Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 6 of 182
Found at i:2123594 original size:15 final size:15
Alignment explanation
Indices: 2123574--2123629 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
2123564 TATCCTCCAG
*
2123574 CTCCACCTCCACCAC
1 CTCCACCACCACCAC
* *
2123589 CACCACCACCTCCAC
1 CTCCACCACCACCAC
* *
2123604 CTCCACCACCTCCAT
1 CTCCACCACCACCAC
*
2123619 GTCCACCACCA
1 CTCCACCACCA
2123630 TTACCAGCTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.23, C:0.62, G:0.02, T:0.12
Consensus pattern (15 bp):
CTCCACCACCACCAC
Found at i:2123599 original size:18 final size:18
Alignment explanation
Indices: 2123576--2123749 Score: 80
Period size: 18 Copynumber: 9.2 Consensus size: 18
2123566 TCCTCCAGCT
2123576 CCACCTCCACCACCACCA
1 CCACCTCCACCACCACCA
*
2123594 CCACCTCCACCTCCACCA
1 CCACCTCCACCACCACCA
* **
2123612 CCTCCATGTCCACCACCATTA
1 CCACC---TCCACCACCACCA
* **
2123633 CCAGCTCCACCACCTTCA
1 CCACCTCCACCACCACCA
* ** **
2123651 CCACTTCCACTTCCACTT
1 CCACCTCCACCACCACCA
* * * *
2123669 CCACTTCCATATCCTCCAGCT
1 CCACCTCC--A-CCACCACCA
*
2123690 CCGCCTCCACCACCACCA
1 CCACCTCCACCACCACCA
* *
2123708 CC-GCTACCACCACCTCCA
1 CCACCT-CCACCACCACCA
2123726 CCACCTCCATGTCCACCACCA
1 CCACCTCCA---CCACCACCA
2123747 CCA
1 CCA
2123750 TTACCAGCTC
Statistics
Matches: 116, Mismatches: 29, Indels: 19
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.02
18 74 0.64
19 3 0.03
20 1 0.01
21 36 0.31
ACGTcount: A:0.22, C:0.57, G:0.03, T:0.17
Consensus pattern (18 bp):
CCACCTCCACCACCACCA
Found at i:2123660 original size:6 final size:6
Alignment explanation
Indices: 2123651--2123677 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2123641 ACCACCTTCA
2123651 CCACTT CCACTT CCACTT CCACTT CCA
1 CCACTT CCACTT CCACTT CCACTT CCA
2123678 TATCCTCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCACTT
Found at i:2123726 original size:9 final size:9
Alignment explanation
Indices: 2123693--2123734 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2123683 TCCAGCTCCG
2123693 CCTCCACCA
1 CCTCCACCA
*
2123702 CCACCACC-
1 CCTCCACCA
*
2123710 GCTACCACCA
1 CCT-CCACCA
2123720 CCTCCACCA
1 CCTCCACCA
2123729 CCTCCA
1 CCTCCA
2123735 TGTCCACCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 1 0.04
9 24 0.89
10 2 0.07
ACGTcount: A:0.24, C:0.64, G:0.02, T:0.10
Consensus pattern (9 bp):
CCTCCACCA
Found at i:2123774 original size:114 final size:112
Alignment explanation
Indices: 2123537--2123813 Score: 341
Period size: 114 Copynumber: 2.4 Consensus size: 112
2123527 ATACCCGGAG
* *
2123537 CCACTTCCTCCTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCACCTCC
1 CCACTTCCACCTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCACCACC
2123602 ACCTCCACCACCTCCATGTCCACCACCATTACCAGCTCCACCACCTTCA
66 ACCTCCACCACCTCCATGTCCACCACCATTACCAGCT-C-CCACCTTCA
* *
2123651 CCACTTCCACTTCCACTTCCACTTCCATATCCTCCAGCTCCGCCTCCACCACCACCACCGCTACC
1 CCACTTCCACCTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCA-C-C-ACC
*
2123716 ACCACCTCCACCACCTCCATGTCCACCACCACCATTACCAGCT-CC-GC-T-A
63 ACCACCTCCACCACCTCCATGT---CCACCACCATTACCAGCTCCCACCTTCA
* * * *
2123765 CCGGC-TCCACCGCC-TTCTCCACTTCCATATCCTCCAGCTCCACCGCCAC
1 CC-ACTTCCACCTCCACT-TCCACTTCCATATCCTCCAGCTCCACCTCCAC
2123814 TACCGCCGCC
Statistics
Matches: 144, Mismatches: 11, Indels: 16
0.84 0.06 0.09
Matches are distributed among these distances:
113 1 0.01
114 94 0.65
115 3 0.02
116 2 0.01
117 26 0.18
120 18 0.12
ACGTcount: A:0.20, C:0.55, G:0.05, T:0.20
Consensus pattern (112 bp):
CCACTTCCACCTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCACCACC
ACCTCCACCACCTCCATGTCCACCACCATTACCAGCTCCCACCTTCA
Found at i:2123895 original size:129 final size:123
Alignment explanation
Indices: 2123702--2124039 Score: 333
Period size: 129 Copynumber: 2.7 Consensus size: 123
2123692 GCCTCCACCA
* * *
2123702 CCACCACCGC-TACCACCACCTCCACCACCTCCATGTCCA-C--CACCACCATTACCAGCTCCGC
1 CCACCACC-CTTACCACCACCTCCACCACCTCCATGTCCACCTGCTCCTCCATTTCCAGCTCCGC
* * * * * *
2123763 TACCGGCTCCACCGCCTTCTCCACTTCCATATCCTCCAGCTCCACCGCCACTACCGCCGCCTCCG
65 TACCAGCTCCACCTCCTTCTCCACTTCCATACCCACAAGCTCCA-C-CC-CT---GCCACCTCCG
* * *
2123828 CCACCACCCTTACCTCCACCTCCACCACCTCCATATCCACCTGCTCCTCCATTTCCAGCTCCACT
1 CCACCACCCTTACCACCACCTCCACCACCTCCATGTCCACCTGCTCCTCCATTTCCAGCTCCGCT
* * * *
2123893 ACCAGCTCCTCCTCCTTCACCAGCTCCACTTCCATACCCAGAAGCTCCACCCGTGCTACCTCCG
66 ACCAGCTCCACCTCCTT------CTCCACTTCCATACCCACAAGCTCCACCCCTGCCACCTCCG
* * * * * *
2123957 CCACCACCATTACCACCACCGCCTCCTCCTCCATGTCCACCTGCTCCTCCATATCCAGCACCGCT
1 CCACCACCCTTACCACCACCTCCACCACCTCCATGTCCACCTGCTCCTCCATTTCCAGCTCCGCT
2124022 ACCAGCTCCACCTCCTTC
66 ACCAGCTCCACCTCCTTC
2124040 ACCAGCTCCA
Statistics
Matches: 176, Mismatches: 26, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
123 1 0.01
125 1 0.01
126 35 0.20
127 1 0.01
129 112 0.64
132 1 0.01
133 2 0.01
134 1 0.01
135 22 0.12
ACGTcount: A:0.18, C:0.54, G:0.08, T:0.20
Consensus pattern (123 bp):
CCACCACCCTTACCACCACCTCCACCACCTCCATGTCCACCTGCTCCTCCATTTCCAGCTCCGCT
ACCAGCTCCACCTCCTTCTCCACTTCCATACCCACAAGCTCCACCCCTGCCACCTCCG
Found at i:2124040 original size:129 final size:128
Alignment explanation
Indices: 2123822--2124114 Score: 426
Period size: 129 Copynumber: 2.3 Consensus size: 128
2123812 ACTACCGCCG
* * * * * *
2123822 CCTCCGCCACCACCCTTACCTCCACCTCCACCACCTCCATATCCACCTGCTCCTCCATTTCCAGC
1 CCTCCGCCACCACCATTACCACCACCACCTCCTCCTCCATATCCACCTGCTCCTCCATATCCAGC
* *
2123887 TCCACTACCAGCTCCTCCTCCTTCACCAGCTCCACTTCCATACCCAGAAGCTCCACCCGTGC-TA
66 ACCACTACCAGCTCCACCTCCTTCACCAGCTCCACTTCCATACCCAGAAGCTCCA-CC-TGCATA
* *
2123951 CCTCCGCCACCACCATTACCACCACCGCCTCCTCCTCCATGTCCACCTGCTCCTCCATATCCAGC
1 CCTCCGCCACCACCATTACCACCACCACCTCCTCCTCCATATCCACCTGCTCCTCCATATCCAGC
* *
2124016 ACCGCTACCAGCTCCACCTCCTTCACCAGCTCCACTTCCATATCCAGAAGCTCCACCTGCAATA
66 ACCACTACCAGCTCCACCTCCTTCACCAGCTCCACTTCCATACCCAGAAGCTCCACCTGC-ATA
* *
2124080 CCTCCGCCTCCACCACTACCACCACCACCTCCTCC
1 CCTCCGCCACCACCATTACCACCACCACCTCCTCC
2124115 ACCGAGCCCA
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
127 3 0.02
128 2 0.01
129 143 0.97
ACGTcount: A:0.19, C:0.53, G:0.07, T:0.20
Consensus pattern (128 bp):
CCTCCGCCACCACCATTACCACCACCACCTCCTCCTCCATATCCACCTGCTCCTCCATATCCAGC
ACCACTACCAGCTCCACCTCCTTCACCAGCTCCACTTCCATACCCAGAAGCTCCACCTGCATA
Found at i:2124062 original size:18 final size:18
Alignment explanation
Indices: 2124022--2124056 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2124012 CAGCACCGCT
*
2124022 ACCAGCTCCACCTCCTTC
1 ACCAGCTCCACCTCCATC
*
2124040 ACCAGCTCCACTTCCAT
1 ACCAGCTCCACCTCCAT
2124057 ATCCAGAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.51, G:0.06, T:0.23
Consensus pattern (18 bp):
ACCAGCTCCACCTCCATC
Found at i:2138172 original size:12 final size:12
Alignment explanation
Indices: 2138155--2138179 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2138145 CACTTTTAAC
2138155 CACTTTCTGTAG
1 CACTTTCTGTAG
2138167 CACTTTCTGTAG
1 CACTTTCTGTAG
2138179 C
1 C
2138180 TTAGCCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (12 bp):
CACTTTCTGTAG
Found at i:2138298 original size:23 final size:23
Alignment explanation
Indices: 2138225--2138421 Score: 177
Period size: 23 Copynumber: 8.5 Consensus size: 23
2138215 TATGCGGAAC
* *
2138225 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
2138247 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2138268 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
2138294 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
2138317 AATCAGAGAGCACCCAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2138340 AATCAGAGAGCACCCAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2138363 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2138386 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
2138411 AAACAGAGAGC
1 AAACAGAGAGC
2138422 GCGCTAGTGT
Statistics
Matches: 147, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
21 17 0.12
23 92 0.63
24 2 0.01
25 29 0.20
26 7 0.05
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:2138347 original size:69 final size:69
Alignment explanation
Indices: 2138225--2138421 Score: 206
Period size: 69 Copynumber: 2.8 Consensus size: 69
2138215 TATGCGGAAC
2138225 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCA-CATAAGTGCTGGGCAACAGAGAGCACACA
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACCATAAGTGCT--G-AACAGAGAGCACACA
*
2138287 CAGTGCT
63 AAGTGCT
*
2138294 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACCCA-AAGTGCT-AATCAGAGAGCACCCAA
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCA-CCATAAGTGCTGAA-CAGAGAGCACACAA
2138357 AGTGCT
64 AGTGCT
* * * * * * * *
2138363 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 AAACAGAGAGTACACAAAGTACTAAT--CAGAGAGCACCATAAGTGCTGAACAGAGAGC
2138422 GCGCTAGTGT
Statistics
Matches: 111, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
68 2 0.02
69 53 0.48
70 13 0.12
71 32 0.29
72 9 0.08
73 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (69 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACCATAAGTGCTGAACAGAGAGCACACAAAG
TGCT
Found at i:2141634 original size:129 final size:129
Alignment explanation
Indices: 2141404--2141663 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 129
2141394 ACTTGGAAAC
2141404 ATACTCAACTATATTCCGTTTCATCCCTTTCCACCAATAAAATGGCTTTAAGTCATGATACATCT
1 ATACTCAACTATATTCCGTTTCATCCCTTTCCACCAATAAAATGGCTTTAAGTCATGATACATCT
2141469 TGTTACTTCCCGGATATACAGCAAACGAACTATGATGAGCTTCATCCAAAATTCTTCGTTTCAA
66 TGTTACTTCCCGGATATACAGCAAACGAACTATGATGAGCTTCATCCAAAATTCTTCGTTTCAA
2141533 ATACTCAACTATATTCCGTTTCATCCCTTTCCACCAATAAAATGGCTTTAAGTCATGATACATCT
1 ATACTCAACTATATTCCGTTTCATCCCTTTCCACCAATAAAATGGCTTTAAGTCATGATACATCT
*
2141598 TGTTACTTCCCGGATGTACAGCAAACGAACTATGATGAGCTTCATCCAAAATTCTTCGTTTCAA
66 TGTTACTTCCCGGATATACAGCAAACGAACTATGATGAGCTTCATCCAAAATTCTTCGTTTCAA
2141662 AT
1 AT
2141664 CTTCTTGATT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (129 bp):
ATACTCAACTATATTCCGTTTCATCCCTTTCCACCAATAAAATGGCTTTAAGTCATGATACATCT
TGTTACTTCCCGGATATACAGCAAACGAACTATGATGAGCTTCATCCAAAATTCTTCGTTTCAA
Found at i:2145817 original size:23 final size:23
Alignment explanation
Indices: 2145786--2145889 Score: 138
Period size: 23 Copynumber: 4.4 Consensus size: 23
2145776 AGTGCTGGGC
*
2145786 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
2145809 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
2145832 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
2145856 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
2145880 AACAGAGAGC
1 AACAGAGAGC
2145890 GCGCTAGTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
23 51 0.71
24 2 0.03
25 16 0.22
26 3 0.04
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:2145866 original size:71 final size:69
Alignment explanation
Indices: 2145739--2145889 Score: 180
Period size: 71 Copynumber: 2.2 Consensus size: 69
2145729 TATGCGGAAC
* * **
2145739 AAACAGAGAGTACCAAAGTACTAATAGAGAGCACATAAGTGCTGGGCAACAAAGAGCAC-ACACA
1 AAACAGAGAGCACCAAAGTACTAATAGAGAGCACACAAGTGCTGAACAACAAAGAGCACGACAC-
2145803 GTGCT
65 GTGCT
* * * *
2145808 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCT-AATAACAGAGAGCACGAG
1 AAACAGAGAGCAC-CAAAGTACTAAT-AGAGAGCACACA-AGTGCTGAACAACAAAGAGCACGAC
2145872 ACGTGCT
63 ACGTGCT
2145879 AAACAGAGAGC
1 AAACAGAGAGC
2145890 GCGCTAGTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
69 12 0.17
70 11 0.16
71 38 0.54
72 9 0.13
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (69 bp):
AAACAGAGAGCACCAAAGTACTAATAGAGAGCACACAAGTGCTGAACAACAAAGAGCACGACACG
TGCT
Found at i:2145878 original size:48 final size:46
Alignment explanation
Indices: 2145786--2145889 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 46
2145776 AGTGCTGGGC
*
2145786 AACAAAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTA
* * *
2145832 ATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTA
1 AACAGAGAGCACACACAGTGCT-A-AACAGAGAGCAC-ACAAAGTGCTA
2145880 AACAGAGAGC
1 AACAGAGAGC
2145890 GCGCTAGTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
46 20 0.40
47 1 0.02
48 28 0.56
49 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (46 bp):
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTA
Found at i:2151033 original size:12 final size:11
Alignment explanation
Indices: 2151008--2151042 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
2150998 TTTATTTTGT
2151008 AAATAAAATAA
1 AAATAAAATAA
2151019 AAATAAAAGTAA
1 AAATAAAA-TAA
2151031 AAATAAATATAA
1 AAATAAA-ATAA
2151043 TTATTGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 13 0.59
13 1 0.05
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:2157583 original size:22 final size:24
Alignment explanation
Indices: 2157553--2157606 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
2157543 AAGTCGGTGG
*
2157553 TTGATTTTTTAATATATTT-TTT-A
1 TTGAATTTTTAATA-ATTTATTTAA
*
2157576 -TGAATTTTTGATAATTTATTTAA
1 TTGAATTTTTAATAATTTATTTAA
2157599 TTGAATTT
1 TTGAATTT
2157607 GGATGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 14 0.54
23 1 0.04
24 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (24 bp):
TTGAATTTTTAATAATTTATTTAA
Found at i:2171709 original size:30 final size:30
Alignment explanation
Indices: 2171675--2171735 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2171665 TAATAGCATT
* *
2171675 AATAATTATATTTAAATTTTATATTCAAAA
1 AATAATTATATCTAAATTTTAAATTCAAAA
*
2171705 AATAATTATATCTAAATTTTAAATTCTAAA
1 AATAATTATATCTAAATTTTAAATTCAAAA
2171735 A
1 A
2171736 CTTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (30 bp):
AATAATTATATCTAAATTTTAAATTCAAAA
Found at i:2184437 original size:3 final size:3
Alignment explanation
Indices: 2184424--2184455 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2184414 ATTCTCCTCT
*
2184424 TGC TAC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
2184456 TTACTTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.31, G:0.31, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:2186092 original size:21 final size:21
Alignment explanation
Indices: 2186059--2186099 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2186049 AACTTGTTTA
*
2186059 GAAAATAACAATATTAAAATT
1 GAAAATAACAATATCAAAATT
2186080 GAAATATAA-AATATCAAAAT
1 GAAA-ATAACAATATCAAAAT
2186100 AAAAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
GAAAATAACAATATCAAAATT
Found at i:2186105 original size:21 final size:22
Alignment explanation
Indices: 2186063--2186106 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2186053 TGTTTAGAAA
* **
2186063 ATAACAATATTAAAATTGAAAT
1 ATAACAATATCAAAATAAAAAT
2186085 ATAA-AATATCAAAATAAAAAT
1 ATAACAATATCAAAATAAAAAT
2186106 A
1 A
2186107 GGATTATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAACAATATCAAAATAAAAAT
Found at i:2186632 original size:31 final size:31
Alignment explanation
Indices: 2186590--2186662 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
2186580 AAAAAAACTT
*
2186590 AACAATACAATGACATAAATAAAAACTTTCA
1 AACAATTCAATGACATAAATAAAAACTTTCA
* ** *
2186621 AATAATTCAATGATTTAAATAAAAATTTTCA
1 AACAATTCAATGACATAAATAAAAACTTTCA
2186652 AACAATTCAAT
1 AACAATTCAAT
2186663 AATTATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (31 bp):
AACAATTCAATGACATAAATAAAAACTTTCA
Found at i:2188042 original size:29 final size:28
Alignment explanation
Indices: 2187996--2188050 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
2187986 GACTCATTTA
*
2187996 TATATATTTTTTAATACA-ACATTTCTCG
1 TATATATTTATTAATACACA-ATTTCTCG
*
2188024 TATATATTATATTATTACACAATTTCT
1 TATATATT-TATTAATACACAATTTCT
2188051 TATGAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 14 0.61
30 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.51
Consensus pattern (28 bp):
TATATATTTATTAATACACAATTTCTCG
Found at i:2193992 original size:17 final size:18
Alignment explanation
Indices: 2193967--2194003 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2193957 TCTTTTAAAA
2193967 ATTATAAAT-ATATAAATT
1 ATTATAAATGATA-AAATT
2193985 ATTA-AAATGATAAAATT
1 ATTATAAATGATAAAATT
2194002 AT
1 AT
2194004 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATAAAATT
Found at i:2200916 original size:2 final size:2
Alignment explanation
Indices: 2200909--2200952 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2200899 TAATTTACAC
2200909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2200951 AT
1 AT
2200953 TTCAAACAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2204626 original size:15 final size:14
Alignment explanation
Indices: 2204597--2204630 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2204587 AGCCTGAACA
2204597 GGTTGGTTGCATTG
1 GGTTGGTTGCATTG
*
2204611 GGTTGCGTTGCGTTG
1 GGTTG-GTTGCATTG
2204626 GGTTG
1 GGTTG
2204631 TGTCACGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.03, C:0.09, G:0.47, T:0.41
Consensus pattern (14 bp):
GGTTGGTTGCATTG
Found at i:2211000 original size:6 final size:6
Alignment explanation
Indices: 2210989--2211013 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2210979 TCCATGGGCC
2210989 GTAGCA GTAGCA GTAGCA GTAGCA G
1 GTAGCA GTAGCA GTAGCA GTAGCA G
2211014 CATCAACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GTAGCA
Found at i:2225576 original size:31 final size:30
Alignment explanation
Indices: 2225514--2225585 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
2225504 TATATACATG
*
2225514 AACTTTAATTTGGTGCAATTATACACGTAA
1 AACTTTAATTTGGTGCAAATATACACGTAA
* * * *
2225544 AACTCTAATTGTGGTTCAAATATATACTTAA
1 AACTTTAATT-TGGTGCAAATATACACGTAA
2225575 AACTTTAATTT
1 AACTTTAATTT
2225586 TGATTTAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATACACGTAA
Found at i:2231722 original size:8 final size:8
Alignment explanation
Indices: 2231709--2231735 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2231699 CGAATATCTT
2231709 TTTAATTA
1 TTTAATTA
2231717 TTTAATTA
1 TTTAATTA
2231725 TTTAATTA
1 TTTAATTA
2231733 TTT
1 TTT
2231736 TTAAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTA
Found at i:2232642 original size:15 final size:15
Alignment explanation
Indices: 2232618--2232666 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2232608 CATTAAATTA
*
2232618 ATTAATAAATTATTT
1 ATTAAAAAATTATTT
*
2232633 TTTAAAAAATTAATCTT
1 ATTAAAAAATT-AT-TT
*
2232650 ATTATAAAATTATTT
1 ATTAAAAAATTATTT
2232665 AT
1 AT
2232667 GTTTTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAAAAAATTATTT
Found at i:2234328 original size:2 final size:2
Alignment explanation
Indices: 2234321--2234348 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2234311 CATCTTAACC
2234321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2234349 CAAAAGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2234886 original size:18 final size:18
Alignment explanation
Indices: 2234863--2234913 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
2234853 TATAATACTT
2234863 TATATTATGTTATTTTTA
1 TATATTATGTTATTTTTA
2234881 TATATTATGTTATTTTTA
1 TATATTATGTTATTTTTA
*
2234899 TATATTATGTAATTT
1 TATATTATGTTATTT
2234914 AGAACACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TATATTATGTTATTTTTA
Found at i:2249960 original size:5 final size:5
Alignment explanation
Indices: 2249950--2249976 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2249940 TTTGTGGGGT
2249950 GATGG GATGG GATGG GATGG GATGG GA
1 GATGG GATGG GATGG GATGG GATGG GA
2249977 GACGGTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.59, T:0.19
Consensus pattern (5 bp):
GATGG
Found at i:2250701 original size:31 final size:31
Alignment explanation
Indices: 2250666--2250725 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2250656 CTTGGTGACT
* *
2250666 TAAAT-AAAAAATTTTAAATAGTTTAGTGATG
1 TAAATGAAAAAATTCT-AATAATTTAGTGATG
2250697 TAAATGAAAAAATTCTAATAATTTAGTGA
1 TAAATGAAAAAATTCTAATAATTTAGTGA
2250726 CTATTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (31 bp):
TAAATGAAAAAATTCTAATAATTTAGTGATG
Found at i:2251606 original size:45 final size:46
Alignment explanation
Indices: 2251516--2251607 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
2251506 TTAATCTAAT
*
2251516 TGATATCATTTTTATTTATTTTACAACTAATAAGTGTTGGATATAG
1 TGATATCATTATTATTTATTTTACAACTAATAAGTGTTGGATATAG
* *
2251562 TGATATCATTATTATTTA-TTTCCAACTAATAAGTGTTGGGTATAG
1 TGATATCATTATTATTTATTTTACAACTAATAAGTGTTGGATATAG
2251607 T
1 T
2251608 TACATCATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 26 0.60
46 17 0.40
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (46 bp):
TGATATCATTATTATTTATTTTACAACTAATAAGTGTTGGATATAG
Found at i:2251857 original size:18 final size:18
Alignment explanation
Indices: 2251834--2251869 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2251824 CACAATGATC
2251834 ATAAATGTCCAATACAAA
1 ATAAATGTCCAATACAAA
*
2251852 ATAAATGTCTAATACAAA
1 ATAAATGTCCAATACAAA
2251870 TTCATCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAATGTCCAATACAAA
Found at i:2260855 original size:16 final size:17
Alignment explanation
Indices: 2260827--2260858 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2260817 AAATGTACTT
2260827 AAATTATATTAAAATAA
1 AAATTATATTAAAATAA
2260844 AAATTA-ATTAAAATA
1 AAATTATATTAAAATA
2260859 TGCCCATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTATATTAAAATAA
Found at i:2268154 original size:2 final size:2
Alignment explanation
Indices: 2268147--2268173 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2268137 TTTTAAGTAT
2268147 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2268174 TCAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2271228 original size:29 final size:28
Alignment explanation
Indices: 2271183--2271238 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
2271173 CCTCTCTTTC
2271183 TATTTTAAGAATTTAATTCTTTTATTTA
1 TATTTTAAGAATTTAATTCTTTTATTTA
*
2271211 TATTTTAAGGAATTTAATTTTTTTATTT
1 TATTTTAA-GAATTTAATTCTTTTATTT
2271239 TTTAGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
TATTTTAAGAATTTAATTCTTTTATTTA
Found at i:2273990 original size:3 final size:3
Alignment explanation
Indices: 2273982--2274025 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2273972 TCCACAAAGA
* * * *
2273982 ATT ATT ATT ATT ATT ACT ATT ACT ATC ATT GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2274026 GGTCCTTAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:2283646 original size:4 final size:4
Alignment explanation
Indices: 2283637--2283663 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2283627 AAAAGATTTC
2283637 AGAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGA
2283664 TGAACTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2294522 original size:20 final size:20
Alignment explanation
Indices: 2294481--2294522 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2294471 ACCATAAATA
*
2294481 ATTTTTTAAATTTATTTTTT
1 ATTTTTTAAATATATTTTTT
2294501 ATTTTTTAAA-ATATTTTATT
1 ATTTTTTAAATATATTTT-TT
2294521 AT
1 AT
2294523 GCTTCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTAAATATATTTTTT
Found at i:2296966 original size:29 final size:31
Alignment explanation
Indices: 2296931--2297006 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 31
2296921 ATGAAAACGT
* * *
2296931 AATTTTTGAG-GAATTTGGGGTTAAAATTGA
1 AATTTTTGAGAAAATTTGGGATTAAAAATGA
2296961 AATTTTTG-GAAAATTTGGGATTAAAAATG-
1 AATTTTTGAGAAAATTTGGGATTAAAAATGA
*
2296990 AACTTTTGA-AAAATTTG
1 AATTTTTGAGAAAATTTG
2297007 AGGTCGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.40
30 24 0.60
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (31 bp):
AATTTTTGAGAAAATTTGGGATTAAAAATGA
Found at i:2297055 original size:28 final size:28
Alignment explanation
Indices: 2297023--2297252 Score: 115
Period size: 28 Copynumber: 8.1 Consensus size: 28
2297013 AAAATGTGAC
2297023 TTTTGGAAATTTAGGGGCAAAATGGTAA
1 TTTTGGAAATTTAGGGGCAAAATGGTAA
* * *
2297051 CTTTGG-GATGTTTGGAGGCAAAATGGTAA
1 TTTTGGAAAT-TTAGG-GGCAAAATGGTAA
* *
2297080 TTTTGGATA-TCAGGGGGCAAAATGGTAA
1 TTTTGGAAATTTA-GGGGCAAAATGGTAA
*
2297108 TTTTGGATGAGTTT-GGGGTCAAAAT-GTAA
1 TTTTGGA--AATTTAGGGG-CAAAATGGTAA
*
2297137 TTTTGGGAAAGTTTA-GGGTAAAAT-GTAA
1 TTTT-GGAAA-TTTAGGGGCAAAATGGTAA
* ** *
2297165 TTTT-TACAAGTTGGGGGGCAAAAAT-CTAA
1 TTTTGGA-AA-TTTAGGGGC-AAAATGGTAA
* * * *
2297194 TTTT-GAGAAGTTCGGGGTAAAAT-GTGA
1 TTTTGGA-AATTTAGGGGCAAAATGGTAA
2297221 TTTT-GAAAGTTTAGGGGCAAAAAT-GTAA
1 TTTTGGAAA-TTTAGGGGC-AAAATGGTAA
2297249 TTTT
1 TTTT
2297253 TGAGAAGTTT
Statistics
Matches: 157, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
26 3 0.02
27 26 0.17
28 64 0.41
29 53 0.34
30 10 0.06
31 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTTGGAAATTTAGGGGCAAAATGGTAA
Found at i:2297084 original size:57 final size:56
Alignment explanation
Indices: 2297003--2297167 Score: 160
Period size: 57 Copynumber: 2.9 Consensus size: 56
2296993 TTTTGAAAAA
* *
2297003 TTTGAGGTCGAAAATGTGACTTTTGGAAATTTAGGGGCAAAATGGTAACTTTGGGAT-G
1 TTTGGGGTC-AAAATGT-AATTTTGGAAATTTAGGGGCAAAATGGTAA-TTTGGGATAG
* * *
2297061 TTTGGAGG-CAAAATGGTAATTTTGGATA-TCAGGGGGCAAAATGGTAATTTTGGATGAG
1 TTTGG-GGTCAAAAT-GTAATTTTGGAAATTTA-GGGGCAAAATGGTAATTTGGGAT-AG
*
2297119 TTTGGGGTCAAAATGTAATTTTGGGAAAGTTTA-GGGTAAAAT-GTAATTT
1 TTTGGGGTCAAAATGTAATTTT-GGAAA-TTTAGGGGCAAAATGGTAATTT
2297168 TTACAAGTTG
Statistics
Matches: 90, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
56 9 0.10
57 46 0.51
58 31 0.34
59 2 0.02
60 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (56 bp):
TTTGGGGTCAAAATGTAATTTTGGAAATTTAGGGGCAAAATGGTAATTTGGGATAG
Found at i:2297263 original size:30 final size:30
Alignment explanation
Indices: 2297098--2297494 Score: 262
Period size: 29 Copynumber: 13.7 Consensus size: 30
2297088 ATCAGGGGGC
* *
2297098 AAAATGGTAATTTTGGATG-AGTTT-GGGGTC
1 AAAAT-GTAATTTTTGA-GAAGTTTAGGGGTA
*
2297128 AAAATGTAA-TTTTGGGAAAGTTTA-GGGT-
1 AAAATGTAATTTTTGAG-AAGTTTAGGGGTA
* ** *
2297156 AAAATGTAATTTTT-ACAAGTTGGGGGGCA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
* *
2297185 AAAATCTAA-TTTTGAGAAG-TTCGGGGT-
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
* *
2297212 AAAATGTGA-TTTTGA-AAGTTTAGGGGCA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
**
2297240 AAAATGTAATTTTTGAGAAGTTTA-GGACA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
* *
2297269 AAAATGTAAATTTTGAGAAGTTTGGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
* * *
2297299 AAAATGTGATTTTAG-GAAGTTTGGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
* * *
2297328 AAAATATGATTTTT-AAAAGTTT-GAGGGTA
1 AAAATGTAATTTTTGAGAAGTTTAG-GGGTA
*
2297357 AAAATGTAATTTTTAAGAAGTTT-GTGGGTA
1 AAAATGTAATTTTTGAGAAGTTTAG-GGGTA
* * * * *
2297387 AAAAAGTGA-TTTTGGGAAGTTCAAGGGTA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
* * *
2297416 AAAA-GTGATTTTT-AGAAGTTT-GAGAGAA
1 AAAATGTAATTTTTGAGAAGTTTAG-GGGTA
* * *
2297444 AAAATATAATTTTAG-GAAAGTTTAGGGATA
1 AAAATGTAATTTTTGAG-AAGTTTAGGGGTA
* *
2297474 AAAATATGA-TTTTGAGAAGTT
1 AAAATGTAATTTTTGAGAAGTT
2297495 CAAGGACCTT
Statistics
Matches: 293, Mismatches: 51, Indels: 47
0.75 0.13 0.12
Matches are distributed among these distances:
26 3 0.01
27 25 0.09
28 51 0.17
29 149 0.51
30 64 0.22
31 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTAGGGGTA
Found at i:2297348 original size:87 final size:86
Alignment explanation
Indices: 2297098--2297499 Score: 356
Period size: 87 Copynumber: 4.6 Consensus size: 86
2297088 ATCAGGGGGC
* *
2297098 AAAATGGTAATTTTG-GATGAGTTT-GGGGTCAAAATGTAATTTTGGGAAAGTTT-AGGGT-AAA
1 AAAAT-GTAATTTTGAGA--AGTTTGGGGGTAAAAATGTGATTTT-GG-AAGTTTAAGGGTAAAA
* * * *
2297159 ATGTAATTTTTACAAGTTGGGGGGCA
61 ATGTAATTTTTAGAAGTTTGAGGACA
* * * * *
2297185 AAAATCTAATTTTGAGAAG-TTCGGGGT-AAAATGTGATTTTGAAAGTTTAGGGGCAAAAATGTA
1 AAAATGTAATTTTGAGAAGTTTGGGGGTAAAAATGTGATTTTGGAAGTTTAAGGGTAAAAATGTA
2297248 ATTTTTGAGAAGTTT-AGGACA
66 ATTTTT-AGAAGTTTGAGGACA
** *
2297269 AAAATGTAAATTTTGAGAAGTTTGGGGGTAAAAATGTGATTTTAGGAAGTTTGGGGGTAAAAATA
1 AAAATGT-AATTTTGAGAAGTTTGGGGGTAAAAATGTGATTTT-GGAAGTTTAAGGGTAAAAATG
* * **
2297334 TGATTTTTAAAAGTTTGAGGGTA
64 TAATTTTTAGAAGTTTGAGGACA
* * * *
2297357 AAAATGTAATTTTTAAGAAGTTTGTGGGTAAAAAAGTGATTTTGGGAAGTTCAAGGGTAAAAA-G
1 AAAATGTAA-TTTTGAGAAGTTTGGGGGTAAAAATGTGATTTT-GGAAGTTTAAGGGTAAAAATG
*
2297421 TGATTTTTAGAAGTTTGAGAGA-A
64 TAATTTTTAGAAGTTTGAG-GACA
* * * * *
2297444 AAAATATAATTTT-AGGAAAGTTTAGGGATAAAAATATGATTTTGAGAAGTTCAAGG
1 AAAATGTAATTTTGA-G-AAGTTTGGGGGTAAAAATGTGATTTTG-GAAGTTTAAGG
2297500 ACCTTTTGGG
Statistics
Matches: 265, Mismatches: 35, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
82 6 0.02
83 4 0.02
84 38 0.14
85 26 0.10
86 21 0.08
87 88 0.33
88 82 0.31
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (86 bp):
AAAATGTAATTTTGAGAAGTTTGGGGGTAAAAATGTGATTTTGGAAGTTTAAGGGTAAAAATGTA
ATTTTTAGAAGTTTGAGGACA
Found at i:2298586 original size:6 final size:6
Alignment explanation
Indices: 2298575--2298634 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
2298565 CCCAATTTTA
* * * *
2298575 AAATTT AAATTT AAATTT -ATTTT AAGTTT -AATTT -ATTTT GAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
2298620 AAATTT AAAGTTT AA
1 AAATTT AAA-TTT AA
2298635 TTAAAAGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
5 12 0.27
6 28 0.62
7 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:2298604 original size:11 final size:11
Alignment explanation
Indices: 2298575--2298627 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
2298565 CCCAATTTTA
2298575 AAATTTAAATTT
1 AAATTT-AATTT
*
2298587 AAATTTATTTT
1 AAATTTAATTT
*
2298598 AAGTTTAATTT
1 AAATTTAATTT
*
2298609 -ATTTTGAATTT
1 AAATTT-AATTT
2298620 AAATTTAA
1 AAATTTAA
2298628 AGTTTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 4 0.12
11 20 0.59
12 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:2298607 original size:16 final size:16
Alignment explanation
Indices: 2298577--2298626 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
2298567 CAATTTTAAA
*
2298577 ATTTAAATTTAAATTT
1 ATTTTAATTTAAATTT
2298593 ATTTTAAGTTT-AATTT
1 ATTTTAA-TTTAAATTT
2298609 ATTTTGAATTTAAATTT
1 ATTTT-AATTTAAATTT
2298626 A
1 A
2298627 AAGTTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTTTAATTTAAATTT
Found at i:2305111 original size:2 final size:2
Alignment explanation
Indices: 2305104--2305131 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2305094 TTTGCGGGGC
2305104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2305132 GTGAAGTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2306481 original size:20 final size:19
Alignment explanation
Indices: 2306458--2306517 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
2306448 TATGATTTTA
2306458 ATATA-TAAAATATAATTT
1 ATATATTAAAATATAATTT
* * *
2306476 ATATATTTAAATTAAAAATT
1 ATATA-TTAAAATATAATTT
* *
2306496 AAAAATTAAAA-ATAATTT
1 ATATATTAAAATATAATTT
2306514 ATAT
1 ATAT
2306518 TAATGGAAAG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 12 0.40
19 5 0.17
20 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAAAATATAATTT
Found at i:2306506 original size:6 final size:7
Alignment explanation
Indices: 2306484--2306508 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2306474 TTATATATTT
2306484 AAATTAA
1 AAATTAA
2306491 AAATTAA
1 AAATTAA
2306498 AAATTAA
1 AAATTAA
2306505 AAAT
1 AAAT
2306509 AATTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:2306851 original size:31 final size:29
Alignment explanation
Indices: 2306793--2306869 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
2306783 CTCACTAAAT
*
2306793 TTTTAAAATTTTTAATTAGACCCTCAAAA
1 TTTTAAAATTTTTAATTAAACCCTCAAAA
*
2306822 CTTTTAAAATTTTTTAA-TAAACCTTTCAAAA
1 -TTTTAAAA-TTTTTAATTAAACC-CTCAAAA
* **
2306853 TTTCAAAACATTTAATT
1 TTTTAAAATTTTTAATT
2306870 TAACTCCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.13
30 21 0.54
31 13 0.33
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (29 bp):
TTTTAAAATTTTTAATTAAACCCTCAAAA
Found at i:2307509 original size:2 final size:2
Alignment explanation
Indices: 2307504--2307541 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2307494 TGTTTTTTTT
2307504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2307542 AAATAAACGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2308302 original size:5 final size:5
Alignment explanation
Indices: 2308292--2308340 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
2308282 CACCTAACAA
*
2308292 TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCT TGCC
1 TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGCC
2308341 GTCTGCTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.00, C:0.57, G:0.20, T:0.22
Consensus pattern (5 bp):
TGCCC
Found at i:2309356 original size:19 final size:19
Alignment explanation
Indices: 2309323--2309383 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
2309313 TCAACAAAAG
**
2309323 TTATAAAAAAATAAAATAT
1 TTATAAAAATTTAAAATAT
* *
2309342 TTTTTAAAATTTAAAATAT
1 TTATAAAAATTTAAAATAT
*
2309361 TTATAAAAATTTCAAA-AT
1 TTATAAAAATTTAAAATAT
2309379 TTATA
1 TTATA
2309384 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
18 7 0.20
19 28 0.80
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATAAAAATTTAAAATAT
Found at i:2316003 original size:118 final size:118
Alignment explanation
Indices: 2315777--2316004 Score: 303
Period size: 118 Copynumber: 1.9 Consensus size: 118
2315767 AAAAAAAGGG
* * * * * *
2315777 TAAGAAGAGCTTTTGATTGGTGTAAGCGGTGTGATTTTAATAGCCTAGTTATTTAAACGAAAACT
1 TAAGAAGAGCTTTTGATTGGTGTAAGCAGTGCGATTTTAATAGCCCAATGACTTAAACGAAAACT
* * * **
2315842 TTTGAATAGTTTGATTTGCAGATTCACGACACTTAAAGGTTTTATAAAGATTT
66 TTTGAATAGTTTAATTTACAGATTCACGACACTCAAAAATTTTATAAAGATTT
* * *
2315895 TAAGGAGAGCTTTTGATTGGTGTAAGCAGTGCGATTTTAATAGCCCAATGACTTAAATGAAAATT
1 TAAGAAGAGCTTTTGATTGGTGTAAGCAGTGCGATTTTAATAGCCCAATGACTTAAACGAAAACT
** *
2315960 TTTGAATAGTTTAATTTACAGATTCGTGACGCTCAAAAATTTTAT
66 TTTGAATAGTTTAATTTACAGATTCACGACACTCAAAAATTTTAT
2316005 GAAAACAAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (118 bp):
TAAGAAGAGCTTTTGATTGGTGTAAGCAGTGCGATTTTAATAGCCCAATGACTTAAACGAAAACT
TTTGAATAGTTTAATTTACAGATTCACGACACTCAAAAATTTTATAAAGATTT
Found at i:2324439 original size:23 final size:23
Alignment explanation
Indices: 2324369--2324537 Score: 166
Period size: 23 Copynumber: 7.3 Consensus size: 23
2324359 ACGGAACAAG
* *
2324369 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
2324390 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
2324415 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
2324438 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
2324461 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
2324484 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
2324507 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
2324530 CAGAGAGC
1 CAGAGAGC
2324538 GCGCTAGTGT
Statistics
Matches: 126, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
21 15 0.12
23 91 0.72
24 1 0.01
25 13 0.10
26 6 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:2324465 original size:46 final size:46
Alignment explanation
Indices: 2324415--2324537 Score: 185
Period size: 46 Copynumber: 2.7 Consensus size: 46
2324405 TGCTGGGCAA
*
2324415 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * *
2324461 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
*
2324507 CAGAGAGCACGAGAC-GTGCTAAACAGAGAGC
1 CAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
2324538 GCGCTAGTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 67 0.97
47 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:2324488 original size:69 final size:66
Alignment explanation
Indices: 2324369--2324513 Score: 193
Period size: 69 Copynumber: 2.1 Consensus size: 66
2324359 ACGGAACAAG
* *
2324369 CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGC
1 CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGTGC
2324434 TAAA
63 TAAA
2324438 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
2324502 CTAAT
62 CTAAA
2324507 CAGAGAG
1 CAGAGAG
2324514 CACGAGACGT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
68 2 0.03
69 38 0.55
70 11 0.16
71 11 0.16
72 7 0.10
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (66 bp):
CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCTAA
A
Found at i:2327703 original size:18 final size:18
Alignment explanation
Indices: 2327669--2327702 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2327659 ATAACCTTTA
2327669 AAAGTAAAAACTAAAAAT
1 AAAGTAAAAACTAAAAAT
2327687 AAAGT-AAAACTAAAAA
1 AAAGTAAAAACTAAAAA
2327703 AAAAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAGTAAAAACTAAAAAT
Found at i:2327708 original size:24 final size:25
Alignment explanation
Indices: 2327667--2327714 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2327657 GCATAACCTT
* **
2327667 TAAAAGTAAAAACTAAAAA-TAAAG
1 TAAAACTAAAAAAAAAAAAGTAAAG
2327691 TAAAACTAAAAAAAAAAAAGTAAA
1 TAAAACTAAAAAAAAAAAAGTAAA
2327715 CGATTTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (25 bp):
TAAAACTAAAAAAAAAAAAGTAAAG
Found at i:2328112 original size:14 final size:12
Alignment explanation
Indices: 2328079--2328108 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2328069 GAAGTATAGT
2328079 AAAACATTAAAA
1 AAAACATTAAAA
2328091 AAAACATTAAAA
1 AAAACATTAAAA
2328103 AAAACA
1 AAAACA
2328109 CATTTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAACATTAAAA
Found at i:2328804 original size:92 final size:91
Alignment explanation
Indices: 2328708--2328891 Score: 271
Period size: 92 Copynumber: 2.0 Consensus size: 91
2328698 ATACAATTCC
* *
2328708 TTAAAAGAAAATATACAATAAAATTAAAAATATTGATGT-GTTTTTTAAAATAAACTATTTATCA
1 TTAAAA-AAAAAATACAATAAAACTAAAAATATTGATGTAGTTTTTTAAAATAAACTATTTATCA
* *
2328772 TCATCTAACCTTCCATTTTTTTATAACT
65 TCACCTAACCTTCCA-TTTTATATAACT
* * * *
2328800 TTAAAAAAAAAATGCAATACAGCTAAAAATATTGATGTATTTTTTTAAAATAAACTATTTATCAT
1 TTAAAAAAAAAATACAATAAAACTAAAAATATTGATGTAGTTTTTTAAAATAAACTATTTATCAT
2328865 CACCTAACCTTCCATTTTATATAACT
66 CACCTAACCTTCCATTTTATATAACT
2328891 T
1 T
2328892 CATTAAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
91 39 0.47
92 44 0.53
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.40
Consensus pattern (91 bp):
TTAAAAAAAAAATACAATAAAACTAAAAATATTGATGTAGTTTTTTAAAATAAACTATTTATCAT
CACCTAACCTTCCATTTTATATAACT
Found at i:2329362 original size:26 final size:26
Alignment explanation
Indices: 2329306--2329363 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2329296 AAAATTTAAA
* *
2329306 ATAAAATATACAAAAATTATATATTT
1 ATAAAATATAAAAAAATTATATAATT
*
2329332 TTAAAATATAAAAGAAATTATA-AATT
1 ATAAAATATAAAA-AAATTATATAATT
2329358 ATAAAA
1 ATAAAA
2329364 ATACATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
ATAAAATATAAAAAAATTATATAATT
Found at i:2329364 original size:27 final size:26
Alignment explanation
Indices: 2329308--2329366 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2329298 AATTTAAAAT
* * * *
2329308 AAAATATACAAAAATTATATATTTTT
1 AAAATATAAAAAAATTATAAATTATA
2329334 AAAATATAAAAGAAATTATAAATTATA
1 AAAATATAAAA-AAATTATAAATTATA
2329361 AAAATA
1 AAAATA
2329367 CATGTATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAATATAAAAAAATTATAAATTATA
Found at i:2329428 original size:21 final size:23
Alignment explanation
Indices: 2329394--2329435 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2329384 AAAAATATTT
2329394 AAAAAATCTAAAATT-CAAATTA
1 AAAAAATCTAAAATTCCAAATTA
*
2329416 AAAAAATC-GAAATTCCAAAT
1 AAAAAATCTAAAATTCCAAAT
2329436 AATTTACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAAAATCTAAAATTCCAAATTA
Found at i:2331172 original size:22 final size:20
Alignment explanation
Indices: 2331147--2331190 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2331137 ATTACTATTT
2331147 TTAATTAAAGTTATTTAAAAAA
1 TTAATTAAA-TT-TTTAAAAAA
* *
2331169 TTAATTTAATTTTTATAAAA
1 TTAATTAAATTTTTAAAAAA
2331189 TT
1 TT
2331191 TTATAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAATTAAATTTTTAAAAAA
Found at i:2331973 original size:20 final size:21
Alignment explanation
Indices: 2331932--2331974 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
2331922 ATTTTTTAAA
2331932 AATATTTATATTATTTCAATTT
1 AATATTTATATTATTT-AATTT
2331954 AATATTTAATATT-TTT-ATTT
1 AATATTT-ATATTATTTAATTT
2331974 A
1 A
2331975 TTGAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATTTATATTATTTAATTT
Found at i:2334870 original size:6 final size:6
Alignment explanation
Indices: 2334859--2334903 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
2334849 TATCATCTCT
* * *
2334859 TTCATC TTCATC TTCACC TTCACC TTCACC TTCATC TTCACC TTC
1 TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC TTC
2334904 GTGGTCATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (6 bp):
TTCACC
Found at i:2334879 original size:12 final size:12
Alignment explanation
Indices: 2334859--2334903 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
2334849 TATCATCTCT
*
2334859 TTCATCTTCATC
1 TTCACCTTCATC
*
2334871 TTCACCTTCACC
1 TTCACCTTCATC
2334883 TTCACCTTCATC
1 TTCACCTTCATC
2334895 TTCACCTTC
1 TTCACCTTC
2334904 GTGGTCATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (12 bp):
TTCACCTTCATC
Found at i:2337051 original size:24 final size:24
Alignment explanation
Indices: 2337024--2337074 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2337014 TCTTTTAATT
** *
2337024 GATACCCTGCTTTGTTTTCGGTTC
1 GATACCCTAATTTGTTTTCGATTC
2337048 GATACCCTAATTTGTTTTCGATTC
1 GATACCCTAATTTGTTTTCGATTC
2337072 GAT
1 GAT
2337075 GAATTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.45
Consensus pattern (24 bp):
GATACCCTAATTTGTTTTCGATTC
Found at i:2342362 original size:94 final size:92
Alignment explanation
Indices: 2342237--2342467 Score: 247
Period size: 94 Copynumber: 2.5 Consensus size: 92
2342227 TATTTCCAAG
* * * *
2342237 AAAAAATTAAAAGAAATTAAAAACATAAAATGATTTTACTATAAACACTC-AAGTAATTTTCTTT
1 AAAAAATTAAAACAAAATAAAAACATAAAATGATTTTACTATAAACACTCGAA-CAACTTTCTTT
2342301 AAAACCCG-GGACTTTCCTTACACCGAAA
65 AAAACCCGAGG-CTTTCCTTACACCGAAA
* * *
2342329 AAAATAATTATAAACAAAATAAAAATATAAAATGATTTTACTATGAATACTCGAACAACTTTCTT
1 AAAA-AATTA-AAACAAAATAAAAACATAAAATGATTTTACTATAAACACTCGAACAACTTTCTT
*
2342394 TAAAACCCGAGGCTTTCCTCT-TA-CGAAA
64 TAAAACCCGAGGCTTTCCT-TACACCGAAA
* * * * *
2342422 AAAAAATCTAAAATAAATTAAAAA-ACAAATTGATTTTTCCTATAAA
1 AAAAAAT-TAAAACAAAATAAAAACATAAAATGA-TTTTACTATAAA
2342468 AACCCAGATA
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
91 7 0.06
92 29 0.25
93 16 0.14
94 61 0.52
95 5 0.04
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.29
Consensus pattern (92 bp):
AAAAAATTAAAACAAAATAAAAACATAAAATGATTTTACTATAAACACTCGAACAACTTTCTTTA
AAACCCGAGGCTTTCCTTACACCGAAA
Found at i:2343423 original size:15 final size:16
Alignment explanation
Indices: 2343402--2343448 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
2343392 AAACATCGTC
2343402 CTAAATTATAATATAA
1 CTAAATTATAATATAA
*
2343418 -TAAATTTTAA-ATAAA
1 CTAAATTATAATAT-AA
2343433 CTAAATTATAAATATA
1 CTAAATTAT-AATATA
2343449 TATTTAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 7 0.28
17 3 0.12
18 2 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
CTAAATTATAATATAA
Found at i:2347269 original size:45 final size:45
Alignment explanation
Indices: 2347220--2347777 Score: 427
Period size: 45 Copynumber: 12.9 Consensus size: 45
2347210 AGATTGCCTC
* * ** *
2347220 GACAGTGAATAGCTCAGCTGAGAAGATGAAGAACGAGATGGTCAT
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
* * *
2347265 GACAGTAAATAACTCCA-CTGAGGAGATGAA-AAGAGAGACA-AC-T
1 GACAGTAAATAGCT-CAGCTGAGAAGATGAAGAA-AGAGACAGCCAT
* * * *
2347308 -TCAATAAAGAGCTCAGCGGAGAAGATGAAGAAAGA-A-A--CAT
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
* *
2347348 --TATTAAATAGCTCAGCTGAGAAGATGAAGAAAGA-A-A--CAT
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
*
2347387 --CATTAAATAGCTCAGCTGAGAAGATG-AGACAAGAGACAG-C-T
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGA-AAGAGACAGCCAT
* * * * *
2347428 -ACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTT
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
* * *
2347472 GACAGTAAATATCTCAGCTGAGAAGATGAACAAAGAGACAGCCTT
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
* * ** *
2347517 GACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGCCAG
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
* *
2347562 GACAGTCAATAGCTCAGCCGAGAAGATG-AGACAAGAGACAG-C-T
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGA-AAGAGACAGCCAT
* * * *
2347605 -ACAGTAAATGGTTCAGCTGAGAAGATGAAGAAAGAGACGGCCTT
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
* * * * *
2347649 GACAGTAAAGAGCTCGAAC-GAGAAGGTGAAGAAAGAAACAGCCTT
1 GACAGTAAATAGCTC-AGCTGAGAAGATGAAGAAAGAGACAGCCAT
* * * *
2347694 GACAGTAAATAACTCGGCTGAGAAGGTTAAGAAAGAGATC-G-C-T
1 GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGA-CAGCCAT
* * *
2347737 GCAACAGTGAATGGCTCAGCTGAGAAGATGAAAAAAGAGAC
1 G--ACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGAC
2347778 CACTGTGGCA
Statistics
Matches: 421, Mismatches: 68, Indels: 49
0.78 0.13 0.09
Matches are distributed among these distances:
38 3 0.01
39 65 0.15
40 3 0.01
41 5 0.01
42 85 0.20
43 13 0.03
44 12 0.03
45 230 0.55
46 5 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (45 bp):
GACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCCAT
Found at i:2347499 original size:87 final size:87
Alignment explanation
Indices: 2347390--2347663 Score: 372
Period size: 87 Copynumber: 3.1 Consensus size: 87
2347380 GAAACATCAT
*
2347390 TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATG
1 TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAGAAGATG
*
2347455 AAGAAAGAGACAGCCTTGACAG
66 AAGAAAGAGACGGCCTTGACAG
* ***
2347477 TAAATATCTCAGCTGAGAAGATGA-ACAAAGAGACAGCCTTGACA-ATAAATAACTCAGCTGAGA
1 TAAATAGCTCAGCTGAGAAGATGAGAC-AAGAGACAG-C-T-ACAGA-AAATGGTTCAGCTGAGA
* **
2347540 AGATGAAGAAAGAGATGGCCAGGACAG
61 AGATGAAGAAAGAGACGGCCTTGACAG
* * *
2347567 TCAATAGCTCAGCCGAGAAGATGAGACAAGAGACAGCTACAGTAAATGGTTCAGCTGAGAAGATG
1 TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAGAAGATG
2347632 AAGAAAGAGACGGCCTTGACAG
66 AAGAAAGAGACGGCCTTGACAG
*
2347654 TAAAGAGCTC
1 TAAATAGCTC
2347664 GAACGAGAAG
Statistics
Matches: 159, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
86 2 0.01
87 81 0.51
88 2 0.01
89 3 0.02
90 69 0.43
91 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.15
Consensus pattern (87 bp):
TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAGAAGATG
AAGAAAGAGACGGCCTTGACAG
Found at i:2347609 original size:132 final size:135
Alignment explanation
Indices: 2347440--2347684 Score: 331
Period size: 132 Copynumber: 1.8 Consensus size: 135
2347430 AGAAAATGGT
*
2347440 TCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAAT-ATCTCAGCTGAGAAGATGAACA
1 TCAGCCGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATGAT-TCAGCTGAGAAGATGAACA
* *
2347504 AAGAGACAGCCTTGACAATAAATAACTC-AGCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGT
65 AAGAGACAGCCTTGACAATAAAGAACTCGAAC-GAGAAGATGAAGAAAGAGATGGCCAGGACAGT
2347568 CAATAGC
129 CAATAGC
* * *
2347575 TCAGCCGAGAAGATG-AGACAAGAGACAG-C-T-ACAGTAAATGGTTCAGCTGAGAAGATGAAGA
1 TCAGCCGAAAAGATGAAGA-AAGAGACAGCCTTGACAGTAAATGATTCAGCTGAGAAGATGAACA
* * * *
2347636 AAGAGACGGCCTTGACAGTAAAGAGCTCGAACGAGAAGGTGAAGAAAGA
65 AAGAGACAGCCTTGACAATAAAGAACTCGAACGAGAAGATGAAGAAAGA
2347685 AACAGCCTTG
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
132 67 0.69
133 4 0.04
134 4 0.04
135 22 0.23
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.14
Consensus pattern (135 bp):
TCAGCCGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATGATTCAGCTGAGAAGATGAACAA
AGAGACAGCCTTGACAATAAAGAACTCGAACGAGAAGATGAAGAAAGAGATGGCCAGGACAGTCA
ATAGC
Found at i:2347650 original size:177 final size:176
Alignment explanation
Indices: 2347351--2347777 Score: 553
Period size: 177 Copynumber: 2.4 Consensus size: 176
2347341 GAAACATTAT
* * * * *
2347351 TAAATAGCTCAGCTGAGAAGATGAAGAAAGA-A----ACATCATTAAATAGCTCAGCTGAGAAGA
1 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGCGCAACAGTCAATAGCTCAGCTGAGAAGA
2347411 TGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACA
66 TGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACA
* * * *
2347476 GTAAATATCTC-AGCTGAGAAGATGAACAAAGAGACAGCCTTGACAA
131 GTAAAGAGCTCGAAC-GAGAAGATGAACAAAGAAACAGCCTTGACAA
* *
2347522 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGC-CAGGACAGTCAATAGCTCAGCCGAGAA
1 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGCGCA--ACAGTCAATAGCTCAGCTGAGAA
* * *
2347586 GATGAGACAAGAGACAGCTACAGTAAATGGTTCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGA
64 GATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGA
* * *
2347651 CAGTAAAGAGCTCGAACGAGAAGGTGAAGAAAGAAACAGCCTTGACAG
129 CAGTAAAGAGCTCGAACGAGAAGATGAACAAAGAAACAGCCTTGACAA
* * * * *
2347699 TAAATAACTCGGCTGAGAAGGTTAAGAAAGAGATCGCTGCAACAGTGAATGGCTCAGCTGAGAAG
1 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGC-GCAACAGTCAATAGCTCAGCTGAGAAG
* *
2347764 ATGAAAAAAGAGAC
65 ATGAGACAAGAGAC
2347778 CACTGTGGCA
Statistics
Matches: 222, Mismatches: 24, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
171 30 0.14
172 1 0.00
175 2 0.01
177 185 0.83
178 2 0.01
179 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (176 bp):
TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGCGCAACAGTCAATAGCTCAGCTGAGAAGA
TGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACA
GTAAAGAGCTCGAACGAGAAGATGAACAAAGAAACAGCCTTGACAA
Found at i:2348857 original size:26 final size:26
Alignment explanation
Indices: 2348821--2348874 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2348811 CGCAAAATAA
2348821 TCATCGTTGTGATAAATTGTTTCATT
1 TCATCGTTGTGATAAATTGTTTCATT
2348847 TCATCGTTGTGATAAATTGTTTCATT
1 TCATCGTTGTGATAAATTGTTTCATT
2348873 TC
1 TC
2348875 GTTTGTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (26 bp):
TCATCGTTGTGATAAATTGTTTCATT
Found at i:2358832 original size:2 final size:2
Alignment explanation
Indices: 2358825--2358856 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2358815 TTTAAAATTC
2358825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2358857 TTAATTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2362854 original size:66 final size:66
Alignment explanation
Indices: 2362702--2362836 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
2362692 TTAAGCCTGG
2362702 AGGGATATATAAGCATTTTATGGTTTATAGGTTCACTGCTCATTAAGAGTATGAGGATTAAGGTT
1 AGGGATATATAAGCATTTTATGGTTTATAGGTTCACTGCTCATTAAGAGTATGAGGATTAAGGTT
2362767 T
66 T
2362768 AGGGATATATAAGCATTTTATGGTTTATAGGTTCACTGCTCATTAAGAGTATGAGGATTAAGGTT
1 AGGGATATATAAGCATTTTATGGTTTATAGGTTCACTGCTCATTAAGAGTATGAGGATTAAGGTT
2362833 T
66 T
2362834 AGG
1 AGG
2362837 TTTATTAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.37
Consensus pattern (66 bp):
AGGGATATATAAGCATTTTATGGTTTATAGGTTCACTGCTCATTAAGAGTATGAGGATTAAGGTT
T
Found at i:2371623 original size:2 final size:2
Alignment explanation
Indices: 2371616--2371654 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2371606 AGACATAATA
2371616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2371655 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2371659 original size:2 final size:2
Alignment explanation
Indices: 2371654--2371693 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2371644 ATATATATAT
2371654 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2371694 GGGGTTAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2376227 original size:23 final size:23
Alignment explanation
Indices: 2376182--2376227 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2376172 TAATATAAGG
**
2376182 ATAAAAATTATATTTTAACTCTC
1 ATAAAAATTATAACTTAACTCTC
2376205 ATAAAAATATATAACTTAA-TCTC
1 ATAAAAAT-TATAACTTAACTCTC
2376228 GACTCTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAAAAATTATAACTTAACTCTC
Found at i:2379167 original size:21 final size:21
Alignment explanation
Indices: 2379138--2379178 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2379128 AATCCCACAT
*
2379138 CAGTTTTTTACATCAAATAAG
1 CAGTATTTTACATCAAATAAG
2379159 CAGTATTTTACATCAAATAA
1 CAGTATTTTACATCAAATAA
2379179 AGAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
CAGTATTTTACATCAAATAAG
Found at i:2384572 original size:8 final size:8
Alignment explanation
Indices: 2384559--2384589 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
2384549 TTTTACCTAA
2384559 TTTGTCTC
1 TTTGTCTC
2384567 TTTGTCTC
1 TTTGTCTC
2384575 TTTGTCTC
1 TTTGTCTC
2384583 TTTGTCT
1 TTTGTCT
2384590 GCTTATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.13, T:0.65
Consensus pattern (8 bp):
TTTGTCTC
Found at i:2385706 original size:20 final size:20
Alignment explanation
Indices: 2385673--2385713 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2385663 GCTTTGTGAA
2385673 AGTTTTGCATAAAAAAACATT
1 AGTTTTGCATAAAAAAA-ATT
2385694 AGTTTTG-ATAAAAAAAATT
1 AGTTTTGCATAAAAAAAATT
2385713 A
1 A
2385714 ACTCATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (20 bp):
AGTTTTGCATAAAAAAAATT
Found at i:2386669 original size:24 final size:24
Alignment explanation
Indices: 2386623--2386672 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2386613 GATTTCTATT
*
2386623 TAAAAAATAAATTAAAACTAAAAA
1 TAAAAAATAAATTAAAACAAAAAA
*
2386647 TAAAAATTAAATTAACAA-AAAAAA
1 TAAAAAATAAATTAA-AACAAAAAA
2386671 TA
1 TA
2386673 TAACGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (24 bp):
TAAAAAATAAATTAAAACAAAAAA
Found at i:2386671 original size:18 final size:18
Alignment explanation
Indices: 2386623--2386671 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2386613 GATTTCTATT
*
2386623 TAAAAAATAAATTAAAAC
1 TAAAAAAAAAATTAAAAC
*
2386641 TAAAAATAAAAATT-AAAT
1 TAAAAA-AAAAATTAAAAC
2386659 TAACAAAAAAAAT
1 TAA-AAAAAAAAT
2386672 ATAACGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAAAAAAATTAAAAC
Found at i:2389046 original size:31 final size:29
Alignment explanation
Indices: 2389006--2389093 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 29
2388996 GGTTAATATT
2389006 TAGAGTTTAACTAAAACTTTTAAAAATTTT-G
1 TAGA-TTTAA-TAAAA-TTTTAAAAATTTTGG
*
2389037 TAAGATTTAATGAGAATGTTTAAAAATTTTGG
1 T-AGATTTAAT-AAAAT-TTTAAAAATTTTGG
*
2389069 TAGAATTAATTAAAATTTTCAAAAA
1 TAGATTTAA-TAAAATTTT-AAAAA
2389094 CGATAAAGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
30 5 0.10
31 37 0.77
32 6 0.12
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.40
Consensus pattern (29 bp):
TAGATTTAATAAAATTTTAAAAATTTTGG
Found at i:2390873 original size:388 final size:389
Alignment explanation
Indices: 2390105--2390882 Score: 1549
Period size: 389 Copynumber: 2.0 Consensus size: 389
2390095 TACGCTAGTT
2390105 AATCTTTAATTTTTTTGTTGATCTATTGTATCAACTTCCTTTTGTTCTAAAAAAAAAACTTTAAA
1 AATCTTTAATTTTTTTGTTGATCTATTGTATCAACTTCCTTTTGTTCTAAAAAAAAAACTTTAAA
2390170 TTTACCATTCAACAAAAACTTCATTTTGATGTATTTTAATATACATAAATTATTATCTCTATTAA
66 TTTACCATTCAACAAAAACTTCATTTTGATGTATTTTAATATACATAAATTATTATCTCTATTAA
2390235 TTGTATATTTATATTTAAAATAGCGAAAATAACTTACATAAAACAATTATTTTTATTATTAAAGC
131 TTGTATATTTATATTTAAAATAGCGAAAATAACTTACATAAAACAATTATTTTTATTATTAAAGC
2390300 TATCACTTTTTATTAAAAAAACGTAGTTTACAAAATAAAAAGCGGTGGTCCGATTAGGGAAAACC
196 TATCACTTTTTATTAAAAAAACGTAGTTTACAAAATAAAAAGCGGTGGTCCGATTAGGGAAAACC
2390365 CACAGAGCCATTATGGATTCAAGTGGCACCGACCCGTCATCCTTCCACTGCAGAGAGAAGGAAGT
261 CACAGAGCCATTATGGATTCAAGTGGCACCGACCCGTCATCCTTCCACTGCAGAGAGAAGGAAGT
2390430 TAGCTGCTCTGGGAAACCAACCTCACGCGTTGCCTTCCACTCTAGGAGACACGAGACCCGAACC
326 TAGCTGCTCTGGGAAACCAACCTCACGCGTTGCCTTCCACTCTAGGAGACACGAGACCCGAACC
2390494 AATCTTTAATTTTTTTGTTGATCTATTGTATCAACTTCCTTTTGTTCTAAAAAAAAAACTTTAAA
1 AATCTTTAATTTTTTTGTTGATCTATTGTATCAACTTCCTTTTGTTCTAAAAAAAAAACTTTAAA
2390559 TTTACCATTCAACAAAAACTTCATTTTGATGTATTTTAATATACATAAATTATTATCTCTATTAA
66 TTTACCATTCAACAAAAACTTCATTTTGATGTATTTTAATATACATAAATTATTATCTCTATTAA
2390624 TTGTATATTTATATTTAAAATAGCGAAAATAACTTACATAAAACAATTATTTTTATTATTAAAGC
131 TTGTATATTTATATTTAAAATAGCGAAAATAACTTACATAAAACAATTATTTTTATTATTAAAGC
2390689 TATCACTTTTTATTAAAAAAACGTAGTTTACAAAATAAAAAGCGGTGGTCCGATTAGGGAAAA-C
196 TATCACTTTTTATTAAAAAAACGTAGTTTACAAAATAAAAAGCGGTGGTCCGATTAGGGAAAACC
2390753 CACAGAGCCATTATGGATTCAAGTGGCACCGACCCGTCATCCTTCCACTGCAGAGAGAAGGAAGT
261 CACAGAGCCATTATGGATTCAAGTGGCACCGACCCGTCATCCTTCCACTGCAGAGAGAAGGAAGT
2390818 TAGCTGCTCTGGGAAACCAACCTCACGCGTTGCCTTCCACTCTAGGAGACACGAGACCCGAACC
326 TAGCTGCTCTGGGAAACCAACCTCACGCGTTGCCTTCCACTCTAGGAGACACGAGACCCGAACC
2390882 A
1 A
2390883 TCGTACAAGA
Statistics
Matches: 389, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
388 131 0.34
389 258 0.66
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (389 bp):
AATCTTTAATTTTTTTGTTGATCTATTGTATCAACTTCCTTTTGTTCTAAAAAAAAAACTTTAAA
TTTACCATTCAACAAAAACTTCATTTTGATGTATTTTAATATACATAAATTATTATCTCTATTAA
TTGTATATTTATATTTAAAATAGCGAAAATAACTTACATAAAACAATTATTTTTATTATTAAAGC
TATCACTTTTTATTAAAAAAACGTAGTTTACAAAATAAAAAGCGGTGGTCCGATTAGGGAAAACC
CACAGAGCCATTATGGATTCAAGTGGCACCGACCCGTCATCCTTCCACTGCAGAGAGAAGGAAGT
TAGCTGCTCTGGGAAACCAACCTCACGCGTTGCCTTCCACTCTAGGAGACACGAGACCCGAACC
Found at i:2404358 original size:2 final size:2
Alignment explanation
Indices: 2404351--2404379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2404341 TTATACATTT
2404351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2404380 TATTTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2407892 original size:18 final size:16
Alignment explanation
Indices: 2407860--2407922 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
2407850 GATAAAATTG
2407860 AAAAAGAAAGAAAATA
1 AAAAAGAAAGAAAATA
2407876 AAAAAGCAAAGGAAAAT-
1 AAAAAG-AAA-GAAAATA
* *
2407893 ATAAAGAAA-AAATTGA
1 AAAAAGAAAGAAAAT-A
*
2407909 AAAAATAAAGAAAA
1 AAAAAGAAAGAAAA
2407923 GGAAGCGCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
14 4 0.11
16 16 0.43
17 11 0.30
18 6 0.16
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAAGAAAGAAAATA
Found at i:2408326 original size:10 final size:9
Alignment explanation
Indices: 2408293--2408328 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2408283 TTTAAAATTC
2408293 AAAATTTTA
1 AAAATTTTA
*
2408302 AAAACTTTA
1 AAAATTTTA
2408311 AAAATTTTA
1 AAAATTTTA
2408320 AATAATTTT
1 AA-AATTTT
2408329 TTTTTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTA
Found at i:2418545 original size:23 final size:22
Alignment explanation
Indices: 2418423--2418547 Score: 115
Period size: 23 Copynumber: 5.5 Consensus size: 22
2418413 AGTGCTGGGG
*
2418423 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACAAAGTGC
* * * *
2418445 AATCCATTAGGCACACACAGTGC
1 AA-ACAGTAAGCACACAAAGTGC
* * * *
2418468 AATCAGTAGGCGCACATAGTGC
1 AAACAGTAAGCACACAAAGTGC
* *
2418490 AAATCAGTAGGCACACAAGGTGC
1 AAA-CAGTAAGCACACAAAGTGC
2418513 GAAACAGTAAGCACACAAAGTGC
1 -AAACAGTAAGCACACAAAGTGC
2418536 GAAACAGTAAGC
1 -AAACAGTAAGC
2418548 GCGCTAGCGT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
22 20 0.23
23 64 0.74
24 3 0.03
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (22 bp):
AAACAGTAAGCACACAAAGTGC
Found at i:2422828 original size:22 final size:22
Alignment explanation
Indices: 2422799--2422862 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2422789 AATGTAAAAA
2422799 ATAT-TATTTATTTAAATATTT
1 ATATATATTTATTTAAATATTT
* * * *
2422820 ATTTATATTTAATTACAT-TTAG
1 ATATATATTTATTTAAATATT-T
2422842 ATATATATTT-TTTAAATATTT
1 ATATATATTTATTTAAATATTT
2422863 TAATCTGTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 10 0.31
22 22 0.69
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATATATTTATTTAAATATTT
Found at i:2430772 original size:15 final size:15
Alignment explanation
Indices: 2430752--2430785 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2430742 TTAGTTATCG
*
2430752 TCTTCGTCTTCATCA
1 TCTTCGTCATCATCA
*
2430767 TCTTCGTCATCTTCA
1 TCTTCGTCATCATCA
2430782 TCTT
1 TCTT
2430786 TTCCCTGTCA
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:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTTCGTCATCATCA
Found at i:2436709 original size:18 final size:18
Alignment explanation
Indices: 2436686--2436731 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2436676 AACATTTTCC
2436686 TTTAATTAAATTAGAAA-A
1 TTTAATTAAATTA-AAATA
2436704 TTTAATT-AATTAAAATTA
1 TTTAATTAAATTAAAA-TA
2436722 TTTAATTAAA
1 TTTAATTAAA
2436732 AAATCAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 5 0.20
18 15 0.60
19 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTAATTAAATTAAAATA
Found at i:2437262 original size:18 final size:18
Alignment explanation
Indices: 2437221--2437256 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2437211 TATTAATTAA
2437221 AATTAAAAACTAAAAAAT
1 AATTAAAAACTAAAAAAT
2437239 AATTAAAAAC-AAAAAAT
1 AATTAAAAACTAAAAAAT
2437256 A
1 A
2437257 TTTTAACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (18 bp):
AATTAAAAACTAAAAAAT
Found at i:2442495 original size:19 final size:18
Alignment explanation
Indices: 2442468--2442504 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2442458 AAAGCAGTAA
*
2442468 TTTTTTTTGTTTATTATT
1 TTTTTTTTGATTATTATT
2442486 TTTTTATTTGATTATTATT
1 TTTTT-TTTGATTATTATT
2442505 AGAAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTTTTGATTATTATT
Found at i:2442857 original size:19 final size:18
Alignment explanation
Indices: 2442800--2442858 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
2442790 CAAAAAATAT
*
2442800 AAAAA-TAAAAGTTATAA
1 AAAAATTAAAATTTATAA
* *
2442817 AAATTATTAAATTTTAATAA
1 AAA-AATTAAAATTT-ATAA
2442837 AAAAATTAAAATTTATGAA
1 AAAAATTAAAATTTAT-AA
2442856 AAA
1 AAA
2442859 CTAGAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 20 0.61
20 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAATTAAAATTTATAA
Found at i:2443080 original size:19 final size:19
Alignment explanation
Indices: 2443056--2443120 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
2443046 ATACGATAAT
2443056 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTACGAA
*
2443075 TTTTAT-ATTTCTTTAC-ATC
1 TTTTATAATTT-TTTACGA-A
*
2443094 TTTTATAATTTTCTTATG-A
1 TTTTATAATTTT-TTACGAA
2443113 TTTTATAA
1 TTTTATAA
2443121 AATTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
18 5 0.13
19 26 0.68
20 7 0.18
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAA
Found at i:2448488 original size:13 final size:13
Alignment explanation
Indices: 2448458--2448496 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2448448 TAAAAATTTC
*
2448458 AATTAATCAATATA
1 AATTAATTAAT-TA
*
2448472 AATTATTTAATTA
1 AATTAATTAATTA
2448485 AATTAATTAATT
1 AATTAATTAATT
2448497 TATTATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTAATTAATTA
Found at i:2451029 original size:25 final size:24
Alignment explanation
Indices: 2450984--2451031 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2450974 TTATTCTATT
*
2450984 AGCTACACAATTGTACCAATTTTA
1 AGCTACACAATTGTACAAATTTTA
2451008 AGCTACACAAATTGATA-AAATTTT
1 AGCTACAC-AATTG-TACAAATTTT
2451032 TAACAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 11 0.52
26 2 0.10
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (24 bp):
AGCTACACAATTGTACAAATTTTA
Found at i:2453937 original size:16 final size:15
Alignment explanation
Indices: 2453907--2453944 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
2453897 AATGCACAAA
*
2453907 ATAAATTATAAAAAT
1 ATAAATTAAAAAAAT
2453922 ATAAATATAAAAAAAT
1 ATAAAT-TAAAAAAAT
2453938 ATAAATT
1 ATAAATT
2453945 TAAGTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAATTAAAAAAAT
Found at i:2454040 original size:13 final size:13
Alignment explanation
Indices: 2453997--2454041 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
2453987 TCTATGAGTA
2453997 AAAAAAATTATGT
1 AAAAAAATTATGT
*
2454010 AACAAAAATATTTAGT
1 AA-AAAAAT-TAT-GT
2454026 AAAAAAATTATGT
1 AAAAAAATTATGT
2454039 AAA
1 AAA
2454042 TATCAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.26
14 8 0.30
15 8 0.30
16 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAAAAATTATGT
Found at i:2457444 original size:43 final size:43
Alignment explanation
Indices: 2457376--2457457 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
2457366 TAAAAATTGG
* *
2457376 AAATTGTGAATCAATAAGCTAACAAGTTTGACTACCAACAATT
1 AAATTGAGAATCAATAAGCTAACAAGTCTGACTACCAACAATT
* *
2457419 AAATTGAGAATCAAT-AGTCTGACAAGTCTGACTATCAAC
1 AAATTGAGAATCAATAAG-CTAACAAGTCTGACTACCAAC
2457458 TAGGTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (43 bp):
AAATTGAGAATCAATAAGCTAACAAGTCTGACTACCAACAATT
Found at i:2461536 original size:1 final size:1
Alignment explanation
Indices: 2461532--2461557 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2461522 GGAAAGTATT
2461532 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
2461558 ATAGAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2462285 original size:4 final size:4
Alignment explanation
Indices: 2462276--2462304 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2462266 TTTTTGTGGA
2462276 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
2462305 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:2466283 original size:3 final size:3
Alignment explanation
Indices: 2466275--2466302 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2466265 CGAACATTAC
2466275 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2466303 ACAGGACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2466758 original size:6 final size:6
Alignment explanation
Indices: 2466749--2466794 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
2466739 TTTTTCCCCT
* * *
2466749 ACCAAG ACCAAG ACCAAG ACCAAG ACCATG ACCATG ACCATG ACCA
1 ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCA
2466795 GTTATCTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.43, C:0.35, G:0.15, T:0.07
Consensus pattern (6 bp):
ACCAAG
Found at i:2466974 original size:2 final size:2
Alignment explanation
Indices: 2466969--2466997 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2466959 AAAGCTTTTT
2466969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2466998 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2468776 original size:63 final size:63
Alignment explanation
Indices: 2468667--2468966 Score: 256
Period size: 63 Copynumber: 4.9 Consensus size: 63
2468657 TGAAGTGCAG
* * *
2468667 GCTCCTGTTGAGGAGTTGCAGAAGGTCCTGGTGCTGTTATATTGTAATGTATGGTAAGAGGTT
1 GCTCCTGTTGAGGAGTTGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
* * * * ** ** * *
2468730 GGTCCTGTTGAGGAGTCGCGGAAGGTCCTGATGCTGCTACGCTGTAATGCGTGGCCTGAGGTT
1 GCTCCTGTTGAGGAGTTGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
* * *
2468793 GTTCCTGTTGAGGAGTTGCTGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
1 GCTCCTGTTGAGGAGTTGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
* ** * * * *
2468856 GCT-CTGGTTGAGGAGCTGTGGAAGGTGCC--G-G-AGCTATGCTGTAATGTATGGACTGAGGTT
1 GCTCCT-GTTGAGGAGTTGCAGAAGGT-CCTGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
* * ** * * *
2468916 GCTCTTGTTGATGAGTCACTGAAGGTCC---CGCTGCTATACTGTAATGAATGG
1 GCTCCTGTTGAGGAGTTGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGG
2468967 CCCGAGGTCG
Statistics
Matches: 190, Mismatches: 42, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
59 3 0.02
60 59 0.31
61 2 0.01
62 3 0.02
63 121 0.64
64 2 0.01
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.31
Consensus pattern (63 bp):
GCTCCTGTTGAGGAGTTGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
Found at i:2474264 original size:16 final size:17
Alignment explanation
Indices: 2474234--2474270 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2474224 GTTATAAAAT
2474234 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
2474252 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
2474268 TTT
1 TTT
2474271 TCATCTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:2478134 original size:63 final size:60
Alignment explanation
Indices: 2478035--2478261 Score: 233
Period size: 63 Copynumber: 3.7 Consensus size: 60
2478025 GTGCCTCCCA
*
2478035 TTGAGGAGTCGCAGAAGGTCCCGGTGCTGGTATACTGTAATGTATGGAAAGAGGTTGCTCCTG
1 TTGAGGAGTCGCAGAAGGTCCC---GCTGCTATACTGTAATGTATGGAAAGAGGTTGCTCCTG
* *
2478098 TTGAGGAGTCGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTAAGAGGTTGCT-CTGG
1 TTGAGGAGTCGCAGAAGGTCC---CGCTGCTATACTGTAATGTATGGAAAGAGGTTGCTCCT-G
* * * ** * ***
2478161 TTGAGGAG-CAACAGAAAGTCCCGATGCTACGCTGTAATGTACGGCCTGAGGTTGCTCCTG
1 TTGAGGAGTC-GCAGAAGGTCCCGCTGCTATACTGTAATGTATGGAAAGAGGTTGCTCCTG
* * *
2478221 TTGAGGAGTTGCTGAAGGTCCCGCTGCTATACCGTAATGTA
1 TTGAGGAGTCGCAGAAGGTCCCGCTGCTATACTGTAATGTA
2478262 CAGACCGAGG
Statistics
Matches: 136, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
60 60 0.44
61 2 0.01
62 3 0.02
63 71 0.52
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (60 bp):
TTGAGGAGTCGCAGAAGGTCCCGCTGCTATACTGTAATGTATGGAAAGAGGTTGCTCCTG
Found at i:2481819 original size:16 final size:16
Alignment explanation
Indices: 2481798--2481831 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2481788 ACTAAAGAAC
2481798 AAATATAAGTGCATTT
1 AAATATAAGTGCATTT
* *
2481814 AAATATAATTGGATTT
1 AAATATAAGTGCATTT
2481830 AA
1 AA
2481832 TCTAAATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (16 bp):
AAATATAAGTGCATTT
Found at i:2485435 original size:20 final size:21
Alignment explanation
Indices: 2485409--2485469 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
2485399 TTTAAAAAAA
*
2485409 TTAAAATATTTTTTATAATTT
1 TTAAAATAATTTTTATAATTT
2485430 TT-AAATAATTTTTAT--TTT
1 TTAAAATAATTTTTATAATTT
*
2485448 TTGAAAATAGTTTTT-TAATTT
1 TT-AAAATAATTTTTATAATTT
2485469 T
1 T
2485470 CTTTTGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 22 0.65
21 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TTAAAATAATTTTTATAATTT
Found at i:2486513 original size:19 final size:19
Alignment explanation
Indices: 2486471--2486507 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2486461 AAAAATATTT
2486471 AAAAATAAAATAAAGTTCA
1 AAAAATAAAATAAAGTTCA
*
2486490 AAAAATATAA-AAAGTTCA
1 AAAAATAAAATAAAGTTCA
2486508 TGAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
AAAAATAAAATAAAGTTCA
Found at i:2492234 original size:30 final size:30
Alignment explanation
Indices: 2492194--2492264 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2492184 AGAGTCGATT
2492194 CTCCTTCTCCAGCTCCAGAA-TCTGACATTG
1 CTCCTTCTCCAGCTCCAGAATTC-GACATTG
*
2492224 CTCCTACTCCAGCTCCAGAATTCGACATTG
1 CTCCTTCTCCAGCTCCAGAATTCGACATTG
2492254 CTCCTTCTCCA
1 CTCCTTCTCCA
2492265 TCTGATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.20, C:0.39, G:0.11, T:0.30
Consensus pattern (30 bp):
CTCCTTCTCCAGCTCCAGAATTCGACATTG
Done.