Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 201 of 349
Found at i:65088010 original size:11 final size:10
Alignment explanation
Indices: 65087966--65088012 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
65087956 AGCTCACTCG
*
65087966 AGCTCAAGTC
1 AGCTCAATTC
65087976 AGCTCAA-TC
1 AGCTCAATTC
*
65087985 GAGCTCAATTT
1 -AGCTCAATTC
65087996 AGCTACAATTC
1 AGCT-CAATTC
65088007 AGCTCA
1 AGCTCA
65088013 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:65090973 original size:19 final size:19
Alignment explanation
Indices: 65090949--65090988 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65090939 AGCTCCCATG
65090949 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65090968 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65090987 TA
1 TA
65090989 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65093755 original size:14 final size:14
Alignment explanation
Indices: 65093736--65093778 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
65093726 AAATCGACAA
*
65093736 TTTGTTCATACCAT
1 TTTGTTCCTACCAT
*
65093750 TTTGTTCCTACCCT
1 TTTGTTCCTACCAT
*
65093764 TTCGTTCCTACCAT
1 TTTGTTCCTACCAT
65093778 T
1 T
65093779 CCATTCGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (14 bp):
TTTGTTCCTACCAT
Found at i:65100669 original size:14 final size:14
Alignment explanation
Indices: 65100647--65100694 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65100637 ACCTAAACCG
* *
65100647 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65100661 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
65100675 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
65100689 ACCATT
1 ACCATT
65100695 CCATTTGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65101322 original size:82 final size:81
Alignment explanation
Indices: 65101186--65101345 Score: 214
Period size: 82 Copynumber: 2.0 Consensus size: 81
65101176 GACGGCCAAC
* * * * * * *
65101186 AAACACGCCCGTGTGCTATGGCTGGTGGCACAATGTAGGCTTGGTTTAAGCCAATTTTCCATCTC
1 AAACACGCCCGTGTGATATGGCTGGTGGCACAACGCAAGCTTGGTTTAAGCCAATTTGCCACCCC
65101251 TTTATGGGCCATTCCT
66 TTTATGGGCCATTCCT
*
65101267 AAACATGCCCGTGTGATATGG-TCGTGTGGCACAACGCAAGCTTGGTTTAAGCCAATTTGCCACC
1 AAACACGCCCGTGTGATATGGCT-G-GTGGCACAACGCAAGCTTGGTTTAAGCCAATTTGCCACC
*
65101331 CCTTTATGGGTCATT
64 CCTTTATGGGCCATT
65101346 TCTACAAGCC
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 1 0.01
81 20 0.29
82 47 0.69
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (81 bp):
AAACACGCCCGTGTGATATGGCTGGTGGCACAACGCAAGCTTGGTTTAAGCCAATTTGCCACCCC
TTTATGGGCCATTCCT
Found at i:65102174 original size:15 final size:16
Alignment explanation
Indices: 65102141--65102179 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
65102131 CACTTCACAC
65102141 TTTTTTTTATATTCGA
1 TTTTTTTTATATTCGA
65102157 TTTTTTTTA-ATTTC-A
1 TTTTTTTTATA-TTCGA
65102172 TTTTTTTT
1 TTTTTTTT
65102180 CACTAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTTATATTCGA
Found at i:65104060 original size:44 final size:43
Alignment explanation
Indices: 65103961--65104085 Score: 125
Period size: 43 Copynumber: 2.9 Consensus size: 43
65103951 AGCTCGTACA
* * * *
65103961 ATGCCTAC-GTCCTAGACGTGGTCTTACATGTAA--TCAAATGTTG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGAAATCTCAAA--TCG
65104004 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAAATCTCAAATCG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACACG-AAATCTCAAATCG
65104048 ATGCCAAC-GTCCCAGACGTGGTCTTACACGAAATCTCA
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGAAATCTCA
65104086 TGCCGGAATC
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
42 2 0.03
43 32 0.45
44 30 0.42
45 2 0.03
46 5 0.07
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACACGAAATCTCAAATCG
Found at i:65106126 original size:21 final size:22
Alignment explanation
Indices: 65106087--65106130 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
65106077 ATGCATACTC
65106087 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
65106109 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
65106130 C
1 C
65106131 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:65108419 original size:30 final size:30
Alignment explanation
Indices: 65108385--65108481 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65108375 TAAACTAAAA
*
65108385 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
65108415 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
65108445 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
65108474 ATGAGCTA
1 -TGAGCTA
65108482 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:65117270 original size:14 final size:14
Alignment explanation
Indices: 65117223--65117270 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65117213 GTACGAATGG
*
65117223 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
65117237 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
65117251 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
65117265 ATTGGT
1 AATGGT
65117271 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:65118915 original size:30 final size:30
Alignment explanation
Indices: 65118881--65118976 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
65118871 GCTCACTCCT
*
65118881 AGCTC-ACTTTCAACTCACGAGCTAAACCTC
1 AGCTCAACTTT-AGCTCACGAGCTAAACCTC
* * * * *
65118911 AGCTCAACTTTAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAACCTC
* *
65118941 AGCTCAACTTTAGCTCACGAGCTAAAGCTT
1 AGCTCAACTTTAGCTCACGAGCTAAACCTC
65118971 AGCTCA
1 AGCTCA
65118977 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTC
Found at i:65123225 original size:11 final size:12
Alignment explanation
Indices: 65123193--65123225 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65123183 GAGCTGTAGC
65123193 AAACTTAATTAT
1 AAACTTAATTAT
*
65123205 AAACTGAATTA-
1 AAACTTAATTAT
65123216 AAACTTAATT
1 AAACTTAATT
65123226 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:65124323 original size:21 final size:21
Alignment explanation
Indices: 65124276--65124327 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
65124266 CTCTTTTTCT
* **
65124276 TTTCTCTTTCAATTTCTTTTC
1 TTTCTTTTTCAATTTCTTGCC
* *
65124297 TCTCTTTTTCATTTTCTTGCC
1 TTTCTTTTTCAATTTCTTGCC
65124318 TTTCTTTTTC
1 TTTCTTTTTC
65124328 CACTCTCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTTTTTCAATTTCTTGCC
Found at i:65127734 original size:11 final size:11
Alignment explanation
Indices: 65127718--65127742 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65127708 TTCGTTCCAT
65127718 AATAATTTTCA
1 AATAATTTTCA
65127729 AATAATTTTCA
1 AATAATTTTCA
65127740 AAT
1 AAT
65127743 CCTCACCACA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTTTCA
Found at i:65134994 original size:30 final size:30
Alignment explanation
Indices: 65134960--65135056 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65134950 TAAACTAAAA
*
65134960 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
65134990 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
65135020 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
65135049 ATGAGCTA
1 -TGAGCTA
65135057 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:65135635 original size:11 final size:12
Alignment explanation
Indices: 65135603--65135635 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65135593 GAGCTGTAGC
65135603 AAACTTAATTAT
1 AAACTTAATTAT
*
65135615 AAACTGAATTA-
1 AAACTTAATTAT
65135626 AAACTTAATT
1 AAACTTAATT
65135636 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:65140724 original size:24 final size:25
Alignment explanation
Indices: 65140671--65140724 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
65140661 AACAAATTCT
* *
65140671 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
65140696 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
65140719 TTTTTT
1 TTTTTT
65140725 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:65147353 original size:24 final size:24
Alignment explanation
Indices: 65147300--65147353 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
65147290 AAACAAATTC
*
65147300 TTTTTTTCATTTTCATCACTCGTT
1 TTTTTTTCATTTTAATCACTCGTT
* *
65147324 TCTTTTTC-TTTTGAATCACTC-TC
1 TTTTTTTCATTTT-AATCACTCGTT
65147347 TTTTTTT
1 TTTTTTT
65147354 ATCACTCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.11, C:0.20, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTTTCATTTTAATCACTCGTT
Found at i:65148331 original size:13 final size:13
Alignment explanation
Indices: 65148313--65148341 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65148303 TGGCTAACCT
65148313 ACATAATTAAATA
1 ACATAATTAAATA
65148326 ACATAATTAAATA
1 ACATAATTAAATA
65148339 ACA
1 ACA
65148342 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:65148619 original size:20 final size:21
Alignment explanation
Indices: 65148571--65148620 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
65148561 AATGAGCTTG
*
65148571 AAATGAGCTAAATTCGAGCTC
1 AAATGAGCTAAATACGAGCTC
*
65148592 AAACGAGCTAAA-ACGAGCTC
1 AAATGAGCTAAATACGAGCTC
*
65148612 AAGTGAGCT
1 AAATGAGCT
65148621 GATGGGAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (21 bp):
AAATGAGCTAAATACGAGCTC
Found at i:65156928 original size:27 final size:29
Alignment explanation
Indices: 65156897--65156958 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
65156887 TACCTGTATT
*
65156897 TGGCCCACTAAGCCC-AATCATA-TTCTA
1 TGGCCCACTAAGCCCAAATCACATTTCTA
* * *
65156924 TGGCCCATTAGGCCCAAATCACATTTTTA
1 TGGCCCACTAAGCCCAAATCACATTTCTA
65156953 TGGCCC
1 TGGCCC
65156959 GTTAGTCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.45
28 6 0.21
29 10 0.34
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCCACTAAGCCCAAATCACATTTCTA
Found at i:65156957 original size:29 final size:28
Alignment explanation
Indices: 65156897--65156976 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 28
65156887 TACCTGTATT
* * *
65156897 TGGCCCACTAAGCCCAATCATA-TTCTA
1 TGGCCCATTAGGCCCAATCACATTTCTA
*
65156924 TGGCCCATTAGGCCCAAATCACATTTTTA
1 TGGCCCATTAGGCCC-AATCACATTTCTA
* * *
65156953 TGGCCCGTTAGTCCCAGTCACATT
1 TGGCCCATTAGGCCCAATCACATT
65156977 CATATTCATG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 13 0.30
28 14 0.32
29 17 0.39
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTTCTA
Found at i:65157229 original size:16 final size:16
Alignment explanation
Indices: 65157210--65157244 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
65157200 CTTTTTGACA
* *
65157210 TTTCGGCATTTCGGCT
1 TTTCAGCATTTCAGCT
65157226 TTTCAGCATTTCAGCT
1 TTTCAGCATTTCAGCT
65157242 TTT
1 TTT
65157245 GCCGATACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (16 bp):
TTTCAGCATTTCAGCT
Found at i:65158372 original size:16 final size:16
Alignment explanation
Indices: 65158351--65158384 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
65158341 GAAAATTCTG
*
65158351 GGATTTCAGGATTTTT
1 GGATTTCAAGATTTTT
65158367 GGATTTCAAGATTTTT
1 GGATTTCAAGATTTTT
65158383 GG
1 GG
65158385 GGCGTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (16 bp):
GGATTTCAAGATTTTT
Found at i:65165882 original size:20 final size:20
Alignment explanation
Indices: 65165857--65165896 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
65165847 GTACTTTGAA
65165857 AATGTATATATTAAAGTATG
1 AATGTATATATTAAAGTATG
65165877 AATGTATATATTAAAGTATG
1 AATGTATATATTAAAGTATG
65165897 GCATGTATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (20 bp):
AATGTATATATTAAAGTATG
Found at i:65168250 original size:38 final size:38
Alignment explanation
Indices: 65168199--65168276 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
65168189 TACTTCTGTG
*
65168199 ATTGCTTTGATAGATCCTGGGTCAACACATTCGTATGT
1 ATTGCTTTGATAGATCCTGGATCAACACATTCGTATGT
65168237 ATTGCTTTGATAGATCCTGGATCAACACATTCGTATGT
1 ATTGCTTTGATAGATCCTGGATCAACACATTCGTATGT
65168275 AT
1 AT
65168277 GCATGAACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (38 bp):
ATTGCTTTGATAGATCCTGGATCAACACATTCGTATGT
Found at i:65172991 original size:20 final size:20
Alignment explanation
Indices: 65172968--65173014 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
65172958 AGGTTAAGAT
*
65172968 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
65172988 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
65173008 TGAGCTG
1 TGAGCTG
65173015 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:65175470 original size:44 final size:42
Alignment explanation
Indices: 65175416--65175536 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 42
65175406 GCGTTTTGTG
* *
65175416 ATTTCATGTAAGACCATGTCTGGGACATTGGCATCAACT-TCTG
1 ATTTCGTGTAAGACCATGTCTGGGACATTGGCATC--CTATCTA
* * *
65175459 TTTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTA
1 ATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCCTATCTA
* *
65175502 ATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATC
1 ATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
65175537 GATGTTTGAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 29 0.43
43 9 0.13
44 29 0.43
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (42 bp):
ATTTCGTGTAAGACCATGTCTGGGACATTGGCATCCTATCTA
Found at i:65177331 original size:42 final size:43
Alignment explanation
Indices: 65177252--65177388 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 43
65177242 TCCTTGACGT
* **
65177252 GGTCTTACATGTAATTCAATATCGATGCCTCTCTCCCAGACAG
1 GGTCTTACATGTAAATCAATATCGATGCCGATCTCCCAGACAG
* *
65177295 GGTCTTACATG-AAATCAGATAT-GATGCCGATGTCCCAGACAT
1 GGTCTTACATGTAAATCA-ATATCGATGCCGATCTCCCAGACAG
* * * * * *
65177337 GGTCTTATACGTAAAT--ATCAGTCGAGGCCTATGTCCCAGACAC
1 GGTCTTACATGTAAATCAAT-A-TCGATGCCGATCTCCCAGACAG
65177380 GGTCTTACA
1 GGTCTTACA
65177389 CGATATCTCA
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.03
41 1 0.01
42 31 0.40
43 44 0.56
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGTAAATCAATATCGATGCCGATCTCCCAGACAG
Found at i:65177764 original size:10 final size:10
Alignment explanation
Indices: 65177751--65177807 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
65177741 AGCTCACTTG
65177751 AGCTCGTTTT
1 AGCTCGTTTT
*
65177761 AGCTCGTTTG
1 AGCTCGTTTT
*
65177771 AGCTCGAATTT
1 AGCTCG-TTTT
*
65177782 AGCTCGAATTT
1 AGCTCG-TTTT
*
65177793 AGCTCGTTTC
1 AGCTCGTTTT
65177803 AGCTC
1 AGCTC
65177808 ATTCTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
10 22 0.54
11 19 0.46
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:65177787 original size:11 final size:11
Alignment explanation
Indices: 65177758--65177798 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
65177748 TTGAGCTCGT
65177758 TTTAGCTCG--
1 TTTAGCTCGAA
65177767 TTTGAGCTCGAA
1 TTT-AGCTCGAA
65177779 TTTAGCTCGAA
1 TTTAGCTCGAA
65177790 TTTAGCTCG
1 TTTAGCTCG
65177799 TTTCAGCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.10
10 6 0.21
11 17 0.59
12 3 0.10
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (11 bp):
TTTAGCTCGAA
Found at i:65178049 original size:13 final size:13
Alignment explanation
Indices: 65178031--65178059 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65178021 AATAGTTATG
65178031 TGTTATTTAATTA
1 TGTTATTTAATTA
65178044 TGTTATTTAATTA
1 TGTTATTTAATTA
65178057 TGT
1 TGT
65178060 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:65185282 original size:17 final size:17
Alignment explanation
Indices: 65185260--65185295 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
65185250 TTCTGGAATT
65185260 CAGCTTGGAAGAAATCC
1 CAGCTTGGAAGAAATCC
65185277 CAGCTTGGAAGAAATCC
1 CAGCTTGGAAGAAATCC
65185294 CA
1 CA
65185296 AGTAACTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (17 bp):
CAGCTTGGAAGAAATCC
Found at i:65187454 original size:10 final size:10
Alignment explanation
Indices: 65187439--65187476 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
65187429 TTGGGTTAAG
65187439 ATTGAGCTGA
1 ATTGAGCTGA
65187449 ATTGAGCTCGA
1 ATTGAGCT-GA
65187460 A-TGAGCTGA
1 ATTGAGCTGA
*
65187469 CTTGAGCT
1 ATTGAGCT
65187477 TGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:65187464 original size:20 final size:20
Alignment explanation
Indices: 65187441--65187487 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
65187431 GGGTTAAGAT
65187441 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
65187461 TGAGCTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
65187481 TGAGCTG
1 TGAGCTG
65187488 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:65194310 original size:10 final size:10
Alignment explanation
Indices: 65194297--65194331 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
65194287 AAGCTCGGTT
65194297 GAGCTCAAAC
1 GAGCTCAAAC
*
65194307 GAGCTGAAAC
1 GAGCTCAAAC
*
65194317 GAGCTCAAAT
1 GAGCTCAAAC
65194327 GAGCT
1 GAGCT
65194332 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:65194340 original size:20 final size:20
Alignment explanation
Indices: 65194294--65194341 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
65194284 AGTAAGCTCG
65194294 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
65194314 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
65194334 GTTGAGCT
1 GTTGAGCT
65194342 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:65195484 original size:5 final size:5
Alignment explanation
Indices: 65195474--65195528 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
65195464 CTCTTGCCTC
*
65195474 TCTTT TCTTT T-TATT TATTT TCTTT TC--T TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65195519 TCTTT TCTTT
1 TCTTT TCTTT
65195529 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 32 0.74
6 3 0.07
7 4 0.09
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:65195502 original size:25 final size:26
Alignment explanation
Indices: 65195474--65195528 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
65195464 CTCTTGCCTC
65195474 TCTTTTCTTTT-TATTTATTTTCTTT
1 TCTTTTCTTTTCTATTTATTTTCTTT
* *
65195499 TC--TTCTTTTGCTTTTTCTTTTCTTT
1 TCTTTTCTTTT-CTATTTATTTTCTTT
65195524 TCTTT
1 TCTTT
65195529 GTTTTCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 7 0.29
25 16 0.67
27 1 0.04
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (26 bp):
TCTTTTCTTTTCTATTTATTTTCTTT
Found at i:65195533 original size:20 final size:19
Alignment explanation
Indices: 65195474--65195539 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
65195464 CTCTTGCCTC
65195474 TCTTTTCTTTTTATT-TATTT
1 TCTTTTCTTTTT-TTGT-TTT
*
65195494 TCTTTTCTTCTTTTGCTTTT
1 TCTTTTCTTTTTTTG-TTTT
65195514 TCTTTTCTTTTCTTTGTTTT
1 TCTTTTCTTTT-TTTGTTTT
65195534 CTCTTT
1 -TCTTT
65195540 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.05
20 28 0.70
21 10 0.25
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (19 bp):
TCTTTTCTTTTTTTGTTTT
Found at i:65196463 original size:13 final size:13
Alignment explanation
Indices: 65196445--65196514 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
65196435 CATAAATCAC
65196445 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
65196457 -TTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
65196469 TTTTTTTTCG-AT
1 TTTTTTTTTGAAT
***
65196481 TTTTTTTAAAAAAT
1 TTTTTTT-TTGAAT
65196495 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
65196508 TTTTTTT
1 TTTTTTT
65196515 CAAACTTGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
11 11 0.23
12 9 0.19
13 18 0.38
14 9 0.19
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:65196487 original size:11 final size:11
Alignment explanation
Indices: 65196446--65196475 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
65196436 ATAAATCACT
65196446 TTTTTTTTGAA
1 TTTTTTTTGAA
65196457 TTTTTTTTGAA
1 TTTTTTTTGAA
65196468 TTTTTTTT
1 TTTTTTTT
65196476 TCGATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:65214946 original size:30 final size:30
Alignment explanation
Indices: 65214912--65215008 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65214902 TAAACTAAAA
65214912 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65214942 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65214972 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65215002 TGAGCTA
1 TGAGCTA
65215009 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65227154 original size:4 final size:4
Alignment explanation
Indices: 65227145--65227176 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
65227135 AAACTAAGTA
65227145 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
65227177 ACTTTACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:65227162 original size:12 final size:13
Alignment explanation
Indices: 65227143--65227176 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
65227133 TTAAACTAAG
65227143 TAAAATAAATAAA
1 TAAAATAAATAAA
65227156 T-AAATAAATAAA
1 TAAAATAAATAAA
65227168 TAAAATAAA
1 TAAAATAAA
65227177 ACTTTACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:65233171 original size:30 final size:30
Alignment explanation
Indices: 65233088--65233172 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
65233078 GCTCATATTC
65233088 AGCTCACGAGCTAAA-CTTTAGCTCAACTTT
1 AGCTCACGAGCTAAAGC-TTAGCTCAACTTT
* * ** *
65233118 AGCTTAGGAG-TTTAGCCTCAGCTCAACTTT
1 AGCTCACGAGCTAAAG-CTTAGCTCAACTTT
65233148 AGCTCACGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAAGCTTAGCTCA
65233173 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
29 2 0.05
30 36 0.86
31 4 0.10
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
AGCTCACGAGCTAAAGCTTAGCTCAACTTT
Found at i:65240940 original size:20 final size:20
Alignment explanation
Indices: 65240915--65240952 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65240905 AGCTCGTTTC
*
65240915 CAGCTCATTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
65240935 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
65240953 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:65240959 original size:10 final size:10
Alignment explanation
Indices: 65240915--65240972 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
65240905 AGCTCGTTTC
65240915 CAGCTC-ATT
1 CAGCTCAATT
*
65240924 CGAGCTCAAGT
1 C-AGCTCAATT
65240935 CAGCTCAA-T
1 CAGCTCAATT
65240944 CGAGCTCAATT
1 C-AGCTCAATT
*
65240955 TAGCTACAATT
1 CAGCT-CAATT
65240966 CAGCTCA
1 CAGCTCA
65240973 TTTATTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.07
10 25 0.61
11 13 0.32
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:65240959 original size:20 final size:20
Alignment explanation
Indices: 65240916--65240976 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
65240906 GCTCGTTTCC
* * *
65240916 AGCTCATTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
65240936 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
65240956 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
65240976 A
1 A
65240977 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:65242322 original size:13 final size:13
Alignment explanation
Indices: 65242306--65242333 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
65242296 AAAAAAATCG
65242306 AAATTCAAAAAAA
1 AAATTCAAAAAAA
65242319 AAATTCAAAAAAA
1 AAATTCAAAAAAA
65242332 AA
1 AA
65242334 GTGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:65242354 original size:14 final size:14
Alignment explanation
Indices: 65242337--65242387 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
65242327 AAAAAAAGTG
65242337 AAAAAAATCGAGCA
1 AAAAAAATCGAGCA
** *
65242351 AAAAAAATAAAGAA
1 AAAAAAATCGAGCA
65242365 AAAAAAAGT-GAGCA
1 AAAAAAA-TCGAGCA
65242379 AAAAAAATC
1 AAAAAAATC
65242388 AAGTGAATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.08
Consensus pattern (14 bp):
AAAAAAATCGAGCA
Found at i:65242356 original size:28 final size:28
Alignment explanation
Indices: 65242325--65242394 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
65242315 AAAAAAATTC
65242325 AAAAAA-AAAGTGAAAAAAA-TCGAGCAA
1 AAAAAATAAAGTGAAAAAAAGT-GAGCAA
**
65242352 AAAAAATAAAGAAAAAAAAAGTGAGCAA
1 AAAAAATAAAGTGAAAAAAAGTGAGCAA
*
65242380 AAAAAATCAAGTGAA
1 AAAAAATAAAGTGAA
65242395 TCGACTCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.17
28 29 0.81
29 1 0.03
ACGTcount: A:0.71, C:0.06, G:0.14, T:0.09
Consensus pattern (28 bp):
AAAAAATAAAGTGAAAAAAAGTGAGCAA
Found at i:65242444 original size:26 final size:26
Alignment explanation
Indices: 65242410--65242466 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
65242400 TCAATCAACC
* *
65242410 GAGCCGGATCACATCATTTGGTATCA
1 GAGCTGGATCACATCAGTTGGTATCA
65242436 GAGCTGGATCACATCAGTTGGTATCA
1 GAGCTGGATCACATCAGTTGGTATCA
65242462 GAGCT
1 GAGCT
65242467 AGCTAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (26 bp):
GAGCTGGATCACATCAGTTGGTATCA
Found at i:65243681 original size:10 final size:10
Alignment explanation
Indices: 65243668--65243705 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
65243658 TTGTAGCTAA
65243668 ATTGAGCTCG
1 ATTGAGCTCG
65243678 ATTGAGCT-G
1 ATTGAGCTCG
65243687 ACTTGAGCTCG
1 A-TTGAGCTCG
*
65243698 AGTGAGCT
1 ATTGAGCT
65243706 GGAAACGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:65243685 original size:20 final size:20
Alignment explanation
Indices: 65243645--65243705 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
65243635 ACCAATAAAA
65243645 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
65243665 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
65243685 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
65243705 T
1 T
65243706 GGAAACGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:65243706 original size:20 final size:20
Alignment explanation
Indices: 65243669--65243706 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65243659 TGTAGCTAAA
*
65243669 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
65243689 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
65243707 GAAACGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:65243948 original size:19 final size:19
Alignment explanation
Indices: 65243924--65243963 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65243914 AGCTCCCATG
65243924 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65243943 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65243962 TA
1 TA
65243964 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65246016 original size:697 final size:698
Alignment explanation
Indices: 65244673--65246055 Score: 2473
Period size: 697 Copynumber: 2.0 Consensus size: 698
65244663 CCTACAAGTG
*
65244673 ACCATTGGACATCATGCATTCACTTTGAGTTTTCTTAAGCATGAAGATTCATTCATTTCCTATTA
1 ACCATTAGACATCATGCATTCACTTTGAGTTTTCTTAAGCATGAAGATTCATTCATTTCCTATTA
65244738 CCATAGCTGAATCTAGACATGCACATTAAGGGTCATTTTTCTAGAATTTTCTTTAATTAATATGT
66 CCATAGCTGAATCTAGACATGCACATTAAGGGTCATTTTTCTAGAATTTTCTTTAATTAATATGT
* * * *
65244803 AAGCATGAAAGGCTAATCGGCTACCTAGACTTAGGCCTATAAATACTTGTTCAATTTTCATGTAA
131 AAGCATGAAAGGCCAATCGACTACCTAGACTAAGGCCTATAAATACTTGTTCAATTTCCATGTAA
* *
65244868 AGGACTTTTTGAAACTTATGTTAATGTTATGCTCCCGAAATTGTGAGGCAAACTTTTCTTATATT
196 AGGACTTTTTGAAACTTATGTTAATGTTATGCTCCCGAAATTATGAGGCAAACTTTTATTATATT
*
65244933 TCGTTCAAAGATTCGTTTGGCGTTCCTAGCATTCTAGTTGTGTCAACCGTGTTCTTTGTCGTACC
261 TCGTTCAAAGATTCGTTTGGCATTCCTAGCATTCTAGTTGTGTCAACCGTGTTCTTTGTCGTACC
65244998 CGAACTTATCACTATTCATAGTGTGGCGTTCAACATACCGAGGTTCCTATCTTGTTAGATAGTGG
326 CGAACTTATCACTATTCATAGTGTGGCGTTCAACATACCGAGGTTCCTATCTTGTTAGATAGTGG
* *
65245063 GTCGAGGTTTTCCCTTACCAAACCTAAAACCAAACTCAAAAGGCTTAATCAACGGGTCGATACCA
391 GTCGAGGTTTTCCCTTACCAAACCTAAAACCAAACTCAAAAAGCTTAATCAACGGATCGATACCA
**
65245128 TTTCGGTATTAGTTCTTGAAAGTACCTTTAGTAGTTCAAACCTGTTCTCTTCTTTACCTAATCGA
456 TTTCGGTATTAGTTCTTGAAAGTACCTTTAGTAGTTCAAACCCATTCTCTTCTTTACCTAATCGA
65245193 ACCTAAACCGACCAATTTGTTCATATCCTTTTGTTCCTACCCTTTCATTCCTACCATTCCATTCG
521 ACCTAAACCGACCAATTTGTTCATATCCTTTTGTTCCTACCCTTTCATTCCTACCATTCCATTCG
*
65245258 TACCCCTCTTTCTACTTTGACCATACCTTCAACTCAACTAAACCCAACGTAACTTCTCGTAGACG
586 TACCCCTCTTTCTACTTCGACCATACCTTCAACTCAACTAAACCCAACGTAACTTCTCGTAGACG
*
65245323 ATCGGGCAATTTACATACGACTCGACTCTTCCCGAGACGGTTCGTATC
651 ATCGGGCAATCTACATACGACTCGACTCTTCCCGAGACGGTTCGTATC
65245371 ACCATTAGACATCATGCATTCACTTTGAGTTTTCTTAAGCATGAAGATTCATTCATTTCCTATTA
1 ACCATTAGACATCATGCATTCACTTTGAGTTTTCTTAAGCATGAAGATTCATTCATTTCCTATTA
*
65245436 CCATAGCTGAATCTAGACATGCACATTAAGGGTCATTTTTCTAGAATTTTCTTTAATTAATGTGT
66 CCATAGCTGAATCTAGACATGCACATTAAGGGTCATTTTTCTAGAATTTTCTTTAATTAATATGT
65245501 AAGCATGAAAGGCCAATCGACTACCTAGACTAAGGCCTATAAATACTTGTTCAATTTCCATGTAA
131 AAGCATGAAAGGCCAATCGACTACCTAGACTAAGGCCTATAAATACTTGTTCAATTTCCATGTAA
* * *
65245566 AGGAC-TTTTGAAACTTTTGTTAATGTTATGCTGCCGAAATTATGAGGCATACTTTTATTATATT
196 AGGACTTTTTGAAACTTATGTTAATGTTATGCTCCCGAAATTATGAGGCAAACTTTTATTATATT
*
65245630 TCGTTCAAAGATTCGTTTGGCATTCCTAGCGTTCTAGTTGTGTCAACCGTGTTCTTTGTCGTACC
261 TCGTTCAAAGATTCGTTTGGCATTCCTAGCATTCTAGTTGTGTCAACCGTGTTCTTTGTCGTACC
65245695 CGAACTTATCACTATTCATAGTGTGGCGTTCAACATACCGAGGTTCCTATCTTGTTAGATAGTGG
326 CGAACTTATCACTATTCATAGTGTGGCGTTCAACATACCGAGGTTCCTATCTTGTTAGATAGTGG
* * * *
65245760 GTCGAGG-TTTCCTTTACCAAACTTATAACCGAACTCAAAAAGCTTAATCAACGGATCGATACCA
391 GTCGAGGTTTTCCCTTACCAAACCTAAAACCAAACTCAAAAAGCTTAATCAACGGATCGATACCA
* *
65245824 TTTCGGTATTGGTTCTTGAAAGTACCTTTAGTAGTTCCAAACCCATTCTCTTCTTTACCTAGTCG
456 TTTCGGTATTAGTTCTTGAAAGTACCTTTAGTAGTT-CAAACCCATTCTCTTCTTTACCTAATCG
* *
65245889 AACCTAAACTGACCAATTTGTTCATATCCTTTTGTTCCTACCCTTTCGTTCCTACCATTCCATTC
520 AACCTAAACCGACCAATTTGTTCATATCCTTTTGTTCCTACCCTTTCATTCCTACCATTCCATTC
* * *
65245954 GTACCCCTCTTTCTACTTCGACCATTCCTTTAACTCAACTAAACCTAACGTAACTTCTCGTAGAC
585 GTACCCCTCTTTCTACTTCGACCATACCTTCAACTCAACTAAACCCAACGTAACTTCTCGTAGAC
65246019 GATCGGGCAATCTACATACGACTCGACTCTTCCCGAG
650 GATCGGGCAATCTACATACGACTCGACTCTTCCCGAG
65246056 TAGTCAAAGA
Statistics
Matches: 654, Mismatches: 30, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
696 86 0.13
697 374 0.57
698 194 0.30
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (698 bp):
ACCATTAGACATCATGCATTCACTTTGAGTTTTCTTAAGCATGAAGATTCATTCATTTCCTATTA
CCATAGCTGAATCTAGACATGCACATTAAGGGTCATTTTTCTAGAATTTTCTTTAATTAATATGT
AAGCATGAAAGGCCAATCGACTACCTAGACTAAGGCCTATAAATACTTGTTCAATTTCCATGTAA
AGGACTTTTTGAAACTTATGTTAATGTTATGCTCCCGAAATTATGAGGCAAACTTTTATTATATT
TCGTTCAAAGATTCGTTTGGCATTCCTAGCATTCTAGTTGTGTCAACCGTGTTCTTTGTCGTACC
CGAACTTATCACTATTCATAGTGTGGCGTTCAACATACCGAGGTTCCTATCTTGTTAGATAGTGG
GTCGAGGTTTTCCCTTACCAAACCTAAAACCAAACTCAAAAAGCTTAATCAACGGATCGATACCA
TTTCGGTATTAGTTCTTGAAAGTACCTTTAGTAGTTCAAACCCATTCTCTTCTTTACCTAATCGA
ACCTAAACCGACCAATTTGTTCATATCCTTTTGTTCCTACCCTTTCATTCCTACCATTCCATTCG
TACCCCTCTTTCTACTTCGACCATACCTTCAACTCAACTAAACCCAACGTAACTTCTCGTAGACG
ATCGGGCAATCTACATACGACTCGACTCTTCCCGAGACGGTTCGTATC
Found at i:65246250 original size:38 final size:38
Alignment explanation
Indices: 65246195--65246272 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
65246185 TACTTCTGTG
* *
65246195 ATTGCTGTGATAGATCCTGGATCAACACATTCGTATGT
1 ATTGCTGTGATAAATCCTGGATCAACACATTCATATGT
*
65246233 ATTGCTTTGATAAATCCTGGATCAACACATTCATATGT
1 ATTGCTGTGATAAATCCTGGATCAACACATTCATATGT
65246271 AT
1 AT
65246273 GCATGAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (38 bp):
ATTGCTGTGATAAATCCTGGATCAACACATTCATATGT
Found at i:65250902 original size:42 final size:42
Alignment explanation
Indices: 65250780--65250931 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 42
65250770 TTGCGTTTTT
*
65250780 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCA-ACTTC
1 TGATTTCGTGTAAGACCATGTCTGGGACATCGGCATCATA--TC
*
65250823 T-ATTTTACGTGTAAGACCATGTCTGGGACATCAGCATCATATC
1 TGA-TTT-CGTGTAAGACCATGTCTGGGACATCGGCATCATATC
* * * * * *
65250866 TGATTTCGTGTAAGACCCTGTCTAGCACAGCGGCATCGATGTT
1 TGATTTCGTGTAAGACCATGTCTGGGACATCGGCATC-ATATC
* * *
65250909 TGATTACATGTAAGACCAGGTCT
1 TGATTTCGTGTAAGACCATGTCT
65250932 ATAACGTTTG
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
42 27 0.30
43 32 0.35
44 31 0.34
45 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATCGGCATCATATC
Found at i:65252176 original size:22 final size:22
Alignment explanation
Indices: 65252146--65252189 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
65252136 TTTGGTATTT
65252146 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
65252168 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
65252190 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:65256397 original size:15 final size:15
Alignment explanation
Indices: 65256377--65256486 Score: 53
Period size: 16 Copynumber: 6.9 Consensus size: 15
65256367 TTTTCACTCA
65256377 CTTTTTCTTTTTCTT
1 CTTTTTCTTTTTCTT
*
65256392 CTTTTTCTTTTATCGCT
1 CTTTTTCTTTT-TC-TT
* *
65256409 CTCTTTTCATTCTCTT
1 CT-TTTTCTTTTTCTT
**
65256425 -TTTTTGAATTTTCTT
1 CTTTTT-CTTTTTCTT
*
65256440 TTTTTTCATTTTTCTT
1 CTTTTTC-TTTTTCTT
* * *
65256456 TTCTTTTGTATTTTC-G
1 CT-TTTTCT-TTTTCTT
65256472 CTCTTTTCTTTTTCT
1 CT-TTTTCTTTTTCT
65256487 CTCATTTGAT
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
14 4 0.05
15 24 0.32
16 25 0.34
17 14 0.19
18 7 0.09
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.72
Consensus pattern (15 bp):
CTTTTTCTTTTTCTT
Found at i:65256443 original size:17 final size:17
Alignment explanation
Indices: 65256418--65256470 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
65256408 TCTCTTTTCA
*
65256418 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
65256435 TTC-TTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
65256451 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
65256468 TTC
1 TTC
65256471 GCTCTTTTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:65256444 original size:16 final size:16
Alignment explanation
Indices: 65256418--65256470 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
65256408 TCTCTTTTCA
65256418 TTCTCTTTTTTTGAATT
1 TTCT-TTTTTTTGAATT
* *
65256435 TTCTTTTTTTTCATTT
1 TTCTTTTTTTTGAATT
*
65256451 TTCTTTTCTTTTGTATT
1 TTCTTTT-TTTTGAATT
65256468 TTC
1 TTC
65256471 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (16 bp):
TTCTTTTTTTTGAATT
Found at i:65259032 original size:24 final size:23
Alignment explanation
Indices: 65258978--65259033 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
65258968 GATTAATTAA
**
65258978 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
65259001 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
65259025 GAAATGGTA
1 GAAATGGTA
65259034 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:65261391 original size:10 final size:10
Alignment explanation
Indices: 65261378--65261432 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
65261368 AGCTCAACTC
*
65261378 AGCTCATTTG
1 AGCTCGTTTG
* *
65261388 AGCTTGTTTC
1 AGCTCGTTTG
65261398 AGCTCGTTTG
1 AGCTCGTTTG
* *
65261408 AGCTTGTTTC
1 AGCTCGTTTG
65261418 AGCTCGTTTG
1 AGCTCGTTTG
65261428 AGCTC
1 AGCTC
65261433 AACTGAGCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.42
Consensus pattern (10 bp):
AGCTCGTTTG
Found at i:65261399 original size:20 final size:20
Alignment explanation
Indices: 65261376--65261431 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
65261366 CCAGCTCAAC
*
65261376 TCAGCTCATTTGAGCTTGTT
1 TCAGCTCGTTTGAGCTTGTT
65261396 TCAGCTCGTTTGAGCTTGTT
1 TCAGCTCGTTTGAGCTTGTT
65261416 TCAGCTCGTTTGAGCT
1 TCAGCTCGTTTGAGCT
65261432 CAACTGAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (20 bp):
TCAGCTCGTTTGAGCTTGTT
Found at i:65262974 original size:10 final size:11
Alignment explanation
Indices: 65262952--65262988 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
65262942 AAAAGAGAAG
65262952 AAATTCAAAAA
1 AAATTCAAAAA
65262963 AAATTCAAAAA
1 AAATTCAAAAA
*
65262974 AAAATCGAAAAA
1 AAATTC-AAAAA
65262986 AAA
1 AAA
65262989 AAGAAGTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:65262975 original size:12 final size:12
Alignment explanation
Indices: 65262952--65262989 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
65262942 AAAAGAGAAG
65262952 AAATTC-AAAAA
1 AAATTCAAAAAA
65262963 AAATTCAAAAAA
1 AAATTCAAAAAA
65262975 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
65262987 AAA
1 AAA
65262990 AGAAGTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:65264084 original size:6 final size:6
Alignment explanation
Indices: 65264052--65264159 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
65264042 AAAGAAATTG
* * ** *
65264052 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
65264099 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
65264150 AAAGAA AAAG
1 AAAGAA AAAG
65264160 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:65264139 original size:14 final size:13
Alignment explanation
Indices: 65264120--65264157 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
65264110 AAAAGTGAGA
65264120 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
65264132 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
65264147 GAAAAAGAAAA
1 GAAAAAGAAAA
65264158 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:65264194 original size:12 final size:12
Alignment explanation
Indices: 65264163--65264194 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
65264153 GAAAAAGCGA
*
65264163 AAAAAGAATTTG
1 AAAAAGAGTTTG
65264175 AAAAAGAGTTTG
1 AAAAAGAGTTTG
65264187 AAAAAGAG
1 AAAAAGAG
65264195 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:65269254 original size:28 final size:27
Alignment explanation
Indices: 65269223--65269308 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 27
65269213 GTGTCTTATT
* *
65269223 TTAATATATGTTTTAAATGTGTCTTAGC
1 TTAATACATGTTTT-AATGTGTCCTAGC
*
65269251 TTAAATACATGTTATTAATATGTCCTAGC
1 TT-AATACATGTT-TTAATGTGTCCTAGC
*
65269280 TTAAAACATGCTTTTAATGTGTCCTAGC
1 TTAATACATG-TTTTAATGTGTCCTAGC
65269308 T
1 T
65269309 GCTACCGGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 24 0.48
29 24 0.48
30 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (27 bp):
TTAATACATGTTTTAATGTGTCCTAGC
Found at i:65269274 original size:29 final size:28
Alignment explanation
Indices: 65269225--65269308 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 28
65269215 GTCTTATTTT
* *
65269225 AATATATGTTTTAAATGTGTCTTAGCTTA
1 AATACATGTTTT-AATGTGTCCTAGCTTA
*
65269254 AATACATGTTATTAATATGTCCTAGCTTA
1 AATACATGTT-TTAATGTGTCCTAGCTTA
65269283 AA-ACATGCTTTTAATGTGTCCTAGCT
1 AATACATG-TTTTAATGTGTCCTAGCT
65269309 GCTACCGGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 20 0.41
29 27 0.55
30 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (28 bp):
AATACATGTTTTAATGTGTCCTAGCTTA
Found at i:65272406 original size:9 final size:10
Alignment explanation
Indices: 65272399--65272455 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
65272389 AAGAGAAAAC
65272399 AAAGAAAAGA
1 AAAGAAAAGA
65272409 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
65272421 AAAGAAGA-A
1 AAAGAAAAGA
65272430 AAAGAAAATGA
1 AAAGAAAA-GA
65272441 AATA-AAAAGA
1 AA-AGAAAAGA
65272451 AAAGA
1 AAAGA
65272456 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:65272422 original size:21 final size:20
Alignment explanation
Indices: 65272388--65272455 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
65272378 ACATTCTTGT
65272388 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
65272409 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
65272430 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
65272451 AAAGA
1 AAAGA
65272456 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:65272423 original size:6 final size:5
Alignment explanation
Indices: 65272399--65272455 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65272389 AAGAGAAAAC
*
65272399 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
65272446 AAAGA AAAGA
1 AAAGA AAAGA
65272456 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:65272430 original size:15 final size:14
Alignment explanation
Indices: 65272399--65272455 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65272389 AAGAGAAAAC
65272399 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
65272415 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
65272430 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
65272446 AAAGAAAAGA
1 AAAGAAAAGA
65272456 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:65272535 original size:11 final size:12
Alignment explanation
Indices: 65272503--65272533 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65272493 TTGAGAGAAC
65272503 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65272515 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65272527 TTGAAAA
1 TTGAAAA
65272534 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:65272570 original size:30 final size:31
Alignment explanation
Indices: 65272536--65272617 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
65272526 TTTGAAAAGC
*
65272536 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
65272566 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
65272596 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
65272618 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:65272590 original size:24 final size:24
Alignment explanation
Indices: 65272541--65272610 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
65272531 AAAGCAAAAA
*
65272541 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
65272565 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
65272589 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
65272611 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:65274772 original size:30 final size:30
Alignment explanation
Indices: 65274738--65274825 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
65274728 CTAGATCATA
65274738 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
65274768 TTCAGCTTAGGAGTTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
65274798 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
65274826 TTTTATTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:65277562 original size:30 final size:30
Alignment explanation
Indices: 65277528--65277624 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65277518 TAAACTAAAA
65277528 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65277558 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65277588 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65277618 TGAGCTA
1 TGAGCTA
65277625 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65279805 original size:30 final size:31
Alignment explanation
Indices: 65279734--65279813 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
65279724 CTTTTGTTTC
*
65279734 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATCTTCTTTTTCAATCTCA
*
65279765 AATTTC-TTTTCGT-TCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATCT-TCTTTTTCAATCTCA
* *
65279794 ATTTTCTTTTTCATTTTCTT
1 AATTTCTTTTTCATCTTCTT
65279814 CTTGCTTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 6 0.14
30 29 0.69
31 7 0.17
ACGTcount: A:0.14, C:0.23, G:0.01, T:0.62
Consensus pattern (31 bp):
AATTTCTTTTTCATCTTCTTTTTCAATCTCA
Found at i:65279907 original size:6 final size:6
Alignment explanation
Indices: 65279898--65279952 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
65279888 TTTCTTTTTA
*
65279898 TTTCTT TTTCTT TTTC-- -TTCTT TTTCTT TTTCTT TTCTCTT CTTTGTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT-TCTT -TTTCTT
65279945 TTCTCTT T
1 TT-TCTT T
65279953 ACAAGGATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.07
6 25 0.61
7 11 0.27
8 2 0.05
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:65279908 original size:16 final size:15
Alignment explanation
Indices: 65279887--65279930 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
65279877 CTTGCCTCTC
*
65279887 TTTTCTTTTTATTTCT
1 TTTTCTTTTT-CTTCT
65279903 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
65279918 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
65279931 TTCTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:65279946 original size:25 final size:23
Alignment explanation
Indices: 65279887--65279948 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 23
65279877 CTTGCCTCTC
*
65279887 TTTTCTT-TTTATTTCTTTTTCT
1 TTTTCTTCTTTTTTTCTTTTTCT
65279909 TTTTCTTC--TTTTTCTTTTTCT
1 TTTTCTTCTTTTTTTCTTTTTCT
65279930 TTTCTCTTCTTTGTTTTCT
1 TTT-TCTTCTTT-TTTTCT
65279949 CTTTACAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 15 0.44
22 12 0.35
24 1 0.03
25 6 0.18
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTTCTTCTTTTTTTCTTTTTCT
Found at i:65281766 original size:20 final size:21
Alignment explanation
Indices: 65281741--65281786 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
65281731 AGTTCCCATC
*
65281741 AGCTCACTTGAGCTCG-TTTT
1 AGCTCACTTGAGCTCGAATTT
*
65281761 AGCTCATTTGAGCTCGAATTT
1 AGCTCACTTGAGCTCGAATTT
65281782 AGCTC
1 AGCTC
65281787 GTTTCAGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (21 bp):
AGCTCACTTGAGCTCGAATTT
Found at i:65282028 original size:13 final size:13
Alignment explanation
Indices: 65282010--65282038 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65282000 AATAGTTGTG
65282010 TGTTATTTAATTA
1 TGTTATTTAATTA
65282023 TGTTATTTAATTA
1 TGTTATTTAATTA
65282036 TGT
1 TGT
65282039 AGGTTAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:65284329 original size:22 final size:23
Alignment explanation
Indices: 65284292--65284335 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
65284282 GACCTCTTTG
65284292 AACCATTACCAATTCGTACCAAA
1 AACCATTACCAATTCGTACCAAA
*
65284315 AACCA-TACCATTTCGTACCAA
1 AACCATTACCAATTCGTACCAA
65284336 TTCCATACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.23
Consensus pattern (23 bp):
AACCATTACCAATTCGTACCAAA
Found at i:65284343 original size:21 final size:21
Alignment explanation
Indices: 65284298--65284360 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
65284288 TTTGAACCAT
* **
65284298 TACCAATTCGTACCAAAAACCA
1 TACCATTTCGTACC-AATTCCA
65284320 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* **
65284341 TACTATTTCAAACCAATTCC
1 TACCATTTCGTACCAATTCC
65284361 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.37, C:0.32, G:0.03, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:65284525 original size:215 final size:215
Alignment explanation
Indices: 65284154--65284585 Score: 864
Period size: 215 Copynumber: 2.0 Consensus size: 215
65284144 CAAACAGATG
65284154 AATGCACAGTAAAACCTTTGGTTCATACTTTCCTAAGTATCGGGTCAAGGTCCTTTTCAACCATT
1 AATGCACAGTAAAACCTTTGGTTCATACTTTCCTAAGTATCGGGTCAAGGTCCTTTTCAACCATT
65284219 TCCAATTCATTTAGGTCCTATAAGTTTCGGGTCGACACTTTTCTTTAGTGTTGGTTCATTCTTGA
66 TCCAATTCATTTAGGTCCTATAAGTTTCGGGTCGACACTTTTCTTTAGTGTTGGTTCATTCTTGA
65284284 CCTCTTTGAACCATTACCAATTCGTACCAAAAACCATACCATTTCGTACCAATTCCATACTATTT
131 CCTCTTTGAACCATTACCAATTCGTACCAAAAACCATACCATTTCGTACCAATTCCATACTATTT
65284349 CAAACCAATTCCCAAATACC
196 CAAACCAATTCCCAAATACC
65284369 AATGCACAGTAAAACCTTTGGTTCATACTTTCCTAAGTATCGGGTCAAGGTCCTTTTCAACCATT
1 AATGCACAGTAAAACCTTTGGTTCATACTTTCCTAAGTATCGGGTCAAGGTCCTTTTCAACCATT
65284434 TCCAATTCATTTAGGTCCTATAAGTTTCGGGTCGACACTTTTCTTTAGTGTTGGTTCATTCTTGA
66 TCCAATTCATTTAGGTCCTATAAGTTTCGGGTCGACACTTTTCTTTAGTGTTGGTTCATTCTTGA
65284499 CCTCTTTGAACCATTACCAATTCGTACCAAAAACCATACCATTTCGTACCAATTCCATACTATTT
131 CCTCTTTGAACCATTACCAATTCGTACCAAAAACCATACCATTTCGTACCAATTCCATACTATTT
65284564 CAAACCAATTCCCAAATACC
196 CAAACCAATTCCCAAATACC
65284584 AA
1 AA
65284586 AACGTACCAA
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 217 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (215 bp):
AATGCACAGTAAAACCTTTGGTTCATACTTTCCTAAGTATCGGGTCAAGGTCCTTTTCAACCATT
TCCAATTCATTTAGGTCCTATAAGTTTCGGGTCGACACTTTTCTTTAGTGTTGGTTCATTCTTGA
CCTCTTTGAACCATTACCAATTCGTACCAAAAACCATACCATTTCGTACCAATTCCATACTATTT
CAAACCAATTCCCAAATACC
Found at i:65284544 original size:22 final size:23
Alignment explanation
Indices: 65284507--65284550 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
65284497 GACCTCTTTG
65284507 AACCATTACCAATTCGTACCAAA
1 AACCATTACCAATTCGTACCAAA
*
65284530 AACCA-TACCATTTCGTACCAA
1 AACCATTACCAATTCGTACCAA
65284551 TTCCATACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.23
Consensus pattern (23 bp):
AACCATTACCAATTCGTACCAAA
Found at i:65284558 original size:21 final size:21
Alignment explanation
Indices: 65284513--65284575 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
65284503 TTTGAACCAT
* **
65284513 TACCAATTCGTACCAAAAACCA
1 TACCATTTCGTACC-AATTCCA
65284535 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* **
65284556 TACTATTTCAAACCAATTCC
1 TACCATTTCGTACCAATTCC
65284576 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.37, C:0.32, G:0.03, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:65286683 original size:20 final size:20
Alignment explanation
Indices: 65286660--65286706 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
65286650 GGGTTAAGAT
*
65286660 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
65286680 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
65286700 TGAGCTG
1 TGAGCTG
65286707 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:65287624 original size:11 final size:11
Alignment explanation
Indices: 65287608--65287632 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65287598 TGTGGTGAGG
65287608 ATTTGAAAATT
1 ATTTGAAAATT
65287619 ATTTGAAAATT
1 ATTTGAAAATT
65287630 ATT
1 ATT
65287633 ATGGAATGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTTGAAAATT
Found at i:65292378 original size:25 final size:24
Alignment explanation
Indices: 65292338--65292395 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 24
65292328 TTGTAGATTC
65292338 AAAAAAAAATCGAAAAAAAAATCG
1 AAAAAAAAATCGAAAAAAAAATCG
* *
65292362 AAAAAAAAATTGAAAAAAAAAATTG
1 AAAAAAAAATCG-AAAAAAAAATCG
65292387 AAAAAAAAA
1 AAAAAAAAA
65292396 ATTTGCATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.10
Consensus pattern (24 bp):
AAAAAAAAATCGAAAAAAAAATCG
Found at i:65292398 original size:13 final size:12
Alignment explanation
Indices: 65292338--65292395 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
65292328 TTGTAGATTC
*
65292338 AAAAAAAAATCG
1 AAAAAAAAATTG
*
65292350 AAAAAAAAATCG
1 AAAAAAAAATTG
65292362 AAAAAAAAATTG
1 AAAAAAAAATTG
65292374 AAAAAAAAAATTG
1 -AAAAAAAAATTG
65292387 AAAAAAAAA
1 AAAAAAAAA
65292396 ATTTGCATAC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
12 32 0.73
13 12 0.27
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:65298389 original size:15 final size:15
Alignment explanation
Indices: 65298369--65298423 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
65298359 ACTCTCCTCA
*
65298369 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
65298384 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
65298399 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
65298413 TTCTTTT-TCTC
1 TTCTTTTCTCTC
65298424 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:65303795 original size:17 final size:18
Alignment explanation
Indices: 65303756--65303797 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
65303746 AAGAAGAAAA
65303756 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
65303773 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
65303790 TCAAAAGA
1 ACAAAAGA
65303798 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:65307382 original size:30 final size:29
Alignment explanation
Indices: 65307283--65307384 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
65307273 CGAGTTTAAA
*
65307283 CTAAAATGAGCTAA-GTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
65307311 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
65307341 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
65307371 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
65307385 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 5 0.09
29 10 0.18
30 38 0.69
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:65309579 original size:12 final size:12
Alignment explanation
Indices: 65309564--65309594 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65309554 TTCTTTTTGC
65309564 TTTTCAAAGGCT
1 TTTTCAAAGGCT
65309576 TTTTCAAAGGCT
1 TTTTCAAAGGCT
65309588 TTTTCAA
1 TTTTCAA
65309595 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:65309671 original size:6 final size:6
Alignment explanation
Indices: 65309655--65309704 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
65309645 TTTCTTTTTA
*
65309655 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
65309704 T
1 T
65309705 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:65309687 original size:37 final size:37
Alignment explanation
Indices: 65309644--65309714 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
65309634 CTTGCCTCTC
65309644 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
65309681 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
65309715 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:65309715 original size:16 final size:16
Alignment explanation
Indices: 65309640--65309700 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
65309630 GCCTCTTGCC
*
65309640 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
65309656 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
65309672 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
65309688 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
65309701 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:65312425 original size:30 final size:30
Alignment explanation
Indices: 65312391--65312487 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
65312381 TAAACTAAAA
65312391 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65312421 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
65312451 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
65312480 ATGAGCTA
1 -TGAGCTA
65312488 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65325979 original size:40 final size:40
Alignment explanation
Indices: 65325869--65325965 Score: 151
Period size: 40 Copynumber: 2.4 Consensus size: 40
65325859 ACCCCGTATT
* *
65325869 AGTCCCGAAGGCATTTGTGTGAGTTACTA-AATCCGGGTTA
1 AGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTA
65325909 AGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTA
1 AGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTA
*
65325949 TGTCCCGAAGGCATTTG
1 AGTCCCGAAGGCATTTG
65325966 AACGAGTAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
40 51 0.96
41 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
AGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTA
Found at i:65330464 original size:13 final size:12
Alignment explanation
Indices: 65330446--65330478 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
65330436 ATAGGTACGT
65330446 AAAAAAAATTGA
1 AAAAAAAATTGA
65330458 AAAAAAAATTGA
1 AAAAAAAATTGA
65330470 AAAGAAAAA
1 AAA-AAAAA
65330479 AAAAATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:65331300 original size:15 final size:15
Alignment explanation
Indices: 65331268--65331301 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
65331258 GTTCAACGAA
*
65331268 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
65331283 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
65331298 GAGG
1 GAGG
65331302 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:65335522 original size:11 final size:12
Alignment explanation
Indices: 65335503--65335535 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65335493 CATTCTAATA
65335503 AATTAAGTTT-T
1 AATTAAGTTTAT
*
65335514 AATTTAGTTTAT
1 AATTAAGTTTAT
65335526 AATTAAGTTT
1 AATTAAGTTT
65335536 GCTACAGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (12 bp):
AATTAAGTTTAT
Found at i:65340361 original size:18 final size:18
Alignment explanation
Indices: 65340340--65340374 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65340330 TTTTTCTTTT
65340340 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
65340358 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
65340375 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:65341312 original size:14 final size:15
Alignment explanation
Indices: 65341249--65341315 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 15
65341239 AGACTTTTCA
*
65341249 CTTTTTTTGT-TCTT
1 CTTTTTTTGTCACTT
* *
65341263 CTTTTTTTTTAAC-T
1 CTTTTTTTGTCACTT
65341277 CGATTTTTTTGTCACTT
1 C--TTTTTTTGTCACTT
*
65341294 CTTTTTTTTTC-CTT
1 CTTTTTTTGTCACTT
65341308 -TTTTTTTG
1 CTTTTTTTG
65341316 AAATTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
13 7 0.16
14 14 0.33
15 10 0.23
16 10 0.23
17 2 0.05
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (15 bp):
CTTTTTTTGTCACTT
Found at i:65343469 original size:30 final size:29
Alignment explanation
Indices: 65343435--65343537 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
65343425 AGCTCACTCC
*
65343435 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTT-AGCTCACGAGCTAAACCT
* * * * *
65343465 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTC-ACTTTAGCTCACGAGCTAAACCT
* *
65343495 CAGCTCAGCTTTAGCTCACGAGCTAAAGCT
1 TAGCTCA-CTTTAGCTCACGAGCTAAACCT
*
65343525 TAGCTCATTTTAG
1 TAGCTCACTTTAG
65343538 TTTAAACTCG
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
29 6 0.11
30 45 0.80
31 5 0.09
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (29 bp):
TAGCTCACTTTAGCTCACGAGCTAAACCT
Found at i:65344696 original size:18 final size:18
Alignment explanation
Indices: 65344673--65344708 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
65344663 GTTGTAAAGT
65344673 TTTATTTTTATTTA-TTTA
1 TTTA-TTTTATTTAGTTTA
65344691 TTTATTTTATTTAGTTTA
1 TTTATTTTATTTAGTTTA
65344709 AATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTAGTTTA
Found at i:65347053 original size:18 final size:18
Alignment explanation
Indices: 65347032--65347070 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
65347022 GATTGAGAGT
* *
65347032 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
65347050 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
65347068 GAA
1 GAA
65347071 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:65348600 original size:30 final size:30
Alignment explanation
Indices: 65348566--65348661 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
65348556 AAACTAAAAA
65348566 GAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
1 GAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
* * * * * *
65348596 GAGCTGAGGC-TAAACTCCTAAGCTGAAGTT
1 GAGCT-AAGCTTTAGCTCGTGAGCTAAAGTT
* * *
65348626 GAGCTGAGGTTTAGCTCGTGAGTTGAAAG-T
1 GAGCTAAGCTTTAGCTCGTGAGCT-AAAGTT
65348656 GAGCTA
1 GAGCTA
65348662 GGAGTGAGCT
Statistics
Matches: 47, Mismatches: 16, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
29 1 0.02
30 40 0.85
31 6 0.13
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (30 bp):
GAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
Found at i:65349015 original size:19 final size:19
Alignment explanation
Indices: 65348991--65349030 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65348981 AGCTCCCATG
65348991 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65349010 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65349029 TA
1 TA
65349031 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65350291 original size:14 final size:14
Alignment explanation
Indices: 65350269--65350316 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65350259 ACCTAAACCG
* *
65350269 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65350283 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
65350297 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
65350311 ACCATT
1 ACCATT
65350317 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65350849 original size:10 final size:10
Alignment explanation
Indices: 65350834--65350860 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65350824 TACTCCTTCA
65350834 AGCTCAAATC
1 AGCTCAAATC
65350844 AGCTCAAATC
1 AGCTCAAATC
65350854 AGCTCAA
1 AGCTCAA
65350861 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:65352496 original size:13 final size:12
Alignment explanation
Indices: 65352478--65352511 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
65352468 TATACAAGTT
65352478 TGAAAAAAAATTC
1 TGAAAAAAAA-TC
65352491 TGAAAAAAAATC
1 TGAAAAAAAATC
65352503 -GAAAAAAAA
1 TGAAAAAAAA
65352512 AGAAAAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (12 bp):
TGAAAAAAAATC
Done.