Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_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: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:1969307 original size:115 final size:115
Alignment explanation
Indices: 1969096--1969335 Score: 290
Period size: 115 Copynumber: 2.1 Consensus size: 115
1969086 AAGATGACTC
*
1969096 CCCTTCGTAGTTTAAGACAGTCTTAATTCTTTGGATGACTCCCCTTCACGGGTCTAAGTCAAGTG
1 CCCTTCGCAGTTTAAGACAGTCTTAATTCTTTGGATGACTCCCCTTCACGGGTCTAAGTCAAGTG
* * *
1969161 AGATGGTTCCTCTTCATGATTTAGAGTAGTCTTAATTCTTTGGATGAATT
66 AGATGATTCCTCTTCACGATTTAGAGCAGTCTTAATTCTTTGGATGAATT
* * * * *
1969211 CCCTTCGCGGTTTAAGCCAGTCTTGATTCTTT-GAGTGACTCCCTTTCGCGGGTCTAAGTCAAGT
1 CCCTTCGCAGTTTAAGACAGTCTTAATTCTTTGGA-TGACTCCCCTTCACGGGTCTAAGTCAAGT
* * * * *
1969275 GAGATGATT-CTCCTTCGCGGTTTA-AGCCAGTCTTGATTCTTTGTAT-AACTC
65 GAGATGATTCCT-CTTCACGATTTAGAG-CAGTCTTAATTCTTTGGATGAA-TT
1969326 CCCTTCGCAG
1 CCCTTCGCAG
1969336 GTCTAAGTCA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
114 8 0.08
115 98 0.92
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (115 bp):
CCCTTCGCAGTTTAAGACAGTCTTAATTCTTTGGATGACTCCCCTTCACGGGTCTAAGTCAAGTG
AGATGATTCCTCTTCACGATTTAGAGCAGTCTTAATTCTTTGGATGAATT
Found at i:1969326 original size:74 final size:72
Alignment explanation
Indices: 1969203--1969416 Score: 261
Period size: 74 Copynumber: 2.9 Consensus size: 72
1969193 TAATTCTTTG
*
1969203 GATGAATTCCCTTCGCGGTTTAAGCCAGTCTTGATTCTTTGAGTGACTCCCTTTCGCGGGTCTAA
1 GATG-ATTCCCTTCGCGGTTTAAGCCAGTCTTGATTCTTTGA-TGACTCCCTTTCGCAGGTCTAA
1969268 GTCAAGTGA
64 GTCAAGTGA
* *
1969277 GATGATTCTCCTTCGCGGTTTAAGCCAGTCTTGATTCTTTGTATAACTCCCCTTCGCAGGTCTAA
1 GATGATTC-CCTTCGCGGTTTAAGCCAGTCTTGATTCTTTG-ATGACTCCCTTTCGCAGGTCTAA
1969342 GTCAAGTGA
64 GTCAAGTGA
* * * ** * *
1969351 GACGAATCCCCTTCACATTTTAAG-TAGGTCTTGATTCTTTGGATGACTCCCTTTCG-TGGTCTA
1 GATG-ATTCCCTTCGCGGTTTAAGCCA-GTCTTGATTCTTT-GATGACTCCCTTTCGCAGGTCTA
1969414 AGT
63 AGT
1969417 TATGTGAAAT
Statistics
Matches: 123, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
73 14 0.11
74 104 0.85
75 5 0.04
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (72 bp):
GATGATTCCCTTCGCGGTTTAAGCCAGTCTTGATTCTTTGATGACTCCCTTTCGCAGGTCTAAGT
CAAGTGA
Found at i:1974521 original size:44 final size:44
Alignment explanation
Indices: 1974467--1974643 Score: 246
Period size: 44 Copynumber: 4.0 Consensus size: 44
1974457 ATACCATGAG
**
1974467 TGGCACCTTTCTATCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* **
1974511 TGGTACCTTTCTGCCAATAATTTACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
*
1974555 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* * ** **
1974599 TGGCACATTTCTGCTAATAATATACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1974643 T
1 T
1974644 TTTAGAGCAG
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 119 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
Found at i:1974618 original size:88 final size:88
Alignment explanation
Indices: 1974467--1974643 Score: 273
Period size: 88 Copynumber: 2.0 Consensus size: 88
1974457 ATACCATGAG
* * *
1974467 TGGCACCTTTCTATCAATAATGCACCATTATGCATTTTCATTTATGGTACCTTTCTGCCAATAAT
1 TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTATGGCACATTTCTGCCAATAAT
*
1974532 TTACCATTATGCATTTTCATTTA
66 ATACCATTATGCATTTTCATTTA
* * *
1974555 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTCTGCTAATAAT
1 TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTATGGCACATTTCTGCCAATAAT
**
1974620 ATACTGTTATGCATTTTCATTTA
66 ATACCATTATGCATTTTCATTTA
1974643 T
1 T
1974644 TTTAGAGCAG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (88 bp):
TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTATGGCACATTTCTGCCAATAAT
ATACCATTATGCATTTTCATTTA
Found at i:1982620 original size:18 final size:19
Alignment explanation
Indices: 1982584--1982627 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
1982574 GTTTAGCGAT
1982584 AATATTTGAGTCATGGAGA
1 AATATTTGAGTCATGGAGA
1982603 AATATTTGAGTC-TGGAGA
1 AATATTTGAGTCATGGAGA
1982621 AATATTT
1 AATATTT
1982628 TCTCTATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (19 bp):
AATATTTGAGTCATGGAGA
Found at i:1988008 original size:4 final size:4
Alignment explanation
Indices: 1987999--1988025 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1987989 GAAATATCCA
1987999 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1988026 CCATAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1988137 original size:17 final size:17
Alignment explanation
Indices: 1988115--1988153 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1988105 TTTTTGAAAG
*
1988115 AATATAA-AAATAAATCA
1 AATATAATAAA-AAAACA
1988132 AATATAATAAAAAAACA
1 AATATAATAAAAAAACA
1988149 AATAT
1 AATAT
1988154 GCAAACTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AATATAATAAAAAAACA
Found at i:1988932 original size:4 final size:4
Alignment explanation
Indices: 1988923--1988949 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1988913 GAAATATCCA
1988923 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1988950 CCATAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1991277 original size:53 final size:54
Alignment explanation
Indices: 1991196--1991304 Score: 211
Period size: 53 Copynumber: 2.0 Consensus size: 54
1991186 ACAAGATGAC
1991196 TCCCCTTCGTAGTTTAAGATAGTCTTAATTCTTTGGATGACTCCCCTTCACGGG
1 TCCCCTTCGTAGTTTAAGATAGTCTTAATTCTTTGGATGACTCCCCTTCACGGG
1991250 TCCCCTTCGTAG-TTAAGATAGTCTTAATTCTTTGGATGACTCCCCTTCACGGG
1 TCCCCTTCGTAGTTTAAGATAGTCTTAATTCTTTGGATGACTCCCCTTCACGGG
1991303 TC
1 TC
1991305 TAAGTCAAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 43 0.78
54 12 0.22
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (54 bp):
TCCCCTTCGTAGTTTAAGATAGTCTTAATTCTTTGGATGACTCCCCTTCACGGG
Found at i:1997924 original size:29 final size:29
Alignment explanation
Indices: 1997892--1997968 Score: 133
Period size: 27 Copynumber: 2.8 Consensus size: 29
1997882 AAAATAAAGA
1997892 ATAAAGAATGTAAAAATGTAAAAAAAATT
1 ATAAAGAATGTAAAAATGTAAAAAAAATT
1997921 ATAAAGAATGTAAAAATGT--AAAAAATT
1 ATAAAGAATGTAAAAATGTAAAAAAAATT
1997948 ATAAAGAATGT-AAAATGTAAA
1 ATAAAGAATGTAAAAATGTAAA
1997969 GAATGATTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.15
27 19 0.41
28 1 0.02
29 19 0.41
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.25
Consensus pattern (29 bp):
ATAAAGAATGTAAAAATGTAAAAAAAATT
Found at i:1997970 original size:16 final size:17
Alignment explanation
Indices: 1997893--1997973 Score: 67
Period size: 19 Copynumber: 4.5 Consensus size: 17
1997883 AAATAAAGAA
1997893 TAAAGAATGTAAAAATG
1 TAAAGAATGTAAAAATG
* *
1997910 TAAAAAAAATTATAAAGAATG
1 T--AAAGAA-TGTAAA-AATG
*
1997931 TAAA-AATGTAAAAAATTA
1 TAAAGAATGT-AAAAA-TG
1997949 TAAAGAATGT-AAAATG
1 TAAAGAATGTAAAAATG
1997965 TAAAGAATG
1 TAAAGAATG
1997974 ATTGCCACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
16 10 0.19
17 9 0.17
18 10 0.19
19 13 0.25
20 5 0.10
21 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.25
Consensus pattern (17 bp):
TAAAGAATGTAAAAATG
Found at i:2001817 original size:13 final size:13
Alignment explanation
Indices: 2001799--2001828 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2001789 GTTACAACCC
2001799 GACCCGACCCATT
1 GACCCGACCCATT
2001812 GACCCGACCCATT
1 GACCCGACCCATT
2001825 GACC
1 GACC
2001829 GTTGACCGTT
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:0.47, G:0.17, T:0.13
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:2001964 original size:67 final size:67
Alignment explanation
Indices: 2001852--2002001 Score: 182
Period size: 67 Copynumber: 2.3 Consensus size: 67
2001842 CGTTGATGGG
* *
2001852 TGACATTTTAGTAATTATTTTGAAACTGATGACATATTGGGAATTAATTCGAAAA-GGATGCTAC
1 TGACATTTTAGTAAATATTTTGAAAATGATGACATATTGGGAATTAATTCGAAAATGG-TGCTAC
2001916 TTT
65 TTT
* * ** *
2001919 TGACATTTTAGTAAATATTTTGAAAATGGTG-CTATATTGGTAATTAATTTTAAAATGGTGCTAT
1 TGACATTTTAGTAAATATTTTGAAAATGATGAC-ATATTGGGAATTAATTCGAAAATGGTGCTAC
2001983 TTT
65 TTT
2001986 TGTA-ATTTT-GTAAATA
1 TG-ACATTTTAGTAAATA
2002002 AATAAATAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
66 8 0.11
67 62 0.85
68 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (67 bp):
TGACATTTTAGTAAATATTTTGAAAATGATGACATATTGGGAATTAATTCGAAAATGGTGCTACT
TT
Found at i:2001973 original size:29 final size:30
Alignment explanation
Indices: 2001935--2001992 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
2001925 TTTAGTAAAT
2001935 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTGGTAATTA
* *
2001965 ATTTT-AAAATGGTGCTATTTTTGTAATT
1 ATTTTGAAAATGGTGCTATATTGGTAATT
2001993 TTGTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.48
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTGGTAATTA
Found at i:2002741 original size:24 final size:24
Alignment explanation
Indices: 2002714--2002799 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
2002704 TAGTTATCTA
*
2002714 ATATGATATTTGACCTGAAATTTT
1 ATATGATACTTGACCTGAAATTTT
* * *
2002738 ATATGATACTTGACATG-GATTCTG
1 ATATGATACTTGACCTGAAATT-TT
* * *
2002762 ATATGTTACCTGACCTGAATTTTT
1 ATATGATACTTGACCTGAAATTTT
2002786 ATATGATACTTGAC
1 ATATGATACTTGAC
2002800 ATGGATTCTG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.06
24 43 0.90
25 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (24 bp):
ATATGATACTTGACCTGAAATTTT
Found at i:2002786 original size:48 final size:48
Alignment explanation
Indices: 2002724--2002827 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
2002714 ATATGATATT
2002724 TGACCTGAAATTTTATATGATACTTGACATGGATTCTGATATGTTACC
1 TGACCTGAAATTTTATATGATACTTGACATGGATTCTGATATGTTACC
* *
2002772 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
1 TGACCTGAAATTTTATATGATACTTGACATGGATTCTGATATGTTACC
2002820 TGACCTGA
1 TGACCTGA
2002828 TTTATGTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (48 bp):
TGACCTGAAATTTTATATGATACTTGACATGGATTCTGATATGTTACC
Found at i:2009182 original size:35 final size:35
Alignment explanation
Indices: 2009124--2009192 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
2009114 ATCGCCCAAC
* * *
2009124 ATTCTAAACCCCAAAATCTAAAATTCTTTAATTAT
1 ATTCTAAACCCCAAAATCCAAAATACTTCAATTAT
* * *
2009159 ATTCTAAATCTCAAATTCCAAAATACTTCAATTA
1 ATTCTAAACCCCAAAATCCAAAATACTTCAATTA
2009193 CATGCCCAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (35 bp):
ATTCTAAACCCCAAAATCCAAAATACTTCAATTAT
Found at i:2009647 original size:149 final size:149
Alignment explanation
Indices: 2009377--2009653 Score: 500
Period size: 149 Copynumber: 1.9 Consensus size: 149
2009367 TCATTTTATT
2009377 AAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAATTG
1 AAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAATTG
* * *
2009442 AATTTTCGAGTTTCTGTTTAAATGTAATTATAAATATTTATCATATTATAATATTATTTGATTCT
66 AATTTTCAAGTTTCTGTTTAAATGTAATTATAAATATTTATAATACTATAATATTATTTGATTCT
2009507 AATTCAGTTTAGTTTATAA
131 AATTCAGTTTAGTTTATAA
*
2009526 AAATAGTTTACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAATTG
1 AAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAATTG
* *
2009591 AATTTTCAAGTTTCTTTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATT
66 AATTTTCAAGTTTCTGTTTAAATGTAATTATAAATATTTATAATACTATAATATTATTTGATT
2009654 ATAAATTAAA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 122 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.47
Consensus pattern (149 bp):
AAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAATTG
AATTTTCAAGTTTCTGTTTAAATGTAATTATAAATATTTATAATACTATAATATTATTTGATTCT
AATTCAGTTTAGTTTATAA
Found at i:2010232 original size:34 final size:36
Alignment explanation
Indices: 2010160--2010238 Score: 117
Period size: 34 Copynumber: 2.2 Consensus size: 36
2010150 GGGTTGGGAT
**
2010160 TGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGAA
1 TGTAATTGAAACATTTTTGGAATTTGAGGTTTAGAA
*
2010196 TGTAATTGAAACA-TTTTGGAATTT-AGGTTTATAA
1 TGTAATTGAAACATTTTTGGAATTTGAGGTTTAGAA
2010230 TGTAATTGA
1 TGTAATTGA
2010239 TGACTGTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 18 0.45
35 11 0.28
36 11 0.28
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (36 bp):
TGTAATTGAAACATTTTTGGAATTTGAGGTTTAGAA
Found at i:2011163 original size:23 final size:23
Alignment explanation
Indices: 2011137--2011193 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
2011127 ACTTTGATGC
*
2011137 TGAATCATTCAGCACAGTTTTGT
1 TGAATCAGTCAGCACAGTTTTGT
* * *
2011160 TGAATTAGTCAGTACTGTTTTGT
1 TGAATCAGTCAGCACAGTTTTGT
2011183 TGAATCAGTCA
1 TGAATCAGTCA
2011194 ATACTGAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (23 bp):
TGAATCAGTCAGCACAGTTTTGT
Found at i:2011198 original size:23 final size:23
Alignment explanation
Indices: 2011153--2011199 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2011143 ATTCAGCACA
* *
2011153 GTTTTGTTGAATTAGTCAGTACT
1 GTTTTGTTGAATCAGTCAATACT
2011176 GTTTTGTTGAATCAGTCAATACT
1 GTTTTGTTGAATCAGTCAATACT
2011199 G
1 G
2011200 AATCATTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (23 bp):
GTTTTGTTGAATCAGTCAATACT
Found at i:2011260 original size:29 final size:29
Alignment explanation
Indices: 2011226--2011292 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
2011216 GAAACAAACA
2011226 CGCTGAATGATGAACGATTCAACATTCAG
1 CGCTGAATGATGAACGATTCAACATTCAG
2011255 CGCTGAATGATGAACGATTCAACATTCAG
1 CGCTGAATGATGAACGATTCAACATTCAG
2011284 CGCTGAATG
1 CGCTGAATG
2011293 GTTCCATTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (29 bp):
CGCTGAATGATGAACGATTCAACATTCAG
Found at i:2011953 original size:25 final size:27
Alignment explanation
Indices: 2011917--2011971 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
2011907 ATCATTTAAG
*
2011917 TAATTTTCATAAAAGA-AAATTTTATA
1 TAATTTTCATAAAAGATAAATTTAATA
* *
2011943 TAATTTT-ATAATAGATATATTTAATA
1 TAATTTTCATAAAAGATAAATTTAATA
2011969 TAA
1 TAA
2011972 AATAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (27 bp):
TAATTTTCATAAAAGATAAATTTAATA
Found at i:2019958 original size:44 final size:44
Alignment explanation
Indices: 2019899--2020295 Score: 596
Period size: 44 Copynumber: 9.0 Consensus size: 44
2019889 ATACCATGAG
* *
2019899 TGGCACCTTTTTGCCAAAAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
2019943 TGGAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
2019987 TCGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTAA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
2020031 TGGCACCTTTCTGCTAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
2020075 TGGCTCATTTTTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
2020119 TGGCACCTTTCTGCCAATACTGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * ** * * * *
2020163 AGGCATCTTTCTATCAAAAACGCACCGCTATTCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
2020207 TAGCACATTTCTGTCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
2020251 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
2020295 T
1 T
2020296 TTTAGAGTAT
Statistics
Matches: 313, Mismatches: 40, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 313 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:2026011 original size:44 final size:44
Alignment explanation
Indices: 2025948--2026124 Score: 300
Period size: 44 Copynumber: 4.0 Consensus size: 44
2025938 ATACCATGAG
* *
2025948 TGGCACCTTTCTGTCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
2025992 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
2026036 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
2026080 TGGCATCTTTCTGCCAATAATGTACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
2026124 T
1 T
2026125 TTTAGAGCAC
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 126 1.00
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:2028293 original size:20 final size:21
Alignment explanation
Indices: 2028256--2028294 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2028246 ATGATATCTA
**
2028256 TTTATTTCTATTTGTTTTTAT
1 TTTATTTCTATTCATTTTTAT
2028277 TTTATTT-TATTCATTTTT
1 TTTATTTCTATTCATTTTT
2028295 TGCGATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTATTTCTATTCATTTTTAT
Found at i:2029852 original size:44 final size:44
Alignment explanation
Indices: 2029789--2030049 Score: 378
Period size: 44 Copynumber: 5.9 Consensus size: 44
2029779 CATGAGTGGC
*
2029789 ACCTTTCTGTCAATAATGCACCGTTATGCATTTTCATTTATGGA
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* * * * *
2029833 ACCTTTATTCAAATAATGCACTGTTATGCATTTTCATTTATAGA
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* **
2029877 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTCATGTC
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* *
2029921 ACCTTTCTGCCAATAATGAACCGTTATGCATTTTCATTTATGGC
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* *
2029965 ACCTTTCTACCAATAACGCACCGTTATGCATTTTCATTTATGGA
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* * *
2030009 ACTTTTCTGCCAATAATGTACTGTTATGCATTTTCATTTAT
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
2030050 TTTAGAGCAG
Statistics
Matches: 191, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 191 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (44 bp):
ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
Found at i:2033715 original size:44 final size:44
Alignment explanation
Indices: 2033648--2033912 Score: 350
Period size: 44 Copynumber: 6.0 Consensus size: 44
2033638 ATACCATGAG
**
2033648 TGGCACCTTTCTGTCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
2033692 TGGAACCTTTATTCAAATAATGCACCGTTATGCATTTACATTTA
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
2033736 TAGAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCAATAA
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
2033780 TGTCACCTTTCTGCCAATAATGAACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
*
2033824 TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
* * *
2033868 TGGCACCTTTCTACCAATAAAGTACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
2033912 T
1 T
2033913 TTTAGAGCAA
Statistics
Matches: 194, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 194 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (44 bp):
TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:2036501 original size:13 final size:12
Alignment explanation
Indices: 2036483--2036526 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2036473 CCAATTTTTA
*
2036483 TTTTAAAACATTT
1 TTTTAAAA-ATAT
*
2036496 TTTTAAAAATAG
1 TTTTAAAAATAT
2036508 TTTTAAAATATAT
1 TTTTAAAA-ATAT
2036521 TTTTAA
1 TTTTAA
2036527 GTAATCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTTAAAAATAT
Found at i:2037581 original size:44 final size:44
Alignment explanation
Indices: 2037518--2037780 Score: 364
Period size: 44 Copynumber: 6.0 Consensus size: 44
2037508 ACCATGAGTA
**
2037518 GAACCTTTCTGTCAATAATGCACCGTTATGCATTTTCATTTATG
1 GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
* * * *
2037562 GAACCTTTATTCAAATAATGCACCGTTATGCATTTTCATTTATA
1 GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
* *
2037606 GAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTCATG
1 GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
** * * *
2037650 TCACCTTTCTGCCAATAATGAACCATTATGCATTTTCATTTATG
1 GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
*
2037694 GCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
1 GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
* * **
2037738 GCACCTTTCTACCAATAATGTACTATTATGCATTTTCATTTAT
1 GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTAT
2037781 TTTAGAGCAG
Statistics
Matches: 197, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 197 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (44 bp):
GAACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATG
Found at i:2039897 original size:18 final size:19
Alignment explanation
Indices: 2039868--2039906 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2039858 ATGTTATCTA
*
2039868 TTTATTTCTATTTATTTTT
1 TTTATTTCTATTCATTTTT
2039887 TTTATTT-TATTCATTTTT
1 TTTATTTCTATTCATTTTT
2039905 TT
1 TT
2039907 CGATTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTATTTCTATTCATTTTT
Found at i:2040374 original size:13 final size:12
Alignment explanation
Indices: 2040356--2040399 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2040346 CCAATTTTTA
*
2040356 TTTTAAAACATTT
1 TTTTAAAA-ATAT
*
2040369 TTTTAAAAATAG
1 TTTTAAAAATAT
2040381 TTTTAAAAGATAT
1 TTTTAAAA-ATAT
2040394 TTTTAA
1 TTTTAA
2040400 GTAATCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (12 bp):
TTTTAAAAATAT
Found at i:2042512 original size:54 final size:54
Alignment explanation
Indices: 2042379--2042778 Score: 461
Period size: 54 Copynumber: 7.3 Consensus size: 54
2042369 CATTGAGATT
* ** * * ** *
2042379 CACACTTAGTGCTTATACGGTCATCCAT-AATCATATTATGAATTCCATGGTTTG
1 CACACTTAGTGCCTATACGGTTGTTCATCAA-CATATGATGAATTCTGTGGGTTG
* *
2042433 CACA--TAGTGCCTATACGGTCT-TTCATCAACATATTATGAATTCTGTGGGTTA
1 CACACTTAGTGCCTATACGGT-TGTTCATCAACATATGATGAATTCTGTGGGTTG
* **
2042485 CACACATAGTGCCTATATAGTTGTTCATCAACATATGATGAATTAC-GTGGGTTG
1 CACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-CTGTGGGTTG
* * * * *
2042539 CATACTTAGTGCATATACAGTTATTCATCAACATATGATGAATTTTGTGGGTTG
1 CACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTG
*
2042593 CACACTTAGTGCCTATACGGTTGTTCATCAACATATGACATATGATGAATTATGTGGGTTG
1 CACACTTAGTGCCTATACGGTTGTTCAT---C--A--ACATATGATGAATTCTGTGGGTTG
* *
2042654 CACAGTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
1 CACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTG
2042708 CACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTAC-GTGGGTTG
1 CACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-CTGTGGGTTG
*
2042762 CACACTTAATGCCTATA
1 CACACTTAGTGCCTATA
2042779 ATACACATAT
Statistics
Matches: 304, Mismatches: 27, Indels: 30
0.84 0.07 0.08
Matches are distributed among these distances:
52 41 0.13
53 3 0.01
54 204 0.67
55 2 0.01
56 1 0.00
57 1 0.00
58 1 0.00
59 1 0.00
61 50 0.16
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (54 bp):
CACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTG
Found at i:2042664 original size:61 final size:61
Alignment explanation
Indices: 2042569--2042745 Score: 269
Period size: 61 Copynumber: 3.0 Consensus size: 61
2042559 TTATTCATCA
*
2042569 ACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
1 ACATATGATGAATTATGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
*
2042630 ACATATGATGAATTATGTGGGTTGCACAGTTAGTGCCTATACGGTTGTTCAT---C--A--
1 ACATATGATGAATTATGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
**
2042684 ACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
1 ACATATGATGAATTATGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
2042745 A
1 A
2042746 TGAATTACGT
Statistics
Matches: 104, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
54 49 0.47
56 1 0.01
57 1 0.01
58 1 0.01
59 1 0.01
61 51 0.49
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (61 bp):
ACATATGATGAATTATGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
Found at i:2042679 original size:169 final size:169
Alignment explanation
Indices: 2042461--2042778 Score: 501
Period size: 169 Copynumber: 1.9 Consensus size: 169
2042451 TCTTTCATCA
* * *
2042461 ACATATTATGAATTCTGTGGGTTACACACATAGTGCCTATATAGTTGTTCATCAACATATGATGA
1 ACATATGATGAATTATGTGGGTTACACACATAGTGCCTATACAGTTGTTCATCAACATATGATGA
* **
2042526 ATTACGTGGGTTGCATACTTAGTGCATATACAGTTATTCATCAACATATGATGAATTTTGTGGGT
66 ATTACGTGGGTTGCACACTTAGTGCATATACAGTTATTCATCAACATATGATGAATTACGTGGGT
*
2042591 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATG
131 TGCACACTTAATGCCTATACGGTTGTTCATCAACATATG
* ** *
2042630 ACATATGATGAATTATGTGGGTTGCACAGTTAGTGCCTATACGGTTGTTCATCAACATATGATGA
1 ACATATGATGAATTATGTGGGTTACACACATAGTGCCTATACAGTTGTTCATCAACATATGATGA
* * * *
2042695 ATTCCGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTACGTGGGT
66 ATTACGTGGGTTGCACACTTAGTGCATATACAGTTATTCATCAACATATGATGAATTACGTGGGT
2042760 TGCACACTTAATGCCTATA
131 TGCACACTTAATGCCTATA
2042779 ATACACATAT
Statistics
Matches: 134, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
169 134 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (169 bp):
ACATATGATGAATTATGTGGGTTACACACATAGTGCCTATACAGTTGTTCATCAACATATGATGA
ATTACGTGGGTTGCACACTTAGTGCATATACAGTTATTCATCAACATATGATGAATTACGTGGGT
TGCACACTTAATGCCTATACGGTTGTTCATCAACATATG
Found at i:2042689 original size:115 final size:113
Alignment explanation
Indices: 2042410--2042745 Score: 436
Period size: 115 Copynumber: 3.0 Consensus size: 113
2042400 CATCCATAAT
* * * * *
2042410 CATATTATGAATTCCATGGTTTGCACA-TAGTGCCTATACGGTCTTTCATCAACATATTATGAAT
1 CATATGATGAATTACGTGGGTTGCACATTAGTGCCTATACGGT-TTTCATCAACATATGATGAAT
* * **
2042474 TCTGTGGGTTACACACATAGTGCCTATATAGTTGTTCAT---C--A--A
65 TCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGA
* * *
2042516 CATATGATGAATTACGTGGGTTGCATACTTAGTGCATATACAGTTATTCATCAACATATGATGAA
1 CATATGATGAATTACGTGGGTTGCACA-TTAGTGCCTATACGGTT-TTCATCAACATATGATGAA
*
2042581 TTTTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGA
64 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGA
*
2042631 CATATGATGAATTATGTGGGTTGCACAGTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
1 CATATGATGAATTACGTGGGTTGCACA-TTAGTGCCTATACGGTT-TTCATCAACATATGATGAA
*
2042696 TTCCGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGA
64 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGA
2042746 TGAATTACGT
Statistics
Matches: 199, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
106 22 0.11
107 1 0.01
108 66 0.33
111 1 0.01
113 1 0.01
115 108 0.54
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (113 bp):
CATATGATGAATTACGTGGGTTGCACATTAGTGCCTATACGGTTTTCATCAACATATGATGAATT
CTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGA
Found at i:2043146 original size:20 final size:20
Alignment explanation
Indices: 2043121--2043170 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2043111 AGGCTCAATA
2043121 GTATCGATACCCCTACCCTG
1 GTATCGATACCCCTACCCTG
2043141 GTATCGATACCCCTACCCTG
1 GTATCGATACCCCTACCCTG
2043161 GTATCGATAC
1 GTATCGATAC
2043171 TTCTATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCCTACCCTG
Found at i:2050445 original size:19 final size:19
Alignment explanation
Indices: 2050421--2050463 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2050411 TAAAAAAAAG
2050421 TTTTAACT-TTTTTTCTATA
1 TTTTAACTATTTTTT-TATA
*
2050440 TTTTAACTATTTTTTTGTA
1 TTTTAACTATTTTTTTATA
2050459 TTTTA
1 TTTTA
2050464 TAATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTAACTATTTTTTTATA
Found at i:2051517 original size:18 final size:19
Alignment explanation
Indices: 2051494--2051533 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2051484 TTCCCAGTAA
*
2051494 TTTTATT-TTCTGATAATC
1 TTTTATTCTACTGATAATC
2051512 TTTTATTCGTACTGATAATC
1 TTTTATTC-TACTGATAATC
2051532 TT
1 TT
2051534 ACATTTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTTATTCTACTGATAATC
Found at i:2052139 original size:31 final size:31
Alignment explanation
Indices: 2052101--2052163 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2052091 GCACAAAGCC
*
2052101 AAGTGACTTCAGAAACAACATTAGCAACCCT
1 AAGTGACTTCAGAAACAACATTAACAACCCT
2052132 AAGTGACTTCAGAAACAACATTAACAACCCT
1 AAGTGACTTCAGAAACAACATTAACAACCCT
2052163 A
1 A
2052164 CGATACTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (31 bp):
AAGTGACTTCAGAAACAACATTAACAACCCT
Found at i:2052796 original size:43 final size:43
Alignment explanation
Indices: 2052735--2052821 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2052725 CAACCAAGAG
2052735 ACGTTACTACCTCTTCAATCATCTCATTAGAATCTCCCGTAAT
1 ACGTTACTACCTCTTCAATCATCTCATTAGAATCTCCCGTAAT
2052778 ACGTTACTACCTCTTCAATCATCTCATTAGAATCTCCCGTAAT
1 ACGTTACTACCTCTTCAATCATCTCATTAGAATCTCCCGTAAT
2052821 A
1 A
2052822 ACAATATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (43 bp):
ACGTTACTACCTCTTCAATCATCTCATTAGAATCTCCCGTAAT
Found at i:2053995 original size:136 final size:136
Alignment explanation
Indices: 2053751--2054023 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
2053741 TTGAGAGGAG
2053751 CACAAATCATGAGAAATACCAGGAGACAACACCTCTTAACCACCAGAATCTTCACAGGGGGCCCA
1 CACAAATCATGAGAAATACCAGGAGACAACACCTCTTAACCACCAGAATCTTCACAGGGGGCCCA
2053816 TCTGACACAATGGTGTGAGTAATATGGTTTTCACGCAACAAATTGGGGGCCAACACATCTTTGTC
66 TCTGACACAATGGTGTGAGTAATATGGTTTTCACGCAACAAATTGGGGGCCAACACATCTTTGTC
2053881 AACACC
131 AACACC
2053887 CACAAATCATGAGAAATACCAGGAGACAACACCTCTTAACCACCAGAATCTTCACAGGGGGCCCA
1 CACAAATCATGAGAAATACCAGGAGACAACACCTCTTAACCACCAGAATCTTCACAGGGGGCCCA
2053952 TCTGACACAATGGTGTGAGTAATATGGTTTTCACGCAACAAATTGGGGGCCAACACATCTTTGTC
66 TCTGACACAATGGTGTGAGTAATATGGTTTTCACGCAACAAATTGGGGGCCAACACATCTTTGTC
2054017 AACACC
131 AACACC
2054023 C
1 C
2054024 GTACACTACA
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (136 bp):
CACAAATCATGAGAAATACCAGGAGACAACACCTCTTAACCACCAGAATCTTCACAGGGGGCCCA
TCTGACACAATGGTGTGAGTAATATGGTTTTCACGCAACAAATTGGGGGCCAACACATCTTTGTC
AACACC
Found at i:2054371 original size:176 final size:176
Alignment explanation
Indices: 2054077--2054423 Score: 570
Period size: 176 Copynumber: 2.0 Consensus size: 176
2054067 TATATTGATG
** * * *
2054077 TTTTTAAGCGTCGTTAAATTTTTGTGACGTAAAAAGCGTCATTAAAATAAACGCCACAAAAGGTA
1 TTTTTAAGCGTCGTTAAATTTTTGTGACACAAAAAGCGTCACTAAAACAAACGCCACAAAAGATA
* * *
2054142 GTAACGTTTGTCATTCATAAACGCCATTAAATGTTCTGACATATAATAATGTTTGTTCTCAAAAA
66 GTAACGTCTGTCATTCATAAACGCCATTAAATGTTCTGACATATAACAATGTTTGTTCCCAAAAA
*
2054207 GACCAGTCGTCGGTATTTCATCTATTAAGGGAAAAAGAAAGTGGCT
131 GACAAGTCGTCGGTATTTCATCTATTAAGGGAAAAAGAAAGTGGCT
2054253 TTTTTAAGCGTCGTTAAATTTTTTGTGACACAAAAAGCGTCACTAAAACAAACGCCACAAAA-AT
1 TTTTTAAGCGTCGTTAAA-TTTTTGTGACACAAAAAGCGTCACTAAAACAAACGCCACAAAAGAT
* *
2054317 AGTAGCGTCTGTCATTCATAAATGCCATTAAATGTTCTGACATATAACAATGTTTGTTCCCAAAA
65 AGTAACGTCTGTCATTCATAAACGCCATTAAATGTTCTGACATATAACAATGTTTGTTCCCAAAA
*
2054382 AGACAAGTTGTCGGTATTTCATCTATTAAGGGAAAAAGAAAG
130 AGACAAGTCGTCGGTATTTCATCTATTAAGGGAAAAAGAAAG
2054424 CACAAATAAT
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 119 0.75
177 39 0.25
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (176 bp):
TTTTTAAGCGTCGTTAAATTTTTGTGACACAAAAAGCGTCACTAAAACAAACGCCACAAAAGATA
GTAACGTCTGTCATTCATAAACGCCATTAAATGTTCTGACATATAACAATGTTTGTTCCCAAAAA
GACAAGTCGTCGGTATTTCATCTATTAAGGGAAAAAGAAAGTGGCT
Found at i:2056738 original size:40 final size:41
Alignment explanation
Indices: 2056686--2056773 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
2056676 CGGCTATAAA
* * *
2056686 AAAAACGCCACTAAAATATGAGTCGTTAG-CGCATTTGTAT
1 AAAAACGACACTAAAATACGAGTCGTTAGTAGCATTTGTAT
* * *
2056726 AAAAACGACACTAAAGTACGAGTCTTTAGTAGCGTTTGTAT
1 AAAAACGACACTAAAATACGAGTCGTTAGTAGCATTTGTAT
*
2056767 ACAAACG
1 AAAAACG
2056774 CTGCTAATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 25 0.62
41 15 0.38
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (41 bp):
AAAAACGACACTAAAATACGAGTCGTTAGTAGCATTTGTAT
Found at i:2056973 original size:41 final size:41
Alignment explanation
Indices: 2056923--2057034 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 41
2056913 CGTTCACGGT
* *
2056923 GTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG-AGAC
1 GTTTATATAAAAATGCCACTAAAGTACGAGTCTATAGTAG-C
* * *
2056964 GTTTCTATAAAAATGCAACTAAAGTAC-AGTCTTTAGTAGC
1 GTTTATATAAAAATGCCACTAAAGTACGAGTCTATAGTAGC
* *
2057004 ATTTATATAAAAATGGCACTAAAGTACGAGT
1 GTTTATATAAAAATGCCACTAAAGTACGAGT
2057035 ATTTTGCGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 32 0.52
41 29 0.48
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (41 bp):
GTTTATATAAAAATGCCACTAAAGTACGAGTCTATAGTAGC
Found at i:2058980 original size:23 final size:24
Alignment explanation
Indices: 2058949--2058996 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
2058939 ATTTTGAATC
*
2058949 AATTTAATAGATTTTAGTG-TTTT
1 AATTGAATAGATTTTAGTGATTTT
2058972 AATTGAATAGATTTTAGTGATTTT
1 AATTGAATAGATTTTAGTGATTTT
2058996 A
1 A
2058997 TGAAGAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (24 bp):
AATTGAATAGATTTTAGTGATTTT
Found at i:2069505 original size:15 final size:17
Alignment explanation
Indices: 2069485--2069516 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2069475 CATAATATAA
2069485 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
2069500 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
2069517 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:2072763 original size:183 final size:183
Alignment explanation
Indices: 2072430--2073081 Score: 963
Period size: 183 Copynumber: 3.6 Consensus size: 183
2072420 TTTCGGTACT
* * * *
2072430 TATCGATACTATTA-AAATATGTATTGATACATAACAATATATCAGGTAAAAATATGAGAAAACC
1 TATCGATACT-TTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACC
* * * *
2072494 GA-TTCA-ATGTGATAAAACCGATAAAGC-ACTACCAGATATGTTGAAGGTATCGATTCCATTCA
65 GATTTCATA-ATGACAAAACCGGTAAAGCGA-TACCGGATATGTTGAAGGTATCGATTCCATTCA
* *
2072556 AATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGGCTATAAAG
128 AATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAAG
*
2072612 TATCGATACTTTATAAACATGTATCGATACATAACAATATAAAAGGTAAAAATATGACAAAACCG
1 TATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCG
* * *
2072677 ATTTCATAATGACAAAACTGGTAAAGCGATACCGTATATGTTGAAGGTATCGATTCTATTCAAAT
66 ATTTCATAATGACAAAACCGGTAAAGCGATACCGGATATGTTGAAGGTATCGATTCCATTCAAAT
* * *
2072742 AAGTATCGACACATTTGGAATTTAAAAGAAAAGCAATAATGGCGCCTATAAAA
131 AAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAAG
*
2072795 TATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAATCG
1 TATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCG
* *
2072860 GTTTCAAAATGACAAAACCGGTAAAGCGATACCGGATATGTTGAAGGTATCGATTCCATTCAAAT
66 ATTTCATAATGACAAAACCGGTAAAGCGATACCGGATATGTTGAAGGTATCGATTCCATTCAAAT
* * *
2072925 AAGTATCAACACTTTTGGAATTTAAAAGAAAAACAATAATAACGCCTATAAAG
131 AAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAAG
** * *
2072978 TATTAATACTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATAACAAAACCT
1 TATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACC-
* * *
2073043 G-TTTCATAGTGACAAAACTGGTAAAGCGCTACCGGATAT
65 GATTTCATAATGACAAAACCGGTAAAGCGATACCGGATAT
2073082 ATTAAACGTA
Statistics
Matches: 426, Mismatches: 39, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
181 3 0.01
182 57 0.13
183 363 0.85
184 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (183 bp):
TATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCG
ATTTCATAATGACAAAACCGGTAAAGCGATACCGGATATGTTGAAGGTATCGATTCCATTCAAAT
AAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAAG
Found at i:2075307 original size:15 final size:15
Alignment explanation
Indices: 2075287--2075317 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2075277 TGGTAGTAGA
2075287 GGGATGACAATGAGG
1 GGGATGACAATGAGG
*
2075302 GGGATGACAGTGAGG
1 GGGATGACAATGAGG
2075317 G
1 G
2075318 AAAACAGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.52, T:0.13
Consensus pattern (15 bp):
GGGATGACAATGAGG
Found at i:2075567 original size:66 final size:66
Alignment explanation
Indices: 2075437--2075567 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 66
2075427 AAGGGGAAGT
* * *
2075437 GGGTGGAAAAATAGATGGAGTGGTGAAAGAAGTTAGGGAGTTGAGGGGTGAACTTAAGATGGTGA
1 GGGTGGAAAAATAGATGAAGTGGTGAAAGAAGTTAGGGAATTGAGGGGTGAACTTAAGAGGGTGA
2075502 C
66 C
* * * * * *
2075503 GGGTGGAAAAATTGATGAAGTGGTGAAGGAAGTTATGGAATTGAGTGGTGAACTTACGGGGGTGA
1 GGGTGGAAAAATAGATGAAGTGGTGAAAGAAGTTAGGGAATTGAGGGGTGAACTTAAGAGGGTGA
2075568 AGGGGGTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.32, C:0.03, G:0.42, T:0.23
Consensus pattern (66 bp):
GGGTGGAAAAATAGATGAAGTGGTGAAAGAAGTTAGGGAATTGAGGGGTGAACTTAAGAGGGTGA
C
Found at i:2078954 original size:29 final size:29
Alignment explanation
Indices: 2078921--2078979 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2078911 CCGTTTAAGT
2078921 GTGAAAACAATTAATAAATGCAGTTGGGA
1 GTGAAAACAATTAATAAATGCAGTTGGGA
2078950 GTGAAAACAATTAATAAATGCAGTTGGGA
1 GTGAAAACAATTAATAAATGCAGTTGGGA
2078979 G
1 G
2078980 CAGCGTCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.24
Consensus pattern (29 bp):
GTGAAAACAATTAATAAATGCAGTTGGGA
Found at i:2079270 original size:65 final size:64
Alignment explanation
Indices: 2079072--2079280 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
2079062 TATACTAAGA
* * ** *
2079072 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* * * *
2079136 GTGCATCGATACATCAAATGCATTTGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
2079199 AT-
63 -TG
* * *
2079201 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATAGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCAT-GGTT
2079265 G
64 G
*
2079266 GTGCATCGGTGCATC
1 GTGCATCGATGCATC
2079281 TCTATGAAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 47 0.40
65 61 0.52
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:2086627 original size:65 final size:63
Alignment explanation
Indices: 2086429--2086638 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 63
2086419 TGCACTAAGA
* * * * *
2086429 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCTAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCT-CACTGCATCGATGCATGATTG
* *
2086493 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCACTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCACTGCATCGATGCATGAT-T
2086558 -
63 G
* ** *
2086558 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGTTGCATCGATGCATAGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--CTGCATCGATGCAT-GAT
2086621 TG
62 TG
*
2086623 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
2086639 CTATGAAAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 46 0.38
65 64 0.52
66 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCACTGCATCGATGCATGATTG
Found at i:2088576 original size:179 final size:179
Alignment explanation
Indices: 2088256--2088579 Score: 517
Period size: 179 Copynumber: 1.8 Consensus size: 179
2088246 CCCAAACTTG
* * *
2088256 AAGTATCGATTCATGTATTATAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAAAGTGA
1 AAGTATCGATACATGTATTATAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAAAGTCA
2088321 TAGGTAAATTTACAATGTAACCAGTAAAAATATACCAATTTAATGAGAGAATAGGTAAACATAAT
66 TAGGTAAATTTACAATGTAACCAGTAAAAATATACCAATTTAATGAGAGAATAGGTAAACATAAT
2088386 GTATCGATACTTTTTGCCTAGAATGAATGCCCAACGAGGTGCACGCATA
131 GTATCGATACTTTTTGCCTAGAATGAATGCCCAACGAGGTGCACGCATA
* * * *
2088435 AAGTGTCGATACATTTATTGTAAGTATCGATCTC-ATAAACATCGAAACCAATAATTATAAAGTC
1 AAGTATCGATACATGTATTATAAGTATCGATC-CAAAAAACATCGAAACCAATAATTATAAAGTC
****
2088499 ATAGGTAAATTTACAATGTAACCAGTAAAAATATATTGGTTTAATGAGAGAATAGGTAAAC-TAA
65 ATAGGTAAATTTACAATGTAACCAGTAAAAATATACCAATTTAATGAGAGAATAGGTAAACATAA
2088563 CTGTATCGATACTTTTT
130 -TGTATCGATACTTTTT
2088580 TAAAATTGTA
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
178 3 0.02
179 128 0.97
180 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (179 bp):
AAGTATCGATACATGTATTATAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAAAGTCA
TAGGTAAATTTACAATGTAACCAGTAAAAATATACCAATTTAATGAGAGAATAGGTAAACATAAT
GTATCGATACTTTTTGCCTAGAATGAATGCCCAACGAGGTGCACGCATA
Found at i:2088899 original size:200 final size:200
Alignment explanation
Indices: 2088385--2088908 Score: 793
Period size: 201 Copynumber: 2.6 Consensus size: 200
2088375 GTAAACATAA
* *
2088385 TGTATCGATACTTTTTGCCTAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATT
1 TGTATCGATACTTTTTTCCTAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATT
* * *
2088450 TATTGTAAGTATCGATCTCATAAACATCGAAACCAATAATTATAAAGTCATAGGTAAATTTACAA
66 TATTGTAAGTATCGATC-CAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAA
* *
2088515 TGTAACCAGTAAAAATATATTGGTTTAATGAGAGAATAGGTAAACTAACTGTATCGATACTTTTT
130 TATAACCAGTAAAAATATATTGATTTAATGAGAGAATAGGTAAACTAACTGTATCGATACTTTTT
2088580 TAAAAT
195 TAAAAT
* * * * *
2088586 TGTAACGATA-TTTTTTACCCAGAATGAATGTCCAAAGAGGTACACACATAAAGTGTCGATACAT
1 TGTATCGATACTTTTTT-CCTAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACAT
* *
2088650 TTATTGTAAGTATTGATACCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTAGA
65 TTATTGTAAGTATCGAT-CCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACA
*
2088715 ATATAACCGGTAAAAATATATTGATTTAATGAGAGAATAGGTAAACTTAA-TGTATCGATAC-TT
129 ATATAACCAGTAAAAATATATTGATTTAATGAGAGAATAGGTAAAC-TAACTGTATCGATACTTT
2088778 TTTAAAAT
193 TTTAAAAT
* *
2088786 TGTATCGATACTTTTTTCCTAGAATGAATGCCCAACGAGGTGCACACGTAAAGTGTCAATACATT
1 TGTATCGATACTTTTTTCCTAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATT
* * * *
2088851 TATTATAAGTATCGATCCAAAAAATATCAAAATCGATAATTATAAAGTAATAGGTAAA
66 TATTGTAAGTATCGATCC-AAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
2088909 CATAATGTTC
Statistics
Matches: 291, Mismatches: 27, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
199 2 0.01
200 116 0.40
201 169 0.58
202 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (200 bp):
TGTATCGATACTTTTTTCCTAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATT
TATTGTAAGTATCGATCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAAT
ATAACCAGTAAAAATATATTGATTTAATGAGAGAATAGGTAAACTAACTGTATCGATACTTTTTT
AAAAT
Found at i:2091602 original size:23 final size:23
Alignment explanation
Indices: 2091576--2091619 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2091566 CAAGTTAAAA
*
2091576 AAGCGCTACCTATTACGTTATAT
1 AAGCGCTACCTAATACGTTATAT
*
2091599 AAGCGCTACCTAATATGTTAT
1 AAGCGCTACCTAATACGTTAT
2091620 TGTGCTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (23 bp):
AAGCGCTACCTAATACGTTATAT
Found at i:2093758 original size:7 final size:7
Alignment explanation
Indices: 2093748--2094148 Score: 701
Period size: 7 Copynumber: 58.0 Consensus size: 7
2093738 TAATTATAAA
*
2093748 TTAAACT
1 TTAAAAT
2093755 TTAAAA-
1 TTAAAAT
*
2093761 TTAAACT
1 TTAAAAT
2093768 TTAAAA-
1 TTAAAAT
2093774 TTAAAAT
1 TTAAAAT
2093781 TTAAAAT
1 TTAAAAT
2093788 TTAAAAT
1 TTAAAAT
2093795 TTAAAAT
1 TTAAAAT
2093802 TTAAAAT
1 TTAAAAT
2093809 TTAAAAT
1 TTAAAAT
2093816 TTAAAAT
1 TTAAAAT
2093823 TTAAAAT
1 TTAAAAT
2093830 TTAAAAT
1 TTAAAAT
2093837 TTAAAAT
1 TTAAAAT
2093844 TTAAAAT
1 TTAAAAT
2093851 TTAAAAT
1 TTAAAAT
2093858 TTAAAA-
1 TTAAAAT
2093864 TTAAAAT
1 TTAAAAT
2093871 TTAAAAT
1 TTAAAAT
2093878 TT-AAAT
1 TTAAAAT
2093884 TTAAAAT
1 TTAAAAT
2093891 TT-AAAT
1 TTAAAAT
2093897 TTAAAA-
1 TTAAAAT
2093903 TTAAAA-
1 TTAAAAT
2093909 TTAAAAT
1 TTAAAAT
2093916 TTAAAAT
1 TTAAAAT
2093923 TTAAAAT
1 TTAAAAT
2093930 TTAAAAT
1 TTAAAAT
2093937 TTAAAAT
1 TTAAAAT
2093944 TTAAAAT
1 TTAAAAT
2093951 TTAAAAT
1 TTAAAAT
2093958 TTAATTAAAT
1 TT-A--AAAT
2093968 TTAAAAT
1 TTAAAAT
2093975 TT-AAAT
1 TTAAAAT
2093981 TTAAAAT
1 TTAAAAT
2093988 TTAAAAT
1 TTAAAAT
2093995 TTAAAAT
1 TTAAAAT
2094002 TTAAAAT
1 TTAAAAT
2094009 TTAAAAT
1 TTAAAAT
2094016 TTAAAAT
1 TTAAAAT
2094023 TTAAAAT
1 TTAAAAT
2094030 TTAAAAT
1 TTAAAAT
2094037 TTAAAAT
1 TTAAAAT
2094044 TTAAAAT
1 TTAAAAT
2094051 TTAAAAT
1 TTAAAAT
2094058 TTAAAAT
1 TTAAAAT
2094065 TTAAAAT
1 TTAAAAT
2094072 TTAAAAT
1 TTAAAAT
2094079 TTAAAAT
1 TTAAAAT
2094086 TTAAAAT
1 TTAAAAT
2094093 TTAAAAT
1 TTAAAAT
2094100 TTAAAAT
1 TTAAAAT
2094107 TTAAAAT
1 TTAAAAT
2094114 TTAAAAT
1 TTAAAAT
2094121 TTAAAAT
1 TTAAAAT
2094128 TTAAAAT
1 TTAAAAT
2094135 TTAAAAT
1 TTAAAAT
2094142 TTAAAAT
1 TTAAAAT
2094149 CAAAATATTT
Statistics
Matches: 381, Mismatches: 3, Indels: 20
0.94 0.01 0.05
Matches are distributed among these distances:
6 47 0.12
7 326 0.86
8 1 0.00
9 1 0.00
10 6 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTAAAAT
Found at i:2094220 original size:25 final size:26
Alignment explanation
Indices: 2094186--2094235 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
2094176 AAATTAACTT
*
2094186 ATATGTTTTTAAAATAA-AAAATAAA
1 ATATATTTTTAAAATAATAAAATAAA
*
2094211 ATATATTTTTAATATAATAAAATAA
1 ATATATTTTTAAAATAATAAAATAA
2094236 TTTCTGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATATTTTTAAAATAATAAAATAAA
Found at i:2095432 original size:18 final size:18
Alignment explanation
Indices: 2095409--2095443 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2095399 AATTATGGGC
2095409 AAGGGGTATTGGTACTGA
1 AAGGGGTATTGGTACTGA
2095427 AAGGGGTATTGGTACTG
1 AAGGGGTATTGGTACTG
2095444 TCCATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.40, T:0.29
Consensus pattern (18 bp):
AAGGGGTATTGGTACTGA
Found at i:2095520 original size:21 final size:21
Alignment explanation
Indices: 2095496--2095547 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
2095486 TGAGGTATGG
2095496 GTATCGATACTGGTTGAATGA
1 GTATCGATACTGGTTGAATGA
*
2095517 GTATTGATACTGGTTGAATGA
1 GTATCGATACTGGTTGAATGA
2095538 GTATCGATAC
1 GTATCGATAC
2095548 CATACGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.35
Consensus pattern (21 bp):
GTATCGATACTGGTTGAATGA
Found at i:2096189 original size:195 final size:195
Alignment explanation
Indices: 2095857--2096250 Score: 752
Period size: 195 Copynumber: 2.0 Consensus size: 195
2095847 TATGCGTGTA
*
2095857 GATAACGATCGATCGAAAAGTTCGGACAAGTCGACCAAGTAATAGTCATCAAGATAAAAATAAGA
1 GATAACGATCGATAGAAAAGTTCGGACAAGTCGACCAAGTAATAGTCATCAAGATAAAAATAAGA
2095922 GATCGATATTGACTAGTGAGGCCAGGTGAGTGCATACTAGTTAATATATGAGGTTTAATGGAAAT
66 GATCGATATTGACTAGTGAGGCCAGGTGAGTGCATACTAGTTAATATATGAGGTTTAATGGAAAT
*
2095987 AAGACTTGAGATGAGTCTATTTTCTATATTATAATGCATGAATTCATGAATATATGCATGTGTTT
131 AAGACTTGAGATGAGTCTATTTCCTATATTATAATGCATGAATTCATGAATATATGCATGTGTTT
2096052 GATAACGATCGATAGAAAAGTTCGGACAAGTCGACCAAGTAATAGTCATCAAGATAAAAATAAGA
1 GATAACGATCGATAGAAAAGTTCGGACAAGTCGACCAAGTAATAGTCATCAAGATAAAAATAAGA
2096117 GATCGATATTGACTAGTGAGGCCAGGTGAGTGCATACTAGTTAATATATGAGGTTTAATGGAAAT
66 GATCGATATTGACTAGTGAGGCCAGGTGAGTGCATACTAGTTAATATATGAGGTTTAATGGAAAT
* *
2096182 AAGACTTGCGATGAGTCTATTTCCTATATTATAATGCATGAATTCATGAATGTATGCATGTGTTT
131 AAGACTTGAGATGAGTCTATTTCCTATATTATAATGCATGAATTCATGAATATATGCATGTGTTT
2096247 GATA
1 GATA
2096251 TGATTATTAT
Statistics
Matches: 195, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 195 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (195 bp):
GATAACGATCGATAGAAAAGTTCGGACAAGTCGACCAAGTAATAGTCATCAAGATAAAAATAAGA
GATCGATATTGACTAGTGAGGCCAGGTGAGTGCATACTAGTTAATATATGAGGTTTAATGGAAAT
AAGACTTGAGATGAGTCTATTTCCTATATTATAATGCATGAATTCATGAATATATGCATGTGTTT
Found at i:2101014 original size:19 final size:20
Alignment explanation
Indices: 2100977--2101025 Score: 91
Period size: 19 Copynumber: 2.5 Consensus size: 20
2100967 TTGTTCAAAG
2100977 AGTATCGATACTAAAGGAGT
1 AGTATCGATACTAAAGGAGT
2100997 AGTATCGATACT-AAGGAGT
1 AGTATCGATACTAAAGGAGT
2101016 AGTATCGATA
1 AGTATCGATA
2101026 TTGGTGGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTAAAGGAGT
Found at i:2101939 original size:22 final size:22
Alignment explanation
Indices: 2101911--2101965 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2101901 AGTCGAGGGT
*
2101911 TACATAGGTCATCCGATACATA
1 TACATAGGTCATCCGAGACATA
* * *
2101933 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCATCCGAGACATA
2101955 TACATGAGGTC
1 TACAT-AGGTC
2101966 CTTCGGGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (22 bp):
TACATAGGTCATCCGAGACATA
Found at i:2101968 original size:23 final size:22
Alignment explanation
Indices: 2101928--2101975 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 22
2101918 GTCATCCGAT
2101928 ACATATACATAGGTCCTTCGGG
1 ACATATACATAGGTCCTTCGGG
2101950 ACATATACATGAGGTCCTTCGGG
1 ACATATACAT-AGGTCCTTCGGG
2101973 ACA
1 ACA
2101976 AATTTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (22 bp):
ACATATACATAGGTCCTTCGGG
Found at i:2103754 original size:15 final size:16
Alignment explanation
Indices: 2103734--2103771 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2103724 ATATATGTTG
2103734 TTAATAATA-AATATT
1 TTAATAATATAATATT
*
2103749 TTAATAAGATAATATT
1 TTAATAATATAATATT
2103765 TT-ATAAT
1 TTAATAAT
2103772 CACTTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTAATAATATAATATT
Found at i:2103764 original size:16 final size:15
Alignment explanation
Indices: 2103734--2103767 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2103724 ATATATGTTG
*
2103734 TTAATAATAAATATT
1 TTAATAAGAAATATT
2103749 TTAATAAGATAATATT
1 TTAATAAGA-AATATT
2103765 TTA
1 TTA
2103768 TAATCACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATAAGAAATATT
Found at i:2103825 original size:2 final size:2
Alignment explanation
Indices: 2103818--2103848 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2103808 GAAGTTCTTG
2103818 AT AT AT 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 AT AT AT A
2103849 GTTATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2108006 original size:57 final size:56
Alignment explanation
Indices: 2107944--2108064 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 56
2107934 AAACTGCAAT
* * * *
2107944 AATTAAAGGACTGAAATTAAAGTACCAAAAATAAAGAGCA-AAAGTAAAAAGACATAA
1 AATTAAAGCAATGAAATTAAAGGACCAAAAATAAAG-GAATAAAGT-AAAAGACATAA
** *
2108001 AATTAAAGCAATGAAATTAAAGGACTGAAATTAAAGGAATAAAGTAAAAGACATAA
1 AATTAAAGCAATGAAATTAAAGGACCAAAAATAAAGGAATAAAGTAAAAGACATAA
*
2108057 ATTTAAAG
1 AATTAAAG
2108065 ATGCAGAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 20 0.36
57 35 0.64
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.19
Consensus pattern (56 bp):
AATTAAAGCAATGAAATTAAAGGACCAAAAATAAAGGAATAAAGTAAAAGACATAA
Found at i:2108022 original size:28 final size:28
Alignment explanation
Indices: 2107984--2108064 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
2107974 ATAAAGAGCA
2107984 AAAGTAAAAAGACATAAAATTAAAGCAAT
1 AAAGT-AAAAGACATAAAATTAAAGCAAT
* * * *
2108013 GAAATTAAAGGAC-TGAAATTAAAGGAAT
1 -AAAGTAAAAGACATAAAATTAAAGCAAT
*
2108041 AAAGTAAAAGACATAAATTTAAAG
1 AAAGTAAAAGACATAAAATTAAAG
2108065 ATGCAGAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 10 0.24
28 22 0.52
29 6 0.14
30 4 0.10
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (28 bp):
AAAGTAAAAGACATAAAATTAAAGCAAT
Found at i:2108037 original size:14 final size:14
Alignment explanation
Indices: 2108000--2108040 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2107990 AAAAGACATA
*
2108000 AAATTAAAGCAATG
1 AAATTAAAGGAATG
*
2108014 AAATTAAAGGACTG
1 AAATTAAAGGAATG
2108028 AAATTAAAGGAAT
1 AAATTAAAGGAAT
2108041 AAAGTAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:2108246 original size:13 final size:14
Alignment explanation
Indices: 2108228--2108265 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
2108218 TAAATAAAAA
2108228 TTAGCGGTTAGT-G
1 TTAGCGGTTAGTAG
2108241 TTAGCGGTTAGTAG
1 TTAGCGGTTAGTAG
*
2108255 TTAGCTGTTAG
1 TTAGCGGTTAG
2108266 AAAAGTTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.18, C:0.08, G:0.34, T:0.39
Consensus pattern (14 bp):
TTAGCGGTTAGTAG
Found at i:2112102 original size:30 final size:30
Alignment explanation
Indices: 2112051--2112108 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2112041 TGATTGACTT
*
2112051 GAAATGAAATCTTCTTCAACATGGAATTAC
1 GAAATGAAATCTTCTGCAACATGGAATTAC
* *
2112081 GAAATGAAGTCTT-TGCTAACATTGAATT
1 GAAATGAAATCTTCTGC-AACATGGAATT
2112109 CCTGTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (30 bp):
GAAATGAAATCTTCTGCAACATGGAATTAC
Found at i:2112535 original size:66 final size:65
Alignment explanation
Indices: 2112413--2112595 Score: 167
Period size: 65 Copynumber: 2.8 Consensus size: 65
2112403 ATCTTAAGGG
* * * * * *
2112413 AAAACTACCTCAAGCGAGACG-AATTTTGTTTCTAG-GAAAACTATCTCAAAGGTTTATGTTTTA
1 AAAACTATCTCAAGCGAGAAGAAACTTTGTTTCAAGAG-AAACTATCTCAAAGATTTA--TTTCA
2112476 A-A
63 AGA
* * *
2112478 ATAAACTATCTCAAGCGAGATGAAACTTTGTTTCAAGAGAAATTCTCTCAAA-ATTTATTTCAAG
1 A-AAACTATCTCAAGCGAGAAGAAACTTTGTTTCAAGAGAAACTATCTCAAAGATTTATTTCAAG
2112542 A
65 A
* * * * *
2112543 AAAACTGTCTCAAGGGAGACAAAAACTTTGTTTCAAAAGAAACAATCTCAAAG
1 AAAACTATCTCAAGCGAGA-AGAAACTTTGTTTCAAGAGAAACTATCTCAAAG
2112596 GTGACAGAGA
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
64 21 0.22
65 29 0.30
66 22 0.23
67 23 0.24
68 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (65 bp):
AAAACTATCTCAAGCGAGAAGAAACTTTGTTTCAAGAGAAACTATCTCAAAGATTTATTTCAAGA
Found at i:2114636 original size:45 final size:45
Alignment explanation
Indices: 2114585--2114674 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
2114575 TTGCCCTTTT
2114585 CTAGGTTTCCTAATTGAGACAAATCATAAAACTAGAGTTCATTGG
1 CTAGGTTTCCTAATTGAGACAAATCATAAAACTAGAGTTCATTGG
2114630 CTAGGTTTCCTAATTGAGACAAATCATAAAACTAGAGTTCATTGG
1 CTAGGTTTCCTAATTGAGACAAATCATAAAACTAGAGTTCATTGG
2114675 ACATCAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (45 bp):
CTAGGTTTCCTAATTGAGACAAATCATAAAACTAGAGTTCATTGG
Found at i:2116495 original size:44 final size:44
Alignment explanation
Indices: 2116379--2116603 Score: 301
Period size: 44 Copynumber: 5.0 Consensus size: 44
2116369 AAATGAATTA
* *
2116379 ATAAATGAAAATGCATAACGATGCATT-TTGGCAAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * **
2116422 ACAAATGAAAATTAAATGCATAACAGTGCATTATTGGAAGAAATATGCC
1 ATAAATG---A--AAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2116471 ATAAATGAAAATGCATAACGGTGCATTATTAGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2116515 ATAAATGAAAATGCATAACGGTGAATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2116559 ATAAATGAAAATGCATAACGGTGCATT-TTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
2116602 AT
1 AT
2116604 TACTGGTTTA
Statistics
Matches: 159, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
43 23 0.14
44 99 0.62
46 2 0.01
48 17 0.11
49 18 0.11
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:2116581 original size:25 final size:25
Alignment explanation
Indices: 2116467--2116582 Score: 67
Period size: 25 Copynumber: 5.1 Consensus size: 25
2116457 GGAAGAAATA
2116467 TGCCATAAATGAAAATGCATAACGG
1 TGCCATAAATGAAAATGCATAACGG
** * *
2116492 TG-CAT---T-ATTA-GCAGAAAGG
1 TGCCATAAATGAAAATGCATAACGG
2116511 TGCCATAAATGAAAATGCATAACGG
1 TGCCATAAATGAAAATGCATAACGG
* * * * *
2116536 TG-AATTATTG-----GCAGAAAGG
1 TGCCATAAATGAAAATGCATAACGG
2116555 TGCCATAAATGAAAATGCATAACGG
1 TGCCATAAATGAAAATGCATAACGG
2116580 TGC
1 TGC
2116583 ATTTTGGCAG
Statistics
Matches: 61, Mismatches: 18, Indels: 24
0.59 0.17 0.23
Matches are distributed among these distances:
19 18 0.30
20 10 0.16
21 1 0.02
23 1 0.02
24 10 0.16
25 21 0.34
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (25 bp):
TGCCATAAATGAAAATGCATAACGG
Found at i:2121278 original size:8 final size:8
Alignment explanation
Indices: 2121265--2121292 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2121255 GGGTATTAAA
2121265 GAAAAGGG
1 GAAAAGGG
2121273 GAAAAGGG
1 GAAAAGGG
2121281 GAAAAGGG
1 GAAAAGGG
2121289 GAAA
1 GAAA
2121293 GGAAAGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (8 bp):
GAAAAGGG
Found at i:2122702 original size:48 final size:45
Alignment explanation
Indices: 2122434--2122706 Score: 290
Period size: 44 Copynumber: 6.0 Consensus size: 45
2122424 AAATGAATGA
* * *
2122434 ATAAATG-AAAATGCATAACGGTGTATT-TTGGCATAAAGGTACC
1 ATAAATGAAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
2122477 ATAAATGAAACTTAAATGCATAACGATGTATTATTGGCAGAAAGGTGCC
1 ATAAATG-AA---AAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
2122526 ATAAATG-AAAATGCATAATGGTGCATTATTGGCAGAAAAGTGCC
1 ATAAATGAAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2122570 ATAAAT-AAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
1 ATAAATGAAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
2122614 ATAAATG-AAAATGCATAACGATGCAAT-TTGGGAGAAAGGTGCC
1 ATAAATGAAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
2122657 ACAAAAGAAACTTAAATGCATAACGGTGCATT-TTGGTAGAGAGGTGCC
1 ATAAATG-AA---AAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
2122705 AT
1 AT
2122707 TACTGGTGAA
Statistics
Matches: 197, Mismatches: 20, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
43 27 0.14
44 96 0.49
45 2 0.01
47 1 0.01
48 50 0.25
49 21 0.11
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.25
Consensus pattern (45 bp):
ATAAATGAAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:2122817 original size:11 final size:12
Alignment explanation
Indices: 2122798--2122861 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 12
2122788 ACTTGATCAA
*
2122798 TTTTCTTTCT-T
1 TTTTTTTTCTCT
2122809 TTTTTTTTCTCT
1 TTTTTTTTCTCT
2122821 TTTTTCATTTCTCT
1 TTTTT--TTTCTCT
*
2122835 TTGCTTTTTCTTCT
1 TT-TTTTTTC-TCT
2122849 TCTTTTTTTCTCT
1 T-TTTTTTTCTCT
2122862 ATCCTCACCT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 9 0.20
12 6 0.14
13 7 0.16
14 19 0.43
15 3 0.07
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCTCT
Found at i:2127358 original size:2 final size:2
Alignment explanation
Indices: 2127351--2127385 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2127341 TCATAATAAC
2127351 TA 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 TA T
2127386 GAAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2131506 original size:15 final size:15
Alignment explanation
Indices: 2131486--2131523 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
2131476 GAGCTAGTTC
2131486 GGAGGTGAATGAGAT
1 GGAGGTGAATGAGAT
2131501 GGAGGTGAATGAGAT
1 GGAGGTGAATGAGAT
2131516 GGAGGTGA
1 GGAGGTGA
2131524 GCTGGCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (15 bp):
GGAGGTGAATGAGAT
Found at i:2132020 original size:2 final size:2
Alignment explanation
Indices: 2132003--2132036 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2131993 TCACAATAAC
*
2132003 TA TA GA TA TA -A 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 TA T
2132037 GAAAGTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2133011 original size:14 final size:14
Alignment explanation
Indices: 2132994--2133029 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2132984 AAAAGATAAA
2132994 AAATTAAAGCGA-TG
1 AAATTAAAG-GACTG
2133008 AAATTAAAGGACTG
1 AAATTAAAGGACTG
2133022 AAATTAAA
1 AAATTAAA
2133030 TAAATAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (14 bp):
AAATTAAAGGACTG
Found at i:2133251 original size:20 final size:20
Alignment explanation
Indices: 2133226--2133276 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2133216 TAAATAAAAA
*
2133226 TTAGCGGTTAGT-GTTAGCAG
1 TTAGC-GTTAGTAGTTAGAAG
2133246 TTAGCGTTAGTAGTTAGAAG
1 TTAGCGTTAGTAGTTAGAAG
*
2133266 CTAGCTGTTAG
1 TTAGC-GTTAG
2133277 AAAAGTTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 16 0.59
21 5 0.19
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (20 bp):
TTAGCGTTAGTAGTTAGAAG
Found at i:2136310 original size:110 final size:109
Alignment explanation
Indices: 2136128--2136334 Score: 389
Period size: 110 Copynumber: 1.9 Consensus size: 109
2136118 ATTCTAAGGA
2136128 AAAATATAAAATATTCAATATTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAAA
1 AAAATATAAAATATTCAATATTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAAA
2136193 TATTTCTCTTTCCAACTGAAAT-ATAAAGAATAATATTCTTCAGG
66 TATTTCTCTTTCCAACTGAAATAAT-AAGAATAATATTCTTCAGG
2136237 AAAATATAAAATATTCCAATATTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAA
1 AAAATATAAAATATT-CAATATTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAA
2136302 ATATTTCTCTTTCCAACTGAAATAATAAGAATA
65 ATATTTCTCTTTCCAACTGAAATAATAAGAATA
2136335 TAATAATTCT
Statistics
Matches: 96, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
109 15 0.16
110 79 0.82
111 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (109 bp):
AAAATATAAAATATTCAATATTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAAA
TATTTCTCTTTCCAACTGAAATAATAAGAATAATATTCTTCAGG
Found at i:2136317 original size:53 final size:52
Alignment explanation
Indices: 2136148--2136326 Score: 152
Period size: 53 Copynumber: 3.3 Consensus size: 52
2136138 ATATTCAATA
*
2136148 TTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAAATATTTCTC
1 TTTCCAACTGAA-ATAAACTAATCCCTAAATTACTTTAGGACAAATATTTCTC
** * * *
2136201 TTTCCAACTGAAATATAAAGAA----TAATATT-CTTCAGGAAAATATAAAATATTCCAATA
1 TTTCCAACTGAAATA-AACTAATCCCTAA-ATTACTTTAGGACAA-AT---AT-TT-C--TC
*
2136258 TTTCCAATTGAAGATAAACTAATCCCTAAATTACTTTAGGACAAATATTTCTC
1 TTTCCAACTGAA-ATAAACTAATCCCTAAATTACTTTAGGACAAATATTTCTC
2136311 TTTCCAACTGAAATAA
1 TTTCCAACTGAAATAA
2136327 TAAGAATATA
Statistics
Matches: 97, Mismatches: 13, Indels: 33
0.68 0.09 0.23
Matches are distributed among these distances:
49 12 0.12
50 5 0.05
52 7 0.07
53 29 0.30
54 2 0.02
55 2 0.02
56 2 0.02
57 18 0.19
58 3 0.03
60 5 0.05
61 12 0.12
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (52 bp):
TTTCCAACTGAAATAAACTAATCCCTAAATTACTTTAGGACAAATATTTCTC
Found at i:2137978 original size:123 final size:123
Alignment explanation
Indices: 2137839--2138498 Score: 875
Period size: 123 Copynumber: 5.4 Consensus size: 123
2137829 AAGTTCTTAT
* * * * * *
2137839 TCTTTAGATGAGTTCTT-TTCATTATGAACTCCTTCTGGAAATGATGATGCTAATCTATTTTCAT
1 TCTTCAGATGAGTTCTTCTT-ATTATGAACTTCTTCTGGAAATGTTGATGCTACTCTATCTTCTT
* * * *
2137903 ATGCGATAGAGTTGAGCAAAAGGTTGAATAAGTTCTTCAGATTAAGAACTTCTTCTTCA
65 CTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCC
* *
2137962 TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAATATTGATGCTGCTCTATCTTCTTC
1 TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAATGTTGATGCTACTCTATCTTCTTC
* * * *
2138027 TGTGATAGAGTCGAGCAACAGGTTGAATAAGTACTTCAGATTATGAACTTATTCTTCC
66 TGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCC
* * * *
2138085 TCTTGAGATGAGTTCTTCTTATTACGAACTTCTTCTGGAAATGTTGATGCTTCTCTATCTCCTTC
1 TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAATGTTGATGCTACTCTATCTTCTTC
* * *
2138150 TGCGAT--AGTCGAGCAAAAGGTTGAATGAGTTCTTAAGATTATGAGCTTCTTCTTCC
66 TGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCC
* * * **
2138206 TTTTCAGATGGGTTCTTCTTATTA-CAAGCTTCTTCTGGAAATGTTGATGCTACTCTATCACCTT
1 TCTTCAGATGAGTTCTTCTTATTATGAA-CTTCTTCTGGAAATGTTGATGCTACTCTATCTTCTT
* *
2138270 CTACGATAGAGTCGAGC-AAAGGTTGAATAAGTTCTTCATATTATGAACTTCTT-TCTCC
65 CTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT-TCC
* * * * *
2138328 TCTTCAAATGAGTTATTCTTATTACGAACTTCTTCTGGAAATGTTGATGCTGCTCTATC-ACTTT
1 TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAATGTTGATGCTACTCTATCTTC-TT
*
2138392 CTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTATTCTTCC
65 CTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCC
* * **
2138451 TATTCAGATGAGTTCTTCTTGTTATGAACTTCTTCTAAAAATGTTGAT
1 TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAATGTTGAT
2138499 CCCTTGAGTG
Statistics
Matches: 472, Mismatches: 56, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
120 2 0.00
121 107 0.23
122 103 0.22
123 257 0.54
124 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (123 bp):
TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAATGTTGATGCTACTCTATCTTCTTC
TGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCC
Found at i:2152262 original size:45 final size:45
Alignment explanation
Indices: 2152211--2152299 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
2152201 GCTGATATGC
** *
2152211 TTGCTGGAAGCTGCTGGAACGGGGACGTGGAGGGGCTGTTGGCAT
1 TTGCTGGAAGCTGCTGGAACGGCAACGTGGAGGGGCTGCTGGCAT
* *
2152256 TTGCTGGAAGCTGTTGGAACTGCAACGTGGAGGGGCTGCTGGCA
1 TTGCTGGAAGCTGCTGGAACGGCAACGTGGAGGGGCTGCTGGCA
2152300 GCTAAAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.22
Consensus pattern (45 bp):
TTGCTGGAAGCTGCTGGAACGGCAACGTGGAGGGGCTGCTGGCAT
Found at i:2157452 original size:91 final size:91
Alignment explanation
Indices: 2157292--2157475 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
2157282 TTGCTTTATC
*
2157292 AACTAATTCATCCAAAAATTCATACATCTCAGCTCCATATGCTTGCCTCTCGTCGGGATTGAACG
1 AACTAATTCATCCAAAAATTCATACATCTCAGCTCCATATGCTTGCCTCTCGTCGGGATTGAACA
2157357 AGTAAACCTTGTCGTGAATGCTCATA
66 AGTAAACCTTGTCGTGAATGCTCATA
2157383 AACTAATTCATCCAAAAATTCATACATCTCAGCTCCATATGCTTGCCTCTCGTCGGGATTGAACA
1 AACTAATTCATCCAAAAATTCATACATCTCAGCTCCATATGCTTGCCTCTCGTCGGGATTGAACA
2157448 AGTAAACCTTGTCGTGAATGCTCATA
66 AGTAAACCTTGTCGTGAATGCTCATA
2157474 AA
1 AA
2157476 GCTCCAGTCC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (91 bp):
AACTAATTCATCCAAAAATTCATACATCTCAGCTCCATATGCTTGCCTCTCGTCGGGATTGAACA
AGTAAACCTTGTCGTGAATGCTCATA
Found at i:2160633 original size:20 final size:20
Alignment explanation
Indices: 2160608--2160673 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
2160598 TTGTTCAAAG
2160608 AGTATCGATACCAAAGGAGT
1 AGTATCGATACCAAAGGAGT
*
2160628 AGTATCGATA-C--TGG-G-
1 AGTATCGATACCAAAGGAGT
*
2160643 GGTATCGATACCAAAGGAGT
1 AGTATCGATACCAAAGGAGT
2160663 AGTATCGATAC
1 AGTATCGATAC
2160674 TGGGGGTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 9 0.24
16 2 0.05
17 2 0.05
18 2 0.05
19 2 0.05
20 20 0.54
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (20 bp):
AGTATCGATACCAAAGGAGT
Found at i:2160649 original size:15 final size:15
Alignment explanation
Indices: 2160629--2160688 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
2160619 CAAAGGAGTA
2160629 GTATCGATACTGGGG
1 GTATCGATACTGGGG
* *
2160644 GTATCGATACCAAAGGAGTA
1 GTATCGATA-C--TGG-G-G
2160664 GTATCGATACTGGGG
1 GTATCGATACTGGGG
2160679 GTATCGATAC
1 GTATCGATAC
2160689 CATTAAGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
15 19 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 2 0.06
20 9 0.25
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (15 bp):
GTATCGATACTGGGG
Found at i:2160655 original size:35 final size:35
Alignment explanation
Indices: 2160609--2160690 Score: 164
Period size: 35 Copynumber: 2.3 Consensus size: 35
2160599 TGTTCAAAGA
2160609 GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
1 GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
2160644 GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
1 GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
2160679 GTATCGATACCA
1 GTATCGATACCA
2160691 TTAAGCAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (35 bp):
GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
Found at i:2160702 original size:35 final size:34
Alignment explanation
Indices: 2160609--2160704 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 34
2160599 TGTTCAAAGA
*
2160609 GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
1 GTATCGATACCAAAGCAG-AGTATCGATACTGGGG
*
2160644 GTATCGATACCAAAGGAGTAGTATCGATACTGGGG
1 GTATCGATACCAAAGCAG-AGTATCGATACTGGGG
2160679 GTATCGATACCATTAAGCA-AGTATCG
1 GTATCGATACCA--AAGCAGAGTATCG
2160705 TACCTTTTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
35 54 0.93
37 4 0.07
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (34 bp):
GTATCGATACCAAAGCAGAGTATCGATACTGGGG
Found at i:2161544 original size:44 final size:45
Alignment explanation
Indices: 2161494--2161580 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
2161484 ACATGCATGT
*
2161494 CCAATAT-TTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
2161538 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
2161581 GCATAGTTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 7 0.17
45 34 0.83
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (45 bp):
CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
Found at i:2161580 original size:25 final size:25
Alignment explanation
Indices: 2161507--2161580 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
2161497 ATATTTTACC
2161507 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
* *
2161532 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTAT-CCCATA-AGCTCGTAAGCTT
2161552 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
2161577 ATTT
1 ATTT
2161581 GCATAGTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 2 0.06
22 2 0.06
23 2 0.06
24 2 0.06
25 15 0.42
26 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTATCCCATAAGCTCGTAAGCTT
Found at i:2165636 original size:6 final size:6
Alignment explanation
Indices: 2165625--2165685 Score: 68
Period size: 6 Copynumber: 9.5 Consensus size: 6
2165615 TTTTTTCTTC
*
2165625 TTTTCT TTTTCTAT TTTTTT TTCTTCT TTTTCT TTTTCT TTTTCT TCTTTCT
1 TTTTCT TTTTC--T TTTTCT TT-TTCT TTTTCT TTTTCT TTTTCT T-TTTCT
*
2165677 TTTTGT TTT
1 TTTTCT TTT
2165686 ATAATGTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 32 0.67
7 11 0.23
8 5 0.10
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:2165641 original size:21 final size:19
Alignment explanation
Indices: 2165616--2165685 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 19
2165606 ATCTCTCATT
2165616 TTTTTCTTCTTTTCTTTTTC
1 TTTTTCTT-TTTTCTTTTTC
*
2165636 TATTTTTTTTTCTTCTTTTTC
1 T-TTTTCTTTT-TTCTTTTTC
2165657 TTTTTC-TTTTTCTTCTTTC
1 TTTTTCTTTTTTCTT-TTTC
*
2165676 TTTTTGTTTT
1 TTTTTCTTTT
2165686 ATAATGTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
18 5 0.12
19 12 0.28
20 10 0.23
21 16 0.37
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTTTTCTTTTTC
Found at i:2165643 original size:15 final size:14
Alignment explanation
Indices: 2165616--2165674 Score: 68
Period size: 15 Copynumber: 4.2 Consensus size: 14
2165606 ATCTCTCATT
*
2165616 TTTTTCTTCTTTTC
1 TTTTTCTTTTTTTC
*
2165630 TTTTTC-TATTTT-
1 TTTTTCTTTTTTTC
2165642 TTTTTCTTCTTTTTC
1 TTTTTCTT-TTTTTC
2165657 TTTTTCTTTTTCTTC
1 TTTTTCTTTTT-TTC
2165672 TTT
1 TTT
2165675 CTTTTTGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 6 0.15
13 6 0.15
14 13 0.33
15 14 0.36
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:2165654 original size:12 final size:12
Alignment explanation
Indices: 2165614--2165680 Score: 68
Period size: 12 Copynumber: 5.6 Consensus size: 12
2165604 GCATCTCTCA
2165614 TTTTTTTCTTCT
1 TTTTTTTCTTCT
*
2165626 TTTCTTT-TTCT
1 TTTTTTTCTTCT
2165637 ATTTTTTT-TTCT
1 -TTTTTTTCTTCT
*
2165649 TCTTTTTCTT-T
1 TTTTTTTCTTCT
2165660 TTCTTTTTCTTCT
1 TT-TTTTTCTTCT
2165673 TTCTTTTT
1 TT-TTTTT
2165681 GTTTTATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
11 12 0.26
12 26 0.55
13 9 0.19
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:2168136 original size:12 final size:12
Alignment explanation
Indices: 2168102--2168136 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2168092 TACCGATGCA
*
2168102 CTGCTACAATAT
1 CTGCTACAGTAT
*
2168114 CTGCTATAGTAT
1 CTGCTACAGTAT
2168126 CTGCTACAGTA
1 CTGCTACAGTA
2168137 ACTTCATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (12 bp):
CTGCTACAGTAT
Found at i:2168544 original size:45 final size:45
Alignment explanation
Indices: 2168487--2168618 Score: 223
Period size: 45 Copynumber: 3.0 Consensus size: 45
2168477 ACATGCATGT
*
2168487 CCAATAT-TTTACCATTTATCCCATAAGCTCGTAAG-TATATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCT-TATTTTA
*
2168531 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
2168576 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
2168619 GCATGGTTAC
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
44 7 0.08
45 75 0.90
46 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (45 bp):
CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
Found at i:2169872 original size:2 final size:2
Alignment explanation
Indices: 2169865--2169905 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2169855 AACTTTCTTT
2169865 TA TA TA TA 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 TA TA TA TA T
2169906 CTTACAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2173138 original size:39 final size:40
Alignment explanation
Indices: 2173095--2173189 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
2173085 AGTCAATTAT
* * **
2173095 ATATGCACCCTAGTGC-TTACACATAAGGTCGTGCCCACC
1 ATATGCAACCAAGTGCATTACACATAAGCACGTGCCCACC
*
2173134 ATATGCAACGAAGTGCATTACACATAAGCACGTGCCCACC
1 ATATGCAACCAAGTGCATTACACATAAGCACGTGCCCACC
* *
2173174 ATATGCATCGAAGTGC
1 ATATGCAACCAAGTGC
2173190 TTAATCGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
39 13 0.27
40 36 0.73
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (40 bp):
ATATGCAACCAAGTGCATTACACATAAGCACGTGCCCACC
Found at i:2173168 original size:40 final size:39
Alignment explanation
Indices: 2173106--2173192 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 39
2173096 TATGCACCCT
**
2173106 AGTGCTTACACATAAGGTCGTGCCCACCATATGCAACGA
1 AGTGCTTACACATAAGCACGTGCCCACCATATGCAACGA
*
2173145 AGTGCATTACACATAAGCACGTGCCCACCATATGCATCGA
1 AGTGC-TTACACATAAGCACGTGCCCACCATATGCAACGA
2173185 AGTGCTTA
1 AGTGCTTA
2173193 ATCGATATGC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 8 0.18
40 36 0.82
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (39 bp):
AGTGCTTACACATAAGCACGTGCCCACCATATGCAACGA
Found at i:2175782 original size:15 final size:15
Alignment explanation
Indices: 2175762--2175791 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2175752 CATTTATAGA
2175762 ATAAAAAATCTTTTT
1 ATAAAAAATCTTTTT
2175777 ATAAAAAATCTTTTT
1 ATAAAAAATCTTTTT
2175792 GGGAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAAAAATCTTTTT
Found at i:2177486 original size:37 final size:38
Alignment explanation
Indices: 2177445--2177534 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 38
2177435 AGAGAATAAA
*
2177445 TCTTAAGGAAGACAAAG-TTGAGGTTTCTAGA-AAATAT
1 TCTTAAGGAAGACAAAGATTG-GGTTTCTAGAGAAACAT
* * *
2177482 TCTTAAGAAATA-AAAGAATTGTGTTTCTAGAGAAACAT
1 TCTTAAGGAAGACAAAG-ATTGGGTTTCTAGAGAAACAT
2177520 TCTTAAGGAAGACAA
1 TCTTAAGGAAGACAA
2177535 TATTAAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
36 4 0.09
37 19 0.44
38 18 0.42
39 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (38 bp):
TCTTAAGGAAGACAAAGATTGGGTTTCTAGAGAAACAT
Found at i:2177661 original size:53 final size:53
Alignment explanation
Indices: 2177482--2177662 Score: 191
Period size: 53 Copynumber: 3.4 Consensus size: 53
2177472 TAGAAAATAT
* *** *
2177482 TCTTAAGAAATAAAAGAATTGTGTTTCTAGAGAAACATTCTTAAGGAAGACAA
1 TCTTAAGAAAGAAAAGAATCAAGTTTCTAGAGAAACAATCTTAAGGAAGACAA
* * * * * * * * * *
2177535 TATTAAGAAAGACAAGAGTTAATTTTTTAGGGAAATAGTCTTAAGAAAGACAA
1 TCTTAAGAAAGAAAAGAATCAAGTTTCTAGAGAAACAATCTTAAGGAAGACAA
* * *
2177588 TCTTAAGAAAGAAAAGAATCAAGTTTCTAGAGAAACAAACTTAAGGAATATAA
1 TCTTAAGAAAGAAAAGAATCAAGTTTCTAGAGAAACAATCTTAAGGAAGACAA
*
2177641 TCTTAAGAAAGAAAATAATCAA
1 TCTTAAGAAAGAAAAGAATCAA
2177663 ATTTATATAG
Statistics
Matches: 102, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
53 102 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (53 bp):
TCTTAAGAAAGAAAAGAATCAAGTTTCTAGAGAAACAATCTTAAGGAAGACAA
Found at i:2177801 original size:38 final size:37
Alignment explanation
Indices: 2177689--2177803 Score: 124
Period size: 38 Copynumber: 3.0 Consensus size: 37
2177679 CTTAAAGTAG
*
2177689 AAAATCTAAAGTTTCTAGAGAAACAATCTAATAGAAG-T
1 AAAAT-TAAAGTTTCTAGAGAAACAATTTAA-AGAAGAT
* * *
2177727 CAAATTAAAGTTTCTAGACAAAGCATTTTAAAGAAGAT
1 AAAATTAAAGTTTCTAGAGAAA-CAATTTAAAGAAGAT
* * *
2177765 AAAATTTAATTTTCTAGAGAAACAATATTAAGGAAGAT
1 AAAATTAAAGTTTCTAGAGAAACAAT-TTAAAGAAGAT
2177803 A
1 A
2177804 GTTTTTAATG
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
37 24 0.38
38 40 0.62
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (37 bp):
AAAATTAAAGTTTCTAGAGAAACAATTTAAAGAAGAT
Found at i:2180418 original size:5 final size:5
Alignment explanation
Indices: 2180408--2180886 Score: 930
Period size: 5 Copynumber: 96.6 Consensus size: 5
2180398 AAATATCAAT
2180408 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180458 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180508 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180558 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180608 ATAAC ATAAC --AAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180656 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC AT-A- ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180704 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180754 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180804 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2180854 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
2180887 TAAACACCAT
Statistics
Matches: 470, Mismatches: 0, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
3 5 0.01
4 2 0.00
5 463 0.99
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAC
Found at i:2183947 original size:39 final size:39
Alignment explanation
Indices: 2183873--2183947 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
2183863 CAACTAACCA
*
2183873 TTAACTTTTCTAACAGCTAACATTTCTAAATGCTAACGG
1 TTAACTTTTCTAACAGCTAACATTTCTAAACGCTAACGG
* * * *
2183912 TTAACTTTTCTAACAGTTAACCTTTGTAACCGCTAA
1 TTAACTTTTCTAACAGCTAACATTTCTAAACGCTAA
2183948 TTACTAACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.37
Consensus pattern (39 bp):
TTAACTTTTCTAACAGCTAACATTTCTAAACGCTAACGG
Found at i:2187830 original size:26 final size:26
Alignment explanation
Indices: 2187782--2187880 Score: 78
Period size: 26 Copynumber: 3.8 Consensus size: 26
2187772 GAAATAACAC
*
2187782 AAAAAGAAAGAAGAAGAAAAAAGAGA
1 AAAAAGAAAGAAAAAGAAAAAAGAGA
*
2187808 AAAAAGATAAGAAAAAG-AGAAAGAGA
1 AAAAAGA-AAGAAAAAGAAAAAAGAGA
*** *
2187834 AATGGGAAA-AAAAGAGAAAAAATAAGA
1 AAAAAGAAAGAAAA-AGAAAAAA-GAGA
*
2187861 AAAAGGGAAA-AAAAAGAAAA
1 AAAA-AGAAAGAAAAAGAAAA
2187881 CAAATCAAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
24 4 0.07
25 4 0.07
26 23 0.39
27 19 0.32
28 9 0.15
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAGAAAAAGAAAAAAGAGA
Found at i:2187863 original size:17 final size:17
Alignment explanation
Indices: 2187782--2187880 Score: 76
Period size: 18 Copynumber: 5.6 Consensus size: 17
2187772 GAAATAACAC
2187782 AAAAAGAAAGAAGAAGAAA
1 AAAAAGAAA-AAG-AGAAA
*
2187801 AAAGAGAAAAA-AGATAA
1 AAAAAGAAAAAGAGA-AA
*
2187818 GAAAAAGAGAAAGAGAAA
1 -AAAAAGAAAAAGAGAAA
***
2187836 TGGGAA-AAAAAGAGAAA
1 -AAAAAGAAAAAGAGAAA
*
2187853 AAATAAGAAAAAGGGAAA
1 AAA-AAGAAAAAGAGAAA
2187871 AAAAAGAAAA
1 AAAAAGAAAA
2187881 CAAATCAAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
16 3 0.05
17 21 0.33
18 28 0.44
19 11 0.17
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAGAGAAA
Found at i:2187875 original size:20 final size:20
Alignment explanation
Indices: 2187799--2187875 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
2187789 AAGAAGAAGA
*
2187799 AAAAAGAGAAAAAAGATAAG
1 AAAAAGAGAAAAAAAATAAG
* **
2187819 AAAAAGAGAAAGAGAAATGGG
1 AAAAAGAGAAA-AAAAATAAG
* *
2187840 AAAAAAAGAGAAAAAATAAG
1 AAAAAGAGAAAAAAAATAAG
*
2187860 AAAAAGGGAAAAAAAA
1 AAAAAGAGAAAAAAAA
2187876 GAAAACAAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (20 bp):
AAAAAGAGAAAAAAAATAAG
Found at i:2195421 original size:102 final size:102
Alignment explanation
Indices: 2195293--2195510 Score: 269
Period size: 102 Copynumber: 2.1 Consensus size: 102
2195283 GACGGTTTTT
* **
2195293 CTTGAAACAAAATTGATCTCATTTGAGATTGTTTTCATAAAAACAAATTTGGTCTTGCTTAAGAC
1 CTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCATAAAAACAAATTTGGTCACGCTTAAGAC
* *
2195358 AGTTTTCATTTGAAAC-ACAAATTATGAAA-TTATTTCA
66 AATTTTCACTTGAAACGA-AAATTAT-AAATTTATTTCA
* * * * * *
2195395 CTTGAAACAAAATTGATCTTACTTGAGATTGTTTTCCTCAAAACAAATTTTGTCACGCTTGAGAT
1 CTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCATAAAAACAAATTTGGTCACGCTTAAGAC
* * *
2195460 AATTTTCCCTTGAAACGAAAATTGTAAATTTTTTTCA
66 AATTTTCACTTGAAACGAAAATTATAAATTTATTTCA
*
2195497 CTCGAAACAAAATT
1 CTTGAAACAAAATT
2195511 TTATTTCACC
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
101 3 0.03
102 95 0.96
103 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (102 bp):
CTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCATAAAAACAAATTTGGTCACGCTTAAGAC
AATTTTCACTTGAAACGAAAATTATAAATTTATTTCA
Found at i:2198584 original size:132 final size:132
Alignment explanation
Indices: 2198394--2198665 Score: 422
Period size: 132 Copynumber: 2.1 Consensus size: 132
2198384 CTCAAATTAA
*
2198394 GGAATGTTCCCTAATAATTTATTCAAAACAAATTATTCAATGTTCAATAAAAGGATCACATTTTA
1 GGAATGTTCCCTAATAATTAATTCAAAACAAATTATTCAATGTTCAATAAAAGGATCACATTTTA
* * * * * * *
2198459 AATACTGATTCGAATTTATAATTTCCTTCC-TTTACG-ATAGTGTGTAAGCGATTCGGTACCATA
66 AATACTGATTCAAATTTATAATTTCC-ACCATTTA-GAAAAATATGTAAGCGATTAGGTACCAGA
2198522 TTTG
129 TTTG
*
2198526 GGAATGTTCCCTAATAATTAATTCAAAACAAATTATTCAATGTTCAATAAAATGATCACATTTTA
1 GGAATGTTCCCTAATAATTAATTCAAAACAAATTATTCAATGTTCAATAAAAGGATCACATTTTA
2198591 AATACTGATTCAAATTTATAATTTCCACCATTTAGAAAAATATGTAAGCGATTAGGTACCAGATT
66 AATACTGATTCAAATTTATAATTTCCACCATTTAGAAAAATATGTAAGCGATTAGGTACCAGATT
2198656 TG
131 TG
2198658 GGCAATGT
1 GG-AATGT
2198666 GGGGGTGCTA
Statistics
Matches: 128, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
131 3 0.02
132 120 0.94
133 5 0.04
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (132 bp):
GGAATGTTCCCTAATAATTAATTCAAAACAAATTATTCAATGTTCAATAAAAGGATCACATTTTA
AATACTGATTCAAATTTATAATTTCCACCATTTAGAAAAATATGTAAGCGATTAGGTACCAGATT
TG
Found at i:2205694 original size:44 final size:38
Alignment explanation
Indices: 2205605--2205679 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
2205595 GCCGGGTATA
2205605 TATATATTTAAATTAAATATATAAATATTATATATATTT
1 TATA-ATTTAAATTAAATATATAAATATTATATATATTT
* * *
2205644 TTTAATTTAAATTAAATTTATTAATATTATATATAT
1 TATAATTTAAATTAAATATATAAATATTATATATAT
2205680 ATATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 30 0.91
39 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TATAATTTAAATTAAATATATAAATATTATATATATTT
Found at i:2205695 original size:38 final size:38
Alignment explanation
Indices: 2205613--2205706 Score: 97
Period size: 38 Copynumber: 2.6 Consensus size: 38
2205603 TATATATATT
* * * * **
2205613 TAAATTAAATATATAAATATTATATATATTTTTTAATT
1 TAAATTAAATTTATTAATATTATATATATTATATAAAA
2205651 TAAATTAAATTTATTAATATTATATATATATATATAAAA
1 TAAATTAAATTTATTAATATTATATATAT-TATATAAAA
2205690 T-AATT--ATTT-TTAATATT
1 TAAATTAAATTTATTAATATT
2205707 TATCGGGCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 8 0.16
36 4 0.08
38 31 0.63
39 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TAAATTAAATTTATTAATATTATATATATTATATAAAA
Found at i:2205824 original size:36 final size:36
Alignment explanation
Indices: 2205772--2205842 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
2205762 CCCGTCGCCG
2205772 TCCCCATCCCCATTTAGCATAAAC-AGTTTTTCCCCA
1 TCCCCATCCCCATTTAGCATAAACGA-TTTTTCCCCA
* *
2205808 TCCCCGTCCCCGTTTAGCATAAACGATTTTTCCCC
1 TCCCCATCCCCATTTAGCATAAACGATTTTTCCCC
2205843 GTTTAGCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.21, C:0.39, G:0.08, T:0.31
Consensus pattern (36 bp):
TCCCCATCCCCATTTAGCATAAACGATTTTTCCCCA
Found at i:2205841 original size:24 final size:24
Alignment explanation
Indices: 2205814--2205868 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
2205804 CCCATCCCCG
2205814 TCCCCGTTTAGCATAAACGATTTT
1 TCCCCGTTTAGCATAAACGATTTT
2205838 TCCCCGTTTAGCATAAACGATTTT
1 TCCCCGTTTAGCATAAACGATTTT
2205862 TCCCCGT
1 TCCCCGT
2205869 CCCCGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (24 bp):
TCCCCGTTTAGCATAAACGATTTT
Found at i:2216156 original size:18 final size:18
Alignment explanation
Indices: 2216133--2216168 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2216123 TTTTTTTACA
2216133 ACTTAAAACCTGTAAACC
1 ACTTAAAACCTGTAAACC
2216151 ACTTAAAACCTGTAAACC
1 ACTTAAAACCTGTAAACC
2216169 TTGCTAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (18 bp):
ACTTAAAACCTGTAAACC
Done.