523 ATTTATGGCT
*
44956533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44956567 CAGAGACAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44956607 original size:15 final size:15
Alignment explanation
Indices: 44956587--44956618 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44956577 TATGAAAATT
*
44956587 GCATGTGAATTTATG
1 GCATGTAAATTTATG
44956602 GCATGTAAATTTATG
1 GCATGTAAATTTATG
44956617 GC
1 GC
44956619 TTTTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (15 bp):
GCATGTAAATTTATG
Found at i:44957514 original size:20 final size:20
Alignment explanation
Indices: 44957489--44957539 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
44957479 TGAATCAAAA
*
44957489 AAAGGAAGAAA-AAAAATATT
1 AAAGGAA-AAATAAAAAAATT
44957509 AAAGGAAAAATAAAAAAATT
1 AAAGGAAAAATAAAAAAATT
44957529 AACA-GAAAAAT
1 AA-AGGAAAAAT
44957540 TGGGAGTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAGGAAAAATAAAAAAATT
Found at i:44958556 original size:21 final size:20
Alignment explanation
Indices: 44958528--44958572 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
44958518 TTTACTTCCG
44958528 TTTTATTTATTAAGTTATGT
1 TTTTATTTATTAAGTTATGT
* *
44958548 TTTTAATTTGTTAAGTTTTGT
1 TTTT-ATTTATTAAGTTATGT
44958569 TTTT
1 TTTT
44958573 TTTTTCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (20 bp):
TTTTATTTATTAAGTTATGT
Found at i:44961558 original size:26 final size:24
Alignment explanation
Indices: 44961529--44961583 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
44961519 TCTAAACTAA
44961529 TTTTAGGTAAATTTAATCGTTTATAT
1 TTTTAGGTAAATTTAAT--TTTATAT
** * *
44961555 TTTTTTGTTAATTTAATTTTTTAT
1 TTTTAGGTAAATTTAATTTTATAT
44961579 TTTTA
1 TTTTA
44961584 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.65
Consensus pattern (24 bp):
TTTTAGGTAAATTTAATTTTATAT
Found at i:44968217 original size:70 final size:70
Alignment explanation
Indices: 44968172--44968718 Score: 488
Period size: 70 Copynumber: 7.7 Consensus size: 70
44968162 TTTTCATATT
* * * *
44968172 AGTTGGGAGCTTTGGCTCGTGCTTACTATTTTGGAAGTCGCGATATTGAATCAACAAGCCTTTGG
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
44968237 ATTAC
66 ATTAC
** * * * * * * *
44968242 AACTAGGAGC-TTGAGCTCGCACTGACTATTTTGGAGGTCACAATATTAAATCAACAAGCATTTG
1 AGTTGGGAGCTTTG-GCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTG
44968306 GATTAC
65 GATTAC
* * * *
44968312 AATTGGGAGCTTTGGCTCGCGCTAACTATTTTGGAGGTTGCGATATTAAATCAGCGAGCCTTTGG
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
44968377 ATTAC
66 ATTAC
* * * * * * * ** * *
44968382 AGCTGGGAGCTTTGGTTCACACTAACTATTTTGGAGGTCGCAATATTGAATCAGTGAGCTTTTGC
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
44968447 A-TATC
66 ATTA-C
** * * * * * * *
44968452 AGTTGGGAGCTTTGGCTTACGCTTATTGTTTTGGAGGTTGGGATATTGAATCAGCGAGCTTTTGG
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
*
44968517 ACTAC
66 ATTAC
* * * * * * ** *
44968522 AGCTAGGAGCTTGAGCTTGAGCTCGTGCTTATTATTTTAGAGGCCATGATATTGAATCAACGAGC
1 AGTTGGGAGC-T----TTG-GCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGC
44968587 CTTTGGATTAC
60 CTTTGGATTAC
* * * * **
44968598 AGTTGAGAGCTTTGGCTCGCGCTTACTGTTTTGGAGGTCGTGATATTAAATCAGCGAGCCTTTTC
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
44968663 A-TATC
66 ATTA-C
* * *
44968668 AGTTGGGAGCTTTGGCTCTCGCTAACTATTTTAGAGGTCGCGATATTAAAT
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAAT
44968719 TGGTTGGGAA
Statistics
Matches: 389, Mismatches: 77, Indels: 22
0.80 0.16 0.05
Matches are distributed among these distances:
69 7 0.02
70 318 0.82
71 9 0.02
75 4 0.01
76 51 0.13
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (70 bp):
AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
ATTAC
Found at i:44968635 original size:286 final size:280
Alignment explanation
Indices: 44968156--44968714 Score: 690
Period size: 286 Copynumber: 2.0 Consensus size: 280
44968146 ATTAAATAAA
* **
44968156 TGAGCCTTTTCATATTAGTTGGGAGCTTTGGCTCGTGCTTACTATTTTGGAAGTCGCGATATTGA
1 TGAGCCTTTTCATATCAGTTGGGAGCTTTGGCTCACGCTTACTATTTTGGAAGTCGCGATATTGA
* * * *
44968221 ATCAACAAGCCTTTGGATTACAACTAGGAGCTTGAGCTCGCACTGACTATTTTGGAGGTCACAAT
66 ATCAACAAGCCTTTGGACTACAACTAGGAGCTTGAGCTAGCACTGACTATTTTAGAGGCCACAAT
* *
44968286 ATTAAATCAACAAGCATTTGGATTACAATTGGGAGCTTTGGCTCGCGCTAACTATTTTGGAGGTT
131 ATTAAATCAACAAGCATTTGGATTACAATTGAGAGCTTTGGCTCGCGCTAACTATTTTGGAGGTC
* * *
44968351 GCGATATTAAATCAGCGAGCCTTTGGAT-TACAGCTGGGAGCTTTGGTTCACACTAACTATTTTG
196 GCGATATTAAATCAGCGAGCCTTTGCATAT-CAGCTGGGAGCTTTGGCTCACACTAACTATTTTA
44968415 GAGGTCGCAATATTGAATCAG
260 GAGGTCGCAATATTGAATCAG
* * * * * *
44968436 TGAG-CTTTTGCATATCAGTTGGGAGCTTTGGCTTACGCTTATTGTTTTGGAGGTTGGGATATTG
1 TGAGCCTTTT-CATATCAGTTGGGAGCTTTGGCTCACGCTTACTATTTTGGAAGTCGCGATATTG
* * * * * *
44968500 AATCAGCGAGCTTTTGGACTACAGCTAGGAGCTTGAGCTTGAGCTCGTGCTTATTATTTTAGAGG
65 AATCAACAAGCCTTTGGACTACAACTAGGAGCTTGAGC-T-AGCAC-TG---ACTATTTTAGAGG
** * * * * * *
44968565 CCATGATATTGAATCAACGAGCCTTTGGATTACAGTTGAGAGCTTTGGCTCGCGCTTACTGTTTT
124 CCACAATATTAAATCAACAAGCATTTGGATTACAATTGAGAGCTTTGGCTCGCGCTAACTATTTT
* * * * *
44968630 GGAGGTCGTGATATTAAATCAGCGAGCCTTTTCATATCAGTTGGGAGCTTTGGCTCTCGCTAACT
189 GGAGGTCGCGATATTAAATCAGCGAGCCTTTGCATATCAGCTGGGAGCTTTGGCTCACACTAACT
*
44968695 ATTTTAGAGGTCGCGATATT
254 ATTTTAGAGGTCGCAATATT
44968715 AAATTGGTTG
Statistics
Matches: 233, Mismatches: 38, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
279 5 0.02
280 82 0.35
281 1 0.00
282 3 0.01
283 2 0.01
286 139 0.60
287 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (280 bp):
TGAGCCTTTTCATATCAGTTGGGAGCTTTGGCTCACGCTTACTATTTTGGAAGTCGCGATATTGA
ATCAACAAGCCTTTGGACTACAACTAGGAGCTTGAGCTAGCACTGACTATTTTAGAGGCCACAAT
ATTAAATCAACAAGCATTTGGATTACAATTGAGAGCTTTGGCTCGCGCTAACTATTTTGGAGGTC
GCGATATTAAATCAGCGAGCCTTTGCATATCAGCTGGGAGCTTTGGCTCACACTAACTATTTTAG
AGGTCGCAATATTGAATCAG
Found at i:44976872 original size:2 final size:2
Alignment explanation
Indices: 44976867--44976905 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
44976857 AATTTTTTTA
44976867 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
44976906 GTCCTGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44983292 original size:21 final size:22
Alignment explanation
Indices: 44983266--44983306 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44983256 ATAATTATAT
44983266 TAATTATA-TTATGTTAAATAA
1 TAATTATATTTATGTTAAATAA
*
44983287 TAATTATATTTATTTTAAAT
1 TAATTATATTTATGTTAAAT
44983307 CATTAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TAATTATATTTATGTTAAATAA
Found at i:44983454 original size:38 final size:40
Alignment explanation
Indices: 44983410--44983490 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 40
44983400 TATTTAGTAC
* *
44983410 AATAAAATATTTATTATATTCAT-TTGTGT-TTTTAATAT
1 AATAAAAAATTTATTATATTCATGTAGTGTCTTTTAATAT
*
44983448 AATAAAAAATTTATTATATTTATGGTAGTGTCTTTTAATAT
1 AATAAAAAATTTATTATATTCAT-GTAGTGTCTTTTAATAT
44983489 AA
1 AA
44983491 ATATTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 21 0.57
40 5 0.14
41 11 0.30
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (40 bp):
AATAAAAAATTTATTATATTCATGTAGTGTCTTTTAATAT
Found at i:44984259 original size:30 final size:30
Alignment explanation
Indices: 44984225--44984284 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
44984215 ACTTAACAAG
44984225 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
44984255 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
44984285 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:44984657 original size:24 final size:24
Alignment explanation
Indices: 44984611--44984657 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
44984601 GATTATTGAA
*
44984611 TTTTCATAAAATAGTAATAAAAAG
1 TTTTCATAAAATAATAATAAAAAG
*
44984635 TTTTCATAAATTTAATAATAAAA
1 TTTTCATAAA-ATAATAATAAAA
44984658 TAAAAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
TTTTCATAAAATAATAATAAAAAG
Found at i:44985034 original size:14 final size:14
Alignment explanation
Indices: 44985015--44985045 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44985005 TGCTTATCTT
*
44985015 TATAGGGTAAATTA
1 TATAGGGTAAACTA
44985029 TATAGGGTAAACTA
1 TATAGGGTAAACTA
44985043 TAT
1 TAT
44985046 TGGTAGCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (14 bp):
TATAGGGTAAACTA
Found at i:44994786 original size:188 final size:189
Alignment explanation
Indices: 44994416--44994826 Score: 630
Period size: 188 Copynumber: 2.2 Consensus size: 189
44994406 GCAGCAACCT
* * *
44994416 TCACAATTCTATCTCAATGCCTAATCATATAATGCAAGTTCAAGAATCTAGAGCTTAATTCAGTC
1 TCACAATTCTACCTCAATGCCTAATCAGATAATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
* ** * *
44994481 GGTTCATGCAATCTTCCTTTAAAGATGGTATTTTGATACATCTCAAGTTAGATTCTCAACATTGC
66 AGTTCATGCAATCACCCTTTAAAGATGGTATTTTGAAACATCTCAAGTTAGAGTCTCAACATTGC
44994546 AATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
131 AATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
*
44994605 TCACAATTCTACCTCAATGCCTAATCAGATGATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
1 TCACAATTCTACCTCAATGCCTAATCAGATAATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
* *
44994670 AGTTCATGCAATCACCC-TT-ATGAGTGGTATTTTGAAACGTCTCAAGTTAGAGTCTCAACATTG
66 AGTTCATGCAATCACCCTTTAAAGA-TGGTATTTTGAAACATCTCAAGTTAGAGTCTCAACATTG
* * * *
44994733 CAATCGTTCCCCTATCCCCATACTAAGGCCTCCTTTACACGAAATATTGCAAGTTCAACA
130 CAATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
* *
44994793 TCACAATTCT-CTCTCAATGCCTAACCAAATAATG
1 TCACAATTCTAC-CTCAATGCCTAATCAGATAATG
44994827 TGCTTAGTTG
Statistics
Matches: 202, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
187 4 0.02
188 123 0.61
189 75 0.37
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (189 bp):
TCACAATTCTACCTCAATGCCTAATCAGATAATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
AGTTCATGCAATCACCCTTTAAAGATGGTATTTTGAAACATCTCAAGTTAGAGTCTCAACATTGC
AATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
Found at i:44995884 original size:3 final size:3
Alignment explanation
Indices: 44995876--44995908 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
44995866 TTCAACGGTA
44995876 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
44995909 TTTTCAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:45008626 original size:48 final size:48
Alignment explanation
Indices: 45008559--45008792 Score: 237
Period size: 48 Copynumber: 5.0 Consensus size: 48
45008549 CACATGGTAG
*
45008559 GATGCCAATGCCA-GATCCCAGATATGGTTTTACATGGGATCACATATC
1 GATGCCAATGCCATG-TCCCAGATATGGTCTTACATGGGATCACATATC
* *
45008607 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCATAGATC
1 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATC
** **
45008655 GATGCCAATGCCATGTCTAAGGCATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATC
** * * ** * *
45008703 GATGCC---GTTA-G-CCCAGCTATGGTCTTACACGAAATTATATATC
1 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATC
* * * * *
45008746 GATGCCAAAGACATGTCCTAGACATGGTCTTACATGGGATCGCATAT
1 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATAT
45008793 AACCCTAACA
Statistics
Matches: 149, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
43 29 0.19
44 1 0.01
45 2 0.01
46 2 0.01
47 1 0.01
48 113 0.76
49 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATC
Found at i:45008772 original size:91 final size:94
Alignment explanation
Indices: 45008582--45008792 Score: 250
Period size: 91 Copynumber: 2.3 Consensus size: 94
45008572 GATCCCAGAT
* * **
45008582 ATGGTTTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGAT
1 ATGGTCTTACATGGGATCACATATCGATGCC-A-GCCATGTCCCAGATATGGTCTTACACGAAAT
* * *
45008647 CATAGATCGATGCCAATGCCATGTCTAAGGC
64 CATAGATCGATGCCAAAGACATGTCTAAGAC
** * *
45008678 ATGGTCTTACATGGGATCACATATCGATGCC-GTTA-G-CCCAGCTATGGTCTTACACGAAATTA
1 ATGGTCTTACATGGGATCACATATCGATGCCAGCCATGTCCCAGATATGGTCTTACACGAAATCA
*
45008740 TATATCGATGCCAAAGACATGTCCT-AGAC
66 TAGATCGATGCCAAAGACATGT-CTAAGAC
*
45008769 ATGGTCTTACATGGGATCGCATAT
1 ATGGTCTTACATGGGATCACATAT
45008793 AACCCTAACA
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
91 66 0.65
92 3 0.03
93 2 0.02
96 30 0.30
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (94 bp):
ATGGTCTTACATGGGATCACATATCGATGCCAGCCATGTCCCAGATATGGTCTTACACGAAATCA
TAGATCGATGCCAAAGACATGTCTAAGAC
Found at i:45010811 original size:22 final size:21
Alignment explanation
Indices: 45010780--45010821 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
45010770 TAAATTATAT
*
45010780 ATGTTAATTTATTTGAATTGA
1 ATGTTAATTTATGTGAATTGA
*
45010801 ATGTTGAATTTGTGTGAATTG
1 ATGTT-AATTTATGTGAATTG
45010822 TATAAGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (21 bp):
ATGTTAATTTATGTGAATTGA
Found at i:45011312 original size:23 final size:24
Alignment explanation
Indices: 45011264--45011316 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
45011254 TCTTTGTGAA
* * *
45011264 CTTCCTATTTATAGCTCTGATGAG
1 CTTCCTAATTATAGCTCAGATAAG
45011288 CTTCCTAATT-TAGCTCAGATAAG
1 CTTCCTAATTATAGCTCAGATAAG
45011311 CTTCCT
1 CTTCCT
45011317 GGTATATGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.40
Consensus pattern (24 bp):
CTTCCTAATTATAGCTCAGATAAG
Found at i:45036876 original size:43 final size:43
Alignment explanation
Indices: 45036818--45036975 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
45036808 GTTACCGAGC
*
45036818 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
* * * *
45036861 TGTGCTTACGTGTAAGACCATTTCTGAGACATTGGCATCAT-TA-
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCAT--TGTAT
* * * * * *
45036904 TATGATTTCGTGTAAGACCCTATCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
*
45036946 ATGTGATAACATGTAAGACCATATCTGGGA
1 -TGTGATTACATGTAAGACCATATCTGGGA
45036976 TATGACATTG
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
43 89 0.96
44 2 0.02
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
Found at i:45039565 original size:27 final size:27
Alignment explanation
Indices: 45039522--45039619 Score: 160
Period size: 27 Copynumber: 3.6 Consensus size: 27
45039512 CGTACCTGAA
* *
45039522 CCCTCATGTGATAAAATGACGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTG
*
45039549 CCTTTATGTGATAAAATGATGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTG
*
45039576 CCCTTATGTGATAAAATGATGATTTTT
1 CCCTTATGTGATAAAATGATGATTTTG
45039603 CCCTTATGTGATAAAAT
1 CCCTTATGTGATAAAAT
45039620 AACCGAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (27 bp):
CCCTTATGTGATAAAATGATGATTTTG
Found at i:45039644 original size:27 final size:27
Alignment explanation
Indices: 45039612--45039682 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
45039602 TCCCTTATGT
*
45039612 GATAAAATAACCGAAATACCCTCATAAG
1 GATAAAATAACCGAAATACCCACAT-AG
*
45039640 G-TAAAATGATCC-AAATACCCACATAG
1 GATAAAAT-AACCGAAATACCCACATAG
* *
45039666 GATAGAATGACCGAAAT
1 GATAAAATAACCGAAAT
45039683 GCCCCTGTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
26 5 0.14
27 26 0.74
28 4 0.11
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (27 bp):
GATAAAATAACCGAAATACCCACATAG
Found at i:45039808 original size:23 final size:23
Alignment explanation
Indices: 45039765--45039814 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
45039755 CTGTATTTGA
45039765 GCATGCCATGTTATATGTATGTT
1 GCATGCCATGTTATATGTATGTT
45039788 GCAT-CCATGTATAATAT-TATGTT
1 GCATGCCATGT-T-ATATGTATGTT
45039811 GCAT
1 GCAT
45039815 TGCATGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (23 bp):
GCATGCCATGTTATATGTATGTT
Found at i:45040479 original size:33 final size:33
Alignment explanation
Indices: 45040442--45040531 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
45040432 ATAATCACTG
*
45040442 ATGCCATAACATAGCTATGGTCTTTTCACTAGA
1 ATGCCATAGCATAGCTATGGTCTTTTCACTAGA
*
45040475 ATGCCATAGCATAGCTATGTTCTTTTCACTAGA
1 ATGCCATAGCATAGCTATGGTCTTTTCACTAGA
45040508 ATGCCATAGC-TCAGCTATGGTCTT
1 ATGCCATAGCAT-AGCTATGGTCTT
45040532 ACCTCTTCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
32 1 0.02
33 52 0.98
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (33 bp):
ATGCCATAGCATAGCTATGGTCTTTTCACTAGA
Found at i:45040655 original size:48 final size:47
Alignment explanation
Indices: 45040601--45040714 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 47
45040591 TTTTACTAAA
* **
45040601 ATGCCATAGCCTCGC-TATGGTCTTACATCTTATACACATATCACACCG
1 ATGCCATAGCC-CACATATGGTCTTACA-CAAATACACATATCACACCG
* * * *
45040649 ATGCCATATCCCACATATGGTCTTACACAAATGCACATATCACTCTG
1 ATGCCATAGCCCACATATGGTCTTACACAAATACACATATCACACCG
* *
45040696 ATGCCATATCCCAGATATG
1 ATGCCATAGCCCACATATG
45040715 ATTTTACATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 35 0.61
48 22 0.39
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (47 bp):
ATGCCATAGCCCACATATGGTCTTACACAAATACACATATCACACCG
Found at i:45040704 original size:47 final size:48
Alignment explanation
Indices: 45040616--45040723 Score: 137
Period size: 47 Copynumber: 2.3 Consensus size: 48
45040606 ATAGCCTCGC
**
45040616 TATGGTCTTACATCTTATACACATATCACACCGATGCCATATCCCACA
1 TATGGTCTTACATCAAATACACATATCACACCGATGCCATATCCCACA
* * * *
45040664 TATGGTCTTACA-CAAATGCACATATCACTCTGATGCCATATCCCAGA
1 TATGGTCTTACATCAAATACACATATCACACCGATGCCATATCCCACA
* *
45040711 TATGATTTTACAT
1 TATGGTCTTACAT
45040724 GGAAATCACT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 39 0.76
48 12 0.24
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (48 bp):
TATGGTCTTACATCAAATACACATATCACACCGATGCCATATCCCACA
Found at i:45040825 original size:31 final size:31
Alignment explanation
Indices: 45040742--45040921 Score: 243
Period size: 31 Copynumber: 5.8 Consensus size: 31
45040732 CTTGTCACTT
* *
45040742 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGTCGAAGCTACCACTTTTCACTGATCAG
** * * * **
45040773 ACAGCCAAAGCAACCGTTTTTCACTGATCAG
1 GTAGTCGAAGCTACCACTTTTCACTGATCAG
*
45040804 GTAGTTGAAGCTACCACTTTTCACTGATCAG
1 GTAGTCGAAGCTACCACTTTTCACTGATCAG
* * *
45040835 GTAGCCGAAGCTACCACTTTTCACTAATTAG
1 GTAGTCGAAGCTACCACTTTTCACTGATCAG
45040866 GTAGTCGAAGCTACCACTTTTCACTGATCAG
1 GTAGTCGAAGCTACCACTTTTCACTGATCAG
45040897 GTAGTCGAAGCTACCACTTTTCACT
1 GTAGTCGAAGCTACCACTTTTCACT
45040922 TGTCATTTGT
Statistics
Matches: 127, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 127 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (31 bp):
GTAGTCGAAGCTACCACTTTTCACTGATCAG
Found at i:45040985 original size:50 final size:50
Alignment explanation
Indices: 45040897--45041063 Score: 199
Period size: 50 Copynumber: 3.3 Consensus size: 50
45040887 CACTGATCAG
* * * * *
45040897 GTAGTCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACGTATCACTT-TCACTTGTCCTTGATCAGATAAGT
* * * *
45040948 GTAACCGAAGCTATCACGTATCGCTTTCGCTTGTCCTTGATTAGATAAGT
1 GTAGCCGAAGCTATCACGTATCACTTTCACTTGTCCTTGATCAGATAAGT
* * * * *
45040998 ATAGCCGAAACTATCACTTATCACTTTCACTTGTTCTTGATCAGATAAAT
1 GTAGCCGAAGCTATCACGTATCACTTTCACTTGTCCTTGATCAGATAAGT
45041048 GTAGCCGAAGCTATCA
1 GTAGCCGAAGCTATCA
45041064 TTTATTATTT
Statistics
Matches: 96, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 76 0.79
51 20 0.21
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACGTATCACTTTCACTTGTCCTTGATCAGATAAGT
Found at i:45047598 original size:21 final size:21
Alignment explanation
Indices: 45047551--45047598 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
45047541 GTCTAGAATG
* * *
45047551 TGAATTGAATTGAATTGAGCA
1 TGAAATGAATTAAATTGAGAA
*
45047572 TGAAATGAATTAAATTGATAA
1 TGAAATGAATTAAATTGAGAA
*
45047593 TTAAAT
1 TGAAAT
45047599 TCATTTATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (21 bp):
TGAAATGAATTAAATTGAGAA
Done.