Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 111 of 161
Found at i:35306262 original size:51 final size:53
Alignment explanation
Indices: 35306193--35306300 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 53
35306183 AAAGCTTTTA
* *
35306193 CTTTGAAATACTTGAAAAAAATCAAAATTTTGTTT-TAAAAATTTAAACTTTC-
1 CTTTGAAATACTTGAAAAAAAT-AAAATTTTATTTGTAAAAATCTAAACTTTCT
* *
35306245 CTTTGAAATAAC-T-AAAAAAATATAATTTTATTTGTTAAAATCTAAACTTTCT
1 CTTTGAAAT-ACTTGAAAAAAATAAAATTTTATTTGTAAAAATCTAAACTTTCT
35306297 CTTT
1 CTTT
35306301 TTTTAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
50 10 0.20
51 23 0.47
52 14 0.29
53 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (53 bp):
CTTTGAAATACTTGAAAAAAATAAAATTTTATTTGTAAAAATCTAAACTTTCT
Found at i:35307204 original size:42 final size:43
Alignment explanation
Indices: 35307144--35307565 Score: 508
Period size: 42 Copynumber: 10.1 Consensus size: 43
35307134 CTCTAAACTA
* * *
35307144 GAAAAGTAGACGGACCTCCACACCTAGGCT-TCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
* * * *
35307186 GAAAAGTCAATAGG-CCTCCACACCT-GGGCCCCTAAATGGAAT
1 GAAAAGTAAAT-GGACCTCCACACCTAGGGTCTCTAAATGCAAT
* * * * *
35307228 GAAAAGTGAATAGACCTCTACATCTA-GGTCTCTAAATGTAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
* *
35307270 GAAAAGTAAATGGACCTCCATACCTA-GGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
* * *
35307312 GAAAAGTAAATGGACCTCTACACCTA-GATATCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
*
35307354 GAAAAGTAAACGGACCTCCACACCT-GGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
*
35307396 GAAAAGTAAATGAACCTCCACACCT-GGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
* **
35307438 GAAAAGTAAACGGACCTCCACACCT-GGGTCTCTAAATGTTAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
* * * *
35307480 GAAAGGTAAATGGACCTCTACACCTA-TGTCTCTAAATGTAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
*
35307522 GAAAGGTAAATGGACCTCCA-ACCT-GGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
35307563 GAA
1 GAA
35307566 TGTTTTCCTT
Statistics
Matches: 329, Mismatches: 44, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
41 24 0.07
42 303 0.92
43 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (43 bp):
GAAAAGTAAATGGACCTCCACACCTAGGGTCTCTAAATGCAAT
Found at i:35319199 original size:33 final size:33
Alignment explanation
Indices: 35319157--35319227 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
35319147 AGGATAGGAA
35319157 TTGGATCAAACACATACCTTTCCCATGGTGGCC
1 TTGGATCAAACACATACCTTTCCCATGGTGGCC
35319190 TTGGATCAAACACATACCTTTCCCATGGTGGCC
1 TTGGATCAAACACATACCTTTCCCATGGTGGCC
35319223 TTGGA
1 TTGGA
35319228 GCTTGGGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (33 bp):
TTGGATCAAACACATACCTTTCCCATGGTGGCC
Found at i:35322158 original size:59 final size:59
Alignment explanation
Indices: 35322062--35322180 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
35322052 ACGGACAATA
* * *
35322062 ACTGTACGTATCCTAAGAACCACCCGTCTCCTTTCCTTCTGATGAATTTGAGTAAAATG
1 ACTGTACGTATCCTAAGAAACACCCATCTCCTATCCTTCTGATGAATTTGAGTAAAATG
* *
35322121 ACTGTACGTATCCTAAGAAACGCCCATCTCCTATCCTTTTGATGAATTTGAGTAAAATG
1 ACTGTACGTATCCTAAGAAACACCCATCTCCTATCCTTCTGATGAATTTGAGTAAAATG
35322180 A
1 A
35322181 TGGTTCCAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (59 bp):
ACTGTACGTATCCTAAGAAACACCCATCTCCTATCCTTCTGATGAATTTGAGTAAAATG
Found at i:35334034 original size:14 final size:14
Alignment explanation
Indices: 35334015--35334049 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35334005 CTACGTAAAA
35334015 CGGATTCATACATG
1 CGGATTCATACATG
* *
35334029 CGGATTCTTAGATG
1 CGGATTCATACATG
35334043 CGGATTC
1 CGGATTC
35334050 GTAAATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (14 bp):
CGGATTCATACATG
Found at i:35334184 original size:4 final size:4
Alignment explanation
Indices: 35334175--35334212 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
35334165 TGGGACTTGG
*
35334175 ATAC ATAC ATAC ATAA ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
35334213 GAGGCTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:35337085 original size:11 final size:11
Alignment explanation
Indices: 35337069--35337093 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35337059 ATAGCATAAC
35337069 AAAGAAAAATA
1 AAAGAAAAATA
35337080 AAAGAAAAATA
1 AAAGAAAAATA
35337091 AAA
1 AAA
35337094 ATGAAATCCC
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:35337932 original size:50 final size:50
Alignment explanation
Indices: 35337857--35338151 Score: 313
Period size: 50 Copynumber: 5.9 Consensus size: 50
35337847 CTTCTGTCTG
*
35337857 ACTGCAATGTCAGGGAAGTAAGATTCGCCGTCGTGGCTTTAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCTTTTTA
* * **
35337907 ACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCT-TTTTA
* * * *
35337958 A-TGCAATGCCAGGGAAGTAATATTCGTCGTCGTGGCTTTAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCTTTTTA
* ** * * **
35338007 ACTGCAATGTCGGGGAAGCAAGATTTACCGTTGTGGCTTTAATCTATTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCTTTTTA
** * * * * *
35338057 ACTGCACCGCCAGGGAAGTAAGACTCGCCATCGTGGCTTTAGTCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCTTTTTA
* * * * * *
35338107 ACTGCAATTTTAGAGAAGCAAGATTCACCGTTGTGTCTTTAATCT
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCT
35338152 ACTCCGCTGC
Statistics
Matches: 192, Mismatches: 51, Indels: 4
0.78 0.21 0.02
Matches are distributed among these distances:
49 4 0.02
50 184 0.96
51 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
ACTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTGGCTTTAATCTTTTTA
Found at i:35338162 original size:100 final size:100
Alignment explanation
Indices: 35337867--35338177 Score: 442
Period size: 100 Copynumber: 3.1 Consensus size: 100
35337857 ACTGCAATGT
35337867 CAGGGAAGTAAGATTCGCCGTCGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATT
1 CAGGGAAGTAAGATTCGCCGTCGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATT
* * * **
35337932 CGCCGTTGTGGCTTTAATCTGTTCCAATGCAATGC
66 CACCGTTGTGGCTTTAATCTATTCCACTGCACCGC
* *
35337967 CAGGGAAGTAATATTCGTCGTCGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATT
1 CAGGGAAGTAAGATTCGCCGTCGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATT
*
35338032 TACCGTTGTGGCTTTAATCTATTCCACTGCACCGC
66 CACCGTTGTGGCTTTAATCTATTCCACTGCACCGC
* * * * ** *
35338067 CAGGGAAGTAAGACTCGCCATCGTGGCTTTAGTCTTTTTAACTGCAATTTTAGAGAAGCAAGATT
1 CAGGGAAGTAAGATTCGCCGTCGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATT
* * *
35338132 CACCGTTGTGTCTTTAATCTACTCCGCTGCACCGC
66 CACCGTTGTGGCTTTAATCTATTCCACTGCACCGC
* *
35338167 CTGGAAAGTAA
1 CAGGGAAGTAA
35338178 AATTACTGGC
Statistics
Matches: 188, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 188 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (100 bp):
CAGGGAAGTAAGATTCGCCGTCGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATT
CACCGTTGTGGCTTTAATCTATTCCACTGCACCGC
Found at i:35338490 original size:45 final size:45
Alignment explanation
Indices: 35338362--35338495 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
35338352 AAAATCCGCC
* *
35338362 ATCTTCGATCTACTGCACCACCAGTATGGGAAGACAAGATCTGCT
1 ATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCT
** **** *
35338407 ATCTTCGATCTACTTCA-TGCCAGTACATAAAGACAAGATATGTT
1 ATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCT
* *
35338451 TTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCT
1 ATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCT
35338496 GCTTTTCAAC
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 35 0.50
45 35 0.50
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
ATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATATGCT
Found at i:35339796 original size:7 final size:7
Alignment explanation
Indices: 35339777--35339827 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
35339767 TTGGCCTCTC
35339777 CATTTTT
1 CATTTTT
35339784 -ACTTTTT
1 CA-TTTTT
35339791 CATTTTT
1 CATTTTT
35339798 CATTTTT
1 CATTTTT
35339805 CA-TTTT
1 CATTTTT
35339811 CATTTTTT
1 CA-TTTTT
35339819 CATTTTT
1 CATTTTT
35339826 CA
1 CA
35339828 CATTTTTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.17
7 26 0.65
8 7 0.17
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:35339796 original size:14 final size:15
Alignment explanation
Indices: 35339777--35339835 Score: 72
Period size: 14 Copynumber: 4.1 Consensus size: 15
35339767 TTGGCCTCTC
35339777 CATTTTTAC-TTTTT
1 CATTTTTACATTTTT
35339791 CATTTTT-CATTTTT
1 CATTTTTACATTTTT
35339805 CA-TTTT-CATTTTTT
1 CATTTTTACA-TTTTT
35339819 CATTTTTCACATTTTT
1 CATTTTT-ACATTTTT
35339835 C
1 C
35339836 TGACTCAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.17
14 21 0.52
15 4 0.10
16 6 0.15
17 2 0.05
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (15 bp):
CATTTTTACATTTTT
Found at i:35339801 original size:21 final size:22
Alignment explanation
Indices: 35339777--35339835 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
35339767 TTGGCCTCTC
35339777 CATTTTTACTTTTTCA-TTTTT
1 CATTTTTACTTTTTCATTTTTT
*
35339798 CATTTTT-CATTTTCATTTTTT
1 CATTTTTACTTTTTCATTTTTT
35339819 CATTTTTCACATTTTTC
1 CATTTTT-AC-TTTTTC
35339836 TGACTCAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 7 0.22
21 19 0.59
23 1 0.03
24 5 0.16
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (22 bp):
CATTTTTACTTTTTCATTTTTT
Found at i:35340713 original size:15 final size:15
Alignment explanation
Indices: 35340693--35340730 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
35340683 CCTTGGCCTC
*
35340693 TCCTTTTTTTCTTTT
1 TCCTTTTTTTCATTT
35340708 TCC-TTTTTTCATTT
1 TCCTTTTTTTCATTT
*
35340722 TCATTTTTT
1 TCCTTTTTT
35340731 ATTTTGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TCCTTTTTTTCATTT
Found at i:35340716 original size:14 final size:14
Alignment explanation
Indices: 35340697--35340735 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35340687 GGCCTCTCCT
*
35340697 TTTTTTCTTTTTCC
1 TTTTTTCTTTTTCA
*
35340711 TTTTTTCATTTTCA
1 TTTTTTCTTTTTCA
*
35340725 TTTTTTATTTT
1 TTTTTTCTTTT
35340736 GACTTTGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCTTTTTCA
Found at i:35349959 original size:15 final size:15
Alignment explanation
Indices: 35349941--35349970 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35349931 ACCTCTCCTA
*
35349941 CCACGAGTTTTCATT
1 CCACGAGTATTCATT
35349956 CCACGAGTATTCATT
1 CCACGAGTATTCATT
35349971 TCAGTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (15 bp):
CCACGAGTATTCATT
Found at i:35352514 original size:15 final size:16
Alignment explanation
Indices: 35352494--35352527 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
35352484 GATAATAAAA
35352494 AAATTAACA-AAATTT
1 AAATTAACACAAATTT
35352509 AAATTAACACAAATTT
1 AAATTAACACAAATTT
35352525 AAA
1 AAA
35352528 ATTGAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTAACACAAATTT
Found at i:35352529 original size:17 final size:16
Alignment explanation
Indices: 35352493--35352530 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
35352483 TGATAATAAA
35352493 AAAATTAACAAAATTT
1 AAAATTAACAAAATTT
35352509 -AAATTAACACAAATTT
1 AAAATTAACA-AAATTT
35352525 AAAATT
1 AAAATT
35352531 GAAGTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATTAACAAAATTT
Found at i:35354802 original size:20 final size:20
Alignment explanation
Indices: 35354739--35354804 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 20
35354729 AAAAATATTT
*
35354739 TTTAAAATATTAATTACAAATA
1 TTTAAAATA-TAATT-TAAATA
35354761 TTTAATAAT-TATATTTAAATA
1 TTTAA-AATATA-ATTTAAATA
*
35354782 TTTAAAATATAATTTATATA
1 TTTAAAATATAATTTAAATA
35354802 TTT
1 TTT
35354805 TAATTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 14 0.36
21 14 0.36
22 8 0.21
23 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAAATATAATTTAAATA
Found at i:35354806 original size:21 final size:21
Alignment explanation
Indices: 35354733--35354807 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
35354723 AATAAAAAAA
*
35354733 ATATTTTTTAAAATATTAA-TT
1 ATATATTTTAAAATA-TAATTT
* *
35354754 ACAAATATTTAATAAT-TATATTT
1 ATATAT-TTTAA-AATATA-ATTT
*
35354777 AAATA-TTTAAAATATAATTT
1 ATATATTTTAAAATATAATTT
35354797 ATATATTTTAA
1 ATATATTTTAA
35354808 TTAAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 11 0.26
21 17 0.40
22 6 0.14
23 8 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATTTTAAAATATAATTT
Found at i:35357136 original size:276 final size:272
Alignment explanation
Indices: 35356643--35357188 Score: 966
Period size: 276 Copynumber: 2.0 Consensus size: 272
35356633 AAAGAAGACG
*
35356643 AACTAGGTGAGGCTCAAACAGAAAACTATCTGACACATGCAGTAAAGAAGATGGTTGGCTAGAAG
1 AACTAGGTGAGGCTCAAACAGAAAACTATCTGACACATGCAGTAAAGAAGATGGTAGGCTAGAAG
35356708 CATGATCATTTGAACAAGCAAATGGGTTAGTAGTATTATGAGGGATATGGGAAAAAGATGGGACG
66 CATGATCATTTGAACAAGCAAATGGGTTAGTAGTATTATGAGGGATATGGGAAAAAGATGGGACG
*
35356773 ATGTGACTTGGTGATGGGACAAAAGGCTGTTGAGTGGGTTGGGTACGTGATATTGATGCGATAGG
131 ATGTGACTTGGTGATGGGACAAAAGGCTGTTGAGTGGGTTGGGTACGTGATATTGATGCCATAGG
*
35356838 TGGGAGCGGGGTCTGGTTGTCAACTAAAGTAAGAAAGTATGAGTCAAGAAAAGGTTGAGTAAGGT
196 TGGGAGCGGGGTCTGGTTGTCAACTAAAGTAAG--A--ATGAGTCAAGAAAAAGTTGAGTAAGGT
35356903 CTAATGGGATTTGGGA
257 CTAATGGGATTTGGGA
**
35356919 AACTAGGTGAGGCTCAAACATCAAACTATCTGACACATGCAGTAAAGAAGATGGTAGGCTAGAAG
1 AACTAGGTGAGGCTCAAACAGAAAACTATCTGACACATGCAGTAAAGAAGATGGTAGGCTAGAAG
*
35356984 CATGATCATTTGAATAAGCAAATGGGTTAGTAGTATTATGAGGGATATGGGAAAAAGATGGGACG
66 CATGATCATTTGAACAAGCAAATGGGTTAGTAGTATTATGAGGGATATGGGAAAAAGATGGGACG
* * *
35357049 GTGTGACTTGGTGATGGGACAAAATGCTGTTGAGTGGGTTGGGTAGGTGATATTGATGCCATAGG
131 ATGTGACTTGGTGATGGGACAAAAGGCTGTTGAGTGGGTTGGGTACGTGATATTGATGCCATAGG
*
35357114 TGGGAGTGGGGTCTGGTTGTCAACTAAAGTAAGAATGAGTCAAGAAAAAGTTGAGTAAGGTCTAA
196 TGGGAGCGGGGTCTGGTTGTCAACTAAAGTAAGAATGAGTCAAGAAAAAGTTGAGTAAGGTCTAA
35357179 TGGGATTTGG
261 TGGGATTTGG
35357189 TAAATTTAAA
Statistics
Matches: 260, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
272 40 0.15
274 1 0.00
276 219 0.84
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.25
Consensus pattern (272 bp):
AACTAGGTGAGGCTCAAACAGAAAACTATCTGACACATGCAGTAAAGAAGATGGTAGGCTAGAAG
CATGATCATTTGAACAAGCAAATGGGTTAGTAGTATTATGAGGGATATGGGAAAAAGATGGGACG
ATGTGACTTGGTGATGGGACAAAAGGCTGTTGAGTGGGTTGGGTACGTGATATTGATGCCATAGG
TGGGAGCGGGGTCTGGTTGTCAACTAAAGTAAGAATGAGTCAAGAAAAAGTTGAGTAAGGTCTAA
TGGGATTTGGGA
Found at i:35360650 original size:23 final size:23
Alignment explanation
Indices: 35360624--35360691 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
35360614 GTTCTCTATT
35360624 AATTTGGATTGATTCGATTTTCA
1 AATTTGGATTGATTCGATTTTCA
* * *
35360647 AATTT-TATAGA-TC--TATT--
1 AATTTGGATTGATTCGATTTTCA
35360664 AATTTGGATTGATTCGATTTTCA
1 AATTTGGATTGATTCGATTTTCA
35360687 AATTT
1 AATTT
35360692 TATAGATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 5 0.15
18 4 0.12
19 5 0.15
21 5 0.15
22 4 0.12
23 10 0.30
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.50
Consensus pattern (23 bp):
AATTTGGATTGATTCGATTTTCA
Found at i:35360673 original size:40 final size:40
Alignment explanation
Indices: 35360618--35360699 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
35360608 GAATTGGTTC
35360618 TCTATTAATTTGGATTGATTCGATTTTCAAATTTTATAGA
1 TCTATTAATTTGGATTGATTCGATTTTCAAATTTTATAGA
35360658 TCTATTAATTTGGATTGATTCGATTTTCAAATTTTATAGA
1 TCTATTAATTTGGATTGATTCGATTTTCAAATTTTATAGA
35360698 TC
1 TC
35360700 AAAAATTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (40 bp):
TCTATTAATTTGGATTGATTCGATTTTCAAATTTTATAGA
Found at i:35365045 original size:29 final size:29
Alignment explanation
Indices: 35365012--35365293 Score: 492
Period size: 29 Copynumber: 9.7 Consensus size: 29
35365002 TATCAAATTA
35365012 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
**
35365041 GGTTAGGGTTTTTAATTAAATTAGGTTTC
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
**
35365070 GGTTAGGGTTTTTAATTAAATTAGGTTTC
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
35365099 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
35365128 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
35365157 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
35365186 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
35365215 GGTTAGGGTTTTTAATCAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
35365244 GGTTAAGGTTTTTAATCAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
35365273 GGTTAGGGTTTTTAATTAAAT
1 GGTTAGGGTTTTTAATTAAAT
35365294 CAAATAATAT
Statistics
Matches: 243, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 243 1.00
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:35367445 original size:14 final size:15
Alignment explanation
Indices: 35367428--35367461 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35367418 AATATTTATC
35367428 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
35367442 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
35367457 TAAAA
1 TAAAA
35367462 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:35367592 original size:28 final size:29
Alignment explanation
Indices: 35367559--35367616 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
35367549 TTGAAAATAT
35367559 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
35367587 TAAAAATATTTAAAATTTTCTTAAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAAA
35367616 T
1 T
35367617 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:35367694 original size:21 final size:21
Alignment explanation
Indices: 35367650--35367698 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
35367640 TAATATGGAG
*
35367650 TTGAGAGATTTTTTGAAGGAAAT
1 TTGAG-GA-TTTTGGAAGGAAAT
35367673 TGTGAGGATTTTGGAAGG-AAT
1 T-TGAGGATTTTGGAAGGAAAT
35367694 TTGAG
1 TTGAG
35367699 AGTTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 9 0.38
23 3 0.12
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.37
Consensus pattern (21 bp):
TTGAGGATTTTGGAAGGAAAT
Found at i:35367725 original size:52 final size:52
Alignment explanation
Indices: 35367653--35367752 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
35367643 TATGGAGTTG
* * * *
35367653 AGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
**
35367705 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTTTAAGGAATTTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAG
35367753 AATTTTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
Found at i:35367730 original size:22 final size:22
Alignment explanation
Indices: 35367705--35367773 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
35367695 TGAGAGTTTA
**
35367705 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTTAAGGAAATTG
*
35367727 AGAGAATTTTTTAAGGAATTTG
1 AGAGAATTTTTTAAGGAAATTG
*
35367749 AGAGAATTTTTTAATGAAATTG
1 AGAGAATTTTTTAAGGAAATTG
35367771 AGA
1 AGA
35367774 TGGGATTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.35
Consensus pattern (22 bp):
AGAGAATTTTTTAAGGAAATTG
Found at i:35369077 original size:3 final size:3
Alignment explanation
Indices: 35369069--35369102 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
35369059 TAATATTAAT
* *
35369069 TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
35369103 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35369979 original size:17 final size:18
Alignment explanation
Indices: 35369946--35369981 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35369936 TGCTCTCATG
*
35369946 TGTATTGTATTGCTTATT
1 TGTATTGTATTGATTATT
35369964 TGTATT-TATTGATTATT
1 TGTATTGTATTGATTATT
35369981 T
1 T
35369982 TTCGTTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (18 bp):
TGTATTGTATTGATTATT
Found at i:35373968 original size:106 final size:106
Alignment explanation
Indices: 35373757--35373956 Score: 355
Period size: 106 Copynumber: 1.9 Consensus size: 106
35373747 TCATGAACAA
35373757 ATGTCATTAAAAAAGGTCCACTAGAGAAAGGATTATAAAGGATTTAGTGGAATATTTTGACATTA
1 ATGTCATTAAAAAAGGTCCACTAGAGAAAGGATTATAAAGGATTTAGTGGAATATTTTGACATTA
35373822 AGCTACACCAGATGAATATTAAGTTAATGTATGATCAATGG
66 AGCTACACCAGATGAATATTAAGTTAATGTATGATCAATGG
* * *
35373863 ATGTCATTAAAAAAGGTCCACTAGAGAAAGGATTATAATGGCTTTAGTGGAATATTTTGACCTTA
1 ATGTCATTAAAAAAGGTCCACTAGAGAAAGGATTATAAAGGATTTAGTGGAATATTTTGACATTA
* *
35373928 AGCTGCATCAGATGAATATTAAGTTAATG
66 AGCTACACCAGATGAATATTAAGTTAATG
35373957 GTTTTCCAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (106 bp):
ATGTCATTAAAAAAGGTCCACTAGAGAAAGGATTATAAAGGATTTAGTGGAATATTTTGACATTA
AGCTACACCAGATGAATATTAAGTTAATGTATGATCAATGG
Found at i:35375058 original size:18 final size:18
Alignment explanation
Indices: 35374985--35375282 Score: 135
Period size: 18 Copynumber: 16.7 Consensus size: 18
35374975 TTAAATGAAA
*
35374985 TTTTTGAAACACGAAAA-
1 TTTTTAAAACACGAAAAT
*
35375002 -TTTTAGAAACAC-AAATTT
1 TTTTTA-AAACACGAAA-AT
* *
35375020 TTTTTTAAACACGACAA-
1 TTTTTAAAACACGAAAAT
* * *
35375037 TTTTTGAAACATGAGAAT
1 TTTTTAAAACACGAAAAT
*
35375055 TTTTTCAAAACACAAAAAT
1 TTTTT-AAAACACGAAAAT
*
35375074 TTTTTAAAACATGAAAA-
1 TTTTTAAAACACGAAAAT
* * * * *
35375091 TTTGTGAAACACTAGAGT
1 TTTTTAAAACACGAAAAT
** * *
35375109 CGTTGAAAACACGTAAAT
1 TTTTTAAAACACGAAAAT
* * *
35375127 TTGTGAAAACAC-AAAAA
1 TTTTTAAAACACGAAAAT
* *
35375144 TTTTTGAAACACGGAAAT
1 TTTTTAAAACACGAAAAT
* **
35375162 TTTTAGAAAACATAAAAAT
1 TTTT-TAAAACACGAAAAT
*
35375181 TTTTGAAAACACGAAAA-
1 TTTTTAAAACACGAAAAT
* ***
35375198 TTTTTGAAACACCTGAAT
1 TTTTTAAAACACGAAAAT
* **
35375216 TTTTGAAAACACGAGGA-
1 TTTTTAAAACACGAAAAT
* **
35375233 TTTTTGAAACACGAATTTT
1 TTTTTAAAACACGAA-AAT
*
35375252 TTTTTGAAAATACGAAAAT
1 TTTTT-AAAACACGAAAAT
*
35375271 TTTTGAAAACAC
1 TTTTTAAAACAC
35375283 AGAATTTTGT
Statistics
Matches: 200, Mismatches: 67, Indels: 27
0.68 0.23 0.09
Matches are distributed among these distances:
16 7 0.04
17 67 0.34
18 75 0.38
19 43 0.22
20 8 0.04
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TTTTTAAAACACGAAAAT
Found at i:35375058 original size:35 final size:34
Alignment explanation
Indices: 35374979--35375223 Score: 125
Period size: 35 Copynumber: 7.0 Consensus size: 34
35374969 TTTTTTTTAA
* *
35374979 ATGAAA-TTTTTGAAACACGAAAATTTTAGAAAC
1 ATGAAATTTTTTAAAACACGAAAATTTTTGAAAC
* * *
35375012 A-CAAATTTTTTTTTAAACACGACAATTTTTGAAAC
1 ATGAAA--TTTTTTAAAACACGAAAATTTTTGAAAC
* *
35375047 ATGAGAATTTTTTCAAAACACAAAAATTTTTTAAAAC
1 ATGA-AATTTTTT-AAAACACGAAAA-TTTTTGAAAC
* * * * * * **
35375084 ATGAAAATTTGTGAAACACTAGAGTCGTTGAAAAC
1 ATGAAATTTTTTAAAACACGAAAATTTTTG-AAAC
* * * *
35375119 ACGTAAATTTGTGAAAACACAAAAATTTTTGAAAC
1 ATG-AAATTTTTTAAAACACGAAAATTTTTGAAAC
* * **
35375154 ACGGAAATTTTTAGAAAACATAAAAATTTTTGAAAAC
1 A-TGAAATTTTT-TAAAACACGAAAATTTTTG-AAAC
* * * ***
35375191 ACGAAAATTTTTGAAACACCTGAATTTTTGAAA
1 ATGAAATTTTTTAAAACACGAAAATTTTTGAAA
35375224 ACACGAGGAT
Statistics
Matches: 160, Mismatches: 40, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
32 3 0.02
33 1 0.01
34 6 0.04
35 70 0.44
36 60 0.38
37 20 0.12
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (34 bp):
ATGAAATTTTTTAAAACACGAAAATTTTTGAAAC
Found at i:35375093 original size:54 final size:54
Alignment explanation
Indices: 35374982--35375283 Score: 240
Period size: 54 Copynumber: 5.6 Consensus size: 54
35374972 TTTTTAAATG
* * ** **
35374982 AAATTTTTGAAACACGA-AAATTTTAG-AAACACAAATTTTTTTTTAAACACGA
1 AAATTTTTGAAACACGAGAATTTTTTGAAAACACAAAAATTTTTGAAAACACGA
* * * * *
35375034 CAATTTTTGAAACATGAGAATTTTTTCAAAACACAAAAATTTTTTAAAACATGA
1 AAATTTTTGAAACACGAGAATTTTTTGAAAACACAAAAATTTTTGAAAACACGA
* * * ** ** * *
35375088 AAATTTGTGAAACACTAG-AGTCGTTGAAAACACGTAAATTTGTGAAAACACAA
1 AAATTTTTGAAACACGAGAATTTTTTGAAAACACAAAAATTTTTGAAAACACGA
* *
35375141 AAATTTTTGAAACACG-GAAATTTTTAGAAAACATAAAAATTTTTGAAAACACGA
1 AAATTTTTGAAACACGAG-AATTTTTTGAAAACACAAAAATTTTTGAAAACACGA
** * **
35375195 AAATTTTTGAAACACCTGAA-TTTTTGAAAACACGAGGATTTTTG-AAACACGA
1 AAATTTTTGAAACACGAGAATTTTTTGAAAACACAAAAATTTTTGAAAACACGA
** * *
35375247 ATTTTTTTTTGAAAATACGA-AAATTTTTGAAAACACA
1 A--AATTTTTG-AAACACGAGAATTTTTTGAAAACACA
35375284 GAATTTTGTT
Statistics
Matches: 195, Mismatches: 46, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
52 25 0.13
53 64 0.33
54 87 0.45
55 19 0.10
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (54 bp):
AAATTTTTGAAACACGAGAATTTTTTGAAAACACAAAAATTTTTGAAAACACGA
Found at i:35375224 original size:35 final size:35
Alignment explanation
Indices: 35375071--35375278 Score: 147
Period size: 35 Copynumber: 5.8 Consensus size: 35
35375061 AAAACACAAA
* * *
35375071 AATTTTTTAAAACATGAAAATTTGTGAAACA-CTAG
1 AATTTTTGAAAACACGAAAATTTTTGAAACACCT-G
* ** * * ***
35375106 AGTCGTTGAAAACACGTAAATTTGTGAAAACACAAA
1 AATTTTTGAAAACACGAAAATTTTTG-AAACACCTG
* * *
35375142 AATTTTTG-AAACACGGAAATTTTTAGAAA-ACATAAA
1 AATTTTTGAAAACACGAAAATTTTT-GAAACACCT--G
35375178 AATTTTTGAAAACACGAAAATTTTTGAAACACCTG
1 AATTTTTGAAAACACGAAAATTTTTGAAACACCTG
**
35375213 AATTTTTGAAAACACGAGGATTTTTGAAACA-C-G
1 AATTTTTGAAAACACGAAAATTTTTGAAACACCTG
*
35375246 AATTTTTTTTTGAAAATACGAAAATTTTTGAAA
1 AA----TTTTTGAAAACACGAAAATTTTTGAAA
35375279 ACACAGAATT
Statistics
Matches: 139, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
33 3 0.02
34 4 0.03
35 66 0.47
36 24 0.17
37 42 0.30
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (35 bp):
AATTTTTGAAAACACGAAAATTTTTGAAACACCTG
Found at i:35375236 original size:72 final size:71
Alignment explanation
Indices: 35374982--35375283 Score: 183
Period size: 72 Copynumber: 4.2 Consensus size: 71
35374972 TTTTTAAATG
* * * *
35374982 AAATTTTTGAAACACGAAAATTTTAGAAACAC--AAATTTTTTTTTAAACACG--ACAATTTTTG
1 AAATTTTTGAAACACAAAAATTTTTGAAACACGGAAA---TTTTTGAAACACGAAAAAATTTTTG
*
35375043 -AAACATGA
63 AAAACACGA
* * * * * * * * * **
35375051 GAATTTTTTCAAAACACAAAAATTTTTTAAAACATGAAAATTTGTGAAACAC--TAGAGTCGTTG
1 -AAATTTTT-GAAACACAAAAA-TTTTTGAAACACGGAAATTTTTGAAACACGAAAAAATTTTTG
*
35375114 AAAACACGT
63 AAAACACGA
*
35375123 AAATTTGTGAAAACACAAAAATTTTTGAAACACGGAAATTTTTAGAAA-AC-ATAAAAATTTTTG
1 AAATTTTTG-AAACACAAAAATTTTTGAAACACGGAAATTTTT-GAAACACGA-AAAAATTTTTG
35375186 AAAACACGA
63 AAAACACGA
*** * ****
35375195 AAATTTTTGAAACACCTGAATTTTTGAAAACAC-GAGGATTTTTGAAACACGAATTTTTTTTTGA
1 AAATTTTTGAAACACAAAAATTTTTG-AAACACGGA-AATTTTTGAAACACGAAAAAATTTTTGA
*
35375259 AAATACGA
64 AAACACGA
35375267 AAATTTTTGAAAACACA
1 AAATTTTTG-AAACACA
35375284 GAATTTTGTT
Statistics
Matches: 179, Mismatches: 38, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
70 27 0.15
71 67 0.37
72 75 0.42
73 7 0.04
74 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (71 bp):
AAATTTTTGAAACACAAAAATTTTTGAAACACGGAAATTTTTGAAACACGAAAAAATTTTTGAAA
ACACGA
Found at i:35375241 original size:107 final size:107
Alignment explanation
Indices: 35375026--35375228 Score: 266
Period size: 107 Copynumber: 1.9 Consensus size: 107
35375016 ATTTTTTTTT
* * * * * *
35375026 AAACACGACAATTTTTGAAACATGAGAATTTTTTCAAAACACAAAAATTTTTTAAAACATGAAAA
1 AAACACAAAAATTTTTGAAACAGGAGAATTTTTACAAAACACAAAAATTTTTGAAAACACGAAAA
*
35375091 TTTGTGAAACACTAGAGTCGTTGAAAACACGTAAATTTGTGA
66 TTTGTGAAACACTAGAATCGTTGAAAACACGTAAATTTGTGA
* *
35375133 AAACACAAAAATTTTTGAAACACGGA-AATTTTTAGAAAACATAAAAATTTTTGAAAACACGAAA
1 AAACACAAAAATTTTTGAAACA-GGAGAATTTTTACAAAACACAAAAATTTTTGAAAACACGAAA
* **
35375197 ATTTTTGAAACACCT-GAATTTTTGAAAACACG
65 ATTTGTGAAACA-CTAGAATCGTTGAAAACACG
35375229 AGGATTTTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 78 0.95
108 4 0.05
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (107 bp):
AAACACAAAAATTTTTGAAACAGGAGAATTTTTACAAAACACAAAAATTTTTGAAAACACGAAAA
TTTGTGAAACACTAGAATCGTTGAAAACACGTAAATTTGTGA
Found at i:35375296 original size:23 final size:24
Alignment explanation
Indices: 35375270--35375315 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
35375260 AATACGAAAA
35375270 TTTTTGAAAACA-CAGAATTTTGT
1 TTTTTGAAAACATCAGAATTTTGT
*
35375293 TTTTTGAAAACATGAGAATTTTG
1 TTTTTGAAAACATCAGAATTTTG
35375316 AAAGACGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTTTGAAAACATCAGAATTTTGT
Found at i:35375565 original size:20 final size:19
Alignment explanation
Indices: 35375503--35375565 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 19
35375493 CGTTGCCTTA
* *
35375503 TTTTTGAAAACACGACTATTT
1 TTTTTG-AAACACGA-AAATT
35375524 TTTTTGAAACACGAGAAAATT
1 TTTTTGAAACAC--GAAAATT
*
35375545 TTTTTGAAGACACGAAGATT
1 TTTTTGAA-ACACGAAAATT
35375565 T
1 T
35375566 CGGAACACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 13 0.36
21 17 0.47
22 6 0.17
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTTTGAAACACGAAAATT
Found at i:35375944 original size:8 final size:7
Alignment explanation
Indices: 35375924--35375978 Score: 56
Period size: 8 Copynumber: 7.1 Consensus size: 7
35375914 AATTGAACCT
35375924 TTTTTTC
1 TTTTTTC
35375931 TCTTTTGTC
1 T-TTTT-TC
35375940 TTTTTTCC
1 TTTTTT-C
35375948 TTTTTTCC
1 TTTTTT-C
35375956 TTTTTTC
1 TTTTTTC
*
35375963 TTTCTTTT
1 TTT-TTTC
35375971 TTTTTTC
1 TTTTTTC
35375978 T
1 T
35375979 CTCTTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 10 0.24
8 29 0.69
9 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:35375965 original size:15 final size:16
Alignment explanation
Indices: 35375924--35375989 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
35375914 AATTGAACCT
*
35375924 TTTTTTCTCTTTTGTC
1 TTTTTTCTCTTTTTTC
35375940 TTTTTTC-CTTTTTTCC
1 TTTTTTCTCTTTTTT-C
35375956 TTTTTTCTTTCTTTTTT-
1 TTTTTTC--TCTTTTTTC
*
35375973 TTTTCTCTCTTTTTTC
1 TTTTTTCTCTTTTTTC
35375989 T
1 T
35375990 CCTCTCTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
15 14 0.33
16 16 0.37
17 6 0.14
19 7 0.16
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:35375973 original size:14 final size:14
Alignment explanation
Indices: 35375956--35376004 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
35375946 CCTTTTTTCC
*
35375956 TTTTTTCTTTCTTTT
1 TTTTTTCTCTC-TTT
35375971 TTTTTTCTCTCTTT
1 TTTTTTCTCTCTTT
* *
35375985 TTTCTCCTCTCTTT
1 TTTTTTCTCTCTTT
35375999 TTTTTT
1 TTTTTT
35376005 TGGCCTACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTCTCTCTTT
Found at i:35375987 original size:16 final size:16
Alignment explanation
Indices: 35375923--35376005 Score: 61
Period size: 16 Copynumber: 5.4 Consensus size: 16
35375913 AAATTGAACC
35375923 TTTTTTTCTCT-TTTGT
1 TTTTTTTCTCTCTTT-T
*
35375939 CTTTTTTC-CT-TTTT
1 TTTTTTTCTCTCTTTT
*
35375953 TCCTTTTTTCTTTC-TTT
1 T--TTTTTTCTCTCTTTT
35375970 TTTTTTTCTCTC--TT
1 TTTTTTTCTCTCTTTT
* *
35375984 TTTTCTCCTCTCTTTT
1 TTTTTTTCTCTCTTTT
35376000 TTTTTT
1 TTTTTT
35376006 GGCCTACCTC
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
14 13 0.24
15 15 0.28
16 21 0.39
17 5 0.09
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTTTTCTCTCTTTT
Found at i:35376132 original size:20 final size:20
Alignment explanation
Indices: 35376104--35376161 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
35376094 GGAAATGGCC
*
35376104 TGTTGCTTTTTTTTCT-GCTT
1 TGTTTCTTTTTTTT-TGGCTT
35376124 TGTTTCTTTTTTTTTGGGCTT
1 TGTTTCTTTTTTTTT-GGCTT
35376145 TGCTTT-TTTTTTTTTGG
1 TG-TTTCTTTTTTTTTGG
35376162 GCTTGGAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 15 0.44
22 3 0.09
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.72
Consensus pattern (20 bp):
TGTTTCTTTTTTTTTGGCTT
Found at i:35376136 original size:21 final size:21
Alignment explanation
Indices: 35376110--35376165 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
35376100 GGCCTGTTGC
*
35376110 TTTTTTTTCTGCTTTG-TTTCT
1 TTTTTTTTCGGCTTTGCTTT-T
*
35376131 TTTTTTTTGGGCTTTGCTTTT
1 TTTTTTTTCGGCTTTGCTTTT
*
35376152 TTTTTTTTGGGCTT
1 TTTTTTTTCGGCTT
35376166 GGAGCTGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.00, C:0.11, G:0.16, T:0.73
Consensus pattern (21 bp):
TTTTTTTTCGGCTTTGCTTTT
Found at i:35376243 original size:7 final size:7
Alignment explanation
Indices: 35376234--35376316 Score: 89
Period size: 7 Copynumber: 11.7 Consensus size: 7
35376224 TTTATTTTTC
*
35376234 TTCTTCC
1 TTCTTCT
35376241 TTCTTCT
1 TTCTTCT
35376248 TTCTTCT
1 TTCTTCT
*
35376255 TTGTTCT
1 TTCTTCT
35376262 TTCTTCT
1 TTCTTCT
35376269 TTCTTTCT
1 TTC-TTCT
*
35376277 TTCTTTCG
1 TTC-TTCT
35376285 TTCTTCT
1 TTCTTCT
35376292 CTT-TTCT
1 -TTCTTCT
35376299 TTC-TCT
1 TTCTTCT
*
35376305 TTTTTCT
1 TTCTTCT
35376312 TTCTT
1 TTCTT
35376317 TCCCGATCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
6 7 0.11
7 42 0.65
8 16 0.25
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (7 bp):
TTCTTCT
Found at i:35376251 original size:4 final size:4
Alignment explanation
Indices: 35376244--35376318 Score: 75
Period size: 4 Copynumber: 18.8 Consensus size: 4
35376234 TTCTTCCTTC
* *
35376244 TTCT TTC- TTCT TT-G TTCT TTC- TTCT TTCT TTCT TTCT TTCG TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
35376289 TCTCTT TTCT TTCT CTTTT TTCT TTCT TTC
1 T-TC-T TTCT TTCT -TTCT TTCT TTCT TTC
35376319 CCGATCAACC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
3 8 0.14
4 42 0.71
5 7 0.12
6 2 0.03
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:35376442 original size:17 final size:18
Alignment explanation
Indices: 35376420--35376456 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
35376410 TTCCCCTATC
35376420 TTTCTTCTTTGC-TCTTT
1 TTTCTTCTTTGCTTCTTT
*
35376437 TTTCTTCTTTTCTTCTTT
1 TTTCTTCTTTGCTTCTTT
35376455 TT
1 TT
35376457 GCTTGCTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTCTTCTTTGCTTCTTT
Found at i:35376831 original size:30 final size:30
Alignment explanation
Indices: 35376797--35376892 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
35376787 GGCCAAAACA
* *
35376797 TAATTTTAAGAAAGTTTAAAGGTCAAAATG
1 TAATTTTAAGAAAATTTAAGGGTCAAAATG
* * **
35376827 TAATTTTGAGAAATTTTAAGGGTTGAAATG
1 TAATTTTAAGAAAATTTAAGGGTCAAAATG
* *
35376857 TAATTTCAA-AAAATTTAGGGGTCAAAATG
1 TAATTTTAAGAAAATTTAAGGGTCAAAATG
35376886 TAATTTT
1 TAATTTT
35376893 TTTTAAAAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
29 22 0.41
30 32 0.59
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.38
Consensus pattern (30 bp):
TAATTTTAAGAAAATTTAAGGGTCAAAATG
Found at i:35376884 original size:29 final size:29
Alignment explanation
Indices: 35376797--35376891 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
35376787 GGCCAAAACA
* * *
35376797 TAATTTTAAGAAAGTTTAAAGGTCAAAATG
1 TAATTTCAA-AAAATTTAAGGGTCAAAATG
* * * **
35376827 TAATTTTGAGAAATTTTAAGGGTTGAAATG
1 TAA-TTTCAAAAAATTTAAGGGTCAAAATG
*
35376857 TAATTTCAAAAAATTTAGGGGTCAAAATG
1 TAATTTCAAAAAATTTAAGGGTCAAAATG
35376886 TAATTT
1 TAATTT
35376892 TTTTTAAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 26 0.50
30 22 0.42
31 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (29 bp):
TAATTTCAAAAAATTTAAGGGTCAAAATG
Found at i:35377473 original size:56 final size:55
Alignment explanation
Indices: 35377377--35377487 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 55
35377367 GTATCCATTG
* *
35377377 GATGATAAATCATCATTTTTAATTTGAATAGTGCTTATGAATAATTAATTATGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATT-TGTAA
*
35377433 GATGATAAATCATCACTTTTAATTTGAATATTGCTCATGAATAATTAATTTGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGTAA
35377488 TCTATAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 5 0.10
56 47 0.90
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGTAA
Found at i:35381085 original size:18 final size:18
Alignment explanation
Indices: 35381056--35381094 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
35381046 AAAGTTGACG
35381056 TAAAATATAATTATACATT
1 TAAAATATAATTATA-ATT
35381075 TAAAA-ATAATTATAATT
1 TAAAATATAATTATAATT
35381092 TAA
1 TAA
35381095 CAGAAGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATATAATTATAATT
Found at i:35388863 original size:33 final size:33
Alignment explanation
Indices: 35388778--35388902 Score: 126
Period size: 33 Copynumber: 3.8 Consensus size: 33
35388768 GTTCTTTTTG
* * * *
35388778 TGCCATAGTCCAACTATGGTCTTACATATGTAT
1 TGCCATAGCCCAGCTATGGTCTTACATTTGTAA
* * * *
35388811 TGCCATGGCCCTGCCATGGTCTTACATTTGTAG
1 TGCCATAGCCCAGCTATGGTCTTACATTTGTAA
* * * *
35388844 TGCCATAACCCAGTTATGGTCTTATCAATAG-AA
1 TGCCATAGCCCAGCTATGGTCTTA-CATTTGTAA
35388877 TGCCATAGCCCAGCTATGGTCTTACA
1 TGCCATAGCCCAGCTATGGTCTTACA
35388903 CATGTATCTA
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
32 2 0.03
33 68 0.92
34 4 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (33 bp):
TGCCATAGCCCAGCTATGGTCTTACATTTGTAA
Found at i:35392007 original size:15 final size:16
Alignment explanation
Indices: 35391987--35392016 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35391977 GAGATAAAGC
35391987 CAAAATA-ACATAAAA
1 CAAAATATACATAAAA
35392002 CAAAATATACATAAA
1 CAAAATATACATAAA
35392017 TTCCACTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (16 bp):
CAAAATATACATAAAA
Found at i:35392716 original size:31 final size:31
Alignment explanation
Indices: 35392607--35392740 Score: 105
Period size: 31 Copynumber: 4.4 Consensus size: 31
35392597 TTAATATAAC
* * * *
35392607 ATTTGGTACCTAAACTTGATATTTCTTCCTA
1 ATTTGGTACTTAAACTTGACACTTATTCCTA
* * *** *
35392638 ATTTGGTATTTATACTT--TTTTTAGTCC-A
1 ATTTGGTACTTAAACTTGACACTTATTCCTA
*
35392666 ATTTGGTACTTAAACTTGACACTTTTTCCTA
1 ATTTGGTACTTAAACTTGACACTTATTCCTA
* * *
35392697 ATTTGGTA-TCTGAACTTGACGCTTATTCTTA
1 ATTTGGTACT-TAAACTTGACACTTATTCCTA
35392728 ATTTGGTACTTAA
1 ATTTGGTACTTAA
35392741 TCTTTTTTTC
Statistics
Matches: 80, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
28 16 0.20
29 7 0.09
30 6 0.08
31 50 0.62
32 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACACTTATTCCTA
Found at i:35395338 original size:12 final size:12
Alignment explanation
Indices: 35395303--35395345 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
35395293 TTATTAATCC
*
35395303 TATTATTATTTG
1 TATTATTATTTT
*
35395315 TACTATTATTTT
1 TATTATTATTTT
35395327 TATTATTATTTT
1 TATTATTATTTT
*
35395339 CATTATT
1 TATTATT
35395346 TCTTCTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:35397581 original size:24 final size:24
Alignment explanation
Indices: 35397549--35397624 Score: 62
Period size: 28 Copynumber: 2.9 Consensus size: 24
35397539 TCTAAGATAT
* *
35397549 TTTAGTTAATATATATTATATTTA
1 TTTATTTAATATATATTATATTAA
35397573 TTTATTTAATAAATAAGTATTATATTAA
1 TTTATTTAAT--AT-A-TATTATATTAA
*
35397601 TTATATTGTTATATTATATTATAT
1 TT-TATT-TAATA-TATATTATAT
35397625 ATATGTATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
24 9 0.21
26 2 0.05
27 9 0.21
28 14 0.33
29 5 0.12
30 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTATTTAATATATATTATATTAA
Found at i:35400970 original size:23 final size:23
Alignment explanation
Indices: 35400944--35401254 Score: 187
Period size: 22 Copynumber: 13.3 Consensus size: 23
35400934 CAACCCTGTT
* *
35400944 TTGGACAGCAATTATTCAACAAA
1 TTGGACAGCAATTATACATCAAA
*
35400967 TTGGACAGCAATAATATGC-TCAAA
1 TTGGACAGCAAT--TATACATCAAA
*
35400991 ATGGACAGC-ATTATACATCAAA
1 TTGGACAGCAATTATACATCAAA
* *
35401013 TTAGACAGCTTAAATATAC-TCAAAA
1 TTGGACAGC--AATTATACATC-AAA
35401038 TTGGACAGC-ATTATACATCAAA
1 TTGGACAGCAATTATACATCAAA
* *
35401060 TTAGACAGCTTAAATATAC-TCAAAA
1 TTGGACAGC--AATTATACATC-AAA
* * *
35401085 TCGGACAGC-ATTATATATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
35401107 ATGGACAGC-ATCAATACACTCAAAA
1 TTGGACAGCAAT-TATACA-TC-AAA
* *
35401132 TTGGACAGC-ATCATACATTAAA
1 TTGGACAGCAATTATACATCAAA
*
35401154 ATGGACAGC-ATTAGTACACTCAAAA
1 TTGGACAGCAATTA-TACA-TC-AAA
*
35401179 TTGGACAGC-ATTATACATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
35401201 ATGGACAGC-ATCAATACATTCAAAA
1 TTGGACAGCAAT-TATACA-TC-AAA
* *
35401226 TTGGACAGC-GTTATACATTAAA
1 TTGGACAGCAATTATACATCAAA
*
35401248 ATGGACA
1 TTGGACA
35401255 ACATCAATAT
Statistics
Matches: 229, Mismatches: 37, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.02
22 82 0.36
23 33 0.14
24 33 0.14
25 77 0.34
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (23 bp):
TTGGACAGCAATTATACATCAAA
Found at i:35401038 original size:25 final size:24
Alignment explanation
Indices: 35400964--35401278 Score: 164
Period size: 25 Copynumber: 13.4 Consensus size: 24
35400954 ATTATTCAAC
* *
35400964 AAATTGGACAGCAATAATATGCTCA
1 AAATTGGACAGC-TTAATATACTCA
*
35400989 AAA-TGGACAGC--ATTATACATC-
1 AAATTGGACAGCTTAATATAC-TCA
*
35401010 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGCTT-AATATACTCA
*
35401035 AAATTGGACAGC--ATTATACATC-
1 AAATTGGACAGCTTAATATAC-TCA
*
35401057 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGCTT-AATATACTCA
* *
35401082 AAATCGGACAGCATT-ATATA-TTA
1 AAATTGGACAGC-TTAATATACTCA
* *
35401105 AAA-TGGACAGCATCAATACACTCA
1 AAATTGGACAGC-TTAATATACTCA
* * * *
35401129 AAATTGGACAGCATCATACA-TTA
1 AAATTGGACAGCTTAATATACTCA
* *
35401152 AAA-TGGACAGCATTAGTACACTCA
1 AAATTGGACAGC-TTAATATACTCA
* *
35401176 AAATTGGACAGC--ATTATACATTA
1 AAATTGGACAGCTTAATATAC-TCA
* * *
35401199 AAA-TGGACAGCATCAATACATTCA
1 AAATTGGACAGC-TTAATATACTCA
* *
35401223 AAATTGGACAGCGT--TATACATTA
1 AAATTGGACAGCTTAATATAC-TCA
* *
35401246 AAA-TGGACAACATCAATATACTCA
1 AAATTGGACAGC-TTAATATACTCA
35401270 AAA-TGGACA
1 AAATTGGACA
35401279 TCAAATTTTG
Statistics
Matches: 224, Mismatches: 39, Indels: 55
0.70 0.12 0.17
Matches are distributed among these distances:
21 8 0.04
22 66 0.29
23 31 0.14
24 48 0.21
25 69 0.31
26 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (24 bp):
AAATTGGACAGCTTAATATACTCA
Found at i:35401043 original size:47 final size:47
Alignment explanation
Indices: 35400944--35401278 Score: 388
Period size: 47 Copynumber: 7.1 Consensus size: 47
35400934 CAACCCTGTT
* ** * *
35400944 TTGGACAGCAATTATTCAACAAATTGGACAGCA-ATAATATGCTCAAAA
1 TTGGACAGC-ATTATACATTAAAATGGACAGCATA-AATATACTCAAAA
* * * *
35400992 -TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
* * * *
35401038 TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
* * * *
35401085 TCGGACAGCATTATATATTAAAATGGACAGCATCAATACACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
* * * *
35401132 TTGGACAGCATCATACATTAAAATGGACAGCATTAGTACACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
* * *
35401179 TTGGACAGCATTATACATTAAAATGGACAGCATCAATACATTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
* * *
35401226 TTGGACAGCGTTATACATTAAAATGGACAACATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
35401273 -TGGACA
1 TTGGACA
35401279 TCAAATTTTG
Statistics
Matches: 259, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
46 37 0.14
47 222 0.86
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (47 bp):
TTGGACAGCATTATACATTAAAATGGACAGCATAAATATACTCAAAA
Found at i:35402328 original size:27 final size:27
Alignment explanation
Indices: 35402265--35402334 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
35402255 TTAATAAGTA
35402265 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATCAAACT
* *
35402293 CGCACACTTAGTGCTT-TACATTATACT
1 CGCACACTTAGTGCTTATA-ATCAAACT
35402320 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35402335 AATCCCATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 2 0.05
27 21 0.54
28 16 0.41
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATCAAACT
Found at i:35415836 original size:23 final size:23
Alignment explanation
Indices: 35415806--35415851 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35415796 TCCTCGCGTA
35415806 CCTACTGCTCCTACATCCAGCCC
1 CCTACTGCTCCTACATCCAGCCC
*
35415829 CCTACTGCTCCTACATCTAGCCC
1 CCTACTGCTCCTACATCCAGCCC
35415852 ATTTGTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (23 bp):
CCTACTGCTCCTACATCCAGCCC
Found at i:35419512 original size:22 final size:24
Alignment explanation
Indices: 35419486--35419535 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
35419476 CATTTTAACC
35419486 TAATTTTATATG-TTTTT-ATTTT
1 TAATTTTATATGATTTTTAATTTT
*
35419508 TAATTTTTTATGTATTTTTAATTTT
1 TAATTTTATATG-ATTTTTAATTTT
35419533 TAA
1 TAA
35419536 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
24 5 0.21
25 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TAATTTTATATGATTTTTAATTTT
Found at i:35420121 original size:31 final size:31
Alignment explanation
Indices: 35420083--35420147 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
35420073 AACGTCCCAG
* *
35420083 TGACTTAAATAAAAACTTTCGAATAGTTTAA
1 TGACTTAAATAAAAACTTTCGAACAGTTCAA
35420114 TGACTTAAATAAAAACTTTCGAACAGTTCAA
1 TGACTTAAATAAAAACTTTCGAACAGTTCAA
35420145 TGA
1 TGA
35420148 TTATTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAACAGTTCAA
Found at i:35424761 original size:23 final size:24
Alignment explanation
Indices: 35424707--35424767 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
35424697 ATATAATATG
* *
35424707 ATAATTAAATTAATTATTATGTAAT
1 ATAATTAAATTAA-TAATATATAAT
* *
35424732 GTGATTAAATTAA-AATATATAAT
1 ATAATTAAATTAATAATATATAAT
35424755 ATAATTAAATTAA
1 ATAATTAAATTAA
35424768 GTTAATAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 19 0.63
25 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATAATTAAATTAATAATATATAAT
Found at i:35435025 original size:20 final size:20
Alignment explanation
Indices: 35435000--35435039 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35434990 AATATATCTT
*
35435000 CTATTTTATAATATTATGTC
1 CTATTTTATAATATCATGTC
35435020 CTATTTTATAATATCATGTC
1 CTATTTTATAATATCATGTC
35435040 TAAAATAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (20 bp):
CTATTTTATAATATCATGTC
Found at i:35438649 original size:17 final size:17
Alignment explanation
Indices: 35438627--35438659 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35438617 TTCTAACATT
*
35438627 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
35438644 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
35438660 GTGCACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:35468470 original size:26 final size:26
Alignment explanation
Indices: 35468441--35468517 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 26
35468431 TTTAAATAAA
* *
35468441 CAGTTAATAGAATTAGTTGGTCAAAT
1 CAGTTACTAGAATCAGTTGGTCAAAT
35468467 CAGTTACTAGAATCAGTTGGTCAAAT
1 CAGTTACTAGAATCAGTTGGTCAAAT
*
35468493 CAATTACTAGAATCAGTTGGTCAAA
1 CAGTTACTAGAATCAGTTGGTCAAA
35468518 CCAGCCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (26 bp):
CAGTTACTAGAATCAGTTGGTCAAAT
Found at i:35469859 original size:20 final size:20
Alignment explanation
Indices: 35469830--35469875 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
35469820 AGGGAATGGG
*
35469830 AAGTGTGTGCCGTTTGGGGT
1 AAGTGAGTGCCGTTTGGGGT
35469850 AAGTGAGTGCCGTTTGGGGT
1 AAGTGAGTGCCGTTTGGGGT
35469870 AAGTGA
1 AAGTGA
35469876 AGGCTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.43, T:0.30
Consensus pattern (20 bp):
AAGTGAGTGCCGTTTGGGGT
Found at i:35470131 original size:14 final size:16
Alignment explanation
Indices: 35470112--35470148 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
35470102 CTTTGCCGAA
35470112 TTTTCTCTT-CTTCT-
1 TTTTCTCTTCCTTCTC
35470126 TTTTCT-TTCCTTCTC
1 TTTTCTCTTCCTTCTC
35470141 TTTTCTCT
1 TTTTCTCT
35470149 ACTAGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 6 0.30
16 1 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCTCTTCCTTCTC
Found at i:35470319 original size:13 final size:13
Alignment explanation
Indices: 35470301--35470325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35470291 TCCTTTCTCG
35470301 TTTTTCAAGTATT
1 TTTTTCAAGTATT
35470314 TTTTTCAAGTAT
1 TTTTTCAAGTAT
35470326 CGACACCTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (13 bp):
TTTTTCAAGTATT
Found at i:35470935 original size:27 final size:27
Alignment explanation
Indices: 35470840--35471230 Score: 443
Period size: 27 Copynumber: 14.4 Consensus size: 27
35470830 GTTTGGTTCA
35470840 TAAAATTA-TCGAAATACCCTCGATGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
35470867 TAAAAATTA-TCGAAATACCCTCGATGGG
1 T-AAAATTACT-GAAATACCCTCGATGGG
35470895 TAAAAATTACTGAAATACCCTCGATGGG
1 T-AAAATTACTGAAATACCCTCGATGGG
35470923 TAAAATTACTGAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * **
35470950 TAATATTATTGAAATACTATCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * * *
35470977 TAAAATTAATGAAATACCTTCAATAGG
1 TAAAATTACTGAAATACCCTCGATGGG
* *
35471004 TAAAATTACTGAAATA-CCTTGATGAG
1 TAAAATTACTGAAATACCCTCGATGGG
** * * *
35471030 TAAAATTACCAAAATACCTTCAATTGG
1 TAAAATTACTGAAATACCCTCGATGGG
*
35471057 TAGAATTA-TCGAAATACCCTCGATGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
*
35471084 TAAAATTACTGAAATACCCTCGATAGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * * *
35471111 TAAAATTACTAAAATAGCTTTGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
35471138 TAAAATTACT-AAGATACCCTCGATGGG
1 TAAAATTACTGAA-ATACCCTCGATGGG
*
35471165 TAAAATTA-TCGAAATACCCCCGATGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
* *
35471192 TAAAATTACCGAAATACCCTCAATAGGG
1 TAAAATTACTGAAATACCCTCGAT-GGG
*
35471220 TAAAATGACTG
1 TAAAATTACTG
35471231 CTAGGGTTCT
Statistics
Matches: 309, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
26 22 0.07
27 218 0.71
28 68 0.22
29 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGATGGG
Found at i:35474278 original size:27 final size:27
Alignment explanation
Indices: 35474208--35474567 Score: 393
Period size: 27 Copynumber: 13.3 Consensus size: 27
35474198 AGCTTGGGTC
*
35474208 GTAAAATTACCGAAATACCCTGGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
35474235 GTAAAAATTACCGAAATA-CCTCCGATGG
1 GT-AAAATTACCGAAATACCCT-CGATGG
* *
35474263 GTAAAATTACCAAAATACCTTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* ** *
35474290 ATAAAATTATTGAAATAGCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* **
35474317 GTAAAATTATCGAAATATCTTTC-ATGG
1 GTAAAATTACCGAAATA-CCCTCGATGG
**
35474344 GTAAAATTATTGAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* * * *
35474371 CTAAAATTACCAAAATACCCTCCATGA
1 GTAAAATTACCGAAATACCCTCGATGG
* * *
35474398 GTAAAATTACTGAAATACCCTTGATTG
1 GTAAAATTACCGAAATACCCTCGATGG
* ** *
35474425 GTAAAACTACTAAAATACCCTTGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
**
35474452 GTAAAATTATTGAAATACCC-CTGATGG
1 GTAAAATTACCGAAATACCCTC-GATGG
*
35474479 GTAAAATTACTGAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* **
35474506 GTAAAATTATCGAAATACCCTTAATGG
1 GTAAAATTACCGAAATACCCTCGATGG
35474533 GTAAAATTACCGAAATACCCTCGATAGG
1 GTAAAATTACCGAAATACCCTCGAT-GG
35474561 GTAAAAT
1 GTAAAAT
35474568 GACTGATAGG
Statistics
Matches: 280, Mismatches: 45, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
26 3 0.01
27 241 0.86
28 36 0.13
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.27
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCTCGATGG
Found at i:35474773 original size:26 final size:25
Alignment explanation
Indices: 35474706--35474784 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
35474696 GGCTCTACCA
35474706 CACACATACTGATACTAGTGGCTCTGC
1 CACA-ATACTG-TACTAGTGGCTCTGC
* * * *
35474733 CACAATTCTATTACTGGTGGCTTTGC
1 CACAATACT-GTACTAGTGGCTCTGC
**
35474759 CACATATACTGTACTAGCAGCTCTGC
1 CACA-ATACTGTACTAGTGGCTCTGC
35474785 TGCGTTATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
26 32 0.80
27 8 0.20
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (25 bp):
CACAATACTGTACTAGTGGCTCTGC
Found at i:35477694 original size:18 final size:20
Alignment explanation
Indices: 35477657--35477694 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
35477647 AAATGGATTC
35477657 TTGAAATGAAAATGTGAGATG
1 TTGAAATGAAAA-GTGAGATG
35477678 TTGAAA-GAAAA-TGAGAT
1 TTGAAATGAAAAGTGAGAT
35477695 TATTAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGAAATGAAAAGTGAGATG
Found at i:35482446 original size:37 final size:37
Alignment explanation
Indices: 35482385--35482487 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
35482375 ATCCCTGTTT
* * * *
35482385 TGGCGTGTTTTTGGTTGGACTAGCTCTTATGAGCATC
1 TGGCGTGTTATCGGGTGGATTAGCTCTTATGAGCATC
35482422 TGGCGTGTTATCGGGTGGATTAGCTCTTATGAGCATC
1 TGGCGTGTTATCGGGTGGATTAGCTCTTATGAGCATC
* *
35482459 TGACGTGTTATCGGGTGGATTAACTCTTA
1 TGGCGTGTTATCGGGTGGATTAGCTCTTA
35482488 CGAGTGATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.38
Consensus pattern (37 bp):
TGGCGTGTTATCGGGTGGATTAGCTCTTATGAGCATC
Found at i:35492467 original size:19 final size:18
Alignment explanation
Indices: 35492433--35492468 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35492423 AGTTTTCTCA
*
35492433 AAATGGAAATAGAAATGG
1 AAATGAAAATAGAAATGG
35492451 AAATGAAAATGAGAAATG
1 AAATGAAAAT-AGAAATG
35492469 ATTCATTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (18 bp):
AAATGAAAATAGAAATGG
Found at i:35494105 original size:362 final size:354
Alignment explanation
Indices: 35493448--35494166 Score: 1303
Period size: 362 Copynumber: 2.0 Consensus size: 354
35493438 TAGTTTTTAG
35493448 TTAAAGGACTCAATTGTTAAAATATTAAAATTGATAGGGAATTAATGTGAATTTAGAATAATTAT
1 TTAAAGGACTCAATTGTTAAAATATTAAAATTGATAGGGAATTAATGTGAATTTAGAATAATTAT
35493513 GGGTTTTAGTTGTATAAGTAAAATTTTGGTTAACATGAGAAATTATGAAATTTTGATAAATTTGG
66 GGGTTTTAGTTGTATAAGTAAAATTTTGGTTAACATGAGAAATTATGAAATTTTGATAAATTTGG
*
35493578 AATTTTGGGTTTATGGACTAAATTGTAAAAAATGTAAAAGTTTAGGGAAAGTAAATAAATAATAA
131 AATTTTGGGTTTAGGGACTAAATTGTAAAAAATGTAAAAGTTTAGGGAAAGTAAATAAATAATAA
35493643 AACTTAAGGGTCATATGCATATAATGAGTTGGAATATGTATCTAAATTTGATATATTGAATTTAA
196 AACTTAAGGGTCATATGCATATAATGAGTTGGAATATGTATCTAAATTTGATATATTGAATTTAA
35493708 TCATTATATAGATCAAGTATCGAATTGTACGGAGGTGAATTAGGGAAAAGAGAAAATTTTGGATT
261 TCATTATATAGATCAAGTATCGAATTGTACGGAGGTGAATTAGGGAAAAGAGAAAATTTTGGATT
35493773 AGTCCCTACGAGTCAACGAAAAACATAAA
326 AGTCCCTACGAGTCAACGAAAAACATAAA
35493802 TTAAAGGACTCAATTGTTAAAATATTAAAATTGATAGGGAATTAATGTGAATTTAGAATAATTAT
1 TTAAAGGACTCAATTGTTAAAATATTAAAATTGATAGGGAATTAATGTGAATTTAGAATAATTAT
*
35493867 GGGTTTTGGTTGTATAAGTAAAATTTTGGTTAACATGAGAAATTATGAAATTTTGATAAATTTGG
66 GGGTTTTAGTTGTATAAGTAAAATTTTGGTTAACATGAGAAATTATGAAATTTTGAT--A-----
* *
35493932 AATTTTGGAATTTTGGGTTTAGGGACTAAATTGTGAAAAATGTAAAATTTTAGGGAAAGTAAATA
124 AA-TTTGGAATTTTGGGTTTAGGGACTAAATTGTAAAAAATGTAAAAGTTTAGGGAAAGTAAATA
*
35493997 AATAATAAAACTTAAGGGTCATATGCATATAATGAGTTGGAATATGTATCTGAATTTGATATATT
188 AATAATAAAACTTAAGGGTCATATGCATATAATGAGTTGGAATATGTATCTAAATTTGATATATT
*
35494062 GAATTTAATCATTATATAGATCAAGTATCGAATTGTACGGAGGTGAATTAGGGAAAAGATAAAAT
253 GAATTTAATCATTATATAGATCAAGTATCGAATTGTACGGAGGTGAATTAGGGAAAAGAGAAAAT
*
35494127 TTTGGATTAGTCCCTACGAGTCAACTAAAAACATAAA
318 TTTGGATTAGTCCCTACGAGTCAACGAAAAACATAAA
35494164 TTA
1 TTA
35494167 GGTACGTTCA
Statistics
Matches: 350, Mismatches: 7, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
354 121 0.35
356 1 0.00
361 2 0.01
362 226 0.65
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (354 bp):
TTAAAGGACTCAATTGTTAAAATATTAAAATTGATAGGGAATTAATGTGAATTTAGAATAATTAT
GGGTTTTAGTTGTATAAGTAAAATTTTGGTTAACATGAGAAATTATGAAATTTTGATAAATTTGG
AATTTTGGGTTTAGGGACTAAATTGTAAAAAATGTAAAAGTTTAGGGAAAGTAAATAAATAATAA
AACTTAAGGGTCATATGCATATAATGAGTTGGAATATGTATCTAAATTTGATATATTGAATTTAA
TCATTATATAGATCAAGTATCGAATTGTACGGAGGTGAATTAGGGAAAAGAGAAAATTTTGGATT
AGTCCCTACGAGTCAACGAAAAACATAAA
Found at i:35494553 original size:20 final size:20
Alignment explanation
Indices: 35494516--35494555 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35494506 CTTGTATGGG
*
35494516 ATTGCACTTTGGTGCCTCTA
1 ATTGCACTTTGGTACCTCTA
35494536 ATTGCACATTT-GTACCTCTA
1 ATTGCAC-TTTGGTACCTCTA
35494556 TTACGCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (20 bp):
ATTGCACTTTGGTACCTCTA
Found at i:35499641 original size:20 final size:20
Alignment explanation
Indices: 35499616--35499762 Score: 89
Period size: 20 Copynumber: 7.3 Consensus size: 20
35499606 TTGTACGGGA
*
35499616 TTTGCACTTCGGTGCCCTTG
1 TTTGCACTTCGGTGCCCCTG
* **
35499636 TTTGCATTTCAATGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
*
35499656 TTTGTACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
** * * * * *
35499676 CATACACTTCAGTGTCTCTA
1 TTTGCACTTCGGTGCCCCTG
** * *
35499696 TTCACACTACAGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
35499716 TTTGCACATT-TGTGCCCCTA
1 TTTGCAC-TTCGGTGCCCCTG
* *
35499736 TCTGCACTTCAGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
35499756 TTATGCA
1 TT-TGCA
35499763 TCTATGATTC
Statistics
Matches: 92, Mismatches: 32, Indels: 5
0.71 0.25 0.04
Matches are distributed among these distances:
19 2 0.02
20 85 0.92
21 5 0.05
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:35502870 original size:17 final size:17
Alignment explanation
Indices: 35502844--35502883 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
35502834 AAATATTCAA
* *
35502844 GTTTGTTAACTTGAATT
1 GTTTGATAACTTAAATT
35502861 GTTTGATAACTTAAATT
1 GTTTGATAACTTAAATT
*
35502878 GATTGA
1 GTTTGA
35502884 CTTCTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (17 bp):
GTTTGATAACTTAAATT
Found at i:35507854 original size:24 final size:24
Alignment explanation
Indices: 35507826--35507877 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
35507816 TTTCTAGAAG
* *
35507826 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
35507850 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
35507874 ATTT
1 ATTT
35507878 GACATCGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:35517444 original size:103 final size:103
Alignment explanation
Indices: 35517262--35517796 Score: 558
Period size: 104 Copynumber: 5.2 Consensus size: 103
35517252 GAGTTAGCTA
* * * *
35517262 AGTTAAGCTTGCAACCTCCAGTTATTTGAGTTAGCTGAGTTGAA-CTCGTAACTCCAAAACAGCT
1 AGTTAAGCTCGCAACCT-CAATTATTTGAGTTAGCTAAGTT-AAGCTCGCAACTCCAAAACAGCT
* * *
35517326 CACAGACTTATGTTCCCAGCTGATGCTTAAAGATTAGTTG
64 CACGGACCTATGTTCCCAGCTGATGCTTAAAGGTTAGTTG
* * *
35517366 AGTTAAGCTCGCAACCTCAATTATTTGAGTTAGCTAAGTTAAGCTCACAACTCCAAAATAGCGCA
1 AGTTAAGCTCGCAACCTCAATTATTTGAGTTAGCTAAGTTAAGCTCGCAACTCCAAAACAGCTCA
* * * * *
35517431 CGGACCAACGTTCCAAGCTGATGCTTAAAGGTTAGCTA
66 CGGACCTATGTTCCCAGCTGATGCTTAAAGGTTAGTTG
* * * * * *
35517469 AGTTAAGCTCACAACCCCCAATTATTTGAGTTAGCTGACTTAAGCTTGTAACTCCAAAACAGGC-
1 AGTTAAGCTCGCAA-CCTCAATTATTTGAGTTAGCTAAGTTAAGCTCGCAACTCCAAAACA-GCT
** * *
35517533 CGTGGACCTATGTTCCCAGCTGATGCTTAAAGATTAGATG
64 CACGGACCTATGTTCCCAGCTGATGCTTAAAGGTTAGTTG
* * *
35517573 AGTTAAGCTCGCAACCTACATTTATTTGAGTTAGCTGAA-TCAAGCTCGCAACTCCAAAATAGCT
1 AGTTAAGCTCGCAACCT-CAATTATTTGAGTTAGCT-AAGTTAAGCTCGCAACTCCAAAACAGCT
* * ** *
35517637 CACGGATCTACAG-TCTTAGCTAATGCTT-AAGGTTAGTTG
64 CACGGACCTA-TGTTCCCAGCTGATGCTTAAAGGTTAGTTG
* * * * * *
35517676 AGTTAAGCTCGCAACCCCTAGTTATTTGAGTTAGCTAAATTAAGCTCGCAACTACGAAACAACTC
1 AGTTAAGCTCGCAACCTC-AATTATTTGAGTTAGCTAAGTTAAGCTCGCAACTCCAAAACAGCTC
* * * *
35517741 ATGGACTTATGTTCCCAACTGATGTTTAAAGGTTAGTTG
65 ACGGACCTATGTTCCCAGCTGATGCTTAAAGGTTAGTTG
* *
35517780 AGTTAAGATCACAACCT
1 AGTTAAGCTCGCAACCT
35517797 ATGTTCATCG
Statistics
Matches: 353, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
102 6 0.02
103 164 0.46
104 179 0.51
105 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (103 bp):
AGTTAAGCTCGCAACCTCAATTATTTGAGTTAGCTAAGTTAAGCTCGCAACTCCAAAACAGCTCA
CGGACCTATGTTCCCAGCTGATGCTTAAAGGTTAGTTG
Found at i:35517671 original size:207 final size:208
Alignment explanation
Indices: 35517254--35517797 Score: 704
Period size: 207 Copynumber: 2.6 Consensus size: 208
35517244 AGTAATTTGA
* * *
35517254 GTTAGCTAAGTTAAGCTTGCAACCTCCAGTTATTTGAGTTAGCTGAGTTGAA-CTCGTAACTCCA
1 GTTAGCTAAGTTAAGCTCGCAACCCCCAGTTATTTGAGTTAGCTGAATT-AAGCTCGTAACTCCA
**
35517318 AAACAGCTCACAGACTTATGTTCCCAGCTGATGCTTAAAGATTAGTTGAGTTAAGCTCGCAACCT
65 AAACAGCTCATGGACTTATGTTCCCAGCTGATGCTTAAAGATTAGTTGAGTTAAGCTCGCAACCT
*
35517383 -CAATTATTTGAGTTAGCTAAGTTAAGCTCACAACTCCAAAATAGCGCACGGACCAACGTTCCAA
130 ACAATTATTTGAGTTAGCTAAGTCAAGCTCACAACTCCAAAATAGCGCACGGACCAACGTTCCAA
*
35517447 GCTGATGCTTAAAG
195 GCTAATGCTTAAAG
* * * *
35517461 GTTAGCTAAGTTAAGCTCACAACCCCCAATTATTTGAGTTAGCTGACTTAAGCTTGTAACTCCAA
1 GTTAGCTAAGTTAAGCTCGCAACCCCCAGTTATTTGAGTTAGCTGAATTAAGCTCGTAACTCCAA
* * *
35517526 AACAGGC-CGTGGACCTATGTTCCCAGCTGATGCTTAAAGATTAGATGAGTTAAGCTCGCAACCT
66 AACA-GCTCATGGACTTATGTTCCCAGCTGATGCTTAAAGATTAGTTGAGTTAAGCTCGCAACCT
* * * * * *
35517590 ACATTTATTTGAGTTAGCTGAA-TCAAGCTCGCAACTCCAAAATAGCTCACGGATCTACAG-TCT
130 ACAATTATTTGAGTTAGCT-AAGTCAAGCTCACAACTCCAAAATAGCGCACGGACCAAC-GTTCC
*
35517653 TAGCTAATGCTT-AAG
193 AAGCTAATGCTTAAAG
* * * * * * *
35517668 GTTAGTTGAGTTAAGCTCGCAACCCCTAGTTATTTGAGTTAGCTAAATTAAGCTCGCAACTACGA
1 GTTAGCTAAGTTAAGCTCGCAACCCCCAGTTATTTGAGTTAGCTGAATTAAGCTCGTAACTCCAA
* * * * * *
35517733 AACAACTCATGGACTTATGTTCCCAACTGATGTTTAAAGGTTAGTTGAGTTAAGATCACAACCTA
66 AACAGCTCATGGACTTATGTTCCCAGCTGATGCTTAAAGATTAGTTGAGTTAAGCTCGCAACCTA
35517798 TGTTCATCGA
Statistics
Matches: 291, Mismatches: 40, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
206 3 0.01
207 223 0.77
208 62 0.21
209 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (208 bp):
GTTAGCTAAGTTAAGCTCGCAACCCCCAGTTATTTGAGTTAGCTGAATTAAGCTCGTAACTCCAA
AACAGCTCATGGACTTATGTTCCCAGCTGATGCTTAAAGATTAGTTGAGTTAAGCTCGCAACCTA
CAATTATTTGAGTTAGCTAAGTCAAGCTCACAACTCCAAAATAGCGCACGGACCAACGTTCCAAG
CTAATGCTTAAAG
Found at i:35527992 original size:43 final size:43
Alignment explanation
Indices: 35527931--35528012 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
35527921 TATGTGATTG
*
35527931 ATATTGAAATGGCAAAGATGAGAGATGAATATGAGATGAAAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAAAAA
*
35527974 ATATTGAAATGGCAAAGATGAGAAATGATTATGAGATGA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGA
35528013 GAAATGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAAAAA
Found at i:35529586 original size:19 final size:19
Alignment explanation
Indices: 35529564--35529607 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
35529554 CCCTTCCATC
*
35529564 GATTTCTGCTTCTTCTTAT
1 GATTTCTACTTCTTCTTAT
35529583 GATTTCTACTTCTTCTTAT
1 GATTTCTACTTCTTCTTAT
35529602 GATTTC
1 GATTTC
35529608 CATTTTCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.14, C:0.20, G:0.09, T:0.57
Consensus pattern (19 bp):
GATTTCTACTTCTTCTTAT
Found at i:35529975 original size:19 final size:20
Alignment explanation
Indices: 35529951--35529994 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35529941 TTTCTGCTTC
*
35529951 TTCTTCTC-GTAGGTTTCTT
1 TTCTTCTCTGTACGTTTCTT
*
35529970 TTCTTCTCTTTACGTTTCTT
1 TTCTTCTCTGTACGTTTCTT
35529990 TTCTT
1 TTCTT
35529995 TTCTTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.05, C:0.23, G:0.09, T:0.64
Consensus pattern (20 bp):
TTCTTCTCTGTACGTTTCTT
Found at i:35529988 original size:20 final size:20
Alignment explanation
Indices: 35529963--35530000 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35529953 CTTCTCGTAG
35529963 GTTTCTTTTCTTCTCTTTAC
1 GTTTCTTTTCTTCTCTTTAC
*
35529983 GTTTCTTTTCTTTTCTTT
1 GTTTCTTTTCTTCTCTTT
35530001 TTTGTAAAAT
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:0.03, C:0.21, G:0.05, T:0.71
Consensus pattern (20 bp):
GTTTCTTTTCTTCTCTTTAC
Found at i:35530042 original size:16 final size:16
Alignment explanation
Indices: 35530021--35530051 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35530011 CGATTTCGTT
35530021 TTTCTTGAAATTTGTA
1 TTTCTTGAAATTTGTA
35530037 TTTCTTGAAATTTGT
1 TTTCTTGAAATTTGT
35530052 TGGAGTTCTG
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:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (16 bp):
TTTCTTGAAATTTGTA
Found at i:35530338 original size:33 final size:33
Alignment explanation
Indices: 35530301--35530385 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
35530291 GTAGATGTTA
35530301 ATATCTGGTTTTGGGGTCATTCCATGTCATTCC
1 ATATCTGGTTTTGGGGTCATTCCATGTCATTCC
*
35530334 ATATCTGGTTTTGGGGTCATTCCATTTCATTCC
1 ATATCTGGTTTTGGGGTCATTCCATGTCATTCC
* *
35530367 ATAACTGGTTATGGGGTCA
1 ATATCTGGTTTTGGGGTCA
35530386 ATCTGGCTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (33 bp):
ATATCTGGTTTTGGGGTCATTCCATGTCATTCC
Found at i:35533388 original size:43 final size:43
Alignment explanation
Indices: 35533290--35533436 Score: 149
Period size: 43 Copynumber: 3.5 Consensus size: 43
35533280 TAGGGTTACC
* * *
35533290 GAGATTACGTGTAAGACCATATCTGGGATA-TGGCATC-ATAT
1 GAGATTACGTGTAAGACCATGTCTGGGACATTGACATCGATAT
*
35533331 GAGGCTT-CGTGTAAGACCATGTCTGGGACATTGACATCGATAT
1 GA-GATTACGTGTAAGACCATGTCTGGGACATTGACATCGATAT
* * * * * *
35533374 GTGATTTCGTGTAAGACCATGGCTGGG-CTATTGCCATTGATAC
1 GAGATTACGTGTAAGACCATGTCTGGGAC-ATTGACATCGATAT
*
35533417 GAGATTACATGTAAGACCAT
1 GAGATTACGTGTAAGACCAT
35533437 ATCTCGGATA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 23 0.26
42 13 0.15
43 52 0.59
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
GAGATTACGTGTAAGACCATGTCTGGGACATTGACATCGATAT
Found at i:35534917 original size:77 final size:77
Alignment explanation
Indices: 35534786--35534938 Score: 297
Period size: 77 Copynumber: 2.0 Consensus size: 77
35534776 TTAAAAGCAT
*
35534786 GTTTTAGATCTCGTAGACCTATTTAAGGGACAATGTGATTATGAATGAATGTGATATGATGATAC
1 GTTTTAGATCTCGTAGACCTATTTAAGGGACAATGTGATTATGAATGAACGTGATATGATGATAC
35534851 ATGATCAATGTA
66 ATGATCAATGTA
35534863 GTTTTAGATCTCGTAGACCTATTTAAGGGACAATGTGATTATGAATGAACGTGATATGATGATAC
1 GTTTTAGATCTCGTAGACCTATTTAAGGGACAATGTGATTATGAATGAACGTGATATGATGATAC
35534928 ATGATCAATGT
66 ATGATCAATGT
35534939 GTATGAAATG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (77 bp):
GTTTTAGATCTCGTAGACCTATTTAAGGGACAATGTGATTATGAATGAACGTGATATGATGATAC
ATGATCAATGTA
Found at i:35535515 original size:29 final size:29
Alignment explanation
Indices: 35535471--35535607 Score: 184
Period size: 29 Copynumber: 4.7 Consensus size: 29
35535461 TATTGGCGAT
* *
35535471 CATCGAAAAATGAAAAGGGATATCTTCGGC
1 CATCG-AATATGAAAAGGGATAGCTTCGGC
* *
35535501 CATCGAATATGAAAAAGGATAGCTTCGAC
1 CATCGAATATGAAAAGGGATAGCTTCGGC
* *
35535530 CATCGAATATGAAAAGGGATAGTTTTGGC
1 CATCGAATATGAAAAGGGATAGCTTCGGC
*
35535559 TATCGAATATGAAAAGGGATAGCTTCGGC
1 CATCGAATATGAAAAGGGATAGCTTCGGC
* *
35535588 TATCGATTATGAAAAGGGAT
1 CATCGAATATGAAAAGGGAT
35535608 GGTGACGACC
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 90 0.95
30 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
CATCGAATATGAAAAGGGATAGCTTCGGC
Found at i:35541873 original size:32 final size:30
Alignment explanation
Indices: 35541821--35541886 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 30
35541811 AAATATATAT
*
35541821 ATATAATTTAGAATTATTATATAATTTTCA
1 ATATAATTTAGAATTATTATATAATTTTAA
*
35541851 ATATAATTTTAGTAATTTTTATATAATTTTAA
1 ATATAA-TTTAG-AATTATTATATAATTTTAA
35541883 ATAT
1 ATAT
35541887 TTGAATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 5 0.16
32 21 0.66
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
ATATAATTTAGAATTATTATATAATTTTAA
Found at i:35541888 original size:20 final size:20
Alignment explanation
Indices: 35541841--35541882 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
35541831 GAATTATTAT
*
35541841 ATAATTTTCAATATAATTTTA
1 ATAATTTT-TATATAATTTTA
*
35541862 GTAATTTTTATATAATTTTA
1 ATAATTTTTATATAATTTTA
35541882 A
1 A
35541883 ATATTTGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATAATTTTTATATAATTTTA
Found at i:35541957 original size:19 final size:20
Alignment explanation
Indices: 35541919--35541956 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
35541909 TTTGGAAAAA
35541919 GAATATTTTATAATTATTTT
1 GAATATTTTATAATTATTTT
*
35541939 GAAT-TTTTGTAATT-TTTT
1 GAATATTTTATAATTATTTT
35541957 TAGTCTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
GAATATTTTATAATTATTTT
Found at i:35546856 original size:88 final size:88
Alignment explanation
Indices: 35546707--35546882 Score: 289
Period size: 88 Copynumber: 2.0 Consensus size: 88
35546697 TACTAACAAG
* * * *
35546707 AATTATATCCGCCACGTTTCCATCTATAGTTATGTCCTTGTTTCTTTGAGCTCAGAATGACGAAT
1 AATTATATCCGCCACGTTTCCATCTATAGTTAAGCCCTGGTTTCTTTGAGCTCAGAATGACGAAA
*
35546772 GCACCGGACATAACGACTTAGCA
66 GCAACGGACATAACGACTTAGCA
*
35546795 AATTATATCCGCCACGTTTCCATCTATAGTTAAGCCCTGGTTTCTTTGAGCTCGGAATGACGAAA
1 AATTATATCCGCCACGTTTCCATCTATAGTTAAGCCCTGGTTTCTTTGAGCTCAGAATGACGAAA
*
35546860 GCAATGGACATAACGACTTAGCA
66 GCAACGGACATAACGACTTAGCA
35546883 TCGAATAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (88 bp):
AATTATATCCGCCACGTTTCCATCTATAGTTAAGCCCTGGTTTCTTTGAGCTCAGAATGACGAAA
GCAACGGACATAACGACTTAGCA
Found at i:35550041 original size:20 final size:21
Alignment explanation
Indices: 35549993--35550041 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
35549983 ATAGACACAT
*
35549993 TGAATATTTTATAAATCATTG
1 TGAATATTTTATAAATCATTA
* * *
35550014 TCAATATTTT-TATATTATTA
1 TGAATATTTTATAAATCATTA
35550034 TGAATATT
1 TGAATATT
35550042 AGAAGTATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (21 bp):
TGAATATTTTATAAATCATTA
Found at i:35553316 original size:20 final size:21
Alignment explanation
Indices: 35553287--35553328 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
35553277 ACATGATATG
*
35553287 AATTACATAATATA-TTAAAA
1 AATTACATAATAAACTTAAAA
*
35553307 AATTATATAATAAACTTAAAA
1 AATTACATAATAAACTTAAAA
35553328 A
1 A
35553329 TAGGTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTACATAATAAACTTAAAA
Found at i:35554124 original size:19 final size:20
Alignment explanation
Indices: 35554082--35554128 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
35554072 AAAAATTACA
*
35554082 AAAAAGTTCAAAATAATTTTT
1 AAAAA-TTCAAAATAATTTAT
35554103 AAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTAT
35554122 AAAAATT
1 AAAAATT
35554129 ATATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 8 0.32
21 5 0.20
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:35554155 original size:19 final size:19
Alignment explanation
Indices: 35554096--35554162 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
35554086 AGTTCAAAAT
*
35554096 AATTTTT-AAAAA-TTCAA
1 AATTTTTAAAAAATTTTAA
* *
35554113 AATATTTATAAAAATTAT-A
1 AATTTTTA-AAAAATTTTAA
*
35554132 TATTTTTAAAAAATTTTAA
1 AATTTTTAAAAAATTTTAA
35554151 AATTTTCTAAAA
1 AATTTT-TAAAA
35554163 TAATAATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
17 6 0.16
18 8 0.21
19 18 0.47
20 6 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTTTAAAAAATTTTAA
Found at i:35554163 original size:36 final size:35
Alignment explanation
Indices: 35554093--35554172 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
35554083 AAAAGTTCAA
35554093 AATAATTTTTAAAAATTCAAAATATTTATAAAAAT
1 AATAATTTTTAAAAATTCAAAATATTTATAAAAAT
* * *
35554128 TATATATTTTTAAAAAATTTTAAAAT-TTTCT-AAAAT
1 AATA-ATTTTT-AAAAA-TTCAAAATATTTATAAAAAT
35554164 AATAATTTT
1 AATAATTTT
35554173 AGAACCTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 8 0.21
36 14 0.37
37 9 0.24
38 7 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (35 bp):
AATAATTTTTAAAAATTCAAAATATTTATAAAAAT
Found at i:35554721 original size:14 final size:15
Alignment explanation
Indices: 35554698--35554739 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
35554688 ATTTTCTTAG
35554698 TTTTAGAATTT-AAT
1 TTTTAGAATTTAAAT
*
35554712 TTTTATAATTTAAAT
1 TTTTAGAATTTAAAT
*
35554727 TTTTGGAATTTAA
1 TTTTAGAATTTAA
35554740 CCTCTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTTAGAATTTAAAT
Found at i:35554729 original size:15 final size:14
Alignment explanation
Indices: 35554698--35554739 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
35554688 ATTTTCTTAG
35554698 TTTTAGAATTTAAT
1 TTTTAGAATTTAAT
*
35554712 TTTTATAATTTAAAT
1 TTTTAGAATTT-AAT
*
35554727 TTTTGGAATTTAA
1 TTTTAGAATTTAA
35554740 CCTCTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTAGAATTTAAT
Found at i:35557006 original size:28 final size:28
Alignment explanation
Indices: 35556974--35557030 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
35556964 TAAAAATGAG
*
35556974 AAAAAATAATAATTTCTATAAAACTTTAT
1 AAAAAATAAT-ATTTCTATAAAAATTTAT
* *
35557003 AAAAAATAATTTTTTTATAAAAATTTAT
1 AAAAAATAATATTTCTATAAAAATTTAT
35557031 GGTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAAAATAATATTTCTATAAAAATTTAT
Found at i:35557025 original size:29 final size:28
Alignment explanation
Indices: 35556974--35557030 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
35556964 TAAAAATGAG
35556974 AAAAAATAATAATTTCTATAAAACTTTAT
1 AAAAAATAATAATTTCTATAAAA-TTTAT
* *
35557003 AAAAAATAAT-TTTTTTATAAAAATTTAT
1 AAAAAATAATAATTTCTAT-AAAATTTAT
35557031 GGTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAAAATAATAATTTCTATAAAATTTAT
Found at i:35562287 original size:25 final size:26
Alignment explanation
Indices: 35562232--35562287 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
35562222 TACTTGGGGC
* *
35562232 AAAATCGTTAAAATTTTACCAAGGGT
1 AAAATCGTCAAAATTTTACCAAGGGA
* *
35562258 AAAATCGTCAAAATTTT-GCTAGGGA
1 AAAATCGTCAAAATTTTACCAAGGGA
35562283 AAAAT
1 AAAAT
35562288 AGGGATAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (26 bp):
AAAATCGTCAAAATTTTACCAAGGGA
Found at i:35572026 original size:26 final size:26
Alignment explanation
Indices: 35571988--35572039 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
35571978 CAACCACACT
*
35571988 AAGTTTCAGCTCTTAATGTTTTGGTG
1 AAGTTTCAACTCTTAATGTTTTGGTG
35572014 AAGTTTCAACTCTTAATGTTTTGGTG
1 AAGTTTCAACTCTTAATGTTTTGGTG
35572040 TTTGGATGAC
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:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (26 bp):
AAGTTTCAACTCTTAATGTTTTGGTG
Found at i:35582770 original size:26 final size:26
Alignment explanation
Indices: 35582737--35582935 Score: 247
Period size: 26 Copynumber: 7.7 Consensus size: 26
35582727 GTAATGGGCC
* **
35582737 TAAATTATCGAAATACCCTTGATGCC
1 TAAATTATCGAAATACCCTCGATGGG
* **
35582763 TAAATTATCGAAGTACCCTTTATGGG
1 TAAATTATCGAAATACCCTCGATGGG
* * *
35582789 TAAATTA-CCAGAATACCCTTGATAGG
1 TAAATTATCGA-AATACCCTCGATGGG
* *
35582815 TAAATTACCAAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
35582841 TAAATTATCGAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
* * *
35582867 TAAATTATCGAAAGACACTCGATGTG
1 TAAATTATCGAAATACCCTCGATGGG
*
35582893 TAAATTATCGAAATACTCTCGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
35582919 TAAATTATCGAAATACC
1 TAAATTATCGAAATACC
35582936 TTTGAAGGGC
Statistics
Matches: 151, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
25 2 0.01
26 147 0.97
27 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (26 bp):
TAAATTATCGAAATACCCTCGATGGG
Found at i:35590423 original size:26 final size:26
Alignment explanation
Indices: 35590390--35590530 Score: 167
Period size: 26 Copynumber: 5.4 Consensus size: 26
35590380 ATAATGGGCC
**
35590390 TAAATTATCGAAATACCCTTGATGCC
1 TAAATTATCGAAATACCCTTGATGGG
* *
35590416 TAAATTATCGAAGTACCCTTTATGGG
1 TAAATTATCGAAATACCCTTGATGGG
*
35590442 TAAATTA-CCAGAATACCCTTGATGGG
1 TAAATTATCGA-AATACCCTTGATGGG
* * *
35590468 TAAATTACCAAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTTGATGGG
*
35590494 TAAATTATCGAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTTGATGGG
*
35590520 TAGAATGATCG
1 TA-AATTATCG
35590531 TTATACCCCT
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
25 2 0.02
26 89 0.89
27 9 0.09
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (26 bp):
TAAATTATCGAAATACCCTTGATGGG
Found at i:35590968 original size:28 final size:28
Alignment explanation
Indices: 35590872--35590969 Score: 90
Period size: 28 Copynumber: 3.3 Consensus size: 28
35590862 CATACTTGTA
** *
35590872 CCACACTGATATTGTAACGGGCTTAGGC
1 CCACACTGATATTGTATTGGGCTAAGGC
* *
35590900 CCACACTG-TTTCTATATTGGGCTAAGGCC
1 CCACACTGATAT-TGTATTGGGCTAAGG-C
35590929 CGCACTATACTGATATTGTATTGGGCTAAGGC
1 C-CAC---ACTGATATTGTATTGGGCTAAGGC
35590961 CCACACTGA
1 CCACACTGA
35590970 CACTCGAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.04
28 24 0.43
29 2 0.04
30 3 0.05
31 3 0.05
32 2 0.04
33 18 0.32
34 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (28 bp):
CCACACTGATATTGTATTGGGCTAAGGC
Found at i:35591766 original size:10 final size:11
Alignment explanation
Indices: 35591736--35591768 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
35591726 TATGTTAAAA
35591736 ATATTAATTTT
1 ATATTAATTTT
35591747 ATAGTTAATTTT
1 ATA-TTAATTTT
35591759 -TATTAATTTT
1 ATATTAATTTT
35591769 GACTATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 5 0.24
12 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:35595230 original size:20 final size:20
Alignment explanation
Indices: 35595185--35595231 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
35595175 ATCATGGTCT
*
35595185 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTATTTACTTAC
35595204 TCT-CTTACTTATTTACTTAC
1 T-TGCTTACTTATTTACTTAC
35595224 TTGCTTAC
1 TTGCTTAC
35595232 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.15, C:0.26, G:0.04, T:0.55
Consensus pattern (20 bp):
TTGCTTACTTATTTACTTAC
Found at i:35595495 original size:49 final size:49
Alignment explanation
Indices: 35595437--35595614 Score: 157
Period size: 50 Copynumber: 3.6 Consensus size: 49
35595427 TAATAACATA
* * *
35595437 CCAAAGCCATGCCCCAGACATGGTCTTACATGGGATGTTTCC-TGTAC-TG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTTCCATAT-CGTG
* * *
35595486 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCCATATC-GTG
* ** *
35595536 CCCATGCCATGTCCCAGACATGGTCTTAC--GGGAGACCTCTCATCTCAGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-TTTC-CATATC-GTG
* * *
35595586 CTAACGCCATGTCCCAAACATGGTCTTAC
1 CCAATGCCATGTCCCAGACATGGTCTTAC
35595615 GTGAGACCTC
Statistics
Matches: 106, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
48 11 0.10
49 34 0.32
50 61 0.58
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (49 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCCATATCGTG
Found at i:35595559 original size:50 final size:49
Alignment explanation
Indices: 35595437--35595564 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 49
35595427 TAATAACATA
* * * *
35595437 CCAAAGCCATGCCCCAGACATGGTCTTACATGGGATGTTTCCTGTACTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATACTG
* *
35595486 CCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTTTCATAT-CGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCATATAC--TG
*
35595536 CCCATGCCATGTCCCAGACATGGTCTTAC
1 CCAATGCCATGTCCCAGACATGGTCTTAC
35595565 GGGAGACCTC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 2 0.03
49 37 0.55
50 28 0.42
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (49 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATACTG
Found at i:35597028 original size:5 final size:5
Alignment explanation
Indices: 35597018--35597089 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
35597008 TGTTAAAAAA
* *
35597018 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
35597064 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
35597090 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:35597071 original size:19 final size:19
Alignment explanation
Indices: 35597047--35597089 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
35597037 ATTATGTTTT
35597047 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
35597066 TATATTATATTATATTATA
1 TATATTATATTATATTATA
35597085 TATAT
1 TATAT
35597090 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:35597121 original size:17 final size:17
Alignment explanation
Indices: 35597099--35597132 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35597089 TACATAAAAC
*
35597099 AAAAGAAAGAATAGAAA
1 AAAAGAAAGAAAAGAAA
35597116 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
35597133 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:35597128 original size:9 final size:9
Alignment explanation
Indices: 35597099--35597132 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
35597089 TACATAAAAC
35597099 AAAAGAAAG
1 AAAAGAAAG
*
35597108 AATAGAAA-
1 AAAAGAAAG
35597116 AAAAGAAAG
1 AAAAGAAAG
35597125 AAAAGAAA
1 AAAAGAAA
35597133 CAGAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Done.