Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 64
Found at i:3508166 original size:2 final size:2
Alignment explanation
Indices: 3508161--3508202 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3508151 ATATGAAGAA
3508161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3508203 GTGGTTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3511207 original size:43 final size:41
Alignment explanation
Indices: 3511078--3511252 Score: 140
Period size: 43 Copynumber: 4.1 Consensus size: 41
3511068 TAAATGTAAT
* *
3511078 TTAGGAGCCTTAATTATAAATGTTAAAAGTGAGATTAAAAAAA
1 TTAGGAG-CTTCATTATAAA-GATAAAAGTGAGATTAAAAAAA
* * * *
3511121 ATA-GAGGCTTTGATTATAAAGATAAAAAGTAAGATTGAAAAAA
1 TTAGGA-GC-TTCATTATAAAGAT-AAAAGTGAGATTAAAAAAA
*
3511164 TTAGGAACTTCACTTATAAAGATAAAAGGTGAGATTAAAAAAA
1 TTAGGAGCTTCA-TTATAAAGATAAAA-GTGAGATTAAAAAAA
* * * * *
3511207 -TATGAGC-TCAATTCTAAAAATAAAATGTGAGATTACATAAA
1 TTAGGAGCTTC-ATTATAAAGATAAAA-GTGAGATTAAAAAAA
3511248 TTAGG
1 TTAGG
3511253 GGCGTCAATT
Statistics
Matches: 106, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
41 27 0.25
42 21 0.20
43 56 0.53
44 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (41 bp):
TTAGGAGCTTCATTATAAAGATAAAAGTGAGATTAAAAAAA
Found at i:3514116 original size:13 final size:13
Alignment explanation
Indices: 3514094--3514123 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3514084 ACCTTAAATC
3514094 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
*
3514107 AAAAAGAGAAAAG
1 AAAAAAAGAAAAG
3514120 AAAA
1 AAAA
3514124 GAAAATAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:3521919 original size:21 final size:21
Alignment explanation
Indices: 3521895--3521950 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3521885 ATCAAGAGAA
*
3521895 GAGAAACTTGATAGAGTCGAG
1 GAGAAACTTGAGAGAGTCGAG
*
3521916 GAGAAACTTGAGAGAGTCGAA
1 GAGAAACTTGAGAGAGTCGAG
* *
3521937 GATACACTTGAGAG
1 GAGAAACTTGAGAG
3521951 GCATAAGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.18
Consensus pattern (21 bp):
GAGAAACTTGAGAGAGTCGAG
Found at i:3522017 original size:31 final size:33
Alignment explanation
Indices: 3521982--3522044 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
3521972 AAAAAGAGAT
*
3521982 GTGGTGAAAGAAGTAGA-GT-TTGAGGGGTGAA
1 GTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGAA
*
3522013 GTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 GTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3522045 TCTTAAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 16 0.57
32 2 0.07
33 10 0.36
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (33 bp):
GTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGAA
Found at i:3525886 original size:6 final size:6
Alignment explanation
Indices: 3525863--3525906 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
3525853 TAAATATGAC
* * * *
3525863 GACGAC GACGAC GACGAT GACGAT GATGAT GATGAT GACGAT GA
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GA
3525907 TGATCCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (6 bp):
GACGAT
Found at i:3525890 original size:9 final size:9
Alignment explanation
Indices: 3525858--3525909 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
3525848 GACAATAAAT
*
3525858 ATGACGACG
1 ATGATGACG
* *
3525867 ACGACGACG
1 ATGATGACG
*
3525876 ACGATGACG
1 ATGATGACG
*
3525885 ATGATGATG
1 ATGATGACG
3525894 ATGATGACG
1 ATGATGACG
3525903 ATGATGA
1 ATGATGA
3525910 TCCAAACAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.33, T:0.17
Consensus pattern (9 bp):
ATGATGACG
Found at i:3527640 original size:252 final size:250
Alignment explanation
Indices: 3527180--3527653 Score: 648
Period size: 252 Copynumber: 1.9 Consensus size: 250
3527170 TAAAGTTTGC
* * *
3527180 CATAAAGTGTCGATCCATATATAAAAAGTAACGACCCAAAAAATATCAAAACTCATAATTATAAT
1 CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAAACATCAAAACCCATAATTATAAT
* *
3527245 GTAATGGGTAACTTTTCAATATAACTGGTATAAATATACCGGTTTTATGAAAAATATGTCTACAA
66 GTAATAGGTAACTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAAAAATATGTCTACAA
* * * * *
3527310 CATTTATCGACACTTATTAGTATTGTGTTGATACTTTTTGTCCAGAATGGATGCCAAAAAGAGTG
131 CATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGAGTG
3527375 AACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTGCACG
196 AACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTGCACG
* * ** *
3527430 CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCC-AAAAACATCGAAACCCATAATTATAA
1 CATAAAGTGTCGATACATATATAAAAAGTAACGA-CCCAAAAAACATCAAAACCCATAATTATAA
* * * * *
3527494 TGTAATAGGTAATTTTTTTAATATAACCGGTATACATATATCGGTTTTATGAGAGAATATGTCTA
65 TGTAATAGGTAA-CTTTTCAATATAACCGGTATAAATATACCGGTTTTATGA-AAAATATGTCTA
* * * *
3527559 TAATATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCATAATGGATGCTAAAAATG
128 CAACATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCAGAATGGATGCCAAAAA-G
* *
3527624 -GTGAACGC-ATAAAGTGTTGATACATTTTCA
192 AGTGAAC-CTACAAAGTGTCGATACATTTTCA
3527654 AAAAGTTTCA
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
250 63 0.33
251 37 0.19
252 91 0.47
253 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (250 bp):
CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAAACATCAAAACCCATAATTATAAT
GTAATAGGTAACTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAAAAATATGTCTACAA
CATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGAGTG
AACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGTTGCACG
Found at i:3530708 original size:200 final size:196
Alignment explanation
Indices: 3530308--3531033 Score: 705
Period size: 200 Copynumber: 3.6 Consensus size: 196
3530298 ACCTAAATAT
* * *
3530308 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * * * * * *
3530371 TAGGTAAATTAACAATGTAACCGGTATAAAAATATCGG-TTAATTAGAAAACATGTCAACATAAT
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAAA
* * ** * *
3530435 GTATCGACAATTGTGTAATTTGTGTTGATACTTATTGTCCAGGATGAATGCACAAACGAGGTGC-
128 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCATAATGAATCCA-AAAAG-GGTGCA
3530499 ACGCATAAA
189 AC-CATAAA
* * *
3530508 GTGTCGATACATTTATTAAAAGTATCGATCCCGAAAACATCGAAACTGATAATTATAATGTATTA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
3530573 GGTAAATTTACAATATAATCGATATAAATATACCGGTTTTATGATAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-CATAAAGT
* *
3530638 ATCGACACTTGATAAATTTGTGTCAATACTTTTGGTCCATAATGAATACCAAAAAGGGTGCAACC
130 ATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCATAATGAAT-CCAAAAAGGGTGCAACC
3530703 ATAAA
192 ATAAA
* * * * *
3530708 GTGTCGATACATTTATAAAAAGTATCGATCTCGAAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
3530773 GGTAAATTTTCAATGTAACTGGTATAAATTTACCGGTTTTATGAGAGAATAGGTCTAAATAATA-
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAA-AG
* * *
3530837 TATCGACACGTTGTTAGTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCCCAACAA-G
129 TATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCC---AT---A-ATGAAT--CCAAAAAGG
*
3530901 GTGCAAGCATAAA
184 GTGCAACCATAAA
* ** * * *
3530914 GTGTCGATACATTTA--AAATTGTATCGATCTAAAAAACATTGTAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* * **
3530977 AGGTAAATTTGCAATGTTACCGGTATAAATATACCGG-TTTACTTCGAAAATAGGTCA
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTA-TGAGAAAATAGGTCA
3531034 ATATAAGCGC
Statistics
Matches: 442, Mismatches: 63, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
199 3 0.01
200 234 0.53
201 71 0.16
202 5 0.01
204 8 0.02
205 81 0.18
206 34 0.08
207 6 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCACATAAAGTA
TCGACACTTGTTAATTTGTGTCGATACTTTTGTCCATAATGAATCCAAAAAGGGTGCAACCATAA
A
Found at i:3531135 original size:87 final size:87
Alignment explanation
Indices: 3531034--3531196 Score: 317
Period size: 87 Copynumber: 1.9 Consensus size: 87
3531024 AAATAGGTCA
3531034 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
3531099 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
*
3531121 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
3531186 CCGGTTAAATG
66 CCGGTTAAATG
3531197 ATATAACATT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:3531168 original size:23 final size:23
Alignment explanation
Indices: 3531118--3531162 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3531108 TGCCTATTTT
*
3531118 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
3531141 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
3531163 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:3533610 original size:41 final size:43
Alignment explanation
Indices: 3533565--3533659 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
3533555 TAATCACACA
* *
3533565 TTTTATTTTTACAA-TCG-AGTTCATA-TTTTTTTAATC-TCATT
1 TTTTATCTTTACAAGT-GAAGTCCATAGTTTTTTTAATCAT-ATT
* *
3533606 TTTTATCTTTATAAGTGAAGTCCTTAGTTTTTTTAATCATATT
1 TTTTATCTTTACAAGTGAAGTCCATAGTTTTTTTAATCATATT
3533649 TTTTATCTTTA
1 TTTTATCTTTA
3533660 TAATTGAGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 13 0.28
42 7 0.15
43 25 0.54
44 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (43 bp):
TTTTATCTTTACAAGTGAAGTCCATAGTTTTTTTAATCATATT
Found at i:3533682 original size:44 final size:43
Alignment explanation
Indices: 3533589--3533704 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
3533579 TCGAGTTCAT
3533589 ATTTTTTTAATCTCATTTTTTATCTTTATAAGTGAAGTCCTTA
1 ATTTTTTTAATCTCATTTTTTATCTTTATAAGTGAAGTCCTTA
* * *
3533632 GTTTTTTTAATCAT-ATTTTTTATCTTTATAATTGAGGCTCC-TA
1 ATTTTTTTAATC-TCATTTTTTATCTTTATAAGTGAAG-TCCTTA
* * *
3533675 ATATTTTTAATTTCACTTTTTA-CATTTATA
1 ATTTTTTTAATCTCATTTTTTATC-TTTATA
3533705 TTTGAGACTC
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.03
43 56 0.90
44 4 0.06
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (43 bp):
ATTTTTTTAATCTCATTTTTTATCTTTATAAGTGAAGTCCTTA
Found at i:3534939 original size:210 final size:211
Alignment explanation
Indices: 3534287--3534995 Score: 1052
Period size: 210 Copynumber: 3.3 Consensus size: 211
3534277 ATTTAAGAAT
* * *
3534287 TAAATTGAACAAATATGAGATTGCAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-A-ACACA-T-AAGAG
*
3534352 GGATCAAATCG-AATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTGCTAAATTATAC
62 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * * *
3534416 CCATTTAAAAAGTTATGGGCCAATTAAAAAAATAGAATTAAGTAAAAAGTATGGATCAATCTCAT
127 CCATTTAAAAAGTTATGGGCCAATT--AAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
3534481 ATGCAAATAAAATTTGGAGGAC
190 ATGCAAATAAAATTTGGAGGAC
*
3534503 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACAACACACATTAATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-A-ACACA-TAA-GAG
*
3534568 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAATACTAAATTATAC
62 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
3534633 CCATTTAAAAAGTTAT-GGCCAATTTAAAAATAGAAATAAGTAATAAGTATGTGTCAATTTCAGA
127 CCATTTAAAAAGTTATGGGCCAA-TTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
3534697 TGCAAATAAAATTTGGAGGAC
191 TGCAAATAAAATTTGGAGGAC
* * *
3534718 TAAATTGAACAAATATAAAATTACAAATACAAATTTAAATAAACTAAACAACACA-AA-AGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATAAGAGGGAT
* * * * * *
3534781 CAAATTGAAATAATTTTAAATTTTGAGGTAGAAATTAATACAAAAATGTACTAAATTATACTCAT
66 CAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
*
3534846 TTAAAAAGTTATGGGCCAATTAATAAATAGAAATAAGTAATAAGTATGGGTTAATTTCAGATGCA
131 TTAAAAAGTTATGGGCCAATTAA-AAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCA
*
3534911 AATAAAATGTGGAGGAC
195 AATAAAATTTGGAGGAC
*
3534928 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA-AA-AGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATAAGAGGGAT
3534991 CAAAT
66 CAAAT
3534996 ATGAAAAATA
Statistics
Matches: 458, Mismatches: 30, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
209 80 0.17
210 125 0.27
211 2 0.00
213 5 0.01
214 1 0.00
215 100 0.22
216 76 0.17
217 69 0.15
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATAAGAGGGAT
CAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
TTAAAAAGTTATGGGCCAATTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
ATAAAATTTGGAGGAC
Found at i:3535120 original size:20 final size:20
Alignment explanation
Indices: 3535077--3535362 Score: 120
Period size: 20 Copynumber: 14.4 Consensus size: 20
3535067 ATATATAATA
3535077 TATATATAAAACTATATAGTT
1 TATATAT-AAACTATATAGTT
*
3535098 TATATATAAAGTATAT-GTAT
1 TATATATAAACTATATAGT-T
3535118 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
3535138 TATATAT--A-T-TAT-GTA
1 TATATATAAACTATATAGTT
* * * *
3535153 TAAACTATATA-TACCAT-GTA
1 TATA-TATAAACTA-TATAGTT
*
3535173 TAAACTATAATACTATATAGTT
1 TATA-TATAA-ACTATATAGTT
**
3535195 TATATA-AGAACTAT-T-GAAC
1 TATATATA-AACTATATAG-TT
* * *
3535214 TATATAGAACCTACATAGTT
1 TATATATAAACTATATAGTT
* *
3535234 TATATATAAATTATATATGAAT
1 TATATATAAACTATATA-G-TT
* *
3535256 TATATATAAACTATACAATT
1 TATATATAAACTATATAGTT
* * *
3535276 TATATTTATA-TAT-TA-TA
1 TATATATAAACTATATAGTT
*
3535293 TATAATTATAAA-TA-ATA-TA
1 TAT-A-TATAAACTATATAGTT
* *
3535312 TATTGTATAAATTATATAGTT
1 TA-TATATAAACTATATAGTT
3535333 TATTAATATAAACTATATAGTT
1 TA-T-ATATAAACTATATAGTT
3535355 TATATATA
1 TATATATA
3535363 TAGTATATAT
Statistics
Matches: 206, Mismatches: 34, Indels: 51
0.71 0.12 0.18
Matches are distributed among these distances:
15 5 0.02
16 6 0.03
17 5 0.02
18 12 0.06
19 30 0.15
20 85 0.41
21 23 0.11
22 40 0.19
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:3535132 original size:29 final size:29
Alignment explanation
Indices: 3535100--3535163 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
3535090 ATATAGTTTA
*
3535100 TATATAAAGTATATGTATTATATATAAAC
1 TATATAAAGTATATATATTATATATAAAC
*** *
3535129 TATATAGTTTATATATATTATGTATAAAC
1 TATATAAAGTATATATATTATATATAAAC
3535158 TATATA
1 TATATA
3535164 TACCATGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (29 bp):
TATATAAAGTATATATATTATATATAAAC
Found at i:3535296 original size:17 final size:17
Alignment explanation
Indices: 3535276--3535329 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
3535266 CTATACAATT
*
3535276 TATATTTATATATTATA
1 TATATTTATAAATTATA
* *
3535293 TATAATTATAAATAATA
1 TATATTTATAAATTATA
3535310 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
3535328 TA
1 TA
3535330 GTTTATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:3535310 original size:22 final size:21
Alignment explanation
Indices: 3535233--3535314 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
3535223 CCTACATAGT
3535233 TTATATATAAATTATATATGAA
1 TTATATATAAATTATATAT-AA
* * *
3535255 TTATATATAAACTATACA-AT
1 TTATATATAAATTATATATAA
*
3535275 TTATATTTATATATTATATATAA
1 TTATA--TATAAATTATATATAA
*
3535298 TTATAAAT-AA-TATATAT
1 TTATATATAAATTATATAT
3535315 TGTATAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
19 7 0.15
20 7 0.15
21 2 0.04
22 26 0.54
23 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (21 bp):
TTATATATAAATTATATATAA
Found at i:3535404 original size:14 final size:15
Alignment explanation
Indices: 3535383--3535419 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3535373 GGTTTAGGGT
3535383 TTAGGGTTTTAA-TA
1 TTAGGGTTTTAAGTA
*
3535397 TTATGG-TTTAAGTA
1 TTAGGGTTTTAAGTA
3535411 TTAGGGTTT
1 TTAGGGTTT
3535420 AGGGTTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 12 0.63
15 2 0.11
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (15 bp):
TTAGGGTTTTAAGTA
Found at i:3535569 original size:20 final size:20
Alignment explanation
Indices: 3535541--3535779 Score: 151
Period size: 18 Copynumber: 12.7 Consensus size: 20
3535531 ATGAACATAT
*
3535541 ATATAAACTATATAGTTTAC
1 ATATGAACTATATAGTTTAC
*
3535561 ATATGAACTATATA-TATAC
1 ATATGAACTATATAGTTTAC
* *
3535580 -TA--AAGT-TGATA-TTTAT
1 ATATGAACTAT-ATAGTTTAC
3535596 ATATGAACTATAT--TTTAC
1 ATATGAACTATATAGTTTAC
* *
3535614 ATATAAACTATATAGTTTAT
1 ATATGAACTATATAGTTTAC
3535634 ATACT-AAC--TATAGTTTAC
1 ATA-TGAACTATATAGTTTAC
3535652 ATATGAACTAT-T-GTTTAC
1 ATATGAACTATATAGTTTAC
* *
3535670 ATATGAACTATATA-TATAT
1 ATATGAACTATATAGTTTAC
3535689 ATAT--ACTATATAGTTTAC
1 ATATGAACTATATAGTTTAC
* * *
3535707 ATATGACCTATATA-TATAT
1 ATATGAACTATATAGTTTAC
*
3535726 ATAT--A-TACTATAGTTGATAT
1 ATATGAACTA-TATAGTT--TAC
*
3535746 TTAT-ATACTATATAGTTTAC
1 ATATGA-ACTATATAGTTTAC
*
3535766 ATATGACCTATATA
1 ATATGAACTATATA
3535780 TATATACTAT
Statistics
Matches: 172, Mismatches: 23, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
15 1 0.01
16 11 0.06
17 15 0.09
18 58 0.34
19 25 0.15
20 50 0.29
21 2 0.01
22 8 0.05
23 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (20 bp):
ATATGAACTATATAGTTTAC
Found at i:3535612 original size:18 final size:18
Alignment explanation
Indices: 3535501--3535729 Score: 99
Period size: 18 Copynumber: 12.8 Consensus size: 18
3535491 AGTTTATATT
*
3535501 TATATATTATATATGAAC
1 TATATTTTATATATGAAC
* **
3535519 TATAATTTGCATATGAAC
1 TATATTTTATATATGAAC
3535537 -ATA---TATATA--AAC
1 TATATTTTATATATGAAC
*
3535549 TATATAGTTTACATATGAAC
1 TATAT--TTTATATATGAAC
* *
3535569 TATA---TATATACTAAAG
1 TATATTTTATATA-TGAAC
3535585 T-TGATATTTATATATGAAC
1 TAT-AT-TTTATATATGAAC
* *
3535604 TATATTTTACATATAAAC
1 TATATTTTATATATGAAC
3535622 TATATAGTTTATATACT-AAC
1 TATAT--TTTATATA-TGAAC
* *
3535642 TATAGTTTACATATGAAC
1 TATATTTTATATATGAAC
*
3535660 TAT-TGTTTACATATGAAC
1 TATAT-TTTATATATGAAC
*
3535678 TATA-TATATATAT-ATAC
1 TATATTTTATATATGA-AC
* *
3535695 TATATAGTTTACATATGACC
1 TATAT--TTTATATATGAAC
*
3535715 TATATATATATATAT
1 TATAT-TTTATATAT
3535730 ATACTATAGT
Statistics
Matches: 159, Mismatches: 26, Indels: 51
0.67 0.11 0.22
Matches are distributed among these distances:
12 3 0.02
13 3 0.02
14 4 0.03
15 6 0.04
16 6 0.04
17 17 0.11
18 64 0.40
19 13 0.08
20 41 0.26
21 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (18 bp):
TATATTTTATATATGAAC
Found at i:3535624 original size:73 final size:73
Alignment explanation
Indices: 3535501--3535724 Score: 202
Period size: 73 Copynumber: 3.1 Consensus size: 73
3535491 AGTTTATATT
* * *
3535501 TATATAT-TATATATGAACTATAATTTGCATATGAAC---ATAT--ATATAAACTATATAGTTTA
1 TATATATATACATA-GAACTATTATTTACATATGAACTATATATACATATAAACTATATAGTTTA
3535560 CATATGAAC
65 CATATGAAC
* * *
3535569 TATATATATAC-TA-AAGT-TGATATTTATATATGAACTATATTTTACATATAAACTATATAGTT
1 TATATATATACATAGAACTAT--TATTTACATATGAACTATA-TATACATATAAACTATATAGTT
*
3535631 TATATACT-AAC
63 TACATA-TGAAC
* * *
3535642 TATAGT-T-TACATATGAACTATTGTTTACATATGAACTATATATATATATATACTATATAGTTT
1 TATA-TATATACATA-GAACTATTATTTACATATGAACTATATATACATATAAACTATATAGTTT
*
3535705 ACATATGACC
64 ACATATGAAC
3535715 TATATATATA
1 TATATATATA
3535725 TATATATACT
Statistics
Matches: 123, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
65 1 0.01
66 3 0.02
67 12 0.10
68 9 0.07
69 2 0.02
70 1 0.01
71 2 0.02
72 5 0.04
73 63 0.51
74 21 0.17
75 3 0.02
76 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (73 bp):
TATATATATACATAGAACTATTATTTACATATGAACTATATATACATATAAACTATATAGTTTAC
ATATGAAC
Found at i:3535685 original size:2 final size:2
Alignment explanation
Indices: 3535678--3535974 Score: 94
Period size: 2 Copynumber: 144.0 Consensus size: 2
3535668 ACATATGAAC
* * **
3535678 TA TA TA TA TA TA TA TA CTA TA TA GTT TA CA TA TGA CC TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA TA
* *
3535721 TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA GTT TA
1 TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA -TA TA
* ** * *
3535765 CA TA TGA CC TA TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA
1 TA TA T-A TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA
* * * * *
3535809 TA TA TA T- TA TA TA TA AA CTA TA TA TA CTA CA TA GA AA CTA CA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA
* * *
3535851 TA GTT TA TA TA TA AA T- TA TA TA TGA -A T- TA TA TA TA AA CTA
1 TA -TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA
* * * * *
3535891 TA CGA TT TA TA TT TA TA TA T- TA TG TA TA -A T- TA TA AA TA -A
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3535930 TA TA TA T- TG TA TA AA T- TA TA TA GTT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
3535971 TA TA
1 TA TA
3535975 GTAATATGGT
Statistics
Matches: 212, Mismatches: 52, Indels: 62
0.65 0.16 0.19
Matches are distributed among these distances:
1 11 0.05
2 175 0.83
3 26 0.12
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3535738 original size:37 final size:38
Alignment explanation
Indices: 3535537--3535740 Score: 166
Period size: 37 Copynumber: 5.6 Consensus size: 38
3535527 GCATATGAAC
*
3535537 ATATATATAAACTA-TATAGTTTACATATGAACTATAT
1 ATATATATATACTACTATAGTTTACATATGAACTATAT
* *
3535574 ATATACTA-A-AGT--TGATA-TTTATATATGAACTATATT
1 ATATA-TATATACTACT-ATAGTTTACATATGAACTATA-T
* * * *
3535610 TTACATATAAACTA-TATAGTTTATATACT-AACTATAGT
1 ATATATATATACTACTATAGTTTACATA-TGAACTATA-T
* *
3535648 -T-TACATATGA--ACTATTGTTTACATATGAACTATAT
1 ATATATATAT-ACTACTATAGTTTACATATGAACTATAT
*
3535683 ATATATATATACTA-TATAGTTTACATATGACCTATAT
1 ATATATATATACTACTATAGTTTACATATGAACTATAT
3535720 ATATATATATA-TACTATAGTT
1 ATATATATATACTACTATAGTT
3535741 GATATTTATA
Statistics
Matches: 137, Mismatches: 14, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
35 22 0.16
36 36 0.26
37 58 0.42
38 20 0.15
39 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATATATATACTACTATAGTTTACATATGAACTATAT
Found at i:3535758 original size:37 final size:39
Alignment explanation
Indices: 3535676--3535759 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
3535666 TTACATATGA
* *
3535676 ACTATATATATATATATACTATATAGTTTACATATGACCT
1 ACTATATATATATATATAC-ATATAGTTGACATATGACAT
* * *
3535716 A-TATATATATATATATAC-TATAGTTGATAT-TTATAT
1 ACTATATATATATATATACATATAGTTGACATATGACAT
3535752 ACTATATA
1 ACTATATA
3535760 GTTTACATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
36 4 0.11
37 16 0.42
39 17 0.45
40 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (39 bp):
ACTATATATATATATATACATATAGTTGACATATGACAT
Found at i:3535759 original size:39 final size:39
Alignment explanation
Indices: 3535537--3535737 Score: 151
Period size: 35 Copynumber: 5.4 Consensus size: 39
3535527 GCATATGAAC
* *
3535537 ATATATATAAACTATATAGTTTACATATGAACTATATAT
1 ATATATATATACTATATAGTTTACATATGACCTATATAT
* * * *
3535576 ATA-CTA-A-AGT-TGATA-TTTATATATGAACTATAT-T
1 ATATATATATACTAT-ATAGTTTACATATGACCTATATAT
* * * * *
3535610 TTACATATAAACTATATAGTTTATATACT-AACTATAGT-T
1 ATATATATATACTATATAGTTTACATA-TGACCTATA-TAT
* *
3535649 -TACATATGA-ACTAT-T-GTTTACATATGAAC--TATAT
1 ATATATAT-ATACTATATAGTTTACATATGACCTATATAT
3535683 ATATATATATACTATATAGTTTACATATGACCTATATAT
1 ATATATATATACTATATAGTTTACATATGACCTATATAT
3535722 ATATATATATACTATA
1 ATATATATATACTATA
3535738 GTTGATATTT
Statistics
Matches: 136, Mismatches: 9, Indels: 34
0.76 0.05 0.19
Matches are distributed among these distances:
33 1 0.01
34 7 0.05
35 32 0.24
36 18 0.13
37 20 0.15
38 30 0.22
39 28 0.21
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (39 bp):
ATATATATATACTATATAGTTTACATATGACCTATATAT
Found at i:3535781 original size:53 final size:53
Alignment explanation
Indices: 3535683--3535834 Score: 189
Period size: 53 Copynumber: 2.8 Consensus size: 53
3535673 TGAACTATAT
*
3535683 ATATATATATACTATATAGTTTACATATGACCTATATATATATATATATACTATAGTTG
1 ATATTTATATACTATATAGTTTACATATGACC------TATATATATATACTATAGTTG
*
3535742 ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTTT
1 ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTTG
* * *
3535795 ATATTTATATACTATATA-TATTATATATAAACTATATATA
1 ATATTTATATACTATATAGT-TTACATATGACCTATATATA
3535835 CTACATAGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
52 1 0.01
53 55 0.63
59 31 0.36
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (53 bp):
ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTTG
Found at i:3535869 original size:11 final size:11
Alignment explanation
Indices: 3535855--3535892 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3535845 ACTACATAGT
3535855 TTATATATAAA
1 TTATATATAAA
*
3535866 TTATATATGAA
1 TTATATATAAA
3535877 TTATATATAAA
1 TTATATATAAA
*
3535888 CTATA
1 TTATA
3535893 CGATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:3536002 original size:6 final size:6
Alignment explanation
Indices: 3535994--3536124 Score: 142
Period size: 6 Copynumber: 21.8 Consensus size: 6
3535984 TTTAGGGTTT
* * * *
3535994 ATATTT ATATTA ATATTG ATATTG ATATCG ATA-TG AATATTG ATATTT
1 ATATTG ATATTG ATATTG ATATTG ATATTG ATATTG -ATATTG ATATTG
* * *
3536042 ATATTG ATATTG ATATCG ATATCG ATATTG ATATTG ATATTG TTATTG
1 ATATTG ATATTG ATATTG ATATTG ATATTG ATATTG ATATTG ATATTG
*
3536090 ATATTG ATATTTG -TATTTG -TATTT ATATTG ATATT
1 ATATTG ATA-TTG ATA-TTG ATATTG ATATTG ATATT
3536125 TGTATTTGTA
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
5 3 0.03
6 101 0.93
7 5 0.05
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (6 bp):
ATATTG
Found at i:3536130 original size:6 final size:6
Alignment explanation
Indices: 3536097--3536141 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
3536087 TTGATATTGA
*
3536097 TATTTG TATTTG TATTTA TA-TTG ATATTTG TATTTG TATTTG TAT
1 TATTTG TATTTG TATTTG TATTTG -TATTTG TATTTG TATTTG TAT
3536142 CCGTATCCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 2 0.06
6 30 0.86
7 3 0.09
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.64
Consensus pattern (6 bp):
TATTTG
Found at i:3536131 original size:24 final size:24
Alignment explanation
Indices: 3536066--3536137 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
3536056 ATCGATATCG
*
3536066 ATATTGATA-TTG-ATATTGTTATTG
1 ATATTGATATTTGTAT-TTG-TATTT
3536090 ATATTGATATTTGTATTTGTATTT
1 ATATTGATATTTGTATTTGTATTT
3536114 ATATTGATATTTGTATTTGTATTT
1 ATATTGATATTTGTATTTGTATTT
3536138 GTATCCGTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 37 0.82
25 6 0.13
26 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (24 bp):
ATATTGATATTTGTATTTGTATTT
Found at i:3536147 original size:6 final size:6
Alignment explanation
Indices: 3536138--3536236 Score: 164
Period size: 6 Copynumber: 16.7 Consensus size: 6
3536128 ATTTGTATTT
3536138 GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC
1 GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC
* * *
3536186 GTATCC -TATCC GTATCC GTATCC ATATCC GTATTC GTATCC GTATTC
1 GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC GTATCC
3536233 GTAT
1 GTAT
3536237 ATAGTTTATA
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
5 5 0.06
6 82 0.94
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.36
Consensus pattern (6 bp):
GTATCC
Found at i:3536344 original size:28 final size:27
Alignment explanation
Indices: 3536313--3536389 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
3536303 AAACTATATT
3536313 ATATTAATATAAGTTAATATTAATTATA
1 ATATTAAT-TAAGTTAATATTAATTATA
**
3536341 ATATATAATTATTTTAATATTAATTATA
1 ATAT-TAATTAAGTTAATATTAATTATA
* *
3536369 A-ATT-ATTTA-TTAATATAAATT
1 ATATTAATTAAGTTAATATTAATT
3536390 TTATAAGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 11 0.26
25 3 0.07
26 1 0.02
27 2 0.05
28 22 0.51
29 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
ATATTAATTAAGTTAATATTAATTATA
Found at i:3545451 original size:17 final size:16
Alignment explanation
Indices: 3545429--3545477 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3545419 TAACTGCAAA
3545429 AAAATAATTAATTAAAT
1 AAAATAATTAA-TAAAT
* *
3545446 AAAATATTTAAAAAAT
1 AAAATAATTAATAAAT
*
3545462 TAAATAATTAAATAAA
1 AAAATAATT-AATAAA
3545478 ATACTAACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATTAATAAAT
Found at i:3545466 original size:16 final size:16
Alignment explanation
Indices: 3545429--3545473 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3545419 TAACTGCAAA
*
3545429 AAAATAATTAATTAAAT
1 AAAATAATTAA-AAAAT
*
3545446 AAAATATTTAAAAAAT
1 AAAATAATTAAAAAAT
*
3545462 TAAATAATTAAA
1 AAAATAATTAAA
3545474 TAAAATACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATTAAAAAAT
Found at i:3545496 original size:29 final size:29
Alignment explanation
Indices: 3545426--3545497 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
3545416 TTATAACTGC
*
3545426 AAAAAA-ATAATTAATTAAATAAAATATTT
1 AAAAAATATAA-TAATTAAATAAAATATCT
3545455 AAAAAAT-TAAATAATTAAATAAAATA-CT
1 AAAAAATAT-AATAATTAAATAAAATATCT
3545483 AACAAAATATAATAA
1 AA-AAAATATAATAA
3545498 AATATATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
28 3 0.08
29 32 0.84
30 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (29 bp):
AAAAAATATAATAATTAAATAAAATATCT
Found at i:3545540 original size:20 final size:20
Alignment explanation
Indices: 3545517--3545558 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3545507 TAAAGAGCTA
*
3545517 TGAGAGAACTTAAGAGTATT
1 TGAGAGAACTTAAGAGGATT
* *
3545537 TGAGAGAAGTTGAGAGGATT
1 TGAGAGAACTTAAGAGGATT
3545557 TG
1 TG
3545559 GTGTGATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.33, T:0.29
Consensus pattern (20 bp):
TGAGAGAACTTAAGAGGATT
Found at i:3546545 original size:135 final size:134
Alignment explanation
Indices: 3546291--3546751 Score: 537
Period size: 135 Copynumber: 3.3 Consensus size: 134
3546281 TATAATGTAA
* * * *
3546291 TAGGTAGCACTTATATAATAAAATAAGTTAATTACTTAATTTGTTAGTACAACATATTAGGTAAA
1 TAGGTAGCGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAA
* *
3546356 CGCCTAAAATGTTACCAAGGATAACATAACCGGTTATTTATTGGAAAAATTATCAAGCACAATAA
66 CGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGGAAAAA-TATCAAGCACAATAA
3546421 CATAT
130 CATAT
*
3546426 TAGGCAGCGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAA
1 TAGGTAGCGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAA
3546491 CGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGGAAATAATATCAAGCACAATAA
66 CGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGGAAA-AATATCAAGCACAATAA
*
3546556 AATAT
130 CATAT
*
3546561 TAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAGTAGGTTAATTACTTAATTT
1 TAGGTAGCGCTTATATAA--TAA-A-ATAG-G-TTA-AT--T--A-T---TT--------AATTT
* *
3546626 GTTATTACAACATATTAGGTAAACGCTTAAAATGTTACCAAGAATAACATAACCGGTTAATTACT
43 GTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACT
* * *
3546691 GGAAACATTATCAAACATAATAACATAT
108 GGAAA-AATATCAAGCACAATAACATAT
* *
3546719 TAGGTAGCGCTTATGTAACAAAATAGG-TAATTA
1 TAGGTAGCGCTTATATAATAAAATAGGTTAATTA
3546752 CTTACTTAAT
Statistics
Matches: 282, Mismatches: 20, Indels: 37
0.83 0.06 0.11
Matches are distributed among these distances:
135 141 0.50
136 2 0.01
137 3 0.01
138 1 0.00
139 3 0.01
140 1 0.00
141 3 0.01
142 2 0.01
144 1 0.00
146 2 0.01
147 1 0.00
148 1 0.00
150 4 0.01
151 2 0.01
153 1 0.00
154 3 0.01
155 1 0.00
156 2 0.01
158 108 0.38
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (134 bp):
TAGGTAGCGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAA
CGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGGAAAAATATCAAGCACAATAAC
ATAT
Found at i:3546713 original size:158 final size:158
Alignment explanation
Indices: 3546417--3546747 Score: 536
Period size: 158 Copynumber: 2.1 Consensus size: 158
3546407 ATCAAGCACA
* * *
3546417 ATAACATATTAGGCAGCGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATA
1 ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATA
* *
3546482 TTAGGTAAACGCCTAAAATGTTACCAAGGATAACATAACCGGTTAATTACTGGAAATAATATCAA
66 TTAGGTAAACGCCTAAAATGTTACCAAGAATAACATAACCGGTTAATTACTGGAAACAATATCAA
*
3546547 GCACAATAAAATATTAGGTAGCGCTTAT
131 ACACAATAAAATATTAGGTAGCGCTTAT
* *
3546575 ATAACGTAATAGGTAGCGCTTATATAATAAAGTAGGTTAATTACTTAATTTGTTATTACAACATA
1 ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATA
* *
3546640 TTAGGTAAACGCTTAAAATGTTACCAAGAATAACATAACCGGTTAATTACTGGAAACATTATCAA
66 TTAGGTAAACGCCTAAAATGTTACCAAGAATAACATAACCGGTTAATTACTGGAAACAATATCAA
* *
3546705 ACATAATAACATATTAGGTAGCGCTTAT
131 ACACAATAAAATATTAGGTAGCGCTTAT
* *
3546733 GTAACAAAATAGGTA
1 ATAACATAATAGGTA
3546748 ATTACTTACT
Statistics
Matches: 158, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (158 bp):
ATAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATA
TTAGGTAAACGCCTAAAATGTTACCAAGAATAACATAACCGGTTAATTACTGGAAACAATATCAA
ACACAATAAAATATTAGGTAGCGCTTAT
Found at i:3547006 original size:73 final size:73
Alignment explanation
Indices: 3546815--3547060 Score: 388
Period size: 72 Copynumber: 3.4 Consensus size: 73
3546805 AAAATTTAAA
* * *
3546815 CTACCTATTACATTAAAATACCTACCGGTGTTTTTGAAGGTTGTTAATAATGCAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
*
3546880 AAAT-GCA
66 AAATAGCG
**
3546887 CTACCTATTACATTAAAATACCTACCGG-TTTTTTGAAGGTTGCTAATAATGTAAACAATAAAAA
1 CTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
*
3546951 AAATAGTG
66 AAATAGCG
3546959 CTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
3547024 AAATAGGCG
66 AAATA-GCG
* *
3547033 CTACCTATTACATTAAACTATCTACCGG
1 CTACCTATTACATTAAAATACCTACCGG
3547061 ATATGTTGAA
Statistics
Matches: 159, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
71 35 0.22
72 57 0.36
73 39 0.25
74 28 0.18
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (73 bp):
CTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
AAATAGCG
Found at i:3547221 original size:20 final size:20
Alignment explanation
Indices: 3547196--3547250 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3547186 AAGATAAAAA
3547196 TATGACAAAACCGGTTTCAT
1 TATGACAAAACCGGTTTCAT
3547216 TATGACAAAACCGGTTTCAT
1 TATGACAAAACCGGTTTCAT
*
3547236 TATGACAAAAACGGT
1 TATGACAAAACCGGT
3547251 AAAGAGCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
TATGACAAAACCGGTTTCAT
Found at i:3547359 original size:16 final size:16
Alignment explanation
Indices: 3547338--3547370 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3547328 TAATAAATAA
*
3547338 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
3547354 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
3547370 A
1 A
3547371 AAATGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:3547491 original size:16 final size:16
Alignment explanation
Indices: 3547440--3547508 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
3547430 TAATAAATAA
*
3547440 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
* *
3547456 ACAAACATAAGCGAAC
1 ACGAACATAAACGAAC
* *
3547472 ACGAACATAAATGAAT
1 ACGAACATAAACGAAC
3547488 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
3547504 TCGAA
1 ACGAA
3547509 AACTTTCAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3548154 original size:43 final size:40
Alignment explanation
Indices: 3548105--3548205 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 40
3548095 TTCACAAACG
* *
3548105 TAAATGAACGAACGAGACCTATGTTCATGTTCGTTCATTTAA
1 TAAATGAACG-ACAAAACCT-TGTTCATGTTCGTTCATTTAA
*
3548147 TTAAATGAAC-ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
*
3548187 TAAATAAACGCACATAAAC
1 TAAATGAACG-ACA-AAAC
3548206 AAACTTCCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 8 0.16
40 21 0.42
41 9 0.18
42 3 0.06
43 9 0.18
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:3548465 original size:112 final size:112
Alignment explanation
Indices: 3548263--3548834 Score: 840
Period size: 112 Copynumber: 5.2 Consensus size: 112
3548253 CATTTACAAG
** * *
3548263 CCTAGATATGTTGAAAGTATTAATACTTTATAAAAATGTATCGATACTTCACAATATAACATGTA
1 CCTA-ATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTA
*
3548328 AAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAGAACTA
65 AAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTA
* **
3548376 CCTAATATGTTGAAAGTATCGATACTTTATAAAAATATATAAATACTTTACAATATAACAGGTAA
1 CCTAATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAA
*
3548441 AAATATGACAAAACCAATTTCATTATGACAAAACCGGTAAAGAACTA
66 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTA
* *
3548488 CATGATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAA
1 CCTAATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAA
3548553 AAATATGACAAAACCAGTTTCATTATGACAAAA---G---AG--CTA
66 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTA
*
3548592 CCTGATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAA
1 CCTAATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAA
* * * *
3548657 AAATATGAAAAAACCAGTTTCATTATGATAAAACCGGTAAATAGCTA
66 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTA
* * * *
3548704 CTTGATATGTTGAAAATATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGT
1 CCTAATATGTTGAAAGTATCGATAC--TTTATAAAAATGTATCGATACTTTACAATATAACAGGT
* *
3548769 AAAAATATGAAAAAACCAGTTTCATTATGACAAAACCGAT-AAG-ACTA
64 AAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTA
*
3548816 CTTAATATGTTGAAAGTAT
1 CCTAATATGTTGAAAGTAT
3548835 AAATATATTT
Statistics
Matches: 421, Mismatches: 28, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
104 98 0.23
106 2 0.00
107 1 0.00
109 1 0.00
110 1 0.00
112 236 0.56
113 6 0.01
114 76 0.18
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (112 bp):
CCTAATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAA
AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTA
Found at i:3548694 original size:216 final size:219
Alignment explanation
Indices: 3548267--3548834 Score: 854
Period size: 216 Copynumber: 2.6 Consensus size: 219
3548257 TACAAGCCTA
** * *
3548267 GATATGTTGAAAGTATTAATACTTTATAAAAATGTATCGATACTTCACAATATAACATGTAAAAA
1 GATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAA
*
3548332 TATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTAATATGTTGAAAGTATCG
66 TATGACAAAACCAGTTTCATTATGACAAAA-C-G--AAG-ACTACCTAATATGTTGAAAGTATCG
*
3548397 ATACTTTATAAAAATATATAAATACTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTC
126 ATACTTTATAAAAATATATAAATACTTTACAATATAACAGGTAAAAATATGAAAAAACCAATTTC
3548462 ATTATGACAAAACCGGTAAAGAACTACAT
191 ATTATGACAAAACCGGTAAAGAACTACAT
3548491 GATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAA
1 GATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAA
*
3548556 TATGACAAAACCAGTTTCATTATGACAAAA-G-AG-CTACCTGATATGTTGAAAGTATCGATACT
66 TATGACAAAACCAGTTTCATTATGACAAAACGAAGACTACCTAATATGTTGAAAGTATCGATACT
* ** *
3548618 TTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAAAAAACCAGTTTCATTAT
131 TTATAAAAATATATAAATACTTTACAATATAACAGGTAAAAATATGAAAAAACCAATTTCATTAT
* * * *
3548683 GATAAAACCGGTAAATAGCTACTT
196 GACAAAACCGGTAAAGAACTACAT
* *
3548707 GATATGTTGAAAATATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAA
1 GATATGTTGAAAGTATCGATAC--TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAA
* *
3548772 AATATGAAAAAACCAGTTTCATTATGACAAAACCGATAAGACTACTTAATATGTTGAAAGTAT
64 AATATGACAAAACCAGTTTCATTATGACAAAA-CG--AAGACTACCTAATATGTTGAAAGTAT
3548835 AAATATATTT
Statistics
Matches: 316, Mismatches: 20, Indels: 16
0.90 0.06 0.05
Matches are distributed among these distances:
216 128 0.41
218 74 0.23
220 1 0.00
221 1 0.00
223 2 0.01
224 110 0.35
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (219 bp):
GATATGTTGAAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAA
TATGACAAAACCAGTTTCATTATGACAAAACGAAGACTACCTAATATGTTGAAAGTATCGATACT
TTATAAAAATATATAAATACTTTACAATATAACAGGTAAAAATATGAAAAAACCAATTTCATTAT
GACAAAACCGGTAAAGAACTACAT
Found at i:3553572 original size:25 final size:26
Alignment explanation
Indices: 3553535--3553640 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 26
3553525 ATAAAATATT
*
3553535 ATAAAATATATTAATTAT-TTATTAAC
1 ATAAAA-ATATTAATTATATTATTAAA
*
3553561 ATAAAAACATT-ATTATATTATTAAA
1 ATAAAAATATTAATTATATTATTAAA
3553586 ATAATAAATATT-ATTAATTACTTATTAAA
1 ATAA-AAATATTAATT-A-TA-TTATTAAA
* *
3553615 ATAAGAATATT-ATTATAATATTAAA
1 ATAAAAATATTAATTATATTATTAAA
3553640 A
1 A
3553641 AATATTCAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.07
25 23 0.33
26 17 0.24
27 2 0.03
28 11 0.16
29 12 0.17
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (26 bp):
ATAAAAATATTAATTATATTATTAAA
Found at i:3553603 original size:54 final size:52
Alignment explanation
Indices: 3553538--3553644 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 52
3553528 AAATATTATA
* * *
3553538 AAATATATTAATTATTTATTAACATAAAAACATTATTATATTATTAAAATAAT
1 AAATATATTAATTACTTATTAAAATAAAAACATTATTATAATATTAAAA-AAT
* *
3553591 AAATATTATTAATTACTTATTAAAATAAGAATATTATTATAATATTAAAAAAT
1 AAATA-TATTAATTACTTATTAAAATAAAAACATTATTATAATATTAAAAAAT
3553644 A
1 A
3553645 TTCAAAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 9 0.19
54 39 0.81
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (52 bp):
AAATATATTAATTACTTATTAAAATAAAAACATTATTATAATATTAAAAAAT
Found at i:3559460 original size:12 final size:12
Alignment explanation
Indices: 3559443--3559467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3559433 GGTCCTCATT
3559443 TCTTTTCTGGAA
1 TCTTTTCTGGAA
3559455 TCTTTTCTGGAA
1 TCTTTTCTGGAA
3559467 T
1 T
3559468 ATTTGAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TCTTTTCTGGAA
Found at i:3569009 original size:18 final size:18
Alignment explanation
Indices: 3568978--3569030 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
3568968 ACTGAATATT
*
3568978 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3568996 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
3569014 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3569031 GATAATCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3571037 original size:30 final size:30
Alignment explanation
Indices: 3571001--3571078 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
3570991 TAAACACAAT
* *
3571001 TTTTCAACACCAACACCTACCACCCCATTG
1 TTTTCAACACCAACACCCACCACCACATTG
* *
3571031 TTTTCAACACCAACACCCACCATCACATTT
1 TTTTCAACACCAACACCCACCACCACATTG
3571061 TTTTCAACACCAAC-CCCA
1 TTTTCAACACCAACACCCA
3571079 TCATCCCTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 4 0.09
30 40 0.91
ACGTcount: A:0.32, C:0.42, G:0.01, T:0.24
Consensus pattern (30 bp):
TTTTCAACACCAACACCCACCACCACATTG
Found at i:3577712 original size:55 final size:55
Alignment explanation
Indices: 3577629--3577738 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
3577619 TTCAGGAGAA
*
3577629 GATGAGATTAAAAGACAACAAGACGTCCTCAACAAGAGGGAACAATCATCTTCAG
1 GATGAGATTAAAAGACAACAAGAAGTCCTCAACAAGAGGGAACAATCATCTTCAG
*
3577684 GATGAGATTAAAAGACAACAAGAAGTCCTCGACAAGAGGGAACAATCATCTTCAG
1 GATGAGATTAAAAGACAACAAGAAGTCCTCAACAAGAGGGAACAATCATCTTCAG
3577739 ATTCAACATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (55 bp):
GATGAGATTAAAAGACAACAAGAAGTCCTCAACAAGAGGGAACAATCATCTTCAG
Found at i:3578103 original size:35 final size:38
Alignment explanation
Indices: 3578048--3578133 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
3578038 AACAAAATCG
*
3578048 TTGA-ATATGTTTCCCTTGAAACA-AA-A-TTGTCTCCC
1 TTGAGATA-GTTTCCCATGAAACAGAAGATTTGTCTCCC
*
3578083 TTGAGATAGTTTCCCATGAAACAGAAGATTTTGTCTCGC
1 TTGAGATAGTTTCCCATGAAACAGAAGA-TTTGTCTCCC
*
3578122 TTGAGACAGTTT
1 TTGAGATAGTTT
3578134 TTACTCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
35 18 0.42
36 5 0.12
37 1 0.02
39 19 0.44
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (38 bp):
TTGAGATAGTTTCCCATGAAACAGAAGATTTGTCTCCC
Found at i:3578210 original size:36 final size:38
Alignment explanation
Indices: 3578101--3578219 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 38
3578091 GTTTCCCATG
* *
3578101 AAACAGAAGATTTTGTCTCGCTTGAGACAGTTTTTACTCA
1 AAACA-AAGA-TTTGTCTCGCTTAAGACAGTTTTTACTTA
* * * * **
3578141 AAACAAGAAGATTTATTTCACTCAAGATTGTTTTT-CTTA
1 AAAC-A-AAGATTTGTCTCGCTTAAGACAGTTTTTACTTA
3578180 AAAC-AAGATTTGTCTCGCTTAAGACAGTTTTTACTTA
1 AAACAAAGATTTGTCTCGCTTAAGACAGTTTTTACTTA
3578217 AAA
1 AAA
3578220 GAATACATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
36 22 0.35
37 7 0.11
39 7 0.11
40 21 0.33
41 6 0.10
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (38 bp):
AAACAAAGATTTGTCTCGCTTAAGACAGTTTTTACTTA
Found at i:3578280 original size:71 final size:74
Alignment explanation
Indices: 3578105--3578280 Score: 209
Period size: 76 Copynumber: 2.4 Consensus size: 74
3578095 CCCATGAAAC
*
3578105 AGAAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGAAGATTTATTTCACTCAAGATT
1 AGAAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGAACATTTATTTCACTCAAGA--
3578170 GTTTTTCTTAAA
64 -TTTTTCTTAAA
* * * * * *
3578182 ACAAGA-TTTGTCTCGCTTAAGACAGTTTTTACTTAAAAGAA-TACATTTCTTTTCACTCAAGA-
1 AGAAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGAACATTT-ATTTCACTCAAGAT
3578244 TTTT-TT-AA
65 TTTTCTTAAA
*
3578252 AGAAGATTTTGTCTCGCTTGAGATAGTTT
1 AGAAGATTTTGTCTCGCTTGAGACAGTTT
3578281 CCCTCGAAAC
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
70 7 0.08
71 22 0.25
72 4 0.05
75 5 0.06
76 44 0.51
77 5 0.06
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (74 bp):
AGAAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGAACATTTATTTCACTCAAGATT
TTTCTTAAA
Found at i:3578308 original size:39 final size:39
Alignment explanation
Indices: 3578252--3578850 Score: 636
Period size: 39 Copynumber: 16.0 Consensus size: 39
3578242 GATTTTTTAA
3578252 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
3578291 ATAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
3578330 TGAATATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
3578369 AGAATATTTTGTCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3578408 AGAATATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3578447 ATAAGATTTTGTCTCGCTTAAGATAGTTTCCCTAGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3578486 AGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
3578525 AGAATATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
3578564 AGAAGATTTTGTCT--C-------AGTTTCCCTCAAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
3578594 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * * *
3578633 ATAAAATTTTGTCTCTCTTGAGACAGTTTCTCTCTAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3578672 -G-A-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3578708 -G-AG-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
3578744 -G-AG-TTTTGTCT-GTATTGATATAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCG-CTTGAGATAGTTTCCCTCGAAAC
* * *
3578780 --AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*** * *
3578816 -G-AG-TTTTGTCTATATTGAGACAGTTTCCCTTGAAA
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAA
3578851 TAAGAAATGT
Statistics
Matches: 492, Mismatches: 52, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.05
32 1 0.00
36 155 0.32
37 2 0.00
39 307 0.62
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:3578585 original size:30 final size:30
Alignment explanation
Indices: 3578549--3578608 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3578539 CACTTGAGAT
*
3578549 AGTTTCCCTCGAAACAGAAGATTTTGTCTC
1 AGTTTCCCTCAAAACAGAAGATTTTGTCTC
*
3578579 AGTTTCCCTCAAAATAGAAGATTTTGTCTC
1 AGTTTCCCTCAAAACAGAAGATTTTGTCTC
3578609 GCTTGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (30 bp):
AGTTTCCCTCAAAACAGAAGATTTTGTCTC
Found at i:3578621 original size:69 final size:69
Alignment explanation
Indices: 3578510--3578647 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
3578500 TGCTTGAGAT
* * *
3578510 AGTTTCCCTCGAAATAGAATATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAGATTTTG
1 AGTTTCCCTCAAAATAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAATTTTG
3578575 TCTC
66 TCTC
* *
3578579 AGTTTCCCTCAAAATAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACATAAAATTTTG
1 AGTTTCCCTCAAAATAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAATTTTG
3578644 TCTC
66 TCTC
3578648 TCTTGAGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (69 bp):
AGTTTCCCTCAAAATAGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAATTTTG
TCTC
Found at i:3578661 original size:108 final size:105
Alignment explanation
Indices: 3578471--3578683 Score: 293
Period size: 108 Copynumber: 2.0 Consensus size: 105
3578461 CGCTTAAGAT
* * *
3578471 AGTTTCCCTAGAAACAGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAATAGAATATTTTG
1 AGTTTCCCTAGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTG
*
3578536 TCTCACTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTC
66 TCTCACTTGAGACAGTTTCCCTCGAAAC-G-A-ATTTTGTCTC
* * *
3578579 AGTTTCCCTCA-AAATAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACATAAAATTTT
1 AGTTTCCCT-AGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTT
* * *
3578643 GTCTCTCTTGAGACAGTTTCTCTCTAAACGAATTTTGTCTC
65 GTCTCACTTGAGACAGTTTCCCTCGAAACGAATTTTGTCTC
3578684 TCTTGAGACA
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
105 10 0.11
106 1 0.01
107 1 0.01
108 81 0.86
109 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (105 bp):
AGTTTCCCTAGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTG
TCTCACTTGAGACAGTTTCCCTCGAAACGAATTTTGTCTC
Found at i:3578684 original size:36 final size:36
Alignment explanation
Indices: 3578599--3578850 Score: 317
Period size: 36 Copynumber: 6.9 Consensus size: 36
3578589 AAAATAGAAG
* * * *
3578599 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACATAAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC---GA
*
3578638 ATTTTGTCTCTCTTGAGACAGTTTCTCTCT-AAACGA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCT-TGAAACGA
3578674 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
*
3578710 GTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
* * * * * * *
3578746 GTTTTGTCTGTATTGATATAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
3578782 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
* * *
3578818 GTTTTGTCTATATTGAGACAGTTTCCCTTGAAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
3578851 TAAGAAATGT
Statistics
Matches: 188, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
35 1 0.01
36 158 0.84
39 29 0.15
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGA
Found at i:3579327 original size:44 final size:44
Alignment explanation
Indices: 3579264--3579730 Score: 223
Period size: 44 Copynumber: 10.6 Consensus size: 44
3579254 TTGTTTGCTT
* * *
3579264 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
** * *
3579308 GATTCCATCACAGAAGGAGGTGGATC-G-AT--ATTTGTTTGCTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACAT-TTCGTTC
* * * * **
3579349 AAATCCATCGCAGAAGGAGTTGGATCAGCATCAAC-TTTTTTCTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGT-TC
* * * ** *
3579393 GATTCTATCACAGAAGGAGGTAGATCATCATTGACATATCGTTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
* *
3579437 GATTTCCATCACAGAAGGAGGTGGATC-G-A-CAATTTTATTTTCGCTC
1 GA-TTCCATCACAGAAGGAGGTGGATCAGCATCAA---CA-TTTCGTTC
* * * * * * * * *
3579483 AAATCCATCGCAGAAGGAGTTGGATCAACGTCAACTTTTAGCTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
** * * * *
3579527 GATTATATCACAGAATGAGGTAGATCAGCATCGACATATCGTTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
* **** ***
3579571 GATTTCCATCACAGAAGAAGGTGGATC-GACATTTTTATCTTTACTC
1 GA-TTCCATCACAGAAGGAGGTGGATCAG-CATCAACAT-TTCGTTC
* * * * * * * * * * *
3579617 AAATCTATCGCAGAAGGAGTTGGATCAACGTTAACTTTTTGCTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
* * * * * *
3579661 GATTCTATCACAGAAGGAGGTAGATCAACATCGATATCTCGTTC
1 GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
*
3579705 GATTCCATCACAGAATGAGGTGGATC
1 GATTCCATCACAGAAGGAGGTGGATC
3579731 GACATTTTTA
Statistics
Matches: 304, Mismatches: 100, Indels: 38
0.69 0.23 0.09
Matches are distributed among these distances:
40 2 0.01
41 27 0.09
42 3 0.01
43 7 0.02
44 156 0.51
45 95 0.31
46 11 0.04
48 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
GATTCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGTTC
Found at i:3579518 original size:134 final size:132
Alignment explanation
Indices: 3579257--3579804 Score: 782
Period size: 134 Copynumber: 4.1 Consensus size: 132
3579247 TGTTCAATTG
* * * *
3579257 TTTGCTTGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTCGATTCCATCACAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGATTCCATCACAGA
* * * *
3579322 AGGAGGTGGATCGA-TA-TTT-GTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCATCAAC
66 AGGAGGTGGATCGACAATTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCAAC
3579384 TT
131 TT
* * *
3579386 TTTTCTCGATTCTATCACAGAAGGAGGTAGATCATCATTGACATATCGTTCGATTTCCATCACAG
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGA-TTCCATCACAG
3579451 AAGGAGGTGGATCGACAATTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCA
65 AAGGAGGTGGATCGACAATTTTATTTT-GCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCA
3579516 ACTT
129 ACTT
* * *
3579520 TTAGCTCGATTATATCACAGAATGAGGTAGATCAGCATCGACATATCGTTCGATTTCCATCACAG
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGA-TTCCATCACAG
* * * * *
3579585 AAGAAGGTGGATCGACATTTTTATCTTTACTCAAATCTATCGCAGAAGGAGTTGGATCAACGTTA
65 AAGGAGGTGGATCGACAATTTTAT-TTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCA
3579650 ACTT
129 ACTT
* * *
3579654 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGATATCTCGTTCGATTCCATCACAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGATTCCATCACAGA
* *
3579719 ATGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCAT
66 AGGAGGTGGATCGACAATTTTATTTT-GCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCA-
3579784 A-TT
129 ACTT
*
3579787 CTTGCTCGATTC-ATCACA
1 TTTGCTCGATTCTATCACA
3579805 TATGGAGTTG
Statistics
Matches: 377, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
129 46 0.12
130 26 0.07
131 1 0.00
132 12 0.03
133 83 0.22
134 206 0.55
135 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (132 bp):
TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGATTCCATCACAGA
AGGAGGTGGATCGACAATTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCAAC
TT
Found at i:3579764 original size:89 final size:88
Alignment explanation
Indices: 3579399--3579804 Score: 230
Period size: 89 Copynumber: 4.6 Consensus size: 88
3579389 TCTCGATTCT
* * * * *
3579399 ATCACAGAAGGAGGTAGATCATCATTGACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATC
1 ATCACAGAAGGAGGTGGATCAACATCGATATCTCGTTCGA-TTCCATCACAGAAGGAGGTGGATC
*
3579464 GACAATTTTATTTTCGCTCAAATCC
65 -ACATTTTTATTTTCGCTCAAATCC
* * * * * * * ** * *
3579489 ATCGCAGAAGGAGTTGGATCAACGTCAACT-TTTAGCTCGATTATATCACAGAATGAGGTAGATC
1 ATCACAGAAGGAGGTGGATCAACATCGA-TATCTCGTTCGATTCCATCACAGAAGGAGGTGGATC
**** * * **
3579553 AGCATCGACA-TATCGTTCGATTTCC
65 A-CATTTTTATTTTCGCTC-AAATCC
* * *** * * * * * *
3579578 ATCACAGAAGAAGGTGGATCGACATTTTTATCT-TTACTCAAATCTATCGCAGAAGGAGTTGGAT
1 ATCACAGAAGGAGGTGGATCAACATCGATATCTCGT--TCGATTCCATCACAGAAGGAGGTGGAT
** * * * * *
3579642 CA-ACGTTAACTTTTTGCTCGATTCT
64 CACATTTTTA-TTTTCGCTCAAATCC
* *
3579667 ATCACAGAAGGAGGTAGATCAACATCGATATCTCGTTCGATTCCATCACAGAATGAGGTGGATCG
1 ATCACAGAAGGAGGTGGATCAACATCGATATCTCGTTCGATTCCATCACAGAAGGAGGTGGATC-
3579732 ACATTTTTATTTTCGCTCAAATCC
65 ACATTTTTATTTTCGCTCAAATCC
* * * * *
3579756 ATCGCAGAAGGAGTTGGATCAACGTC-ATATTCTTGCTCGATT-CATCACA
1 ATCACAGAAGGAGGTGGATCAACATCGATA-TCTCGTTCGATTCCATCACA
3579805 TATGGAGTTG
Statistics
Matches: 225, Mismatches: 79, Indels: 26
0.68 0.24 0.08
Matches are distributed among these distances:
88 42 0.19
89 123 0.55
90 60 0.27
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (88 bp):
ATCACAGAAGGAGGTGGATCAACATCGATATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCA
CATTTTTATTTTCGCTCAAATCC
Found at i:3580140 original size:30 final size:30
Alignment explanation
Indices: 3580104--3580182 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
3580094 GTAAACACCA
* * *
3580104 TTTTTCAACATCAACACCTACCACCCCATT
1 TTTTTCAACACCAACACCCACCACCACATT
*
3580134 TTTTTCAACACCAACACCCACCATCACATT
1 TTTTTCAACACCAACACCCACCACCACATT
3580164 TTTTTCAACACCAAC-CCCA
1 TTTTTCAACACCAACACCCA
3580183 TCATCTCTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 4 0.09
30 41 0.91
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.28
Consensus pattern (30 bp):
TTTTTCAACACCAACACCCACCACCACATT
Found at i:3586091 original size:88 final size:88
Alignment explanation
Indices: 3585977--3586394 Score: 595
Period size: 88 Copynumber: 4.8 Consensus size: 88
3585967 TAAAAACATT
* * * *
3585977 GATCCCCCTCATTCTATGATGTAATCGAATGAGATGTCGGTGCTGATCTACCTCCTTCTGTGATA
1 GATCCCCCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATA
3586042 GATTTGAGTGAAATGAAAATGTC
66 GATTTGAGTGAAATGAAAATGTC
* * * * *
3586065 GATCCCCCTCTTTCTGTGATGGAATCGAATGAGATGTTGGTGCTGATCTATCTTCTTTTGTGATA
1 GATCCCCCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATA
* *
3586130 GATTTGAGTAAAATGAAAATGTT
66 GATTTGAGTGAAATGAAAATGTC
* * *
3586153 GATCCCCCTCATTCTATGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCTTTCTGTGATA
1 GATCCCCCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATA
*
3586218 GATTTGAGTGAAATGAAAATGTT
66 GATTTGAGTGAAATGAAAATGTC
* ** *
3586241 GAT-CCCCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTTATTCTATGATA
1 GATCCCCCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATA
3586305 GATTTGAGTGAAATGAAAATGTC
66 GATTTGAGTGAAATGAAAATGTC
** * * * * *
3586328 GATTGCCCTCATTTTGTGATGAAATCTAACGAGATGTTGGTGCTGATCTACATCTTTCTGTGATA
1 GATCCCCCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATA
3586393 GA
66 GA
3586395 ATCGAGAAAA
Statistics
Matches: 295, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
87 80 0.27
88 215 0.73
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (88 bp):
GATCCCCCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATA
GATTTGAGTGAAATGAAAATGTC
Found at i:3586199 original size:44 final size:44
Alignment explanation
Indices: 3586149--3586303 Score: 132
Period size: 44 Copynumber: 3.5 Consensus size: 44
3586139 AAAATGAAAA
*
3586149 TGTTGATCCCCCTCATTCTATGATGGAATCGAACGAGATGTTGG
1 TGTTGATCCACCTCATTCTATGATGGAATCGAACGAGATGTTGG
* * * * * * ** * ****
3586193 TGTTGATCTACCTCTTTCTGTGATAGATTTGAGTGAAATGAAAA
1 TGTTGATCCACCTCATTCTATGATGGAATCGAACGAGATGTTGG
* *
3586237 TGTTGATCC-CCTCCTTCTGTGATGGAATCGAACGAGATGTTGG
1 TGTTGATCCACCTCATTCTATGATGGAATCGAACGAGATGTTGG
* * *
3586280 TGCTGATCTACCTTATTCTATGAT
1 TGTTGATCCACCTCATTCTATGAT
3586304 AGATTTGAGT
Statistics
Matches: 79, Mismatches: 31, Indels: 2
0.71 0.28 0.02
Matches are distributed among these distances:
43 30 0.38
44 49 0.62
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (44 bp):
TGTTGATCCACCTCATTCTATGATGGAATCGAACGAGATGTTGG
Found at i:3586361 original size:175 final size:176
Alignment explanation
Indices: 3585977--3586394 Score: 640
Period size: 175 Copynumber: 2.4 Consensus size: 176
3585967 TAAAAACATT
* * * *
3585977 GATCCCCCTCATTCTATGATGTAATCGAATGAGATGTCGGTGCTGATCTACCTCCTTCTGTGATA
1 GATCCCCCTCATTCTATGATGAAATCGAACGAGATGTTGGTGCTGATCTACCTCTTTCTGTGATA
* *
3586042 GATTTGAGTGAAATGAAAATGTCGATCCCCCTCTTTCTGTGATGGAATCGAATGAGATGTTGGTG
66 GATTTGAGTGAAATGAAAATGTCGATCCCCCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTG
* * * * *
3586107 CTGATCTATCTTCTTTTGTGATAGATTTGAGTAAAATGAAAATGTT
131 CTGATCTACCTTATTCTATGATAGATTTGAGTAAAATGAAAATGTC
* *
3586153 GATCCCCCTCATTCTATGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCTTTCTGTGATA
1 GATCCCCCTCATTCTATGATGAAATCGAACGAGATGTTGGTGCTGATCTACCTCTTTCTGTGATA
*
3586218 GATTTGAGTGAAATGAAAATGTTGAT-CCCCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTG
66 GATTTGAGTGAAATGAAAATGTCGATCCCCCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTG
*
3586282 CTGATCTACCTTATTCTATGATAGATTTGAGTGAAATGAAAATGTC
131 CTGATCTACCTTATTCTATGATAGATTTGAGTAAAATGAAAATGTC
** * * * *
3586328 GATTGCCCTCATTTTGTGATGAAATCTAACGAGATGTTGGTGCTGATCTACATCTTTCTGTGATA
1 GATCCCCCTCATTCTATGATGAAATCGAACGAGATGTTGGTGCTGATCTACCTCTTTCTGTGATA
3586393 GA
66 GA
3586395 ATCGAGAAAA
Statistics
Matches: 220, Mismatches: 22, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
175 135 0.61
176 85 0.39
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (176 bp):
GATCCCCCTCATTCTATGATGAAATCGAACGAGATGTTGGTGCTGATCTACCTCTTTCTGTGATA
GATTTGAGTGAAATGAAAATGTCGATCCCCCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTG
CTGATCTACCTTATTCTATGATAGATTTGAGTAAAATGAAAATGTC
Found at i:3586536 original size:20 final size:20
Alignment explanation
Indices: 3586508--3586582 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
3586498 GTATCATGCT
3586508 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
3586528 CGAAGGACTTACGCATCATGG-T
1 CGAAAGACTTA--C-TGATGGCC
3586550 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* *
3586570 CAAAAGATTTACT
1 CGAAAGACTTACT
3586583 CATCAAGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.12
20 22 0.51
22 11 0.26
23 5 0.12
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:3586567 original size:42 final size:41
Alignment explanation
Indices: 3586438--3586570 Score: 160
Period size: 42 Copynumber: 3.2 Consensus size: 41
3586428 AGGCCTTATG
* *
3586438 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTA-T
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACT
* ** * *
3586478 AGATGACCCGATTGATTTAAGTATCATGCTCGAAAGACTTACT
1 -GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACT
*
3586521 GATGGCCCGAAGGACTTACGCATCATGGTCGAAAGACTTACT
1 GATGGCCCGAAGGACTTA-GCATCATGCTCGAAAGACTTACT
3586563 GATGGCCC
1 GATGGCCC
3586571 AAAAGATTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 14 0.18
42 61 0.80
43 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACT
Found at i:3586587 original size:42 final size:42
Alignment explanation
Indices: 3586438--3586587 Score: 133
Period size: 42 Copynumber: 3.6 Consensus size: 42
3586428 AGGCCTTATG
* * * *
3586438 GATGGCCCGAAGGACTTA-TCATCTTGCTCGAAAGACTTA-T
1 GATGGCCCAAAAGACTTACGCATCATGCTCGAAAGACTTACT
* * ** * * *
3586478 AGATGACCCGATTGATTTAAGTATCATGCTCGAAAGACTTACT
1 -GATGGCCCAAAAGACTTACGCATCATGCTCGAAAGACTTACT
* * *
3586521 GATGGCCCGAAGGACTTACGCATCATGGTCGAAAGACTTACT
1 GATGGCCCAAAAGACTTACGCATCATGCTCGAAAGACTTACT
* *
3586563 GATGGCCCAAAAGATTTACTCATCA
1 GATGGCCCAAAAGACTTACGCATCA
3586588 AGAAACCCTT
Statistics
Matches: 89, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
41 14 0.16
42 74 0.83
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
GATGGCCCAAAAGACTTACGCATCATGCTCGAAAGACTTACT
Found at i:3586746 original size:39 final size:39
Alignment explanation
Indices: 3586673--3587157 Score: 621
Period size: 39 Copynumber: 12.2 Consensus size: 39
3586663 TTAGTTTCTT
* * *
3586673 ATAAAATCTTTTATTTC-AGCGAAACTATCTCAAGCGAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
* * ** *
3586711 ACAAAATCTTTTGTTTCAATTGAAACTATCTCAAGCAAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
* *
3586750 ATAAAATCTTCTGTTTCAAGGGAAACTATCGCAAGCGAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
* * *
3586789 ATAAAATCTTATGTTTCGAGGAAAACTATCTCAAGAGAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
* * *
3586828 ATAAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCAAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
*
3586867 ATAAAATCTTATGTTTCAAGGGAAACTATTTCAAGCGAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
*
3586906 ATAAAATCTTATGTTTCAAGGAAAACTATCTCAAGCGAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
* *
3586945 ATAAAAATCTTCTCTTTCAAGGGAAACTATCTCAAGCGAG
1 AT-AAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
* *
3586985 ATAAAAATCTTCTCTTTCAAGGGAAACTATCTCAAGCGAG
1 AT-AAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
*
3587025 ATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
**
3587064 ATAAAAATCTTATGTTTCAAGGGAAACTATAAACTATCTCAAATGAG
1 AT-AAAATCTTATGTTTCAAGGG-------AAACTATCTCAAGCGAG
* *
3587111 ATAAAAATCTTATGTTTCAAAGGAAACTATCTCAAGAGAG
1 AT-AAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
3587151 ATAAAAT
1 ATAAAAT
3587158 ATTCTTTAAA
Statistics
Matches: 397, Mismatches: 40, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
38 15 0.04
39 233 0.59
40 112 0.28
47 37 0.09
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (39 bp):
ATAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCGAG
Found at i:3587116 original size:47 final size:47
Alignment explanation
Indices: 3587047--3587140 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
3587037 GTTTCGAGGG
* *
3587047 AAACTATCTCAAGCGAGATAAAAATCTTATGTTTCAAGGGAAACTAT
1 AAACTATCTCAAACGAGATAAAAATCTTATGTTTCAAAGGAAACTAT
*
3587094 AAACTATCTCAAATGAGATAAAAATCTTATGTTTCAAAGGAAACTAT
1 AAACTATCTCAAACGAGATAAAAATCTTATGTTTCAAAGGAAACTAT
3587141 CTCAAGAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.29
Consensus pattern (47 bp):
AAACTATCTCAAACGAGATAAAAATCTTATGTTTCAAAGGAAACTAT
Found at i:3587433 original size:76 final size:75
Alignment explanation
Indices: 3587171--3587415 Score: 334
Period size: 76 Copynumber: 3.2 Consensus size: 75
3587161 CTTTAAAAAC
* * * * *
3587171 AATCTTGTTTTAAGAAAAGCAGTCTTGAGTGAAATAAATCTTCTTGTTTTGAGTAAAAAATGTCT
1 AATCTTATTTTAAGAAAAACA-ACATGAGTGAAATAAATCTTCTTGTTTTGAGTAAAAACTGTCT
**
3587236 CGTGCGAGACA
65 CAAGCGAGACA
*
3587247 AATCTTGTTTTAAGAAAAACAACATGAGTGAAATAAATCTTCTTGTTTCT-AGTAAAAACTGTCT
1 AATCTTATTTTAAGAAAAACAACATGAGTGAAATAAATCTTCTTGTTT-TGAGTAAAAACTGTCT
*
3587311 CAAGCTAGACA
65 CAAGCGAGACA
*
3587322 AATCTTATTTTAAGAAAAACAACATGTAGTGAAATGAAAT-GTCTTGTTTTGAGTAAAAACTGTC
1 AATCTTATTTTAAGAAAAACAACATG-AGTGAAAT-AAATCTTCTTGTTTTGAGTAAAAACTGTC
3587386 TCAAGCGAGACAA
64 TCAAGCGAGAC-A
3587399 AATC-TATTTTAAGAAAA
1 AATCTTATTTTAAGAAAA
3587416 GCAATCTTGT
Statistics
Matches: 154, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
75 72 0.47
76 73 0.47
77 9 0.06
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (75 bp):
AATCTTATTTTAAGAAAAACAACATGAGTGAAATAAATCTTCTTGTTTTGAGTAAAAACTGTCTC
AAGCGAGACA
Found at i:3593647 original size:21 final size:23
Alignment explanation
Indices: 3593623--3593675 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
3593613 ATCCTCTCTA
3593623 TGTATCGATACACT-A-TGAATG
1 TGTATCGATACACTCATTGAATG
* * *
3593644 TGTACCAATACATTCATTGAATG
1 TGTATCGATACACTCATTGAATG
3593667 TGTATCGAT
1 TGTATCGAT
3593676 GAGTGTATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 13 0.52
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (23 bp):
TGTATCGATACACTCATTGAATG
Found at i:3596373 original size:19 final size:18
Alignment explanation
Indices: 3596346--3596381 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3596336 ATGTAATTAG
*
3596346 TGTATCGATACACCTAGGA
1 TGTACCGATACA-CTAGGA
3596365 TGTACCGATACACTAGG
1 TGTACCGATACACTAGG
3596382 TCAACTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (18 bp):
TGTACCGATACACTAGGA
Found at i:3597132 original size:36 final size:36
Alignment explanation
Indices: 3597092--3597208 Score: 144
Period size: 36 Copynumber: 3.1 Consensus size: 36
3597082 CTTTTTGAGT
3597092 AAAACTGTCTCAAGCGAGACAAAGTCTGTTTTAAGA
1 AAAACTGTCTCAAGCGAGACAAAGTCTGTTTTAAGA
** * * *
3597128 AAAACAATCTCAAGTGAGATAAAATGTCTTGTTTTGAGTA
1 AAAACTGTCTCAAGCGAGA-CAAA-GTC-TGTTTTAAG-A
*
3597168 AAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGA
1 AAAACTGTCTCAAGCGAGACAAAGTCTGTTTTAAGA
3597204 AAAAC
1 AAAAC
3597209 AATCTTGAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
36 22 0.33
37 11 0.17
38 5 0.08
39 11 0.17
40 17 0.26
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
AAAACTGTCTCAAGCGAGACAAAGTCTGTTTTAAGA
Found at i:3597179 original size:40 final size:39
Alignment explanation
Indices: 3597074--3597192 Score: 131
Period size: 36 Copynumber: 3.1 Consensus size: 39
3597064 CAACAAAATG
*
3597074 AAATGTCTCT-TTTTGAGT-AAAACTGTCTCAAGCGAGAC
1 AAATGTCT-TGTTTTGAGTAAAAACTGTCTCAAGCGAGAA
* ** *
3597112 AAA-GTC-TGTTTTAAG-AAAAACAATCTCAAGTGAGATA
1 AAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGA-A
3597149 AAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACA
1 AAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGA-A
3597189 AAAT
1 AAAT
3597193 CTGTTTTAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
35 1 0.02
36 22 0.34
37 6 0.09
38 6 0.09
39 8 0.12
40 22 0.34
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (39 bp):
AAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGAA
Found at i:3597270 original size:75 final size:75
Alignment explanation
Indices: 3597069--3597271 Score: 300
Period size: 76 Copynumber: 2.7 Consensus size: 75
3597059 TAACTCAACA
*
3597069 AAATGAAATGTC-TCTTTTTGAGTAAAACTGTCTCAAGCGAGACAAAGTCTGTTTTAAGAAAAAC
1 AAATGAAATGTCTTC-TTTTGAGTAAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAAC
3597133 AATCTCAAGTG
65 AATCTCAAGTG
* * *
3597144 AGATAAAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAAC
1 AAATGAAATGTCTTCTTTTGAGT-AAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAAC
**
3597209 AATCTTGAGTG
65 AATCTCAAGTG
* * *
3597220 AAATGAAATATCTTCTTTCGAGTTAAACTGTCTCAAGCGAGACAAAATCTGT
1 AAATGAAATGTCTTCTTTTGAGTAAAACTGTCTCAAGCGAGACAAAATCTGT
3597272 CTTTGAGAGA
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 46 0.40
76 68 0.60
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (75 bp):
AAATGAAATGTCTTCTTTTGAGTAAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAACA
ATCTCAAGTG
Found at i:3597403 original size:32 final size:32
Alignment explanation
Indices: 3597362--3597425 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
3597352 TTATATAAGG
3597362 ATGTTGAATCCCCAAAGATGCCACAACATTCA
1 ATGTTGAATCCCCAAAGATGCCACAACATTCA
* *
3597394 ATGTTGAATCTCCAAAGATGCCCCAACATTCA
1 ATGTTGAATCCCCAAAGATGCCACAACATTCA
3597426 TAATTTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.23
Consensus pattern (32 bp):
ATGTTGAATCCCCAAAGATGCCACAACATTCA
Found at i:3598485 original size:18 final size:18
Alignment explanation
Indices: 3598454--3598495 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
3598444 CTTCTTGCCC
3598454 TTTTTCTTTATTTTTTTG
1 TTTTTCTTTATTTTTTTG
*
3598472 TTTTT-TTT-TCTTTTT-
1 TTTTTCTTTATTTTTTTG
3598487 TTTTTCTTT
1 TTTTTCTTT
3598496 GCTCATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 3 0.14
18 5 0.23
ACGTcount: A:0.02, C:0.07, G:0.02, T:0.88
Consensus pattern (18 bp):
TTTTTCTTTATTTTTTTG
Found at i:3598492 original size:11 final size:11
Alignment explanation
Indices: 3598454--3598495 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
3598444 CTTCTTGCCC
3598454 TTTTTCTTTATT
1 TTTTTCTTT-TT
*
3598466 TTTTT-GTTTT
1 TTTTTCTTTTT
3598476 TTTTTCTTTTT
1 TTTTTCTTTTT
3598487 TTTTTCTTT
1 TTTTTCTTT
3598496 GCTCATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 7 0.26
11 15 0.56
12 5 0.19
ACGTcount: A:0.02, C:0.07, G:0.02, T:0.88
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:3608054 original size:2 final size:2
Alignment explanation
Indices: 3608047--3608071 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3608037 TAGATAATAA
3608047 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3608072 AACTCTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3612045 original size:159 final size:159
Alignment explanation
Indices: 3611755--3612072 Score: 530
Period size: 159 Copynumber: 2.0 Consensus size: 159
3611745 AATAATTTTA
* *
3611755 CCTTAGTAAATAATGTATAGGATTTAATACATAATCTTTATGCAAGTGACTTTTAACTTAGTACT
1 CCTTAGTAAATAATGTATAGGATTTAATACATAAGCTTTATGCAAGTGACTTTTAACTTAGTAAT
*
3611820 TTTATTTAACTAAAGATGGTGTGGCTAGTCTTTAACTAAATAAAATTATGAAAACCACTTAGCTA
66 TTTATTTAACTAAAGATGGTGCGGCTAGTCTTTAACTAAATAAAATTATGAAAACCACTTAGCTA
3611885 GATATTAATCCTAAATTTTATTTTAAATT
131 GATATTAATCCTAAATTTTATTTTAAATT
* *
3611914 CCTTAGTAAATAATGTATAGGATTTAATACATAAGCTTTATGTAGGTGACTTTTAACTTTAGTAA
1 CCTTAGTAAATAATGTATAGGATTTAATACATAAGCTTTATGCAAGTGACTTTTAAC-TTAGTAA
* * * *
3611979 TTTTATTTAACTAAATATGTTGCGGCTAGTCTTTAACTAAATAAAATTATG-AAATCACTTATCT
65 TTTTATTTAACTAAAGATGGTGCGGCTAGTCTTTAACTAAATAAAATTATGAAAACCACTTAGCT
*
3612043 AGATATTAATCCTTAATTTTATTTTAAATT
130 AGATATTAATCCTAAATTTTATTTTAAATT
3612073 GTTAATCCAT
Statistics
Matches: 148, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
159 94 0.64
160 54 0.36
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (159 bp):
CCTTAGTAAATAATGTATAGGATTTAATACATAAGCTTTATGCAAGTGACTTTTAACTTAGTAAT
TTTATTTAACTAAAGATGGTGCGGCTAGTCTTTAACTAAATAAAATTATGAAAACCACTTAGCTA
GATATTAATCCTAAATTTTATTTTAAATT
Found at i:3612729 original size:23 final size:23
Alignment explanation
Indices: 3612698--3612756 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 23
3612688 TTTTGAGATT
*
3612698 GTTGCATTTTTTTATTAATTTAG
1 GTTGAATTTTTTTATTAATTTAG
3612721 GTTGAA---TTTTATTAATTTAG
1 GTTGAATTTTTTTATTAATTTAG
*
3612741 GTTGAATTTTATTATT
1 GTTGAATTTTTTTATT
3612757 TTTATAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 20 0.65
23 11 0.35
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (23 bp):
GTTGAATTTTTTTATTAATTTAG
Found at i:3612732 original size:20 final size:20
Alignment explanation
Indices: 3612707--3612754 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
3612697 TGTTGCATTT
3612707 TTTTATTAATTTAGGTTGAA
1 TTTTATTAATTTAGGTTGAA
3612727 TTTTATTAATTTAGGTTGAA
1 TTTTATTAATTTAGGTTGAA
3612747 TTTTATTA
1 TTTTATTA
3612755 TTTTTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.58
Consensus pattern (20 bp):
TTTTATTAATTTAGGTTGAA
Found at i:3613595 original size:44 final size:45
Alignment explanation
Indices: 3613516--3613604 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
3613506 TATTTCATTC
* * *
3613516 AAAAAATTATTAATTTACTAATAGATAATAAAAAATGGTAAATTA
1 AAAAAACTATTAATTTACTAATAAATAATAAAAAATAGTAAATTA
* *
3613561 AAAAAACTATTAATTTTCTAATAAATAAT-AAAAATATTAAATTA
1 AAAAAACTATTAATTTACTAATAAATAATAAAAAATAGTAAATTA
3613605 TTAACTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 13 0.33
45 26 0.67
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (45 bp):
AAAAAACTATTAATTTACTAATAAATAATAAAAAATAGTAAATTA
Found at i:3615933 original size:131 final size:132
Alignment explanation
Indices: 3615594--3615944 Score: 479
Period size: 132 Copynumber: 2.7 Consensus size: 132
3615584 TTTAAGAGAT
* *
3615594 AAAACAACAATATCTAATTATTTCCAATCGGAGAATAAATGACCTTTCATGCCTTAAAACAATCA
1 AAAACAATAATATCTAATTATTTCCAATC-GAGAATAAATGACCTCTCATGCCTTAAAACAATCA
* * * * * *
3615659 TTTATTACTACAATTGAAATGAATAGATATTACCATTTCGTCTTAAAATTCAATATCGATTCGAG
65 TTTATTACTCCAATCGAAATGAAGAGATATCACCATTTCGTATTAAAAATCAATATCGATTCGAG
3615724 TAA
130 TAA
* * * *
3615727 AAAACAATAATATCTAATGATTTCTAATCGAGAATAAATGACCTCTCATACCTTAAAACAGTCAT
1 AAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCAT
* * *
3615792 TTATTGCTCCAATCGAAATGAAGAGATATCACTATTTCGTATTAAAAATCAATATTGATTCGAG-
66 TTATTACTCCAATCGAAATGAAGAGATATCACCATTTCGTATTAAAAATCAATATCGATTCGAGT
*
3615856 AG
131 AA
** * * * *
3615858 AAAATGATAATATCGAATTATTCCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCATTCAT
1 AAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCAT
*
3615923 TTATTACTCCAACCGAAATGAA
66 TTATTACTCCAATCGAAATGAA
3615945 AAATATATTA
Statistics
Matches: 191, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
131 77 0.40
132 88 0.46
133 26 0.14
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (132 bp):
AAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCAT
TTATTACTCCAATCGAAATGAAGAGATATCACCATTTCGTATTAAAAATCAATATCGATTCGAGT
AA
Found at i:3616935 original size:107 final size:107
Alignment explanation
Indices: 3616744--3616938 Score: 237
Period size: 107 Copynumber: 1.8 Consensus size: 107
3616734 AAATAACCCT
* * * *
3616744 AAAATATATAACATGCACAAAAAAGGGTAAATTATAGAATCGATCCCTACATGTGGCTAACATGC
1 AAAATATATAACATGCACAAAAAAGGGTAAATTACAAAATCGATCCCTACATATGACTAACATGC
* *
3616809 AAAAATACGCTAAAATTAGGGGGCTAAATAGCAATTATACCA
66 AAAAACACGCGAAAATTAGGGGGCTAAATAGCAATTATACCA
* * * * * ***
3616851 AAAATTTATAACATGCATAAAAACGGGTAAATTACAAAATTGATCCCTATATATGACTATTTTGC
1 AAAATATATAACATGCACAAAAAAGGGTAAATTACAAAATCGATCCCTACATATGACTAACATGC
* * *
3616916 AAATACACGCGCAAGTTAGGGGG
66 AAAAACACGCGAAAATTAGGGGG
3616939 ACCAAAGCGT
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
107 71 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (107 bp):
AAAATATATAACATGCACAAAAAAGGGTAAATTACAAAATCGATCCCTACATATGACTAACATGC
AAAAACACGCGAAAATTAGGGGGCTAAATAGCAATTATACCA
Found at i:3617997 original size:3 final size:3
Alignment explanation
Indices: 3617989--3618033 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
3617979 TGTACAAAGA
* *
3617989 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT ATT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3618034 GTGGGATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3618015 original size:17 final size:17
Alignment explanation
Indices: 3617993--3618027 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3617983 CAAAGAAATA
3617993 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
*
3618010 ATAATAATAATATTAAT
1 ATAATAATAATAATAAT
3618027 A
1 A
3618028 ACAATAGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:3618015 original size:20 final size:20
Alignment explanation
Indices: 3617990--3618028 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3617980 GTACAAAGAA
3617990 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
*
3618010 ATAATAATAATATTAATAA
1 ATAATAATAATAATAATAA
3618029 CAATAGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:3618019 original size:23 final size:23
Alignment explanation
Indices: 3617989--3618033 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3617979 TGTACAAAGA
*
3617989 AATAATAATAATAATAATAATAT
1 AATAATAATAATAATAACAATAT
*
3618012 AATAATAATATTAATAACAATA
1 AATAATAATAATAATAACAATA
3618034 GTGGGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAATAATAATAATAACAATAT
Found at i:3621689 original size:12 final size:11
Alignment explanation
Indices: 3621660--3621708 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
3621650 CCCCTTTTTG
*
3621660 TTTTTTCATTA
1 TTTTTTCATTT
3621671 TTTTTTCATTT
1 TTTTTTCATTT
3621682 TTTCTTTCATTT
1 TTT-TTTCATTT
3621694 TCTTTTTC-TTT
1 T-TTTTTCATTT
3621705 TTTT
1 TTTT
3621709 ATTTTCTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
10 3 0.09
11 17 0.49
12 13 0.37
13 2 0.06
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:3621699 original size:23 final size:24
Alignment explanation
Indices: 3621663--3621708 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3621653 CTTTTTGTTT
3621663 TTTCATTA-TTTTTTCATTTTTTC
1 TTTCATTATTTTTTTCATTTTTTC
*
3621686 TTTCATT-TTCTTTTTCTTTTTTT
1 TTTCATTATT-TTTTTCATTTTTT
3621709 ATTTTCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTCATTATTTTTTTCATTTTTTC
Found at i:3640735 original size:306 final size:307
Alignment explanation
Indices: 3640160--3640774 Score: 1214
Period size: 306 Copynumber: 2.0 Consensus size: 307
3640150 ATCTTGGGGA
3640160 GACCCTTCCTAGTTACCATATGTATTTTAATCGACTGCGAGAAGGGTGATCTTACCATAAGAGTG
1 GACCCTTCCTAGTTACCATA-GTATTTTAATCGACTGCGAGAAGGGTGATCTTACCATAAGAGTG
3640225 ACTGACCAATATGTCACTGTTAATGTTTTCCGTACTCTCAAGTACATGGATGATTCTTAAGAACG
65 ACTGACCAATATGTCACTGTTAATGTTTTCCGTACTCTCAAGTACATGGATGATTCTTAAGAACG
3640290 CCATAGAATTTGTGAAGTGGATTCATTTATAGTAAGAGAAGCTAATAATTTTACCATGACAATTT
130 CCATAGAATTTGTGAAGTGGATTCATTTATAGTAAGAGAAGCTAATAATTTTACCATGACAATTT
3640355 CATTTAGCTGTGAAATTATGAGAGGTTATTTGAAGAAGAAAGTGTCGAAAAGCCCAATGACTTTT
195 CATTTAGCTGTGAAATTATGAGAGGTTATTTGAAGAAGAAAGTGTCGAAAAGCCCAATGACTTTT
3640420 CTTTGGAGAAGCAGCAGGCTAGCTTCCTCATAGCTAACCCAGGTATAC
260 CTTTGGAGAAGCAGCAGGCTAGCTTCCTCATAGCTAACCCAGGTATAC
3640468 GACCCTTCCTAGTTACCATA-TATTTTAATCGACTGCGAGAAGGGTGATCTTACCATAAGAGTGA
1 GACCCTTCCTAGTTACCATAGTATTTTAATCGACTGCGAGAAGGGTGATCTTACCATAAGAGTGA
3640532 CTGACCAATATGTCACTGTTAATGTTTTCCGTACTCTCAAGTACATGGATGATTCTTAAGAACGC
66 CTGACCAATATGTCACTGTTAATGTTTTCCGTACTCTCAAGTACATGGATGATTCTTAAGAACGC
3640597 CATAGAATTTGTGAAGTGGATTCATTTATAGTAAGAGAAGCTAATAATTTTACCATGACAATTTC
131 CATAGAATTTGTGAAGTGGATTCATTTATAGTAAGAGAAGCTAATAATTTTACCATGACAATTTC
3640662 ATTTAGCTGTGAAATTATGAGAGGTTATTTGAAGAAGAAAGTGTCGAAAAGCCCAATGACTTTTC
196 ATTTAGCTGTGAAATTATGAGAGGTTATTTGAAGAAGAAAGTGTCGAAAAGCCCAATGACTTTTC
3640727 TTTGGAGAAGCAGCAGGCTAGCTTCCTCATAGCTAACCCAGGTATAC
261 TTTGGAGAAGCAGCAGGCTAGCTTCCTCATAGCTAACCCAGGTATAC
3640774 G
1 G
3640775 TTTTGAACCT
Statistics
Matches: 307, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
306 287 0.93
308 20 0.07
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (307 bp):
GACCCTTCCTAGTTACCATAGTATTTTAATCGACTGCGAGAAGGGTGATCTTACCATAAGAGTGA
CTGACCAATATGTCACTGTTAATGTTTTCCGTACTCTCAAGTACATGGATGATTCTTAAGAACGC
CATAGAATTTGTGAAGTGGATTCATTTATAGTAAGAGAAGCTAATAATTTTACCATGACAATTTC
ATTTAGCTGTGAAATTATGAGAGGTTATTTGAAGAAGAAAGTGTCGAAAAGCCCAATGACTTTTC
TTTGGAGAAGCAGCAGGCTAGCTTCCTCATAGCTAACCCAGGTATAC
Found at i:3640923 original size:32 final size:32
Alignment explanation
Indices: 3640887--3640950 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3640877 TTATCTGGGT
*
3640887 AGTAATGAAACTTTACCTGTTATTATTTCCTC
1 AGTAATGAAACTTTACCTATTATTATTTCCTC
3640919 AGTAATGAAACTTTACCTATTATTATTTCCTC
1 AGTAATGAAACTTTACCTATTATTATTTCCTC
3640951 TACCCTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.44
Consensus pattern (32 bp):
AGTAATGAAACTTTACCTATTATTATTTCCTC
Found at i:3647852 original size:18 final size:17
Alignment explanation
Indices: 3647817--3647859 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3647807 AACATTTCCA
3647817 TCCATTTTGCCACAATATT
1 TCCA-TTTGCCACAATA-T
* *
3647836 TCCATTTGCTACCATAT
1 TCCATTTGCCACAATAT
3647853 TCCATTT
1 TCCATTT
3647860 CACCATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 10 0.45
19 4 0.18
ACGTcount: A:0.23, C:0.28, G:0.05, T:0.44
Consensus pattern (17 bp):
TCCATTTGCCACAATAT
Found at i:3647872 original size:16 final size:17
Alignment explanation
Indices: 3647835--3647874 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3647825 GCCACAATAT
3647835 TTCCATTTGCTACCATA
1 TTCCATTTGCTACCATA
3647852 TTCCATTT-C-ACCATCA
1 TTCCATTTGCTACCAT-A
3647868 TTCCATT
1 TTCCATT
3647875 CCCACCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 8 0.36
ACGTcount: A:0.23, C:0.33, G:0.03, T:0.42
Consensus pattern (17 bp):
TTCCATTTGCTACCATA
Found at i:3647951 original size:43 final size:43
Alignment explanation
Indices: 3647903--3647990 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
3647893 ATCTTCTCAC
3647903 AACATTTTCATTTATAAATAACATCACTAACTATACTTAGGTG
1 AACATTTTCATTTATAAATAACATCACTAACTATACTTAGGTG
3647946 AACATTTTCATTTATAAATAACATCACTAACTATACTTAGGTG
1 AACATTTTCATTTATAAATAACATCACTAACTATACTTAGGTG
3647989 AA
1 AA
3647991 ATAGTAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (43 bp):
AACATTTTCATTTATAAATAACATCACTAACTATACTTAGGTG
Found at i:3654333 original size:131 final size:131
Alignment explanation
Indices: 3654090--3654450 Score: 472
Period size: 131 Copynumber: 2.8 Consensus size: 131
3654080 ATAATTTTAA
* * * *
3654090 GAGATAAAACGTTAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * * * *
3654155 TTCATTTATTACTACAATCAAAATGAAGATATATTATTATTTCGTCTTCAAATTCAATATAAATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCATTATTTCGTCTTAAAAATCAATATAAATT
3654220 C
131 C
* * *
3654221 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * **
3654286 GTCATTTATTGCTCCAATCGAAATGAAGAGATGTCATTATTAT-GTCTTAAAAATCAATATTGAT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCATTATT-TCGTCTTAAAAATCAATATAAAT
3654350 TC
130 TC
* * * * *
3654352 GAGAGAAAATGGTAATATCGAATTATTTCCAATCGATAATAAATGACCTCTCATGTCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
3654417 ATCATTTATTACTCCAACCGAAATGAAAAGATAT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATAT
3654451 TACCATTCTC
Statistics
Matches: 198, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
131 197 0.99
132 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATCGAAATGAAGAGATATCATTATTTCGTCTTAAAAATCAATATAAATT
C
Found at i:3660629 original size:44 final size:44
Alignment explanation
Indices: 3660572--3660677 Score: 104
Period size: 44 Copynumber: 2.4 Consensus size: 44
3660562 GAGTGTGCTA
* * * * * *
3660572 ATCCATCTTCTTCTGTGATGAAATCGAGCGAAATGACAATGTTG
1 ATCCACCTCCTTCTGTGATGAAATCAAACAAAATGACAATATTG
* * *
3660616 ATCCACCTCCTTCTATGATGGAATCAAACAAAATGTCAATATTG
1 ATCCACCTCCTTCTGTGATGAAATCAAACAAAATGACAATATTG
* * *
3660660 ATCTACGTCCTTTTGTGA
1 ATCCACCTCCTTCTGTGA
3660678 CAGAATCGAG
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
ATCCACCTCCTTCTGTGATGAAATCAAACAAAATGACAATATTG
Found at i:3660692 original size:44 final size:44
Alignment explanation
Indices: 3660593--3660692 Score: 101
Period size: 44 Copynumber: 2.3 Consensus size: 44
3660583 TCTGTGATGA
* * **
3660593 AATCGAGCGAAATGACAATGTTGATCCACCTCCTTCTATGATGG
1 AATCGAGCAAAATGACAATATTGATCCACCTCCTTCTATGACAG
* * * * * * *
3660637 AATCAAACAAAATGTCAATATTGATCTACGTCCTTTTGTGACAG
1 AATCGAGCAAAATGACAATATTGATCCACCTCCTTCTATGACAG
3660681 AATCGAGCAAAA
1 AATCGAGCAAAA
3660693 GGGTGTTGTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (44 bp):
AATCGAGCAAAATGACAATATTGATCCACCTCCTTCTATGACAG
Found at i:3661047 original size:99 final size:99
Alignment explanation
Indices: 3660876--3661059 Score: 287
Period size: 99 Copynumber: 1.9 Consensus size: 99
3660866 TTTTGTTTGG
* *
3660876 AGTGAAACAAATTCAAAATTTGTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTGGTTTTA
1 AGTGAAACAAATTCAAAATTTGTGTTTAAAGGGAAACTATCTCAAGCGAGACAAAATTGATTTTA
*
3660941 ACAAAAACAATCTCCAGTGACATCAAGTTTTTTT
66 ACAAAAACAATCTCAAGTGACATCAAGTTTTTTT
* * * **
3660975 AGTGAAACAATTTCAAAATTTGTGTTTAAAGGGAAACTGTCTCAAGCGATATGAAATTGATTTTA
1 AGTGAAACAAATTCAAAATTTGTGTTTAAAGGGAAACTATCTCAAGCGAGACAAAATTGATTTTA
*
3661040 AGAAAAACAATCTCAAGTGA
66 ACAAAAACAATCTCAAGTGA
3661060 GATAAAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 76 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (99 bp):
AGTGAAACAAATTCAAAATTTGTGTTTAAAGGGAAACTATCTCAAGCGAGACAAAATTGATTTTA
ACAAAAACAATCTCAAGTGACATCAAGTTTTTTT
Found at i:3664637 original size:19 final size:18
Alignment explanation
Indices: 3664587--3664634 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3664577 AAATCAGGTA
*
3664587 ATTTTATTAAAATATTTT
1 ATTTTACTAAAATATTTT
3664605 ATTTTACTAAAATATTTT
1 ATTTTACTAAAATATTTT
3664623 ATTTTACTAAAA
1 ATTTTACTAAAA
3664635 ATACCAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTACTAAAATATTTT
Found at i:3665418 original size:29 final size:26
Alignment explanation
Indices: 3665382--3665446 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 26
3665372 ACAATGTAGA
3665382 AAATTAAAAGCT-AGAATTTAAAGGATTG
1 AAATTAAAA-CTGA-AATTTAAAGG-TTG
3665410 AAATATAAATACTGAAATTTAAAGGTTG
1 AAAT-TAAA-ACTGAAATTTAAAGGTTG
3665438 AAATTAAAA
1 AAATTAAAA
3665447 TAACATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 1 0.03
27 4 0.12
28 11 0.32
29 16 0.47
30 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (26 bp):
AAATTAAAACTGAAATTTAAAGGTTG
Found at i:3666281 original size:48 final size:49
Alignment explanation
Indices: 3666208--3666306 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 49
3666198 TAGGGATTTT
3666208 TTATATATAAAATAATATTTAATTATTAAT-A-A-TATATTATTATATA
1 TTATATATAAAATAATATTTAATTATTAATAATATTATATTATTATATA
*
3666254 TTATATAT-ATATAATATTGTAATATTATTAATAATATTATATTATTATATA
1 TTATATATAAAATAATATT-T-A-ATTATTAATAATATTATATTATTATATA
3666305 TT
1 TT
3666307 TAATTATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
45 9 0.20
46 9 0.20
47 1 0.02
48 9 0.20
49 1 0.02
50 1 0.02
51 16 0.35
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (49 bp):
TTATATATAAAATAATATTTAATTATTAATAATATTATATTATTATATA
Found at i:3666289 original size:20 final size:18
Alignment explanation
Indices: 3666218--3666330 Score: 92
Period size: 17 Copynumber: 6.8 Consensus size: 18
3666208 TTATATATAA
3666218 AATAATATTTA-ATTATT
1 AATAATATTTATATTATT
3666235 AAT-A-A--TATATTATT
1 AATAATATTTATATTATT
3666249 -AT-ATA-TTATA-TA-T
1 AATAATATTTATATTATT
3666262 ATATAATATTGTAATATTATT
1 A-ATAATATT-T-ATATTATT
3666283 AATAATA-TTATATTATT
1 AATAATATTTATATTATT
3666300 -AT-ATATTTA-ATTATT
1 AATAATATTTATATTATT
3666315 AATAATATTATATATT
1 AATAATATT-TATATT
3666331 TATATAAATT
Statistics
Matches: 80, Mismatches: 0, Indels: 30
0.73 0.00 0.27
Matches are distributed among these distances:
13 6 0.08
14 9 0.11
15 16 0.20
16 11 0.14
17 17 0.21
18 4 0.05
19 7 0.09
20 8 0.10
21 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (18 bp):
AATAATATTTATATTATT
Found at i:3666344 original size:70 final size:65
Alignment explanation
Indices: 3666208--3666336 Score: 53
Period size: 65 Copynumber: 2.0 Consensus size: 65
3666198 TAGGGATTTT
* *
3666208 TTATATATAAAATAATATT-T-A-ATTATTAATAATA--T-ATTATTATATATTATA-TATATAT
1 TTATATAT-ATATAATATTGTAATATTATTAATAATATTTAATTATTA-ATAATATATTAT-TAT
3666266 AATA
63 -ATA
* * * *
3666270 TTGTA-ATATTATTAATAATATTATATTATT-AT-ATATTTAATTATTAATAATATTATATATTT
1 TTATATATA-TA-TAATATTGTAATATTATTAATAATATTTAATTATTAATAATA-TAT-TA-TT
3666332 ATATA
61 ATATA
3666337 AATTTGTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
60 1 0.02
61 3 0.06
62 10 0.20
63 4 0.08
64 3 0.06
65 12 0.24
66 9 0.18
67 3 0.06
68 5 0.10
69 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.53
Consensus pattern (65 bp):
TTATATATATATAATATTGTAATATTATTAATAATATTTAATTATTAATAATATATTATTATATA
Found at i:3667584 original size:2 final size:2
Alignment explanation
Indices: 3667577--3667625 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3667567 ATAGGGGTAC
3667577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3667619 AT AT AT A
1 AT AT AT A
3667626 AAATCAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3667737 original size:7 final size:7
Alignment explanation
Indices: 3667725--3667761 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
3667715 TAGTTAAGTG
3667725 AAAAAGA
1 AAAAAGA
3667732 AAAAAGA
1 AAAAAGA
3667739 AAAAAGA
1 AAAAAGA
3667746 AAAAAG-
1 AAAAAGA
3667752 AAAAAGA
1 AAAAAGA
3667759 AAA
1 AAA
3667762 GCAAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:3669057 original size:27 final size:27
Alignment explanation
Indices: 3669033--3669092 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3669023 ACGTCGTTTG
*
3669033 TCTTCTCGTTAATTCTGACGCCGTTCT
1 TCTTCTCGCTAATTCTGACGCCGTTCT
* * *
3669060 TCTTCTCGCTAATTCTGAAGCCTTTCA
1 TCTTCTCGCTAATTCTGACGCCGTTCT
3669087 TCTTCT
1 TCTTCT
3669093 TGCCAACACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.13, C:0.30, G:0.12, T:0.45
Consensus pattern (27 bp):
TCTTCTCGCTAATTCTGACGCCGTTCT
Found at i:3669735 original size:86 final size:87
Alignment explanation
Indices: 3669589--3669768 Score: 308
Period size: 86 Copynumber: 2.1 Consensus size: 87
3669579 CCGGAATAGC
* * *
3669589 AAGGGCCCCAAAAAAATTAGATTTATTACTATTTTTACAATAAAAAAATAAATAAAGTATTATGG
1 AAGGGCCCCAAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAACAAAGTATTATGG
3669654 ATCAATGGTAAAATTGAGATTT
66 ATCAATGGTAAAATTGAGATTT
*
3669676 AAGGGCCCC-AAAAAATTAGATTTATTACTATTATTACAATAAAAAAGCAAACAAAGTATTATGG
1 AAGGGCCCCAAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAACAAAGTATTATGG
*
3669740 ATCAGTGGTAAAATTGAGATTT
66 ATCAATGGTAAAATTGAGATTT
3669762 AAGGGCC
1 AAGGGCC
3669769 TCTTTTTAAG
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 79 0.90
87 9 0.10
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (87 bp):
AAGGGCCCCAAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAACAAAGTATTATGG
ATCAATGGTAAAATTGAGATTT
Found at i:3670836 original size:62 final size:62
Alignment explanation
Indices: 3670739--3670882 Score: 180
Period size: 62 Copynumber: 2.3 Consensus size: 62
3670729 GGGCCTAAGA
* * * * * * * *
3670739 GCCTACCCAAAAATGTTCTTAAGCCCACGGGGCCTACCCAAGAAAGATCTCAGGGCTATAGG
1 GCCTACCCAAGAATGATCTCAAGCCCACGAGGCCTACCCAAGAAAAATCACAGGGCCACAGG
* * *
3670801 GCCTACCCAAGAATGATCTCAGGGCCACGAGGCCTACCCAAGAAAAATCACAGGGCCGCAGG
1 GCCTACCCAAGAATGATCTCAAGCCCACGAGGCCTACCCAAGAAAAATCACAGGGCCACAGG
*
3670863 ACCTACCCAAGAATGATCTC
1 GCCTACCCAAGAATGATCTC
3670883 GGCGGCGCAT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.32, C:0.31, G:0.22, T:0.15
Consensus pattern (62 bp):
GCCTACCCAAGAATGATCTCAAGCCCACGAGGCCTACCCAAGAAAAATCACAGGGCCACAGG
Found at i:3670899 original size:31 final size:30
Alignment explanation
Indices: 3670769--3670905 Score: 141
Period size: 31 Copynumber: 4.4 Consensus size: 30
3670759 AAGCCCACGG
*
3670769 GGCCTACCCAAGAAAGATCTCAGGGCTATA
1 GGCCTACCCAAGAAAGATCTCAGGGCCATA
* *
3670799 GGGCCTACCCAAGAATGATCTCAGGGCCACGA
1 -GGCCTACCCAAGAAAGATCTCAGGGCCA-TA
* * **
3670831 GGCCTACCCAAGAAAAATCACAGGGCCGCA
1 GGCCTACCCAAGAAAGATCTCAGGGCCATA
* *
3670861 GGACCTACCCAAGAATGATCTCGGCGGCGCATA
1 GG-CCTACCCAAGAAAGATCTCAG-GGC-CATA
3670894 -GCCTACCCAAGA
1 GGCCTACCCAAGA
3670906 GTTACATTAG
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
30 3 0.03
31 78 0.89
32 5 0.06
33 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.12
Consensus pattern (30 bp):
GGCCTACCCAAGAAAGATCTCAGGGCCATA
Found at i:3673551 original size:13 final size:13
Alignment explanation
Indices: 3673504--3673553 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
3673494 CAACAATCAA
3673504 CGGGTCGGGCAGT
1 CGGGTCGGGCAGT
* *
3673517 CGAGTCGGACCAGGT
1 CGGGTCGG-GCA-GT
*
3673532 TGGGTCGGGCAGT
1 CGGGTCGGGCAGT
3673545 CGGGTCGGG
1 CGGGTCGGG
3673554 TCAAACCGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 17 0.59
14 4 0.14
15 8 0.28
ACGTcount: A:0.10, C:0.22, G:0.52, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGCAGT
Found at i:3683062 original size:2 final size:2
Alignment explanation
Indices: 3683055--3683079 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3683045 CCGGTGACTT
3683055 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3683080 CCTCGCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3683831 original size:12 final size:12
Alignment explanation
Indices: 3683814--3683838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3683804 CATTTAAAAC
3683814 TTTCAACGAAGT
1 TTTCAACGAAGT
3683826 TTTCAACGAAGT
1 TTTCAACGAAGT
3683838 T
1 T
3683839 AAAGATCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTCAACGAAGT
Found at i:3684500 original size:2 final size:2
Alignment explanation
Indices: 3684493--3684525 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3684483 AATATTACTT
3684493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3684526 CATTATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3684888 original size:19 final size:19
Alignment explanation
Indices: 3684845--3684888 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3684835 ATTGGAACAC
3684845 CTAAAAACATGTAATTTTA
1 CTAAAAACATGTAATTTTA
* * *
3684864 AT-AAAACATTTTATTTTA
1 CTAAAAACATGTAATTTTA
3684882 CTAAAAA
1 CTAAAAA
3684889 TATCATATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (19 bp):
CTAAAAACATGTAATTTTA
Found at i:3685660 original size:139 final size:139
Alignment explanation
Indices: 3685496--3685845 Score: 496
Period size: 139 Copynumber: 2.5 Consensus size: 139
3685486 TCATAGGTTA
* * *
3685496 AAGGACTA-AGTTTGAAATT-GAACCTAAAATGGAGGCTCTAACATTAATCCTAATTAATTTTAA
1 AAGGACTAGA-TTTGAAATTAG-ACCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAA
* *
3685559 TCAATTAT-TCGATT-AGAATAATTAAAATGGAACCTCGAGCAAAAAC-ATGGACCAAATTAAG-
64 TCAATTATGT-GATTCA-AATAATTAAAATGAAACCTCGAGCAAAAACGA-GAACCAAATTAAGA
* *
3685620 AATTCGCCTAAGTTT
126 AATT-ACCTAAATTT
3685635 AAGGACTAGATTTGAAATTAGACCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATC
1 AAGGACTAGATTTGAAATTAGACCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATC
* * *
3685700 AAATATGTGATTCAAATAATTAAAATGAAACCTCGAGCAAAAGCGAGAATCAAATTAAGAAATTA
66 AATTATGTGATTCAAATAATTAAAATGAAACCTCGAGCAAAAACGAGAACCAAATTAAGAAATTA
3685765 CCTAAATTT
131 CCTAAATTT
* *
3685774 AAGGACTAGCTTTGAAATTAGGCCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATC
1 AAGGACTAGATTTGAAATTAGACCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATC
3685839 AATTATG
66 AATTATG
3685846 CAATTATCCA
Statistics
Matches: 192, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
139 183 0.95
140 9 0.05
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (139 bp):
AAGGACTAGATTTGAAATTAGACCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATC
AATTATGTGATTCAAATAATTAAAATGAAACCTCGAGCAAAAACGAGAACCAAATTAAGAAATTA
CCTAAATTT
Done.