Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 120 of 279
Found at i:38046485 original size:22 final size:23
Alignment explanation
Indices: 38046451--38046493 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
38046441 AAAAAATTAT
38046451 AAATATTATAAA-TTTAAAAACA
1 AAATATTATAAATTTTAAAAACA
38046473 AAATA-TATAAAATTTTAAAAA
1 AAATATTAT-AAATTTTAAAAA
38046494 ATCAATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 8 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATTATAAATTTTAAAAACA
Found at i:38046976 original size:20 final size:20
Alignment explanation
Indices: 38046940--38046978 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38046930 TTTTTAGATT
*
38046940 TTTTAAAAATTATATTAAAA
1 TTTTAAAAATTAGATTAAAA
38046960 TTTT-AAAATTAGGATTAAA
1 TTTTAAAAATTA-GATTAAA
38046979 TTATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTAAAAATTAGATTAAAA
Found at i:38050098 original size:20 final size:20
Alignment explanation
Indices: 38050075--38050160 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 20
38050065 ATTAAAATAT
38050075 AAAATATTTTATAATTTTT-
1 AAAATATTTTATAATTTTTA
* * *
38050094 AAAA-ATTATAAAATATTTAA
1 AAAATATTTTATAAT-TTTTA
38050114 AAAATATATTTAATAATTTTTA
1 AAAATAT-TTT-ATAATTTTTA
* * *
38050136 TAATTA-TTTAGAATTTTTA
1 AAAATATTTTATAATTTTTA
38050155 ATAAAT
1 A-AAAT
38050161 TTAGTATAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
18 8 0.16
19 16 0.32
20 10 0.20
21 2 0.04
22 10 0.20
23 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
AAAATATTTTATAATTTTTA
Found at i:38050112 original size:27 final size:27
Alignment explanation
Indices: 38050055--38050116 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
38050045 AAATTTAAAG
38050055 TTTAAAATTTATTAAAATATAAAATAT
1 TTTAAAATTTATTAAAATATAAAATAT
*
38050082 TTTATAATTT-TTAAAAATTATAAAATAT
1 TTTAAAATTTATT-AAAA-TATAAAATAT
*
38050110 TTAAAAA
1 TTTAAAA
38050117 ATATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 2 0.07
27 13 0.43
28 15 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTAAAATTTATTAAAATATAAAATAT
Found at i:38050114 original size:18 final size:18
Alignment explanation
Indices: 38050055--38050121 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
38050045 AAATTTAAAG
*
38050055 TTTAAAATTTATTAAAATA
1 TTTAAAAATTA-TAAAATA
* * *
38050074 --TAAAATATTTTATAATT
1 TTTAAAA-ATTATAAAATA
38050091 TTTAAAAATTATAAAATA
1 TTTAAAAATTATAAAATA
*
38050109 TTTAAAAAATATA
1 TTTAAAAATTATA
38050122 TTTAATAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
17 10 0.27
18 22 0.59
19 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAAAATTATAAAATA
Found at i:38058894 original size:24 final size:24
Alignment explanation
Indices: 38058860--38058909 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
38058850 TACATAGTGC
*
38058860 ATGGAATGATACAACACGAATTAG
1 ATGGAACGATACAACACGAATTAG
*
38058884 ATGGAACGATACAATACGAATTAG
1 ATGGAACGATACAACACGAATTAG
38058908 AT
1 AT
38058910 ATAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (24 bp):
ATGGAACGATACAACACGAATTAG
Found at i:38059783 original size:219 final size:219
Alignment explanation
Indices: 38059538--38059975 Score: 815
Period size: 219 Copynumber: 2.0 Consensus size: 219
38059528 GATAATATAT
*
38059538 GTGAAATAGTTTAAAATAAAAGGTGTCTAAAAATACATATGCATAATAATTAAAACAAATAGTGT
1 GTGAAATAGTTTAAAATAAAAGGTGTCTAAAAATACATATGCATAATAATTAAAACAAATAATGT
38059603 ATATGAAAATTAAAATGAATAATAGTTTAAAATATGTAAAACTTAGAATACATGATAATAACGCA
66 ATATGAAAATTAAAATGAATAATAGTTTAAAATATGTAAAACTTAGAATACATGATAATAACGCA
38059668 ATTTAAAATAAATAATACAAGAAAAACAAGCTTAAAATAAATAAATAATAAAATAATTTCCTAAA
131 ATTTAAAATAAATAATACAAGAAAAACAAGCTTAAAATAAATAAATAATAAAATAATTTCCTAAA
38059733 AAAATAAAATAATAAATAAATTAA
196 AAAATAAAATAATAAATAAATTAA
*
38059757 GTGAAATAGTTTTAAAA-AAAAGGTGTCTAAAAATATATATGCATAATAATTAAAACAAATAATG
1 GTGAAATAG-TTTAAAATAAAAGGTGTCTAAAAATACATATGCATAATAATTAAAACAAATAATG
*
38059821 TATATGAAAATTAAAATGAATAATAGTTTAAAATATGTAAAACTTAGTATACATGATAATAACGC
65 TATATGAAAATTAAAATGAATAATAGTTTAAAATATGTAAAACTTAGAATACATGATAATAACGC
*
38059886 AATTTAAAATAAATAATACAAGAAAAACAGGCTTAAAATAAATAAATAATAAAATAATTTCCTAA
130 AATTTAAAATAAATAATACAAGAAAAACAAGCTTAAAATAAATAAATAATAAAATAATTTCCTAA
*
38059951 AAAACTAAAATAATAAATAAATTAA
195 AAAAATAAAATAATAAATAAATTAA
38059976 ATAGATTAGG
Statistics
Matches: 213, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
219 206 0.97
220 7 0.03
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (219 bp):
GTGAAATAGTTTAAAATAAAAGGTGTCTAAAAATACATATGCATAATAATTAAAACAAATAATGT
ATATGAAAATTAAAATGAATAATAGTTTAAAATATGTAAAACTTAGAATACATGATAATAACGCA
ATTTAAAATAAATAATACAAGAAAAACAAGCTTAAAATAAATAAATAATAAAATAATTTCCTAAA
AAAATAAAATAATAAATAAATTAA
Found at i:38064047 original size:18 final size:18
Alignment explanation
Indices: 38064014--38064068 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 18
38064004 CGTGATCCGA
*
38064014 TTGAAAA-ACGAGAATTT
1 TTGAAAACACGAAAATTT
*
38064031 TTTAAAACACGAAAA-TT
1 TTGAAAACACGAAAATTT
38064048 TTGAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
38064066 TTG
1 TTG
38064069 GGATCCGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:38064613 original size:3 final size:3
Alignment explanation
Indices: 38064599--38064824 Score: 69
Period size: 3 Copynumber: 74.3 Consensus size: 3
38064589 ATGTATACCA
* * *
38064599 AAT AAT ACAT AAT AAT ACT AA- AAT AA- AAT AAT AAGT AAC AAT AGT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
* * * *
38064644 GAA- AAT AAT AAG CAT AAT AAT AA- ATAT AAT GAT ATAT AAA AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT
* * * *
38064690 ACT -AT ATAT AA- AAGT ATAT ATAT ACGT -AC AAT AA- AAT ATAT ACT
1 AAT AAT A-AT AAT AA-T A-AT A-AT A-AT AAT AAT AAT AAT A-AT AAT
* * * ** *
38064734 AAT ATT AAT AAT AA- ATAT AAC AAG GGT AAA AAT AAGT -AT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
* * *
38064779 -AT ATT AGAT AGT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38064824 A
1 A
38064825 TGTGAAGGTT
Statistics
Matches: 160, Mismatches: 40, Indels: 46
0.65 0.16 0.19
Matches are distributed among these distances:
2 16 0.10
3 114 0.71
4 29 0.18
5 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38064641 original size:26 final size:27
Alignment explanation
Indices: 38064598--38064651 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
38064588 TATGTATACC
*
38064598 AAATAATACATAATAATACT-AAAATA
1 AAATAATACATAACAATACTGAAAATA
*
38064624 AAATAATA-AGTAACAATAGTGAAAATA
1 AAATAATACA-TAACAATACTGAAAATA
38064651 A
1 A
38064652 TAAGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 16 0.67
27 7 0.29
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (27 bp):
AAATAATACATAACAATACTGAAAATA
Found at i:38065150 original size:29 final size:30
Alignment explanation
Indices: 38065118--38065174 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
38065108 ATTAGCAGCG
* *
38065118 TGAAAATGATAA-AATAACAAATATTTAAA
1 TGAAAATAATAAGAACAACAAATATTTAAA
* *
38065147 TGAAGATAATAAGAACAGCAAATATTTA
1 TGAAAATAATAAGAACAACAAATATTTA
38065175 GAAAGTAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (30 bp):
TGAAAATAATAAGAACAACAAATATTTAAA
Found at i:38066556 original size:21 final size:21
Alignment explanation
Indices: 38066531--38066584 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
38066521 AGGATAGGAT
**
38066531 CTGCAACTTCAATGTGCTCCA
1 CTGCAACTTCAATCAGCTCCA
*
38066552 CTGCAACTTCGATCAGCTCCA
1 CTGCAACTTCAATCAGCTCCA
* *
38066573 TTGTAACTTCAA
1 CTGCAACTTCAA
38066585 GGCTCTGCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (21 bp):
CTGCAACTTCAATCAGCTCCA
Found at i:38066853 original size:13 final size:13
Alignment explanation
Indices: 38066825--38066859 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
38066815 TGAGTTGATT
38066825 TTTGAAAACAGAA
1 TTTGAAAACAGAA
*
38066838 TTTGCAAAACAGAT
1 TTTG-AAAACAGAA
38066852 TTTGAAAA
1 TTTGAAAA
38066860 TACCTCGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAGAA
Found at i:38066905 original size:88 final size:87
Alignment explanation
Indices: 38066688--38066920 Score: 260
Period size: 86 Copynumber: 2.7 Consensus size: 87
38066678 CAATCTTTAT
* ** * *
38066688 CCTCGGCATGTGACCCGGGGCTCAACTCATTTCTCGCAATATGAATTGACTCTTT-AAAACTAGA
1 CCTCGGCATGT-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACTAGA
38066752 CATTAAAAACAGAAATTGAAAATA
64 CATTAAAAACAGAAATTGAAAATA
* * *
38066776 CCTCAGC--GTGCCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAC-AGA-
1 CCTCGGCATGTACCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACTAGAC
* **
38066837 ATTTGCAAAACAGATTTTGAAAATA
65 A-TT-AAAAACAGAAATTGAAAATA
* *
38066862 CCTCGGCATGTAACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTTATTTTTGAAAA
1 CCTCGGCATGT-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
38066921 GCATAATTGA
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
84 1 0.01
85 12 0.10
86 58 0.48
88 48 0.39
89 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (87 bp):
CCTCGGCATGTACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACTAGACA
TTAAAAACAGAAATTGAAAATA
Found at i:38067035 original size:73 final size:72
Alignment explanation
Indices: 38066878--38067293 Score: 591
Period size: 73 Copynumber: 5.7 Consensus size: 72
38066868 CATGTAACCC
* * * *
38066878 GAGGCTCAACTCACCTCTCGTAATATGAGTTTATTTTTGAAAAGCA-TAATTGAAAATACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CAGAAATTGAAATTACCTCAG
38066942 CGTGCCCT
65 CGTGCCCT
* *
38066950 GAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGTAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCTCAG
*
38067015 CGTGTCCT
65 CGTGCCCT
* * * * *
38067023 GAGGCCCAACTCACCTCTCACAATGTAAGTTGATTTTTTTGAAAACCAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAA-CAGAAATTGAAATTACCTC
38067088 AGCGTGCCCT
63 AGCGTGCCCT
* * *
38067098 GAGGCTCAACTCACCTCTCGCAATAGGAGTTGGTTTTTGACGAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCTCAG
38067163 CGTGCCCT
65 CGTGCCCT
* * *
38067171 GAGGCTCAACTCACCTCTCGCAATAGGAGTTGGTTTTTGACGAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCTCAG
38067236 CGTGCCCT
65 CGTGCCCT
*
38067244 GAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTGAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAAT
38067294 AAAAACTAGG
Statistics
Matches: 311, Mismatches: 27, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
72 48 0.15
73 198 0.64
74 5 0.02
75 60 0.19
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (72 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGC
GTGCCCT
Found at i:38067111 original size:148 final size:145
Alignment explanation
Indices: 38066878--38067293 Score: 570
Period size: 148 Copynumber: 2.8 Consensus size: 145
38066868 CATGTAACCC
* ** ** *
38066878 GAGGCTCAACTCACCTCTCGTAATATG-AGTTTATTTTTGAAAAGCA-TAATTGAAAATACCTCA
1 GAGGCCCAACTCACCTCTCACAATA-GAAGTTGGTTTTTGAAAA-CAGAAATTGAAAATACCTCA
* *
38066941 GCGTGCCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGTAA
64 GCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAA
*
38067006 TTACCTCAGCGTGTCCT
129 TTACCTCAGCGTGCCCT
*
38067023 GAGGCCCAACTCACCTCTCACAAT-GTAAGTTGATTTTTTTGAAAACCAGAAATTGAAAATACCT
1 GAGGCCCAACTCACCTCTCACAATAG-AAGTTG--GTTTTTGAAAA-CAGAAATTGAAAATACCT
* * *
38067087 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTGGTTTTTGACGAACAGAAATTGA
62 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGA
38067152 AATTACCTCAGCGTGCCCT
127 AATTACCTCAGCGTGCCCT
* * * * *
38067171 GAGGCTCAACTCACCTCTCGCAATAGGAGTTGGTTTTTGACGAACAGAAATTGAAATTACCTCAG
1 GAGGCCCAACTCACCTCTCACAATAGAAGTTGGTTTTTGA-AAACAGAAATTGAAAATACCTCAG
*
38067236 CGTGCCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTGA-AAACAGAAAT
65 CGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAAT
38067294 AAAAACTAGG
Statistics
Matches: 241, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
143 1 0.00
145 34 0.14
146 72 0.30
147 14 0.06
148 119 0.49
149 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (145 bp):
GAGGCCCAACTCACCTCTCACAATAGAAGTTGGTTTTTGAAAACAGAAATTGAAAATACCTCAGC
GTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATT
ACCTCAGCGTGCCCT
Found at i:38067277 original size:221 final size:217
Alignment explanation
Indices: 38066838--38067293 Score: 621
Period size: 221 Copynumber: 2.1 Consensus size: 217
38066828 GAAAACAGAA
** * * *
38066838 TTTGCAAAACAGATTTTGAAAATACCTCGGCATGTAACCC-GAGGCTCAACTCACCTCTCGTAAT
1 TTTG-AAAACAGAAATTGAAAATACCTCAGC--GT-GCCCTGAGGCTCAACTCACCTCTCGCAAT
* * *
38066902 ATGAGTTTATTTTTGAAAAGCATAATTGAAAATACCTCAGCGTGCCCTGAGGCTTAACTCACCTC
62 AGGAGTTGATTTTTGAAAAGCATAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTC
* * *
38066967 TCGCAATATGAGTTGATTTTTGACAAACAGAAATTGTAATTACCTCAGCGTGTCCTGAGGCCCAA
127 TCGCAATAGGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCCCAA
* *
38067032 CTCACCTCTCACAATGTAAGTTGATTTT
192 CTCACCTATCACAATATAAGTTGA--TT
38067060 TTTGAAAACCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGG
1 TTTGAAAA-CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGG
* *
38067125 AGTTGGTTTTTGACGAACAG-A-AATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTC
65 AGTTGATTTTTGA--AA-AGCATAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTC
* * *
38067188 TCGCAATAGGAGTTGGTTTTTGACGAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAA
127 TCGCAATAGGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCCCAA
* *
38067253 CTCACCTATCGCAATATGAGTTGATT
192 CTCACCTATCACAATATAAGTTGATT
38067279 TTTGAAAACAGAAAT
1 TTTGAAAACAGAAAT
38067294 AAAAACTAGG
Statistics
Matches: 209, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
218 7 0.03
219 13 0.06
220 38 0.18
221 123 0.59
222 26 0.12
223 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (217 bp):
TTTGAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGA
GTTGATTTTTGAAAAGCATAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGC
AATAGGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCCCAACTCA
CCTATCACAATATAAGTTGATT
Found at i:38078702 original size:18 final size:17
Alignment explanation
Indices: 38078669--38078723 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
38078659 CGTGATCCGA
*
38078669 TTGAAAAACGAGAATTT
1 TTGAAAAACGAAAATTT
*
38078686 TTTAAAATACGAAAA-TT
1 TTGAAAA-ACGAAAATTT
38078703 TTGAAAACACGAAAATTT
1 TTGAAAA-ACGAAAATTT
38078721 TTG
1 TTG
38078724 GGATCCGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (17 bp):
TTGAAAAACGAAAATTT
Found at i:38079295 original size:26 final size:27
Alignment explanation
Indices: 38079252--38079305 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
38079242 TATGTATACC
*
38079252 AAATAATACATAATAATACT-AAAATA
1 AAATAATACATAACAATACTGAAAATA
*
38079278 AAATAATA-AGTAACAATAGTGAAAATA
1 AAATAATACA-TAACAATACTGAAAATA
38079305 A
1 A
38079306 TAAGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 16 0.67
27 7 0.29
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (27 bp):
AAATAATACATAACAATACTGAAAATA
Found at i:38079340 original size:18 final size:17
Alignment explanation
Indices: 38079314--38079367 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
38079304 AATAAGCATA
38079314 ATAATAAATATAATGATAT
1 ATAA-AAATATAAT-ATAT
*
38079333 ATAAAAATAATACTATAT
1 ATAAAAAT-ATAATATAT
*
38079351 ATAAAAGTAT-ATATAT
1 ATAAAAATATAATATAT
38079367 A
1 A
38079368 CGTACAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 15 0.48
19 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAAAATATAATATAT
Found at i:38079569 original size:26 final size:26
Alignment explanation
Indices: 38079540--38079607 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
38079530 ATAAAGAGAT
*
38079540 ATAAATAAATGGTAAAACAAAGTAA-A-
1 ATAAATAAAT-GTAAAA-AAAGGAATAG
**
38079566 ATAAATGTATGTAAAAAAAGGAATAG
1 ATAAATAAATGTAAAAAAAGGAATAG
*
38079592 ATAAATAAATATAAAA
1 ATAAATAAATGTAAAA
38079608 GAAATATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 6 0.18
25 7 0.21
26 21 0.62
ACGTcount: A:0.65, C:0.01, G:0.12, T:0.22
Consensus pattern (26 bp):
ATAAATAAATGTAAAAAAAGGAATAG
Found at i:38079803 original size:29 final size:30
Alignment explanation
Indices: 38079771--38079827 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38079761 ATTAGCAGCG
* *
38079771 TGAAAATGATAA-AATAACAAATATTTAAA
1 TGAAAATAATAAGAACAACAAATATTTAAA
*
38079800 TGAAGATAATAAGAACAACAAATATTTA
1 TGAAAATAATAAGAACAACAAATATTTA
38079828 GAAAGTAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (30 bp):
TGAAAATAATAAGAACAACAAATATTTAAA
Found at i:38082203 original size:29 final size:30
Alignment explanation
Indices: 38082171--38082227 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38082161 ATTAGCAGCG
* *
38082171 TGAAAATGATAA-AATAACAAATATTTAAA
1 TGAAAATAATAAGAACAACAAATATTTAAA
*
38082200 TGAAGATAATAAGAACAACAAATATTTA
1 TGAAAATAATAAGAACAACAAATATTTA
38082228 GAAAGTAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (30 bp):
TGAAAATAATAAGAACAACAAATATTTAAA
Found at i:38088813 original size:14 final size:14
Alignment explanation
Indices: 38088794--38088824 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
38088784 TTTCACACAC
38088794 AAAATGAAAATCGG
1 AAAATGAAAATCGG
38088808 AAAATGAAAATCGG
1 AAAATGAAAATCGG
38088822 AAA
1 AAA
38088825 TGTTATGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.19, T:0.13
Consensus pattern (14 bp):
AAAATGAAAATCGG
Found at i:38101649 original size:27 final size:27
Alignment explanation
Indices: 38101611--38101664 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
38101601 AAAGAAGACC
38101611 ACATGGGGACTTTGCAACCTCAATGTA
1 ACATGGGGACTTTGCAACCTCAATGTA
38101638 ACATGGGGACTTTGCAACCTCAATGTA
1 ACATGGGGACTTTGCAACCTCAATGTA
38101665 TGCCAAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (27 bp):
ACATGGGGACTTTGCAACCTCAATGTA
Found at i:38105568 original size:18 final size:17
Alignment explanation
Indices: 38105529--38105569 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
38105519 AATTTTCATG
38105529 CAAATATATAAAAACAA
1 CAAATATATAAAAACAA
* *
38105546 TAAATATCATAAAAATAA
1 CAAATAT-ATAAAAACAA
38105564 CAAATA
1 CAAATA
38105570 ATTTATGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (17 bp):
CAAATATATAAAAACAA
Found at i:38105953 original size:14 final size:14
Alignment explanation
Indices: 38105934--38105975 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38105924 ATTTTAAAAT
38105934 TATACATAATATAA
1 TATACATAATATAA
*
38105948 TATAC--AATAAAA
1 TATACATAATATAA
*
38105960 TATAAATAATATAA
1 TATACATAATATAA
38105974 TA
1 TA
38105976 GATAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TATACATAATATAA
Found at i:38105974 original size:31 final size:30
Alignment explanation
Indices: 38105939--38106067 Score: 77
Period size: 31 Copynumber: 4.1 Consensus size: 30
38105929 AAAATTATAC
38105939 ATAATATAATATACAATAAAATATAAATAA
1 ATAATATAATATACAATAAAATATAAATAA
* *
38105969 TATAATA-GATAATACAAAAAAATGATAAAATAA
1 -ATAATATAAT-ATACAATAAAAT-AT-AAATAA
* * * *
38106002 ATATTTTTACATATA-AATAAAGTTTAAAGTAAA
1 ATA-ATATA-ATATACAATAAAATATAAA-T-AA
* *
38106035 ATAA-ATAATATACAA-AATATTTAAAATAA
1 ATAATATAATATACAATAAAATAT-AAATAA
38106064 ATAA
1 ATAA
38106068 ATTATAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
29 6 0.08
30 13 0.17
31 27 0.36
32 7 0.09
33 18 0.24
34 3 0.04
35 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (30 bp):
ATAATATAATATACAATAAAATATAAATAA
Found at i:38105982 original size:26 final size:27
Alignment explanation
Indices: 38105928--38105982 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
38105918 TTACAAATTT
* *
38105928 TAAAATTATACATAATATAATATACAA
1 TAAAATTATAAATAATATAATAGACAA
*
38105955 TAAAA-TATAAATAATATAATAGATAA
1 TAAAATTATAAATAATATAATAGACAA
38105981 TA
1 TA
38105983 CAAAAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAATTATAAATAATATAATAGACAA
Found at i:38108540 original size:13 final size:13
Alignment explanation
Indices: 38108522--38108548 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38108512 GCCATCAACA
38108522 CCGTGATTCCAGG
1 CCGTGATTCCAGG
38108535 CCGTGATTCCAGG
1 CCGTGATTCCAGG
38108548 C
1 C
38108549 TTCGAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.22
Consensus pattern (13 bp):
CCGTGATTCCAGG
Found at i:38109483 original size:13 final size:13
Alignment explanation
Indices: 38109465--38109491 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38109455 GCCATCAACA
38109465 CCGTGATTCCAGG
1 CCGTGATTCCAGG
38109478 CCGTGATTCCAGG
1 CCGTGATTCCAGG
38109491 C
1 C
38109492 TTCGAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.22
Consensus pattern (13 bp):
CCGTGATTCCAGG
Found at i:38113197 original size:19 final size:19
Alignment explanation
Indices: 38113173--38113270 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
38113163 AATCTTTAAG
38113173 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38113192 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38113211 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38113228 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38113247 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
38113268 GAT
1 GAT
38113271 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38113202 original size:36 final size:35
Alignment explanation
Indices: 38113162--38113270 Score: 114
Period size: 36 Copynumber: 2.9 Consensus size: 35
38113152 TATGGAAATA
38113162 CAATCTTTAAGGATATGCAATCTTAGATATGATATG
1 CAATCTTTAA-GATATGCAATCTTAGATATGATATG
38113198 CAATC-TT-AGATATGATACAATCTTAGATATGATATG
1 CAATCTTTAAGATATG---CAATCTTAGATATGATATG
*
38113234 CAATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 CAATCTT---TAAGATATGCAATCTT--AGATATGAT
38113271 CTTGTAATCT
Statistics
Matches: 62, Mismatches: 1, Indels: 16
0.78 0.01 0.20
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 29 0.47
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (35 bp):
CAATCTTTAAGATATGCAATCTTAGATATGATATG
Found at i:38120993 original size:85 final size:85
Alignment explanation
Indices: 38120850--38121015 Score: 305
Period size: 85 Copynumber: 2.0 Consensus size: 85
38120840 AAATAGTGAG
38120850 TTACATGGCATGGATACACGCTTGTATCCTTAGCCTGTTTGACTCTAAAGCTAAAACAATGAGTT
1 TTACATGGCATGGATACACGCTTGTATCCTTAGCCTGTTTGACTCTAAAGCTAAAACAATGAGTT
38120915 ACACAGCCTAGACACATGCC
66 ACACAGCCTAGACACATGCC
* *
38120935 TTACATGGCATGGATATACGCTTGTGTCCTTAGCCTGTTTGACTCTAAAGCTAAAACAATGAGTT
1 TTACATGGCATGGATACACGCTTGTATCCTTAGCCTGTTTGACTCTAAAGCTAAAACAATGAGTT
*
38121000 ACACGGCCTAGACACA
66 ACACAGCCTAGACACA
38121016 CGCCCGTGTC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (85 bp):
TTACATGGCATGGATACACGCTTGTATCCTTAGCCTGTTTGACTCTAAAGCTAAAACAATGAGTT
ACACAGCCTAGACACATGCC
Found at i:38121544 original size:32 final size:27
Alignment explanation
Indices: 38121477--38121531 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
38121467 AATCCAACTC
*
38121477 AAACAATAAATTAACCCGTAAAATCTT
1 AAACAATGAATTAACCCGTAAAATCTT
38121504 AAACAATGAATTAACCCGTAAAATCTT
1 AAACAATGAATTAACCCGTAAAATCTT
38121531 A
1 A
38121532 CCTTAACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.25
Consensus pattern (27 bp):
AAACAATGAATTAACCCGTAAAATCTT
Found at i:38124354 original size:46 final size:46
Alignment explanation
Indices: 38124302--38124575 Score: 451
Period size: 46 Copynumber: 6.0 Consensus size: 46
38124292 AGTGTGCTCT
38124302 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
38124348 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
38124394 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
38124440 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
38124486 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
38124532 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
38124576 TCATGTCAAA
Statistics
Matches: 218, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 1 0.00
46 217 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:38135543 original size:47 final size:47
Alignment explanation
Indices: 38135474--38135567 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
38135464 GGTAAGATTC
38135474 AGTTTGAGTGAATTGATAAAAAGTAGTTGTTTACAGGGGAAGAAAAA
1 AGTTTGAGTGAATTGATAAAAAGTAGTTGTTTACAGGGGAAGAAAAA
38135521 AGTTTGAGTGAATTGATAAAAAGTAGTTGTTTACAGGGGAAGAAAAA
1 AGTTTGAGTGAATTGATAAAAAGTAGTTGTTTACAGGGGAAGAAAAA
38135568 GGAACTTACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.43, C:0.02, G:0.28, T:0.28
Consensus pattern (47 bp):
AGTTTGAGTGAATTGATAAAAAGTAGTTGTTTACAGGGGAAGAAAAA
Found at i:38135964 original size:17 final size:18
Alignment explanation
Indices: 38135934--38135979 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
38135924 ATTTAAATTA
38135934 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
38135952 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
38135968 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
38135980 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:38136303 original size:27 final size:25
Alignment explanation
Indices: 38136249--38136303 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
38136239 CAGATGGCCC
* **
38136249 AAAGTAAAAAAATCTAAATATTTTT
1 AAAGTAAAAAAATCTAAATAATCCT
38136274 AAAGTAAAAAAATCTAGATATAATCCT
1 AAAGTAAAAAAATCTA-A-ATAATCCT
38136301 AAA
1 AAA
38136304 AAAAGGCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 1 0.04
27 8 0.32
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.29
Consensus pattern (25 bp):
AAAGTAAAAAAATCTAAATAATCCT
Found at i:38136938 original size:7 final size:7
Alignment explanation
Indices: 38136922--38136953 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38136912 GTCATCAAGT
38136922 CAACAGC
1 CAACAGC
*
38136929 CAATAGC
1 CAACAGC
38136936 CAACAGC
1 CAACAGC
38136943 CAACAGC
1 CAACAGC
38136950 CAAC
1 CAAC
38136954 GCCGACACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.44, C:0.41, G:0.12, T:0.03
Consensus pattern (7 bp):
CAACAGC
Found at i:38147860 original size:22 final size:22
Alignment explanation
Indices: 38147832--38147876 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
38147822 AGGGGGAGTG
38147832 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
38147854 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
38147876 T
1 T
38147877 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:38148143 original size:25 final size:25
Alignment explanation
Indices: 38148115--38148200 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 25
38148105 CTTGCTGAAG
38148115 TAAAATGGAAAAAACCTGATTGATA
1 TAAAATGGAAAAAACCTGATTGATA
* *
38148140 TAAAATGGAAAAAACTTCTGTTTTGAGA
1 TAAAATGGAAAAAAC--CTG-ATTGATA
* * *
38148168 CATACATGGAAAAGACCTGATTGATA
1 TA-AAATGGAAAAAACCTGATTGATA
38148194 TAAAATG
1 TAAAATG
38148201 AGCCTTTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
25 19 0.40
26 6 0.12
27 6 0.12
28 6 0.12
29 11 0.23
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (25 bp):
TAAAATGGAAAAAACCTGATTGATA
Found at i:38164296 original size:17 final size:17
Alignment explanation
Indices: 38164263--38164296 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38164253 ATCAATTTTA
**
38164263 AAAATAAAAATTTTATC
1 AAAATAAAAATAATATC
38164280 AAAATAAAAATAATATC
1 AAAATAAAAATAATATC
38164297 TACTTATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAAAATAATATC
Found at i:38168912 original size:68 final size:69
Alignment explanation
Indices: 38168829--38168962 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 69
38168819 TAAAGATCGG
*
38168829 TGGCGACTCTC-TTTTTTCGTTTTCAAAATCAAGTCGATTCCCGTTTTTGAAAAATGATTTCGAC
1 TGGCGACTCTCTTTTTTTCGTTTTCAAAATCAAGTCGATTCCCGTTTTCGAAAAATGATTTCGAC
38168893 AGCT
66 AGCT
* *
38168897 TGGCGACTC-CATTTTTTTCGTTTTCAAAATCAAGTCGATTTCCGTTTTCGAAAAATGGTTTCGA
1 TGGCGACTCTC-TTTTTTTCGTTTTCAAAATCAAGTCGATTCCCGTTTTCGAAAAATGATTTCGA
38168961 CA
65 CA
38168963 AACTCGATTA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
67 1 0.02
68 9 0.15
69 51 0.84
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (69 bp):
TGGCGACTCTCTTTTTTTCGTTTTCAAAATCAAGTCGATTCCCGTTTTCGAAAAATGATTTCGAC
AGCT
Found at i:38173049 original size:15 final size:14
Alignment explanation
Indices: 38173029--38173070 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
38173019 GTACATAAAA
*
38173029 ATATAAATATTTTAT
1 ATATAAATA-ATTAT
38173044 ATATAAA-AATTAT
1 ATATAAATAATTAT
38173057 ATATAAATTAATTA
1 ATATAAA-TAATTA
38173071 ATTGTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAAATAATTAT
Found at i:38181030 original size:22 final size:22
Alignment explanation
Indices: 38181003--38181047 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38180993 AACTTTCAAG
38181003 CATGTATATTTCATTTTATGAC
1 CATGTATATTTCATTTTATGAC
38181025 CATGTATATTTCATTTTATGAC
1 CATGTATATTTCATTTTATGAC
38181047 C
1 C
38181048 TAACATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.49
Consensus pattern (22 bp):
CATGTATATTTCATTTTATGAC
Found at i:38181055 original size:22 final size:22
Alignment explanation
Indices: 38181008--38181057 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
38180998 TCAAGCATGT
**
38181008 ATATTTCATTTTATGACCATGT
1 ATATTTCATTTTATGACCATAC
38181030 ATATTTCATTTTATGACC-TAAC
1 ATATTTCATTTTATGACCAT-AC
38181052 ATATTT
1 ATATTT
38181058 AAACTATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (22 bp):
ATATTTCATTTTATGACCATAC
Found at i:38181646 original size:18 final size:18
Alignment explanation
Indices: 38181594--38181646 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
38181584 CAGTTACTCT
* *
38181594 ATAACAGTCAGTTATACA
1 ATAACAGTCAATTATTCA
*
38181612 ATAACAATC-ATTCATTCA
1 ATAACAGTCAATT-ATTCA
*
38181630 GTAACAGTCAATTATTC
1 ATAACAGTCAATTATTC
38181647 CGTAGCAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 23 0.82
19 3 0.11
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.32
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:38184401 original size:15 final size:15
Alignment explanation
Indices: 38184381--38184410 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38184371 AACCGTGGCC
*
38184381 TTCTTTCTTTCCTTT
1 TTCTTTATTTCCTTT
38184396 TTCTTTATTTCCTTT
1 TTCTTTATTTCCTTT
38184411 CTTAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTTATTTCCTTT
Found at i:38184521 original size:15 final size:15
Alignment explanation
Indices: 38184501--38184555 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
38184491 TTATTGATTA
38184501 TATTATATTTTATAT
1 TATTATATTTTATAT
*
38184516 TATTATA-TTAATA-
1 TATTATATTTTATAT
* *
38184529 TAGTATACTTTA-AT
1 TATTATATTTTATAT
38184543 TATTATTATTTTA
1 TATTA-TATTTTA
38184556 CTTATATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 7 0.22
14 12 0.38
15 13 0.41
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTATATTTTATAT
Found at i:38184535 original size:21 final size:21
Alignment explanation
Indices: 38184492--38184535 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
38184482 ACTTGTCTTT
**
38184492 TATTGATTATATTATATTTTA
1 TATTGATTATATTATATAGTA
38184513 TATT-ATTATATTAATATAGTA
1 TATTGATTATATT-ATATAGTA
38184534 TA
1 TA
38184536 CTTTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTGATTATATTATATAGTA
Found at i:38185199 original size:3 final size:3
Alignment explanation
Indices: 38185193--38185277 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
38185183 AGTATGTAGG
* * ** *
38185193 TAA TAA TAA -AA AAA TAA TAA TAG TAA TAA TAA -AA TAA TGC TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
38185239 TAA TCA TAA -ATA TAA TAG TAA TGA TAA AAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
38185278 CAACAAAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 5 0.08
3 55 0.90
4 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:38185242 original size:23 final size:23
Alignment explanation
Indices: 38185193--38185280 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
38185183 AGTATGTAGG
* * *
38185193 TAATAATAAAAAAATAATAATAG
1 TAATAATAAAATAATAATAACAA
**
38185216 TAATAATAAAATAATGCTAACAA
1 TAATAATAAAATAATAATAACAA
* **
38185239 TAATCAT-AAAT-ATAATAGTAA
1 TAATAATAAAATAATAATAACAA
*
38185260 TGAT-A-AAAATAATAATAACAA
1 TAATAATAAAATAATAATAACAA
38185281 CAAAAAAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.10
21 17 0.34
22 4 0.08
23 24 0.48
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (23 bp):
TAATAATAAAATAATAATAACAA
Found at i:38193550 original size:46 final size:44
Alignment explanation
Indices: 38193491--38193605 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
38193481 ACAGGACAGA
* *
38193491 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
38193537 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
38193581 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
38193606 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:38193586 original size:44 final size:45
Alignment explanation
Indices: 38193491--38193624 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
38193481 ACAGGACAGA
* *
38193491 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
38193537 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
38193581 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
38193625 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:38201388 original size:15 final size:15
Alignment explanation
Indices: 38201368--38201397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38201358 AACCGTGGCC
*
38201368 TTCTTTCTTTCCTTT
1 TTCTTTATTTCCTTT
38201383 TTCTTTATTTCCTTT
1 TTCTTTATTTCCTTT
38201398 CTTAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTTATTTCCTTT
Found at i:38201508 original size:15 final size:15
Alignment explanation
Indices: 38201488--38201542 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
38201478 TTATTGATTA
38201488 TATTATATTTTATAT
1 TATTATATTTTATAT
*
38201503 TATTATA-TTAATA-
1 TATTATATTTTATAT
* *
38201516 TAGTATACTTTA-AT
1 TATTATATTTTATAT
38201530 TATTATTATTTTA
1 TATTA-TATTTTA
38201543 CTTATATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 7 0.22
14 12 0.38
15 13 0.41
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTATATTTTATAT
Found at i:38201522 original size:21 final size:21
Alignment explanation
Indices: 38201479--38201522 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
38201469 ACTTGTCTTT
**
38201479 TATTGATTATATTATATTTTA
1 TATTGATTATATTATATAGTA
38201500 TATT-ATTATATTAATATAGTA
1 TATTGATTATATT-ATATAGTA
38201521 TA
1 TA
38201523 CTTTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTGATTATATTATATAGTA
Found at i:38202186 original size:3 final size:3
Alignment explanation
Indices: 38202180--38202264 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
38202170 AGTATGTAGG
* * ** *
38202180 TAA TAA TAA -AA AAA TAA TAA TAG TAA TAA TAA -AA TAA TGC TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
38202226 TAA TCA TAA -ATA TAA TAG TAA TGA TAA AAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
38202265 CAACAAAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 5 0.08
3 55 0.90
4 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:38202229 original size:23 final size:23
Alignment explanation
Indices: 38202180--38202267 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
38202170 AGTATGTAGG
* * *
38202180 TAATAATAAAAAAATAATAATAG
1 TAATAATAAAATAATAATAACAA
**
38202203 TAATAATAAAATAATGCTAACAA
1 TAATAATAAAATAATAATAACAA
* **
38202226 TAATCAT-AAAT-ATAATAGTAA
1 TAATAATAAAATAATAATAACAA
*
38202247 TGAT-A-AAAATAATAATAACAA
1 TAATAATAAAATAATAATAACAA
38202268 CAAAAAAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.10
21 17 0.34
22 4 0.08
23 24 0.48
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (23 bp):
TAATAATAAAATAATAATAACAA
Found at i:38205381 original size:5 final size:5
Alignment explanation
Indices: 38205371--38205399 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
38205361 AGTTTTAGGG
38205371 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
38205400 TTCTGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:38209046 original size:19 final size:18
Alignment explanation
Indices: 38209010--38209048 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
38209000 CTAAAACTTT
38209010 ATTTTAATATTTTTATAC
1 ATTTTAATATTTTTATAC
38209028 ATTTTAAT-TTTAATTATAC
1 ATTTTAATATTT--TTATAC
38209047 AT
1 AT
38209049 ACTTTATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTAATATTTTTATAC
Found at i:38209990 original size:25 final size:25
Alignment explanation
Indices: 38209960--38210024 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
38209950 TCACTAGGTT
* *
38209960 AATCAGAGTTTAAGTGAGAAATTAA
1 AATCAGAGTTTAACTGAGAAACTAA
38209985 AATCAGAGTTTAACTGAGAAACTAA
1 AATCAGAGTTTAACTGAGAAACTAA
38210010 AA-CTAGAGTTTAACT
1 AATC-AGAGTTTAACT
38210025 AAGAGAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (25 bp):
AATCAGAGTTTAACTGAGAAACTAA
Found at i:38210036 original size:25 final size:25
Alignment explanation
Indices: 38209989--38210036 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38209979 AATTAAAATC
* *
38209989 AGAGTTTAACTGAGAAACTAAAACT
1 AGAGTTTAACTAAGAAACGAAAACT
38210014 AGAGTTTAACTAAGAGAA-GAAAA
1 AGAGTTTAACTAAGA-AACGAAAA
38210037 TCGAGAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAGTTTAACTAAGAAACGAAAACT
Found at i:38220809 original size:35 final size:35
Alignment explanation
Indices: 38220770--38220857 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
38220760 ATATACCTTT
38220770 ATTAAAACGGCGTCGTTTTGCTTAATTCAATAAGC
1 ATTAAAACGGCGTCGTTTTGCTTAATTCAATAAGC
* *
38220805 ATTAAAATGGCGTTGTTTTGCTTAATTCAATAAGC
1 ATTAAAACGGCGTCGTTTTGCTTAATTCAATAAGC
38220840 ATTAAAACGGCGTCGTTT
1 ATTAAAACGGCGTCGTTT
38220858 AAACAAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (35 bp):
ATTAAAACGGCGTCGTTTTGCTTAATTCAATAAGC
Found at i:38221260 original size:18 final size:20
Alignment explanation
Indices: 38221239--38221286 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
38221229 CTTATTTTTA
38221239 TATTATATATAATT-AT-TT
1 TATTATATATAATTGATATT
* *
38221257 TATTATATATTATTGTTATT
1 TATTATATATAATTGATATT
38221277 TATTATATAT
1 TATTATATAT
38221287 TACTTTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTATATATAATTGATATT
Found at i:38221265 original size:16 final size:16
Alignment explanation
Indices: 38221244--38221276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38221234 TTTTATATTA
38221244 TATATAATTATT-TTAT
1 TATAT-ATTATTGTTAT
38221260 TATATATTATTGTTAT
1 TATATATTATTGTTAT
38221276 T
1 T
38221277 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATATATTATTGTTAT
Found at i:38221287 original size:20 final size:20
Alignment explanation
Indices: 38221204--38221288 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 20
38221194 AATTTTTTTA
* *
38221204 TATTGTTATTTGTTTTATATT
1 TATTGTTATTTATTATATA-T
* *
38221225 TAATCTTATTT-TTATATTAT
1 TATTGTTATTTATTATA-TAT
**
38221245 ATATAATTATTTTATTATATAT
1 -TATTGTTA-TTTATTATATAT
38221267 TATTGTTATTTATTATATAT
1 TATTGTTATTTATTATATAT
38221287 TA
1 TA
38221289 CTTTTCACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 19 0.37
21 22 0.42
22 6 0.12
23 5 0.10
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTGTTATTTATTATATAT
Found at i:38221341 original size:11 final size:11
Alignment explanation
Indices: 38221327--38221431 Score: 54
Period size: 13 Copynumber: 8.6 Consensus size: 11
38221317 TCTTATTTAC
38221327 ATATTATTATT
1 ATATTATTATT
38221338 ATATT-TTACTT
1 ATATTATTA-TT
*
38221349 GTATTATATATT
1 ATATTAT-TATT
38221361 -TATTAATTATTT
1 ATATT-ATTA-TT
38221373 ATATATATTATAT
1 ATAT-TATTAT-T
*
38221386 ATACATATATACTTT
1 ATA-TTAT-TA--TT
38221401 CATATTATATATT
1 -ATATTAT-TATT
38221414 ATAATTATT-TT
1 AT-ATTATTATT
38221425 ATATTAT
1 ATATTAT
38221432 GTCATTTTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 29
0.71 0.03 0.27
Matches are distributed among these distances:
10 8 0.10
11 21 0.27
12 11 0.14
13 23 0.30
14 3 0.04
15 7 0.09
16 4 0.05
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (11 bp):
ATATTATTATT
Found at i:38221428 original size:23 final size:23
Alignment explanation
Indices: 38221350--38221431 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
38221340 ATTTTACTTG
38221350 TATTATATATTTATTAATTA-TTTA
1 TATTATATA-TTA-TAATTATTTTA
38221374 TA-TATATTATATATACATATATACTTTCA
1 TATTATA-TAT-TATA-AT-TAT--TTT-A
38221403 TATTATATATTATAATTATTTTA
1 TATTATATATTATAATTATTTTA
38221426 TATTAT
1 TATTAT
38221432 GTCATTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
23 14 0.29
24 11 0.22
25 2 0.04
26 3 0.06
27 2 0.04
28 7 0.14
29 6 0.12
30 4 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATATATTATAATTATTTTA
Found at i:38221451 original size:20 final size:18
Alignment explanation
Indices: 38221426--38221466 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
38221416 AATTATTTTA
38221426 TATTATGTCATTTTTTATAC
1 TATTATGT-ATTTTTTAT-C
*
38221446 TATTATGTTTTTTTTATC
1 TATTATGTATTTTTTATC
38221464 TAT
1 TAT
38221467 ATATTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (18 bp):
TATTATGTATTTTTTATC
Found at i:38221904 original size:24 final size:26
Alignment explanation
Indices: 38221856--38221904 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
38221846 GCTCACTTAA
* *
38221856 TTTTATATTTATATGTATATTAATCC
1 TTTTATATGTATATGTATATAAATCC
38221882 TTTTATATGT-TAT-TATATAAATC
1 TTTTATATGTATATGTATATAAATC
38221905 ATTAGGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTTATATGTATATGTATATAAATCC
Found at i:38225527 original size:14 final size:14
Alignment explanation
Indices: 38225508--38225537 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38225498 AAGATATTCT
38225508 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
38225522 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
38225536 TT
1 TT
38225538 GAACCAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:38234004 original size:206 final size:206
Alignment explanation
Indices: 38233650--38234543 Score: 1398
Period size: 206 Copynumber: 4.3 Consensus size: 206
38233640 GCAGATCGGG
*
38233650 CTGAAGCAAGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
*
38233715 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAA
66 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
38233780 AGAGCAAGTCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAGCAGATCTCACCTTC
131 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAGCAGATCTCACCTTC
*
38233845 AGATGTTTGTA
196 AGATGTTTATA
38233856 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
38233921 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
38233986 AGAGCAAGTCGAAGTCTGGCATCTCCACTTCAAAGGGGAGCAGATACATAGCAGATCTCACCTTC
131 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAGCAGATCTCACCTTC
38234051 AGATGTTTATA
196 AGATGTTTATA
* * * * *
38234062 TTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGTGCTAATAAGGAACGAACCGAAGACATAACT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
* *
38234127 GATTTGGCTTTCACGTGTTTACGATGAAGTAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
38234192 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGAGAGCAGATACATAGCAAATCTCACCTTC
131 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAGCAGATCTCACCTTC
*
38234257 AAATGTTTATA
196 AGATGTTTATA
* * * * * *
38234268 TTGAAAC-AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAATACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
*
38234332 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTAGTGTCAG
66 GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
38234397 GGAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGG-GCAGATACATAGCAGATCTAACCT
131 AGAGCAAATCGAAGTCTGGCATCTCCA-CTTCAACGG-GGAGCAGATACATAGCAGATCTCACCT
*
38234461 TCAGATATTTATA
194 TCAGATGTTTATA
** * * * * * * * *
38234474 CTGAAG-TGGATCCAAGATGATTTGGCATTCTTGAGTTTACAAGGAACAAATCGAGGACATAGCA
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
38234538 GATTTG
66 GATTTG
38234544 ACTCTCAGGT
Statistics
Matches: 639, Mismatches: 46, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
205 137 0.21
206 501 0.78
207 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (206 bp):
CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACGAACCGAAGACATAGCT
GATTTGGTTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAGCAGATCTCACCTTC
AGATGTTTATA
Found at i:38236210 original size:18 final size:20
Alignment explanation
Indices: 38236187--38236234 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
38236177 CTTATTTTTA
38236187 TATTATATATAATT-AT-TT
1 TATTATATATAATTGATATT
* *
38236205 TATTATATATTATTGTTATT
1 TATTATATATAATTGATATT
38236225 TATTATATAT
1 TATTATATAT
38236235 TACTTTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTATATATAATTGATATT
Found at i:38236213 original size:16 final size:16
Alignment explanation
Indices: 38236192--38236224 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38236182 TTTTATATTA
38236192 TATATAATTATT-TTAT
1 TATAT-ATTATTGTTAT
38236208 TATATATTATTGTTAT
1 TATATATTATTGTTAT
38236224 T
1 T
38236225 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATATATTATTGTTAT
Found at i:38236266 original size:13 final size:13
Alignment explanation
Indices: 38236248--38236272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38236238 TTTTCACAAA
38236248 ACATTATTATTTT
1 ACATTATTATTTT
38236261 ACATTATTATTT
1 ACATTATTATTT
38236273 AGATATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
ACATTATTATTTT
Found at i:38236289 original size:11 final size:11
Alignment explanation
Indices: 38236252--38236377 Score: 55
Period size: 11 Copynumber: 10.5 Consensus size: 11
38236242 CACAAAACAT
38236252 TATTATT-TTA
1 TATTATTATTA
*
38236262 CATTATTATTTAGA
1 TATTATTA-TT--A
38236276 TATTATTATTA
1 TATTATTATTA
*
38236287 TATT-TTACTTG
1 TATTATTA-TTA
38236298 TATTATATATT-
1 TATTAT-TATTA
38236309 TATTAATTATTTA
1 TATT-ATTA-TTA
38236322 TATATATTATATACA
1 TAT-TATTAT-T--A
*
38236337 TATATACTT-TCA
1 TAT-TA-TTATTA
38236349 TATTATATATTA
1 TATTAT-TATTA
38236361 TAATTATT-TTA
1 T-ATTATTATTA
38236372 TATTAT
1 TATTAT
38236378 GTCATTTTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 36
0.69 0.04 0.27
Matches are distributed among these distances:
10 15 0.16
11 24 0.26
12 18 0.19
13 17 0.18
14 9 0.10
15 8 0.09
16 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (11 bp):
TATTATTATTA
Found at i:38236313 original size:33 final size:33
Alignment explanation
Indices: 38236250--38236324 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
38236240 TTCACAAAAC
*
38236250 ATTATTATTTTACATTATTATTTAGATATT-ATT
1 ATTA-TATTTTACATTATTATATAGATATTAATT
* **
38236283 ATTATATTTTACTTGTATTATATATTTATTAATT
1 ATTATATTTTACAT-TATTATATAGATATTAATT
38236317 ATTTATAT
1 A-TTATAT
38236325 ATATTATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 9 0.26
33 16 0.46
34 4 0.11
35 6 0.17
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (33 bp):
ATTATATTTTACATTATTATATAGATATTAATT
Found at i:38236374 original size:23 final size:23
Alignment explanation
Indices: 38236298--38236377 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 23
38236288 ATTTTACTTG
38236298 TATTATATATTTATTAATTA-TTTA
1 TATTATATA-TTA-TAATTATTTTA
38236322 TA-TATAT-TATATACATATATACTTTCA
1 TATTATATAT-TATA-AT-TAT--TTT-A
38236349 TATTATATATTATAATTATTTTA
1 TATTATATATTATAATTATTTTA
38236372 TATTAT
1 TATTAT
38236378 GTCATTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 19
0.71 0.00 0.29
Matches are distributed among these distances:
21 3 0.06
22 4 0.09
23 14 0.30
24 5 0.11
26 6 0.13
27 5 0.11
28 9 0.19
29 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATATATTATAATTATTTTA
Found at i:38236411 original size:17 final size:19
Alignment explanation
Indices: 38236372--38236411 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
38236362 AATTATTTTA
38236372 TATTATGTCATTTTTTATAC
1 TATTATGT-ATTTTTTATAC
38236392 TATTATGT-TTTTTTAT-C
1 TATTATGTATTTTTTATAC
38236409 TAT
1 TAT
38236412 ATATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
20 8 0.40
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (19 bp):
TATTATGTATTTTTTATAC
Found at i:38236713 original size:23 final size:22
Alignment explanation
Indices: 38236671--38236714 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
38236661 CTAAACCAAT
*
38236671 ATTTTTTATTATTCTTTTATAA
1 ATTTTTTATTATTCTATTATAA
38236693 ATTTTTGTCATTA-TCTATTATA
1 ATTTTT-T-ATTATTCTATTATA
38236715 TATTGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTTTATTATTCTATTATAA
Found at i:38236854 original size:24 final size:26
Alignment explanation
Indices: 38236806--38236854 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
38236796 GCTCATTTAA
* *
38236806 TTTTATATTTATATGTATATTAATCC
1 TTTTATATGTATATGTATATAAATCC
38236832 TTTTATATGT-TAT-TATATAAATC
1 TTTTATATGTATATGTATATAAATC
38236855 ATTAGGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTTATATGTATATGTATATAAATCC
Found at i:38246570 original size:26 final size:25
Alignment explanation
Indices: 38246531--38246583 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
38246521 AATATAATTT
38246531 TTATATTTTATAAAGT-TATAAAAAAA
1 TTATATTTTATAAA-TCT-TAAAAAAA
38246557 TTATATTATT-TAAATCTTAAAAAAA
1 TTATATT-TTATAAATCTTAAAAAAA
38246582 TT
1 TT
38246584 CCTAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 11 0.44
26 12 0.48
27 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTATATTTTATAAATCTTAAAAAAA
Found at i:38251591 original size:6 final size:6
Alignment explanation
Indices: 38251580--38251613 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
38251570 GTTTCCTCCT
38251580 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
38251614 TTCTCTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:38267431 original size:23 final size:24
Alignment explanation
Indices: 38267400--38267447 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
38267390 AACATTTAAT
38267400 TAAAATTTTAA-ATTTTTAAAAAA
1 TAAAATTTTAATATTTTTAAAAAA
* *
38267423 TAAATTTTTAATTTTTTTAAAAAA
1 TAAAATTTTAATATTTTTAAAAAA
38267447 T
1 T
38267448 TTATATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAATTTTAATATTTTTAAAAAA
Found at i:38267808 original size:4 final size:4
Alignment explanation
Indices: 38267799--38267827 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
38267789 CTAAAACAAC
38267799 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
38267828 GATCTGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:38268508 original size:23 final size:23
Alignment explanation
Indices: 38268460--38268508 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
38268450 AGATGAGATA
**
38268460 AAATTTATTAAATTAAGTTCTCG
1 AAATTTATTAAATTAAGGCCTCG
*
38268483 AAATTTATTAATTTTAAGGCCT-G
1 AAATTTATTAA-ATTAAGGCCTCG
38268506 AAA
1 AAA
38268509 AATCACTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (23 bp):
AAATTTATTAAATTAAGGCCTCG
Found at i:38278407 original size:33 final size:31
Alignment explanation
Indices: 38278329--38278407 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 31
38278319 AAACTGTCTC
*
38278329 ACCAACCACTA-CACCTACTCAACCTGAATT
1 ACCAACCACCACCACCTACTCAACCTGAATT
*
38278359 ACCAACC-CTCCCCACCTCCACTCAACCTGAATT
1 ACCAACCAC-CACCACCT--ACTCAACCTGAATT
38278392 ACCAACCACCACCACC
1 ACCAACCACCACCACC
38278408 ATACAACCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 1 0.02
30 7 0.17
31 5 0.12
33 27 0.66
34 1 0.02
ACGTcount: A:0.33, C:0.49, G:0.03, T:0.15
Consensus pattern (31 bp):
ACCAACCACCACCACCTACTCAACCTGAATT
Found at i:38282523 original size:22 final size:22
Alignment explanation
Indices: 38282465--38282540 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
38282455 ATATCATATT
* *
38282465 TTATATGTATCATATTTTTTAATG
1 TTATAT-TAT-ATATATTTTAATA
*
38282489 TTGTATTAT-TATATTTTAATA
1 TTATATTATATATATTTTAATA
*
38282510 TTATATTATATATATTTTCATA
1 TTATATTATATATATTTTAATA
38282532 TTATATTAT
1 TTATATTAT
38282541 GTACATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 18 0.39
22 20 0.43
23 3 0.07
24 5 0.11
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (22 bp):
TTATATTATATATATTTTAATA
Found at i:38282658 original size:21 final size:22
Alignment explanation
Indices: 38282607--38282663 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
38282597 TATTACTAGT
38282607 TATATATTATTTATATATTTCCA
1 TATATA-TATTTATATATTTCCA
* *
38282630 TGTTTATATTT-TATATTGTCC-
1 TATATATATTTATATATT-TCCA
38282651 TATATATATTTAT
1 TATATATATTTAT
38282664 GTAGTGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 15 0.54
22 9 0.32
23 4 0.14
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.60
Consensus pattern (22 bp):
TATATATATTTATATATTTCCA
Found at i:38288600 original size:3 final size:3
Alignment explanation
Indices: 38288592--38288619 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38288582 TCTCCAAAAC
38288592 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
38288620 CGTTTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38290278 original size:9 final size:10
Alignment explanation
Indices: 38290251--38290277 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
38290241 GGCTAAAAAT
38290251 AATTTTTTAA
1 AATTTTTTAA
38290261 AATTTTTTAA
1 AATTTTTTAA
38290271 AATTTTT
1 AATTTTT
38290278 ATAGCTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:38294010 original size:2 final size:2
Alignment explanation
Indices: 38293998--38294040 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
38293988 TTGTTCTCCT
*
38293998 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38294040 T
1 T
38294041 AAGCCTTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:38304788 original size:24 final size:24
Alignment explanation
Indices: 38304751--38304813 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
38304741 TCATGTACAC
*
38304751 ATTATT-TATATTATTTTCA-TGATT
1 ATTATTGTAT-TTATTTTCACT-ACT
* *
38304775 ATTATTGTGTTTATTTTTACTACT
1 ATTATTGTATTTATTTTCACTACT
38304799 ATTATTGTATTTATT
1 ATTATTGTATTTATT
38304814 ATTAGTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTATTGTATTTATTTTCACTACT
Found at i:38304828 original size:24 final size:24
Alignment explanation
Indices: 38304772--38304828 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
38304762 TATTTTCATG
* *
38304772 ATTATTATTGTGTTTATTTTTACT
1 ATTATTATTGTATTTATTATTACT
* *
38304796 ACTATTATTGTATTTATTATTAGT
1 ATTATTATTGTATTTATTATTACT
*
38304820 ATTAGTATT
1 ATTATTATT
38304829 ATAATTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (24 bp):
ATTATTATTGTATTTATTATTACT
Found at i:38305055 original size:16 final size:16
Alignment explanation
Indices: 38305036--38305076 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
38305026 TTTTTAATAC
38305036 TATATTATATATATAT
1 TATATTATATATATAT
38305052 TATATTATATATATAT
1 TATATTATATATATAT
38305068 T-TATTATAT
1 TATATTATAT
38305077 TTTTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTATATATATAT
Found at i:38305062 original size:23 final size:23
Alignment explanation
Indices: 38305015--38305090 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
38305005 AATGTGTATG
* *
38305015 TATTATATATAT-TTTTAATACTA
1 TATTATATATATATTATATTA-TA
38305038 TATTATATATATATTATATTATA
1 TATTATATATATATTATATTATA
*
38305061 TA-TATAT-T-TATTATATT-TT
1 TATTATATATATATTATATTATA
38305080 TATGTATATAT
1 TAT-TATATAT
38305091 TTTTAATATC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.07
20 9 0.20
21 6 0.13
22 6 0.13
23 16 0.35
24 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (23 bp):
TATTATATATATATTATATTATA
Found at i:38305099 original size:23 final size:23
Alignment explanation
Indices: 38305017--38305092 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 23
38305007 TGTGTATGTA
38305017 TTATATATATTTTTA-ATACTATAT
1 TTAT-TATATTTTTATATA-TATAT
38305041 TATATATATATTATATTATATATATAT
1 T-TAT-TATATT-T-TTATATATATAT
*
38305068 TTATTATATTTTTATGTATATAT
1 TTATTATATTTTTATATATATAT
38305091 TT
1 TT
38305093 TTAATATCAC
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
23 13 0.28
24 2 0.04
25 16 0.34
26 4 0.09
27 9 0.19
28 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (23 bp):
TTATTATATTTTTATATATATAT
Found at i:38305270 original size:3 final size:3
Alignment explanation
Indices: 38305264--38305320 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
38305254 TTTATTCATA
* *
38305264 TAT TAT TAT CAT TAT TTT CTACGT TAT -AT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TA--T TAT TAT TAT TAT TAT TAT TAT TAT
*
38305311 CAT TAT TAT T
1 TAT TAT TAT T
38305321 TTCATTGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.05
3 38 0.86
4 1 0.02
5 2 0.05
6 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:38317723 original size:45 final size:44
Alignment explanation
Indices: 38317674--38317865 Score: 147
Period size: 45 Copynumber: 4.3 Consensus size: 44
38317664 TTGAGATTGT
*
38317674 AGTGGAGCAGATCAAATATAGCAAATCTTGTTTCCCTGAAGTTGC
1 AGTGGAGCAGATCAAATATA-CAAATCTTGTCTCCCTGAAGTTGC
* * * * *
38317719 AGTGGAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGC
1 AGTGGAGCAGATCAAA--T--A-TACAAATCTTGTCTCCCTGAAGTTGC
* * *
38317768 AGTAGAGCAGATC-AA-A-ACAGATCTTGTCTCCTTGAAGTTGC
1 AGTGGAGCAGATCAAATATACAAATCTTGTCTCCCTGAAGTTGC
* * *** * *
38317809 AGTGGAACAGATCGAATACGGTAAATCTTGCCTTCCTGAAGTTGC
1 AGTGGAGCAGATCAAATA-TACAAATCTTGTCTCCCTGAAGTTGC
*
38317854 AGTGAAGCAGAT
1 AGTGGAGCAGAT
38317866 TCAAGCCACC
Statistics
Matches: 116, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
41 33 0.28
42 2 0.02
43 2 0.02
45 43 0.37
47 1 0.01
48 2 0.02
49 31 0.27
50 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTGGAGCAGATCAAATATACAAATCTTGTCTCCCTGAAGTTGC
Found at i:38317804 original size:41 final size:41
Alignment explanation
Indices: 38317743--38317821 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
38317733 AAGCTAAATT
*
38317743 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAA
1 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAACAGATCAAA
* *
38317784 ACAGATCTTGTCTC-CTTGAAGTTGCAGTGGAACAGATC
1 ACAGATCTTATCTCTC-TGAAGTTGCAGTAGAACAGATC
38317822 GAATACGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
ACAGATCTTATCTCTCTGAAGTTGCAGTAGAACAGATCAAA
Found at i:38317963 original size:41 final size:44
Alignment explanation
Indices: 38317900--38318000 Score: 102
Period size: 44 Copynumber: 2.4 Consensus size: 44
38317890 TAAGCAATAG
* * *
38317900 GTTGCAAG-GGAGCAGATCAAAAC-A-AA-CCTTATCTCCCTGAA
1 GTTGC-AGTGGAGCAGGTCAAAACTACAAGCCTCATCTCCCTAAA
* *
38317941 GTTGCAGTGGAGCAGGTTAAAACTACAAGTCTCATCTCCCTAAA
1 GTTGCAGTGGAGCAGGTCAAAACTACAAGCCTCATCTCCCTAAA
* *
38317985 TTTGTAGTGGAGCAGG
1 GTTGCAGTGGAGCAGG
38318001 CTGAAGATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
40 2 0.04
41 18 0.37
42 1 0.02
43 2 0.04
44 26 0.53
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (44 bp):
GTTGCAGTGGAGCAGGTCAAAACTACAAGCCTCATCTCCCTAAA
Found at i:38319515 original size:15 final size:15
Alignment explanation
Indices: 38319484--38319516 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38319474 TAGGCCCTTA
*
38319484 TTTATTTATTATATT
1 TTTATGTATTATATT
38319499 TTTATGTA-TATATT
1 TTTATGTATTATATT
38319513 TTTA
1 TTTA
38319517 ATATCACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATGTATTATATT
Found at i:38325421 original size:17 final size:17
Alignment explanation
Indices: 38325401--38325452 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
38325391 AAATTTTTTG
*
38325401 AAAAAAAATTATTTTAT
1 AAAAAAAATAATTTTAT
*
38325418 AAAATAAATAATTTTAAAT
1 AAAAAAAATAATTTT--AT
38325437 AAAAACAAATGAATTT
1 AAAAA-AAAT-AATTT
38325453 ATCTCCACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 13 0.46
19 6 0.21
20 4 0.14
21 5 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAAAAAATAATTTTAT
Found at i:38327368 original size:19 final size:17
Alignment explanation
Indices: 38327338--38327401 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 17
38327328 ATTAATTATT
38327338 TTAAAAATTAAAATTTA
1 TTAAAAATTAAAATTTA
38327355 TTAAAAAGTATAAAA-TTA
1 TTAAAAA-T-TAAAATTTA
*
38327373 TAAAAAAATTATAAATTT-
1 T-TAAAAATTA-AAATTTA
38327391 TTAAAAATTAA
1 TTAAAAATTAA
38327402 TTAGAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 1 0.03
17 17 0.43
18 10 0.25
19 12 0.30
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAAAAATTAAAATTTA
Found at i:38328990 original size:9 final size:10
Alignment explanation
Indices: 38328968--38329015 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
38328958 TAAAAAGTTC
38328968 TTTTTATAAT
1 TTTTTATAAT
38328978 TTTTTATAAT
1 TTTTTATAAT
*
38328988 TTTTAAAAATAAT
1 TTTT---TATAAT
38329001 TTTTTAT-AT
1 TTTTTATAAT
38329010 TTTTTA
1 TTTTTA
38329016 AAAAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 8 0.24
10 16 0.48
13 9 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:38328999 original size:23 final size:23
Alignment explanation
Indices: 38328973--38329024 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
38328963 AGTTCTTTTT
38328973 ATAATTTTTTATAATTTTTAAAA
1 ATAATTTTTTATAATTTTTAAAA
*
38328996 ATAATTTTTTATATTTTTTAAAA
1 ATAATTTTTTATAATTTTTAAAA
38329019 A-AATTT
1 ATAATTT
38329025 AAATTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATAATTTTTTATAATTTTTAAAA
Found at i:38331129 original size:23 final size:23
Alignment explanation
Indices: 38331092--38331173 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 23
38331082 NCTTTTTTGT
38331092 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
38331115 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
38331137 TATTAGGTATATTCTAAAT-TCTA
1 TATTATATATATTCTTAATAT-TA
38331160 TATTAGGTATATAT
1 TATTA--TATATAT
38331174 ATTTTCTATA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
22 17 0.38
23 19 0.42
24 4 0.09
25 5 0.11
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:38331187 original size:27 final size:26
Alignment explanation
Indices: 38331157--38331315 Score: 94
Period size: 25 Copynumber: 6.0 Consensus size: 26
38331147 ATTCTAAATT
* *
38331157 CTATATTAGGTATATATATTTTCTATA
1 CTATATTATGTATATATATTTT-AATA
* *
38331184 CTATTTTATGTATATAT-GTTTAATA
1 CTATATTATGTATATATATTTTAATA
* * * *
38331209 CTATATTATTTATATATATATATATTTT
1 CTATATTATGTATATATAT-TTTA-ATA
* *
38331237 CTACATGTTATCTTATGTATATATTTT-A-A
1 CT--ATATTAT-GTA--TATATATTTTAATA
* *
38331266 CTATATTATGTATGTAT-TTTTAACA
1 CTATATTATGTATATATATTTTAATA
*
38331291 CTATATTATGTACATAT-TTTTAATA
1 CTATATTATGTATATATATTTTAATA
38331316 TTATCACGTA
Statistics
Matches: 102, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.04
24 5 0.05
25 41 0.40
26 5 0.05
27 24 0.24
28 3 0.03
29 2 0.02
30 6 0.06
31 3 0.03
32 2 0.02
33 7 0.07
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (26 bp):
CTATATTATGTATATATATTTTAATA
Found at i:38331470 original size:16 final size:15
Alignment explanation
Indices: 38331449--38331491 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
38331439 TAATTATTAT
38331449 TATTTTAATATTTTGA
1 TATTTTAATATTTT-A
38331465 TATTTTAATATTTTA
1 TATTTTAATATTTTA
38331480 TATTTTATATAT
1 TATTTTA-ATAT
38331492 CTACATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:38331484 original size:7 final size:8
Alignment explanation
Indices: 38331449--38331491 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
38331439 TAATTATTAT
38331449 TATTTTAA
1 TATTTTAA
*
38331457 TATTTTGA
1 TATTTTAA
38331465 TATTTTAA
1 TATTTTAA
38331473 TATTTT-A
1 TATTTTAA
38331480 TATTTTATA
1 TATTTTA-A
38331489 TAT
1 TAT
38331492 CTACATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 7 0.23
8 20 0.65
9 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:38331555 original size:25 final size:24
Alignment explanation
Indices: 38331505--38331567 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
38331495 CATGTTATCT
*
38331505 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
38331531 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
**
38331556 TACATATTTTTT
1 TATGTATTTTTT
38331568 TTATATCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 21 0.64
26 7 0.21
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:38343402 original size:72 final size:72
Alignment explanation
Indices: 38343291--38344226 Score: 1428
Period size: 72 Copynumber: 12.9 Consensus size: 72
38343281 TTCAAAAAAA
38343291 AAAATT-AACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343355 TGTTTTC
66 TGTTTTC
38343362 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343427 TGTTTTC
66 TGTTTTC
38343434 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343499 TGTTTTC
66 TGTTTTC
38343506 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343571 TGTTTTC
66 TGTTTTC
38343578 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343643 TGTTTTC
66 TGTTTTC
38343650 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343715 TGTTTTC
66 TGTTTTC
38343722 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343787 TGTTTTC
66 TGTTTTC
38343794 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38343859 TGTTTTC
66 TGTTTTC
* * * * *
38343866 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATT
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGG--GACACGTTGAGGTAATTTCAATT
*
38343931 TTTGTCTTTC
64 TCTGT-TTTC
* * * ** * * ** *
38343941 AAAAAAATCAGCTCATATTGCGATAAATGAGTTGATCCTCAAGACACATTGAGGTAATTTCAATT
1 --AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATT
38344006 TCTGTTTTC
64 TCTGTTTTC
* ** * **
38344015 AAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
38344080 TGTTTTC
66 TGTTTTC
** * ** * * *
38344087 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
*
38344152 TGTTTTTGAAAAA
66 TG-TTTT-----C
* * ** *
38344165 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC--TGAGGTATTTTCAATTT
1 AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTT
38344227 TCGTTTGTCA
Statistics
Matches: 818, Mismatches: 35, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
71 6 0.01
72 665 0.81
73 4 0.00
74 27 0.03
75 26 0.03
76 17 0.02
77 32 0.04
78 41 0.05
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (72 bp):
AAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
TGTTTTC
Found at i:38343586 original size:216 final size:216
Alignment explanation
Indices: 38343205--38345031 Score: 1666
Period size: 216 Copynumber: 8.0 Consensus size: 216
38343195 TGTTACTTCC
** ** *
38343205 GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
1 GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
* * *
38343270 AATTTCTATTTTTCAAAAAAAAAAATTAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACAC
66 AATTTCT-GTTTTC------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
*
38343335 GTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTC
124 GTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
38343400 GGGACACGTTGAGGTAATTTCAATTTCT
189 GGGACACGTTGAGGTAATTTCAATTTCT
* * *
38343428 GTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTC
1 GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
* *
38343493 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGG
66 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGTTGAGG
*
38343558 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACAC
131 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
38343623 GTTGAGGTAATTTCAATTTCT
196 GTTGAGGTAATTTCAATTTCT
* * *
38343644 GTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGGTAATTTC
1 GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
* *
38343709 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACACGTTGAGG
66 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGTTGAGG
*
38343774 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGGACAC
131 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
38343839 GTTGAGGTAATTTCAATTTCT
196 GTTGAGGTAATTTCAATTTCT
* *
38343860 GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTT
1 GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGCTGAGGTATTT
* * * ** * ** *
38343925 TCAATTTTTGTCTTTCAAAAAAATCAGCTCATATTGCGATAAATGAGTTGATCCTCAAGACACAT
64 TCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGT
* ** **
38343990 TGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAA
126 TGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
38344055 GACACGTTGAGGTAATTTCAATTTCT
191 GACACGTTGAGGTAATTTCAATTTCT
** ** *
38344081 GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
1 GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
* **
38344146 AATTTCTGTTTTTGAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC-
66 AATTTCTG-TTTT-----CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
* *
38344210 -TGAGGTATTTTCAATTTTCGTTTGTCAATTTATTTTTCAAAAATCCAACTCATATTGCGAGAGG
125 TTGAGGTAATTTCAA-TTTC---TG---------TTTTC-AAAATTCAACTCATATTGCGAGAGG
** *
38344274 TGAGTTGAGCCTCGGCTCACGTGCTGA-GTATTTTCAATTTCTATT
176 TGAGTTGAGCCTCGGGACACGT--TGAGGTAATTTCAATTTC---T
* * * *
38344319 TTCAATTTCTATTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGC
1 GT---TTTC-A------AAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGC
38344384 TGAGGTATTTTCAATTTCTGTCTTTC---AA--AA---A-A-----A-A--TGAGTTGAGCCTCG
54 TGAGGTATTTTCAATTTCTGT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * * * *
38344432 GGACACGCTGAGGGATTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAG
118 GGACACGTTGAGGTAATTTCAATTTCT-GTTTTC-AAA-ATTCAACTCATATTGCGAGAGGTGAG
*
38344497 TTGAGCCTCGGGTCACACGCTGAGACGT--TTTCAATTTCT
180 TTGAGCCTCGGG--ACACGTTGAG--GTAATTTCAATTTCT
* * ***
38344536 GCTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGACGTT
1 G-TTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATT
* * *
38344601 TTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
63 TTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACG
* * * *
38344666 CTGAGGTATTTTCAATTTCTACTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGGG
125 TTGAGGTAATTTCAATTTCT-GTTTTCAA---A-A----T------TCAACTCATATTGCGAGAG
* * * *
38344731 GTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTCT
175 GTGAGTTGAGCCTCGG--GACACGTTGAGGTAATTTCAATTTCT
* *
38344775 ACTTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 -GTTTTCAA---A-A----T-------TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
*
38344840 ACGCTAAGGTAATTTT-AATTTCTGTTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTG
50 ACGCTGAGGT-ATTTTCAATTTCTG-------TTTTC-AAAAATCAACTCATATTGCGAGAGGTG
* * * * *
38344904 AGTTGAGCCTCAGGACACGCTAAGGTAATTTTAATTTCTGTTTATATTTTTCAAAAAATCAACTC
106 AGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTCTG-------TTTTC-AAAATTCAACTC
* * * * *
38344969 ATATTGCGAGATGTGAGTTGAGCATCGGGGCACGCTGAGGTATTTTCAATTTCT
163 ATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTCT
38345023 GCTTTTCAA
1 G-TTTTCAA
38345032 TTTATATTTT
Statistics
Matches: 1367, Mismatches: 112, Indels: 225
0.80 0.07 0.13
Matches are distributed among these distances:
208 64 0.05
209 1 0.00
211 2 0.00
213 2 0.00
214 1 0.00
215 4 0.00
216 398 0.29
217 2 0.00
218 33 0.02
219 70 0.05
220 24 0.02
221 172 0.13
222 48 0.04
223 65 0.05
224 2 0.00
225 15 0.01
226 3 0.00
227 30 0.02
228 18 0.01
229 6 0.00
230 14 0.01
231 1 0.00
233 5 0.00
234 39 0.03
235 13 0.01
236 4 0.00
237 3 0.00
238 2 0.00
239 61 0.04
240 2 0.00
241 4 0.00
242 4 0.00
243 1 0.00
248 64 0.05
249 1 0.00
250 61 0.04
252 17 0.01
253 4 0.00
254 34 0.02
257 21 0.02
258 5 0.00
259 38 0.03
260 1 0.00
261 1 0.00
263 5 0.00
264 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (216 bp):
GTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGTTGAGG
TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
GTTGAGGTAATTTCAATTTCT
Found at i:38344320 original size:13 final size:13
Alignment explanation
Indices: 38344302--38344331 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38344292 ACGTGCTGAG
38344302 TATTTTCAATTTC
1 TATTTTCAATTTC
38344315 TATTTTCAATTTC
1 TATTTTCAATTTC
38344328 TATT
1 TATT
38344332 CGTCAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTCAATTTC
Found at i:38344365 original size:86 final size:82
Alignment explanation
Indices: 38344085--38344411 Score: 294
Period size: 86 Copynumber: 3.9 Consensus size: 82
38344075 ATTTCTGTTT
* ** * *
38344085 TCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA-TGCTGAGGTATTTTCAAT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACTGCTGA-GTATTTTCAAT
* * **
38344149 TTCTGTTT---TTGA--AA
64 TTCTTTTTCAATTTATTCG
** * * *
38344163 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACTG-AG-GTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACTGCTGAGTATTTTCAA-T
* **
38344226 TTCGTTTGTCAATTTATTTT
64 TTC-TTTTTCAATTTATTCG
38344246 TCAAAAATCCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGTATTTTCAA
1 TCAAAAAT-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TCAC-TGCTGAGTATTTTCAA
38344311 TTTCTATTTTCAATTTCTATTCG
63 TTTCT-TTTTCAA-TT-TATTCG
38344334 TC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TCAC-TGCTGA-GTATTTTCAA
38344398 TTTCTGTCTTTCAA
63 TTTCT-T-TTTCAA
38344412 AAAAAATGAG
Statistics
Matches: 209, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
76 10 0.05
77 4 0.02
78 45 0.22
79 2 0.01
81 3 0.01
83 7 0.03
84 35 0.17
85 3 0.01
86 55 0.26
87 33 0.16
88 12 0.06
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (82 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACTGCTGAGTATTTTCAATTT
CTTTTTCAATTTATTCG
Found at i:38344466 original size:56 final size:57
Alignment explanation
Indices: 38344360--38344469 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 57
38344350 TTGCGAGAGG
* * *
38344360 TGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAA
1 TGAGTTGAGCCTCGG-TCACACGCTGAGGGATTTTCAATTTCTCTCTTTCAAAAAAAA
*
38344418 TGAGTTGAGCCTCGG-GACACGCTGAGGGATTTTCAATTTCTACT-TTTCAAAA
1 TGAGTTGAGCCTCGGTCACACGCTGAGGGATTTTCAATTTCT-CTCTTTCAAAA
38344470 GAATCAACTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
56 31 0.66
57 1 0.02
58 15 0.32
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (57 bp):
TGAGTTGAGCCTCGGTCACACGCTGAGGGATTTTCAATTTCTCTCTTTCAAAAAAAA
Found at i:38344555 original size:75 final size:75
Alignment explanation
Indices: 38344418--38344694 Score: 425
Period size: 75 Copynumber: 3.7 Consensus size: 75
38344408 TCAAAAAAAA
*
38344418 TGAGTTGAGCCTCGGG--ACACGCTGAG-GGATTTTCAATTTCTACTTTTCAAAAGAATCAACTC
1 TGAGTTGAGCCTCGGGTCACACGCTGAGACG-TTTTCAATTTCTACTTTTC-AAA-AATCAACTC
*
38344480 ATATTGCGAGAGG
63 ACATTGCGAGAGG
*
38344493 TGAGTTGAGCCTCGGGTCACACGCTGAGACGTTTTCAATTTCTGCTTTTCAAAAATCAACTCACA
1 TGAGTTGAGCCTCGGGTCACACGCTGAGACGTTTTCAATTTCTACTTTTCAAAAATCAACTCACA
38344558 TTGCGAGAGG
66 TTGCGAGAGG
*
38344568 TGAGTTGAGCCTCGGGTCACACGCTGAGACGTTTTCAATTTCTGCTTTTCAAAAATCAACTCACA
1 TGAGTTGAGCCTCGGGTCACACGCTGAGACGTTTTCAATTTCTACTTTTCAAAAATCAACTCACA
38344633 TTGCGAGAGG
66 TTGCGAGAGG
* * ***
38344643 TGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTCTACTTTTCAA
1 TGAGTTGAGCCTCGGGTCACACGCTGAGACGTTTTCAATTTCTACTTTTCAA
38344695 TTTATATTTT
Statistics
Matches: 190, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
75 158 0.83
76 3 0.02
77 28 0.15
78 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (75 bp):
TGAGTTGAGCCTCGGGTCACACGCTGAGACGTTTTCAATTTCTACTTTTCAAAAATCAACTCACA
TTGCGAGAGG
Found at i:38344693 original size:14 final size:14
Alignment explanation
Indices: 38344674--38344708 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
38344664 TGCTGAGGTA
*
38344674 TTTTCAATTTCTAC
1 TTTTCAATTTATAC
*
38344688 TTTTCAATTTATAT
1 TTTTCAATTTATAC
38344702 TTTTCAA
1 TTTTCAA
38344709 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTATAC
Done.