Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 6 of 208
Found at i:1994782 original size:8 final size:8
Alignment explanation
Indices: 1994726--1994790 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
1994716 GGTTAGGGTG
*
1994726 AAAGAAAG
1 AAAGAAAA
1994734 AAAGAAGAA
1 AAAGAA-AA
1994743 AGGAAGAAAA
1 A--AAGAAAA
1994753 AAAGAAAA
1 AAAGAAAA
*
1994761 AAA-AGAA
1 AAAGAAAA
*
1994768 AGA-AAAA
1 AAAGAAAA
1994775 AAAGAAAA
1 AAAGAAAA
*
1994783 AAATAAAA
1 AAAGAAAA
1994791 GAACAGTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 10 0.21
8 27 0.57
9 2 0.04
10 3 0.06
11 5 0.11
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAGAAAA
Found at i:2004146 original size:76 final size:75
Alignment explanation
Indices: 2004074--2004758 Score: 706
Period size: 75 Copynumber: 9.1 Consensus size: 75
2004064 TATTTTTCAA
* * *
2004074 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGTG-CGCACGCTGAGGTATTTTTAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
*
2004138 TATGTTTTTC
66 TCTGTTTTTC
*** *
2004148 AAAAAAATCAACTCATAAT-CTGAGAGGTGAGTTGAGCCTCGGGTCGTGCGCTGAGGCATTTTCA
1 --AAAAATCAACTCATAATGC-GAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCA
*
2004212 ATTTCTGTTCTTC
63 ATTTCTGTTTTTC
* * * *
2004225 AAAGATCAACTCATAAT-CGAAGAGGTGGGTTGAGCTTCGGGTCACACGCTGAGGTATTTTTAA-
1 AAAAATCAACTCATAATGCG-AGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
2004288 --CT-TTTTTC
65 TTCTGTTTTTC
** * * * *
2004296 AAAAATCAACTCATAATTTGAGAGGTGAGTTTGAGCTTTGGGTCACACGCGGAGGTGTTTTCAAT
1 AAAAATCAACTCATAATGCGAGAGGTGAG-TTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
2004361 TTCTGTTTTTC
65 TTCTGTTTTTC
* * * * *
2004372 AAAAATCAACTCATAATGTGAGAGGTGAGTTGAGTCTTGGGTCACACGCCGAGATATTTTTCAAT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TTTTCAAT
2004437 TTCTGTTTTTTTC
65 TTCTG--TTTTTC
* * * *
2004450 AAAAATCAACTCATAATGCGAGAAGAGAGTTGAGCCTTGGGTCACATGCTGAGGTATCTTTCAAT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAT-TTTCAAT
2004515 TTCTGTTTTTTC
65 TTCTG-TTTTTC
* * *
2004527 AAAAATTAACTCATAGTGCGAGGGGTGAGTTGAGCCTCGGGTCAAGCAC-C-GAGGTATTTTTCA
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-A-CACGCTGAGGTA-TTTTCA
*
2004590 ATTTCTATTTTTTC
63 ATTTCT-GTTTTTC
* * * * * * *
2004604 AAAAATCAACTCATAATCCGAAAGGTGAGTTGAGCCTCAGGTCGCGCGCTGATGCATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
*
2004669 TCTATTTTTC
66 TCTGTTTTTC
* * ** * ** * * *
2004679 AAAGATCAACTCATAAT-CTGAGAAGTGAGTTGAGATTCAGGTCGTACGCCGAGATATTTTCGAT
1 AAAAATCAACTCATAATGC-GAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
*
2004743 TTCTATTTTTC
65 TTCTGTTTTTC
2004754 AAAAA
1 AAAAA
2004759 AAAATTGACA
Statistics
Matches: 521, Mismatches: 68, Indels: 41
0.83 0.11 0.07
Matches are distributed among these distances:
71 29 0.06
72 33 0.06
74 2 0.00
75 151 0.29
76 98 0.19
77 136 0.26
78 70 0.13
79 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (75 bp):
AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
TCTGTTTTTC
Found at i:2004763 original size:154 final size:150
Alignment explanation
Indices: 2004074--2004758 Score: 699
Period size: 154 Copynumber: 4.5 Consensus size: 150
2004064 TATTTTTCAA
* * * * *
2004074 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGTG-CGCACGCTGAGGTATTTTT-AAT
1 AAAAATCAACTCATAAT-CGAGAGGTGAGTTGAGCTTCGGGTCACACGCCGAGATATTTTTCAAT
* * * * ***
2004137 TTATGTTTTTCAAAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGTGCGCTGA
65 TTCTATTTTTC--AAAAATCAACTCATAATCCGAAAGGTGAGTTGAGCCTCGGGTCACACGCTGA
*
2004202 GGCATTTTCAATTTCTGTTCTTC
128 GGCATTTTCAATTTCTGTTTTTC
* * * *
2004225 AAAGATCAACTCATAATCGAAGAGGTGGGTTGAGCTTCGGGTCACACGCTGAGGTATTTTT-AA-
1 AAAAATCAACTCATAATCG-AGAGGTGAGTTGAGCTTCGGGTCACACGCCGAGATATTTTTCAAT
** * * * *
2004288 --CT-TTTTTCAAAAATCAACTCATAATTTGAGAGGTGAGTTTGAGCTTTGGGTCACACGCGGAG
65 TTCTATTTTTCAAAAATCAACTCATAATCCGAAAGGTGAG-TTGAGCCTCGGGTCACACGCTGAG
**
2004350 GTGTTTTCAATTTCTGTTTTTC
129 GCATTTTCAATTTCTGTTTTTC
*
2004372 AAAAATCAACTCATAATGTGAGAGGTGAGTTGAGTCTT-GGGTCACACGCCGAGATATTTTTCAA
1 AAAAATCAACTCATAAT-CGAGAGGTGAGTTGAG-CTTCGGGTCACACGCCGAGATATTTTTCAA
* * * * *
2004436 TTTCTGTTTTTTTCAAAAATCAACTCATAATGCGAGAA-GAGAGTTGAGCCTTGGGTCACATGCT
64 TTTC--TATTTTTCAAAAATCAACTCATAATCCGA-AAGGTGAGTTGAGCCTCGGGTCACACGCT
*
2004500 GAGGTATCTTTCAATTTCTGTTTTTTC
126 GAGGCAT-TTTCAATTTCTG-TTTTTC
* * * * * *
2004527 AAAAATTAACTCATAGTGCGAGGGGTGAGTTGAGCCTCGGGTCA-AGCACCGAGGTATTTTTCAA
1 AAAAATCAACTCATAAT-CGAGAGGTGAGTTGAGCTTCGGGTCACA-CGCCGAGATATTTTTCAA
* * *
2004591 TTTCTATTTTTTCAAAAATCAACTCATAATCCGAAAGGTGAGTTGAGCCTCAGGTCGCGCGCTGA
64 TTTCTA-TTTTTCAAAAATCAACTCATAATCCGAAAGGTGAGTTGAGCCTCGGGTCACACGCTGA
* *
2004656 TGCATTTTCAATTTCTATTTTTC
128 GGCATTTTCAATTTCTGTTTTTC
* * * * ** *
2004679 AAAGATCAACTCATAATCTGAGAAGTGAGTTGAGATTCAGGTCGTACGCCGAGATA-TTTTCGAT
1 AAAAATCAACTCATAATC-GAGAGGTGAGTTGAGCTTCGGGTCACACGCCGAGATATTTTTCAAT
2004743 TTCTATTTTTCAAAAA
65 TTCTATTTTTCAAAAA
2004759 AAAATTGACA
Statistics
Matches: 454, Mismatches: 59, Indels: 43
0.82 0.11 0.08
Matches are distributed among these distances:
146 28 0.06
147 87 0.19
148 12 0.03
149 1 0.00
150 13 0.03
151 48 0.11
152 67 0.15
153 40 0.09
154 95 0.21
155 63 0.14
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (150 bp):
AAAAATCAACTCATAATCGAGAGGTGAGTTGAGCTTCGGGTCACACGCCGAGATATTTTTCAATT
TCTATTTTTCAAAAATCAACTCATAATCCGAAAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGC
ATTTTCAATTTCTGTTTTTC
Found at i:2004938 original size:29 final size:30
Alignment explanation
Indices: 2004879--2005019 Score: 112
Period size: 29 Copynumber: 4.7 Consensus size: 30
2004869 ATTTTATATT
*
2004879 TTTTTTAAAATTACATCTTGACACCTAAAC
1 TTTTTTAAAATTACATTTTGACACCTAAAC
* * *
2004909 TTTTTTAAAATTATATTTTGAC-CTTTAAC
1 TTTTTTAAAATTACATTTTGACACCTAAAC
* *
2004938 TTTTTTAAAATTAGATTTTAAC-CCTCAAAC
1 TTTTTTAAAATTACATTTTGACACCT-AAAC
* * **
2004968 TTTTCTT--ATTTACATTTTGGC-CCTTTAATT
1 TTTT-TTAAAATTACATTTTGACACC--TAAAC
*
2004998 TTTTTTAAAATTACACTTTGAC
1 TTTTTTAAAATTACATTTTGAC
2005020 CCAAGAAGTT
Statistics
Matches: 88, Mismatches: 17, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
29 41 0.47
30 33 0.38
31 14 0.16
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.50
Consensus pattern (30 bp):
TTTTTTAAAATTACATTTTGACACCTAAAC
Found at i:2004971 original size:59 final size:60
Alignment explanation
Indices: 2004879--2005012 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 60
2004869 ATTTTATATT
* *
2004879 TTTTTTAAAATTACATCTTGACACCTAAACTTTT-TTAAAATTATATTTT-GACCTTTAA-C
1 TTTTTTAAAATTACATCTTAACACCTAAACTTTTCTT--AATTACATTTTGGACCTTTAATC
* * * * *
2004938 TTTTTTAAAATTAGATTTTAAC-CCTCAAACTTTTCTTATTTACATTTTGGCCCTTTAATT
1 TTTTTTAAAATTACATCTTAACACCT-AAACTTTTCTTAATTACATTTTGGACCTTTAATC
2004998 TTTTTTAAAATTACA
1 TTTTTTAAAATTACA
2005013 CTTTGACCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 12 0.19
59 35 0.56
60 16 0.25
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (60 bp):
TTTTTTAAAATTACATCTTAACACCTAAACTTTTCTTAATTACATTTTGGACCTTTAATC
Found at i:2005536 original size:14 final size:13
Alignment explanation
Indices: 2005517--2005567 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
2005507 AGAAGAAATG
2005517 AAGAAATAAAAGAA
1 AAGAAA-AAAAGAA
*
2005531 AAGAAAAAGA-AA
1 AAGAAAAAAAGAA
*
2005543 AAGGAAAAAAGAA
1 AAGAAAAAAAGAA
*
2005556 AA-AATAAAAGAA
1 AAGAAAAAAAGAA
2005568 CAGCCAGGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 18 0.58
13 7 0.23
14 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:2005540 original size:20 final size:20
Alignment explanation
Indices: 2005496--2005567 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 20
2005486 GGGCTAAGGT
* *
2005496 GAAAGAAA-CAAAGAAGAAAT
1 GAAAGAAATAAAAGAA-AAAA
2005516 G-AAGAAATAAAAGAAAAGAA
1 GAAAGAAATAAAAGAAAA-AA
*
2005536 -AAAG-AA-AAAGGAAAAAA
1 GAAAGAAATAAAAGAAAAAA
2005553 GAAA-AAATAAAAGAA
1 GAAAGAAATAAAAGAA
2005568 CAGCCAGGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
17 2 0.05
18 13 0.31
19 16 0.38
20 11 0.26
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (20 bp):
GAAAGAAATAAAAGAAAAAA
Found at i:2005948 original size:17 final size:17
Alignment explanation
Indices: 2005926--2005962 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2005916 CACTGCAGTA
* *
2005926 AGCCAGGCCAGGCCAGC
1 AGCCAGCCCAGCCCAGC
2005943 AGCCAGCCCAGCCCAGC
1 AGCCAGCCCAGCCCAGC
2005960 AGC
1 AGC
2005963 AAAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.46, G:0.30, T:0.00
Consensus pattern (17 bp):
AGCCAGCCCAGCCCAGC
Found at i:2007241 original size:36 final size:36
Alignment explanation
Indices: 2007194--2007266 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2007184 AAATGTTACA
2007194 TAGTTTATTATTTGATCTTTATCTGAATCATTGTAT
1 TAGTTTATTATTTGATCTTTATCTGAATCATTGTAT
*
2007230 TAGTTTCTTATTTGATCTTTATCTGAATCATTGTAT
1 TAGTTTATTATTTGATCTTTATCTGAATCATTGTAT
2007266 T
1 T
2007267 CACTTTTGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (36 bp):
TAGTTTATTATTTGATCTTTATCTGAATCATTGTAT
Found at i:2010252 original size:214 final size:214
Alignment explanation
Indices: 2009883--2010282 Score: 782
Period size: 214 Copynumber: 1.9 Consensus size: 214
2009873 TGTTTGAACT
2009883 TTCAATGCTGTTATAATTGAAAAATCTATACATACAGATGGAAAATTAAATCAAGAACAATACTT
1 TTCAATGCTGTTATAATTGAAAAATCTATACATACAGATGGAAAATTAAATCAAGAACAATACTT
*
2009948 GCATGCATACGTGATCTGAATGTTCACTTATCTTAATTTTATTGGGTTTCGTGTGACAAATGTAT
66 GCATGCATACGTGATCTGAATGTTCACTTATCTTAATATTATTGGGTTTCGTGTGACAAATGTAT
2010013 AGGAAGATAGTTGGGAGCAGGTGGGTTTAAAATAAAGAAATGATTTGGAAAATAATTCTAAATGT
131 AGGAAGATAGTTGGGAGCAGGTGGGTTTAAAATAAAGAAATGATTTGGAAAATAATTCTAAATGT
2010078 GGAATTTTCTCACTACTTG
196 GGAATTTTCTCACTACTTG
2010097 TTCAATGCTGTTATAATTGAAAAATCTATACATACAGATGGAAAATTAAATCAAGAACAATACTT
1 TTCAATGCTGTTATAATTGAAAAATCTATACATACAGATGGAAAATTAAATCAAGAACAATACTT
*
2010162 GCATGCATACGTGATCTGAATGTTCACTTATCTTAGTATTATTGGGTTTCGTGTGACAAATGTAT
66 GCATGCATACGTGATCTGAATGTTCACTTATCTTAATATTATTGGGTTTCGTGTGACAAATGTAT
2010227 AGGAAGATAGTTGGGAGCAGGTGGGTTTAAAATAAAGAAATGATTTGGAAAATAAT
131 AGGAAGATAGTTGGGAGCAGGTGGGTTTAAAATAAAGAAATGATTTGGAAAATAAT
2010283 GTTGGATAAA
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 184 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (214 bp):
TTCAATGCTGTTATAATTGAAAAATCTATACATACAGATGGAAAATTAAATCAAGAACAATACTT
GCATGCATACGTGATCTGAATGTTCACTTATCTTAATATTATTGGGTTTCGTGTGACAAATGTAT
AGGAAGATAGTTGGGAGCAGGTGGGTTTAAAATAAAGAAATGATTTGGAAAATAATTCTAAATGT
GGAATTTTCTCACTACTTG
Found at i:2010348 original size:16 final size:17
Alignment explanation
Indices: 2010309--2010348 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2010299 TGGCAGTAGC
*
2010309 AAAGAAAGCAAAAAACG
1 AAAGAAAGCAAAAAACA
*
2010326 AATGAAAG-AAAAAACA
1 AAAGAAAGCAAAAAACA
2010342 AAAGAAA
1 AAAGAAA
2010349 AGAACTCAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAGAAAGCAAAAAACA
Found at i:2010877 original size:20 final size:20
Alignment explanation
Indices: 2010852--2010890 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2010842 GAGCTAACCT
2010852 CCCTCGATTGCTCAGCTTCG
1 CCCTCGATTGCTCAGCTTCG
2010872 CCCTCGATTGCTCAGCTTC
1 CCCTCGATTGCTCAGCTTC
2010891 TCTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.41, G:0.18, T:0.31
Consensus pattern (20 bp):
CCCTCGATTGCTCAGCTTCG
Found at i:2014828 original size:16 final size:16
Alignment explanation
Indices: 2014790--2014828 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2014780 TGGCAGTAGC
* *
2014790 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
2014806 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
2014822 AAAGAAA
1 AAAGAAA
2014829 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:2018916 original size:50 final size:50
Alignment explanation
Indices: 2018860--2018958 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
2018850 CACTATGGTT
*
2018860 AATTAAATTGATCAAATCGATCAGTCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATCACTCCACCATTAAATTCACTATTTCATC
*
2018910 AATTAAATTGATCAAATCGATCCCTCCACCATTAAATTCACTATTTCAT
1 AATTAAATTGATCAAATCGATCACTCCACCATTAAATTCACTATTTCAT
2018959 TGTTAAATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.34
Consensus pattern (50 bp):
AATTAAATTGATCAAATCGATCACTCCACCATTAAATTCACTATTTCATC
Found at i:2028159 original size:50 final size:50
Alignment explanation
Indices: 2028103--2028202 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
2028093 CACTATGGTT
2028103 AATTAAATTGATCAAATCGATCAT-TCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATC-TCTCCACCATTAAATTCACTATTTCATC
2028153 AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
2028203 GTTAAATCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (50 bp):
AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
Found at i:2030693 original size:14 final size:14
Alignment explanation
Indices: 2030676--2030713 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2030666 AAGGTATGAG
**
2030676 TATGTATATATGTA
1 TATGTATATATAAA
2030690 TATGTATATATAAA
1 TATGTATATATAAA
2030704 TATGTATATA
1 TATGTATATA
2030714 ATGCTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (14 bp):
TATGTATATATAAA
Found at i:2030855 original size:2 final size:2
Alignment explanation
Indices: 2030805--2030847 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2030795 TTAGGTTCGA
2030805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2030847 A
1 A
2030848 GGTATATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2031073 original size:75 final size:75
Alignment explanation
Indices: 2030985--2031125 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 75
2030975 ACTTACATAT
* * * * *
2030985 ATGTATATATTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATAT-G-AGATTCGATT
1 ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATAT-A-TGTATATGGAAGATTCGATT
2031048 ATGCAGGTATAC
64 ATGCAGGTATAC
* * *
2031060 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATATATGTATATGGAAGATTCGATTAT
1 ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATATGTATATGGAAGATTCGATTAT
2031125 G
66 G
2031126 TATATATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 6 0.11
74 2 0.04
75 48 0.86
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (75 bp):
ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATATGTATATGGAAGATTCGATTAT
GCAGGTATAC
Found at i:2031309 original size:41 final size:41
Alignment explanation
Indices: 2031224--2031316 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 41
2031214 GTACTTTACA
* * * * * * *
2031224 TCTAGTAGGTTTGATGCTGGTGAAATATTTCAGACTTTATG
1 TCTAGTAGGCTTAATGCCGGTGAAACAATTCAGACTATAAG
*
2031265 TCTAGTAGGCTTAATGCCGGTGAAACAATTCGGACTATAAG
1 TCTAGTAGGCTTAATGCCGGTGAAACAATTCAGACTATAAG
*
2031306 TCTAGCAGGCT
1 TCTAGTAGGCT
2031317 AAAAGCCAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (41 bp):
TCTAGTAGGCTTAATGCCGGTGAAACAATTCAGACTATAAG
Found at i:2031527 original size:69 final size:67
Alignment explanation
Indices: 2031441--2031618 Score: 202
Period size: 63 Copynumber: 2.6 Consensus size: 67
2031431 TTGAAGAACA
* *
2031441 TGTATATACATTTGGTGATAATACTTGTTAGGCATATGTATATATGCATTCAGCTATTCATGTTT
1 TGTATATACATTCGGTGATAATATTTGTTA-GCATATGTATATA-GCATTCAGCTATTCATGTTT
2031506 AAAG
64 AAAG
* * * *
2031510 TGTATATATATTCGGTGATAATATTTGTT---ATGTGTATA-AGCATTCGGTTATTCATGTTTAA
1 TGTATATACATTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCAGCTATTCATGTTTAA
2031571 AG
66 AG
* **
2031573 TGTATATGCATTCAATGATAATATTTGTTAAGCATATATGTATATA
1 TGTATATACATTCGGTGATAATATTTGTT-AGC--ATATGTATATA
2031619 CACATTTGGC
Statistics
Matches: 91, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
63 47 0.52
64 1 0.01
65 8 0.09
69 34 0.37
70 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (67 bp):
TGTATATACATTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCAGCTATTCATGTTTAA
AG
Found at i:2031584 original size:31 final size:31
Alignment explanation
Indices: 2031481--2031585 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
2031471 GGCATATGTA
* *
2031481 TATATGCATTCAGCTATTCATGTTTAAAGTG
1 TATATGCATTCGGTTATTCATGTTTAAAGTG
** * * *
2031512 TATATATATTCGGTGATAAT-AT-TTGTTATGTG
1 TATATGCATTCGGT--TATTCATGTT-TAAAGTG
*
2031544 TATAAGCATTCGGTTATTCATGTTTAAAGTG
1 TATATGCATTCGGTTATTCATGTTTAAAGTG
2031575 TATATGCATTC
1 TATATGCATTC
2031586 AATGATAATA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
30 3 0.05
31 29 0.53
32 20 0.36
33 3 0.05
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.45
Consensus pattern (31 bp):
TATATGCATTCGGTTATTCATGTTTAAAGTG
Found at i:2031783 original size:2 final size:2
Alignment explanation
Indices: 2031776--2031802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2031766 GCATGTTGTT
2031776 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 T
2031803 GTACTCATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2037467 original size:26 final size:27
Alignment explanation
Indices: 2037438--2037496 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
2037428 AATATTAAAT
*
2037438 TATTTATATAATTT-TATTATATATTA
1 TATTTATAAAATTTGTATTATATATTA
* * *
2037464 TATTTTTAAAATTTGTATTTTCTATTA
1 TATTTATAAAATTTGTATTATATATTA
*
2037491 TTTTTA
1 TATTTA
2037497 ATGGTTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTATAAAATTTGTATTATATATTA
Found at i:2037482 original size:27 final size:26
Alignment explanation
Indices: 2037438--2037495 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2037428 AATATTAAAT
* *
2037438 TATTTATATAATTTTATTATATATTA
1 TATTTTTAAAATTTTATTATATATTA
* *
2037464 TATTTTTAAAATTTGTATTTTCTATTA
1 TATTTTTAAAATTT-TATTATATATTA
2037491 T-TTTT
1 TATTTT
2037496 AATGGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TATTTTTAAAATTTTATTATATATTA
Found at i:2044469 original size:24 final size:25
Alignment explanation
Indices: 2044441--2044493 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
2044431 ACTATTTATA
2044441 TAATTTTATTATATAT-TA-TATTTT
1 TAATTTTATTAT-TATCTATTATTTT
* *
2044465 TAATTTTTTTATTTTCTATTATTTT
1 TAATTTTATTATTATCTATTATTTT
2044490 TAAT
1 TAAT
2044494 GGTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 13 0.52
25 10 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TAATTTTATTATTATCTATTATTTT
Found at i:2051284 original size:2 final size:2
Alignment explanation
Indices: 2051277--2051319 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2051267 ACTTTCTTCC
*
2051277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2051319 A
1 A
2051320 GTTTAACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2051430 original size:23 final size:22
Alignment explanation
Indices: 2051387--2051430 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2051377 TTATTGTCTA
*
2051387 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
2051409 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
2051431 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:2065397 original size:14 final size:14
Alignment explanation
Indices: 2065378--2065417 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2065368 TTGATTGGCA
2065378 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
2065392 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
2065406 GGAAAATGTTTT
1 GTAAAATGTTTT
2065418 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:2065426 original size:20 final size:20
Alignment explanation
Indices: 2065401--2065440 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2065391 CGTAAAATGA
*
2065401 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
2065421 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2065441 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2065430 original size:34 final size:35
Alignment explanation
Indices: 2065386--2065452 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2065376 CAGTAAAATG
*
2065386 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2065420 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2065453 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2065456 original size:14 final size:15
Alignment explanation
Indices: 2065380--2065456 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2065370 GATTGGCAGT
* *
2065380 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
2065394 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
2065408 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
2065428 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
2065443 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
2065457 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:2065564 original size:20 final size:20
Alignment explanation
Indices: 2065539--2065577 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2065529 GTTTTTACAT
2065539 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
2065559 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
2065578 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:2069508 original size:11 final size:11
Alignment explanation
Indices: 2069492--2069516 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2069482 ACCATCTGTG
2069492 TATAACCAAAA
1 TATAACCAAAA
2069503 TATAACCAAAA
1 TATAACCAAAA
2069514 TAT
1 TAT
2069517 CATCCAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (11 bp):
TATAACCAAAA
Found at i:2069716 original size:14 final size:14
Alignment explanation
Indices: 2069694--2069749 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
2069684 GAATATGCTG
* *
2069694 AGAAGAGAAGATGA
1 AGAACAGAAGAAGA
2069708 AGAACAGAAGAAGA
1 AGAACAGAAGAAGA
2069722 A-AA-AG--GAATGA
1 AGAACAGAAGAA-GA
2069733 AGAACAGAAGAAGA
1 AGAACAGAAGAAGA
2069747 AGA
1 AGA
2069750 CGGAGCCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
10 3 0.09
11 3 0.09
12 4 0.11
13 4 0.11
14 18 0.51
15 3 0.09
ACGTcount: A:0.62, C:0.04, G:0.30, T:0.04
Consensus pattern (14 bp):
AGAACAGAAGAAGA
Found at i:2069836 original size:18 final size:18
Alignment explanation
Indices: 2069813--2069857 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2069803 TTTGCAACCC
2069813 AAGGGGAAGGGAAAAGGG
1 AAGGGGAAGGGAAAAGGG
*
2069831 AAGGGGAAGGGAAAGGGG
1 AAGGGGAAGGGAAAAGGG
*
2069849 AAAGGGAAG
1 AAGGGGAAG
2069858 AAGAAGGCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGAAAAGGG
Found at i:2069837 original size:6 final size:6
Alignment explanation
Indices: 2069813--2069857 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
2069803 TTTGCAACCC
* * * *
2069813 AAGGGG AAGGGA AAAGGG AAGGGG AAGGGA AAGGGG AAAGGG AAG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAG
2069858 AAGAAGGCGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:2069863 original size:24 final size:24
Alignment explanation
Indices: 2069813--2069864 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2069803 TTTGCAACCC
* **
2069813 AAGGGGAAGGGAAAAGGGAAGGGG
1 AAGGGAAAGGGAAAAGGGAAGAAG
*
2069837 AAGGGAAAGGGGAAAGGGAAGAAG
1 AAGGGAAAGGGAAAAGGGAAGAAG
2069861 AAGG
1 AAGG
2069865 CGTCATTCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (24 bp):
AAGGGAAAGGGAAAAGGGAAGAAG
Found at i:2070420 original size:23 final size:22
Alignment explanation
Indices: 2070377--2070420 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2070367 TTATTGTCTA
*
2070377 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
2070399 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
2070421 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:2070676 original size:19 final size:20
Alignment explanation
Indices: 2070630--2070676 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
2070620 CTAATTATTG
*
2070630 ACCGAAATGGATTAGAATAC
1 ACCGAAATGGATTAGAACAC
*
2070650 ACCAAAATGG-TT-GAAGCAC
1 ACCGAAATGGATTAGAA-CAC
2070669 ACCGAAAT
1 ACCGAAAT
2070677 TTTAACAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
20 9 0.39
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (20 bp):
ACCGAAATGGATTAGAACAC
Found at i:2073186 original size:14 final size:14
Alignment explanation
Indices: 2073167--2073201 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2073157 ATGCATATAG
2073167 ATATATATAGATAT
1 ATATATATAGATAT
2073181 ATATATATAGATAT
1 ATATATATAGATAT
*
2073195 GTATATA
1 ATATATA
2073202 AATTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
ATATATATAGATAT
Found at i:2073199 original size:10 final size:10
Alignment explanation
Indices: 2073161--2073185 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2073151 TAAAAAATGC
2073161 ATATAGATAT
1 ATATAGATAT
2073171 ATATAGATAT
1 ATATAGATAT
2073181 ATATA
1 ATATA
2073186 TATAGATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
ATATAGATAT
Found at i:2073262 original size:29 final size:31
Alignment explanation
Indices: 2073229--2073303 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
2073219 ACATATATAA
*
2073229 GTATGTATATATATAAATAGATTAT-AAAAT
1 GTATGTATGTATATAAATAGATTATAAAAAT
* * * *
2073259 -TATGTACGTGTATATATATATTATAAAAAT
1 GTATGTATGTATATAAATAGATTATAAAAAT
2073289 GTATGTATGTATATA
1 GTATGTATGTATATA
2073304 TATGTATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 19 0.53
30 5 0.14
31 12 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (31 bp):
GTATGTATGTATATAAATAGATTATAAAAAT
Found at i:2073391 original size:19 final size:19
Alignment explanation
Indices: 2073347--2073383 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2073337 TGAATGAGTA
*
2073347 AATAGTAATGATAATAATT
1 AATAATAATGATAATAATT
2073366 AATAATAATGATAATAAT
1 AATAATAATGATAATAAT
2073384 AGCAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (19 bp):
AATAATAATGATAATAATT
Found at i:2074929 original size:44 final size:43
Alignment explanation
Indices: 2074843--2074985 Score: 150
Period size: 44 Copynumber: 3.4 Consensus size: 43
2074833 AATCCGACCT
* * * *
2074843 ACTGCAACTTCAGAGG-TATAGGATT-CATCTTCAATCTTCTCC
1 ACTGCAACTTCAG-GGAGATAAGATTGGATCTTCAATCTGCTCC
* *
2074885 ACTGCAAGTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTGG-ATCTTCAATCTGCTCC
* * * *
2074929 ATTGCAACTTCAGTGAGATAAGATTGGA--TGCAATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGATTGGATCTTCAATCTGCTCC
2074970 ACTGCAACTTCAGGGA
1 ACTGCAACTTCAGGGA
2074986 CGAGATTTGT
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
41 26 0.31
42 19 0.23
43 1 0.01
44 38 0.45
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (43 bp):
ACTGCAACTTCAGGGAGATAAGATTGGATCTTCAATCTGCTCC
Found at i:2075106 original size:44 final size:44
Alignment explanation
Indices: 2075053--2075645 Score: 218
Period size: 44 Copynumber: 13.5 Consensus size: 44
2075043 ATTTGATCTG
2075053 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
* * ** * *
2075097 CTGCACTACTGCTTAGGGAGATAG-GGCT--AATGGCTTAAATCTGCTT
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAAT--CTTCAA-C--CTA
* * * * * *
2075143 CTCCACTA-T-CTT-GGGAAGATAAGATTC-ACCATCTTCAATCTG
1 CTCCACTACTGCTTAGGG-AGA-CAGAATCTGCAATCTTCAACCTA
* *
2075185 CTCTACTATTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
* * *
2075229 CTCCACTACTGCTTAGGGAGACAGGA-CT--AATGACTTAAATCTGCTT
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAAT--CTTCAA-C--CTA
* * * * ** * *
2075275 CTCCACTA-T-CTT-GGGAAGATAAGATTC-ACCATCTTTGATCTG
1 CTCCACTACTGCTTAGGG-AGA-CAGAATCTGCAATCTTCAACCTA
* * * *
2075317 CTCCACTATTGCTTAGGGTGATAGAATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
* * * *
2075361 CTCCACTACTGCTTAGGGAGATAGTA-CT--AATGACTTAAATCTGCTT
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAAT--CTTCAA-C--CTA
* * * * * * * *
2075407 CTTCACTAC--CTT-GGGAAGATAAGATTC-ACCATCTTCGATCTG
1 CTCCACTACTGCTTAGGG-AGA-CAGAATCTGCAATCTTCAACCTA
*
2075449 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACTTA
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
* * * * *
2075493 CTCCACTACTGCTTAGGGGGATA-AGA-CT--AATGGCTTAAATATGCTT
1 CTCCACTACTGCTTAGGGAGACAGA-ATCTGCAAT--CTT-CA-A-CCTA
* * * * ** ** *
2075539 CTCCACTA-T-CTT-GGGAAGATAAGATTC-ACCATCTTTGATTTG
1 CTCCACTACTGCTTAGGG-AGA-CAGAATCTGCAATCTTCAACCTA
2075581 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
2075625 CTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
2075646 TAGGACTAAT
Statistics
Matches: 402, Mismatches: 89, Indels: 116
0.66 0.15 0.19
Matches are distributed among these distances:
41 12 0.03
42 38 0.09
43 63 0.16
44 199 0.50
45 39 0.10
46 43 0.11
47 8 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
Found at i:2075160 original size:132 final size:132
Alignment explanation
Indices: 2075015--2075779 Score: 1190
Period size: 132 Copynumber: 5.8 Consensus size: 132
2075005 TTACTTCCCT
*
2075015 ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* *
2075080 CTGCAATCTTCAACCTACTGCACTACTGCTTAGGGAGATAGGGCTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
2075145 CC
131 CC
* ** * *
2075147 ACTATCTTGGGAAGATAAGATTCACCATCTTCAATCTGCTCTACTATTGCTTAGGGAGACAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* *
2075212 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAGGACTAATGACTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
2075277 CC
131 CC
* * * *
2075279 ACTATCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTATTGCTTAGGGTGATAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* * *
2075344 CTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGTACTAATGACTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
*
2075409 TC
131 CC
*
2075411 ACTACCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* * * *
2075476 CTGCAATCTTCAACTTACTCCACTACTGCTTAGGGGGATAAGACTAATGGCTTAAATATGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
2075541 CC
131 CC
* *
2075543 ACTATCTTGGGAAGATAAGATTCACCATCTTTGATTTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
*
2075608 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATATGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
*
2075673 CT
131 CC
* * ** * *
2075675 TCTACCTTAGGAAGATAAGATTCACTTTTTTTGATCTGCTCCACTACTGCTTAGGGAGATA-AGA
1 ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGA-A
* * *
2075739 TCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATA
65 TCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATA
2075780 AGGCTTGATA
Statistics
Matches: 582, Mismatches: 50, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
131 1 0.00
132 581 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
ACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
CC
Found at i:2077119 original size:17 final size:14
Alignment explanation
Indices: 2077092--2077167 Score: 73
Period size: 14 Copynumber: 5.3 Consensus size: 14
2077082 TGGCCTCTCC
2077092 TTTTCTTTTTCTTTT
1 TTTTCTTTTT-TTTT
* *
2077107 ATCTTCTTTTTTCTT
1 -TTTTCTTTTTTTTT
*
2077122 TTTTCTTTGTTTTT
1 TTTTCTTTTTTTTT
*
2077136 CTTTC-TTTTTTTT
1 TTTTCTTTTTTTTT
*
2077149 TTCTCTTTTTTCTTT
1 TTTTCTTTTTT-TTT
2077164 TTTT
1 TTTT
2077168 TTAGATATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
13 10 0.21
14 20 0.42
15 9 0.19
16 9 0.19
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:2077134 original size:10 final size:10
Alignment explanation
Indices: 2077099--2077165 Score: 52
Period size: 10 Copynumber: 6.9 Consensus size: 10
2077089 TCCTTTTCTT
2077099 TTTCTTTTATC
1 TTTCTTTT-TC
2077110 -TTCTTTTT-
1 TTTCTTTTTC
*
2077118 TCT-TTTTTC
1 TTTCTTTTTC
*
2077127 TTTGTTTTTC
1 TTTCTTTTTC
*
2077137 TTTCTTTTTTT
1 TTTC-TTTTTC
*
2077148 TTTCTCTTT-
1 TTTCTTTTTC
2077157 TTTCTTTTT
1 TTTCTTTTT
2077166 TTTTAGATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 5 0.11
9 12 0.26
10 20 0.43
11 9 0.20
ACGTcount: A:0.01, C:0.15, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:2077138 original size:34 final size:34
Alignment explanation
Indices: 2077097--2077169 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
2077087 TCTCCTTTTC
2077097 TTTTTCTTT-TATCTTCTTTTT-TCTTTTTTCTTTG
1 TTTTTCTTTCT-T-TTCTTTTTCTCTTTTTTCTTTG
* *
2077131 TTTTTCTTTCTTTTTTTTTTCTCTTTTTTCTTTT
1 TTTTTCTTTCTTTTCTTTTTCTCTTTTTTCTTTG
2077165 TTTTT
1 TTTTT
2077170 AGATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 7 0.20
34 27 0.77
35 1 0.03
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.84
Consensus pattern (34 bp):
TTTTTCTTTCTTTTCTTTTTCTCTTTTTTCTTTG
Found at i:2077168 original size:24 final size:24
Alignment explanation
Indices: 2077092--2077169 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
2077082 TGGCCTCTCC
* *
2077092 TTTTCTTTT-TCTTTTATCTTCTTT
1 TTTTTTTTTCTCTTTTTTCTT-TTT
* *
2077116 TTTCTTTTTTCTTTGTTTTTCTTTCT
1 TTT-TTTTTTCTCT-TTTTTCTTTTT
2077142 TTTTTTTTTCTCTTTTTTCTTTTT
1 TTTTTTTTTCTCTTTTTTCTTTTT
2077166 TTTT
1 TTTT
2077170 AGATATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 17 0.38
25 14 0.31
26 7 0.16
27 7 0.16
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTCTCTTTTTTCTTTTT
Found at i:2077178 original size:21 final size:20
Alignment explanation
Indices: 2077113--2077180 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
2077103 TTTTATCTTC
*
2077113 TTTTTTCTTTTTTCTTTG-TT
1 TTTTTTCTTTTTT-TTTGATA
** *
2077133 TTTCTTTCTTTTTTTTTTCTC
1 TTT-TTTCTTTTTTTTTGATA
2077154 TTTTTTCTTTTTTTTTAGATA
1 TTTTTTCTTTTTTTTT-GATA
2077175 TTTTTT
1 TTTTTT
2077181 ATTGAACCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.04, C:0.10, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTGATA
Found at i:2077179 original size:34 final size:33
Alignment explanation
Indices: 2077113--2077180 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
2077103 TTTTATCTTC
*** *
2077113 TTTTTTCTTTTTTCTTTGTTTTTCTTTCTTTTT
1 TTTTTTCTTTTTTCTTTGTTTTTAGATATTTTT
*
2077146 TTTTTCTCTTTTTTCTTTTTTTTTAGATATTTTT
1 TTTTT-TCTTTTTTCTTTGTTTTTAGATATTTTT
2077180 T
1 T
2077181 ATTGAACCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.04, C:0.10, G:0.03, T:0.82
Consensus pattern (33 bp):
TTTTTTCTTTTTTCTTTGTTTTTAGATATTTTT
Found at i:2088156 original size:43 final size:43
Alignment explanation
Indices: 2088014--2088168 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
2088004 TTTCGAGATG
* * *
2088014 TGATATCGTGTAAGACCATGTCTGGGACATTGGCATCGATCTGA
1 TGATAACGTGTAAGACCATGTCTGGGACATTGGCATTGATAT-A
* **
2088058 -GATCACGTGTAAGACCATGTCTGGGACATTGG--TGTCCTATA
1 TGATAACGTGTAAGACCATGTCTGGGACATTGGCAT-TGATATA
*** * *
2088099 TGATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATTGATATA
1 TGATAACGTGTAAGACCATGTCTGGGACATTGGCATTGATATA
* *
2088142 TGATAACATGTAAGACCATATCTGGGA
1 TGATAACGTGTAAGACCATGTCTGGGA
2088169 TATAGCATTG
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 29 0.33
43 56 0.64
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
TGATAACGTGTAAGACCATGTCTGGGACATTGGCATTGATATA
Found at i:2092179 original size:114 final size:114
Alignment explanation
Indices: 2092020--2092627 Score: 982
Period size: 114 Copynumber: 5.3 Consensus size: 114
2092010 AAAATAAGCA
* * * * *
2092020 TTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* * * *
2092085 CACAAAAAAATCTAAGCCTAACGACGCCGTCTTCTGAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
* *
2092134 TTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTAGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
*
2092199 CGCAAAAATACCTAAGTCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
*
2092248 TTAGTGGCATTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
2092313 CGTAAAAATACCTAAGCCTAACGACGCCGTTTTTTGAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
* *
2092362 TTAGTGGCGTTTTTAAGTAAGCGCCGTTGATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
2092427 CGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
* * ** *
2092476 TTAGTGGCATTTTTAAGTAAGTGCCGCTGTTGCTCAGGTCTTTAGTGGCGTTTTTGGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
2092541 CGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
2092590 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGG
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGG
2092628 GATTTAAAAT
Statistics
Matches: 458, Mismatches: 36, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 458 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (114 bp):
TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
Found at i:2093231 original size:7 final size:7
Alignment explanation
Indices: 2093221--2093294 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
2093211 GGATTCTGGT
2093221 TTAAGGG
1 TTAAGGG
*
2093228 TTAATGTGA
1 TTAA-G-GG
*
2093237 TTTAAGGT
1 TT-AAGGG
*
2093245 TTATGGG
1 TTAAGGG
2093252 TTAAGGG
1 TTAAGGG
2093259 TTAAGGG
1 TTAAGGG
*
2093266 TTAGGGG
1 TTAAGGG
*
2093273 TTAGGGG
1 TTAAGGG
2093280 TT-A-GG
1 TTAAGGG
*
2093285 TTAGGGG
1 TTAAGGG
2093292 TTA
1 TTA
2093295 GATGTTAAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
5 4 0.07
7 40 0.74
8 4 0.07
9 4 0.07
10 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (7 bp):
TTAAGGG
Found at i:2093264 original size:21 final size:20
Alignment explanation
Indices: 2093238--2093321 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 20
2093228 TTAATGTGAT
*
2093238 TTAAGGTTTATGGGTTAAGGG
1 TTAAGG-TTAGGGGTTAAGGG
*
2093259 TTAAGGGTTAGGGGTTAGGGG
1 TTAA-GGTTAGGGGTTAAGGG
*
2093280 TT-AGGTTAGGGGTT-AGATG
1 TTAAGGTTAGGGGTTAAG-GG
* *
2093299 TTAAGAGTTAGGGATTTAGGG
1 TTAAG-GTTAGGGGTTAAGGG
2093320 TT
1 TT
2093322 TATAAATTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 14 0.27
20 3 0.06
21 30 0.58
22 4 0.08
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.36
Consensus pattern (20 bp):
TTAAGGTTAGGGGTTAAGGG
Found at i:2093288 original size:19 final size:21
Alignment explanation
Indices: 2093250--2093311 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2093240 AAGGTTTATG
*
2093250 GGTTAAGGGTTAAGGGTTAGG
1 GGTTAGGGGTTAAGGGTTAGG
2093271 GGTTAGGGGTT-A-GGTTAGG
1 GGTTAGGGGTTAAGGGTTAGG
** *
2093290 GGTTAGATGTTAAGAGTTAGG
1 GGTTAGGGGTTAAGGGTTAGG
2093311 G
1 G
2093312 ATTTAGGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 2 0.06
21 17 0.49
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.31
Consensus pattern (21 bp):
GGTTAGGGGTTAAGGGTTAGG
Found at i:2093295 original size:7 final size:7
Alignment explanation
Indices: 2093249--2093295 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
2093239 TAAGGTTTAT
*
2093249 GGGTTAA
1 GGGTTAG
*
2093256 GGGTTAA
1 GGGTTAG
2093263 GGGTTAG
1 GGGTTAG
2093270 GGGTTAG
1 GGGTTAG
2093277 GGGTTA-
1 GGGTTAG
2093283 -GGTTAG
1 GGGTTAG
2093289 GGGTTAG
1 GGGTTAG
2093296 ATGTTAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 5 0.14
7 32 0.86
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:2093301 original size:14 final size:12
Alignment explanation
Indices: 2093257--2093295 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2093247 ATGGGTTAAG
*
2093257 GGTTAAGGGTTA
1 GGTTAGGGGTTA
2093269 GGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
2093283 GGTTAGGGGTTA
1 GGTTAGGGGTTA
2093295 G
1 G
2093296 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:2093301 original size:26 final size:26
Alignment explanation
Indices: 2093257--2093310 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
2093247 ATGGGTTAAG
* * *
2093257 GGTTAAGGGTTAGGGGTTAGGGGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
* *
2093283 GGTTAGGGGTTAGATGTTAAGAGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
2093309 GG
1 GG
2093311 GATTTAGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.31
Consensus pattern (26 bp):
GGTTAAGGGTTAGAGGTTAAGAGTTA
Found at i:2093554 original size:90 final size:90
Alignment explanation
Indices: 2093327--2093666 Score: 382
Period size: 90 Copynumber: 3.7 Consensus size: 90
2093317 GGGTTTATAA
* * * * * *
2093327 ATTCGGTGTTAGG-TTAGAGTTTAGGGTTTAGATTAATTAGT-GTATTTTAA-TTATAAATTACA
1 ATTCGGGGTTTGGTTTAGGGTTTAGGGTTTAGATTAATTAGTACT-TTTTAATTTATATATTAAA
* *
2093389 TAAGGTTTAGGGGTTAAGGGTTAGGG
65 TAAAGTTTAGGGGTTAGGGGTTAGGG
* * * * * * *
2093415 ATTC-AGGATCGGGTTATGGTTTAGGGTTTAGATTAATTACTATTTTTTAATTTATATATTAAAT
1 ATTCGGGGTTTGGTTTAGGGTTTAGGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAAT
*
2093479 AAAGTTTAAGGGTTAGGGGTTAGGG
66 AAAGTTTAGGGGTTAGGGGTTAGGG
2093504 ATTCGGGGTTTGGTTTAGGGTTTAGGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAAT
1 ATTCGGGGTTTGGTTTAGGGTTTAGGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAAT
2093569 AAAGTTTAGGGGTTAGGGGTTAGGG
66 AAAGTTTAGGGGTTAGGGGTTAGGG
* * * * * * *
2093594 GTTAGGGATTTGGGGTCGGGTTAGGGTTTAAGATTTGGATTAATTAGTACTTGTTAATTTATATA
1 ATTCGGGGTTT--GGT----TTAGGGTTTAGGGTTTAGATTAATTAGTACTTTTTAATTTATATA
2093659 TTAAATAA
60 TTAAATAA
2093667 GTTCTTTATA
Statistics
Matches: 214, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
87 4 0.02
88 35 0.16
89 38 0.18
90 85 0.40
92 3 0.01
96 49 0.23
ACGTcount: A:0.28, C:0.03, G:0.27, T:0.42
Consensus pattern (90 bp):
ATTCGGGGTTTGGTTTAGGGTTTAGGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAAT
AAAGTTTAGGGGTTAGGGGTTAGGG
Found at i:2093586 original size:7 final size:7
Alignment explanation
Indices: 2093574--2093600 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2093564 TAAATAAAGT
2093574 TTAGGGG
1 TTAGGGG
2093581 TTAGGGG
1 TTAGGGG
2093588 TTAGGGG
1 TTAGGGG
2093595 TTAGGG
1 TTAGGG
2093601 ATTTGGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:2093608 original size:14 final size:14
Alignment explanation
Indices: 2093574--2093609 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2093564 TAAATAAAGT
*
2093574 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGGA
2093588 TTAGGGGTTAGGGA
1 TTAGGGGTTAGGGA
*
2093602 TTTGGGGT
1 TTAGGGGT
2093610 CGGGTTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.53, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAGGGA
Found at i:2093768 original size:21 final size:21
Alignment explanation
Indices: 2093715--2093768 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
2093705 TAAAGATTAT
2093715 TAATTTAAAA-TTGATATGGAA
1 TAATTTAAAATTTGATAT-GAA
*
2093736 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATGAA
2093757 TAATTTAAAATT
1 TAATTTAAAATT
2093769 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATGAA
Found at i:2093783 original size:8 final size:8
Alignment explanation
Indices: 2093758--2093809 Score: 54
Period size: 9 Copynumber: 6.5 Consensus size: 8
2093748 TGAATATAAT
2093758 AATT-TAA
1 AATTGTAA
2093765 AATTGTAAA
1 AATTGT-AA
2093774 AATTGTAA
1 AATTGTAA
2093782 AATTGTAAA
1 AATTGT-AA
*
2093791 AATTATAA
1 AATTGTAA
*
2093799 AAAT-TAA
1 AATTGTAA
2093806 AATT
1 AATT
2093810 AAAATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
7 10 0.26
8 14 0.36
9 15 0.38
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (8 bp):
AATTGTAA
Found at i:2093784 original size:17 final size:16
Alignment explanation
Indices: 2093758--2093827 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 16
2093748 TGAATATAAT
2093758 AATTTAAAATTGTAAA
1 AATTTAAAATTGTAAA
2093774 AATTGTAAAATTGTAAA
1 AATT-TAAAATTGTAAA
*
2093791 AATTATAAAAAT-T-AA
1 AATT-TAAAATTGTAAA
2093806 AA-TTAAAA-T-TAAA
1 AATTTAAAATTGTAAA
*
2093819 AAATTAAAA
1 AATTTAAAA
2093828 AGAAATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.04
13 9 0.18
14 7 0.14
15 4 0.08
16 5 0.10
17 22 0.45
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AATTTAAAATTGTAAA
Found at i:2093804 original size:9 final size:9
Alignment explanation
Indices: 2093763--2093803 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
2093753 ATAATAATTT
2093763 AAAATTGTA
1 AAAATTGTA
2093772 AAAATTGT-
1 AAAATTGTA
2093780 AAAATTGTA
1 AAAATTGTA
*
2093789 AAAATTATA
1 AAAATTGTA
2093798 AAAATT
1 AAAATT
2093804 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (9 bp):
AAAATTGTA
Found at i:2093828 original size:21 final size:21
Alignment explanation
Indices: 2093761--2093827 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 21
2093751 ATATAATAAT
*
2093761 TTAAAATTGTAAAAATTGTAAAA
1 TTAAAATTATAAAAA-T-TAAAA
2093784 TTGTAAAAATTATAAAAATTAAAA
1 -T-T-AAAATTATAAAAATTAAAA
2093808 TTAAAATTA-AAAAATTAAAA
1 TTAAAATTATAAAAATTAAAA
2093828 AGAAATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 11 0.28
21 7 0.17
22 1 0.03
23 1 0.03
24 6 0.15
25 2 0.05
26 12 0.30
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAAAATTATAAAAATTAAAA
Found at i:2093892 original size:47 final size:48
Alignment explanation
Indices: 2093833--2093931 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
2093823 TAAAAAGAAA
** * *
2093833 TAAAAACACTAAAATTTTTATTTTTACCTAATTTTTATAAATACTACT
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
* *
2093881 TAAAAA-ACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
2093928 TAAA
1 TAAA
2093932 CAAAACTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (48 bp):
TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
Found at i:2094340 original size:192 final size:193
Alignment explanation
Indices: 2094006--2094538 Score: 807
Period size: 192 Copynumber: 2.7 Consensus size: 193
2093996 CGTTTCTAAC
*
2094006 AAAAACGCCACAAAATATTCTTAATAATGAAGACAAAACGGTGCAGTTTTTGGCTGCGAATTTAA
1 AAAAACGCCGCAAAATATTCTTAATAATGAAG-----A-GGTGCAGTTTTTGGCTGCGAATTTAA
*
2094071 TGGGTTTTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGACGCTAAGGAAAAAA
60 TGGGTTTTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAA
* *
2094136 CGCTGCAAAGTTCTGTTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCT
125 CGCCGCAAAGTTCTATTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCT
2094201 ACTA
190 ACTA
*
2094205 AAAAACGCCGCAAAATATTCTTAATAATGAAG-GGTGCAGTTTTTGGCTGTGAATTTAATGGGTT
1 AAAAACGCCGCAAAATATTCTTAATAATGAAGAGGTGCAGTTTTTGGCTGCGAATTTAATGGGTT
* * *
2094269 TTGCAGCGCTAAGGGAAAAATGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAAAGCCGC
66 TTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAACGCCGC
* *
2094334 AAAGTTCTATTCTCAGTTTTCGTAAAATGGTGTCGTTTTGCCTGGGCATTAGTGGCGCTACTA
131 AAAGTTCTATTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCTACTA
*
2094397 AAAAACGCCGCAAAATATTCTTAATAATGAAGACAAAACGGTGCAATTTTTGGCTGCGAATTTAA
1 AAAAACGCCGCAAAATATTCTTAATAATGAAG-----A-GGTGCAGTTTTTGGCTGCGAATTTAA
* * ** *
2094462 TGGGTTTTGCGGCGCTAAGGTAAAAACACCGCTAAATATGGTCATTAGCGGCGCTAAGGAACAAA
60 TGGGTTTTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAA
2094527 CGCCGCAAAGTT
125 CGCCGCAAAGTT
2094539 AGTACTGAAA
Statistics
Matches: 307, Mismatches: 20, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
192 183 0.60
199 124 0.40
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (193 bp):
AAAAACGCCGCAAAATATTCTTAATAATGAAGAGGTGCAGTTTTTGGCTGCGAATTTAATGGGTT
TTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAACGCCGC
AAAGTTCTATTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCTACTA
Found at i:2097836 original size:28 final size:28
Alignment explanation
Indices: 2097776--2097830 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2097766 TTGTCATCCT
* ***
2097776 GCTATAATTCATGCCTTGTCTTTTAATC
1 GCTATAATTCATGCCATGTCTGCAAATC
2097804 GCTATAATTCATGCCATGTCTGCAAAT
1 GCTATAATTCATGCCATGTCTGCAAAT
2097831 GACTATGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (28 bp):
GCTATAATTCATGCCATGTCTGCAAATC
Found at i:2098181 original size:46 final size:46
Alignment explanation
Indices: 2098128--2098301 Score: 154
Period size: 46 Copynumber: 3.6 Consensus size: 46
2098118 AAAAAATGTC
* *
2098128 CAACTTAATAACTTATATAATTCACATAATAACTTACATAACTTAA
1 CAACTTAACAACTTACATAATTCACATAATAACTTACATAACTTAA
* * * *
2098174 CAACTTAACAACTCACATAATTTACATAACACATATA-TATATGCCATACCAT-A
1 CAACTTAACAACTTACATAATTCACAT---A-ATA-ACT-TA---CATAACTTAA
* * *
2098227 TAACTTAATAACTTATATAATTCACATAATAACTTACATAACTTAA
1 CAACTTAACAACTTACATAATTCACATAATAACTTACATAACTTAA
* *
2098273 TAACTTAACAACTTACATAATTTACATAA
1 CAACTTAACAACTTACATAATTCACATAA
2098302 CTTAATAATT
Statistics
Matches: 101, Mismatches: 16, Indels: 22
0.73 0.12 0.16
Matches are distributed among these distances:
45 6 0.06
46 50 0.50
48 3 0.03
49 5 0.05
50 5 0.05
51 3 0.03
53 23 0.23
54 6 0.06
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (46 bp):
CAACTTAACAACTTACATAATTCACATAATAACTTACATAACTTAA
Found at i:2098208 original size:53 final size:55
Alignment explanation
Indices: 2098144--2098287 Score: 127
Period size: 53 Copynumber: 2.7 Consensus size: 55
2098134 AATAACTTAT
*
2098144 ATAATTCACATA-ATAACTTACATAACTTAACAACTTAACAACTCACATAATTTAC
1 ATAA-TCACATACATAACTTACATAACTTAACAACTTAACAACTCACATAATTCAC
* ** * * * * * *
2098199 ATAA-CACATATATATA-TGCCATACCAT-ATAACTTAATAACTTATATAATTCAC
1 ATAATCACATACATA-ACTTACATAACTTAACAACTTAACAACTCACATAATTCAC
* *
2098252 ATAATAACTTACATAACTTA-ATAACTTAACAACTTA
1 ATAATCACATACATAACTTACATAACTTAACAACTTA
2098288 CATAATTTAC
Statistics
Matches: 67, Mismatches: 17, Indels: 11
0.71 0.18 0.12
Matches are distributed among these distances:
53 37 0.55
54 25 0.37
55 5 0.07
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (55 bp):
ATAATCACATACATAACTTACATAACTTAACAACTTAACAACTCACATAATTCAC
Found at i:2098239 original size:8 final size:8
Alignment explanation
Indices: 2098226--2098309 Score: 68
Period size: 8 Copynumber: 10.5 Consensus size: 8
2098216 GCCATACCAT
2098226 ATAACTTA
1 ATAACTTA
2098234 ATAACTTA
1 ATAACTTA
*
2098242 TATAA-TTC
1 -ATAACTTA
*
2098250 A-CA-T-A
1 ATAACTTA
2098255 ATAACTTA
1 ATAACTTA
2098263 CATAACTTA
1 -ATAACTTA
2098272 ATAACTTA
1 ATAACTTA
*
2098280 ACAACTTA
1 ATAACTTA
*
2098288 CATAATTTA
1 -ATAACTTA
2098297 CATAACTTA
1 -ATAACTTA
2098306 ATAA
1 ATAA
2098310 TTTTAAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 2 0.03
8 30 0.48
9 26 0.42
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAACTTA
Found at i:2098246 original size:17 final size:17
Alignment explanation
Indices: 2098226--2098309 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 17
2098216 GCCATACCAT
*
2098226 ATAACTTAATAACTTAT
1 ATAACTTAATAACTTAC
2098243 ATAA-TTCACATAATAACTTAC
1 ATAACTT-A-AT---AACTTAC
2098264 ATAACTTAATAACTTA-
1 ATAACTTAATAACTTAC
* *
2098280 ACAACTTACATAATTTAC
1 ATAACTTA-ATAACTTAC
2098298 ATAACTTAATAA
1 ATAACTTAATAA
2098310 TTTTAAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
16 9 0.16
17 22 0.40
18 9 0.16
20 2 0.04
21 11 0.20
22 2 0.04
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAACTTAATAACTTAC
Found at i:2098267 original size:9 final size:8
Alignment explanation
Indices: 2098253--2098309 Score: 69
Period size: 9 Copynumber: 6.8 Consensus size: 8
2098243 ATAATTCACA
2098253 TAATAACT
1 TAATAACT
2098261 TACATAACT
1 TA-ATAACT
2098270 TAATAACT
1 TAATAACT
*
2098278 TAACAACT
1 TAATAACT
*
2098286 TACATAATT
1 TA-ATAACT
2098295 TACATAACT
1 TA-ATAACT
2098304 TAATAA
1 TAATAA
2098310 TTTTAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 21 0.49
9 22 0.51
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (8 bp):
TAATAACT
Found at i:2098312 original size:17 final size:17
Alignment explanation
Indices: 2098253--2098309 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
2098243 ATAATTCACA
2098253 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
2098270 TAATAACTTA-ACAACT
1 TAATAACTTACATAACT
*
2098286 TACATAATTTACATAACT
1 TA-ATAACTTACATAACT
2098304 TAATAA
1 TAATAA
2098310 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.20
17 21 0.60
18 7 0.20
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:2098419 original size:17 final size:17
Alignment explanation
Indices: 2098397--2098468 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
2098387 ATAACTCACA
2098397 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
2098414 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
2098431 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
2098447 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
2098465 TAAT
1 TAAT
2098469 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:2098441 original size:25 final size:26
Alignment explanation
Indices: 2098405--2098468 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
2098395 CATAATAACT
*
2098405 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
2098430 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
2098456 TACATAACTTAAT
1 TACATAACTTAAT
2098469 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:2099035 original size:43 final size:43
Alignment explanation
Indices: 2098974--2099194 Score: 293
Period size: 43 Copynumber: 5.1 Consensus size: 43
2098964 CACCAAACAA
*
2098974 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
* ** *
2099017 TAACGGCGTTTGTGGGAAAAAAATGCCGCTAAAGGACATGGCCTT
1 TAGCGGCGTTTGTGGG--AAAAGCGCCGCTAAAGAACATGGCCTT
* *
2099062 TAGCGGCATTT-TCGGGAAAAGAGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGAACATGGCCTT
* *
2099105 TAGCGGTGTTT-TCAGGAAAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGAACATGGCCTT
* *
2099148 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
2099191 TAGC
1 TAGC
2099195 TGCATTTATT
Statistics
Matches: 156, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
43 120 0.77
44 1 0.01
45 35 0.22
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
Found at i:2101084 original size:15 final size:15
Alignment explanation
Indices: 2101064--2101093 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2101054 GTGAGAAATG
2101064 TTCGTAAACTAATTT
1 TTCGTAAACTAATTT
2101079 TTCGTAAACTAATTT
1 TTCGTAAACTAATTT
2101094 GATCGTTTGA
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:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
TTCGTAAACTAATTT
Found at i:2102367 original size:33 final size:33
Alignment explanation
Indices: 2102325--2102392 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2102315 TTCGTGTAAG
*
2102325 ACCCTGTATGGGCAGTGACATCGGTATATGATA
1 ACCCTGTATGGGCAGTGACATCAGTATATGATA
2102358 ACCCTGTATGGGCAGTGACATCAGTATATGATA
1 ACCCTGTATGGGCAGTGACATCAGTATATGATA
2102391 AC
1 AC
2102393 ATGTATGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (33 bp):
ACCCTGTATGGGCAGTGACATCAGTATATGATA
Found at i:2109954 original size:28 final size:27
Alignment explanation
Indices: 2109888--2109954 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
2109878 CTTTAATAGT
* * *
2109888 AACAGTACAGTGTGGGCCTTAGCCCTA
1 AACAGTACAGTGTAGGCCTAAGCCCGA
* **
2109915 TACAAAAACAGTGTAGGCCTAAGCCCGA
1 AAC-AGTACAGTGTAGGCCTAAGCCCGA
2109943 AACAGTATCAGT
1 AACAGTA-CAGT
2109955 ATGTTGTAAG
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (27 bp):
AACAGTACAGTGTAGGCCTAAGCCCGA
Found at i:2110173 original size:22 final size:22
Alignment explanation
Indices: 2110100--2110173 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
2110090 CAGCAGAGCT
*
2110100 GCCAGTAATCAGAATGGCTAAAA
1 GCCA-TAAACAGAATGGCTAAAA
* * * *
2110123 GCCGTAAATAGGATAGCTATAAA
1 GCCATAAACAGAATGGCTA-AAA
* *
2110146 -CTATAAACAGAATGGCTACAA
1 GCCATAAACAGAATGGCTAAAA
2110167 GCCATAA
1 GCCATAA
2110174 GTATAGTAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
21 2 0.05
22 29 0.78
23 6 0.16
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.19
Consensus pattern (22 bp):
GCCATAAACAGAATGGCTAAAA
Found at i:2110220 original size:32 final size:32
Alignment explanation
Indices: 2110165--2110335 Score: 200
Period size: 32 Copynumber: 5.4 Consensus size: 32
2110155 GAATGGCTAC
* * *
2110165 AAGCCATAAGT-ATAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
2110196 AAGCCATCAGTAGCAGTTATATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
2110228 CAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
2110260 AAGCCATCAGTAATGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
2110292 AAGCCATCAGTAATGGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
2110324 AAGCCATCAGTA
1 AAGCCATCAGTA
2110336 GCATCGCAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 10 0.08
32 113 0.92
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:2110282 original size:64 final size:64
Alignment explanation
Indices: 2110179--2110335 Score: 226
Period size: 64 Copynumber: 2.5 Consensus size: 64
2110169 CATAAGTATA
* * *
2110179 GTAATATGATTGGCACAAAGCCATCAGTAGCAGTTATATGATC-AGCACACAGCCATCAGTAACG
1 GTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGA-CACAAAGCCATCAGTAACG
* * ** *
2110243 GTAATATGATCGACACAAAGCCATCAGTAATGGTAATATGATCGACACAAAGCCATCAGTAATG
1 GTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCCATCAGTAACG
2110307 GTAATATGATTGGCACAAAGCCATCAGTA
1 GTAATATGATTGGCACAAAGCCATCAGTA
2110336 GCATCGCAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 81 0.99
65 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (64 bp):
GTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCCATCAGTAACG
Found at i:2110551 original size:24 final size:24
Alignment explanation
Indices: 2110496--2110562 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
2110486 TCATACCAAA
* *
2110496 CACAAACAAAGCAATCATTTACAT
1 CACAGACAAATCAATCATTTACAT
*
2110520 CA-AGGACAAATCAATCATTTATAT
1 CACA-GACAAATCAATCATTTACAT
* *
2110544 CACAGACAATTCAAACATT
1 CACAGACAAATCAATCATT
2110563 AACCTCGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (24 bp):
CACAGACAAATCAATCATTTACAT
Found at i:2110684 original size:27 final size:27
Alignment explanation
Indices: 2110654--2110941 Score: 203
Period size: 27 Copynumber: 10.7 Consensus size: 27
2110644 ACCCTACAAA
**
2110654 GGTATTACTATCATTTTACCCTATAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* * * * *
2110681 GGTA-TATCGATCAATTCA-CCTAACAGA
1 GGTATTA-CGGTCATTTTACCCT-ATAGG
* *
2110708 AGTATTACGG-CTATTTTACCTTATAGG
1 GGTATTACGGTC-ATTTTACCCTATAGG
* * *
2110735 GGCATTACGGTCATTTTACCTTACAGG
1 GGTATTACGGTCATTTTACCCTATAGG
2110762 GGTATTAC-GTCATTTTACCCTATAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* *
2110788 GGTATTATGGTCATTTTACCCTAT-GAA
1 GGTATTACGGTCATTTTACCCTATAG-G
** * * * *
2110815 GGTATTTTGATCAATTCA-CCTA-ACTGA
1 GGTATTACGGTCATTTTACCCTATA--GG
* * *
2110842 AGTGTTACGGTCATTTTACTCTATAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* * * *
2110869 GGCATTACGATTATTTTACCCTACAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* *
2110896 GGTATTACGGTCATTTTATCCTACAGG
1 GGTATTACGGTCATTTTACCCTATAGG
*
2110923 GGCATTACGGTCATTTTAC
1 GGTATTACGGTCATTTTAC
2110942 AAACATTAGG
Statistics
Matches: 202, Mismatches: 46, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
26 34 0.17
27 158 0.78
28 9 0.04
29 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTATTACGGTCATTTTACCCTATAGG
Found at i:2110827 original size:134 final size:135
Alignment explanation
Indices: 2110641--2110941 Score: 394
Period size: 134 Copynumber: 2.2 Consensus size: 135
2110631 TTATAGTAAC
** * ** *
2110641 TTTACCCTACAAAGGTATTACTATCATTTTACCCTATAGGGGTATATCGATCAATTCACCTAACA
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAGAGGTATATCGATCAATTCACCTAACA
* *
2110706 GAAGTATTACGG-CTATTTTAC-CTTATAGGGGCATTACGGTCATTTTACCTTACAGGGGTATTA
66 GAAGTATTACGGTC-ATTTTACTC-TATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTA
2110769 C-GTCAT
129 CGGTCAT
* * * * *
2110775 TTTACCCTATAGGGGTATTATGGTCATTTTACCCTAT-GAAGGTATTTTGATCAATTCACCTAAC
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAG-AGGTATATCGATCAATTCACCTAAC
* * *
2110839 TGAAGTGTTACGGTCATTTTACTCTATAGGGGCATTACGATTATTTTACCCTACAGGGGTATTAC
65 AGAAGTATTACGGTCATTTTACTCTATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTAC
2110904 GGTCAT
130 GGTCAT
*
2110910 TTTATCCTACAGGGGCATTACGGTCATTTTAC
1 TTTACCCTACAGGGGCATTACGGTCATTTTAC
2110942 AAACATTAGG
Statistics
Matches: 145, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
133 1 0.01
134 109 0.75
135 35 0.24
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (135 bp):
TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAGAGGTATATCGATCAATTCACCTAACA
GAAGTATTACGGTCATTTTACTCTATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTACG
GTCAT
Found at i:2111325 original size:18 final size:18
Alignment explanation
Indices: 2111298--2111335 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2111288 CTATGTGGCT
2111298 CACAAGCCTA-CTAGGCC
1 CACAAGCCTATCTAGGCC
*
2111315 CACATAGCCTATTTAGGCC
1 CACA-AGCCTATCTAGGCC
2111334 CA
1 CA
2111336 ATAAGACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.29, C:0.37, G:0.16, T:0.18
Consensus pattern (18 bp):
CACAAGCCTATCTAGGCC
Found at i:2115549 original size:43 final size:44
Alignment explanation
Indices: 2115482--2115581 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
2115472 AATGTTGAAG
* *
2115482 TAAAATTAAAAAATAGTTACGTGTTT-TTTTATAAGTAACTATA
1 TAAAATTAAAAAATAGTGACGTGTTTCTTTTATAAATAACTATA
* * *
2115525 TAAAATTAAAAAATTA-TGATGTGTTTCTTTTATAAATAATTTTA
1 TAAAATTAAAAAA-TAGTGACGTGTTTCTTTTATAAATAACTATA
*
2115569 TGAAATTAAAAAA
1 TAAAATTAAAAAA
2115582 ATCCACAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
43 21 0.43
44 28 0.57
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (44 bp):
TAAAATTAAAAAATAGTGACGTGTTTCTTTTATAAATAACTATA
Found at i:2116201 original size:67 final size:65
Alignment explanation
Indices: 2116122--2116254 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 65
2116112 TTTTTATGGA
* **
2116122 TCTTGCAAGAAAGAGTAACGCAATACACCAGCATTATTGTGTCAATTTTAGACCATAAATATAGT
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTA--CAGTCAATTTTAGACCATAAATATAGT
2116187 AT
64 AT
*
2116189 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGCCCATAAATATAGTAT
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
2116254 T
1 T
2116255 TCTATTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 27 0.44
67 35 0.56
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (65 bp):
TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
Found at i:2119889 original size:61 final size:60
Alignment explanation
Indices: 2119795--2119910 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
2119785 TACAGATGTT
* * *
2119795 TTTAAATTTTTTTATATATATGTATAATTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTAAATTTTTTTACATAAATGTATAATCTAATTTTTAGTTTGTTGATAAATTATATACA
* * * *
2119855 TTTAAATATTTTTTACATAAATTTATAGTCTAATTTTTATTTTGTTTATAAATTAT
1 TTTAAAT-TTTTTTACATAAATGTATAATCTAATTTTTAGTTTGTTGATAAATTAT
2119911 TTGTTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 7 0.15
61 41 0.85
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (60 bp):
TTTAAATTTTTTTACATAAATGTATAATCTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:2119930 original size:23 final size:22
Alignment explanation
Indices: 2119887--2119930 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2119877 TTATAGTCTA
*
2119887 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
2119909 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
2119931 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:2122059 original size:28 final size:28
Alignment explanation
Indices: 2122027--2122083 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2122017 TATGTTAGGA
2122027 ATTCTACTTTACCTACGAAAAGTAAGAT
1 ATTCTACTTTACCTACGAAAAGTAAGAT
2122055 ATTCTACTTTACCTACGAAAAGTAAGAT
1 ATTCTACTTTACCTACGAAAAGTAAGAT
2122083 A
1 A
2122084 CTTTGCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (28 bp):
ATTCTACTTTACCTACGAAAAGTAAGAT
Found at i:2124521 original size:16 final size:16
Alignment explanation
Indices: 2124496--2124530 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2124486 AGTAAAACTG
2124496 GAAAACTTGTTATCTC
1 GAAAACTTGTTATCTC
*
2124512 GAAAATTTGTTATCTC
1 GAAAACTTGTTATCTC
2124528 GAA
1 GAA
2124531 GGTTGGGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (16 bp):
GAAAACTTGTTATCTC
Found at i:2144576 original size:32 final size:32
Alignment explanation
Indices: 2144540--2144629 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
2144530 ATCAGTAACT
**
2144540 GTAATATGATCGACACAAAGCCATCGGTAATG
1 GTAATATGATCGACACAAAGCCATCAATAATG
2144572 GTAATATGATCGACACAAAGCCATCAATAATG
1 GTAATATGATCGACACAAAGCCATCAATAATG
* *
2144604 GTAATATGATTGGCACAAAGCCATCA
1 GTAATATGATCGACACAAAGCCATCA
2144630 GTAGTATCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (32 bp):
GTAATATGATCGACACAAAGCCATCAATAATG
Found at i:2144679 original size:27 final size:25
Alignment explanation
Indices: 2144644--2144714 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
2144634 TATCACAGTA
*
2144644 AAGCTACCAGTAATAGTATATGTGGCC
1 AAGCCACCAGTAATAGTAT-TGTGG-C
2144671 AAGCCACCAGTAATAGTGATTGTGGC
1 AAGCCACCAGTAATAGT-ATTGTGGC
*
2144697 AGAGCCACCAAT-ATAGTA
1 A-AGCCACCAGTAATAGTA
2144715 CTTCCTCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 1 0.03
26 7 0.17
27 30 0.75
28 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGCCACCAGTAATAGTATTGTGGC
Found at i:2144849 original size:24 final size:24
Alignment explanation
Indices: 2144794--2144860 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
2144784 TCATACCAAA
*
2144794 CACAGACAAAGCAATCATTTACAT
1 CACAGACAAATCAATCATTTACAT
*
2144818 CA-AGGACAAATCAATCATTTATAT
1 CACA-GACAAATCAATCATTTACAT
* *
2144842 CACAGACAATTCAAACATT
1 CACAGACAAATCAATCATT
2144861 AACCTCGAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.24
Consensus pattern (24 bp):
CACAGACAAATCAATCATTTACAT
Found at i:2145072 original size:27 final size:27
Alignment explanation
Indices: 2145006--2145124 Score: 109
Period size: 27 Copynumber: 4.4 Consensus size: 27
2144996 CCTAACAGAA
*
2145006 GTATTAC-AGTCATTTTACCCTATA-GA
1 GTATTACGA-TCATTTTACCCTATAGGG
* * * * *
2145032 GCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGATCATTTTACCCTATAGGG
*
2145059 GTATTACGATCATTTTACCCTATAAGG
1 GTATTACGATCATTTTACCCTATAGGG
* * *
2145086 GTATTATGGTCATTTTACCCTATGGGG
1 GTATTACGATCATTTTACCCTATAGGG
2145113 GTA-TATCGATCA
1 GTATTA-CGATCA
2145125 ATTCACCTAA
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
26 20 0.28
27 52 0.72
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (27 bp):
GTATTACGATCATTTTACCCTATAGGG
Found at i:2145116 original size:54 final size:54
Alignment explanation
Indices: 2145006--2145211 Score: 172
Period size: 54 Copynumber: 3.8 Consensus size: 54
2144996 CCTAACAGAA
* *
2145006 GTATTAC-AGTCATTTTACCCTAT-AGAGCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGA-TCATTTTACCCTATAAGAGCATTATGGTCATTTTACCCTATAGGG
* * *
2145059 GTATTACGATCATTTTACCCTATAAGGGTATTATGGTCATTTTACCCTATGGGG
1 GTATTACGATCATTTTACCCTATAAGAGCATTATGGTCATTTTACCCTATAGGG
* * * * * **
2145113 GTA-TATCGATCAATTCA-CCTAACTAA-AGTATTATGGTCATTTCACTCTATAAAG
1 GTATTA-CGATCATTTTACCCT-A-TAAGAGCATTATGGTCATTTTACCCTATAGGG
* * * * *
2145167 GCATTACGGTCATTTTACCCTA-CAGGGACATTACGGTCATTTTAC
1 GTATTACGATCATTTTACCCTATAAGAG-CATTATGGTCATTTTAC
2145212 AAACATTAGG
Statistics
Matches: 122, Mismatches: 22, Indels: 17
0.76 0.14 0.11
Matches are distributed among these distances:
52 1 0.01
53 27 0.22
54 86 0.70
55 8 0.07
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
GTATTACGATCATTTTACCCTATAAGAGCATTATGGTCATTTTACCCTATAGGG
Found at i:2145119 original size:134 final size:135
Alignment explanation
Indices: 2144965--2145211 Score: 372
Period size: 134 Copynumber: 1.8 Consensus size: 135
2144955 ATTACAATTA
* *
2144965 TTTACCGTATGGGGGTATATCGATCAATTCACCTAAC-AGAAGTATTACAGTCATTTTACCCTAT
1 TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTA-AAGTATTACAGTCATTTCACCCTAT
* * * **
2145029 AGA-GCATTATGGTCATTTTATCCTACAGGGGTATTACGATCATTTTACCCTATAAGGGTATTAT
65 AAAGGCATTACGGTCATTTTACCCTACAGGGACATTACGATCATTTTACCCTATAAGGGTATTAT
2145093 GGTCAT
130 GGTCAT
** *
2145099 TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTAAAGTATTATGGTCATTTCACTCTATA
1 TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTAAAGTATTACAGTCATTTCACCCTATA
*
2145164 AAGGCATTACGGTCATTTTACCCTACAGGGACATTACGGTCATTTTAC
66 AAGGCATTACGGTCATTTTACCCTACAGGGACATTACGATCATTTTAC
2145212 AAACATTAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
134 59 0.59
135 41 0.41
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (135 bp):
TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTAAAGTATTACAGTCATTTCACCCTATA
AAGGCATTACGGTCATTTTACCCTACAGGGACATTACGATCATTTTACCCTATAAGGGTATTATG
GTCAT
Found at i:2160720 original size:10 final size:10
Alignment explanation
Indices: 2160706--2160744 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2160696 TTGGAAAATA
2160706 AATATGATAT
1 AATATGATAT
*
2160716 GATATGATAT
1 AATATGATAT
*
2160726 AATATAATAT
1 AATATGATAT
2160736 AATAT-ATAT
1 AATATGATAT
2160745 TCATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (10 bp):
AATATGATAT
Found at i:2162854 original size:42 final size:44
Alignment explanation
Indices: 2162807--2162905 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
2162797 AATGTTGAAG
* *
2162807 TAAAATTAAAAAA-TAGTTACGTG-TT-TTTTATAAGTAACTATA
1 TAAAATTAAAAAATTA-TGACGTGTTTCTTTTATAAATAACTATA
* *
2162849 TAAAATTAAAAAATTATGATGTGTTTCTTTTATAAATAATTATA
1 TAAAATTAAAAAATTATGACGTGTTTCTTTTATAAATAACTATA
*
2162893 TGAAATTAAAAAA
1 TAAAATTAAAAAA
2162906 AATCCACAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 18 0.37
43 4 0.08
44 27 0.55
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (44 bp):
TAAAATTAAAAAATTATGACGTGTTTCTTTTATAAATAACTATA
Found at i:2163689 original size:24 final size:26
Alignment explanation
Indices: 2163650--2163698 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
2163640 AAATTTTAAA
*
2163650 ATATTTATAAAAAATT-TCAAAATTT
1 ATATTTATAAAAAATTATAAAAATTT
2163675 ATATTT-TAAAAAATTATAAAAATT
1 ATATTTATAAAAAATTATAAAAATT
2163699 AAGAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTTATAAAAAATTATAAAAATTT
Found at i:2164396 original size:61 final size:61
Alignment explanation
Indices: 2164328--2164444 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
2164318 TACCGATGTT
* * *
2164328 TTTAAATATTTTTTATATATATTTTTAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
* *
2164389 TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTATTTTGTTTATAAATTAT
1 TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTAGTTTGTTGATAAATTAT
2164445 TTGTTATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (61 bp):
TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:2164464 original size:23 final size:22
Alignment explanation
Indices: 2164421--2164464 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2164411 CTATAGTTTA
*
2164421 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
2164443 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
2164465 AAATTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:2171325 original size:26 final size:26
Alignment explanation
Indices: 2171296--2171347 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2171286 CCCTTACACC
* *
2171296 AATATCGCAGCATAGCTGCCAGTAGT
1 AATAACGCAGCAGAGCTGCCAGTAGT
*
2171322 AATAACGCAGTAGAGCTGCCAGTAGT
1 AATAACGCAGCAGAGCTGCCAGTAGT
2171348 CAGAATGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (26 bp):
AATAACGCAGCAGAGCTGCCAGTAGT
Found at i:2171402 original size:22 final size:22
Alignment explanation
Indices: 2171348--2171412 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
2171338 TGCCAGTAGT
*
2171348 CAGAATGGCTAAAAGCCGTAAA
1 CAGAATGGCTAAAAGCCATAAA
* * * * *
2171370 TAGGATAGCTATAAGCTATAAA
1 CAGAATGGCTAAAAGCCATAAA
*
2171392 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTAAAAGCCATAA
2171413 GTACAGTAAT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAAAGCCATAAA
Found at i:2171532 original size:32 final size:32
Alignment explanation
Indices: 2171404--2171542 Score: 145
Period size: 32 Copynumber: 4.4 Consensus size: 32
2171394 GAATGGCTAC
* *
2171404 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
* ** * *
2171435 AAACCATCAGTAGTAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
* * * * *
2171467 CAGACATCAATAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
*
2171499 AAGCCATCAGTAACAATAATATGATTGACACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
*
2171531 AAGCCATTAGTA
1 AAGCCATCAGTA
2171543 GCATTGCAGC
Statistics
Matches: 85, Mismatches: 22, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 9 0.11
32 76 0.89
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATTGACACA
Found at i:2171894 original size:27 final size:27
Alignment explanation
Indices: 2171864--2172149 Score: 184
Period size: 27 Copynumber: 10.6 Consensus size: 27
2171854 TAGGAGAGGC
* *
2171864 ATTACGGTCACTTTACGCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
2171891 ATTACGATTATTTTACCCTAAAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * * **
2171918 A-TATTGATCAATTCA-TCTAACAGAAGT
1 ATTA-CGGTCATTTTACCCT-ACAGGGGT
* *
2171945 ATTACGGTCATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
2171972 ATTATGGTTATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * **
2171999 ATTATGGTCGTTTTATCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * **
2172026 A-TATCGATCAATTCA-CCTAACCGAAGT
1 ATTA-CGGTCATTTTACCCT-ACAGGGGT
* * *
2172053 ATTACGGTCATTTTACCCTATAGGTGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
2172080 ATTACGGTCATTTCACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
2172107 ATTACATTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
2172134 ATTACGGTCATTTTAC
1 ATTACGGTCATTTTAC
2172150 AAATATTGGG
Statistics
Matches: 189, Mismatches: 62, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
26 9 0.05
27 171 0.90
28 9 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:2171999 original size:81 final size:80
Alignment explanation
Indices: 2171832--2172000 Score: 203
Period size: 81 Copynumber: 2.1 Consensus size: 80
2171822 TTACCTTTTG
* ** * * *
2171832 AGGGTATATCGGTCAATTCACCTAGGAGAGGCATTACGGTCACTTTACGCTACAGGGGTATTACG
1 AGGGTATATCGATCAATTCACCTAACAGAAGCATTACGGTCACTTTACCCTACAGGGGCATTACG
2171897 ATTATTTTACCCTAA
66 ATTATTTTACCCTAA
* * * * * *
2171912 AGGGGTATATTGATCAATTCATCTAACAGAAGTATTACGGTCATTTTACCCTATAGGGGCATTAT
1 A-GGGTATATCGATCAATTCACCTAACAGAAGCATTACGGTCACTTTACCCTACAGGGGCATTAC
*
2171977 GGTTATTTTACCCTACA
65 GATTATTTTACCCTA-A
2171994 AGGGTAT
1 AGGGTAT
2172001 TATGGTCGTT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 71 0.96
82 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (80 bp):
AGGGTATATCGATCAATTCACCTAACAGAAGCATTACGGTCACTTTACCCTACAGGGGCATTACG
ATTATTTTACCCTAA
Found at i:2172001 original size:54 final size:54
Alignment explanation
Indices: 2171861--2172146 Score: 219
Period size: 54 Copynumber: 5.3 Consensus size: 54
2171851 ACCTAGGAGA
* * * * *
2171861 GGCATTACGGTCACTTT-ACGCTACAGGGGTATTACGATTATTTTACCCTAAAGG
1 GGCATTACGGTCA-TTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
* * * * * *
2171915 GGTA-TATTGATCAATTCA-TCTA-ACAGAAGTATTACGGTCATTTTACCCTATAGG
1 GGCATTA-CGGTCATTTCACCCTACA-AG-GGTATTACGGTCATTTTACCCTATAGG
* * * * * * *
2171969 GGCATTATGGTTATTTTACCCTACAAGGGTATTATGGTCGTTTTATCCTATGGG
1 GGCATTACGGTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
* * *
2172023 GGTA-TATCGATCAATTCA-CCTAACCGAA--GTATTACGGTCATTTTACCCTATAGG
1 GGCATTA-CGGTCATTTCACCCT-A-C-AAGGGTATTACGGTCATTTTACCCTATAGG
* ** *
2172077 TGCATTACGGTCATTTCACCCTACAAGGGTATTACATTCATTTTACCCTACAGG
1 GGCATTACGGTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
2172131 GGCATTACGGTCATTT
1 GGCATTACGGTCATTT
2172147 TACAAATATT
Statistics
Matches: 178, Mismatches: 39, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
52 3 0.02
53 14 0.08
54 145 0.81
55 13 0.07
56 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
GGCATTACGGTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
Found at i:2172121 original size:108 final size:107
Alignment explanation
Indices: 2171861--2172132 Score: 357
Period size: 108 Copynumber: 2.5 Consensus size: 107
2171851 ACCTAGGAGA
* * *
2171861 GGCATTACGGTCACTTTACGCTACAGGGGTATTACGATT-ATTTTACCCTAAAGGGGTATATTGA
1 GGCATTACGGTCA-TTTACCCTACAAGGGTATTAC-ATTCATTTTACCCTAAAGGGGTATATCGA
*
2171925 TCAATTCATCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
64 TCAATTCACCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
* * *** * * **
2171969 GGCATTATGGTTATTTTACCCTACAAGGGTATTATGGTCGTTTTATCCTATGGGGGTATATCGAT
1 GGCATTACGGTCA-TTTACCCTACAAGGGTATTACATTCATTTTACCCTAAAGGGGTATATCGAT
*
2172034 CAATTCACCTAACCGAAGTATTACGGTCATTTTACCCTATAGG
65 CAATTCACCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
* *
2172077 TGCATTACGGTCATTTCACCCTACAAGGGTATTACATTCATTTTACCCTACAGGGG
1 GGCATTACGGTCATTT-ACCCTACAAGGGTATTACATTCATTTTACCCTAAAGGGG
2172133 CATTACGGTC
Statistics
Matches: 137, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
107 4 0.03
108 133 0.97
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (107 bp):
GGCATTACGGTCATTTACCCTACAAGGGTATTACATTCATTTTACCCTAAAGGGGTATATCGATC
AATTCACCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
Found at i:2173375 original size:18 final size:18
Alignment explanation
Indices: 2173320--2173390 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
2173310 TAGTCACTGG
2173320 GCTATAAAATACTTTATA
1 GCTATAAAATACTTTATA
* *
2173338 GCCTA-AAACCAAAATTTATA
1 G-CTATAAA--ATACTTTATA
2173358 GCTATAAAATACTTTATA
1 GCTATAAAATACTTTATA
2173376 GCTATAAAATACTTT
1 GCTATAAAATACTTT
2173391 GGTCAGACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 27 0.60
19 6 0.13
20 12 0.27
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (18 bp):
GCTATAAAATACTTTATA
Found at i:2177324 original size:123 final size:123
Alignment explanation
Indices: 2177105--2177349 Score: 481
Period size: 123 Copynumber: 2.0 Consensus size: 123
2177095 GTGGAAAATC
2177105 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
1 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
2177170 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGTA
66 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGTA
2177228 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
1 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
*
2177293 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGGTGAGTGACACACAATGT
66 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGT
2177350 GCTTTTATCG
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (123 bp):
CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGTA
Found at i:2183935 original size:66 final size:66
Alignment explanation
Indices: 2183853--2183985 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
2183843 CTTTTATGGA
2183853 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
2183918 T
66 T
2183919 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
2183984 T
66 T
2183985 T
1 T
2183986 TCTATTTATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (66 bp):
TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
T
Found at i:2184554 original size:26 final size:25
Alignment explanation
Indices: 2184507--2184556 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2184497 AAATTTTAAA
*
2184507 ATATTTATAAAAAATTTCAAAATTT
1 ATATTTATAAAAAATTTAAAAATTT
2184532 ATATTT-TAAAAAAGTTATAAAAATT
1 ATATTTATAAAAAA-TT-TAAAAATT
2184557 AAGAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 8 0.36
26 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATTTATAAAAAATTTAAAAATTT
Found at i:2185107 original size:61 final size:61
Alignment explanation
Indices: 2185033--2185149 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
2185023 TTATCGATGT
** *
2185033 TTTTAAATATTTTTTTATATATTTTTAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTTAAATATTTTTACATATATTTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
* *
2185094 TTTT-AATATTTTTTACATATATTTATAGTTTAATTTTTATTTTGTTTATAAATTAT
1 TTTTAAATA-TTTTTACATATATTTATAGTTTAATTTTTAGTTTGTTGATAAATTAT
2185150 TTGTTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 4 0.08
61 46 0.92
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (61 bp):
TTTTAAATATTTTTACATATATTTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:2185169 original size:23 final size:22
Alignment explanation
Indices: 2185126--2185169 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2185116 TTATAGTTTA
*
2185126 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
2185148 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
2185170 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Done.