Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 294 of 297
Found at i:99900227 original size:41 final size:40
Alignment explanation
Indices: 99900154--99900274 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 40
99900144 TAACGTTATT
* * *
99900154 GCACACTTAGTGCCATCACATTAAACCGAAGCTATCTCAGTACC
1 GCACACTTAGTGCCA-CATA-T-AGCCGAAGCTATCTCAAT-CC
*
99900198 GCACACTTAGTGCCACATATAGCCGAAGCTAT-TCCAATTC
1 GCACACTTAGTGCCACATATAGCCGAAGCTATCT-CAATCC
* * * * *
99900238 GCACACTAAGTGCTATATATAGCCAAAACTATCTCAA
1 GCACACTTAGTGCCACATATAGCCGAAGCTATCTCAA
99900275 AACACACTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
40 32 0.48
41 15 0.23
42 1 0.02
43 3 0.05
44 15 0.23
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (40 bp):
GCACACTTAGTGCCACATATAGCCGAAGCTATCTCAATCC
Found at i:99907431 original size:17 final size:17
Alignment explanation
Indices: 99907409--99907442 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
99907399 TTGTTGGTTC
99907409 GGTTTTGAAATTCAAAA
1 GGTTTTGAAATTCAAAA
99907426 GGTTTTGAAATTCAAAA
1 GGTTTTGAAATTCAAAA
99907443 CCGTTTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
GGTTTTGAAATTCAAAA
Found at i:99907592 original size:17 final size:18
Alignment explanation
Indices: 99907560--99907634 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 18
99907550 AATTAGAAAT
*
99907560 TAAAAGATAATAATATTAA
1 TAAAA-ATATTAATATTAA
* *
99907579 TTAAAAT-TTAATATTCA
1 TAAAAATATTAATATTAA
*
99907596 TAAAAATATTAAACATTAA
1 TAAAAATATT-AATATTAA
*
99907615 TAAAAAAATATTAAAATTAA
1 T--AAAAATATTAATATTAA
99907635 AACCTGACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 14 0.31
18 4 0.09
19 11 0.24
20 7 0.16
21 9 0.20
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAAAATATTAATATTAA
Found at i:99909432 original size:46 final size:45
Alignment explanation
Indices: 99909328--99909545 Score: 192
Period size: 46 Copynumber: 4.8 Consensus size: 45
99909318 AGATTTGTGT
**
99909328 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGA-GACGAA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAGATGA-G-A
* *
99909375 GGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGA
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAG-ATGAGA
* ** **
99909422 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCCTTGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-ACAGATGAGA
* * * * *
99909468 GCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTACGGGAT-A-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AGATGAGA
* *
99909512 GCTAGTGTAAGACATGTCTGTGACATGCATCGGC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC
99909546 ATGGTTACAT
Statistics
Matches: 141, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
44 30 0.21
46 76 0.54
47 20 0.14
48 13 0.09
49 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATGAGA
Found at i:99909481 original size:92 final size:90
Alignment explanation
Indices: 99909328--99909582 Score: 262
Period size: 90 Copynumber: 2.8 Consensus size: 90
99909318 AGATTTGTGT
*
99909328 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAAGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACGAAGGCCAGTGTAAGACATGT
*
99909393 CTGGGACATGCATCAGCCACAGTATGAGA
64 CTGGGACATGCATCAGCCACAGGAT-A-A
* * * * *
99909422 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCCTTGAGATGTTA-GCCAGTGTCAGACATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG-AAGGCCAGTGTAAGACATGTC
* * * * *
99909486 TGGGACATGCGTCGGCTACGGGATAT
65 TGGGACATGCATCAGCCACAGGATAA
* * * ** * * *
99909512 GCTAGTGTAAGACATGTCTGTGACATGCATCGGCATGGTTAC-ATGTGTCAGTGTAAGACCTGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAAG-GCCAGTGTAAGACATGTC
99909576 TGGGACA
65 TGGGACA
99909583 CGGCATCGAC
Statistics
Matches: 133, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
90 56 0.42
91 1 0.01
92 49 0.37
93 15 0.11
94 12 0.09
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAAGGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACAGGATAA
Found at i:99911867 original size:9 final size:9
Alignment explanation
Indices: 99911855--99911911 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
99911845 TTTGATAAAC
99911855 ATGATATGT
1 ATGATATGT
*
99911864 ATGATATGCAC
1 ATGATATG--T
*
99911875 ATGACATGT
1 ATGATATGT
*
99911884 ATGATATGCAC
1 ATGATATG--T
99911895 ATGATATGT
1 ATGATATGT
99911904 ATGATATG
1 ATGATATG
99911912 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:99911878 original size:20 final size:20
Alignment explanation
Indices: 99911853--99911915 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
99911843 ATTTTGATAA
99911853 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
99911873 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
99911893 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
99911913 ACA
1 ACA
99911916 CGAGATGGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:99911995 original size:24 final size:24
Alignment explanation
Indices: 99911968--99912092 Score: 173
Period size: 24 Copynumber: 5.2 Consensus size: 24
99911958 GGAGGAAGTG
*
99911968 CAAAAGGGCTTATGCCTCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
99911992 CAAAAGGGCTTATGCCCCAGTTAC
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
99912016 CAAAAGGGCTTATACCCCAATTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
99912040 C-AAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
99912063 TAAAAGGGCCTT-TGCCCCAGTTAT
1 CAAAAGGG-CTTATGCCCCAGTTAT
*
99912087 TAAAAG
1 CAAAAG
99912093 AGACTAGGCC
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 20 0.22
24 68 0.75
25 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:99912081 original size:47 final size:48
Alignment explanation
Indices: 99911968--99912092 Score: 173
Period size: 47 Copynumber: 2.6 Consensus size: 48
99911958 GGAGGAAGTG
*
99911968 CAAAAGGGCTTATGCCTCAGTTATCAAAAGGGCTTATGCCCCAGTTAC
1 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAC
* * *
99912016 CAAAAGGGCTTATACCCCAATTATC-AAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAC
* *
99912063 TAAAAGGGCCTT-TGCCCCAGTTATTAAAAG
1 CAAAAGGG-CTTATGCCCCAGTTATCAAAAG
99912093 AGACTAGGCC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 38 0.57
48 29 0.43
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (48 bp):
CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAC
Found at i:99919201 original size:32 final size:32
Alignment explanation
Indices: 99919165--99919228 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
99919155 TTATGCCAAT
99919165 CTGAAGCGTAAGGATATTGAATATGCGGTAGG
1 CTGAAGCGTAAGGATATTGAATATGCGGTAGG
99919197 CTGAAGCGTAAGGATATTGAATATGCGGTAGG
1 CTGAAGCGTAAGGATATTGAATATGCGGTAGG
99919229 AGACATGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.25
Consensus pattern (32 bp):
CTGAAGCGTAAGGATATTGAATATGCGGTAGG
Found at i:99921488 original size:9 final size:9
Alignment explanation
Indices: 99921476--99921532 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
99921466 TTTGATAAAC
99921476 ATGATATGT
1 ATGATATGT
*
99921485 ATGATATGCAC
1 ATGATATG--T
*
99921496 ATGACATGT
1 ATGATATGT
*
99921505 ATGATATGCAC
1 ATGATATG--T
99921516 ATGATATGT
1 ATGATATGT
99921525 ATGATATG
1 ATGATATG
99921533 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:99921499 original size:20 final size:20
Alignment explanation
Indices: 99921474--99921544 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
99921464 ATTTTGATAA
99921474 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
99921494 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
99921514 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
99921534 ACATGAGATGT
1 ACATGATATGT
99921545 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:99921521 original size:11 final size:11
Alignment explanation
Indices: 99921485--99921539 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
99921475 CATGATATGT
99921485 ATGATATGCAC
1 ATGATATGCAC
* *
99921496 ATGACATG--T
1 ATGATATGCAC
99921505 ATGATATGCAC
1 ATGATATGCAC
*
99921516 ATGATATG--T
1 ATGATATGCAC
99921525 ATGATATGCAC
1 ATGATATGCAC
99921536 ATGA
1 ATGA
99921540 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:99921616 original size:24 final size:24
Alignment explanation
Indices: 99921589--99921695 Score: 178
Period size: 24 Copynumber: 4.4 Consensus size: 24
99921579 GGAGGAAGTG
99921589 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
99921613 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
99921637 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
99921661 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
99921685 TAAAAGAGGCT
1 CAAAAG-GGCT
99921696 AGGCCTCCAT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
24 76 0.95
25 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:99921937 original size:31 final size:31
Alignment explanation
Indices: 99921902--99921965 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
99921892 CATTTACAGT
99921902 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
99921933 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
99921964 AA
1 AA
99921966 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:99923578 original size:35 final size:35
Alignment explanation
Indices: 99923532--99923599 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
99923522 CGAGATTTAT
99923532 GATTGCCAGTGATGGCATTTGATGGAAAAAAAAAA
1 GATTGCCAGTGATGGCATTTGATGGAAAAAAAAAA
*
99923567 GATTGTCAGTGATGGCATTTGATGGAAAAAAAA
1 GATTGCCAGTGATGGCATTTGATGGAAAAAAAA
99923600 GAGAGAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.25
Consensus pattern (35 bp):
GATTGCCAGTGATGGCATTTGATGGAAAAAAAAAA
Found at i:99925068 original size:30 final size:31
Alignment explanation
Indices: 99925009--99925072 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
99924999 ACTTAACAAG
*
99925009 CAAATGCTTCTAAAATAGTAATAAAAATTAA
1 CAAATGCTTCTAAAATAATAATAAAAATTAA
*
99925040 CAAATGCCTT-TAAAATAATAA-GAAAATTAA
1 CAAATG-CTTCTAAAATAATAATAAAAATTAA
99925070 CAA
1 CAA
99925073 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 11 0.37
31 16 0.53
32 3 0.10
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAATAAAAATTAA
Found at i:99925127 original size:22 final size:22
Alignment explanation
Indices: 99925102--99925144 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
99925092 TATCCAAACA
99925102 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
99925124 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
99925145 AGTAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:99927489 original size:16 final size:16
Alignment explanation
Indices: 99927468--99927499 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
99927458 AGTTTAGGGG
99927468 CAAAAATATAATTTTT
1 CAAAAATATAATTTTT
*
99927484 CAAAAATATGATTTTT
1 CAAAAATATAATTTTT
99927500 GGGTCAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
CAAAAATATAATTTTT
Found at i:99942123 original size:40 final size:40
Alignment explanation
Indices: 99942073--99942162 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
99942063 CGTTTGAATG
*
99942073 AAAAACGCCGCTAAAGAACAAGCATTAGCGGTGCTTTTTA
1 AAAAACGCCGCTAAAGAACAAGCATTAGCGGCGCTTTTTA
* *
99942113 AAAAATGCCGCTAAAGAACGAGCATTAGCGGCGCTTTTTA
1 AAAAACGCCGCTAAAGAACAAGCATTAGCGGCGCTTTTTA
99942153 AAAAACGCCG
1 AAAAACGCCG
99942163 TTATAAGTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGAACAAGCATTAGCGGCGCTTTTTA
Found at i:99942181 original size:40 final size:40
Alignment explanation
Indices: 99942073--99942197 Score: 135
Period size: 40 Copynumber: 3.1 Consensus size: 40
99942063 CGTTTGAATG
* * *
99942073 AAAAACGCCGCTAAAGAACAAGCATTAGCGGTGCTTTTTA
1 AAAAACGCCGCTAAAGAACGACCATTAGCGGCGCTTTTTA
* *
99942113 AAAAATGCCGCTAAAGAACGAGCATTAGCGGCGCTTTTTA
1 AAAAACGCCGCTAAAGAACGACCATTAGCGGCGCTTTTTA
* ** * **
99942153 AAAAACGCCGTTATAAGTTC-ACCTTTAGCCACGCTTTTTA
1 AAAAACGCCGCTA-AAGAACGACCATTAGCGGCGCTTTTTA
99942193 AAAAA
1 AAAAA
99942198 AGGCCGCAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 69 0.95
41 4 0.05
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGAACGACCATTAGCGGCGCTTTTTA
Found at i:99942960 original size:15 final size:14
Alignment explanation
Indices: 99942940--99942974 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
99942930 ACTATTTTAA
*
99942940 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
99942954 GGGTTTAGGGATTAT
1 -GGTTTAGGGATTAT
99942969 GGTTTA
1 GGTTTA
99942975 AAGGTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:99943034 original size:14 final size:14
Alignment explanation
Indices: 99942983--99943056 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
99942973 TAAAGGTGAT
99942983 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
* **
99942996 TTTAAGGTTTAGGTA
1 -TTAAGGGTTAGGGG
*
99943011 TTACGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
99943025 TTAAGGGTTAGGTG
1 TTAAGGGTTAGGGG
* *
99943039 TTCATGGTTCAGGGG
1 TTAAGGGTT-AGGGG
99943054 TTA
1 TTA
99943057 TATTTTAGGA
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
14 37 0.82
15 8 0.18
ACGTcount: A:0.19, C:0.04, G:0.41, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:99943217 original size:7 final size:7
Alignment explanation
Indices: 99943205--99943230 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
99943195 TATCATTATA
99943205 GTTTAGG
1 GTTTAGG
99943212 GTTTAGG
1 GTTTAGG
99943219 GTTTAGG
1 GTTTAGG
99943226 GTTTA
1 GTTTA
99943231 AGCTTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:99943289 original size:15 final size:15
Alignment explanation
Indices: 99943256--99943302 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
99943246 TATTTTAAGG
**
99943256 TTTATGGATTATGAA
1 TTTATGGATTATGGT
*
99943271 TTTAGGGATTATGGT
1 TTTATGGATTATGGT
*
99943286 TTTATGGTTTATGGT
1 TTTATGGATTATGGT
99943301 TT
1 TT
99943303 AAAGGTTGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (15 bp):
TTTATGGATTATGGT
Found at i:99944243 original size:40 final size:40
Alignment explanation
Indices: 99944172--99944275 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
99944162 AAAGAAAATT
* ** *
99944172 AAAATTGAGCAATAGTGGCGTTTTTGGT-AAAACGCTGCA-A
1 AAAATTGAGCTATAGTGGCGTTTTTAATAAAAACAC--CATA
99944212 AAAATTGAGCTATAGTGGCGTTTTTAATAAAAACACCATA
1 AAAATTGAGCTATAGTGGCGTTTTTAATAAAAACACCATA
99944252 AAAAGTT--GCTATAGTGGCGTTTTT
1 AAAA-TTGAGCTATAGTGGCGTTTTT
99944276 GGTGGAAGCG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 19 0.33
40 30 0.53
41 8 0.14
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (40 bp):
AAAATTGAGCTATAGTGGCGTTTTTAATAAAAACACCATA
Found at i:99944568 original size:3 final size:3
Alignment explanation
Indices: 99944556--99944601 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
99944546 AATGGAAGTT
*
99944556 GAA G-A GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
99944602 GGAGGAGGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:99944615 original size:18 final size:16
Alignment explanation
Indices: 99944594--99944637 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 16
99944584 AGAAGAAGAA
99944594 GAAGAAGAGGAGGAGGAG
1 GAAGAAGAGG-GG-GGAG
99944612 GAAGAGAAGAGGGGGGAG
1 G-A-AGAAGAGGGGGGAG
99944630 GAAGAAGA
1 GAAGAAGA
99944638 AGAAGAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.25
17 1 0.04
18 6 0.25
19 3 0.12
20 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (16 bp):
GAAGAAGAGGGGGGAG
Found at i:99948141 original size:8 final size:8
Alignment explanation
Indices: 99948128--99948157 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
99948118 CCATTTTTGA
*
99948128 TAATCTTG
1 TAATCTCG
99948136 TAATCTCG
1 TAATCTCG
99948144 TAATCTCG
1 TAATCTCG
99948152 TAATCT
1 TAATCT
99948158 TCTTCTACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (8 bp):
TAATCTCG
Found at i:99949175 original size:43 final size:43
Alignment explanation
Indices: 99949106--99949252 Score: 154
Period size: 43 Copynumber: 3.5 Consensus size: 43
99949096 AATATTTTTT
* * * *
99949106 TAAAGGTCATGTTCTCTAGCAGCGTTTGTGAGAAAAGTGCCGC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
* * * * *
99949149 TAAAAGTCATGGTATTTAGCGTCGTTTTTGGGAAAAGCGCCGC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
* * * * *
99949192 TAGAAGTCATAGTCTTTAGCGGCATTTG-CAAAAAAGTG-CGC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
99949233 TAAAAGTCATGGTCTTTAGC
1 TAAAAGTCATGGTCTTTAGC
99949253 AGCATTTTTT
Statistics
Matches: 83, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
41 21 0.25
42 6 0.07
43 56 0.67
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
TAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
Found at i:99949248 original size:41 final size:41
Alignment explanation
Indices: 99949138--99949259 Score: 129
Period size: 41 Copynumber: 2.9 Consensus size: 41
99949128 CGTTTGTGAG
* ** **
99949138 AAAAGTGCCGCTAAAAGTCATGGTATTTAGCGTCGTTTTTGGG
1 AAAAGTGCCGCTAAAAGTCATGGTCTTTAGCG--GCATTTGAA
* * *
99949181 AAAAGCGCCGCTAGAAGTCATAGTCTTTAGCGGCATTTGCAA
1 AAAAGTGCCGCTAAAAGTCATGGTCTTTAGCGGCATTTG-AA
*
99949223 AAAAGTG-CGCTAAAAGTCATGGTCTTTAGCAGCATTT
1 AAAAGTGCCGCTAAAAGTCATGGTCTTTAGCGGCATTT
99949260 TTTAAAATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 32 0.48
42 6 0.09
43 28 0.42
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (41 bp):
AAAAGTGCCGCTAAAAGTCATGGTCTTTAGCGGCATTTGAA
Found at i:99960837 original size:46 final size:45
Alignment explanation
Indices: 99960766--99960890 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 45
99960756 CATCGGTAGG
* **
99960766 AAGCCTACTAGGCACAAGGCTCGATACAATACAGTACACCGGCATA
1 AAGCCTGCTAGGCACAAGGC-CGATACAATACAGTACACCAACATA
* *
99960812 AAGCCTGCTAGGCACAAGGACCGATACATTATAGTACACCAACATA
1 AAGCCTGCTAGGCACAAGG-CCGATACAATACAGTACACCAACATA
* * *
99960858 AAGCTTGCTAGGCTCAAGGCCCGATTCAATACA
1 AAGCCTGCTAGGCACAAGG-CCGATACAATACA
99960891 CTCAATACAT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 66 0.99
47 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (45 bp):
AAGCCTGCTAGGCACAAGGCCGATACAATACAGTACACCAACATA
Found at i:99966150 original size:49 final size:49
Alignment explanation
Indices: 99966001--99966364 Score: 573
Period size: 49 Copynumber: 7.6 Consensus size: 49
99965991 TTAAACCCAT
99966001 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
99966048 ATGTGAAAGTG--TATATATGTGAATAGGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTG-ATAAGGCCTAATGGCCGATGTGATGA
*
99966096 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
99966145 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
99966194 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
99966243 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
99966292 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAATGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
99966339 ATGTGAAAGTGCATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
99966365 TCCCGAAGGG
Statistics
Matches: 300, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
47 70 0.23
48 37 0.12
49 183 0.61
50 10 0.03
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:99966539 original size:37 final size:37
Alignment explanation
Indices: 99966483--99966561 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
99966473 CTGAGCTCTA
* **
99966483 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTACGTCCGGGT
*
99966520 AAGACCCGATAACTTCGTGTGGAGATTACGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTACGTCCGGGT
99966557 AAGAC
1 AAGAC
99966562 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTACGTCCGGGT
Found at i:99973857 original size:47 final size:47
Alignment explanation
Indices: 99973803--99974252 Score: 801
Period size: 47 Copynumber: 9.6 Consensus size: 47
99973793 TATTTGAATA
99973803 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
99973850 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
99973897 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
99973944 AATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
99973991 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
99974038 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
99974085 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
99974132 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
99974179 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
99974226 GATGTGAAAGTGCATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
99974253 TCCCGAAGGG
Statistics
Matches: 388, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 388 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:99974427 original size:37 final size:37
Alignment explanation
Indices: 99974373--99974449 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
99974363 GAGTTCTAAG
* * *
99974373 GACCCGATGACTACGTGTGGGGATTTTGTCCGGGTAA
1 GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
*
99974410 GACCCGATAACTTCGTGTGGAGATTATGTCCGGGTAA
1 GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
99974447 GAC
1 GAC
99974450 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
Found at i:99987455 original size:41 final size:41
Alignment explanation
Indices: 99987410--99987492 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
99987400 TGGTCAGGTA
99987410 ATCCTCCTAAGTATTCCAATCTTAGAATTTTCAGTTGTCTT
1 ATCCTCCTAAGTATTCCAATCTTAGAATTTTCAGTTGTCTT
*
99987451 ATCCTCCTAATTATTCCAATCTTAGAATTTTCAGTTGTCTT
1 ATCCTCCTAAGTATTCCAATCTTAGAATTTTCAGTTGTCTT
99987492 A
1 A
99987493 CTTATGCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (41 bp):
ATCCTCCTAAGTATTCCAATCTTAGAATTTTCAGTTGTCTT
Found at i:99989826 original size:7 final size:7
Alignment explanation
Indices: 99989816--99989851 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
99989806 GTTAAAAAAT
99989816 ATTTAAA
1 ATTTAAA
99989823 ATTTAAA
1 ATTTAAA
99989830 ATTTAAA
1 ATTTAAA
99989837 ATTTAAA
1 ATTTAAA
99989844 ATTTAAA
1 ATTTAAA
99989851 A
1 A
99989852 AGAAACATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:99991268 original size:27 final size:26
Alignment explanation
Indices: 99991208--99991269 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
99991198 ATAAGACTCC
99991208 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
99991234 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
99991262 ATTTTATT
1 ATTTTATT
99991270 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:99994960 original size:15 final size:14
Alignment explanation
Indices: 99994940--99994986 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
99994930 GCAACCTAAT
99994940 TTTTATTTTTATTTA
1 TTTTATTTTTA-TTA
*
99994955 TTTTA-TCTTATTA
1 TTTTATTTTTATTA
99994968 TTTTATTATTTATTA
1 TTTTATT-TTTATTA
99994983 TTTT
1 TTTT
99994987 CAGATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 8 0.29
14 5 0.18
15 15 0.54
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:99995947 original size:97 final size:97
Alignment explanation
Indices: 99995769--99995951 Score: 271
Period size: 97 Copynumber: 1.9 Consensus size: 97
99995759 TCTAAGAATG
**
99995769 TGTTGGACTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGTTTGAT
1 TGTTGGACTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGTTCAAT
* **
99995834 ATGTTTTTAGAAAAAAATAAAAATTAGGAGTA
66 ATGATTCCAGAAAAAAATAAAAATTAGGAGTA
* *
99995866 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGTTCAAT
1 TGTTGGACTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGTTCAAT
99995931 AT-ATTCCA-AAGTAAAAATAAA
66 ATGATTCCAGAA--AAAAATAAA
99995952 TAAATTAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
95 2 0.03
96 3 0.04
97 72 0.94
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (97 bp):
TGTTGGACTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGTTCAAT
ATGATTCCAGAAAAAAATAAAAATTAGGAGTA
Found at i:99996617 original size:27 final size:26
Alignment explanation
Indices: 99996557--99996618 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
99996547 ATAAGACTCC
99996557 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
99996583 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
99996611 ATTTTATT
1 ATTTTATT
99996619 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:99996633 original size:10 final size:10
Alignment explanation
Indices: 99996614--99996645 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
99996604 TTTTAGGATT
99996614 TTAT-TTTAA
1 TTATCTTTAA
99996623 TTATCTTTAA
1 TTATCTTTAA
99996633 TTATCTTTAA
1 TTATCTTTAA
99996643 TTA
1 TTA
99996646 ATTGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:100007261 original size:10 final size:10
Alignment explanation
Indices: 100007242--100007273 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
100007232 TTTTAGGATT
100007242 TTAT-TTTAA
1 TTATCTTTAA
100007251 TTATCTTTAA
1 TTATCTTTAA
100007261 TTATCTTTAA
1 TTATCTTTAA
100007271 TTA
1 TTA
100007274 ATTGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:100012651 original size:21 final size:21
Alignment explanation
Indices: 100012611--100012652 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
100012601 TAAGGTGGTA
* *
100012611 TTAAAGTTTTGTTAAGAAATT
1 TTAAAGTTTCGATAAGAAATT
*
100012632 TTAAAGTTTCGATAATAAATT
1 TTAAAGTTTCGATAAGAAATT
100012653 AATTAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
TTAAAGTTTCGATAAGAAATT
Found at i:100013292 original size:25 final size:25
Alignment explanation
Indices: 100013264--100013350 Score: 138
Period size: 25 Copynumber: 3.5 Consensus size: 25
100013254 ACCTTAGCGC
*
100013264 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
*
100013289 GCTCTCTGATTATTAGCATGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
* *
100013314 GCGCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTCAGT
100013339 GCTCTCTGATTA
1 GCTCTCTGATTA
100013351 GCACATCTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:100013353 original size:22 final size:23
Alignment explanation
Indices: 100013264--100013391 Score: 98
Period size: 25 Copynumber: 5.4 Consensus size: 23
100013254 ACCTTAGCGC
*
100013264 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTG--TATTAGCACGTCAGT
*
100013289 GCTCTCTGATTATTAGCATGTCAGT
1 GCTCTCTG--TATTAGCACGTCAGT
* *
100013314 GCGCTCTGATTATTAGCACGTTAGT
1 GCTCTCTG--TATTAGCACGTCAGT
* *
100013339 GCTCTCTG-ATTAGCACATCTGT
1 GCTCTCTGTATTAGCACGTCAGT
* * *
100013361 GGTCTCTGTA-TAGCACTTCAAT
1 GCTCTCTGTATTAGCACGTCAGT
*
100013383 GTTCTCTGT
1 GCTCTCTGT
100013392 TCATTAGTGC
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
22 35 0.40
23 1 0.01
25 52 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (23 bp):
GCTCTCTGTATTAGCACGTCAGT
Found at i:100014055 original size:18 final size:19
Alignment explanation
Indices: 100014017--100014055 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
100014007 GATGATATGA
*
100014017 TTAAATTATGATGTGAATG
1 TTAAATAATGATGTGAATG
*
100014036 TTAAATAATTATGT-AATG
1 TTAAATAATGATGTGAATG
100014054 TT
1 TT
100014056 TGTATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
TTAAATAATGATGTGAATG
Found at i:100016392 original size:19 final size:19
Alignment explanation
Indices: 100016368--100016413 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
100016358 TATATTATCG
*
100016368 CTATGTATTCCTATAATCA
1 CTATGTATTCCTACAATCA
100016387 CTATGTATTCCTACAATCA
1 CTATGTATTCCTACAATCA
*
100016406 CCATGTAT
1 CTATGTAT
100016414 GCAAATGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (19 bp):
CTATGTATTCCTACAATCA
Found at i:100016443 original size:3 final size:3
Alignment explanation
Indices: 100016435--100016608 Score: 339
Period size: 3 Copynumber: 58.0 Consensus size: 3
100016425 CTAGTTAGAT
100016435 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
100016483 GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
100016531 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
100016579 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
100016609 AAAAGTAGTA
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 169 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:100020388 original size:50 final size:46
Alignment explanation
Indices: 100020177--100020395 Score: 160
Period size: 46 Copynumber: 4.6 Consensus size: 46
100020167 TATATGTGCT
* *
100020177 AGTGTAGGACATGTCTGGGACATGCATCGGCTAC-A-ATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GC-ACGATAGATGAGAGCC
* ** *
100020223 AGTGTAAGACATGTCTGGGACATGCATCG-ACGTTGAGACAAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGCACGAT-AGATGAGAGCC
* * * * * * *
100020269 AGTGTATGACATGTTTGGAACATGCATCAGCCTCG--CGATGGACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-G-CACGATAGAT-GA-GAGCC
* *
100020317 AGTGGAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCG-CA-CGATAGATGAGAGCC
100020366 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
100020396 AGTATCTTAG
Statistics
Matches: 134, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
43 2 0.01
45 1 0.01
46 61 0.46
47 2 0.01
48 24 0.18
49 20 0.15
50 21 0.16
51 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCACGATAGATGAGAGCC
Found at i:100021832 original size:16 final size:17
Alignment explanation
Indices: 100021801--100021833 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
100021791 AGGGTGTTAC
100021801 AGCCCGTACGAGCCCACG
1 AGCCCGTAC-AGCCCACG
100021819 AGCCCGTA-AGCCCAC
1 AGCCCGTACAGCCCAC
100021834 ACAGCCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.45, G:0.24, T:0.06
Consensus pattern (17 bp):
AGCCCGTACAGCCCACG
Found at i:100026357 original size:48 final size:48
Alignment explanation
Indices: 100026237--100026715 Score: 377
Period size: 48 Copynumber: 9.9 Consensus size: 48
100026227 AGGCTAAGAT
* * * * *
100026237 GCCGATGCCATGTCCCAGACATGGTCTTGCATTGGCTCTCATATATCG-G
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAG-TCTCACATATCGAG
* *
100026286 TGCTGATGCCATGTTCCAAACATGCTCTTACACTAGTCT-ACATATCGAG
1 -GCCGATGCCATG-TCCAAACATGGTCTTACACTAGTCTCACATATCGAG
* * ** *
100026335 GCCGATGCCATGTCCAAGACATGGTCTTACAGTAG-CTCTA-GTATAAAT
1 GCCGATGCCATGTCCAA-ACATGGTCTTACACTAGTCTC-ACATATCGAG
* * *
100026383 GCCAATGCCATACTCCAAACATGGTCTTACACT-GGCTCACATATCGAG
1 GCCGATGCCAT-GTCCAAACATGGTCTTACACTAGTCTCACATATCGAG
* * * * *
100026431 GCTGATGCCATGTCCCAGATATGGTCTTACACTAG-CCCACATATCAAG
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGTCTCACATATCGAG
** * ** *
100026479 GCCGATGCCATGTCCCAAACATGGTCTTACACTAG-CTTTCGTATAAAT
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGTCTCACATATCGAG
* *
100026527 GCTGATGCCATGCTCCAAACATGGTCTTACACT-GGCTCACATATCGAG
1 GCCGATGCCATG-TCCAAACATGGTCTTACACTAGTCTCACATATCGAG
* * * * * ** *
100026575 GCTGATGCCATGTCCCAGACATGGTCTTACACTA-ACTCTCGTATAAAT
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGTCTCACATATCGAG
* * * * * *
100026623 GTCTATGCCATACTCTAAACATGGTCTTACACT-GGCTCACATATCGAA
1 GCCGATGCCAT-GTCCAAACATGGTCTTACACTAGTCTCACATATCGAG
*
100026671 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACATATC
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGTCTCACATATC
100026716 CCTAGTATCA
Statistics
Matches: 343, Mismatches: 68, Indels: 38
0.76 0.15 0.08
Matches are distributed among these distances:
47 13 0.04
48 288 0.84
49 14 0.04
50 27 0.08
51 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCAAACATGGTCTTACACTAGTCTCACATATCGAG
Found at i:100026631 original size:144 final size:144
Alignment explanation
Indices: 100026235--100026715 Score: 544
Period size: 144 Copynumber: 3.3 Consensus size: 144
100026225 AAAGGCTAAG
* * * *
100026235 ATGCCGATGCCATGTCCCAGACATGGTCTTGCATTGGCTCTCATATATCG-GTGCTGATGCCATG
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGG--CTCACATATCGAG-GCTGATGCCATG
* * * * *
100026299 TTCCAAACATGCTCTTACACT-AGTCTACATATCGAGGCCGATGCCATGT-CCAAGACATGGTCT
63 TCCCAGACATGGTCTTACACTAACTCT-CATATCAAGGCCGATGCCATGTCCCAA-ACATGGTCT
* *
100026362 TACAGTAGCTCTAGTATAA
126 TACACTAGCTCTCGTATAA
* *
100026381 ATGCCAATGCCAT-ACTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTC
1 ATGCCGATGCCATGTC-CCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTC
* * * *
100026445 CCAGATATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCATGTCCCAAACATGGTCTTACA
65 CCAGACATGGTCTTACACTAACTCTCATATCAAGGCCGATGCCATGTCCCAAACATGGTCTTACA
*
100026510 CTAGCTTTCGTATAA
130 CTAGCTCTCGTATAA
*
100026525 ATGCTGATGCCATG-CTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTC
1 ATGCCGATGCCATGTC-CCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTC
* * * * * * *
100026589 CCAGACATGGTCTTACACTAACTCTCGTATAAATGTCTATGCCAT-ACTCTAAACATGGTCTTAC
65 CCAGACATGGTCTTACACTAACTCTCATATCAAGGCCGATGCCATGTC-CCAAACATGGTCTTAC
* * * *
100026653 ACTGGCTCACATATCGA
129 ACTAGCTCTCGTAT-AA
* *
100026670 A-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATC
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
100026716 CCTAGTATCA
Statistics
Matches: 288, Mismatches: 39, Indels: 18
0.83 0.11 0.05
Matches are distributed among these distances:
143 1 0.00
144 247 0.86
145 10 0.03
146 30 0.10
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (144 bp):
ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCC
CAGACATGGTCTTACACTAACTCTCATATCAAGGCCGATGCCATGTCCCAAACATGGTCTTACAC
TAGCTCTCGTATAA
Found at i:100035568 original size:30 final size:30
Alignment explanation
Indices: 100035534--100035594 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
100035524 TTCCCGAGCC
100035534 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
100035564 TAGGGGCAAAATTGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
100035594 T
1 T
100035595 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:100039388 original size:27 final size:27
Alignment explanation
Indices: 100039358--100039443 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
100039348 AGTTTGCCAA
100039358 AAAGGCATTCCTTTCATATTCTACCAT
1 AAAGGCATTCCTTTCATATTCTACCAT
* * * *
100039385 AAAGACGTTCCTTCCATATTGC-GCCAT
1 AAAGGCATTCCTTTCATATT-CTACCAT
* * *
100039412 AAAGGCATTCATTTTATATTATACCAT
1 AAAGGCATTCCTTTCATATTCTACCAT
100039439 AAAGG
1 AAAGG
100039444 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (27 bp):
AAAGGCATTCCTTTCATATTCTACCAT
Found at i:100041530 original size:40 final size:40
Alignment explanation
Indices: 100041447--100041709 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
100041437 TTGAATGCTG
* * * * * *
100041447 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
100041487 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
100041527 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
100041567 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
100041607 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
100041647 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
100041686 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
100041710 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:100041729 original size:79 final size:80
Alignment explanation
Indices: 100041486--100041744 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
100041476 AAGTGAATAT
* * * * * *
100041486 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
100041550 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
100041566 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
100041631 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
100041646 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
100041710 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
100041725 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
100041745 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:100049482 original size:40 final size:40
Alignment explanation
Indices: 100049399--100049661 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
100049389 TTGAATGCTG
* * * * * *
100049399 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
100049439 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
100049479 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
100049519 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
100049559 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
100049599 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
100049638 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
100049662 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:100049681 original size:79 final size:80
Alignment explanation
Indices: 100049438--100049696 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
100049428 AAGTGAATAT
* * * * * *
100049438 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
100049502 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
100049518 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
100049583 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
100049598 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
100049662 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
100049677 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
100049697 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:100053671 original size:11 final size:12
Alignment explanation
Indices: 100053651--100053683 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
100053641 TGACCCAAGA
100053651 TGAATTAATTT-
1 TGAATTAATTTG
*
100053662 TGAATCAATTTG
1 TGAATTAATTTG
100053674 TGAATTAATT
1 TGAATTAATT
100053684 CACTTGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (12 bp):
TGAATTAATTTG
Found at i:100056042 original size:42 final size:43
Alignment explanation
Indices: 100055985--100056114 Score: 113
Period size: 42 Copynumber: 3.0 Consensus size: 43
100055975 ACTTTAAAAC
*
100055985 AAATTTTATATAAAACTCAGTCATGCAAATTTTCATAGCAT-A
1 AAATGTTATATAAAACTCAGTCATGCAAATTTTCATAGCATAA
* * *** *
100056027 AAATGTTATATAAAACT-ATTTA-GCAAAATTGAAAATAGAATTACA
1 AAATGTTATATAAAACTCAGTCATGC-AAATT-TTCATAGCA-TA-A
*
100056072 AAATTAGTTATATAAAACTCAGTCATGTAAATTTTCATAGCAT
1 AAA-T-GTTATATAAAACTCAGTCATGCAAATTTTCATAGCAT
100056115 TTCATAGCAT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
40 2 0.03
41 8 0.12
42 21 0.32
43 1 0.02
45 4 0.06
46 2 0.03
47 18 0.28
48 8 0.12
49 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (43 bp):
AAATGTTATATAAAACTCAGTCATGCAAATTTTCATAGCATAA
Found at i:100073036 original size:12 final size:12
Alignment explanation
Indices: 100073019--100073044 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
100073009 ACCTATACAC
100073019 CCATGTGTTAGG
1 CCATGTGTTAGG
100073031 CCATGTGTTAGG
1 CCATGTGTTAGG
100073043 CC
1 CC
100073045 GTGCAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (12 bp):
CCATGTGTTAGG
Found at i:100074007 original size:37 final size:37
Alignment explanation
Indices: 100073956--100074057 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
100073946 ACACCAATCA
* * * *
100073956 CTCATAAAAGCTAATCTAAACGATAACACGCTAGATG
1 CTCATAAGAGCTAATCCAAACAAAAACACGCTAGATG
* **
100073993 CTCATAAGACCTAATCCATCCAAAAACACGCTAGATG
1 CTCATAAGAGCTAATCCAAACAAAAACACGCTAGATG
* *
100074030 CTCATAAGAGCTAATCCAACCGAAAACA
1 CTCATAAGAGCTAATCCAAACAAAAACA
100074058 AGCCAAAGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (37 bp):
CTCATAAGAGCTAATCCAAACAAAAACACGCTAGATG
Found at i:100082353 original size:41 final size:40
Alignment explanation
Indices: 100082279--100082377 Score: 117
Period size: 41 Copynumber: 2.5 Consensus size: 40
100082269 AAGTGTAAGT
* * **
100082279 AGGGCACCAGAGTGCATAACAGGGATATGAATGTGAAATC
1 AGGGCACCAGAGTGCAAAACAGGGACACAAATGTGAAATC
* * *
100082319 AGGGGCACCGGAGTGCAAAACAGGGCCACAAATGTGCAATC
1 A-GGGCACCAGAGTGCAAAACAGGGACACAAATGTGAAATC
*
100082360 AAGGCACCAGAGTGCAAA
1 AGGGCACCAGAGTGCAAA
100082378 CAGTATAAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 16 0.33
41 33 0.67
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.12
Consensus pattern (40 bp):
AGGGCACCAGAGTGCAAAACAGGGACACAAATGTGAAATC
Found at i:100083418 original size:14 final size:14
Alignment explanation
Indices: 100083380--100083419 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
100083370 TCTGTTTTTC
100083380 TTTT-ACTT-TAATA
1 TTTTAACTTATAA-A
100083393 TTTTAA-TTATAAA
1 TTTTAACTTATAAA
100083406 TTTTAACTTATAAA
1 TTTTAACTTATAAA
100083420 ATCACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAACTTATAAA
Found at i:100086465 original size:49 final size:49
Alignment explanation
Indices: 100086393--100086493 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
100086383 TATGGGAACA
* *
100086393 CATATAGTGGTTGTCAATACATCAAATCTTTTATCACTCGTTAAACATT
1 CATATAGTGATTGTCAATACATCAAATCTTTTACCACTCGTTAAACATT
100086442 CATATAGTGATTGTCAATACATCAAATCTTTTACCACTCGTTAAACATT
1 CATATAGTGATTGTCAATACATCAAATCTTTTACCACTCGTTAAACATT
100086491 CAT
1 CAT
100086494 TTAGATTTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (49 bp):
CATATAGTGATTGTCAATACATCAAATCTTTTACCACTCGTTAAACATT
Found at i:100088861 original size:9 final size:9
Alignment explanation
Indices: 100088837--100088901 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
100088827 TACTTAATTC
100088837 TTTTAAAAGA
1 TTTTAAAA-A
*
100088847 TATTAAAAA
1 TTTTAAAAA
* *
100088856 TTTTAATAT
1 TTTTAAAAA
100088865 TTTTAAAAA
1 TTTTAAAAA
* *
100088874 TTTTAATAT
1 TTTTAAAAA
100088883 TTTTAAAAA
1 TTTTAAAAA
*
100088892 TTTTATAAA
1 TTTTAAAAA
100088901 T
1 T
100088902 CACATTTAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
9 37 0.84
10 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:100088872 original size:18 final size:18
Alignment explanation
Indices: 100088849--100088896 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
100088839 TTAAAAGATA
100088849 TTAAAAATTTTAATATTT
1 TTAAAAATTTTAATATTT
100088867 TTAAAAATTTTAATATTT
1 TTAAAAATTTTAATATTT
100088885 TTAAAAATTTTA
1 TTAAAAATTTTA
100088897 TAAATCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAAAATTTTAATATTT
Found at i:100089194 original size:18 final size:17
Alignment explanation
Indices: 100089171--100089231 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 17
100089161 TTCCAATATC
* *
100089171 TTTTTATTATTTTTTATA
1 TTTTTAATATTATTTA-A
100089189 TTTTTAATATTATTTAA
1 TTTTTAATATTATTTAA
100089206 TTTTTAAATAATATTATTTAA
1 -TTTT---TAATATTATTTAA
100089227 TTTTT
1 TTTTT
100089232 TATAAACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 2 0.05
18 18 0.49
20 4 0.11
21 13 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTAATATTATTTAA
Found at i:100093816 original size:45 final size:45
Alignment explanation
Indices: 100093765--100093891 Score: 202
Period size: 45 Copynumber: 2.8 Consensus size: 45
100093755 TATCGTATGG
* *
100093765 TACTATTTGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
100093810 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
100093855 TACTATTCGGGCCTTCGAGCCTAGCAGGCGA-AATGCC
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCC
100093892 AGTGGATGAA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 5 0.07
45 71 0.93
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:100116205 original size:15 final size:16
Alignment explanation
Indices: 100116176--100116208 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
100116166 ATGATAGTTT
100116176 TGGAGAAGAAAGAAAA
1 TGGAGAAGAAAGAAAA
100116192 TGGAGAAG-AAGAAAA
1 TGGAGAAGAAAGAAAA
100116207 TG
1 TG
100116209 ATAGCTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (16 bp):
TGGAGAAGAAAGAAAA
Found at i:100118225 original size:44 final size:42
Alignment explanation
Indices: 100118157--100118290 Score: 135
Period size: 44 Copynumber: 3.1 Consensus size: 42
100118147 TTCTGATGTG
* * * *
100118157 TGATTTCGTGTAAGACCATGTCTGGGACGTTGGTATCG-ATT
1 TGATTTAGTGTAAGACCATATCTGGGACATTGGCATCGTATT
*
100118198 TGAGATTTAAGTGTAAGACCATATCTGGGACATTGGCATTGTATT
1 T--GATTT-AGTGTAAGACCATATCTGGGACATTGGCATCGTATT
* * * **
100118243 TGATTTCGTGTAAGACCCTATCTGGGATAGCGGCATCGATATT
1 TGATTTAGTGTAAGACCATATCTGGGACATTGGCATCG-TATT
100118286 TGATT
1 TGATT
100118291 ACACGTAAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 26 0.34
43 19 0.25
44 27 0.35
45 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (42 bp):
TGATTTAGTGTAAGACCATATCTGGGACATTGGCATCGTATT
Found at i:100118265 original size:42 final size:41
Alignment explanation
Indices: 100118157--100118269 Score: 136
Period size: 44 Copynumber: 2.7 Consensus size: 41
100118147 TTCTGATGTG
* * *
100118157 TGATTTCGTGTAAGACCATGTCTGGGACGTTGGTATCGATT
1 TGATTTCGTGTAAGACCATATCTGGGACATTGGCATCGATT
* *
100118198 TGAGATTTAAGTGTAAGACCATATCTGGGACATTGGCATTGTATT
1 T--GATTT-CGTGTAAGACCATATCTGGGACATTGGCATCG-ATT
*
100118243 TGATTTCGTGTAAGACCCTATCTGGGA
1 TGATTTCGTGTAAGACCATATCTGGGA
100118270 TAGCGGCATC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 19 0.31
43 10 0.16
44 27 0.44
45 4 0.07
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATATCTGGGACATTGGCATCGATT
Found at i:100118287 original size:43 final size:42
Alignment explanation
Indices: 100118157--100118290 Score: 128
Period size: 42 Copynumber: 3.1 Consensus size: 42
100118147 TTCTGATGTG
* * *
100118157 TGATTTCGTGTAAGACCATGTCTGGGAC-GTTGGTATCG-ATT
1 TGATTTCGTGTAAGACCATATCTGGGACAG-CGGCATCGTATT
* ** *
100118198 TGAGATTTAAGTGTAAGACCATATCTGGGACATTGGCATTGTATT
1 T--GATTT-CGTGTAAGACCATATCTGGGACAGCGGCATCGTATT
* *
100118243 TGATTTCGTGTAAGACCCTATCTGGGATAGCGGCATCGATATT
1 TGATTTCGTGTAAGACCATATCTGGGACAGCGGCATCG-TATT
100118286 TGATT
1 TGATT
100118291 ACACGTAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 26 0.34
43 19 0.25
44 26 0.34
45 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATATCTGGGACAGCGGCATCGTATT
Found at i:100118300 original size:43 final size:42
Alignment explanation
Indices: 100118210--100118303 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
100118200 AGATTTAAGT
** * * **
100118210 GTAAGACCATATCTGGGACATTGGCATTGTATTTGATTTCGT
1 GTAAGACCATATCTGGGACAGCGGCATCGTATTTGATTACAC
* *
100118252 GTAAGACCCTATCTGGGATAGCGGCATCGATATTTGATTACAC
1 GTAAGACCATATCTGGGACAGCGGCATCG-TATTTGATTACAC
100118295 GTAAGACCA
1 GTAAGACCA
100118304 CGTTTGGGAC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 24 0.57
43 18 0.43
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
GTAAGACCATATCTGGGACAGCGGCATCGTATTTGATTACAC
Found at i:100139776 original size:44 final size:44
Alignment explanation
Indices: 100139720--100139807 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
100139710 TCCGATGTGT
* *
100139720 GATTTCGAGTAAGACCACGCCTGGGACATTGGTATCG-ATTTGA
1 GATTTCGAGTAAGACCACGCCTGGGACATCGATATCGTATTTGA
* * * *
100139763 GATTTACGTGTAAGATCATGTCTGGGACATCGATATCGTATTTGA
1 GATTT-CGAGTAAGACCACGCCTGGGACATCGATATCGTATTTGA
100139808 TTTCGTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 5 0.14
44 26 0.70
45 6 0.16
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
GATTTCGAGTAAGACCACGCCTGGGACATCGATATCGTATTTGA
Found at i:100143961 original size:27 final size:27
Alignment explanation
Indices: 100143923--100143975 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
100143913 CAGTTCAAAC
*
100143923 CACAGAAACAGAATAAATTGGCCTTAT
1 CACAGAAACAGAACAAATTGGCCTTAT
100143950 CACAGAAACAGAACAAATTGGCCTTA
1 CACAGAAACAGAACAAATTGGCCTTA
100143976 GCCCAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (27 bp):
CACAGAAACAGAACAAATTGGCCTTAT
Found at i:100144193 original size:27 final size:26
Alignment explanation
Indices: 100144158--100144269 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
100144148 AGCATGGCTG
* *
100144158 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
100144184 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* * *
100144212 CTAGAACAAATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
100144239 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
100144266 CCAG
1 CCAG
100144270 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.09
27 49 0.70
28 15 0.21
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:100145733 original size:24 final size:24
Alignment explanation
Indices: 100145706--100145770 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
100145696 TACCCTAATT
100145706 AGCTCCTAAATCCTCTCCCTGATC
1 AGCTCCTAAATCCTCTCCCTGATC
*
100145730 AGCTCCTAAATCCTCTCCCTTATC
1 AGCTCCTAAATCCTCTCCCTGATC
*
100145754 AGCTCCTAAATCTTCTC
1 AGCTCCTAAATCCTCTC
100145771 TAGACAGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.22, C:0.40, G:0.06, T:0.32
Consensus pattern (24 bp):
AGCTCCTAAATCCTCTCCCTGATC
Found at i:100152070 original size:27 final size:26
Alignment explanation
Indices: 100152030--100152141 Score: 107
Period size: 27 Copynumber: 4.2 Consensus size: 26
100152020 AGCATGGCTG
* * *
100152030 CCAGAACAAATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGGTAGAGCCA
* *
100152056 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGTAGAGCCA
*
100152084 CTAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGTAGAGCCA
* * *
100152111 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGTAGAGCCA
100152138 CCAG
1 CCAG
100152142 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.09
27 50 0.71
28 14 0.20
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGTAGAGCCA
Found at i:100152400 original size:16 final size:16
Alignment explanation
Indices: 100152379--100152418 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
100152369 ATACATAAGG
* *
100152379 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAAA
100152395 GCTGTAATGGAATAAA
1 GCTGTAATGGAATAAA
*
100152411 GTTGTAAT
1 GCTGTAAT
100152419 AAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:100156464 original size:32 final size:32
Alignment explanation
Indices: 100156423--100156487 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
100156413 TTGCAATTTG
100156423 TTTTATATTTGCCCTTAGCCTTTACATCTATC
1 TTTTATATTTGCCCTTAGCCTTTACATCTATC
* *
100156455 TTTTATATTTGCCCTTGGCTTTTACATCTATC
1 TTTTATATTTGCCCTTAGCCTTTACATCTATC
100156487 T
1 T
100156488 CGTCATCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.08, T:0.52
Consensus pattern (32 bp):
TTTTATATTTGCCCTTAGCCTTTACATCTATC
Found at i:100156706 original size:12 final size:12
Alignment explanation
Indices: 100156689--100156715 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
100156679 TAGATTTATG
100156689 CAAAACAATACC
1 CAAAACAATACC
100156701 CAAAACAATACC
1 CAAAACAATACC
100156713 CAA
1 CAA
100156716 TAATTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.33, G:0.00, T:0.07
Consensus pattern (12 bp):
CAAAACAATACC
Found at i:100159764 original size:13 final size:13
Alignment explanation
Indices: 100159746--100159771 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100159736 CTGAAAAGAG
100159746 GGAGAAGGGTGGA
1 GGAGAAGGGTGGA
100159759 GGAGAAGGGTGGA
1 GGAGAAGGGTGGA
100159772 ACGAAATAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.62, T:0.08
Consensus pattern (13 bp):
GGAGAAGGGTGGA
Found at i:100159790 original size:53 final size:53
Alignment explanation
Indices: 100159706--100159811 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
100159696 TGAAAAAGAG
* * *
100159706 GGAGAAGGGTGAAACGAAATGGGAATAAGACTGAAAAGAGGGAGAAGGGTGGA
1 GGAGAAGGGTGAAACGAAATAGGAACAAGACTGAAAAGAGGGAAAAGGGTGGA
* * *
100159759 GGAGAAGGGTGGAACGAAATAGGAACCAGACTGAAAAGAGGGAAAATGGTGGA
1 GGAGAAGGGTGAAACGAAATAGGAACAAGACTGAAAAGAGGGAAAAGGGTGGA
100159812 ACGAAAGAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.43, C:0.06, G:0.42, T:0.09
Consensus pattern (53 bp):
GGAGAAGGGTGAAACGAAATAGGAACAAGACTGAAAAGAGGGAAAAGGGTGGA
Found at i:100161313 original size:24 final size:24
Alignment explanation
Indices: 100161281--100161354 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
100161271 ACACAGTTCA
100161281 CCCTAATCAGCTCCTAAATCCTCT
1 CCCTAATCAGCTCCTAAATCCTCT
*
100161305 CCCTGATCAGCTCCTAAATCCTCT
1 CCCTAATCAGCTCCTAAATCCTCT
* *
100161329 CCCTTATCAGCTCCTAAATCTTCT
1 CCCTAATCAGCTCCTAAATCCTCT
100161353 CC
1 CC
100161355 AGACAGACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.22, C:0.42, G:0.05, T:0.31
Consensus pattern (24 bp):
CCCTAATCAGCTCCTAAATCCTCT
Found at i:100165113 original size:89 final size:89
Alignment explanation
Indices: 100164962--100165137 Score: 343
Period size: 89 Copynumber: 2.0 Consensus size: 89
100164952 TTTCACTGTT
100164962 TGACTATTCTGACCACTCTTCACTACGAATCCAATTTATCATTTTACAGAATTCAAAATGTGTTG
1 TGACTATTCTGACCACTCTTCACTACGAATCCAATTTATCATTTTACAGAATTCAAAATGTGTTG
100165027 TATTTGATCTCATTTGAAACTATA
66 TATTTGATCTCATTTGAAACTATA
*
100165051 TGACTATTCTGACCACTCTTCACTACGAATCCAATTTCTCATTTTACAGAATTCAAAATGTGTTG
1 TGACTATTCTGACCACTCTTCACTACGAATCCAATTTATCATTTTACAGAATTCAAAATGTGTTG
100165116 TATTTGATCTCATTTGAAACTA
66 TATTTGATCTCATTTGAAACTA
100165138 GACTCATTAA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (89 bp):
TGACTATTCTGACCACTCTTCACTACGAATCCAATTTATCATTTTACAGAATTCAAAATGTGTTG
TATTTGATCTCATTTGAAACTATA
Found at i:100165233 original size:73 final size:73
Alignment explanation
Indices: 100165142--100165286 Score: 272
Period size: 73 Copynumber: 2.0 Consensus size: 73
100165132 AAACTAGACT
*
100165142 CATTAAGGAGTCTAAGCATATAAATTTTATCTTATAATAATTTTTTTACAATTTATAATGATTTT
1 CATTAAGGAGTCTAAGCATATAAATTTTATCTTATAATAATTTTTGTACAATTTATAATGATTTT
100165207 CTAAAAAC
66 CTAAAAAC
*
100165215 CATTAAGGAGTCTAAGCATATAAATTTTATCTTATAATCATTTTTGTACAATTTATAATGATTTT
1 CATTAAGGAGTCTAAGCATATAAATTTTATCTTATAATAATTTTTGTACAATTTATAATGATTTT
100165280 CTAAAAA
66 CTAAAAA
100165287 TAGAACAGGG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (73 bp):
CATTAAGGAGTCTAAGCATATAAATTTTATCTTATAATAATTTTTGTACAATTTATAATGATTTT
CTAAAAAC
Found at i:100165622 original size:13 final size:13
Alignment explanation
Indices: 100165606--100165634 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
100165596 ATACATTTAT
100165606 CATATATAACTAA
1 CATATATAACTAA
100165619 CATATATAACTAA
1 CATATATAACTAA
100165632 CAT
1 CAT
100165635 TTATTCCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
CATATATAACTAA
Found at i:100172567 original size:40 final size:40
Alignment explanation
Indices: 100172519--100172746 Score: 366
Period size: 40 Copynumber: 5.7 Consensus size: 40
100172509 GCAAACACAT
* * * *
100172519 TTGCCTTCGGGTCTTAACCCAGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
100172559 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
100172599 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
100172639 TTGCCTTCGGGTCATAGCCCGGACATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
100172679 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
100172719 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
100172747 TCCAATGCTC
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 179 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:100178542 original size:44 final size:44
Alignment explanation
Indices: 100178458--100178542 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
100178448 TATATACGGG
* ** *
100178458 GCATCCGAGCTCGTTGAGTTATTCCAAGTTCATTACGGATGCGA
1 GCATACGAGCTCGTTGAGTTAGGCCAAGTTCATAACGGATGCGA
* *
100178502 GCATACGAGCTCGTTGAGTT-GGCCTGAGTTCATAATGGATG
1 GCATACGAGCTCGTTGAGTTAGGCC-AAGTTCATAACGGATG
100178543 TGATACATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.06
44 32 0.94
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (44 bp):
GCATACGAGCTCGTTGAGTTAGGCCAAGTTCATAACGGATGCGA
Found at i:100179946 original size:13 final size:13
Alignment explanation
Indices: 100179928--100179952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100179918 TTATTTTTAA
100179928 TTGGCCACACGGT
1 TTGGCCACACGGT
100179941 TTGGCCACACGG
1 TTGGCCACACGG
100179953 GTGTGTGATA
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:0.16, C:0.32, G:0.32, T:0.20
Consensus pattern (13 bp):
TTGGCCACACGGT
Found at i:100186027 original size:56 final size:56
Alignment explanation
Indices: 100185960--100186073 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
100185950 TTATAAAAGC
100185960 ATGAATTATGGATTGATTTGAATAATGTGATTAATAAACAAGTTAAATTTGACATT
1 ATGAATTATGGATTGATTTGAATAATGTGATTAATAAACAAGTTAAATTTGACATT
100186016 ATGAATTATGGATTGATTTGAATAATGTGATTAATAAACAAGTTAAATTTGACATT
1 ATGAATTATGGATTGATTTGAATAATGTGATTAATAAACAAGTTAAATTTGACATT
100186072 AT
1 AT
100186074 AGATCAAGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (56 bp):
ATGAATTATGGATTGATTTGAATAATGTGATTAATAAACAAGTTAAATTTGACATT
Found at i:100186508 original size:44 final size:45
Alignment explanation
Indices: 100186454--100186545 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 45
100186444 ATGTATAAAG
*
100186454 CATCCAAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGTGA-A
1 CATCCAAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGTGATA
*
100186498 CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGTGATA
1 CATCCAAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGTGATA
100186543 CAT
1 CAT
100186546 GTAAGTGGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 41 0.91
45 4 0.09
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (45 bp):
CATCCAAGCTCGTTGAGTTGGTCCGAGTTCATAATGGATGTGATA
Found at i:100204958 original size:8 final size:8
Alignment explanation
Indices: 100204945--100204972 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
100204935 AAGGAAGTGT
100204945 AGTGGTTA
1 AGTGGTTA
100204953 AGTGGTTA
1 AGTGGTTA
100204961 AGTGGTTA
1 AGTGGTTA
100204969 AGTG
1 AGTG
100204973 CTTCTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (8 bp):
AGTGGTTA
Found at i:100205058 original size:61 final size:61
Alignment explanation
Indices: 100204963--100205085 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
100204953 AGTGGTTAAG
* *
100204963 TGGTTAAGTGCTTCTTAACTATCCTTTAAGTCTCTAGTTCGAACCTTTATGTG-TCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTCGAACCCTTATGTGCT-TATTAT
*
100205024 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCTTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTCGAACCCTTATGTGCTTATTAT
100205085 T
1 T
100205086 TTTATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 57 0.98
62 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.46
Consensus pattern (61 bp):
TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTCGAACCCTTATGTGCTTATTAT
Found at i:100208616 original size:33 final size:33
Alignment explanation
Indices: 100208576--100208642 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
100208566 AACCCTCTTT
*
100208576 CCAAGCCTAGCAGAAATTTATATATTACATTTA
1 CCAAGCCTAGCAAAAATTTATATATTACATTTA
100208609 CCAAGCCTAGCAAAAATTTATATATTACATTTA
1 CCAAGCCTAGCAAAAATTTATATATTACATTTA
100208642 C
1 C
100208643 AACACTTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (33 bp):
CCAAGCCTAGCAAAAATTTATATATTACATTTA
Found at i:100210471 original size:57 final size:56
Alignment explanation
Indices: 100210383--100210497 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 56
100210373 TAAAGTGTGC
** *
100210383 AGACTTCGTTAAATGATTGAAAATTACCCAGATG-GCATCTTTCTTTTTCGGTGATAA
1 AGACTTCGTTAAACAATCGAAAATTACCCAGA-GAGCATCTTTC-TTTTCGGTGATAA
*
100210440 AGACTTCGTTAAACAATCGATAATTACCCAGAGAGCATCTTTCTTTTCGGTGATAA
1 AGACTTCGTTAAACAATCGAAAATTACCCAGAGAGCATCTTTCTTTTCGGTGATAA
100210496 AG
1 AG
100210498 TTAATCTCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 16 0.30
57 37 0.70
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (56 bp):
AGACTTCGTTAAACAATCGAAAATTACCCAGAGAGCATCTTTCTTTTCGGTGATAA
Found at i:100212258 original size:41 final size:41
Alignment explanation
Indices: 100212195--100212272 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
100212185 GCAATTTTGT
*
100212195 AGGAACCATTCTATATGGTACTA-TAGATATCGGCGTCGTCC
1 AGGAACCATTCTATATGCTACTATTA-ATATCGGCGTCGTCC
*
100212236 AGGAGCCATTCTATATGCTACTATTAATATCGGCGTC
1 AGGAACCATTCTATATGCTACTATTAATATCGGCGTC
100212273 ATCCCTGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (41 bp):
AGGAACCATTCTATATGCTACTATTAATATCGGCGTCGTCC
Found at i:100215215 original size:6 final size:6
Alignment explanation
Indices: 100215194--100215315 Score: 70
Period size: 6 Copynumber: 19.8 Consensus size: 6
100215184 TATTAGAACT
* * * *
100215194 AGAATC AAAATA AGAATC AGAATC AGGATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * * * *
100215243 AGAATC AGAATC AAAATT ACGTGA-C AGAATT AGAATT AGAATC AGTATC
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC
*
100215292 AGGTAA-C AGAATC AAAATC AGAAT
1 A-G-AATC AGAATC AGAATC AGAAT
100215316 GTGAATGCAA
Statistics
Matches: 88, Mismatches: 19, Indels: 18
0.70 0.15 0.14
Matches are distributed among these distances:
5 4 0.05
6 74 0.84
7 7 0.08
8 3 0.03
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:100215235 original size:37 final size:37
Alignment explanation
Indices: 100215194--100215315 Score: 121
Period size: 37 Copynumber: 3.5 Consensus size: 37
100215184 TATTAGAACT
* *
100215194 AGAATCAAAATAAGAATCAGAATCAGGATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* * * *
100215231 AGAATCAGAATCAGAATCAGAATCAAAATTACGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* * *
100215268 AGAAT-----T-AGAATTAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
100215299 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
100215316 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
31 24 0.36
32 1 0.01
36 1 0.01
37 41 0.61
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
Found at i:100215244 original size:31 final size:31
Alignment explanation
Indices: 100215206--100215315 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 31
100215196 AATCAAAATA
*
100215206 AGAATCAGAATCAGGATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
* *
100215237 AGAATCAGAATCAGAATCAAAATTACGTGACAGAATT
1 AGAATCAGAATCAGAATC------AGGTGACAGAATC
* * *
100215274 AGAATTAGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
*
100215305 AAAATCAGAAT
1 AGAATCAGAAT
100215316 GTGAATGCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
31 36 0.57
37 27 0.43
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATC
Found at i:100215779 original size:27 final size:27
Alignment explanation
Indices: 100215749--100215889 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
100215739 GGGCAAAATG
* * * *
100215749 GTAATTTTACCCCATAAGGGTATCTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
100215776 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
100215803 GTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
100215830 GTAATTCTACCCTAGAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
100215857 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
100215884 ATAATT
1 GTAATT
100215890 TAGTAAATCG
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:100217973 original size:6 final size:6
Alignment explanation
Indices: 100217952--100218013 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
100217942 TATTAGAACT
* * * *
100217952 AGAATC AAAATA AGAATC AGAATC AGGATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
*
100218001 AGAATT AGAATC A
1 AGAATC AGAATC A
100218014 AAATTACGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 1 0.02
6 39 0.89
7 3 0.07
8 1 0.02
ACGTcount: A:0.50, C:0.13, G:0.19, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:100217993 original size:37 final size:37
Alignment explanation
Indices: 100217952--100218045 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
100217942 TATTAGAACT
* ** *
100217952 AGAATCAAAATAAGAATCAGAATCAGGATCAGGTGAC
1 AGAATCAGAATAAGAATCAGAATCAAAATCACGTGAC
* * *
100217989 AGAATCAGAATCAGAATTAGAATCAAAATTACGTGAC
1 AGAATCAGAATAAGAATCAGAATCAAAATCACGTGAC
* *
100218026 AGAATTAGAATTAGAATCAG
1 AGAATCAGAATAAGAATCAG
100218046 TATTAGGTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATAAGAATCAGAATCAAAATCACGTGAC
Found at i:100218002 original size:31 final size:31
Alignment explanation
Indices: 100217964--100218073 Score: 85
Period size: 31 Copynumber: 3.4 Consensus size: 31
100217954 AATCAAAATA
*
100217964 AGAATCAGAATCAGGATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
* * *
100217995 AGAATCAGAATTAGAATCAAAATTACGTGACAGAATT
1 AGAATCAGAATCAGAATC------AGGTGACAGAATC
* * * *
100218032 AGAATTAGAATCAGTATTAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
*
100218063 AAAATCAGAAT
1 AGAATCAGAAT
100218074 GTGAATGCAA
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
31 35 0.58
37 25 0.42
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATC
Found at i:100218652 original size:27 final size:27
Alignment explanation
Indices: 100218511--100218645 Score: 180
Period size: 27 Copynumber: 5.0 Consensus size: 27
100218501 AGGGCAAAAT
* * * *
100218511 GGTAATTTTACCCCATAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
100218538 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
100218565 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
100218592 GGTAATTCTACCCTAGAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
**
100218619 ATTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
100218646 AATAATTTAG
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:100220676 original size:34 final size:34
Alignment explanation
Indices: 100220638--100220722 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
100220628 TAGTATCAAT
*
100220638 TGGGCCTTAGCCCATTATAGTAGACAGTACCAGA
1 TGGGCCTTAGCCCATTATAGCAGACAGTACCAGA
100220672 TGGGCCTTAGCCCATTATAGCAGACAGTACCAGA
1 TGGGCCTTAGCCCATTATAGCAGACAGTACCAGA
100220706 TGGGCCTTAGCCCATTA
1 TGGGCCTTAGCCCATTA
100220723 CAAAATAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.24
Consensus pattern (34 bp):
TGGGCCTTAGCCCATTATAGCAGACAGTACCAGA
Found at i:100221342 original size:27 final size:27
Alignment explanation
Indices: 100221308--100221421 Score: 131
Period size: 27 Copynumber: 4.2 Consensus size: 27
100221298 GGTTATCTCG
100221308 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTATAGGGGTATTTCA
* * * * *
100221335 GTATTTCTATCCTA-CGAAGGTATTTCG
1 GTAATTCTACCCTATAG-GGGTATTTCA
*
100221362 GTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTATAGGGGTATTTCA
* *
100221389 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTATAGGGGTATTTCA
*
100221416 ATAATT
1 GTAATT
100221422 TTGTAAATCG
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 68 0.97
28 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (27 bp):
GTAATTCTACCCTATAGGGGTATTTCA
Found at i:100221421 original size:54 final size:54
Alignment explanation
Indices: 100221281--100221414 Score: 189
Period size: 54 Copynumber: 2.5 Consensus size: 54
100221271 GGGCAAAATG
* * * *
100221281 GTAATTTTACCCCACAAGGTTATCTCGGTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
* * *
100221335 GTATTTCTATCCTACGAA-GGTATTTCGGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTAC-AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
100221389 GTAATTCTACCCTACAAGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
100221415 AATAATTTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.03
54 65 0.94
55 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
Found at i:100224353 original size:5 final size:5
Alignment explanation
Indices: 100224343--100224367 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
100224333 GATGCCAACC
100224343 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
100224368 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:100259078 original size:40 final size:41
Alignment explanation
Indices: 100258982--100259086 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 41
100258972 TGAATGATGT
*
100258982 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
* * * *
100259022 CCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTATAA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGTGACCATAA
*
100259062 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
100259087 AACGAGTAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 46 0.84
41 8 0.15
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
Found at i:100260509 original size:47 final size:47
Alignment explanation
Indices: 100260440--100260542 Score: 170
Period size: 47 Copynumber: 2.2 Consensus size: 47
100260430 GGGGTGTTAC
* * *
100260440 ATCCTTATCTTACCAAATGCCATGTTTCAAACATAGTCTTACATGGT
1 ATCCTTGTCATACCAAATGCCATGTTCCAAACATAGTCTTACATGGT
*
100260487 ATCCTTGTCATACCAAATGCCATGTTCCAAACATGGTCTTACATGGT
1 ATCCTTGTCATACCAAATGCCATGTTCCAAACATAGTCTTACATGGT
100260534 ATCCTTGTC
1 ATCCTTGTC
100260543 TTAGTGCCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (47 bp):
ATCCTTGTCATACCAAATGCCATGTTCCAAACATAGTCTTACATGGT
Found at i:100260688 original size:44 final size:44
Alignment explanation
Indices: 100260639--100260722 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
100260629 ATGGTCTTAA
* * *
100260639 TCAATTCCTCTTTAAATGCCATGTTATGAA-CATGGACTTTTCCG
1 TCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCCG
* *
100260683 TCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
100260723 GAGATATCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 32 0.94
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (44 bp):
TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCCG
Found at i:100267188 original size:103 final size:103
Alignment explanation
Indices: 100267009--100267215 Score: 378
Period size: 103 Copynumber: 2.0 Consensus size: 103
100266999 ACACCCGAAT
*
100267009 TACGAACTCAGTAGACTCAACAGGTAGAGCCTTACTGGATGCTAAGGTTTCGCATGCATATGAAT
1 TACGAACTCAGTAGACTCAACAGGTAGAGCCTTACTGGATGCTAAGGTTTCGCATACATATGAAT
100267074 GAGTAGAACCAGGGTCAATCAATGCAATCACATTAGTA
66 GAGTAGAACCAGGGTCAATCAATGCAATCACATTAGTA
* * *
100267112 TACGAGCTCAGTAGACTCAACAGGTAGAGTCTTACTGGTTGCTAAGGTTTCGCATACATATGAAT
1 TACGAACTCAGTAGACTCAACAGGTAGAGCCTTACTGGATGCTAAGGTTTCGCATACATATGAAT
100267177 GAGTAGAACCAGGGTCAATCAATGCAATCACATTAGTA
66 GAGTAGAACCAGGGTCAATCAATGCAATCACATTAGTA
100267215 T
1 T
100267216 CAAAGAGAGT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (103 bp):
TACGAACTCAGTAGACTCAACAGGTAGAGCCTTACTGGATGCTAAGGTTTCGCATACATATGAAT
GAGTAGAACCAGGGTCAATCAATGCAATCACATTAGTA
Found at i:100270046 original size:27 final size:27
Alignment explanation
Indices: 100270016--100270193 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
100270006 ATATTGAGTC
* * * *
100270016 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
100270043 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
100270070 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
100270098 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
100270125 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
100270152 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
100270179 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
100270194 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:100270155 original size:82 final size:81
Alignment explanation
Indices: 100270037--100270192 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
100270027 TGCTATATAA
* *
100270037 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
100270102 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
100270119 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
100270183 CACTTAGTGC
65 CACTTAGTGC
100270193 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:100274127 original size:102 final size:102
Alignment explanation
Indices: 100273951--100274183 Score: 387
Period size: 102 Copynumber: 2.3 Consensus size: 102
100273941 GTGAGAACAT
* *
100273951 ATGTGTAGTACTATGT-ACAGGCTACTATGTGTTTAAGACAGTTTTAGGTCCCGTGTGTAGTACT
1 ATGTGTAGTACTATGTGA-AGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTATAGTACT
100274015 AAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTAGC
65 AAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTAGC
100274053 ATGTGTAGTACTATGTGAAGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTATAGTACTA
1 ATGTGTAGTACTATGTGAAGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTATAGTACTA
* * *
100274118 AGTGCAGGCTACTATGTGTACTAGATTGTTAGGTCGC
66 AGTGCAGGCTACTACGTGTACCAGATTGTTAGGTAGC
* *
100274155 ATGTGTAGTACTAAGTGTAGGCTACTATG
1 ATGTGTAGTACTATGTGAAGGCTACTATG
100274184 AGTACTGGAG
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 122 0.99
103 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (102 bp):
ATGTGTAGTACTATGTGAAGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTATAGTACTA
AGTGCAGGCTACTACGTGTACCAGATTGTTAGGTAGC
Found at i:100274189 original size:50 final size:50
Alignment explanation
Indices: 100273951--100274189 Score: 234
Period size: 50 Copynumber: 4.7 Consensus size: 50
100273941 GTGAGAACAT
* * * *
100273951 ATGTGTAGTACTATGTACAGGCTACTATGTGT-TTAAGACAGTT-TTAGGTCCC
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACT-AG--A-TTGTTAGGTCGC
* * * *
100274003 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTAGC
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATTGTTAGGTCGC
* * * *
100274053 ATGTGTAGTACTATGTGAAGGCTACTATGTGT-TTAAGACAGTT-TTAGGTCAC
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACT-AG--A-TTGTTAGGTCGC
* *
100274105 GTGTATAGTACTAAGTGCAGGCTACTATGTGTACTAGATTGTTAGGTCGC
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATTGTTAGGTCGC
* *
100274155 ATGTGTAGTACTAAGTGTAGGCTACTATGAGTACT
1 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACT
100274190 GGAGAGCTTT
Statistics
Matches: 153, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
49 4 0.03
50 78 0.51
52 68 0.44
53 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (50 bp):
ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATTGTTAGGTCGC
Done.