Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 205 of 207
Found at i:61717272 original size:20 final size:21
Alignment explanation
Indices: 61717247--61717288 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
61717237 ATTCACAACG
61717247 TTAAA-TTCAAAGATTTTATA
1 TTAAATTTCAAAGATTTTATA
61717267 TTAAATTTCAAAGATTTTATA
1 TTAAATTTCAAAGATTTTATA
61717288 T
1 T
61717289 GTACATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
TTAAATTTCAAAGATTTTATA
Found at i:61726025 original size:31 final size:30
Alignment explanation
Indices: 61725978--61726047 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
61725968 TGATGAAATC
* *
61725978 CAAATTCAATGACCAAAATGGACCTAATTG
1 CAAATTCAATGACCAAAATGAAACTAATTG
*
61726008 CAAAGTTCAAGTG-CCAAAATGAAACTAATTAT
1 CAAA-TTCAA-TGACCAAAATGAAACTAATT-G
61726040 CAAATTCA
1 CAAATTCA
61726048 GGAGCTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.12
31 24 0.71
32 6 0.18
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (30 bp):
CAAATTCAATGACCAAAATGAAACTAATTG
Found at i:61733453 original size:23 final size:23
Alignment explanation
Indices: 61733410--61733453 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
61733400 AATTTTTTTA
*
61733410 AAAAAAATTTATATAAAAATATT
1 AAAAAAATTTATAAAAAAATATT
*
61733433 AAAAAGATTTA-AAAAATAATA
1 AAAAAAATTTATAAAAA-AATA
61733454 ATTTTACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAATTTATAAAAAAATATT
Found at i:61736103 original size:23 final size:23
Alignment explanation
Indices: 61736073--61736124 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
61736063 CCAACAACTT
61736073 TAACATTGACAAGCTACTAAAAG
1 TAACATTGACAAGCTACTAAAAG
61736096 TAACATTGACAAGCTACTAAAAG
1 TAACATTGACAAGCTACTAAAAG
61736119 TAACAT
1 TAACAT
61736125 GTAGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (23 bp):
TAACATTGACAAGCTACTAAAAG
Found at i:61743099 original size:5 final size:5
Alignment explanation
Indices: 61743089--61743119 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
61743079 TATGTGAAAC
61743089 AAATA AAATA AAATA AAATA AAAT- AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AA
61743120 GCACTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:61744746 original size:46 final size:46
Alignment explanation
Indices: 61744693--61744782 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
61744683 TTAGGGGTTA
*
61744693 GGTCTGTTTTAAGTCTTGGGTTTGGGCTGGTTCAGATTGGGCTTTG
1 GGTCTGTTTTAAGTCTTGGGTTTGGGCTAGTTCAGATTGGGCTTTG
**
61744739 GGTCTGTTTTGGGTCTTGGGTTTGGGCTAGTTCAGATTGGGCTT
1 GGTCTGTTTTAAGTCTTGGGTTTGGGCTAGTTCAGATTGGGCTT
61744783 GTACAGCTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.08, C:0.11, G:0.38, T:0.43
Consensus pattern (46 bp):
GGTCTGTTTTAAGTCTTGGGTTTGGGCTAGTTCAGATTGGGCTTTG
Found at i:61745110 original size:44 final size:44
Alignment explanation
Indices: 61745062--61745151 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 44
61745052 ACTCATATCC
* * * *
61745062 TCAACTTGCCCCACTACAACTTCAGGGGGATAAGATTCGTGACT
1 TCAACCTGCCCCACTACAACTTCAGAGAGACAAGATTCGTGACT
*** * *
61745106 TCAACCTGCTTTACTGCAACTTCAGAGAGACAAGATTTGTGACT
1 TCAACCTGCCCCACTACAACTTCAGAGAGACAAGATTCGTGACT
61745150 TC
1 TC
61745152 GCTTCCATCT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (44 bp):
TCAACCTGCCCCACTACAACTTCAGAGAGACAAGATTCGTGACT
Found at i:61745574 original size:46 final size:45
Alignment explanation
Indices: 61745422--61745751 Score: 230
Period size: 44 Copynumber: 7.6 Consensus size: 45
61745412 TTTTAATCCA
* * *
61745422 CTCCACTGTAA-CTTCAGGGAGATAGGA--T-AGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* * * **
61745465 CTCCGCTGTAATCTCAGGGAGATAAGATCT--CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* *
61745509 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGATCTG
* * * *
61745555 TTCCACTGTAATCTCAGGGAGATAAGACCTG-A---TGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGATCTG
* * * *
61745596 CTCTACTGTAA-CTTCAGAGAGATAAGATC------CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTTGATCTG
* * * * *
61745635 CTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCCTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* *
61745679 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGATCTG
*
61745725 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
61745752 CCTGTATAAT
Statistics
Matches: 226, Mismatches: 43, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
39 26 0.12
40 2 0.01
41 29 0.13
43 23 0.10
44 72 0.32
45 2 0.01
46 69 0.31
47 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (45 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGATCTG
Found at i:61747543 original size:46 final size:46
Alignment explanation
Indices: 61747476--61747565 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
61747466 CAAGCTGTAC
*
61747476 AAGCCCAATCTGAACTAGCCCAAACCCAAGACCCAAAACAGACCCA
1 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACCCA
**
61747522 AAGCCCAATCTGAACCAGCCCAAACCCAAGACTTAAAACAGACC
1 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACC
61747566 TAACCCCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.43, C:0.38, G:0.11, T:0.08
Consensus pattern (46 bp):
AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACCCA
Found at i:61748932 original size:27 final size:25
Alignment explanation
Indices: 61748901--61748964 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
61748891 ATGTGTCCCC
*
61748901 TTTTTATATAT-ATGTAAATCTCCATA
1 TTTTTATATATCATATAAAT-T-CATA
*
61748927 TATTTTACATATGCATATAAATTCATA
1 T-TTTTATATAT-CATATAAATTCATA
61748954 TTTTTATATAT
1 TTTTTATATAT
61748965 TTTATAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 10 0.31
27 14 0.44
28 1 0.03
29 7 0.22
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (25 bp):
TTTTTATATATCATATAAATTCATA
Found at i:61749138 original size:5 final size:5
Alignment explanation
Indices: 61749124--61749154 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
61749114 ACATAAGTGC
61749124 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
61749155 GTTTCACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:61761303 original size:46 final size:45
Alignment explanation
Indices: 61761236--61761533 Score: 205
Period size: 46 Copynumber: 6.8 Consensus size: 45
61761226 ATTATACAGG
*
61761236 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
61761282 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * * * *
61761326 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG------GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
* * * *
61761365 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATTCAGA
*
61761406 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * ** * *
61761452 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA--GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-AATTCAGA
* * *
61761496 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA
61761534 CACTATCCTA
Statistics
Matches: 198, Mismatches: 37, Indels: 37
0.73 0.14 0.14
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 23 0.12
40 1 0.01
41 27 0.14
42 1 0.01
43 1 0.01
44 69 0.35
45 1 0.01
46 71 0.36
47 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
Found at i:61761516 original size:44 final size:43
Alignment explanation
Indices: 61761236--61761589 Score: 206
Period size: 44 Copynumber: 8.2 Consensus size: 43
61761226 ATTATACAGG
* ** * *
61761236 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA
* * * *
61761282 TCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCAAGGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAG--A
* * * *
61761326 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA
* * * * * *
61761365 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGAGA
* ** * *
61761406 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA
* *
61761452 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA
* ** **
61761496 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA
* * **
61761539 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-AAAGCAGAGA
61761583 TCTTATC
1 TCTTATC
61761590 AGCGGAGCAG
Statistics
Matches: 238, Mismatches: 53, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 24 0.10
40 1 0.00
41 30 0.13
42 8 0.03
43 29 0.12
44 77 0.32
45 6 0.03
46 61 0.26
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA
Found at i:61761546 original size:87 final size:88
Alignment explanation
Indices: 61761236--61761589 Score: 248
Period size: 87 Copynumber: 4.1 Consensus size: 88
61761226 ATTATACAGG
* *
61761236 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTG-AGATT
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAG-TT
* * * *
61761300 ACAGCGGAGCAGATCAAGGA-TAGTA-A
63 ACAGTGGAGCAGATTAA-AACAAG-AGA
* * ** * * ** * *
61761326 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GATCTTATCTCTCTGAAGTTACA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
* * * * *
61761386 GTAGAGAAGATCACATC-AG-G-
66 GTGGAGCAGATTAAAACAAGAGA
* * *
61761406 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTA
* * *
61761471 CAGTGGAGCAGATTGAAGCCAGAGA
64 CAGTGGAGCAGATTAAAACAAGAGA
* * * *
61761496 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A-CACTATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTAC
* *
61761559 AGTGGAGCGGATTAAAATAAGAGA
65 AGTGGAGCAGATTAAAACAAGAGA
61761583 TCTTATC
1 TCTTATC
61761590 AGCGGAGCAG
Statistics
Matches: 209, Mismatches: 41, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
80 30 0.14
82 2 0.01
83 29 0.14
84 2 0.01
86 2 0.01
87 77 0.37
88 2 0.01
89 2 0.01
90 63 0.30
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAACAAGAGA
Found at i:61762272 original size:46 final size:46
Alignment explanation
Indices: 61762205--61762294 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
61762195 GCAGCTGTAC
*
61762205 AAGCCCAATCTGAACTAGCCCAAACCCAAGACCCAAAACAGACCCA
1 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACCCA
**
61762251 AAGCCCAATCTGAACCAGCCCAAACCCAAGACTTAAAACAGACC
1 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACC
61762295 TAACCCCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.43, C:0.38, G:0.11, T:0.08
Consensus pattern (46 bp):
AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACCCA
Found at i:61763676 original size:27 final size:25
Alignment explanation
Indices: 61763645--61763708 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
61763635 ATGTGTCCCC
*
61763645 TTTTTATATAT-ATGTAAATCTCCATA
1 TTTTTATATATCATATAAAT-T-CATA
*
61763671 TATTTTACATATGCATATAAATTCATA
1 T-TTTTATATAT-CATATAAATTCATA
61763698 TTTTTATATAT
1 TTTTTATATAT
61763709 TTTATAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 10 0.31
27 14 0.44
28 1 0.03
29 7 0.22
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (25 bp):
TTTTTATATATCATATAAATTCATA
Found at i:61763883 original size:5 final size:5
Alignment explanation
Indices: 61763869--61763899 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
61763859 ACATAAGTGC
61763869 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
61763900 GTTTCACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:61765001 original size:27 final size:28
Alignment explanation
Indices: 61764971--61765030 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
61764961 AAACAAAGAA
61764971 AAAAAATAAAGATATTA-TTTTTATCTC
1 AAAAAATAAAGATATTATTTTTTATCTC
* *
61764998 AAAAAATAGAGATATTATTTTTTATCTT
1 AAAAAATAAAGATATTATTTTTTATCTC
61765026 AAAAA
1 AAAAA
61765031 CGTGATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (28 bp):
AAAAAATAAAGATATTATTTTTTATCTC
Found at i:61767861 original size:17 final size:17
Alignment explanation
Indices: 61767831--61767875 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
61767821 CCGATATAAT
* *
61767831 AAATATATTTATTTTTA
1 AAATATTTTTAATTTTA
61767848 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
61767864 AAATATTTTTAA
1 AAATATTTTTAA
61767876 AATACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:61771075 original size:18 final size:19
Alignment explanation
Indices: 61771025--61771075 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
61771015 CACGCAGATG
*
61771025 GAACTCAACAACAA-ATCAA
1 GAAC-CAACAACAACAACAA
*
61771044 GAACCATCAA-AACAACAA
1 GAACCAACAACAACAACAA
61771062 GAA-CAACAACAACA
1 GAACCAACAACAACA
61771076 GATGCCACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.61, C:0.27, G:0.06, T:0.06
Consensus pattern (19 bp):
GAACCAACAACAACAACAA
Found at i:61773312 original size:383 final size:379
Alignment explanation
Indices: 61772570--61773492 Score: 1042
Period size: 383 Copynumber: 2.4 Consensus size: 379
61772560 AAGCTAGCTG
* * *
61772570 ATACACCCTATTAAATTCGCTGTCTTATAAGTTAACTTTTGAGGTTTTAGGGTTTTAAATTTCAT
1 ATACACCCTATTAAATTCTCCGTCTTATAAGTTAACTTTTGAGGTTTTAGGGTTTT-AA-TTCTT
* *
61772635 TTTAACTCGATATTAAAGCTAAGTTCCTTAAACCCTAAACCCTAAATTCTCTCGTCTTCAGGTTC
64 TTTAACTCGATATTAAAGCTAAGTTCCTTAAACCATAAACCCTAAATTCTCTCGTCTTCAAG-TC
* * **
61772700 TCTTAAAGGTTGGGTTAGAATTT-AAACTAGGTTCTACCTTAAACCCAAGGCCTTTTCCATCCAC
128 T-TT-AAGGTCGGGTTAGAGTTTGAAACTAGCATCTACC-TAAA-CCAAGGCCTTTTCCATCCAC
* * * * **
61772764 CAAGTAAACTTCTATCGAAGATCTTTATCTTTCGTAATGGTTGGTAGCGTATTGGTTTTAAAGTA
189 CAAGTAAACTTCTATCGAACATCCTTATCTTTCATAATGGTTGGTACCGTATCAGTTTTAAAGTA
* *
61772829 AAACGAAACGAGCACGATCATGTTATACGCCCACTAGCATGACACCAAACTACTTTAGTTTCTTC
254 AAACGAAACGAGCACCATCATGTTATACGCCCACTAGCACGACACCAAACTACTTTAGTTTCTTC
* *
61772894 TGCAACAAGTAAAAGGTTTGCAGTAATACAAATAGGGCAAGATTAACACCGAGTATAACTT
319 TGCAACAAGAAAAAAGTTTGCAGTAATACAAATAGGGCAAGATTAACACCGAGTATAACTT
*
61772955 ATACACTACCCTAATAAATTCTCCGTCTTATAA-TTAACTTTTGAGGTTTTAGGGTTTTAATCTC
1 AT--AC-ACCCTATTAAATTCTCCGTCTTATAAGTTAACTTTTGAGGTTTTAGGGTTTTAAT-TC
* *
61773019 TTTTTAACTCGATATTAAA-CTAGGTT-CTGTAAACCATAAACCCTAGATTCTCTCGTCTTCAAG
62 TTTTTAACTCGATATTAAAGCTAAGTTCCT-TAAACCATAAACCCTAAATTCTCTCGTCTTCAAG
* * * * * *
61773082 TCTTTAAGGTCGGGTTAGAGTTTGCACCTA-CATGTAGC-AGA-GAAGGCCTTTAATTTCCATCC
126 TCTTTAAGGTCGGGTTAGAGTTTGAAACTAGCATCTACCTAAACCAAGGCC--T--TTTCCATCC
* * *
61773144 TCCAAGTAAACTTTTATCGAACATCCTTGTC-TTCTATAATGGTTGGTACCGTATCAGTTTTAAA
187 ACCAAGTAAACTTCTATCGAACATCCTTATCTTTC-ATAATGGTTGGTACCGTATCAGTTTTAAA
* * **
61773208 GTAAAAAC-AATAC-AGCAACCATCATGTTATATGCCCACTAGCACGATACTGAACTACTTTAGT
251 GT-AAAACGAA-ACGAGC-ACCATCATGTTATACGCCCACTAGCACGACACCAAACTACTTTAGT
* **
61773271 TTCTTTTGCAACAAGAAAAAAGTTTGCAG-AGATACAAATAGGGCAAGATTCGCACCGAGTATAA
313 TTCTTCTGCAACAAGAAAAAAGTTTGCAGTA-ATACAAATAGGGCAAGATTAACACCGAGTATAA
61773335 CTT
377 CTT
* ** * * * * *
61773338 ATACACCCTATTAAATTCTCCATCTTATATAAGCAAACCTTTGATG-TTCAGGGTTTTACTTTTC
1 ATACACCCTATTAAATTCTCCGTC-T-TATAAGTTAACTTTTGAGGTTTTAGGGTTTTAATTCT-
* ** * **
61773402 TTTTAACTCAATATTAAAGCTAAGTTCCTTAAATTATAAACCCTAAATTCTCTTGTCTTCGGGTT
63 TTTTAACTCGATATTAAAGCTAAGTTCCTTAAACCATAAACCCTAAATTCTCTCGTCTTC---AA
*
61773467 GTCTTTAAGGTCAGGTTAGAGTTTGA
125 GTCTTTAAGGTCGGGTTAGAGTTTGA
61773493 CTTGATATTA
Statistics
Matches: 457, Mismatches: 57, Indels: 47
0.81 0.10 0.08
Matches are distributed among these distances:
378 6 0.01
380 21 0.05
381 8 0.02
382 122 0.27
383 157 0.34
384 7 0.02
385 40 0.09
386 46 0.10
387 27 0.06
388 23 0.05
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (379 bp):
ATACACCCTATTAAATTCTCCGTCTTATAAGTTAACTTTTGAGGTTTTAGGGTTTTAATTCTTTT
TAACTCGATATTAAAGCTAAGTTCCTTAAACCATAAACCCTAAATTCTCTCGTCTTCAAGTCTTT
AAGGTCGGGTTAGAGTTTGAAACTAGCATCTACCTAAACCAAGGCCTTTTCCATCCACCAAGTAA
ACTTCTATCGAACATCCTTATCTTTCATAATGGTTGGTACCGTATCAGTTTTAAAGTAAAACGAA
ACGAGCACCATCATGTTATACGCCCACTAGCACGACACCAAACTACTTTAGTTTCTTCTGCAACA
AGAAAAAAGTTTGCAGTAATACAAATAGGGCAAGATTAACACCGAGTATAACTT
Found at i:61776558 original size:29 final size:30
Alignment explanation
Indices: 61776500--61776562 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
61776490 AGTTTACGAG
* * *
61776500 AATTGGATTAAATCAAAATTTTATATATAA
1 AATTGCATAAAATCAAAAATTTATATATAA
*
61776530 AATTGCATAAAATCAAAAATTT-TGTATAA
1 AATTGCATAAAATCAAAAATTTATATATAA
61776559 AATT
1 AATT
61776563 ACACATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (30 bp):
AATTGCATAAAATCAAAAATTTATATATAA
Found at i:61780641 original size:31 final size:30
Alignment explanation
Indices: 61780603--61780687 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 30
61780593 TTGGTCTAGA
61780603 TACCAAATTGAACATTAAATCCAAACTCAGG
1 TACCAAATTGAACATTAAA-CCAAACTCAGG
* *
61780634 TACCAAATTGGAACA--AAA-AAAACTTAGG
1 TACCAAATT-GAACATTAAACCAAACTCAGG
* *
61780662 TACCAAATTGAATATTGAAGCCAAAC
1 TACCAAATTGAACATT-AAACCAAAC
61780688 ACAAGTACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
27 4 0.09
28 17 0.39
30 5 0.11
31 13 0.30
32 5 0.11
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (30 bp):
TACCAAATTGAACATTAAACCAAACTCAGG
Found at i:61782479 original size:2 final size:2
Alignment explanation
Indices: 61782472--61782507 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
61782462 TGTCTATTTC
61782472 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
61782508 TGTGTGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61784164 original size:363 final size:358
Alignment explanation
Indices: 61783326--61784207 Score: 1229
Period size: 351 Copynumber: 2.5 Consensus size: 358
61783316 TTTCCTTCCC
61783326 CCTAGGTTACAAATTCATAAGTATAGCTCCAATTAAACTCAAAACAGAGATCAATCTCATCATAG
1 CCTAGGTTACAAA-TCATAAGTATAGCTCCAATTAAACTCAAAACAGAGATCAATCTCATCATAG
* * * * *
61783391 CTAT-GAATTTAAATTATCTTATTCCGT--GATTTCCAAGCAAACAAACGGAGCATAAAGTTACA
65 CT-TCGAATTTAAAATA-CCTAATCC-TACAATTTCCAACCAAACAAAC-GAGCATAAAGTTACA
* * * *
61783453 AATTGC-AATCTACAACAATTTCATTAATCCTGAATC--CAAAACTTCTCCATCCTGAAGCTAAG
126 AATTCCAAATCTACAATAATTTCATTAATCCTGAATCTAGAAAACTTATCCATCCTGAAGCTAAG
* ** * *
61783515 TAATAAACAATCCAAAACATTATCTCTATGCATGCACTTTTACTTAAAATTCAGTATTAAACCTT
191 TAATAAACAATCCAAAACATAATCTCTACACATGCACTTCTACTTAAAATTCAGTATTAAAACTT
* * * * *
61783580 ACTAGAAGATAATTCAACTACATTCTACATTTCATCATCTTCATTATTCACTCCACATCCAACAT
256 ACTAAAAGATAATTCAACTACATTCTACATTTAATCATCCTCATCATTCAATCCACATCCAACAT
*
61783645 TTCTCTAAGCACATGCATTTTACAATGTTGATTTCATT
321 TTCTCTAAGCACATGCATTTTACAATGTTGATTCCATT
*
61783683 CCTAGGTT----A-CATAAGTATA-----ACTTAAACTCAAAACAGAGATCAATCTCATCATAGC
1 CCTAGGTTACAAATCATAAGTATAGCTCCAATTAAACTCAAAACAGAGATCAATCTCATCATAGC
* * *
61783738 TTCAAATTCAAAATACCTAATTCTACAATTTCCAACCAAACAAACGTAGCATAAAGTTACAAATT
66 TTCGAATTTAAAATACCTAATCCTACAATTTCCAACCAAACAAACG-AGCATAAAGTTACAAATT
*
61783803 CCAAAATCTACAATAATTTCATTAATCCTGAATCTAGAAAACTTATCCATCCTGGAGCTAAGTAA
130 CC-AAATCTACAATAATTTCATTAATCCTGAATCTAGAAAACTTATCCATCCTGAAGCTAAGTAA
* *
61783868 TAAACGATCCAAAACATAATTTCTACACATGCACTTCTACTTAAAATTCAGTATTAAAACTCTAC
194 TAAACAATCCAAAACATAATCTCTACACATGCACTTCTACTTAAAATTCAGTATTAAAACT-TAC
*
61783933 TAAAAGATAGTTCAACTACATTCTACATTTAATCATCCTCATCATTCAATCCACATCCAACATTT
258 TAAAAGATAATTCAACTACATTCTACATTTAATCATCCTCATCATTCAATCCACATCCAACATTT
* *
61783998 CTCTAAGCACATGCATTTTACAGTGTGTGGTTCCATT
323 CTCTAAGCACATGCATTTTACAATGT-TGATTCCATT
* *
61784035 CCTAGGTTACAAACTCATAAGTATAGCTCCAATTATACTCAAAGCAGAGATCAATCTCATCATAG
1 CCTAGGTTACAAA-TCATAAGTATAGCTCCAATTAAACTCAAAACAGAGATCAATCTCATCATAG
* *
61784100 CTTCGAATTTAAAATACCTAATCCTACAATTTCCAACCAAAAAAACAGAGCATAGAGTTACAAAT
65 CTTCGAATTTAAAATACCTAATCCTACAATTTCCAACCAAACAAAC-GAGCATAAAGTTACAAAT
* *
61784165 TTCAAATCTGCAATAATTTCATTAATCCTGAATCTAGAAAACT
129 TCCAAATCTACAATAATTTCATTAATCCTGAATCTAGAAAACT
61784208 AGTCTATCCT
Statistics
Matches: 463, Mismatches: 40, Indels: 39
0.85 0.07 0.07
Matches are distributed among these distances:
344 1 0.00
345 7 0.02
346 81 0.17
348 29 0.06
350 80 0.17
351 97 0.21
352 16 0.03
353 1 0.00
356 1 0.00
357 8 0.02
358 10 0.02
362 39 0.08
363 92 0.20
364 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (358 bp):
CCTAGGTTACAAATCATAAGTATAGCTCCAATTAAACTCAAAACAGAGATCAATCTCATCATAGC
TTCGAATTTAAAATACCTAATCCTACAATTTCCAACCAAACAAACGAGCATAAAGTTACAAATTC
CAAATCTACAATAATTTCATTAATCCTGAATCTAGAAAACTTATCCATCCTGAAGCTAAGTAATA
AACAATCCAAAACATAATCTCTACACATGCACTTCTACTTAAAATTCAGTATTAAAACTTACTAA
AAGATAATTCAACTACATTCTACATTTAATCATCCTCATCATTCAATCCACATCCAACATTTCTC
TAAGCACATGCATTTTACAATGTTGATTCCATT
Found at i:61786287 original size:2 final size:2
Alignment explanation
Indices: 61786280--61786316 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
61786270 CATGTTTTAT
61786280 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
61786317 TTATTATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:61797308 original size:16 final size:16
Alignment explanation
Indices: 61797287--61797317 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61797277 TAATATTAAA
61797287 CTCTAATCCAATACAC
1 CTCTAATCCAATACAC
61797303 CTCTAATCCAATACA
1 CTCTAATCCAATACA
61797318 GCGAACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
CTCTAATCCAATACAC
Found at i:61798089 original size:19 final size:18
Alignment explanation
Indices: 61798034--61798090 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
61798024 TAACGTATAG
*
61798034 TTTT-AATATTTATATAAA
1 TTTTAAATATTTA-AAAAA
* *
61798052 TTTTAAAAAATTAAGAAAA
1 TTTTAAATATTTAA-AAAA
61798071 TTCTTAAATATTTAAAAAA
1 TT-TTAAATATTTAAAAAA
61798090 T
1 T
61798091 AATTAGGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.16
19 16 0.52
20 10 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTTAAATATTTAAAAAA
Found at i:61798636 original size:216 final size:216
Alignment explanation
Indices: 61798261--61798736 Score: 729
Period size: 216 Copynumber: 2.2 Consensus size: 216
61798251 CGCCAATTTC
* * * * *
61798261 TGGTTCAACTAGTTTAATTAGTTGGTCCGATTGATTTCCAACAATTATATATACATCGGTTAATA
1 TGGTTCAACTAGTTAAATCAGTCGGTCCAATTGATTTCCAACAATTATACATACATCGGTTAATA
* * ** *
61798326 ATTCTATAAAAATAACTAATAAGGTTTTGGAGCTTTGAGATCCTAAATTCGAATTCCACCCAAAA
66 ATTATATAAAAATAACTAATAAGGCTTTGGAAATTTGAGACCCTAAATTCGAATTCCACCCAAAA
*
61798391 TTTCTGAATCCTTCTAAATGTGTAAATTAAAGTAGGGAGGTTAGTCTCTAGTTTCAACATAATTA
131 TTTCTGAATCCTTCTAAATGTGCAAATTAAAGTAGGGAGGTTAGTCTCTAGTTTCAACATAATTA
* * *
61798456 AAGGGGCTAACCTCGTCATTA
196 AAGGGACTAACCTCATAATTA
* *
61798477 TGGTTCAACTAGTTAAATCAGTCGGTCCAATTGATTTCCAACAGTTATACATACATCGGTTGATA
1 TGGTTCAACTAGTTAAATCAGTCGGTCCAATTGATTTCCAACAATTATACATACATCGGTTAATA
* *
61798542 ATTATATAAAAATAACTTATAAGGCTTTGGAAATTTGAGACCCTAAATTCGAGTTCCACCC-AAA
66 ATTATATAAAAATAACTAATAAGGCTTTGGAAATTTGAGACCCTAAATTCGAATTCCACCCAAAA
* * *
61798606 GTTCTCGAATCTTTCTAAGTGTGCAAATTAAAGTAGGGAGGTTAGTCTCTAGTTTCAACATAATT
131 TTTCT-GAATCCTTCTAAATGTGCAAATTAAAGTAGGGAGGTTAGTCTCTAGTTTCAACATAATT
*
61798671 AAAGTGACTAACCTCATAATTA
195 AAAGGGACTAACCTCATAATTA
*
61798693 TGGTTCAACTAGTTCAATCAGTCGGTCCAATTGATTTCCAACAA
1 TGGTTCAACTAGTTAAATCAGTCGGTCCAATTGATTTCCAACAA
61798737 CAATAAAGCT
Statistics
Matches: 235, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
215 7 0.03
216 228 0.97
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (216 bp):
TGGTTCAACTAGTTAAATCAGTCGGTCCAATTGATTTCCAACAATTATACATACATCGGTTAATA
ATTATATAAAAATAACTAATAAGGCTTTGGAAATTTGAGACCCTAAATTCGAATTCCACCCAAAA
TTTCTGAATCCTTCTAAATGTGCAAATTAAAGTAGGGAGGTTAGTCTCTAGTTTCAACATAATTA
AAGGGACTAACCTCATAATTA
Found at i:61799086 original size:3 final size:3
Alignment explanation
Indices: 61799078--61799119 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
61799068 TTGCAGCTTT
*
61799078 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ACC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
61799120 GAATTCTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:61810892 original size:25 final size:23
Alignment explanation
Indices: 61810863--61810913 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
61810853 ATTATATTTT
*
61810863 AAATAAATAATATGAATACGACTTA
1 AAATAAACAATA--AATACGACTTA
* *
61810888 AAATATACAATAAATACGATTTA
1 AAATAAACAATAAATACGACTTA
61810911 AAA
1 AAA
61810914 ACAATGGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (23 bp):
AAATAAACAATAAATACGACTTA
Found at i:61815938 original size:22 final size:22
Alignment explanation
Indices: 61815908--61815950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
61815898 CCTTTATGGA
*
61815908 TTTAGTATGCAAACCCCATATT
1 TTTAATATGCAAACCCCATATT
* *
61815930 TTTAATATGCAATCCCTATAT
1 TTTAATATGCAAACCCCATAT
61815951 ACACGAACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAATATGCAAACCCCATATT
Found at i:61815985 original size:15 final size:15
Alignment explanation
Indices: 61815954--61816152 Score: 161
Period size: 15 Copynumber: 13.5 Consensus size: 15
61815944 CCTATATACA
* *
61815954 CGAACCCTGTATATG
1 CGAACCCTATATGTG
*
61815969 CGAACCCTACATGTG
1 CGAACCCTATATGTG
* *
61815984 CGAACTCTACATGTG
1 CGAACCCTATATGTG
* *
61815999 CGAACACTATAGGTG
1 CGAACCCTATATGTG
*
61816014 CGAACCCTACATGTG
1 CGAACCCTATATGTG
*
61816029 CGAACCC-ATATGCG
1 CGAACCCTATATGTG
* * * *
61816043 CGAATCTTGTAGGTG
1 CGAACCCTATATGTG
*
61816058 CGAACCC-ATATGTA
1 CGAACCCTATATGTG
* *
61816072 CGAACCCTGTAGGTG
1 CGAACCCTATATGTG
*
61816087 CGAACCC-ATATGTA
1 CGAACCCTATATGTG
*
61816101 CGAACCCTATAGGTG
1 CGAACCCTATATGTG
* *
61816116 TGAACCCTGTATGTG
1 CGAACCCTATATGTG
* ** *
61816131 GGAACTTTATAAGTG
1 CGAACCCTATATGTG
61816146 CGAACCC
1 CGAACCC
61816153 CTCGTGTGAA
Statistics
Matches: 140, Mismatches: 41, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
14 32 0.23
15 108 0.77
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (15 bp):
CGAACCCTATATGTG
Found at i:61815988 original size:30 final size:29
Alignment explanation
Indices: 61815954--61816122 Score: 149
Period size: 29 Copynumber: 5.8 Consensus size: 29
61815944 CCTATATACA
* *
61815954 CGAACCCTGTATATGCGAACCCTACATGTG
1 CGAACCCTGTATGTGCGAACCC-ATATGTG
* ** * *
61815984 CGAACTCTACATGTGCGAACACTATAGGTG
1 CGAACCCTGTATGTGCGAAC-CCATATGTG
** *
61816014 CGAACCCTACATGTGCGAACCCATATGCG
1 CGAACCCTGTATGTGCGAACCCATATGTG
* * * *
61816043 CGAATCTTGTAGGTGCGAACCCATATGTA
1 CGAACCCTGTATGTGCGAACCCATATGTG
* *
61816072 CGAACCCTGTAGGTGCGAACCCATATGTA
1 CGAACCCTGTATGTGCGAACCCATATGTG
* * *
61816101 CGAACCCTATAGGTGTGAACCC
1 CGAACCCTGTATGTGCGAACCC
61816123 TGTATGTGGG
Statistics
Matches: 116, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
29 75 0.65
30 40 0.34
31 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (29 bp):
CGAACCCTGTATGTGCGAACCCATATGTG
Found at i:61816077 original size:14 final size:14
Alignment explanation
Indices: 61816058--61816107 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
61816048 CTTGTAGGTG
61816058 CGAACCCATATGTA
1 CGAACCCATATGTA
* * *
61816072 CGAACCCTGTAGGTG
1 CGAACCC-ATATGTA
61816087 CGAACCCATATGTA
1 CGAACCCATATGTA
61816101 CGAACCC
1 CGAACCC
61816108 TATAGGTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (14 bp):
CGAACCCATATGTA
Found at i:61816114 original size:58 final size:58
Alignment explanation
Indices: 61815953--61816122 Score: 169
Period size: 58 Copynumber: 2.9 Consensus size: 58
61815943 CCCTATATAC
* * * * * *
61815953 ACGAACCCTGTATATGCGAACCCTACATGTGCGAACTCTACATGTGCGAACACTATAGGT
1 ACGAACCCTGTATGTGCGAACCC-ATATGTGCGAACCCTATAGGTGCGAAC-CCATAGGT
* ** * * * * *
61816013 GCGAACCCTACATGTGCGAACCCATATGCGCGAATCTTGTAGGTGCGAACCCATATGT
1 ACGAACCCTGTATGTGCGAACCCATATGTGCGAACCCTATAGGTGCGAACCCATAGGT
* * *
61816071 ACGAACCCTGTAGGTGCGAACCCATATGTACGAACCCTATAGGTGTGAACCC
1 ACGAACCCTGTATGTGCGAACCCATATGTGCGAACCCTATAGGTGCGAACCC
61816123 TGTATGTGGG
Statistics
Matches: 86, Mismatches: 24, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
58 48 0.56
59 19 0.22
60 19 0.22
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (58 bp):
ACGAACCCTGTATGTGCGAACCCATATGTGCGAACCCTATAGGTGCGAACCCATAGGT
Found at i:61819359 original size:31 final size:31
Alignment explanation
Indices: 61819292--61819360 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
61819282 ATTAAGTACT
* * * *
61819292 AAATTAAGAAAAAGTGTCAAGTTCATGTACC
1 AAATTAGGAAAAAGTGTCAAGTTAAGGCACC
*
61819323 GAATTAGGAAAAAGTGTCAAGTTAAGGCACC
1 AAATTAGGAAAAAGTGTCAAGTTAAGGCACC
61819354 AAATTAG
1 AAATTAG
61819361 ACCAAAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (31 bp):
AAATTAGGAAAAAGTGTCAAGTTAAGGCACC
Found at i:61820188 original size:6 final size:7
Alignment explanation
Indices: 61820171--61820196 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61820161 AAAATATTCA
61820171 AAAAATT
1 AAAAATT
61820178 AAAAATT
1 AAAAATT
61820185 AAAAATT
1 AAAAATT
61820192 AAAAA
1 AAAAA
61820197 AAAGTTGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:61821319 original size:18 final size:18
Alignment explanation
Indices: 61821286--61821335 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
61821276 ATTCACCTAA
*
61821286 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
61821305 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
61821323 ACCCAACCCAACC
1 ACCCAACCCAACC
61821336 TAATCATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.40, C:0.46, G:0.02, T:0.12
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:61821456 original size:9 final size:9
Alignment explanation
Indices: 61821442--61821499 Score: 98
Period size: 9 Copynumber: 6.4 Consensus size: 9
61821432 GTAGTGATTC
61821442 AATTCGGTT
1 AATTCGGTT
*
61821451 AATTCGGGT
1 AATTCGGTT
61821460 AATTCGGTT
1 AATTCGGTT
*
61821469 AATTCGGGT
1 AATTCGGTT
61821478 AATTCGGTT
1 AATTCGGTT
61821487 AATTCGGTT
1 AATTCGGTT
61821496 AATT
1 AATT
61821500 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:61837211 original size:29 final size:28
Alignment explanation
Indices: 61837157--61837211 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
61837147 TTCTTTATAG
* *
61837157 TTTTAGAATTTAGTCTTTATATTTTTAC
1 TTTTAGAATTTAGTCTCTATACTTTTAC
61837185 TTTTAGGAATTTAGTCTCCT-TACTTTT
1 TTTTA-GAATTTAGTCT-CTATACTTTT
61837212 TATTTTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 17 0.74
30 1 0.04
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (28 bp):
TTTTAGAATTTAGTCTCTATACTTTTAC
Found at i:61837779 original size:44 final size:44
Alignment explanation
Indices: 61837723--61837811 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
61837713 ATTGATGTTC
* *
61837723 ACATGATTTTGATAGATCATCTTATATGCATGTGTTAAATTGAT
1 ACATGATTTTGATAGATCATCTTATATGCATGTGTCAAATAGAT
61837767 ACATGATTTTGATAGATCATCTTATATGCATGTGTCAAATAGAT
1 ACATGATTTTGATAGATCATCTTATATGCATGTGTCAAATAGAT
61837811 A
1 A
61837812 ATCGAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (44 bp):
ACATGATTTTGATAGATCATCTTATATGCATGTGTCAAATAGAT
Found at i:61838599 original size:20 final size:21
Alignment explanation
Indices: 61838569--61838607 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
61838559 TAATAAAATA
61838569 AAAAATAGAAATTAAATAATT
1 AAAAATAGAAATTAAATAATT
61838590 AAAAAT-GAAATTAAATAA
1 AAAAATAGAAATTAAATAA
61838608 ACATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAATAGAAATTAAATAATT
Found at i:61840879 original size:28 final size:29
Alignment explanation
Indices: 61840813--61840888 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
61840803 CTCATATCAG
61840813 CCCATACATTT-CACAATTTCTCACATTTAA
1 CCCATA-ATTTACAC-ATTTCTCACATTTAA
* *
61840843 CACACAATTTACACATTTCTCA-ATTTAA
1 CCCATAATTTACACATTTCTCACATTTAA
*
61840871 CCCATAATTGACA-ATTTC
1 CCCATAATTTACACATTTC
61840889 ATTAAAACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.12
28 16 0.40
29 12 0.30
30 7 0.17
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCATAATTTACACATTTCTCACATTTAA
Found at i:61842465 original size:26 final size:26
Alignment explanation
Indices: 61842435--61842484 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
61842425 CCAATGAATC
*
61842435 GGGGAATCAGCACTTAGCAACCCCTA
1 GGGGAATCAGCACATAGCAACCCCTA
61842461 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
61842485 CCCTTTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTA
Found at i:61842530 original size:104 final size:102
Alignment explanation
Indices: 61842298--61842667 Score: 571
Period size: 103 Copynumber: 3.6 Consensus size: 102
61842288 TAGCCGTTAT
** * *
61842298 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT-AGGGG
*
61842363 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
61842401 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTAGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTAGGGGA
61842466 ATCAGCACATAGCAACCCCCCCTTTTCATTTCAAAGATA
66 ATCAGCACATAGCAA--CCCCCTTTTCATTTCAAAGATA
*
61842505 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTAGGGG
*
61842570 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
61842609 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
61842668 TTTATATACA
Statistics
Matches: 250, Mismatches: 12, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
102 20 0.08
103 91 0.36
104 89 0.36
105 50 0.20
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTAGGGGA
ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:61842567 original size:26 final size:26
Alignment explanation
Indices: 61842538--61842589 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
61842528 ACCAATGAAA
*
61842538 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
61842564 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
61842590 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:61843029 original size:29 final size:29
Alignment explanation
Indices: 61842996--61843059 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
61842986 TAATCCACCA
61842996 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
61843025 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
61843055 CCCAA
1 CCCAA
61843060 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:61843033 original size:30 final size:30
Alignment explanation
Indices: 61843003--61843059 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
61842993 CCACCCAACT
61843003 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
61843032 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
61843060 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:61845471 original size:46 final size:46
Alignment explanation
Indices: 61845368--61845529 Score: 276
Period size: 46 Copynumber: 3.6 Consensus size: 46
61845358 TACGTATGAT
61845368 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
61845411 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
61845457 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
61845503 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
61845530 AGTACTCAAA
Statistics
Matches: 113, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
43 10 0.09
44 5 0.04
45 21 0.19
46 77 0.68
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:61849328 original size:16 final size:17
Alignment explanation
Indices: 61849296--61849330 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
61849286 CAATTAACCC
61849296 CTCAATTAATCTAATTTT
1 CTCAATTAA-CTAATTTT
61849314 CTCAATTAA-TAATTTT
1 CTCAATTAACTAATTTT
61849330 C
1 C
61849331 CTAGACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (17 bp):
CTCAATTAACTAATTTT
Found at i:61864219 original size:17 final size:17
Alignment explanation
Indices: 61864183--61864225 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
61864173 ATCTAACTTT
* * *
61864183 AAAATAATGTAAATCTA
1 AAAATAATTTAAACCCA
61864200 AAAATAATTTAAACCCA
1 AAAATAATTTAAACCCA
*
61864217 AAATTAATT
1 AAAATAATT
61864226 CGATAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATAATTTAAACCCA
Found at i:61865116 original size:18 final size:19
Alignment explanation
Indices: 61865082--61865117 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
61865072 GATAATAACT
*
61865082 AAAATATTATTATTTTAAA
1 AAAATATTATTAATTTAAA
61865101 AAAATATT-TTAATTTAA
1 AAAATATTATTAATTTAA
61865118 GGATACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTATTAATTTAAA
Found at i:61874317 original size:31 final size:30
Alignment explanation
Indices: 61874282--61874351 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
61874272 CTTAACAGCC
* *
61874282 CAGTAATTTAAAT-AAAATTTTTTGAATAAGT
1 CAGTAACTTAAATGAAAA-CTTTTGAA-AAGT
61874313 CAGTAACTTAAATGAAAACTTTTGAAAAGTT
1 CAGTAACTTAAATGAAAACTTTTGAAAAG-T
*
61874344 CAATAACT
1 CAGTAACT
61874352 ATATTGTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.09
31 27 0.79
32 4 0.12
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.36
Consensus pattern (30 bp):
CAGTAACTTAAATGAAAACTTTTGAAAAGT
Found at i:61883040 original size:34 final size:34
Alignment explanation
Indices: 61883002--61883070 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
61882992 AGATATTTTC
61883002 TTGTTAAGTTACACTTATCTTAATATTGTTTAAG
1 TTGTTAAGTTACACTTATCTTAATATTGTTTAAG
61883036 TTGTTAAGTTACACTTATCTTAATATTGTTTAAG
1 TTGTTAAGTTACACTTATCTTAATATTGTTTAAG
61883070 T
1 T
61883071 ATAAATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.51
Consensus pattern (34 bp):
TTGTTAAGTTACACTTATCTTAATATTGTTTAAG
Found at i:61885321 original size:31 final size:31
Alignment explanation
Indices: 61885286--61885351 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
61885276 AAAAAAACTT
*
61885286 AATAGTCTC-GTGACTTGAAT-AAAATTTTTTG
1 AATAGT-TCAGTGACTTAAATGAAAA-TTTTTG
*
61885317 AATAGTTCAGTGATTTAAATGAAAATTTTTG
1 AATAGTTCAGTGACTTAAATGAAAATTTTTG
61885348 AATA
1 AATA
61885352 ATTTAATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.06
31 25 0.81
32 4 0.13
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (31 bp):
AATAGTTCAGTGACTTAAATGAAAATTTTTG
Found at i:61887546 original size:30 final size:30
Alignment explanation
Indices: 61887512--61887569 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
61887502 ATTATAAATT
*
61887512 ATAAATTAAACAGATCTTATGGAATTAACC
1 ATAAATTAAACAGATCTTATGCAATTAACC
**
61887542 ATAAATTAAGGAGATCTTATGCAATTAA
1 ATAAATTAAACAGATCTTATGCAATTAA
61887570 TCAGTAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (30 bp):
ATAAATTAAACAGATCTTATGCAATTAACC
Found at i:61893322 original size:2 final size:2
Alignment explanation
Indices: 61893310--61893341 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
61893300 TTAGTCTTTA
*
61893310 AT AT TT 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
61893342 TATTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:61895458 original size:12 final size:12
Alignment explanation
Indices: 61895441--61895468 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
61895431 GGAGCAACGC
61895441 CGGCACGACGGA
1 CGGCACGACGGA
61895453 CGGCACGACGGA
1 CGGCACGACGGA
61895465 CGGC
1 CGGC
61895469 GACTGAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.43, T:0.00
Consensus pattern (12 bp):
CGGCACGACGGA
Found at i:61896008 original size:3 final size:3
Alignment explanation
Indices: 61895945--61895999 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
61895935 GTACTTTTGC
* * *
61895945 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TTT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
61895993 TAG TAT T
1 TAT TAT T
61896000 GGTATTATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:61896209 original size:36 final size:36
Alignment explanation
Indices: 61896130--61896209 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
61896120 AATTTGTTTA
* *
61896130 ATATATATACGTATACTCATATTTCTTTTTATATAT
1 ATATATATACATATACTCATATTTATTTTTATATAT
* *
61896166 ATCTATATACATATACAT-ATTTTTATTTTTATA-AGT
1 ATATATATACATATAC-TCATATTTATTTTTATATA-T
61896202 ATATATAT
1 ATATATAT
61896210 TTATATGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (36 bp):
ATATATATACATATACTCATATTTATTTTTATATAT
Found at i:61909080 original size:218 final size:218
Alignment explanation
Indices: 61908743--61909317 Score: 955
Period size: 218 Copynumber: 2.7 Consensus size: 218
61908733 AAAGAATTTC
* * * *
61908743 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTG-AGAT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAAG-T
*
61908807 TACAATGGAGCGG-----ATTAAAGGATCTTATCTCCCTGAAGTTACAGTAGAGAAGATCACATC
64 TACAGTGGAGCGGATTAAATTAAAGGATCTTATCTCCCTGAAGTTACAGTAGAGAAGATCACATC
61908867 AGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGG
129 AGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGG
61908932 TTACAGTGGAGCAGATTGAAGCCAG
194 TTACAGTGGAGCAGATTGAAGCCAG
61908957 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
*
61909022 CAGTGGAGCGGATTAAATTAAAAGATCTTATCTCCCTGAAGTTACAGTAGAGAAGATCACATCAG
66 CAGTGGAGCGGATTAAATTAAAGGATCTTATCTCCCTGAAGTTACAGTAGAGAAGATCACATCAG
*
61909087 GTCTTATCTCCTTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGGTT
131 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGGTT
61909152 ACAGTGGAGCAGATTGAAGCCAG
196 ACAGTGGAGCAGATTGAAGCCAG
*
61909175 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
* * * * ** *
61909240 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTGGATCACATCAA
66 CAGTGGAGCGGATTAAATTAAAGGATCTTATCTCCCTGAAGTTACAGTAGAGAAGATCACATCAG
61909305 GTCTTATCTCCCT
131 GTCTTATCTCCCT
61909318 AAGCAGTAGT
Statistics
Matches: 338, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
213 26 0.08
214 44 0.13
218 268 0.79
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (218 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAATTAAAGGATCTTATCTCCCTGAAGTTACAGTAGAGAAGATCACATCAG
GTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGGTT
ACAGTGGAGCAGATTGAAGCCAG
Found at i:61909228 original size:87 final size:87
Alignment explanation
Indices: 61908744--61909286 Score: 338
Period size: 87 Copynumber: 6.3 Consensus size: 87
61908734 AAGAATTTCA
* * * *
61908744 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-ATCCTATCTCCTTG-AGAT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGACA-TAGATCTTATCTCCCTGAAG-T
* *
61908807 TACAATGGAGCGGATT--A-A-AG
64 TACAGTGGAGCAGATTGAAGACAG
* * *
61908827 GATCTTATCTCCCTGA-AGTTACAGTAGAGAAGATC----ACATCAGGTCTTATCTCCCTG-AGA
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGACAT-AGATCTTATCTCCCTGAAG-
** ***
61908886 TTACAGTGGAATAGACCAAAGA-ATTTCG
63 TTACAGTGGAGCAGATTGAAGACA----G
* ** * *
61908914 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGATT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGACATAGATCTTATCTCCCTGAAG-TT
* * *
61908978 ACAGCGGAGCAGATCGAAGACAC
65 ACAGTGGAGCAGATTGAAGACAG
* * * * * *
61909001 TATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAATTA-AAAGATCTTATCTCCCTGAAGT
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAA-GACATAGATCTTATCTCCCTGAAGT
* * * *
61909064 TACAGTAGAGAAGA-TCACA-TCAG
64 TACAGTGGAGCAGATTGA-AGACAG
* ** * * *
61909087 G-TCTTATCTCCTTGAGATTACAGTGGAATAGACCAAAGA-ATTTCGGATCTTATCTCCCTGAGG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGACA--T-AGATCTTATCTCCCTGAAG
*
61909150 TTACAGTGGAGCAGATTGAAGCCAG
63 TTACAGTGGAGCAGATTGAAGACAG
* *
61909175 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACACT--ATCCTATCTCCCTGAAGT
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGACA-TAGATCTTATCTCCCTGAAGT
* * * *
61909238 TACAGTGGAGCGGATTAAAATAAAG
64 TACAGTGGAGCAGATT-GAAGACAG
* *
61909263 GATCTTATCTCTCTGAGGTTACAG
1 GATCTTATCTCCCTGAGATTACAG
61909287 CAGAGTGGAT
Statistics
Matches: 358, Mismatches: 72, Indels: 56
0.74 0.15 0.12
Matches are distributed among these distances:
78 1 0.00
79 3 0.01
80 25 0.07
82 2 0.01
83 32 0.09
84 2 0.01
85 27 0.08
86 4 0.01
87 177 0.49
88 11 0.03
89 1 0.00
90 69 0.19
91 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (87 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGACATAGATCTTATCTCCCTGAAGTTA
CAGTGGAGCAGATTGAAGACAG
Found at i:61909285 original size:44 final size:44
Alignment explanation
Indices: 61908695--61909286 Score: 303
Period size: 44 Copynumber: 13.6 Consensus size: 44
61908685 GGTTTATTAT
* * **
61908695 ACAGG-TCTTATCTCCCTGAGATTACAGTGGAACAGA-CCAAAG
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * *
61908737 AATTTCA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCAAAG
1 -A---CAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * * * * * *
61908783 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATT---A-
1 ACAG-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * * * *
61908824 A-AGGATCTTATCTCCCTGAAGTTACAGTAGAGAAGA-TCACA-
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * ** **
61908865 TCAGG-TCTTATCTCCCTGAGATTACAGTGGAATAGA-CCAAAG
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
*
61908907 A-ATTTCGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GAAG
1 ACA----GGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * * **
61908953 CCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCGAAG
1 ACAG-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
** * * * **
61908997 ACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAATT
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * * * * * *
61909041 AAAAGATCTTATCTCCCTGAAGTTACAGTAGAGAAGA-TCACA-
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * * ** **
61909083 TCAGG-TCTTATCTCCTTGAGATTACAGTGGAATAGA-CCAAAG
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
*
61909125 A-ATTTCGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GAAG
1 ACA----GGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* * **
61909171 CCAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TCGAAG
1 ACAG-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
** * * * *
61909215 ACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT
1 ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
* *
61909259 AAAGGATCTTATCTCTCTGAGGTTACAG
1 ACAGGATCTTATCTCCCTGAGGTTACAG
61909287 CAGAGTGGAT
Statistics
Matches: 422, Mismatches: 94, Indels: 65
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 24 0.06
40 2 0.00
41 61 0.14
42 7 0.02
43 62 0.15
44 159 0.38
45 7 0.02
46 97 0.23
47 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
ACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAAG
Found at i:61909387 original size:83 final size:84
Alignment explanation
Indices: 61909294--61909462 Score: 223
Period size: 83 Copynumber: 2.0 Consensus size: 84
61909284 CAGCAGAGTG
* * * * * *
61909294 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGAAGCAGACGAAAGAAACCGATCTTATCTCC
1 GATCACATCAAGTCTCATCTCCCTAAGCAATAGCGAAGCAGACAAAAGAAACCAATCCTATCTCC
*
61909359 CT-AAGTAGTAGTGGAGCA
66 CTGAAGTAGCAGTGGAGCA
* * * *
61909377 GATCACATCAAGTCTCATCTCTCTAAGCAATAGCGGAGCAGACAAAAGAAACTAATCCTATCTCT
1 GATCACATCAAGTCTCATCTCCCTAAGCAATAGCGAAGCAGACAAAAGAAACCAATCCTATCTCC
*
61909442 CTGAAGTTGCAGTGGAGCA
66 CTGAAGTAGCAGTGGAGCA
61909461 GA
1 GA
61909463 CTAAAACCAC
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
83 57 0.78
84 16 0.22
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (84 bp):
GATCACATCAAGTCTCATCTCCCTAAGCAATAGCGAAGCAGACAAAAGAAACCAATCCTATCTCC
CTGAAGTAGCAGTGGAGCA
Found at i:61909397 original size:40 final size:40
Alignment explanation
Indices: 61909294--61909418 Score: 126
Period size: 43 Copynumber: 3.0 Consensus size: 40
61909284 CAGCAGAGTG
*
61909294 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGAAGCA
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
* ** *
61909334 GA-CGAAAGAAACCGATCTTATCTCCCTAAGTAGTAGTGGAGCA
1 GATC-ACATCAA--G-TCTTATCTCCCTAAGCAGTAGTGGAGCA
* * * *
61909377 GATCACATCAAGTCTCATCTCTCTAAGCAATAGCGGAGCA
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
61909417 GA
1 GA
61909419 CAAAAGAAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 31 0.46
41 1 0.01
42 1 0.01
43 32 0.48
44 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
Found at i:61910228 original size:12 final size:12
Alignment explanation
Indices: 61910211--61910240 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61910201 CCGGAGCAAC
61910211 GCCGGCACGACG
1 GCCGGCACGACG
61910223 GCCGGCACGACG
1 GCCGGCACGACG
*
61910235 GACGGC
1 GCCGGC
61910241 GACTGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.43, T:0.00
Consensus pattern (12 bp):
GCCGGCACGACG
Found at i:61910787 original size:3 final size:3
Alignment explanation
Indices: 61910721--61910778 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
61910711 GTACTTTTGC
* * *
61910721 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TTT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
61910769 TAT TAG TAT T
1 TAT TAT TAT T
61910779 GGTATTATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:61910988 original size:36 final size:36
Alignment explanation
Indices: 61910909--61910988 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
61910899 AATTTGTTTA
* *
61910909 ATATATATACGTATACTCATATTTCTTTTTATATAT
1 ATATATATACATATACTCATATTTATTTTTATATAT
* *
61910945 ATCTATATACATATACAT-ATTTTTATTTTTATA-AGT
1 ATATATATACATATAC-TCATATTTATTTTTATATA-T
61910981 ATATATAT
1 ATATATAT
61910989 TTATATGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (36 bp):
ATATATATACATATACTCATATTTATTTTTATATAT
Found at i:61917372 original size:8 final size:8
Alignment explanation
Indices: 61917353--61917395 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
61917343 TGTAAAGTTT
61917353 TTAAAAATA
1 TTAAAAA-A
61917362 TTAAAAAA
1 TTAAAAAA
*
61917370 TTAAAAAT
1 TTAAAAAA
61917378 TTCATAAAAA
1 TT-A-AAAAA
61917388 TTAAAAAA
1 TTAAAAAA
61917396 AACATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 15 0.50
9 9 0.30
10 6 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (8 bp):
TTAAAAAA
Found at i:61917376 original size:18 final size:18
Alignment explanation
Indices: 61917353--61917394 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
61917343 TGTAAAGTTT
61917353 TTAAAAATATT-A-AAAAA
1 TTAAAAAT-TTCATAAAAA
61917370 TTAAAAATTTCATAAAAA
1 TTAAAAATTTCATAAAAA
61917388 TTAAAAA
1 TTAAAAA
61917395 AAACATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 9 0.39
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAATTTCATAAAAA
Found at i:61925598 original size:41 final size:41
Alignment explanation
Indices: 61925541--61925621 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
61925531 TTTCAAGCAA
61925541 ATTGAAGCCATATATTGTGTTTATGCAAAATTCCAGCATAT
1 ATTGAAGCCATATATTGTGTTTATGCAAAATTCCAGCATAT
61925582 ATTGAAGCCATATATTGTGTTTATGCAAAATTCCAGCATA
1 ATTGAAGCCATATATTGTGTTTATGCAAAATTCCAGCATA
61925622 CTTCCCAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (41 bp):
ATTGAAGCCATATATTGTGTTTATGCAAAATTCCAGCATAT
Found at i:61931518 original size:21 final size:21
Alignment explanation
Indices: 61931492--61931565 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
61931482 TAAGTTCAAG
61931492 TTTTTTTTATTCGTTTTAAAT
1 TTTTTTTTATTCGTTTTAAAT
* ** *
61931513 TTTTTTTAATTAATTTTAAGT
1 TTTTTTTTATTCGTTTTAAAT
**
61931534 TTTTAATTATTTCGTGTTTAAAT
1 TTTTTTTTA-TTCGT-TTTAAAT
*
61931557 TATTTTTTA
1 TTTTTTTTA
61931566 GATCGAGTTT
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
21 23 0.61
22 3 0.08
23 12 0.32
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTTTTATTCGTTTTAAAT
Found at i:61931858 original size:16 final size:16
Alignment explanation
Indices: 61931839--61931872 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
61931829 CAAAGTCAAG
61931839 TTTTTA-ATTTGAATA
1 TTTTTATATTTGAATA
*
61931854 TTTTTATATTTTAATA
1 TTTTTATATTTGAATA
61931870 TTT
1 TTT
61931873 AAATATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTATATTTGAATA
Found at i:61935113 original size:22 final size:22
Alignment explanation
Indices: 61935086--61935131 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
61935076 TATTTATTTA
61935086 TTATTTGTTCT-TTTCTTTTCTT
1 TTATTTGTTCTCTTT-TTTTCTT
* *
61935108 TTATTTTTTCTCTTTTTTTTTT
1 TTATTTGTTCTCTTTTTTTCTT
61935130 TT
1 TT
61935132 GAGAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (22 bp):
TTATTTGTTCTCTTTTTTTCTT
Found at i:61946951 original size:40 final size:40
Alignment explanation
Indices: 61946907--61946988 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
61946897 TTCCTAATAA
61946907 GGTTTTAATAAGACACATTATCTATTAATAGACATCCAAG
1 GGTTTTAATAAGACACATTATCTATTAATAGACATCCAAG
* *
61946947 GGTTTTAATAAGGCACATTATTTATTAATAGACATCCAAG
1 GGTTTTAATAAGACACATTATCTATTAATAGACATCCAAG
61946987 GG
1 GG
61946989 AGAGTGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (40 bp):
GGTTTTAATAAGACACATTATCTATTAATAGACATCCAAG
Found at i:61952160 original size:60 final size:60
Alignment explanation
Indices: 61952067--61952189 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
61952057 AAATATCAAG
61952067 TAAATTTGCATCCCAAACAATTCACATAGACTCAATACATTATGAAGACTAGTATTATCA
1 TAAATTTGCATCCCAAACAATTCACATAGACTCAATACATTATGAAGACTAGTATTATCA
61952127 TAAATTTGCATCCCAAACAATTCACATAGACTCAATACATTATGAAGACTAGTATTATCA
1 TAAATTTGCATCCCAAACAATTCACATAGACTCAATACATTATGAAGACTAGTATTATCA
61952187 TAA
1 TAA
61952190 TTAACCAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (60 bp):
TAAATTTGCATCCCAAACAATTCACATAGACTCAATACATTATGAAGACTAGTATTATCA
Found at i:61952707 original size:130 final size:131
Alignment explanation
Indices: 61952567--61953036 Score: 637
Period size: 131 Copynumber: 3.6 Consensus size: 131
61952557 AAGAAAGAAA
*
61952567 GCTCAAAAATCACATTGTTCAACTC-AAAAACCTAAATCTAAACTTAACCAGCAACACTGAATCA
1 GCTCAAAAATCACATTGTTCAACTCAAAAAAACTAAATCTAAACTTAACCAGCAACACTGAATCA
*
61952631 ATAAAAATTCAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAAAAAAAA
66 ATAAAAATTAAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAAAAAAAA
61952696 G
131 G
* ** *
61952697 GCTCAAAAATCACATTGTTCATCTCAAAAAAAAAAAATCTAAACTTAACCAGCAACACAGAATCA
1 GCTCAAAAATCACATTGTTCAACTCAAAAAAACTAAATCTAAACTTAACCAGCAACACTGAATCA
* * * * *
61952762 ATAAAAATTCAAATTGGTACATAGAAATCTCAAAGTCAATGCTAACAAAAAAGAC---AAAAGAA
66 ATAAAAATTAAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAAAAAAAA
61952824 G
131 G
* *
61952825 GCTCAAAAATCACATTGTTCGACTCAAAAAAACTAAATCTAAACTTAAACCAGCTACACTGAATC
1 GCTCAAAAATCACATTGTTCAACTCAAAAAAACTAAATCTAAACTT-AACCAGCAACACTGAATC
* * * * * * *
61952890 AATAAAAATTAAAAAATAGTACATAGAAATCACAGACTCAATACTAGCAAAAACTAAAAAAAAAA
65 AATAAAAATT-AAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAAC--GACAAAAAA
61952955 AAAAG
127 AAAAG
* * * * *
61952960 CCTCAAAAATCACATTGTTCATCTC--AAAAACTAAATCTAAACTAAACCTGCAACCCTGAATCA
1 GCTCAAAAATCACATTGTTCAACTCAAAAAAACTAAATCTAAACTTAACCAGCAACACTGAATCA
61953023 ATAAAAATTAAAAT
66 ATAAAAATTAAAAT
61953037 CAATTCAAAA
Statistics
Matches: 297, Mismatches: 35, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
128 49 0.16
129 26 0.09
130 58 0.20
131 91 0.31
132 26 0.09
133 18 0.06
135 29 0.10
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.20
Consensus pattern (131 bp):
GCTCAAAAATCACATTGTTCAACTCAAAAAAACTAAATCTAAACTTAACCAGCAACACTGAATCA
ATAAAAATTAAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAAAAAAAA
G
Found at i:61953028 original size:261 final size:257
Alignment explanation
Indices: 61952560--61953036 Score: 713
Period size: 261 Copynumber: 1.8 Consensus size: 257
61952550 CAAGAGAAAG
*
61952560 AAAGAAAGCTCAAAAATCACATTGTTCAACTCAAAAACCTAAATCTAAACTTAACCAGCAACACT
1 AAAGAAAGCTCAAAAATCACATTGTTCAACTCAAAAAACTAAATCTAAACTTAACCAGCAACACT
* * * * * * *
61952625 GAATCAATAAAAATTCAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAA
66 GAATCAATAAAAATTAAAAATAGTACATAGAAATCACAAACTCAATACTAGCAAAAACAAAAAAA
* *
61952690 AAAAAAGGCTCAAAAATCACATTGTTCATCTCAAAAAAAAAAAATCTAAACTTAACCAGCAACAC
131 AAAAAAGCCTCAAAAATCACATTGTTCATCTC-AAAAAAAAAAATCTAAACTAAACCAGCAACAC
*
61952755 AGAATCAATAAAAATTCAAATTGGTACATAGAAATCTCAAAGTCAATGCTAACAAAAAAGACA
195 AGAATCAATAAAAATTAAAATTGGTACATAGAAATCTCAAAGTCAATGCTAACAAAAAAGACA
* * *
61952818 AAAGAAGGCTCAAAAATCACATTGTTCGACTCAAAAAAACTAAATCTAAACTTAAACCAGCTACA
1 AAAGAAAGCTCAAAAATCACATTGTTCAACTC-AAAAAACTAAATCTAAACTT-AACCAGCAACA
*
61952883 CTGAATCAATAAAAATTAAAAAATAGTACATAGAAATCACAGACTCAATACTAGCAAAAACTAAA
64 CTGAATCAATAAAAATT-AAAAATAGTACATAGAAATCACAAACTCAATACTAGCAAAAAC--AA
** *
61952948 AAAAAAAAAAAGCCTCAAAAATCACATTGTTCATCTC-AAAAACTAAATCTAAACTAAACCTGCA
126 AAAAAAAAAAAGCCTCAAAAATCACATTGTTCATCTCAAAAAAAAAAATCTAAACTAAACCAGCA
* *
61953012 ACCCTGAATCAATAAAAATTAAAAT
191 ACACAGAATCAATAAAAATTAAAAT
61953037 CAATTCAAAA
Statistics
Matches: 194, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
258 30 0.15
259 19 0.10
260 27 0.14
261 82 0.42
263 36 0.19
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.20
Consensus pattern (257 bp):
AAAGAAAGCTCAAAAATCACATTGTTCAACTCAAAAAACTAAATCTAAACTTAACCAGCAACACT
GAATCAATAAAAATTAAAAATAGTACATAGAAATCACAAACTCAATACTAGCAAAAACAAAAAAA
AAAAAAGCCTCAAAAATCACATTGTTCATCTCAAAAAAAAAAATCTAAACTAAACCAGCAACACA
GAATCAATAAAAATTAAAATTGGTACATAGAAATCTCAAAGTCAATGCTAACAAAAAAGACA
Found at i:61956847 original size:11 final size:11
Alignment explanation
Indices: 61956824--61956858 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
61956814 ATATATTTTT
61956824 AAAAATTTATAA
1 AAAAATTT-TAA
61956836 AAAAATTTTAA
1 AAAAATTTTAA
*
61956847 AAAAATTCTAA
1 AAAAATTTTAA
61956858 A
1 A
61956859 GAATATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:61956850 original size:12 final size:12
Alignment explanation
Indices: 61956824--61956853 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
61956814 ATATATTTTT
61956824 AAAAATTTATAA
1 AAAAATTTATAA
61956836 AAAAATTT-TAA
1 AAAAATTTATAA
61956847 AAAAATT
1 AAAAATT
61956854 CTAAAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAATTTATAA
Found at i:61960386 original size:30 final size:29
Alignment explanation
Indices: 61960333--61960394 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
61960323 TTGTTTATTA
*
61960333 TTATATATTTTATAATCAAATTAAATCGC
1 TTATATATTTTATAATCAAATTAAATCAC
*
61960362 TTATATTTTATTATTAAT-AAATTAAATCAC
1 TTATATATT-TTA-TAATCAAATTAAATCAC
61960392 TTA
1 TTA
61960395 CTGTTCTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.28
30 17 0.59
31 4 0.14
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (29 bp):
TTATATATTTTATAATCAAATTAAATCAC
Found at i:61963184 original size:22 final size:21
Alignment explanation
Indices: 61963134--61963184 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
61963124 CTGTTACTCT
*
61963134 CTACCCTCTTTAACCCTAAAAC
1 CTACCC-CTTTAACCCCAAAAC
* *
61963156 CTTCCCCTTTAAACCCCAAACC
1 CTACCCCTTT-AACCCCAAAAC
61963178 CTACCCC
1 CTACCCC
61963185 AATATCCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.27, C:0.49, G:0.00, T:0.24
Consensus pattern (21 bp):
CTACCCCTTTAACCCCAAAAC
Found at i:61966863 original size:269 final size:270
Alignment explanation
Indices: 61966379--61966873 Score: 789
Period size: 269 Copynumber: 1.8 Consensus size: 270
61966369 TCCGAAGAGT
* *
61966379 TAGACTCAGATCCAAGCTTTTTTTAATTTTGAAGGATTAAAAATTTTAAATTGGAATTAAATTGG
1 TAGACTCAGATCCAAGC-TTTTTTAATTTTGAAGGATT-AAAATTTTAAATTGAAATTAAATTAG
* *
61966444 ATTTAGAATTTTAGGGTTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATCGAAACTAAAT
64 ATTTAGAATTTTAGGATTTAACTTGAACTGGAGTGCTAGAAAAGCATTTTAAATCGAAACTAAAT
* * *
61966509 TTGAAGGGTTTTTTTTTCTATTTTAAGATTTGGATTAGCTTGGTTAGTTGAATCTTTATTTTTAT
129 TTGAAGGATTTTTTTTTCTATTTTAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTATAT
* *
61966574 GAAAAATTCTTTGGTTTTCTTGTTTGTAGGATTTGAATTTATTTTCCTTCACATGTATATTATTT
194 GAAAAATTCATTGATTTTCTTGTTTGTAGGATTTGAATTTATTTTCCTTCACATGTATATTATTT
61966639 TTTTCTAAGTGC
259 TTTTCTAAGTGC
*
61966651 TAGACTCAGATCCAAGC-TTTTTAGTTTTGAAGGATT-AAATTTTAAAATTGAAATTAAATTAGA
1 TAGACTCAGATCCAAGCTTTTTTAATTTTGAAGGATTAAAATTTT-AAATTGAAATTAAATTAGA
* *
61966714 TTTAGAATTTTAGGATTTAACTTGAACTGGAGTGCTAGAAAAGCATTTTAAATTGAAACTATATT
65 TTTAGAATTTTAGGATTTAACTTGAACTGGAGTGCTAGAAAAGCATTTTAAATCGAAACTAAATT
*
61966779 TGAAGGATTTTTTTTATC-CTTTTAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTATAT
130 TGAAGGATTTTTTTT-TCTATTTTAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTATAT
* **
61966843 GGAAGTTTCATTGATTTTCTTGTTTGTAGGA
194 GAAAAATTCATTGATTTTCTTGTTTGTAGGA
61966874 GTTATGCCCT
Statistics
Matches: 205, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
268 7 0.03
269 161 0.79
270 20 0.10
272 17 0.08
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (270 bp):
TAGACTCAGATCCAAGCTTTTTTAATTTTGAAGGATTAAAATTTTAAATTGAAATTAAATTAGAT
TTAGAATTTTAGGATTTAACTTGAACTGGAGTGCTAGAAAAGCATTTTAAATCGAAACTAAATTT
GAAGGATTTTTTTTTCTATTTTAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTATATGA
AAAATTCATTGATTTTCTTGTTTGTAGGATTTGAATTTATTTTCCTTCACATGTATATTATTTTT
TTCTAAGTGC
Found at i:61972463 original size:58 final size:58
Alignment explanation
Indices: 61972373--61972484 Score: 215
Period size: 58 Copynumber: 1.9 Consensus size: 58
61972363 TAACGGAAGA
61972373 GCCTTATTGATATAATATCGATAGTTTGAGGATGTAACTAGAATGCTGTGAAGTTTAG
1 GCCTTATTGATATAATATCGATAGTTTGAGGATGTAACTAGAATGCTGTGAAGTTTAG
*
61972431 GCCTTATTGATATAATATCGATAGTTTGAGGATGTAACTAGAATGCTTTGAAGT
1 GCCTTATTGATATAATATCGATAGTTTGAGGATGTAACTAGAATGCTGTGAAGT
61972485 ATAATGACCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (58 bp):
GCCTTATTGATATAATATCGATAGTTTGAGGATGTAACTAGAATGCTGTGAAGTTTAG
Found at i:61976525 original size:16 final size:18
Alignment explanation
Indices: 61976486--61976519 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61976476 TAAGTTTATA
61976486 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
61976503 ATATTTATATATTATGT
1 ATATTTATATATTATGT
61976520 AATTTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:61978019 original size:24 final size:25
Alignment explanation
Indices: 61977973--61978028 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
61977963 ATCAACATTC
* * * *
61977973 AAAAAATTAATAACTAAATTTAACT
1 AAAAAAATAAGAACCAAATTTAACA
61977998 AAAAAAATAAGAACCAAA-TTAACA
1 AAAAAAATAAGAACCAAATTTAACA
61978022 AAAAAAA
1 AAAAAAA
61978029 ACATAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (25 bp):
AAAAAAATAAGAACCAAATTTAACA
Found at i:61979536 original size:50 final size:50
Alignment explanation
Indices: 61979461--61979560 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
61979451 TAACAGAATG
*
61979461 ACCAGTTTTCTCTTTGATCTAATATATAAAGATAGATTTACTCATTTTCT
1 ACCAGTTTTCTCTTTGATCTAATATATAAAGATAGATTTACCCATTTTCT
*
61979511 ACCAGTTTTCTCTTTGATCTAATATATAAAGATAGATTTGCCCATTTTCT
1 ACCAGTTTTCTCTTTGATCTAATATATAAAGATAGATTTACCCATTTTCT
61979561 GAGTAGAGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (50 bp):
ACCAGTTTTCTCTTTGATCTAATATATAAAGATAGATTTACCCATTTTCT
Found at i:61982824 original size:21 final size:21
Alignment explanation
Indices: 61982785--61982824 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61982775 AAGTAAGGGT
*
61982785 TTTTTTAATATTGTATATTAA
1 TTTTTTAATATGGTATATTAA
61982806 TTTTTTAATTATGGT-TATT
1 TTTTTTAA-TATGGTATATT
61982825 TTTTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTTAATATGGTATATTAA
Found at i:61983300 original size:9 final size:10
Alignment explanation
Indices: 61983281--61983306 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
61983271 AAATTATTTT
61983281 AAAAATAAAA
1 AAAAATAAAA
61983291 AAAAATAAAA
1 AAAAATAAAA
61983301 AAAAAT
1 AAAAAT
61983307 TTTAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:61983320 original size:40 final size:40
Alignment explanation
Indices: 61983270--61983346 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
61983260 TAAACATTAA
*
61983270 AAAATTATTTTAAAAATAAAAAA-AAATAAAAAAAAATTTT
1 AAAAGTATTTTAAAAATAAAAAATAAA-AAAAAAAAATTTT
* *
61983310 AAAAGTATTTTAAAATTAAAAAATAAAAATAAAAAAT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAAAAAAAAT
61983347 ATATATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 30 0.91
41 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (40 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAAAAAAAAATTTT
Found at i:61987142 original size:59 final size:61
Alignment explanation
Indices: 61987066--61987199 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 61
61987056 AAAAAATTAA
* *
61987066 ATAGTTTGA-TGATCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAAG-AAAAAAAA-C
1 ATAG-TTGAGTGACCATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAAGAAAAAAAAATC
* * *
61987125 ATAGTTGAGTGACCATTTTGTAACTTTTCATCGTTAGTTGATCAAAAAAGAAAAAAAAATC
1 ATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAAGAAAAAAAAATC
61987186 ATAGTT-AGGTGACC
1 ATAGTTGA-GTGACC
61987200 TCTACTAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
58 4 0.06
59 40 0.61
60 9 0.14
61 13 0.20
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (61 bp):
ATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAAGAAAAAAAAATC
Found at i:61987428 original size:14 final size:14
Alignment explanation
Indices: 61987409--61987436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61987399 ACTTTTACCC
61987409 TTTTTTCTCACTTT
1 TTTTTTCTCACTTT
61987423 TTTTTTCTCACTTT
1 TTTTTTCTCACTTT
61987437 GACTCCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTCTCACTTT
Found at i:61987759 original size:22 final size:22
Alignment explanation
Indices: 61987738--61987792 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
61987728 TTTTTTATTA
61987738 AATAAAATA-AAAT-TAATAATT
1 AATAAAATATAAATATAA-AATT
*
61987759 -ATAAAATATAAATATAAAACT
1 AATAAAATATAAATATAAAATT
*
61987780 AATAAAATGTAAA
1 AATAAAATATAAA
61987793 ATTTATTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 8 0.28
21 7 0.24
22 14 0.48
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AATAAAATATAAATATAAAATT
Found at i:61987774 original size:13 final size:15
Alignment explanation
Indices: 61987738--61987795 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 15
61987728 TTTTTTATTA
61987738 AATAAA-ATAAAATT
1 AATAAATATAAAATT
*
61987752 AATAATTATAAAA-T
1 AATAAATATAAAATT
*
61987766 -ATAAATATAAAACT
1 AATAAATATAAAATT
*
61987780 AATAAAATGTAAAATT
1 AAT-AAATATAAAATT
61987796 TATTCTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 11 0.31
14 7 0.19
15 8 0.22
16 10 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AATAAATATAAAATT
Found at i:61987974 original size:17 final size:17
Alignment explanation
Indices: 61987952--61987987 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61987942 AATATTGTAT
61987952 TTCATTATTCAAAATAA
1 TTCATTATTCAAAATAA
**
61987969 TTCATTATTGTAAATAA
1 TTCATTATTCAAAATAA
61987986 TT
1 TT
61987988 TGCTTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (17 bp):
TTCATTATTCAAAATAA
Found at i:61991066 original size:11 final size:11
Alignment explanation
Indices: 61991050--61991075 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61991040 GAAAAAATAA
61991050 AAAAGTATTTT
1 AAAAGTATTTT
61991061 AAAAGTATTTT
1 AAAAGTATTTT
61991072 AAAA
1 AAAA
61991076 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:61998226 original size:2 final size:2
Alignment explanation
Indices: 61998219--61998248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61998209 AGTAAACCCA
61998219 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
61998249 GAATAAGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61998818 original size:26 final size:25
Alignment explanation
Indices: 61998787--61998838 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
61998777 CCTATTTTTT
* *
61998787 AATAAACATTAAAAAATTATTTTAAA
1 AATAAAAAATAAAAAA-TATTTTAAA
61998813 AATAAAAAATAAAAAATATTTTAAA
1 AATAAAAAATAAAAAATATTTTAAA
61998838 A
1 A
61998839 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAAAAAATAAAAAATATTTTAAA
Found at i:61998858 original size:7 final size:7
Alignment explanation
Indices: 61998846--61998885 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
61998836 AAAGTATTTT
61998846 AAAATTA
1 AAAATTA
61998853 AAAATTA
1 AAAATTA
61998860 AAAATTA
1 AAAATTA
*
61998867 AAAAATA
1 AAAATTA
*
61998874 AAAATAA
1 AAAATTA
61998881 AAAAT
1 AAAAT
61998886 ATATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:61998884 original size:13 final size:13
Alignment explanation
Indices: 61998845--61998886 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
61998835 AAAAGTATTT
* *
61998845 TAAAATTAAAAAT
1 TAAAAATAAAAAA
61998858 TAAAAATTAAAAAA
1 TAAAAA-TAAAAAA
61998872 TAAAAATAAAAAA
1 TAAAAATAAAAAA
61998885 TA
1 TA
61998887 TATATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:62020280 original size:60 final size:61
Alignment explanation
Indices: 62020155--62020280 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 61
62020145 TCACTCAGCT
* ** * ** *
62020155 ATTTTTTTTCTTTTTTTGATCACACAATTATGAAAAGTTGTAAAACGGTCATTAAACTATG
1 ATTTTTTTTCTTTTTTCGATCACACAATTATGAAAAGTTACAAAACAGTCACCAAACTATA
* * *
62020216 ATTTTTTTTCTTTTTTCG-TCACTCAATTATGAAAAGTTACAAAATAGTCACCCAACT-TCA
1 ATTTTTTTTCTTTTTTCGATCACACAATTATGAAAAGTTACAAAACAGTCACCAAACTAT-A
62020276 ATTTT
1 ATTTT
62020281 GTCTTTTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 36 0.67
61 17 0.31
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (61 bp):
ATTTTTTTTCTTTTTTCGATCACACAATTATGAAAAGTTACAAAACAGTCACCAAACTATA
Found at i:62024895 original size:6 final size:6
Alignment explanation
Indices: 62024884--62024914 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
62024874 CGAAAGGGAA
*
62024884 GGACCC GGACCC GGACCC GGACCC AGACCC G
1 GGACCC GGACCC GGACCC GGACCC GGACCC G
62024915 AACCTAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.48, G:0.32, T:0.00
Consensus pattern (6 bp):
GGACCC
Found at i:62026430 original size:16 final size:17
Alignment explanation
Indices: 62026398--62026438 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
62026388 TTTTATGCTC
62026398 TTTAAATTTTCAAAAAT
1 TTTAAATTTTCAAAAAT
*
62026415 TTTATATTTT-AAAAAT
1 TTTAAATTTTCAAAAAT
62026431 TGTTAAAT
1 T-TTAAAT
62026439 AAACCCAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTTCAAAAAT
Found at i:62031690 original size:4 final size:4
Alignment explanation
Indices: 62031681--62031717 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
62031671 TTGATTCTTG
62031681 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
62031718 TTGAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:62035037 original size:13 final size:13
Alignment explanation
Indices: 62035004--62035041 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
62034994 TTAATCGACT
*
62035004 TTTATAATGTAT-
1 TTTATAATATATA
*
62035016 TTTTTAATATATA
1 TTTATAATATATA
62035029 TTTATAATATATA
1 TTTATAATATATA
62035042 ATAAACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTATAATATATA
Found at i:62035603 original size:92 final size:92
Alignment explanation
Indices: 62035441--62035620 Score: 288
Period size: 92 Copynumber: 2.0 Consensus size: 92
62035431 CATTAATTTT
* * *
62035441 ATTATAAGTTGTTATCATATCTGCTCTTTGTTGATACAATACTTAGAACTACCCATAGTCCCTCC
1 ATTATAAGTTATTATCATATCTGCTCTTTGTTAATACAATACTTAGAACTACCCATAGCCCCTCC
*
62035506 GCAACTCTTAAATAGGAGGATAACGTC
66 GCAACTCTTAAATAGGAAGATAACGTC
* * *
62035533 ATTATATGTTATTATCATATCTGCTTTTTGTTAATACAATGCTTAGAACTACCCATAGCCCCTCC
1 ATTATAAGTTATTATCATATCTGCTCTTTGTTAATACAATACTTAGAACTACCCATAGCCCCTCC
*
62035598 TCAACTCTTAAATAGGAAGATAA
66 GCAACTCTTAAATAGGAAGATAA
62035621 TGCGCTTCAG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 80 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (92 bp):
ATTATAAGTTATTATCATATCTGCTCTTTGTTAATACAATACTTAGAACTACCCATAGCCCCTCC
GCAACTCTTAAATAGGAAGATAACGTC
Found at i:62037021 original size:16 final size:17
Alignment explanation
Indices: 62037002--62037039 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
62036992 CTTGCGGATT
62037002 TTTTTAA-AATATTTTG
1 TTTTTAATAATATTTTG
62037018 TTTTTAATTTAATATTTTG
1 TTTTTAA--TAATATTTTG
62037037 TTT
1 TTT
62037040 ACATCTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
19 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTAATAATATTTTG
Found at i:62037158 original size:20 final size:19
Alignment explanation
Indices: 62037120--62037162 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
62037110 ATTTATTAAA
*
62037120 AAATATATTTTTATAAATTT
1 AAATATATATTTATAAA-TT
62037140 AAATATATATTTACT-AATT
1 AAATATATATTTA-TAAATT
62037159 AAAT
1 AAAT
62037163 TTTGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 14 0.67
21 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATATATTTATAAATT
Found at i:62042638 original size:118 final size:117
Alignment explanation
Indices: 62042219--62042727 Score: 542
Period size: 117 Copynumber: 4.3 Consensus size: 117
62042209 GTGATTCGAT
* * * * ** *
62042219 GTTT-CAAGTGAATAATTGCAGTTGATTGGTTTGTGATTGCCAGAAAACCGAGTTTAGGGTGTTT
1 GTTTACAAGTGATTTATTGCAGTTGGTTGGTATGTGATTGCTGGAAAACCGAGTTTAGGGCGTTT
* * * *
62042283 GAGATATACATATAGGAGTGAAGATTTCAGTCTT-CAACTGTTGGTGAGTTCA
66 GAGATATACATATAGGAGTGAAGATTTTAGTCTTGAAAC-ATCGGTGAGTTCA
* * * * * *
62042335 GTTTACGAGTGATTTACTGCATTTGGTTGGTACGTGGTTGCTGGAAAACTGAGTTTAGGGCGTTT
1 GTTTACAAGTGATTTATTGCAGTTGGTTGGTATGTGATTGCTGGAAAACCGAGTTTAGGGCGTTT
* * *
62042400 GAGATATACATATAGGAGTGAGGATTTTAGTCTCGAAACATCGGTCAGTTCA
66 GAGATATACATATAGGAGTGAAGATTTTAGTCTTGAAACATCGGTGAGTTCA
* * * *
62042452 GTTTTCAAGTGAATTATTGCAGTTGGTTGGTACGTGATTGCTGGAAAACCGAGTTTAGGGCATTT
1 GTTTACAAGTGATTTATTGCAGTTGGTTGGTATGTGATTGCTGGAAAACCGAGTTTAGGGCGTTT
** * *
62042517 GAGAT-TAACGCATAGGAGTTAAGATTTTAGTCTTGAAACATCGGTGAGTTCG
66 GAGATAT-ACATATAGGAGTGAAGATTTTAGTCTTGAAACATCGGTGAGTTCA
* * * * *
62042569 GTTTACGAGTGAGTTTGTTGCAGTTGGTTGGTATGTGATTGCTGGAAAACCAAGTTTATGGTGTT
1 GTTTACAAGTGA-TTTATTGCAGTTGGTTGGTATGTGATTGCTGGAAAACCGAGTTTAGGGCGTT
* ** * * *
62042634 TGAGATTTATGTATGGGAGTGAAGATTTTAGTCTTG-AACAGTTGGTGAGCTT-G
65 TGAGATATACATATAGGAGTGAAGATTTTAGTCTTGAAACA-TCGGTGAG-TTCA
* * **
62042687 GTTTACAAGTGAGTTTTTTTCAGTTGGTTTTTATGTGATTG
1 GTTTACAAGTGA-TTTATTGCAGTTGGTTGGTATGTGATTG
62042728 TCGGGAACTG
Statistics
Matches: 332, Mismatches: 54, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
116 5 0.02
117 202 0.61
118 122 0.37
119 3 0.01
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.37
Consensus pattern (117 bp):
GTTTACAAGTGATTTATTGCAGTTGGTTGGTATGTGATTGCTGGAAAACCGAGTTTAGGGCGTTT
GAGATATACATATAGGAGTGAAGATTTTAGTCTTGAAACATCGGTGAGTTCA
Found at i:62053001 original size:27 final size:26
Alignment explanation
Indices: 62052936--62053001 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
62052926 CTGAATATAA
*
62052936 TAAATATATATTTAATTTTTTAATTTT
1 TAAATAAAT-TTTAATTTTTTAATTTT
* ** *
62052963 AAAATACTTTTTAATTTTTTTATTTTT
1 TAAATAAATTTTAA-TTTTTTAATTTT
62052990 TAAATAAATTTT
1 TAAATAAATTTT
62053002 TGGTGTTTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TAAATAAATTTTAATTTTTTAATTTT
Found at i:62054231 original size:29 final size:30
Alignment explanation
Indices: 62054163--62054232 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
62054153 ATAAACATTT
62054163 AATTAATTTTTAAAAATTAAAAAATTCAAAA
1 AATT-ATTTTTAAAAATTAAAAAATTCAAAA
* * *
62054194 AAATGTTTTTAAAAATT-AAAAA-TCATTAA
1 AATTATTTTTAAAAATTAAAAAATTCA-AAA
62054223 AATTATTTTT
1 AATTATTTTT
62054233 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 3 0.09
29 15 0.45
30 12 0.36
31 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
AATTATTTTTAAAAATTAAAAAATTCAAAA
Found at i:62054233 original size:30 final size:29
Alignment explanation
Indices: 62054163--62054233 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
62054153 ATAAACATTT
*
62054163 AATTAATTTTTAAAAATTAAAAAATTCAA
1 AATTATTTTTTAAAAATTAAAAAATTCAA
**
62054192 AAAAATGTTTTTAAAAATTAAAAATCATT-AA
1 AATTAT-TTTTTAAAAATTAAAAA--ATTCAA
62054223 AATTATTTTTT
1 AATTATTTTTT
62054234 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 3 0.09
30 22 0.65
31 6 0.18
32 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (29 bp):
AATTATTTTTTAAAAATTAAAAAATTCAA
Found at i:62056353 original size:14 final size:14
Alignment explanation
Indices: 62056334--62056360 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62056324 TTTTATTTAA
62056334 TTGTGTAGTGTAGT
1 TTGTGTAGTGTAGT
62056348 TTGTGTAGTGTAG
1 TTGTGTAGTGTAG
62056361 AGGGGTGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (14 bp):
TTGTGTAGTGTAGT
Found at i:62060657 original size:16 final size:15
Alignment explanation
Indices: 62060636--62060666 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
62060626 AGAAATAGAA
62060636 CCCAAATTTTCTTTGG
1 CCCAAATTTT-TTTGG
62060652 CCCAAATTTTTTTGG
1 CCCAAATTTTTTTGG
62060667 AAATTGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (15 bp):
CCCAAATTTTTTTGG
Found at i:62075334 original size:12 final size:10
Alignment explanation
Indices: 62075306--62075347 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
62075296 AATTTTTTTA
62075306 ATTTTAAAAT
1 ATTTTAAAAT
62075316 ATTTTAAAAT
1 ATTTTAAAAT
62075326 ACTTTTTAAAAT
1 A--TTTTAAAAT
62075338 -TTTTAAAAT
1 ATTTTAAAAT
62075347 A
1 A
62075348 AATTTTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.31
10 11 0.38
12 9 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:62075341 original size:21 final size:22
Alignment explanation
Indices: 62075307--62075347 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
62075297 ATTTTTTTAA
62075307 TTTTAAAATATTTTAAAATACT
1 TTTTAAAATATTTTAAAATACT
62075329 TTTTAAAAT-TTTTAAAATA
1 TTTTAAAATATTTTAAAATA
62075348 AATTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATATTTTAAAATACT
Found at i:62075353 original size:21 final size:22
Alignment explanation
Indices: 62075305--62075353 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
62075295 AAATTTTTTT
62075305 AATTTTAAAATATTTTAAAATA
1 AATTTTAAAATATTTTAAAATA
**
62075327 CTTTTTAAAAT-TTTTAAAATA
1 AATTTTAAAATATTTTAAAATA
62075348 AATTTT
1 AATTTT
62075354 TGGTATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTAAAATATTTTAAAATA
Found at i:62075353 original size:22 final size:22
Alignment explanation
Indices: 62075307--62075354 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
62075297 ATTTTTTTAA
*
62075307 TTTTAAAATATTTTAAAATACT
1 TTTTAAAATATTTTAAAATAAT
62075329 TTTTAAAAT-TTTTAAAATAAAT
1 TTTTAAAATATTTTAAAAT-AAT
62075351 TTTT
1 TTTT
62075355 GGTATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTAAAATATTTTAAAATAAT
Found at i:62079735 original size:18 final size:17
Alignment explanation
Indices: 62079704--62079765 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
62079694 ATCACACTGG
*
62079704 AAAAA-AATATTTTTTT
1 AAAAATAATAATTTTTT
62079720 AAATAATAATAATTTTGTT
1 AAA-AATAATAATTTT-TT
* *
62079739 AAAGATAATTATTTTTT
1 AAAAATAATAATTTTTT
*
62079756 TAAAA-AATAA
1 AAAAATAATAA
62079766 AAATATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 18 0.49
19 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAAATAATAATTTTTT
Done.