Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 171 of 208
Found at i:54824410 original size:17 final size:17
Alignment explanation
Indices: 54824388--54824423 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
54824378 ATTTCCTTTC
54824388 TTTCATTTTTTTAGTTA
1 TTTCATTTTTTTAGTTA
54824405 TTTCATTTTTTTAGTTA
1 TTTCATTTTTTTAGTTA
54824422 TT
1 TT
54824424 AATTTGCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTCATTTTTTTAGTTA
Found at i:54824428 original size:16 final size:17
Alignment explanation
Indices: 54824392--54824428 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54824382 CCTTTCTTTC
*
54824392 ATTTTTTTAGTTATTTC
1 ATTTTTTTAGTTATTTA
54824409 ATTTTTTTAGTTA-TTA
1 ATTTTTTTAGTTATTTA
54824425 ATTT
1 ATTT
54824429 GCTTGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (17 bp):
ATTTTTTTAGTTATTTA
Found at i:54831793 original size:25 final size:25
Alignment explanation
Indices: 54831764--54831821 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
54831754 ACATCTTTGC
54831764 ATTCATTTCAAGTAATTATTCTTTT
1 ATTCATTTCAAGTAATTATTCTTTT
54831789 ATTCATTTCAAGTAATTATTCTTTT
1 ATTCATTTCAAGTAATTATTCTTTT
54831814 ATTC-TTTC
1 ATTCATTTC
54831822 CAGGCAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTCATTTCAAGTAATTATTCTTTT
Found at i:54836840 original size:175 final size:175
Alignment explanation
Indices: 54836549--54836922 Score: 606
Period size: 175 Copynumber: 2.1 Consensus size: 175
54836539 ACAGATCAGT
***
54836549 GAAGAATTACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTAATCCTATTT
1 GAAGAATTACAGATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCCAGTAATCCTATTT
54836614 CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
66 CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
*
54836679 GATCGCATCAGGTCTTTTCTCCCTAAGATTACAGTGGAATAGACC
131 GATCGCATCAGGTCTTATCTCCCTAAGATTACAGTGGAATAGACC
* * *
54836724 GAAGAATTATAGTTCTTATCTCCCTGAGATTACAGCAAAGCATATTGAAGCCAGTAATCCTATTT
1 GAAGAATTACAGATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCCAGTAATCCTATTT
* * * *
54836789 CCCTGAGATTATAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
66 CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
* *
54836854 GATCGCATCAGGTCTTATCTCCCTGAGATTATAGTGGAATAGACC
131 GATCGCATCAGGTCTTATCTCCCTAAGATTACAGTGGAATAGACC
* *
54836899 GAAGAATTA-AGATCCTGTCTCCCT
1 GAAGAATTACAGATCTTATCTCCCT
54836923 AAGCAGTAGC
Statistics
Matches: 183, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
174 12 0.07
175 171 0.93
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (175 bp):
GAAGAATTACAGATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCCAGTAATCCTATTT
CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
GATCGCATCAGGTCTTATCTCCCTAAGATTACAGTGGAATAGACC
Found at i:54836887 original size:85 final size:85
Alignment explanation
Indices: 54836613--54836892 Score: 285
Period size: 85 Copynumber: 3.2 Consensus size: 85
54836603 TAATCCTATT
*
54836613 TCCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
1 TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
*
54836678 AGATCGCATCAGGTCTTTTC
66 AGATCGCATCAGGTCTTATC
* * ** * * * *
54836698 TCCCTAAGATTACAGTGGAATAGACCGAAGAATTATA-GTTCTTATCTCCCTG-AGATTACAGCA
1 TCCCTGAGATTACAGTGGAACAGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAAG-TTACAGTA
* * * * * * * *
54836761 AAGCATATTGAAGCCAGTAATCCTATT
62 GAGCAGATCGCA-TCAG--GTCTTATC
* * *
54836788 TCCCTGAGATTATAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
1 TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
54836853 AGATCGCATCAGGTCTTATC
66 AGATCGCATCAGGTCTTATC
*
54836873 TCCCTGAGATTATAGTGGAA
1 TCCCTGAGATTACAGTGGAA
54836893 TAGACCGAAG
Statistics
Matches: 149, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
85 46 0.31
86 4 0.03
87 36 0.24
88 35 0.23
89 4 0.03
90 24 0.16
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (85 bp):
TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
AGATCGCATCAGGTCTTATC
Found at i:54837061 original size:44 final size:44
Alignment explanation
Indices: 54836993--54837087 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
54836983 TTAAGCCGCG
* *
54836993 AGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATCGCA
1 AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATCACA
*
54837037 AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTACA
1 AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATCACA
54837081 AGTCCTA
1 AGTCCTA
54837088 ACCCGCAGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (44 bp):
AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATCACA
Found at i:54842341 original size:105 final size:104
Alignment explanation
Indices: 54842114--54842595 Score: 547
Period size: 105 Copynumber: 4.6 Consensus size: 104
54842104 AGATAAGTTG
* * * * * *
54842114 TTAGGATTTGTGATCATAAATTAGCTAACTCAAATAAACTTAGGTTATGATCTTAAATCAACTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
** ** *
54842179 CCTT-TAATATCAGTTGTGAATGTAGGTCAGTGAGCTAT
66 CCTTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * * *
54842217 TTAGGAGTT-ACGATCTTAAATAAACTAACTCAAATAAATTTGGGTTACGATCTTCAATCAGCTA
1 TTAGGAGTTGA-GATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTA
* * * * *
54842281 ACCTTTATAATATTAGCTGTGAACGTAGGTCAGCAAGCTGT
65 ACC-TTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * *
54842322 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAGACTTAGGTTTCAATCTTAAATCAATTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
* *
54842387 CCTTATAATATTAATTGTGAACATAGGTCAGCGAGCTAT
66 CCTTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * * ** *
54842426 TTAGAAGTTGCGATCTTAAAT-AGCTAAGTCAAATAAACTTAGGTCGCGATCTTAAATCAGCTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
* * *
54842490 CCTTTAAAATATCAACCGTGAACATAGGTCAGTGAGCTAT
66 CC-TTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * *
54842530 TTAAGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCGATATTAAATCAACTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
54842595 C
66 C
54842596 TCAAATAAAC
Statistics
Matches: 319, Mismatches: 54, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
103 93 0.29
104 103 0.32
105 122 0.38
106 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (104 bp):
TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
CCTTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
Found at i:54842520 original size:208 final size:208
Alignment explanation
Indices: 54842114--54842595 Score: 635
Period size: 208 Copynumber: 2.3 Consensus size: 208
54842104 AGATAAGTTG
* * * *
54842114 TTAGGATTTGTGATCATAAATTAGCTAACTCAAATAAACTTAGGTTAT-GATCTTAAATCAACTA
1 TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTT-TCGATCTTAAATCAACTA
* ** * *
54842178 ACCTTTAATATCAGTTGTGAATGTAGGTCAGTGAGCTATTTAGGAGTTACGATCTTAAATAAACT
65 ACCTTTAATATCAATTGTGAACATAGGTCAGCGAGCTATTTAGAAGTTACGATCTTAAATAAACT
* * * * * * * * *
54842243 AACTCAAATAAATTTGGGTTACGATCTTCAATCAGCTAACCTTTATAATATTAGCTGTGAACGTA
130 AACTCAAATAAACTTAGGTCACGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATA
*
54842308 GGTCAGCAAGCTGT
195 GGTCAGCAAGCTAT
* * * *
54842322 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAGACTTAGGTTTCAATCTTAAATCAATTAA
1 TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAACTAA
* * *
54842387 CCTTATAATATTAATTGTGAACATAGGTCAGCGAGCTATTTAGAAGTTGCGATCTTAAAT-AGCT
66 CCTT-TAATATCAATTGTGAACATAGGTCAGCGAGCTATTTAGAAGTTACGATCTTAAATAAACT
* *
54842451 AAGTCAAATAAACTTAGGTCGCGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATA
130 AACTCAAATAAACTTAGGTCACGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATA
**
54842516 GGTCAGTGAGCTAT
195 GGTCAGCAAGCTAT
* * *
54842530 TTAAGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCGATATTAAATCAACTAA
1 TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAACTAA
54842595 C
66 C
54842596 TCAAATAAAC
Statistics
Matches: 235, Mismatches: 37, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
207 1 0.00
208 186 0.79
209 48 0.20
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (208 bp):
TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAACTAA
CCTTTAATATCAATTGTGAACATAGGTCAGCGAGCTATTTAGAAGTTACGATCTTAAATAAACTA
ACTCAAATAAACTTAGGTCACGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATAG
GTCAGCAAGCTAT
Found at i:54842632 original size:37 final size:37
Alignment explanation
Indices: 54842542--54842624 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
54842532 AAGAGTTGTG
*
54842542 ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCG
1 ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCA
* *
54842579 ATATTAAATCAACTAACTCAAATAAACTTAGGTTTCA
1 ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCA
54842616 ATCTTAAAT
1 ATCTTAAAT
54842625 TAGCTAACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (37 bp):
ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCA
Found at i:54842710 original size:142 final size:142
Alignment explanation
Indices: 54842436--54842858 Score: 546
Period size: 142 Copynumber: 3.0 Consensus size: 142
54842426 TTAGAAGTTG
* * ** *
54842436 CGATCTTAAAT-AGCTAAGTCAAATAAACTTAGGTCGCGATCTTAAATCAGCTAACCTTTAAAAT
1 CGATATTAAATCAGCTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAGCTAACCTTTATAAT
* * * * * * *
54842500 ATCA-ACCGTGAACATAGGTCAGTGAGCTATTTAAGAGTTGTGATCTTAAATCAACTAACTCAAA
66 ATTAGA-TGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAA
54842564 TAAACTTAGGTTC
130 TAAACTTAGGTTC
* * * * *
54842577 CGATATTAAATCAACTAACTCAAATAAACTTAGGTTTCAATCTTAAATTAGCTAACCTATATAAC
1 CGATATTAAATCAGCTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAGCTAACCTTTATAAT
* * * * **
54842642 ATTAGTTGTGAACATAGGTTAGCAAGTTGTTTAGGAGTTGCGATTTTAAATCAGGTAACTCAAAT
66 ATTAGATGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAAT
*
54842707 AAACTTAGGTTG
131 AAACTTAGGTTC
* * *
54842719 CGATATTAAATCAGCTAACTCAAATTAACTTAGGTTGT-GATCTAAAATCAACTAACCTTTATAA
1 CGATATTAAATCAGCTAACTCAAATAAACTTAGGTT-TCGATCTTAAATCAGCTAACCTTTATAA
* *
54842783 TATTAGATGTGAACGTAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATTAACTAACTCAAA
65 TATTAGATGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAA
54842848 TAAACTTAGGT
130 TAAACTTAGGT
54842859 ATGAACATTT
Statistics
Matches: 239, Mismatches: 40, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
141 10 0.04
142 228 0.95
143 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (142 bp):
CGATATTAAATCAGCTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAGCTAACCTTTATAAT
ATTAGATGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAAT
AAACTTAGGTTC
Found at i:54842728 original size:37 final size:37
Alignment explanation
Indices: 54842678--54842774 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
54842668 TTGTTTAGGA
* *
54842678 GTTGCGATTTTAAATCAGGTAACTCAAATAAACTTAG
1 GTTGCGATATTAAATCAGCTAACTCAAATAAACTTAG
*
54842715 GTTGCGATATTAAATCAGCTAACTCAAATTAACTTAG
1 GTTGCGATATTAAATCAGCTAACTCAAATAAACTTAG
* * * *
54842752 GTTGTGATCTAAAATCAACTAAC
1 GTTGCGATATTAAATCAGCTAAC
54842775 CTTTATAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (37 bp):
GTTGCGATATTAAATCAGCTAACTCAAATAAACTTAG
Found at i:54842925 original size:10 final size:10
Alignment explanation
Indices: 54842910--54842940 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
54842900 ATCTTTCATA
54842910 CATTATATTT
1 CATTATATTT
54842920 CATTATATTT
1 CATTATATTT
54842930 CATTATATTT
1 CATTATATTT
54842940 C
1 C
54842941 TTCAGATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (10 bp):
CATTATATTT
Found at i:54850989 original size:12 final size:13
Alignment explanation
Indices: 54850962--54850995 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
54850952 ATAACAGTGG
54850962 GATATTATGCCAT
1 GATATTATGCCAT
*
54850975 GATTTTATG-CAT
1 GATATTATGCCAT
54850987 GATATTATG
1 GATATTATG
54850996 TTTTAGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (13 bp):
GATATTATGCCAT
Found at i:54853727 original size:69 final size:70
Alignment explanation
Indices: 54853595--54853727 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
54853585 TAGTTTATTA
* * * * *
54853595 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTC
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTC
54853660 CTTAG
66 CTTAG
54853665 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
54853728 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTC
CTTAG
Found at i:54855268 original size:47 final size:47
Alignment explanation
Indices: 54855191--54855752 Score: 818
Period size: 47 Copynumber: 12.0 Consensus size: 47
54855181 TTAGGATTTT
** *
54855191 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * **
54855238 ATTTGATAAATGTGAGCATGCATATGTGTGATAAGGTTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
54855285 AAGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
54855332 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
54855379 ATGTGGTGAATATGAACATGCATATACGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
54855426 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
54855473 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
54855520 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
54855567 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
54855614 ATGTGATGAATGTGAGCATGCATATATATGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
54855661 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
54855708 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
54855753 TAGTGTGAAA
Statistics
Matches: 456, Mismatches: 59, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 456 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:54855387 original size:25 final size:25
Alignment explanation
Indices: 54855312--54855387 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
54855302 ATGTATATAT
54855312 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
54855337 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
54855359 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
54855384 GTGA
1 GTGA
54855388 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:54855716 original size:25 final size:25
Alignment explanation
Indices: 54855642--54855716 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 25
54855632 TGCATATATA
*
54855642 TGATAAGGCCGAATGGCCAATGTGA
1 TGATAAGGCCGAATGGCCAATGTGG
* * *
54855667 TGA-ATGTG-AGCAT-G-CATATGT-G
1 TGATAAG-GCCGAATGGCCA-ATGTGG
54855689 TGATAAGGCCGAATGGCCAATGTGG
1 TGATAAGGCCGAATGGCCAATGTGG
54855714 TGA
1 TGA
54855717 ATATGAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.24
Consensus pattern (25 bp):
TGATAAGGCCGAATGGCCAATGTGG
Found at i:54855973 original size:37 final size:37
Alignment explanation
Indices: 54855915--54856066 Score: 205
Period size: 37 Copynumber: 4.1 Consensus size: 37
54855905 GGAAATATAT
* * *
54855915 TCCGGGTGAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
54855952 TCCGAGAAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
54855989 CCCGGGTAAGACCCGATGACTACGTGTAGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * * *
54856026 TTCGGGTAAGACCCGATAACTTCGTGTGGAGATTTCG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
54856063 TCCG
1 TCCG
54856067 AGCTAAAGGT
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:54857815 original size:41 final size:41
Alignment explanation
Indices: 54857766--54857846 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
54857756 ATTACGAAGT
54857766 TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAAC
1 TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAAC
**
54857807 TAGTATGAAAAATATATTAAAGATCGGTTAAGTAATTAAA
1 TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAA
54857847 TTGAGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (41 bp):
TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAAC
Found at i:54860857 original size:15 final size:14
Alignment explanation
Indices: 54860837--54860866 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
54860827 CTTCATGTAG
54860837 TTGATTTGTCATAAT
1 TTGATTTGTCA-AAT
54860852 TTGATTTGTCAAAT
1 TTGATTTGTCAAAT
54860866 T
1 T
54860867 AGGCTTCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTGATTTGTCAAAT
Found at i:54862715 original size:7 final size:7
Alignment explanation
Indices: 54862703--54862759 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
54862693 TAGTTTACAT
54862703 TTTTTTA
1 TTTTTTA
54862710 TTTTTTA
1 TTTTTTA
54862717 TTTTTATAA
1 TTTTT-T-A
*
54862726 TTTATT-
1 TTTTTTA
*
54862732 TTTTTAA
1 TTTTTTA
*
54862739 TTTTTAA
1 TTTTTTA
54862746 TTTTTTA
1 TTTTTTA
54862753 TTATTTT
1 TT-TTTT
54862760 TAAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
6 4 0.10
7 27 0.64
8 6 0.14
9 5 0.12
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:54862721 original size:15 final size:15
Alignment explanation
Indices: 54862701--54862759 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
54862691 TCTAGTTTAC
54862701 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
**
54862716 A--TTTTTATAATTT
1 ATTTTTTTATTTTTT
*
54862729 ATTTTTTTAATTTTT
1 ATTTTTTTATTTTTT
*
54862744 AATTTTTTATTATTTT
1 ATTTTTTTATT-TTTT
54862760 TAAATTATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 11 0.32
15 19 0.56
16 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:54862731 original size:20 final size:20
Alignment explanation
Indices: 54862706--54862773 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 20
54862696 TTTACATTTT
54862706 TTTATTTTTTATTTTTATAA
1 TTTATTTTTTATTTTTATAA
*
54862726 TTTATTTTTTTAATTTT-TAA
1 TTTA-TTTTTTATTTTTATAA
*
54862746 TTT-TTTATTATTTTTA-AA
1 TTTATTTTTTATTTTTATAA
54862764 -TTATTTTTTA
1 TTTATTTTTTA
54862774 ATGTAACATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 2 0.05
18 18 0.44
20 10 0.24
21 11 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTTTTTATTTTTATAA
Found at i:54862743 original size:37 final size:38
Alignment explanation
Indices: 54862696--54862772 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
54862686 GGCAATCTAG
* *
54862696 TTTACATTTTTTTATTTTTTATT-TTTATAATTTATTTT
1 TTTACA-TTTTTAATTTTTTATTATTTATAAATTATTTT
*
54862734 TTTA-ATTTTTAATTTTTTATTATTTTTAAATTATTTT
1 TTTACATTTTTAATTTTTTATTATTTATAAATTATTTT
54862771 TT
1 TT
54862773 AATGTAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 15 0.43
37 16 0.46
38 4 0.11
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.75
Consensus pattern (38 bp):
TTTACATTTTTAATTTTTTATTATTTATAAATTATTTT
Found at i:54862775 original size:36 final size:36
Alignment explanation
Indices: 54862703--54862772 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
54862693 TAGTTTACAT
* *
54862703 TTTTTTATTTTTTATTTTTATAATTTATTTTTTTAA
1 TTTTTAATTTTTTATTTTTATAAATTATTTTTTTAA
*
54862739 TTTTTAATTTTTTATTATTTTTAAATTATTTTTT
1 TTTTTAATTTTTTATT-TTTATAAATTATTTTTT
54862773 AATGTAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 15 0.50
37 15 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (36 bp):
TTTTTAATTTTTTATTTTTATAAATTATTTTTTTAA
Found at i:54867145 original size:6 final size:7
Alignment explanation
Indices: 54867086--54867114 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
54867076 TGCCCTGTCG
54867086 TTAGGGT
1 TTAGGGT
54867093 TTAGGGT
1 TTAGGGT
54867100 TTAGGGT
1 TTAGGGT
54867107 TTAGGGT
1 TTAGGGT
54867114 T
1 T
54867115 AAGGTTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:54870057 original size:34 final size:34
Alignment explanation
Indices: 54869956--54870076 Score: 137
Period size: 34 Copynumber: 3.7 Consensus size: 34
54869946 AACAACGTTT
*
54869956 TATTTTATTAAATGAAATAATATAGAATAATTTC
1 TATTTTATTACATGAAATAATATAGAATAATTTC
* *
54869990 TATTATATTA-A--AAAT-GTA-A-AAGTAAATTTC
1 TATTTTATTACATGAAATAATATAGAA-T-AATTTC
*
54870020 TATTTTAGTACATGAAATAATATAGAATAATTTC
1 TATTTTATTACATGAAATAATATAGAATAATTTC
*
54870054 TATTTTATTACATCAAATAATAT
1 TATTTTATTACATGAAATAATAT
54870077 CAAAATATTC
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.03
29 2 0.03
30 16 0.22
31 5 0.07
33 5 0.07
34 38 0.53
35 2 0.03
36 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (34 bp):
TATTTTATTACATGAAATAATATAGAATAATTTC
Found at i:54870277 original size:21 final size:21
Alignment explanation
Indices: 54870251--54870292 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54870241 CCAGCTTCCA
* * *
54870251 GCGGGGGTTCTGGTTGCTCCG
1 GCGGGGATTCTAGTTCCTCCG
54870272 GCGGGGATTCTAGTTCCTCCG
1 GCGGGGATTCTAGTTCCTCCG
54870293 ATAGGGGATC
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:0.05, C:0.26, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGGGATTCTAGTTCCTCCG
Found at i:54871890 original size:11 final size:11
Alignment explanation
Indices: 54871858--54871914 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
54871848 GTTTTTAAAT
* *
54871858 AGGAATTTGAA
1 AGGAAATTGAG
54871869 AGGAAATTGAG
1 AGGAAATTGAG
54871880 AGGAAATTGAG
1 AGGAAATTGAG
54871891 A-GAATATT-AG
1 AGGAA-ATTGAG
54871901 AGAGAAATTGAG
1 AG-GAAATTGAG
54871913 AG
1 AG
54871915 AAAGGATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 6 0.15
11 27 0.68
12 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:54871913 original size:10 final size:10
Alignment explanation
Indices: 54871871--54871917 Score: 67
Period size: 11 Copynumber: 4.4 Consensus size: 10
54871861 AATTTGAAAG
54871871 GAAATTGAGA
1 GAAATTGAGA
54871881 GGAAATTGAGA
1 -GAAATTGAGA
54871892 GAATATTAGAGA
1 GAA-ATT-GAGA
54871904 GAAATTGAGA
1 GAAATTGAGA
54871914 GAAA
1 GAAA
54871918 GGATTAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.32
11 16 0.47
12 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:54879593 original size:41 final size:41
Alignment explanation
Indices: 54879529--54879722 Score: 214
Period size: 41 Copynumber: 4.7 Consensus size: 41
54879519 TTTTAAACCT
*
54879529 TTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GTATCA
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGT-TCA
* * * * *
54879570 TTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGTTCT
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGTTCA
* *
54879611 TTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GTATTA
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGT-TCA
* * * * *
54879652 TTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGTTCT
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGTTCA
*
54879693 TTAGCGGCATTTTT-TGCTAAGCGCCGCTAA
1 TTAGCGGCGTTTTTAT-CTAAGCGCCGCTAA
54879723 AGTTCGTGTT
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 3 0.02
41 118 0.94
42 4 0.03
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (41 bp):
TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGTTCA
Found at i:54879664 original size:82 final size:82
Alignment explanation
Indices: 54879527--54879722 Score: 358
Period size: 82 Copynumber: 2.4 Consensus size: 82
54879517 TTTTTTAAAC
54879527 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAGC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAGC
54879592 GCCACTAATTCTCTGTT
66 GCCACTAATTCTCTGTT
*
54879609 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATTATTAGTGGCGTTTTTATCTGAGC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAGC
54879674 GCCACTAATTCTCTGTT
66 GCCACTAATTCTCTGTT
*
54879691 CTTTAGCGGCATTTTT-TGCTAAGCGCCGCTAA
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAA
54879723 AGTTCGTGTT
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
81 1 0.01
82 110 0.99
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAGC
GCCACTAATTCTCTGTT
Found at i:54879958 original size:82 final size:82
Alignment explanation
Indices: 54879862--54880038 Score: 336
Period size: 82 Copynumber: 2.2 Consensus size: 82
54879852 GTGTACTCTA
54879862 TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
1 TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
*
54879927 TTTCTGTAATTGAAAAT
66 TTTCTGTAATTGAAAAG
*
54879944 TTAGTGGCGTTTTAAGGTAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
1 TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
54880009 TTTCTGTAATTGAAAAG
66 TTTCTGTAATTGAAAAG
54880026 TTAGTGGCGTTTT
1 TTAGTGGCGTTTT
54880039 TTCCGGTAGC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 93 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (82 bp):
TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
TTTCTGTAATTGAAAAG
Found at i:54880960 original size:8 final size:10
Alignment explanation
Indices: 54880938--54880974 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
54880928 TATTTTTACT
54880938 TATATATGGA
1 TATATATGGA
*
54880948 TATATATGAA
1 TATATATGGA
54880958 TATATATGGA
1 TATATATGGA
54880968 TATATAT
1 TATATAT
54880975 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:54881083 original size:27 final size:27
Alignment explanation
Indices: 54881042--54881093 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
54881032 AATAAACAAA
* *
54881042 TAAATAAGTTAGTAATTATTTATTTGT
1 TAAATAAATTAGTAATTAATTATTTGT
*
54881069 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATTAATTATTT
54881094 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATTAGTAATTAATTATTTGT
Found at i:54884038 original size:74 final size:74
Alignment explanation
Indices: 54883958--54884104 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 74
54883948 AATAAAATAT
54883958 AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTA
1 AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTA
54884023 ATAATTATG
66 ATAATTATG
*
54884032 AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATTTTATTTTATTAAATATTATTA
1 AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTA
54884097 ATAATTAT
66 ATAATTAT
54884105 ATTAGTAATG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (74 bp):
AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTA
ATAATTATG
Found at i:54884184 original size:18 final size:18
Alignment explanation
Indices: 54884161--54884282 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
54884151 AATAACTTAC
54884161 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
54884179 AACTTACATTACTTACA--T
1 AACTTACA-TA-ATACATTT
*
54884197 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
54884214 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--T---TT
54884237 ACAACTTACATAATACATTT
1 --AACTTACATAATACATTT
* *
54884257 GACTGACATAATACATTT
1 AACTTACATAATACATTT
54884275 AACTTACA
1 AACTTACA
54884283 ACTTACACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
13 1 0.01
14 2 0.03
15 2 0.03
16 4 0.05
17 2 0.03
18 33 0.41
19 11 0.14
20 7 0.09
21 1 0.01
23 1 0.01
24 1 0.01
25 15 0.19
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:54884225 original size:26 final size:26
Alignment explanation
Indices: 54884142--54884599 Score: 683
Period size: 26 Copynumber: 18.1 Consensus size: 26
54884132 ATTTTATTAA
54884142 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
54884168 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
54884195 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
54884221 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
54884246 ATAATAC---AT---TT--GACTGAC
1 ATAATACATAATAACTTACAACTTAC
*
54884264 ATAATACATT-TAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
54884289 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884315 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
54884341 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884367 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884393 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884419 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
54884445 ATAATACAT-TTAACTTGCAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
54884470 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884496 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
54884522 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
54884547 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884572 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
54884598 AT
1 AT
54884600 TTAACTTACA
Statistics
Matches: 395, Mismatches: 23, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
18 12 0.03
20 3 0.01
23 3 0.01
25 113 0.29
26 240 0.61
27 15 0.04
28 9 0.02
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:54884434 original size:19 final size:19
Alignment explanation
Indices: 54884334--54884630 Score: 87
Period size: 19 Copynumber: 15.6 Consensus size: 19
54884324 AATAACTTAC
*
54884334 AACTTACACAATACATAAT
1 AACTTACATAATACATAAT
*
54884353 AACTTACA-ACTTACATAAT
1 AACTTACATA-ATACATAAT
* * *
54884372 -ACATA-AT-A-AC-TTAC
1 AACTTACATAATACATAAT
54884386 AACTTACATAATACATAAT
1 AACTTACATAATACATAAT
*
54884405 AACTTACA-ACTTACATAAT
1 AACTTACATA-ATACATAAT
* * *
54884424 -ACATA-AT-A-AC-TTAC
1 AACTTACATAATACATAAT
54884438 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--TAA--T
*
54884461 GCAACTTACACAATACATAAT
1 --AACTTACATAATACATAAT
*
54884482 AACTTACA-ACTTACATAAT
1 AACTTACATA-ATACATAAT
* * *
54884501 -ACATA-AT-A-AC-TTAC
1 AACTTACATAATACATAAT
54884515 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--TAA--T
*
54884538 ACAACTTACACAATACATTTAACTT
1 --AACTTACATAATACA--TAA--T
54884563 ACAACTTACATAATACATAAT
1 --AACTTACATAATACATAAT
* *
54884584 AACTTACA-ACTTACAT-TT
1 AACTTACATA-ATACATAAT
*
54884602 AACTTACATAATACAT-TT
1 AACTTACATAATACATAAT
54884620 AACTTACATAA
1 AACTTACATAA
54884631 CTTACATAAC
Statistics
Matches: 213, Mismatches: 30, Indels: 71
0.68 0.10 0.23
Matches are distributed among these distances:
14 6 0.03
15 18 0.08
16 6 0.03
17 6 0.03
18 49 0.23
19 64 0.30
21 6 0.03
23 6 0.03
25 52 0.24
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (19 bp):
AACTTACATAATACATAAT
Found at i:54884561 original size:18 final size:18
Alignment explanation
Indices: 54884540--54884627 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 18
54884530 TTTAACTTAC
54884540 AACTTACACAATACATTT
1 AACTTACACAATACATTT
*
54884558 AACTTACAACTTACATAATACATAAT
1 AACTT---AC--AC--AATACAT-TT
*
54884584 AACTTACA-ACTTACATTT
1 AACTTACACA-ATACATTT
*
54884602 AACTTACATAATACATTT
1 AACTTACACAATACATTT
54884620 AACTTACA
1 AACTTACA
54884628 TAACTTACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
18 30 0.54
19 6 0.11
21 3 0.05
23 4 0.07
25 7 0.12
26 6 0.11
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
AACTTACACAATACATTT
Found at i:54884607 original size:11 final size:10
Alignment explanation
Indices: 54884591--54884644 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
54884581 AATAACTTAC
54884591 AACTTACATTT
1 AACTTACA-TT
54884602 AACTTACA-T
1 AACTTACATT
54884611 AA--TACATTT
1 AACTTACA-TT
54884620 AACTTACA-T
1 AACTTACATT
54884629 AACTTACA-T
1 AACTTACATT
54884638 AACTTAC
1 AACTTAC
54884645 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:54884628 original size:18 final size:18
Alignment explanation
Indices: 54884565--54884630 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
54884555 TTTAACTTAC
*
54884565 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
54884584 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
54884602 AACTTACATAATACATTT
1 AACTTACATAATACATTT
54884620 AACTTACATAA
1 AACTTACATAA
54884631 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:54890118 original size:21 final size:21
Alignment explanation
Indices: 54890092--54890162 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
54890082 CTACAACTTA
* *
54890092 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
54890113 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
54890134 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
54890155 AAGCAGAG
1 AAGCAGAG
54890163 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:54890405 original size:14 final size:14
Alignment explanation
Indices: 54890386--54890419 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
54890376 ATTGCTATTG
54890386 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
54890400 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
*
54890414 TTTGCT
1 GTTGCT
54890420 ACAGGAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.53
Consensus pattern (14 bp):
GTTGCTTTTGAAAT
Found at i:54890637 original size:42 final size:42
Alignment explanation
Indices: 54890573--54890858 Score: 450
Period size: 42 Copynumber: 6.8 Consensus size: 42
54890563 AGAAAAAAAA
**
54890573 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-TAAG
*
54890615 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * * *
54890657 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTAC-AAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
*
54890698 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
54890740 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
54890782 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
54890824 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
54890859 GTTTGTAAAC
Statistics
Matches: 226, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
41 36 0.16
42 185 0.82
43 5 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:54890763 original size:167 final size:167
Alignment explanation
Indices: 54890487--54890856 Score: 519
Period size: 167 Copynumber: 2.2 Consensus size: 167
54890477 TTTTGTATAA
* * * *
54890487 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAAAATGCCACTAAAGAACATGTTCTT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTAAAAACGCCACTAAAGAACATGTTCTT
54890552 TAGCGGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCC-CTTAAGC
66 TAGCGGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCTC-TAAGC
*
54890616 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCT
130 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* * * * *
54890654 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTACAAACGCCGCTAAAGAACATGTTCT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGC-GTTTGTAAAAACGCCACTAAAGAACATGTTCT
******* * **
54890719 TTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGC
65 TTAGCGGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCTCTAAGC
54890783 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
130 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
*
54890821 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
54890857 TTGTTTGTAA
Statistics
Matches: 178, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
166 3 0.02
167 138 0.78
168 37 0.21
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (167 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTAAAAACGCCACTAAAGAACATGTTCTT
TAGCGGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCTCTAAGCG
CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
Found at i:54890804 original size:84 final size:84
Alignment explanation
Indices: 54890487--54890858 Score: 464
Period size: 83 Copynumber: 4.5 Consensus size: 84
54890477 TTTTGTATAA
* * * * * ** *
54890487 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCG-TTTGTA-AAAATGCCACTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGTTC
*******
54890550 TTTAGCGGCGATTAGAAAAA
66 TTTAGCGGCG-TTTTTTTCT
* **
54890570 AAACGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTTAAGCGCCGCTAAAGAACATGTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTAC-TAAGCGCCGCTAAAGAACATGTT
54890634 CTTTAGCGGCGTTTTTTTCT
65 CTTTAGCGGCGTTTTTTTCT
* * * *
54890654 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTAC-AAACGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGTTC
54890718 TTTAGCGGCGTTTTTTTCT
66 TTTAGCGGCGTTTTTTTCT
* *
54890737 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGTTC
54890802 TTTAGCGGCGTTTTTTTCT
66 TTTAGCGGCGTTTTTTTCT
* *
54890821 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
54890859 GTTTGTAAAC
Statistics
Matches: 252, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
83 110 0.44
84 107 0.42
85 35 0.14
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGTTC
TTTAGCGGCGTTTTTTTCT
Found at i:54890858 original size:125 final size:125
Alignment explanation
Indices: 54890570--54890858 Score: 454
Period size: 125 Copynumber: 2.3 Consensus size: 125
54890560 ATTAGAAAAA
* *
54890570 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTTAAGCGCCGCTAAAGAACATGTTC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCCTTAAGCGCCGCTAAAGAACATGATC
* *
54890635 TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTAC
66 TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTAC
* *
54890695 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TTCTAAGCGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCCT-TAAGCGCCGCTAAAGAACATGAT
* *
54890759 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
65 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTAC
* * *
54890820 TAAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 -AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
54890859 GTTTGTAAAC
Statistics
Matches: 151, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
124 1 0.01
125 115 0.76
126 35 0.23
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (125 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCCTTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTAC
Found at i:54897558 original size:50 final size:50
Alignment explanation
Indices: 54897434--54897625 Score: 233
Period size: 50 Copynumber: 3.8 Consensus size: 50
54897424 GATAATAACA
** * * *
54897434 TGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGATGTTATCATGTTGG
1 TGCCAACA-CCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *** * *
54897485 TGCCCATGTCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54897535 TGCCAACACCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGG
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
**
54897585 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTC
54897626 AGACATGGTC
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 89 0.74
51 31 0.26
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54897623 original size:100 final size:101
Alignment explanation
Indices: 54897434--54897625 Score: 271
Period size: 100 Copynumber: 1.9 Consensus size: 101
54897424 GATAATAACA
*** * * * *
54897434 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTATCATGTTGGTGCCCATGTCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAACCTATCATCTCGGTGCCAATGCCATGT
*
54897499 CCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
54897535 TGCCAACA-CCATGTCCCAGACATGGTCTTACAT-GGAACCTCTCATCTCGGTGCCAATGCCATG
1 TGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGAACCTATCATCTCGGTGCCAATGCCATG
*
54897598 TCCCAGACATGGTCTTACATGGGACCTC
65 TCCCAGACATGGTCTTACAGGGGACCTC
54897626 AGACATGGTC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
100 48 0.60
101 31 0.39
102 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAACCTATCATCTCGGTGCCAATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:54897628 original size:24 final size:24
Alignment explanation
Indices: 54897601--54897649 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
54897591 TGCCATGTCC
54897601 CAGACATGGTCTTACATGGGACCT
1 CAGACATGGTCTTACATGGGACCT
54897625 CAGACATGGTCTTACATGGGACCT
1 CAGACATGGTCTTACATGGGACCT
54897649 C
1 C
54897650 TCATCTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
CAGACATGGTCTTACATGGGACCT
Found at i:54897672 original size:74 final size:74
Alignment explanation
Indices: 54897551--54897699 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
54897541 CACCATGTCC
54897551 CAGACATGGTCTTACATGGAACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTAC
1 CAGACATGGTCTTACATGGAACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTAC
54897616 ATGGGACCT
66 ATGGGACCT
*
54897625 CAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTAC
1 CAGACATGGTCTTACATGGAACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTAC
54897690 ATGGGACCT
66 ATGGGACCT
54897699 C
1 C
54897700 TTTACCCAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (74 bp):
CAGACATGGTCTTACATGGAACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTAC
ATGGGACCT
Found at i:54897816 original size:13 final size:13
Alignment explanation
Indices: 54897795--54897825 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54897785 GCTTAGATCA
*
54897795 TCATCAAATAAAT
1 TCATAAAATAAAT
54897808 TCATAAAATAAAT
1 TCATAAAATAAAT
54897821 TCATA
1 TCATA
54897826 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54898073 original size:30 final size:30
Alignment explanation
Indices: 54898038--54898095 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54898028 CCTCGACTCT
*
54898038 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
54898068 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
54898096 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:54917167 original size:13 final size:13
Alignment explanation
Indices: 54917146--54917176 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54917136 GCTTAGATCA
*
54917146 TCATCAAATAAAT
1 TCATAAAATAAAT
54917159 TCATAAAATAAAT
1 TCATAAAATAAAT
54917172 TCATA
1 TCATA
54917177 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54917424 original size:30 final size:30
Alignment explanation
Indices: 54917389--54917446 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54917379 CCTCGACTCT
*
54917389 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
54917419 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
54917447 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:54936179 original size:24 final size:24
Alignment explanation
Indices: 54936147--54936195 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
54936137 ATTATAGCGA
54936147 ACGGGTGGGCTTGGGCGGGTTTGG
1 ACGGGTGGGCTTGGGCGGGTTTGG
54936171 ACGGGTGGGCTTGGGCGGGTTTGG
1 ACGGGTGGGCTTGGGCGGGTTTGG
54936195 A
1 A
54936196 TCTGGCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.12, G:0.57, T:0.24
Consensus pattern (24 bp):
ACGGGTGGGCTTGGGCGGGTTTGG
Found at i:54936808 original size:20 final size:21
Alignment explanation
Indices: 54936749--54936808 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
54936739 AAAAATATTA
* *
54936749 ATATATAAA-TAATTTTTTTC
1 ATATATAAATTAATATTTATC
54936769 ATATATAAATTTTGAA-ATTTAT-
1 ATATATAAA--TT-AATATTTATC
54936791 ATATATAAATTAATATTT
1 ATATATAAATTAATATTT
54936809 TTAAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
22 9 0.27
23 5 0.15
24 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATATAAATTAATATTTATC
Found at i:54936811 original size:22 final size:23
Alignment explanation
Indices: 54936749--54936811 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 23
54936739 AAAAATATTA
54936749 ATATATAAA-TAAT-TTTTT-TC
1 ATATATAAATTAATATTTTTATC
* **
54936769 ATATATAAATT-TTGAAATTTAT-
1 ATATATAAATTAAT-ATTTTTATC
54936791 ATATATAAATTAATATTTTTA
1 ATATATAAATTAATATTTTTA
54936812 AATTTTTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 10 0.31
21 1 0.03
22 19 0.59
23 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATATAAATTAATATTTTTATC
Found at i:54936836 original size:127 final size:124
Alignment explanation
Indices: 54936685--54936911 Score: 400
Period size: 127 Copynumber: 1.8 Consensus size: 124
54936675 TATTATGCTT
54936685 AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAATAAAAAATATTAA
1 AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAAT-AAAAATATTAA
*
54936750 TATATAAATAATTTTTTTCATATATAAATTTTGAAATTTATATATATAAATTAATATTTTTA
65 TATATAAATAA-TTTTTT-ATATATAAATTTTAAAATTTATATATATAAATTAATATTTTTA
* *
54936812 AATTTTTAGTTATTTTTAATACATACTTATAGTTTAATTTGTACTTTCTTAATAAAGATATTAAT
1 AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAATAAAAATATTAAT
54936877 ATATAAATAATTTTTTATATATAAATTTTAAAATT
66 ATATAAATAATTTTTTATATATAAATTTTAAAATT
54936912 ATTAAGGCAA
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
124 18 0.19
125 6 0.06
126 21 0.22
127 52 0.54
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (124 bp):
AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAATAAAAATATTAAT
ATATAAATAATTTTTTATATATAAATTTTAAAATTTATATATATAAATTAATATTTTTA
Found at i:54939609 original size:51 final size:51
Alignment explanation
Indices: 54939521--54939651 Score: 118
Period size: 51 Copynumber: 2.6 Consensus size: 51
54939511 ATGAGATGAG
* * * *
54939521 ATTCGTTGCCTTCAACTTTAATCTGCTCCGCTACAACGACAGGGAAATAAA
1 ATTCGCTGCCTTCAGCTTTAATCTACTCCGCTACAACGACAAGGAAATAAA
* ** * * * **
54939572 ATTCGCTGCCTTCAGCTTTAATCTATTCCTTTGCAACGCCAAGGAGATAGG
1 ATTCGCTGCCTTCAGCTTTAATCTACTCCGCTACAACGACAAGGAAATAAA
* ** *
54939623 ATTTGCTGTATTCAGCTTTAATCCACTCC
1 ATTCGCTGCCTTCAGCTTTAATCTACTCC
54939652 ACTTCAGCTT
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (51 bp):
ATTCGCTGCCTTCAGCTTTAATCTACTCCGCTACAACGACAAGGAAATAAA
Found at i:54939659 original size:21 final size:21
Alignment explanation
Indices: 54939633--54939675 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
54939623 ATTTGCTGTA
54939633 TTCAGCTTTAATCCACTCCAC
1 TTCAGCTTTAATCCACTCCAC
*
54939654 TTCAGCTTTAATCCATTCCAC
1 TTCAGCTTTAATCCACTCCAC
54939675 T
1 T
54939676 GCAATGCCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.35, G:0.05, T:0.37
Consensus pattern (21 bp):
TTCAGCTTTAATCCACTCCAC
Found at i:54939856 original size:45 final size:45
Alignment explanation
Indices: 54939800--54939896 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
54939790 GTCTTCTTCA
* * * *
54939800 ATCTGCTTCGCTGTCAATACAAGAAGGCAAGATCTGCTATCCTCG
1 ATCTACTTCGCTGCCAATACAAGAAGACAAGATCTACTATCCTCG
* *
54939845 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATCTTCG
1 ATCTACTTCGCTGCCAATACAAGAAGACAAGATCTACTATCCTCG
54939890 ATCTACT
1 ATCTACT
54939897 CCACTGCTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (45 bp):
ATCTACTTCGCTGCCAATACAAGAAGACAAGATCTACTATCCTCG
Found at i:54940161 original size:132 final size:129
Alignment explanation
Indices: 54939869--54940231 Score: 519
Period size: 132 Copynumber: 2.8 Consensus size: 129
54939859 CAATACAGGA
* * * * * *
54939869 AGACAAGATCTACTATCTTCGATCTACTCCACTGCTACTCAGGGAGATAGGACTAGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
* * * *
54939934 TCTACTTCCCTACTACCTTGGAAAGATAAGGTTCGCCTTTGATCTACTCCACTACTGCTTAGGG
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCTTTGATCTACTCCACTACTGCTTAGGG
* * * *
54939998 AGACGGGATCTACATTTTTCAACCTACTCCACTGCTGCTTAGGGAGATAGGACTGGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
*
54940063 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAG
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACC-T-TT-GATCTACTCCACTACTGCTTAG
54940128 GG
128 GG
* *
54940130 AGACAGGATCTACAATCTTCAACCTAATCCACTGTTGCTCAGGGAGATAGGACTGGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
* * *
54940195 TCTGTTTCCCTACTTCTTTGGGAAGATAAGATTCACC
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACC
54940232 GCCTTCTTCA
Statistics
Matches: 207, Mismatches: 24, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
129 88 0.43
130 1 0.00
131 2 0.01
132 116 0.56
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (129 bp):
AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCTTTGATCTACTCCACTACTGCTTAGGG
Found at i:54941242 original size:18 final size:18
Alignment explanation
Indices: 54941221--54941255 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54941211 TTCTAGGGAC
54941221 AACAAGTTCAATATAAAA
1 AACAAGTTCAATATAAAA
54941239 AACAAGTTCAATATAAA
1 AACAAGTTCAATATAAA
54941256 TAGTATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (18 bp):
AACAAGTTCAATATAAAA
Found at i:54943327 original size:11 final size:10
Alignment explanation
Indices: 54943311--54943344 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
54943301 CGTGCTTTTT
*
54943311 AAAAAAATTC
1 AAAAAAATAC
54943321 AAAAAAATAC
1 AAAAAAATAC
54943331 AAAAAAATA-
1 AAAAAAATAC
54943340 AAAAA
1 AAAAA
54943345 TTGCATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:54943376 original size:30 final size:27
Alignment explanation
Indices: 54943341--54943466 Score: 90
Period size: 30 Copynumber: 4.3 Consensus size: 27
54943331 AAAAAAATAA
* *
54943341 AAAATTGCATTTTGACCCATAAATTTTCCT
1 AAAATTACATTTTAACCC-TAAATTTT--T
*
54943371 AAAATTATATTTTAAACCCTAAACTATTTT
1 AAAATTACATTTT-AACCCTAAA-T-TTTT
* ** *
54943401 GAAATTACATTTTGGCCCATCAACTTTTT
1 AAAATTACATTTTAACCC-T-AAATTTTT
54943430 AAAATTACATTTTAAGCCCTAAATTTTCTT
1 AAAATTACATTTTAA-CCCTAAA-TTT-TT
54943460 AAAATTA
1 AAAATTA
54943467 TGTTTTGACC
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.03
29 23 0.30
30 41 0.54
31 7 0.09
32 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (27 bp):
AAAATTACATTTTAACCCTAAATTTTT
Found at i:54943465 original size:59 final size:59
Alignment explanation
Indices: 54943341--54943487 Score: 154
Period size: 59 Copynumber: 2.5 Consensus size: 59
54943331 AAAAAAATAA
* *
54943341 AAAATTGCATTTTGACCCATAAATTTTCCTAAAATTATATTTTAAACCCTAAACTATTTT
1 AAAATTACATTTTGACCCATAAATTTT-CTAAAATTACATTTTAAACCCTAAACTATTTT
* * * * *
54943401 GAAATTACATTTTGGCCCATCAACTTTT-TAAAATTACATTTTAAGCCCTAAA-TTTTCTT
1 AAAATTACATTTTGACCCAT-AAATTTTCTAAAATTACATTTTAAACCCTAAACTATT-TT
** *
54943460 AAAATTATGTTTTGACCCTATAAGTTTT
1 AAAATTACATTTTGACCC-ATAAATTTT
54943488 GCTACATTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
58 3 0.04
59 44 0.61
60 19 0.26
61 6 0.08
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (59 bp):
AAAATTACATTTTGACCCATAAATTTTCTAAAATTACATTTTAAACCCTAAACTATTTT
Found at i:54943850 original size:16 final size:15
Alignment explanation
Indices: 54943825--54943863 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
54943815 TTTGAGGAAG
*
54943825 AAGAAGAAGAAGAAAA
1 AAGAAAAAGAA-AAAA
54943841 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAA
54943856 AGAGAAAA
1 A-AGAAAA
54943864 TAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAA
Found at i:54943973 original size:18 final size:19
Alignment explanation
Indices: 54943938--54943973 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54943928 AGCCCAATCA
*
54943938 AAAAAAAAGAAATTAAGCC
1 AAAAAAAAGAAATAAAGCC
54943957 AAAAAAAAGAAA-AAAGC
1 AAAAAAAAGAAATAAAGC
54943974 AACACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.75, C:0.08, G:0.11, T:0.06
Consensus pattern (19 bp):
AAAAAAAAGAAATAAAGCC
Found at i:54944206 original size:21 final size:22
Alignment explanation
Indices: 54944171--54944212 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54944161 TAGTCCAAAA
54944171 AAAGAAAAAAGAGAAAAAAAGG
1 AAAGAAAAAAGAGAAAAAAAGG
*
54944193 AAAGGAAAAA-AGAAAAAAAG
1 AAAGAAAAAAGAGAAAAAAAG
54944213 AAGCCCGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAGAGAAAAAAAGG
Found at i:54952800 original size:16 final size:16
Alignment explanation
Indices: 54952779--54952812 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54952769 TTTTAGGATG
*
54952779 AAATTTTATGCAATCA
1 AAATTTCATGCAATCA
54952795 AAATTTCATGCAATCA
1 AAATTTCATGCAATCA
54952811 AA
1 AA
54952813 GGACAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (16 bp):
AAATTTCATGCAATCA
Found at i:54956623 original size:14 final size:14
Alignment explanation
Indices: 54956600--54956636 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
54956590 CTAAATCCTA
*
54956600 AACCCTAAATCTAG
1 AACCCCAAATCTAG
*
54956614 AATCCCAAATCTAG
1 AACCCCAAATCTAG
54956628 AACCCCAAA
1 AACCCCAAA
54956637 CCCAAAACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.32, G:0.05, T:0.16
Consensus pattern (14 bp):
AACCCCAAATCTAG
Found at i:54956788 original size:20 final size:20
Alignment explanation
Indices: 54956746--54956798 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
54956736 CCTTAAGCTT
* **
54956746 GAACCTCAAACCCCGAACCC
1 GAACCCCAAACCCAAAACCC
*
54956766 GAACCCCAAACCCAAAACTC
1 GAACCCCAAACCCAAAACCC
*
54956786 GAACACCAAACCC
1 GAACCCCAAACCC
54956799 GTAACCTCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.47, G:0.08, T:0.04
Consensus pattern (20 bp):
GAACCCCAAACCCAAAACCC
Found at i:54956876 original size:138 final size:139
Alignment explanation
Indices: 54956627--54956903 Score: 475
Period size: 138 Copynumber: 2.0 Consensus size: 139
54956617 CCCAAATCTA
54956627 GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTTGAACCATAAATCAAA
1 GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTTGAACCATAAATCAAA
* * *
54956692 ATCCTAACCCCCAAACTTATAACACATAACCCCAAACCATTGAACCTTAAGCTTGAACCTCAAAC
66 ACCCTAAACCCCAAACTTATAACACATAACCCCAAACCATTGAACCTTAAACTTGAACCTCAAAC
54956757 CCCGAACCC
131 CCCGAACCC
* * *
54956766 GAACCCCAAACCCAAAACTCGAACACCAAACCCGTAACCTCGAACTC-TTGAATCATAAATCAAA
1 GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTTGAACCATAAATCAAA
* *
54956830 ACCCTAAACCCCAAACTTATAACACATAACCCCAAACTATTGAACCTTAAACTTGAACTTCAAAC
66 ACCCTAAACCCCAAACTTATAACACATAACCCCAAACCATTGAACCTTAAACTTGAACCTCAAAC
54956895 CCCGAACCC
131 CCCGAACCC
54956904 CAAACCCTTA
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
138 85 0.65
139 45 0.35
ACGTcount: A:0.42, C:0.36, G:0.06, T:0.16
Consensus pattern (139 bp):
GAACCCCAAACCCAAAACTCGAACAACAAACCCGTAACCTCAAACTCTTTGAACCATAAATCAAA
ACCCTAAACCCCAAACTTATAACACATAACCCCAAACCATTGAACCTTAAACTTGAACCTCAAAC
CCCGAACCC
Found at i:54960382 original size:30 final size:30
Alignment explanation
Indices: 54960348--54960411 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
54960338 AAAATTACAC
* * *
54960348 TTTAATCTTTTAAAAACAATAAAAATTTAA
1 TTTAATCCTCTAAAAACAATAAAAATATAA
** *
54960378 TTTAATCCTCTAAAAATTATAAAGATATAA
1 TTTAATCCTCTAAAAACAATAAAAATATAA
54960408 TTTA
1 TTTA
54960412 TTAAAATAGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTAATCCTCTAAAAACAATAAAAATATAA
Found at i:54964800 original size:18 final size:19
Alignment explanation
Indices: 54964770--54964806 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54964760 CATGAGCATA
54964770 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
54964788 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
54964807 CCATGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:54966731 original size:29 final size:28
Alignment explanation
Indices: 54966684--54966744 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
54966674 ATGGCCAACC
* *
54966684 ATGTTGATATTATGTTTTTGTTAAAGTGT
1 ATGTTGATATGATGATTTTGTT-AAGTGT
* *
54966713 ATGTTGTTATGATGATTTTGTTGAGTGT
1 ATGTTGATATGATGATTTTGTTAAGTGT
54966741 ATGT
1 ATGT
54966745 AGCTTGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (28 bp):
ATGTTGATATGATGATTTTGTTAAGTGT
Found at i:54972592 original size:21 final size:21
Alignment explanation
Indices: 54972542--54972592 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
54972532 CCAGTCTATC
*
54972542 CCATCACTCTCTCAGCCTCTT
1 CCATCACTTTCTCAGCCTCTT
54972563 CCATCACTTTCTCAG-CTACTT
1 CCATCACTTTCTCAGCCT-CTT
*
54972584 GCATCACTT
1 CCATCACTT
54972593 CCCACTGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (21 bp):
CCATCACTTTCTCAGCCTCTT
Found at i:54975887 original size:37 final size:33
Alignment explanation
Indices: 54975810--54975877 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
54975800 TTTTTATTCA
54975810 TAATAAATATGCTTTTATTTTATTTAATAATGG
1 TAATAAATATGCTTTTATTTTATTTAATAATGG
54975843 TAATAAATAT-CTTTTCA-TTTATTTAATAATGG
1 TAATAAATATGCTTTT-ATTTTATTTAATAATGG
54975875 TAA
1 TAA
54975878 AATCGTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.50
Consensus pattern (33 bp):
TAATAAATATGCTTTTATTTTATTTAATAATGG
Found at i:54976181 original size:23 final size:25
Alignment explanation
Indices: 54976155--54976205 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
54976145 TTTTCACCAC
*
54976155 AAAATCAT-AAA-ATTATTTAATTT
1 AAAATCATAAAATATTATTGAATTT
**
54976178 AAAATTTTAAAATATTATTGAATTT
1 AAAATCATAAAATATTATTGAATTT
54976203 AAA
1 AAA
54976206 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 3 0.13
25 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATCATAAAATATTATTGAATTT
Found at i:54976337 original size:22 final size:22
Alignment explanation
Indices: 54976311--54976373 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
54976301 TATTTAAAAT
54976311 AAATAAATTAATATTATTAAAG
1 AAATAAATTAATATTATTAAAG
* *
54976333 AAATAAATTAA-AGTACTTAAAT
1 AAATAAATTAATATTA-TTAAAG
54976355 ATTAATAAA-TAATATTATT
1 A--AATAAATTAATATTATT
54976374 GAAAATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 17 0.50
23 5 0.15
24 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (22 bp):
AAATAAATTAATATTATTAAAG
Found at i:54980685 original size:25 final size:25
Alignment explanation
Indices: 54980652--54980703 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
54980642 TTAGGTGCAC
54980652 TTACCTTAGTCAAATTTTTAGTTGG
1 TTACCTTAGTCAAATTTTTAGTTGG
*
54980677 TTACTTTAGTCAAATTTTTAGTTGG
1 TTACCTTAGTCAAATTTTTAGTTGG
54980702 TT
1 TT
54980704 CACAACGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (25 bp):
TTACCTTAGTCAAATTTTTAGTTGG
Found at i:54981605 original size:23 final size:25
Alignment explanation
Indices: 54981579--54981629 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
54981569 TTTTCACCAC
*
54981579 AAAATCAT-AAA-ATTATTTAATTT
1 AAAATCATAAAATATTATTGAATTT
**
54981602 AAAATTTTAAAATATTATTGAATTT
1 AAAATCATAAAATATTATTGAATTT
54981627 AAA
1 AAA
54981630 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 3 0.13
25 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATCATAAAATATTATTGAATTT
Found at i:54981761 original size:22 final size:24
Alignment explanation
Indices: 54981734--54981797 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
54981724 TTATTTAAAA
54981734 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
*
54981757 -AAATAAATTAA-AGTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
54981780 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
54981798 GAAAATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 6 0.18
24 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:54988451 original size:22 final size:21
Alignment explanation
Indices: 54988413--54988453 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54988403 ATTTTCTCAT
* *
54988413 AAAAATCATAAAAATTATTAA
1 AAAAATAAAAAAAATTATTAA
54988434 AAAAATAAAAAAATATTATT
1 AAAAATAAAAAAA-ATTATT
54988454 GAAAGTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATAAAAAAAATTATTAA
Found at i:54988508 original size:9 final size:9
Alignment explanation
Indices: 54988411--54988611 Score: 57
Period size: 9 Copynumber: 21.8 Consensus size: 9
54988401 ATATTTTCTC
*
54988411 ATAAAAATC
1 ATAAAAATT
54988420 ATAAAAATT
1 ATAAAAATT
*
54988429 ATTAAAAAAATA
1 A-T--AAAAATT
*
54988441 AAAAAATATT
1 ATAAAA-ATT
** *
54988451 ATTGAAAGT
1 ATAAAAATT
*
54988460 ATTAAAATT
1 ATAAAAATT
54988469 -TAAAAA-T
1 ATAAAAATT
54988476 ACT-AAAATT
1 A-TAAAAATT
*
54988485 GATATAAACTT
1 -ATA-AAAATT
54988496 ATAAAAATT
1 ATAAAAATT
*
54988505 ATAATAAAAT
1 ATAA-AAATT
54988515 A-ATAAAATT
1 ATA-AAAATT
54988524 A-ATAAAATT
1 ATA-AAAATT
54988533 AATAAACCATATT
1 -ATAAA--A-ATT
54988546 -TAAAAATCT
1 ATAAAAAT-T
54988555 -TAAAAACTT
1 ATAAAAA-TT
* *
54988564 ATCAAAATC
1 ATAAAAATT
54988573 AT--AAA--
1 ATAAAAATT
*
54988578 A-AAAAATC
1 ATAAAAATT
54988586 ATAAAAACTT
1 ATAAAAA-TT
54988596 ATAAAAATT
1 ATAAAAATT
54988605 ATAAAAA
1 ATAAAAA
54988612 AAATTTACTT
Statistics
Matches: 148, Mismatches: 18, Indels: 52
0.68 0.08 0.24
Matches are distributed among these distances:
5 1 0.01
6 3 0.02
7 4 0.03
8 12 0.08
9 74 0.50
10 33 0.22
11 10 0.07
12 8 0.05
13 3 0.02
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:54988516 original size:8 final size:9
Alignment explanation
Indices: 54988506--54988538 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
54988496 ATAAAAATTA
54988506 TAATAAAA-
1 TAATAAAAT
54988514 TAATAAAAT
1 TAATAAAAT
54988523 TAATAAAAT
1 TAATAAAAT
54988532 TAATAAA
1 TAATAAA
54988539 CCATATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
TAATAAAAT
Found at i:54988585 original size:13 final size:13
Alignment explanation
Indices: 54988567--54988592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54988557 AAAACTTATC
54988567 AAAATCATAAAAA
1 AAAATCATAAAAA
54988580 AAAATCATAAAAA
1 AAAATCATAAAAA
54988593 CTTATAAAAA
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATCATAAAAA
Found at i:54988591 original size:32 final size:32
Alignment explanation
Indices: 54988547--54988614 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
54988537 AACCATATTT
* *
54988547 AAAAATCTTAAAAACTTATCAAAATCATAAAA
1 AAAAATCATAAAAACTTATAAAAATCATAAAA
*
54988579 AAAAATCATAAAAACTTATAAAAATTATAAAA
1 AAAAATCATAAAAACTTATAAAAATCATAAAA
54988611 AAAA
1 AAAA
54988615 TTTACTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (32 bp):
AAAAATCATAAAAACTTATAAAAATCATAAAA
Found at i:54988601 original size:19 final size:19
Alignment explanation
Indices: 54988546--54988611 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
54988536 AAACCATATT
*
54988546 TAAAAATCTTAAAAACTTA
1 TAAAAATCATAAAAACTTA
*
54988565 TCAAAATCAT--AAA---A
1 TAAAAATCATAAAAACTTA
54988579 -AAAAATCATAAAAACTTA
1 TAAAAATCATAAAAACTTA
*
54988597 TAAAAATTATAAAAA
1 TAAAAATCATAAAAA
54988612 AAATTTACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 3 0.08
17 3 0.08
18 1 0.03
19 21 0.57
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAATCATAAAAACTTA
Found at i:54991242 original size:24 final size:24
Alignment explanation
Indices: 54991210--54991265 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
54991200 GAAGACCGTG
* *
54991210 TATATATAT-AATATAGGTAGAATA
1 TATATATATGAA-ATAGGAAAAATA
*
54991234 TATATATATGCAATAGGAAAAATA
1 TATATATATGAAATAGGAAAAATA
54991258 TATATATA
1 TATATATA
54991266 CATAGTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (24 bp):
TATATATATGAAATAGGAAAAATA
Found at i:54992200 original size:10 final size:9
Alignment explanation
Indices: 54992178--54992362 Score: 75
Period size: 9 Copynumber: 20.6 Consensus size: 9
54992168 TCAAGTTTTT
54992178 ATTTTT-TA
1 ATTTTTATA
*
54992186 TTTTTTATA
1 ATTTTTATA
54992195 ATTTTTATA
1 ATTTTTATA
**
54992204 AGTTAATATCA
1 A-TTTTTAT-A
*
54992215 ATTTTAAT-
1 ATTTTTATA
*
54992223 A-TTTTATT
1 ATTTTTATA
*
54992231 ATTATTATGA
1 ATTTTTAT-A
*
54992241 TTTTTTATA
1 ATTTTTATA
*
54992250 AGTTTTA-A
1 ATTTTTATA
54992258 GATTTTTATA
1 -ATTTTTATA
*
54992268 CA-TATT-TA
1 -ATTTTTATA
*
54992276 ATTCTTCATA
1 ATT-TTTATA
*
54992286 ATTTATTA-G
1 ATTT-TTATA
54992295 ATTTTTATA
1 ATTTTTATA
*
54992304 AGTTTATATA
1 A-TTTTTATA
*
54992314 AATTTTA-A
1 ATTTTTATA
54992322 TATTTTTA-A
1 -ATTTTTATA
* *
54992331 GTTTTAATA
1 ATTTTTATA
54992340 ATTTTTAT-
1 ATTTTTATA
54992348 ATTTTTATGA
1 ATTTTTAT-A
54992358 ATTTT
1 ATTTT
54992363 AAATCATTTT
Statistics
Matches: 129, Mismatches: 30, Indels: 34
0.67 0.16 0.18
Matches are distributed among these distances:
7 6 0.05
8 28 0.22
9 56 0.43
10 37 0.29
11 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:54992340 original size:26 final size:25
Alignment explanation
Indices: 54992297--54992354 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
54992287 TTTATTAGAT
54992297 TTTTATAAGTTTATATAAATTTTAATA
1 TTTT-TAAGTTTATAT-AATTTTAATA
*
54992324 TTTTTAAGTTT-TAATAATTTTTATA
1 TTTTTAAGTTTAT-ATAATTTTAATA
54992349 TTTTTA
1 TTTTTA
54992355 TGAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 16 0.55
26 9 0.31
27 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTTAAGTTTATATAATTTTAATA
Found at i:54993469 original size:41 final size:39
Alignment explanation
Indices: 54993424--54993551 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 39
54993414 AGCGGCATTT
* * *
54993424 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGTTT-AACAAAAAACGCCGCTAAAAAT-AAGCA
* * ** *
54993465 TTAGCGGCGCTTTTA-TAAAAACGCCGCTAAAGGTAAAGAA
1 TTAGCGGCG-TTTAACAAAAAACGCCGCTAAAAAT-AAGCA
* * *
54993505 TTAGCGGCGCTTAACAGAAAACGCCGCTAAAAATTAGCA
1 TTAGCGGCGTTTAACAAAAAACGCCGCTAAAAATAAGCA
54993544 TTAGCGGC
1 TTAGCGGC
54993552 ATTTTCTGAA
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
39 14 0.20
40 42 0.61
41 10 0.14
42 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (39 bp):
TTAGCGGCGTTTAACAAAAAACGCCGCTAAAAATAAGCA
Found at i:54993677 original size:41 final size:41
Alignment explanation
Indices: 54993617--54993769 Score: 184
Period size: 41 Copynumber: 3.8 Consensus size: 41
54993607 TTTGGGGCCC
*
54993617 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTATCCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTATCCT
* * **
54993658 TTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCTGGCCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTATCCT
** * ** *
54993699 TTAGCGGTATTTTTTAAGAAGCGCCGCTAATGCTAAGAT-TT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCT-CTATCCT
54993740 TTAGCGGCGTTTTTGAA-AAGCGCCGCTAAT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
54993770 ATATTTTTTA
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
40 13 0.14
41 80 0.86
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTATCCT
Found at i:54993754 original size:82 final size:81
Alignment explanation
Indices: 54993612--54993769 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 81
54993602 GAGTTTTTGG
* **
54993612 GGCCCTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTATCCTTTAGCGACGTTTTTGAAGA
1 GGCCCTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTAGATCCTTTAGCGACGTTTTTGAA-A
*
54993677 AGCGCCGGTAATGCTCT
65 AGCGCCGCTAATGCTCT
* * * *
54993694 GGCCTTTAGCGGTATTTTTTAAGAAGCGCCGCTAATGCTAAGAT-TTTTAGCGGCGTTTTTGAAA
1 GGCCCTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCT-AGATCCTTTAGCGACGTTTTTGAAA
54993758 AGCGCCGCTAAT
65 AGCGCCGCTAAT
54993770 ATATTTTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 12 0.18
82 53 0.79
83 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (81 bp):
GGCCCTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTAGATCCTTTAGCGACGTTTTTGAAAA
GCGCCGCTAATGCTCT
Found at i:54994077 original size:15 final size:16
Alignment explanation
Indices: 54994057--54994090 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
54994047 CAAATATGGT
54994057 GTTTATGGATTT-AGG
1 GTTTATGGATTTAAGG
54994072 GTTTATGGATTTAAGG
1 GTTTATGGATTTAAGG
54994088 GTT
1 GTT
54994091 AGAGGTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GTTTATGGATTTAAGG
Found at i:54994543 original size:21 final size:22
Alignment explanation
Indices: 54994517--54994589 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 22
54994507 TATATATGGA
54994517 TTTAGGGATTATG-GTTTAA-GG
1 TTTAGGGATTATGAG-TTAAGGG
*
54994538 TTTAGGGGTTATGAGTTAAGGGG
1 TTTAGGGATTATGAGTTAA-GGG
* * *
54994561 TTTAGGGGTTAAGAGCT-AGGG
1 TTTAGGGATTATGAGTTAAGGG
54994582 ATTTAGGG
1 -TTTAGGG
54994590 TTTCAAGGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
21 19 0.42
22 9 0.20
23 17 0.38
ACGTcount: A:0.23, C:0.01, G:0.40, T:0.36
Consensus pattern (22 bp):
TTTAGGGATTATGAGTTAAGGG
Found at i:54994566 original size:23 final size:22
Alignment explanation
Indices: 54994536--54994589 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
54994526 TATGGTTTAA
* *
54994536 GGTTTAGGGGTTATGAGTTAAGG
1 GGTTTAGGGGTTAAGAGCT-AGG
54994559 GGTTTAGGGGTTAAGAGCTAGG
1 GGTTTAGGGGTTAAGAGCTAGG
*
54994581 GATTTAGGG
1 GGTTTAGGG
54994590 TTTCAAGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.31
Consensus pattern (22 bp):
GGTTTAGGGGTTAAGAGCTAGG
Found at i:54994965 original size:19 final size:18
Alignment explanation
Indices: 54994941--54994979 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
54994931 AATTATAAGA
54994941 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
54994960 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
54994978 AA
1 AA
54994980 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:54994999 original size:83 final size:80
Alignment explanation
Indices: 54994905--54995057 Score: 261
Period size: 83 Copynumber: 1.9 Consensus size: 80
54994895 GGATAGATAG
*
54994905 GTAATTATTTAAATTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
1 GTAATTATTTAAATTGGATAGGACCAAATTATAAGAAAAAATAAAATAC--AAA-AAAAATGAAA
54994970 TAAAAAATAATTCTTTAT
63 TAAAAAATAATTCTTTAT
*
54994988 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAAAAATGAAATAA
1 GTAATTATTTAAATTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAAAAATGAAATAA
54995053 AAAAT
66 AAAAT
54995058 TTTCTAATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
80 17 0.25
81 3 0.04
83 48 0.71
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (80 bp):
GTAATTATTTAAATTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAAAAATGAAATAA
AAAATAATTCTTTAT
Found at i:54995044 original size:16 final size:15
Alignment explanation
Indices: 54995018--54995056 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
54995008 GGACCAAATT
*
54995018 ATAAGAAAAAATAAA
1 ATAAAAAAAAATAAA
*
54995033 ATACAAAAAAAATGAA
1 ATA-AAAAAAAATAAA
54995049 ATAAAAAA
1 ATAAAAAA
54995057 TTTTCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (15 bp):
ATAAAAAAAAATAAA
Found at i:54999137 original size:12 final size:12
Alignment explanation
Indices: 54999122--54999155 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54999112 TAACCTACAT
54999122 AACTTACATAGA
1 AACTTACATAGA
*
54999134 AACTTATATAGA
1 AACTTACATAGA
*
54999146 AACTTGCATA
1 AACTTACATA
54999156 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:54999214 original size:16 final size:16
Alignment explanation
Indices: 54999195--54999306 Score: 74
Period size: 16 Copynumber: 7.2 Consensus size: 16
54999185 ATACATAGCG
54999195 TACATAACTTACATAA
1 TACATAACTTACATAA
**
54999211 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
54999226 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
**
54999240 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
54999255 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
* * *
54999269 TACATAGCCTACGTAA
1 TACATAACTTACATAA
*
54999285 CTTACTTAACTTACATAA
1 --TACATAACTTACATAA
54999303 TACA
1 TACA
54999307 CCACTTACGT
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
13 16 0.24
14 4 0.06
15 4 0.06
16 32 0.47
18 12 0.18
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:54999240 original size:29 final size:29
Alignment explanation
Indices: 54999198--54999272 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
54999188 CATAGCGTAC
*
54999198 ATAACTTACATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
54999227 ATAACTTGCATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
54999256 ATAACTTGCATAATACA
1 ATAACTTGCATAATACA
54999273 TAGCCTACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAACTTGCATAATACACCACTTACATAA
Found at i:54999354 original size:31 final size:31
Alignment explanation
Indices: 54999316--54999406 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
54999306 ACCACTTACG
54999316 TAACTTAAATAACTTAAATTTGTCAATCATA
1 TAACTTAAATAACTTAAATTTGTCAATCATA
** *
54999347 TAACTTAAATAACTT--ACGTGAT-AAT-ACA
1 TAACTTAAATAACTTAAATTTG-TCAATCATA
* *
54999375 TAACTTATATAACTTAAATTTATCAATCATA
1 TAACTTAAATAACTTAAATTTGTCAATCATA
54999406 T
1 T
54999407 CATAACTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
28 16 0.34
29 7 0.15
30 6 0.13
31 18 0.38
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.38
Consensus pattern (31 bp):
TAACTTAAATAACTTAAATTTGTCAATCATA
Found at i:54999564 original size:9 final size:9
Alignment explanation
Indices: 54999552--54999671 Score: 121
Period size: 9 Copynumber: 14.2 Consensus size: 9
54999542 CAAAATAAAA
54999552 AACTTACAT
1 AACTTACAT
54999561 AACTTACAT
1 AACTTACAT
*
54999570 AA--GACAT
1 AACTTACAT
*
54999577 AAATTACAT
1 AACTTACAT
* *
54999586 AACCTACTT
1 AACTTACAT
54999595 AA--TACAT
1 AACTTACAT
54999602 AACTTACAT
1 AACTTACAT
*
54999611 AACTTAGAT
1 AACTTACAT
54999620 AA--TACAT
1 AACTTACAT
54999627 AACTTACAT
1 AACTTACAT
* *
54999636 AATTTACTT
1 AACTTACAT
54999645 AA--TACAT
1 AACTTACAT
54999652 AACTTACAT
1 AACTTACAT
54999661 AACTTACAT
1 AACTTACAT
54999670 AA
1 AA
54999672 ATATCCCTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
7 24 0.26
9 68 0.74
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:54999578 original size:16 final size:17
Alignment explanation
Indices: 54999556--54999671 Score: 100
Period size: 16 Copynumber: 6.9 Consensus size: 17
54999546 ATAAAAAACT
54999556 TACATAACTTACATAA-
1 TACATAACTTACATAAC
* *
54999572 GACATAAATTACATAACC
1 TACATAACTTACATAA-C
*
54999590 TACTTAA--TACATAAC
1 TACATAACTTACATAAC
*
54999605 TTACATAACTTAGATAA-
1 -TACATAACTTACATAAC
*
54999622 TACATAACTTACATAATT
1 TACATAACTTACATAA-C
*
54999640 TACTTAA--TACATAAC
1 TACATAACTTACATAAC
54999655 TTACATAACTTACATAA
1 -TACATAACTTACATAA
54999672 ATATCCCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.01
16 55 0.69
18 24 0.30
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (17 bp):
TACATAACTTACATAAC
Found at i:54999583 original size:25 final size:25
Alignment explanation
Indices: 54999552--54999671 Score: 177
Period size: 25 Copynumber: 4.8 Consensus size: 25
54999542 CAAAATAAAA
*
54999552 AACTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * *
54999577 AAATTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
*
54999602 AACTTACATAACTTAGATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
54999627 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
54999652 AACTTACATAACTTACATAA
1 AACTTACATAACTTACATAA
54999672 ATATCCCTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 82 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:54999587 original size:50 final size:50
Alignment explanation
Indices: 54999525--54999671 Score: 179
Period size: 50 Copynumber: 2.9 Consensus size: 50
54999515 ATCAAATTAA
* ** * *
54999525 ATAAGTTACATAATACACAAAATAAAAAACTTACATAACTTACATAAGAC
1 ATAAATTACATAATACACTTAATACATAACTTACATAACTTACATAAGAC
* * *
54999575 ATAAATTACATAA-CCTACTTAATACATAACTTACATAACTTAGATAATAC
1 ATAAATTACATAATAC-ACTTAATACATAACTTACATAACTTACATAAGAC
* **
54999625 ATAACTTACATAATTTACTTAATACATAACTTACATAACTTACATAA
1 ATAAATTACATAATACACTTAATACATAACTTACATAACTTACATAA
54999672 ATATCCCTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 82 0.99
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (50 bp):
ATAAATTACATAATACACTTAATACATAACTTACATAACTTACATAAGAC
Found at i:55005287 original size:66 final size:65
Alignment explanation
Indices: 55005192--55005363 Score: 193
Period size: 66 Copynumber: 2.6 Consensus size: 65
55005182 GAACAAATTA
* * * * *
55005192 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATTTGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAA-ATATGAAGAACTCCA
55005256 G
65 G
* * *
55005257 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGTTGAGGTTCAACGAAAATATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAATATGAAGAACTCCA
55005322 G
65 G
* * ** *
55005323 CAGCAGCTTAAAGCAGATGCGGCAGTAAGAGAAGCGGAGGT
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGT
55005364 GGCAGCTAGA
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
65 2 0.02
66 84 0.94
67 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.15
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAATATGAAGAACTCCAG
Found at i:55005405 original size:21 final size:21
Alignment explanation
Indices: 55005350--55005445 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
55005340 TGCGGCAGTA
* *
55005350 AGAGAAGCGGAGG-TGGCAGCT
1 AGAGAAGCAGAGGCT-GCAGCG
* *
55005371 AGAGAAGTACAGGCTGCAGCG
1 AGAGAAGCAGAGGCTGCAGCG
**
55005392 AGAGAAGCAGAGGCTAAAGCG
1 AGAGAAGCAGAGGCTGCAGCG
*
55005413 AGGGAAGCAGAGGCTGCAGCG
1 AGAGAAGCAGAGGCTGCAGCG
*
55005434 AGGGAAGCAGAG
1 AGAGAAGCAGAG
55005446 CAGCGTCAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 62 0.98
22 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGAAGCAGAGGCTGCAGCG
Found at i:55005857 original size:44 final size:43
Alignment explanation
Indices: 55005808--55005920 Score: 127
Period size: 44 Copynumber: 2.6 Consensus size: 43
55005798 GTTTTTGGTC
55005808 AAAGCGCCGCTAAAGATAAGGGTCTTCAGCGGCATTTGTGGAAA
1 AAAGCGCCGCTAAAGATAAGGGTCTTCAGCGGCATTTGTGG-AA
* * * * * * **
55005852 AAAGCGCCACTAAAGATCATGGTCTTTAGTGGCATTTTTGGGG
1 AAAGCGCCGCTAAAGATAAGGGTCTTCAGCGGCATTTGTGGAA
* *
55005895 AAAGCGCCGCTAAAGATTAGGTTCTT
1 AAAGCGCCGCTAAAGATAAGGGTCTT
55005921 TAGTGGCGTT
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
43 22 0.39
44 35 0.61
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATAAGGGTCTTCAGCGGCATTTGTGGAA
Found at i:55005921 original size:43 final size:43
Alignment explanation
Indices: 55005788--55006049 Score: 233
Period size: 43 Copynumber: 6.0 Consensus size: 43
55005778 AGGTGTTGGC
** *
55005788 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATCAGGGT
* * * * ** * *
55005831 CTTCAGCGGCATTTGTGGAAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGTGGCGTTTTTGG-GGAAAGCGCCGCTAAAGATCAGGGT
* * *
55005875 CTTTAGTGGCATTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATCAGGGT
* * *
55005918 CTTTAGTGGCGTTTTGTGGTCG-AAGTGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTT-TGG-GGAAAGCGCCGCTAAAGATCAGGGT
* * * *
55005962 CTATT-GCGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATCAGGGT
* * **
55006005 CTTTAGTGGTGTTTATGGTCAAAGCGCCGCTATAA-ATCAGGGT
1 CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTA-AAGATCAGGGT
55006048 CT
1 CT
55006050 ATTCCGGCGT
Statistics
Matches: 173, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.02
43 98 0.57
44 69 0.40
45 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATCAGGGT
Found at i:55005956 original size:87 final size:86
Alignment explanation
Indices: 55005788--55006049 Score: 310
Period size: 87 Copynumber: 3.0 Consensus size: 86
55005778 AGGTGTTGGC
** * * * * * **
55005788 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTCAGCGGCATTTGTGGAAAA
1 CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGG-TCA
* * *
55005853 AAGCGCCACTAAAGATCATGGT
65 AAGCGCCGCTATAGATCAGGGT
* *
55005875 CTTTAGTGGCATTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCG
1 CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCA
*
55005940 AAGTGCCGCTATAGATCAGGGT
65 AAGCGCCGCTATAGATCAGGGT
* * * *
55005962 CTATT-GCGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGTGTTTATGGTCA
1 CT-TTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCA
*
55006026 AAGCGCCGCTATAAATCAGGGT
65 AAGCGCCGCTATAGATCAGGGT
55006048 CT
1 CT
55006050 ATTCCGGCGT
Statistics
Matches: 150, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
86 30 0.20
87 111 0.74
88 9 0.06
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (86 bp):
CTTTAGTGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAA
AGCGCCGCTATAGATCAGGGT
Found at i:55006076 original size:86 final size:87
Alignment explanation
Indices: 55005899--55006083 Score: 264
Period size: 86 Copynumber: 2.1 Consensus size: 87
55005889 TTGGGGAAAG
* * * *
55005899 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAGTGCCGCTATAGATCAGGGTCT
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTATGGTCAAAGCGCCGCTATAAATCAGGGTCT
* * *** *
55005964 ATTGCGGCGTTTTAGGGGAAAG
66 ATTCCGGCGTTTGAGAAAAAAA
*
55005986 CGCCGCTAAAGATTAGGTTCTTTAGTGGTG-TTTATGGTCAAAGCGCCGCTATAAATCAGGGTCT
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTATGGTCAAAGCGCCGCTATAAATCAGGGTCT
55006050 ATTCCGGCGTTTGAGAAAAAAA
66 ATTCCGGCGTTTGAGAAAAAAA
55006072 CGCCGCTAAAGA
1 CGCCGCTAAAGA
55006084 CCCTGATCTA
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 58 0.67
87 29 0.33
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (87 bp):
CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTATGGTCAAAGCGCCGCTATAAATCAGGGTCT
ATTCCGGCGTTTGAGAAAAAAA
Found at i:55010627 original size:16 final size:17
Alignment explanation
Indices: 55010606--55010637 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55010596 CGTTCTATAC
55010606 TAAAACAAAT-TACCGG
1 TAAAACAAATATACCGG
55010622 TAAAACAAATATACCG
1 TAAAACAAATATACCG
55010638 TTGAAGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (17 bp):
TAAAACAAATATACCGG
Found at i:55010896 original size:21 final size:21
Alignment explanation
Indices: 55010870--55010911 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55010860 ACCGGAGGAA
55010870 AGGAAAGA-AGAGAGGGCGAAG
1 AGGAAAGAGAGA-AGGGCGAAG
*
55010891 AGGAAAGAGAGAATGGCGAAG
1 AGGAAAGAGAGAAGGGCGAAG
55010912 GTGAGGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.48, C:0.05, G:0.45, T:0.02
Consensus pattern (21 bp):
AGGAAAGAGAGAAGGGCGAAG
Found at i:55011818 original size:7 final size:7
Alignment explanation
Indices: 55011806--55011831 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55011796 AAATTTAATT
55011806 TAAATAA
1 TAAATAA
55011813 TAAATAA
1 TAAATAA
55011820 TAAATAA
1 TAAATAA
55011827 TAAAT
1 TAAAT
55011832 TTTAAATTTA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAATAA
Done.