Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008000.1 Hibiscus syriacus cultivar Beakdansim tig00110457_pilon, whole genome shotgun sequence
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: 1646480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1071624 original size:13 final size:13
Alignment explanation
Indices: 1071606--1071630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1071596 ACGGTCAACG
1071606 GTCAACGGGTCGA
1 GTCAACGGGTCGA
1071619 GTCAACGGGTCG
1 GTCAACGGGTCG
1071631 GGTTGGGTCA
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:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:1071640 original size:18 final size:18
Alignment explanation
Indices: 1071611--1071657 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1071601 CAACGGTCAA
*
1071611 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1071629 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1071647 CGGGTCGGGTC
1 CGGGTCGGGTC
1071658 GGGTTGTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1076778 original size:8 final size:8
Alignment explanation
Indices: 1076745--1076799 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1076735 TCAAAGTTTT
1076745 GGTCAACAG
1 GGTCAAC-G
1076754 TGGTCAACG
1 -GGTCAACG
1076763 ACGGTCAACG
1 --GGTCAACG
1076773 GGTCAAC-
1 GGTCAACG
1076780 GGTCAACG
1 GGTCAACG
1076788 GGTCAACG
1 GGTCAACG
1076796 GGTC
1 GGTC
1076800 GGGTCGGGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.45
9 1 0.02
10 15 0.36
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1076783 original size:15 final size:15
Alignment explanation
Indices: 1076763--1076796 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1076753 GTGGTCAACG
1076763 ACGGTCAACGGGTCA
1 ACGGTCAACGGGTCA
1076778 ACGGTCAACGGGTCA
1 ACGGTCAACGGGTCA
1076793 ACGG
1 ACGG
1076797 GTCGGGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.12
Consensus pattern (15 bp):
ACGGTCAACGGGTCA
Found at i:1076804 original size:5 final size:5
Alignment explanation
Indices: 1076794--1076854 Score: 68
Period size: 5 Copynumber: 11.0 Consensus size: 5
1076784 AACGGGTCAA
1076794 CGGGT CGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT CGGGT CAACGGGT
1 CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT CGGGT ---CGGGT
1076845 CGGGT CGGGT
1 CGGGT CGGGT
1076855 TGTGACCGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
5 40 0.80
8 10 0.20
ACGTcount: A:0.07, C:0.21, G:0.54, T:0.18
Consensus pattern (5 bp):
CGGGT
Found at i:1076812 original size:23 final size:23
Alignment explanation
Indices: 1076786--1076854 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
1076776 CAACGGTCAA
1076786 CGGGTCAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCGGGT
1076809 CGGGTCAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCGGGT
1076832 CGGGTCAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCGGGT
1076855 TGTGACCGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.52, T:0.17
Consensus pattern (23 bp):
CGGGTCAACGGGTCGGGTCGGGT
Found at i:1076817 original size:46 final size:45
Alignment explanation
Indices: 1076765--1076854 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
1076755 GGTCAACGAC
1076765 GGTCAACGGGTCAACGGTC-AACGGGTCAACGGGTCGGGTCGGGTCG
1 GGTCAACGGGTC--CGGTCGAACGGGTCAACGGGTCGGGTCGGGTCG
* **
1076811 GGTCAACGGGTCGGGTCGGGTCGGGTCAACGGGTCGGGTCGGGT
1 GGTCAACGGGTCCGGTC-GAACGGGTCAACGGGTCGGGTCGGGT
1076855 TGTGACCGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 4 0.10
46 35 0.90
ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17
Consensus pattern (45 bp):
GGTCAACGGGTCCGGTCGAACGGGTCAACGGGTCGGGTCGGGTCG
Found at i:1080041 original size:14 final size:15
Alignment explanation
Indices: 1080015--1080043 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1080005 TTTAGATAAA
1080015 TATTTTATTAATATT
1 TATTTTATTAATATT
1080030 TATTTT-TTAATATT
1 TATTTTATTAATATT
1080044 AAGAAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATTAATATT
Found at i:1082214 original size:8 final size:7
Alignment explanation
Indices: 1082190--1082231 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1082180 TTTTCATACA
1082190 TGCA-TT
1 TGCATTT
1082196 TGCATTT
1 TGCATTT
1082203 TGCATCTT
1 TGCAT-TT
1082211 TGCATTT
1 TGCATTT
* *
1082218 TTCATTG
1 TGCATTT
1082225 TGCATTT
1 TGCATTT
1082232 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1082214 original size:15 final size:14
Alignment explanation
Indices: 1082190--1082231 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1082180 TTTTCATACA
1082190 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1082203 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
1082218 TTCATTGTGCATTT
1 TGCATTTTGCATTT
1082232 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1082327 original size:27 final size:27
Alignment explanation
Indices: 1082291--1082350 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1082281 CATTCACATA
*
1082291 TTTACATTTGTATTTGCATTTGCATTT
1 TTTACATTTGTATTTACATTTGCATTT
* *
1082318 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGTATTTACATTTGCATTT
1082344 TTTACAT
1 TTTACAT
1082351 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTACATTTGTATTTACATTTGCATTT
Found at i:1083992 original size:2 final size:2
Alignment explanation
Indices: 1083985--1084018 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1083975 TTATCCTTTA
1083985 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
1084019 CCTTTGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1084347 original size:17 final size:16
Alignment explanation
Indices: 1084323--1084354 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1084313 AAGAAAGAAG
1084323 AAAAAAAAAGGAAAAA
1 AAAAAAAAAGGAAAAA
1084339 AAAAGAAAAAGGAAAA
1 AAAA-AAAAAGGAAAA
1084355 TTGAATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAA
Found at i:1089123 original size:22 final size:22
Alignment explanation
Indices: 1089095--1089215 Score: 188
Period size: 22 Copynumber: 5.5 Consensus size: 22
1089085 ATCTACATTC
1089095 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1089117 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1089139 TTCAAAGATGATATATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
*
1089161 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1089183 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1089205 TTCAAAGATGA
1 TTCAAAGATGA
1089216 AAGCTTTATT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 89 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1090165 original size:74 final size:73
Alignment explanation
Indices: 1090009--1090181 Score: 247
Period size: 74 Copynumber: 2.4 Consensus size: 73
1089999 TGAAGAAGGA
* * * *
1090009 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
1 AGAACAAGTTCATAATAAGAAGAACTTATTCAACCTTTTGCTTAAATTCATCATTCAATGGATCA
*
1090074 GCATTTCC
66 GCATTGCC
* *
1090082 AGAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTTTGCTTAAATTCATCATTCAATGGATC
1 AGAACAAGTTCATAATAAGAAGAACTTATTCAACC-TTTTGCTTAAATTCATCATTCAATGGATC
1090147 AGCATTGCC
65 AGCATTGCC
** *
1090156 AGGTCAAGTTCATAATGAGAAGAACT
1 AGAACAAGTTCATAATAAGAAGAACT
1090182 CATCTGAAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 33 0.37
74 56 0.63
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (73 bp):
AGAACAAGTTCATAATAAGAAGAACTTATTCAACCTTTTGCTTAAATTCATCATTCAATGGATCA
GCATTGCC
Found at i:1090282 original size:113 final size:113
Alignment explanation
Indices: 1090082--1090798 Score: 1016
Period size: 113 Copynumber: 6.3 Consensus size: 113
1090072 CAGCATTTCC
* * * ** *
1090082 AGAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTTTGCTTAAATTCATCATTCAATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTTGCTCGAATTCATCATTCGATGGATC
* * * * *
1090147 AGCATTGCCAG-GTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
65 AACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
* *
1090196 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
*
1090261 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
* *
1090309 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATTATTCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCGAATTCATCATTCGATGGATC
* * * *
1090373 AACATTGCCAG-GTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
65 AACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
* * * *
1090422 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
1090487 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
66 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
* * * *
1090535 AGAAAAAGTTCATAATGAGCAGAATTTGTTCAACCTTTTGC-CTGAATTCATCACTT-GATTGAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC-GAATTCATCA-TTCGATGGAT
*
1090598 TAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
64 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
* *
1090648 AGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-CTGAATTCATCACTT-GATGGAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC-GAATTCATCA-TTCGATGGAT
*
1090711 TAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
64 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
*
1090761 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1090799 GTTTGATGCT
Statistics
Matches: 558, Mismatches: 38, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
112 7 0.01
113 510 0.91
114 41 0.07
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
Found at i:1090399 original size:226 final size:225
Alignment explanation
Indices: 1090082--1090798 Score: 1118
Period size: 226 Copynumber: 3.2 Consensus size: 225
1090072 CAGCATTTCC
* * * * *
1090082 AGAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTTTGCTTAAATTCATCATTCAATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTTGCTTGAATTCATCATTCGATGGATC
*
1090147 AGCATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
65 AACATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*
1090212 GAGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAG
130 GAGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCATT-GATGGATTAACTTTTCCAGAGAAAG
*
1090277 TTCATAATGAGAAGAACTCATCTGAAGAAGGA
194 TTCATAATGAGAAGAACTCATATGAAGAAGGA
*
1090309 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATTATTCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATCATTCGATGGATC
1090373 AACATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
65 AACATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1090438 GAGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCATTTGATGGATTAACTTTTCCAGAGAAAG
130 GAGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCA-TTGATGGATTAACTTTTCCAGAGAAAG
1090503 TTCATAATGAGAAGAACTCATATGAAGAAGGA
194 TTCATAATGAGAAGAACTCATATGAAGAAGGA
* * * * * *
1090535 AGAAAAAGTTCATAATGAGCAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTT-GATTGATT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCA-TTCGATGGATC
* * * * *
1090599 AACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAAAAGTTCATAA
65 AACATTGCCAG-GTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
** *
1090663 TGAGAAGAATTTGTTCAACCTTTTGC-CTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAA
129 TGAGAAGAGCTTATTCAACCTTTTGCTC-GAATTCATCA-TTGATGGATTAACTTTTCCAGAGAA
1090727 AGTTCATAATGAGAAGAACTCATATGAAGAAGGA
192 AGTTCATAATGAGAAGAACTCATATGAAGAAGGA
*
1090761 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1090799 GTTTGATGCT
Statistics
Matches: 455, Mismatches: 29, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
225 5 0.01
226 410 0.90
227 40 0.09
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (225 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
ACATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAGCTTATTCAACCTTTTGCTCGAATTCATCATTGATGGATTAACTTTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATATGAAGAAGGA
Found at i:1092892 original size:2 final size:2
Alignment explanation
Indices: 1092885--1092911 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1092875 ATCTTAGTCT
1092885 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
1092912 TGTTTAAATA
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:1093227 original size:14 final size:15
Alignment explanation
Indices: 1093201--1093229 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1093191 TTTAGATAAA
1093201 TATTTTATTAATATT
1 TATTTTATTAATATT
1093216 TATTTT-TTAATATT
1 TATTTTATTAATATT
1093230 AAGAAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATTAATATT
Found at i:1097966 original size:31 final size:31
Alignment explanation
Indices: 1097931--1097998 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1097921 TTCAAAAAAA
** * *
1097931 TAAGATATTTTCACTTTCGTTTTTATTTGAT
1 TAAGATATGATCACCTTCGTTTTTATTTAAT
1097962 TAAGATATGATCACCTTCGTTTTTATTTAAT
1 TAAGATATGATCACCTTCGTTTTTATTTAAT
*
1097993 AAAGAT
1 TAAGAT
1097999 GTGGTTATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (31 bp):
TAAGATATGATCACCTTCGTTTTTATTTAAT
Found at i:1098029 original size:150 final size:150
Alignment explanation
Indices: 1097758--1098068 Score: 586
Period size: 150 Copynumber: 2.1 Consensus size: 150
1097748 TTTGTCCACT
* * *
1097758 TTTGGTCACCGATTTCAAAAAAATAAGATATTTTCAGTTTCGTTTTTATTTGATTAAGATATGGT
1 TTTGGTCACTGATTTCAAAAAAATAAGATATTTTCACTTTCGTTTTTATTTGATTAAGATATGAT
*
1097823 CACCTTCGTTTTTATTTAATTAAGATGTGGTTATCCCGAGTTAACTGTCGTTAACGACAGTTAAA
66 CACCTTCGTTTTTATTTAATAAAGATGTGGTTATCCCGAGTTAACTGTCGTTAACGACAGTTAAA
1097888 TATTTTGATATAATCACACA
131 TATTTTGATATAATCACACA
1097908 TTTGGTCACTGATTTCAAAAAAATAAGATATTTTCACTTTCGTTTTTATTTGATTAAGATATGAT
1 TTTGGTCACTGATTTCAAAAAAATAAGATATTTTCACTTTCGTTTTTATTTGATTAAGATATGAT
1097973 CACCTTCGTTTTTATTTAATAAAGATGTGGTTATCCCGAGTTAACTGTCGTTAACGACAGTTAAA
66 CACCTTCGTTTTTATTTAATAAAGATGTGGTTATCCCGAGTTAACTGTCGTTAACGACAGTTAAA
1098038 TATTTTGATATAATCACACA
131 TATTTTGATATAATCACACA
1098058 TTTGGTCACTG
1 TTTGGTCACTG
1098069 TCATTTACAT
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 157 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (150 bp):
TTTGGTCACTGATTTCAAAAAAATAAGATATTTTCACTTTCGTTTTTATTTGATTAAGATATGAT
CACCTTCGTTTTTATTTAATAAAGATGTGGTTATCCCGAGTTAACTGTCGTTAACGACAGTTAAA
TATTTTGATATAATCACACA
Found at i:1098365 original size:17 final size:19
Alignment explanation
Indices: 1098343--1098385 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1098333 ACTCGGTACC
*
1098343 TTATTTATTA-TATA-TTT
1 TTATTTATTATTAAATTTT
1098360 TTATTT-TTATTAAATTTT
1 TTATTTATTATTAAATTTT
1098378 TTATTTAT
1 TTATTTAT
1098386 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 9 0.41
19 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTATTATTAAATTTT
Found at i:1098380 original size:18 final size:19
Alignment explanation
Indices: 1098346--1098383 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1098336 CGGTACCTTA
*
1098346 TTTATTATATATTTTTATT
1 TTTATTAAATATTTTTATT
1098365 TTTATTAAAT-TTTTTATT
1 TTTATTAAATATTTTTATT
1098383 T
1 T
1098384 ATAATTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTAAATATTTTTATT
Found at i:1098568 original size:24 final size:25
Alignment explanation
Indices: 1098541--1098594 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1098531 TTTTTAATAA
* *
1098541 ATTTTATTTTCAATTATGTA-AT-TT
1 ATTTTATTAT-AATTATATATATATT
1098565 ATTTT-TTATAATTATATATATATT
1 ATTTTATTATAATTATATATATATT
1098589 ATTTTA
1 ATTTTA
1098595 AAAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 8 0.32
23 5 0.20
24 12 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTTTATTATAATTATATATATATT
Found at i:1098626 original size:25 final size:25
Alignment explanation
Indices: 1098592--1098643 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1098582 ATATATTATT
1098592 TTAAAAATATTTT-TATATTAACTTA
1 TTAAAAATATTTTAT-TATTAACTTA
*
1098617 TTAAATATATTTTATTATTAACTTA
1 TTAAAAATATTTTATTATTAACTTA
1098642 TT
1 TT
1098644 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAAAAATATTTTATTATTAACTTA
Found at i:1105463 original size:19 final size:19
Alignment explanation
Indices: 1105423--1105464 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1105413 AAAAAAATTA
* *
1105423 AAAAACTTAATTTATTTAT
1 AAAAACCTAAATTATTTAT
1105442 AAAAACCTAAATT-TTTACT
1 AAAAACCTAAATTATTTA-T
1105461 AAAA
1 AAAA
1105465 TTATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAACCTAAATTATTTAT
Found at i:1107276 original size:23 final size:24
Alignment explanation
Indices: 1107242--1107293 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1107232 ATGAATAATG
* * *
1107242 ATATTTTTATA-TTTAACTTTTAA
1 ATATTTTAATATTTTAAATTTAAA
1107265 ATATTTTAATATTTTAAATTTAAA
1 ATATTTTAATATTTTAAATTTAAA
1107289 ATATT
1 ATATT
1107294 ATATTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTTTAATATTTTAAATTTAAA
Found at i:1113378 original size:29 final size:29
Alignment explanation
Indices: 1113343--1113428 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
1113333 TTGGACCAGT
1113343 GACTAAAATGTAACTTTTGAAAGTTTAGG
1 GACTAAAATGTAACTTTTGAAAGTTTAGG
* *
1113372 GGCTAAAGTATG-AAC-TTTGAAAAGTGTAGG
1 GACTAAA--ATGTAACTTTTG-AAAGTTTAGG
* *
1113402 GACTAAAATTTGTAATTTTTAAAAGTT
1 GACTAAAA--TGTAACTTTTGAAAGTT
1113429 ATATGTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
28 1 0.02
29 10 0.23
30 20 0.45
31 10 0.23
32 3 0.07
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
GACTAAAATGTAACTTTTGAAAGTTTAGG
Found at i:1115598 original size:36 final size:36
Alignment explanation
Indices: 1115548--1115686 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
1115538 AGTTGAGTAT
1115548 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* * *
1115584 TATCAACTTCGGTACATTCGTGTATCAATATTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1115620 TATCAGCTTTGGTACATTCGTGTATCAATTTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1115656 TATCAGCTTTGGCACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
1115687 CCAGTACCAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1122963 original size:36 final size:36
Alignment explanation
Indices: 1122919--1123058 Score: 244
Period size: 36 Copynumber: 3.9 Consensus size: 36
1122909 AGTTGGGTAT
1122919 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
1122955 TTTCAGCTTTGGTACATTCGTGTATCAAAGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
1122991 TATCCGCTTTGGTACATTCGTGTATCAATATTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1123027 TATCAGCTTTGGTACATTCGTGTATCAATGTT
1 TATCAGCTTTGGTACATTCGTGTATCAATGTT
1123059 CAGTATCGTC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1139562 original size:22 final size:22
Alignment explanation
Indices: 1139537--1139600 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1139527 CTGAATGATT
*
1139537 CAGTGTTGACTGATTTAGCAAA
1 CAGTGTTGAATGATTTAGCAAA
1139559 CAGTGTTGAATGATTTAGCAAA
1 CAGTGTTGAATGATTTAGCAAA
* *
1139581 CAGTGCTGAATGATTCAGCA
1 CAGTGTTGAATGATTTAGCA
1139601 CAGAAGTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (22 bp):
CAGTGTTGAATGATTTAGCAAA
Found at i:1139700 original size:16 final size:16
Alignment explanation
Indices: 1139679--1139733 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
1139669 AGAATCTCTA
1139679 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
*
1139695 AATCATTCAACATTTG
1 AATCATTCAGCATTTG
* *
1139711 AATCATTAAGCGTTT-
1 AATCATTCAGCATTTG
1139726 AATCATTC
1 AATCATTC
1139734 TGAAGTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 7 0.21
16 27 0.79
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:1140047 original size:29 final size:27
Alignment explanation
Indices: 1139985--1140068 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 27
1139975 ATGATTGAAT
*
1139985 ACTTTAAGTATATATTTT-AAAAAAAAA
1 ACTTTAAGTAT-TATTTTGATAAAAAAA
* *
1140012 ATTTTAAGTACTTATTTTGACTAAAAATA
1 ACTTTAAGTA-TTATTTTGA-TAAAAAAA
1140041 ACTTTAAGTATTTATTTTGATAAAAAAA
1 ACTTTAAGTA-TTATTTTGATAAAAAAA
1140069 CACTCCAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
27 15 0.31
28 9 0.19
29 24 0.50
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (27 bp):
ACTTTAAGTATTATTTTGATAAAAAAA
Found at i:1142027 original size:17 final size:17
Alignment explanation
Indices: 1142001--1142038 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1141991 TTTATATTTT
1142001 TATAACATTAATTAATA
1 TATAACATTAATTAATA
* *
1142018 TATAATATTACTTAATA
1 TATAACATTAATTAATA
1142035 TATA
1 TATA
1142039 TTAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAACATTAATTAATA
Found at i:1146993 original size:74 final size:74
Alignment explanation
Indices: 1146927--1147142 Score: 342
Period size: 74 Copynumber: 2.9 Consensus size: 74
1146917 TTTTCCGGTC
* * * * * *
1146927 AGATAGGGTCGAGCAGAGGTTATAAAATTTTTGGATTAGGCCGAATTCGGGTGAAAAATATATAT
1 AGATAAGGTTGAGCGGAGGTTATAAAATTTTCGGATCAGGTCGAATTCGGGTGAAAAATATATAT
1146992 TTTCCAATT
66 TTTCCAATT
*
1147001 AGATAAGGTTGAGCGGAGGTTATAAAATTTTCAGATCAGGTCGAATTCGGGTGAAAAATATATAT
1 AGATAAGGTTGAGCGGAGGTTATAAAATTTTCGGATCAGGTCGAATTCGGGTGAAAAATATATAT
1147066 TTTCCAATT
66 TTTCCAATT
***
1147075 AGATAAGGTTGAGCGGAGGTTATAAAATTTTCGGATCAGGTCGAATTCAAATGAAAAATATATAT
1 AGATAAGGTTGAGCGGAGGTTATAAAATTTTCGGATCAGGTCGAATTCGGGTGAAAAATATATAT
1147140 TTT
66 TTT
1147143 TAGATCAGAT
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 131 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (74 bp):
AGATAAGGTTGAGCGGAGGTTATAAAATTTTCGGATCAGGTCGAATTCGGGTGAAAAATATATAT
TTTCCAATT
Found at i:1147031 original size:37 final size:37
Alignment explanation
Indices: 1146990--1147106 Score: 89
Period size: 37 Copynumber: 3.2 Consensus size: 37
1146980 AAAAATATAT
1146990 ATTTTCCAATTAGATAAGGTTGAGCGGAGGTTATAAA
1 ATTTTCCAATTAGATAAGGTTGAGCGGAGGTTATAAA
* * * * * *** *
1147027 ATTTT-CAGATCAGGTCGAA--TTCGGGTGAAAAATAT-AT
1 ATTTTCCA-ATTAGAT--AAGGTT-GAGCGGAGGTTATAAA
1147064 ATTTTCCAATTAGATAAGGTTGAGCGGAGGTTATAAA
1 ATTTTCCAATTAGATAAGGTTGAGCGGAGGTTATAAA
1147101 ATTTTC
1 ATTTTC
1147107 GGATCAGGTC
Statistics
Matches: 54, Mismatches: 18, Indels: 16
0.61 0.20 0.18
Matches are distributed among these distances:
35 2 0.04
36 9 0.17
37 32 0.59
38 9 0.17
39 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (37 bp):
ATTTTCCAATTAGATAAGGTTGAGCGGAGGTTATAAA
Found at i:1149528 original size:24 final size:23
Alignment explanation
Indices: 1149490--1149535 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1149480 ACATGCAATT
1149490 AATTCGTGCAGGTACATAAAGGG
1 AATTCGTGCAGGTACATAAAGGG
* *
1149513 AATTACGTGCATGTACATGAAGG
1 AATT-CGTGCAGGTACATAAAGG
1149536 TGATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (23 bp):
AATTCGTGCAGGTACATAAAGGG
Found at i:1150442 original size:6 final size:6
Alignment explanation
Indices: 1150431--1150464 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1150421 GAATTTAAAC
1150431 TAATAT TAATAT TAATAT TAATAT ATATATAT TA
1 TAATAT TAATAT TAATAT TAATAT -TA-ATAT TA
1150465 TAACTATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATAT
Found at i:1153403 original size:22 final size:23
Alignment explanation
Indices: 1153378--1153434 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
1153368 TTTTATTTAG
1153378 TATATTATGTT-TTAT-TATCATA
1 TATATTATGTTCTTATATAT-ATA
*
1153400 TATATTATTATTCTTATATATATA
1 TATATTA-TGTTCTTATATATATA
1153424 TATATATATGT
1 TATAT-TATGT
1153435 AATTATCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 3 0.10
24 14 0.48
25 5 0.17
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATTATGTTCTTATATATATA
Found at i:1161347 original size:105 final size:105
Alignment explanation
Indices: 1161165--1161727 Score: 920
Period size: 105 Copynumber: 5.4 Consensus size: 105
1161155 AGGTCTTACC
* * *
1161165 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAAGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1161230 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
1161270 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1161335 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
1161375 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1161440 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
1161480 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1161545 ACGAAGGGACCGCTGGTTGTCAACAAACA--TCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
* *
1161583 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * * *
1161647 AGCGAAGGGATGGTTGGTTGTCTAA-AATA-ATTTCCCAGTTC
66 A-CGAAGGGACCGCTGGTTGTC-AACAA-ACATTTCCCAATTT
* *
1161688 CAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1161728 GGAACAATAC
Statistics
Matches: 433, Mismatches: 20, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.00
103 90 0.21
104 3 0.01
105 339 0.78
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
Found at i:1161830 original size:32 final size:32
Alignment explanation
Indices: 1161786--1161868 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
1161776 AATTCCTGGC
*
1161786 TCAAATTCACGGCGAAGGGGCCACCCACGGTT
1 TCAACTTCACGGCGAAGGGGCCACCCACGGTT
1161818 TCAACTTCACGGCGAAGGGGCCACCCACGGTT
1 TCAACTTCACGGCGAAGGGGCCACCCACGGTT
*
1161850 TCAACTTCACGACGAAGGG
1 TCAACTTCACGGCGAAGGG
1161869 AATCGTACAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (32 bp):
TCAACTTCACGGCGAAGGGGCCACCCACGGTT
Found at i:1163688 original size:2 final size:2
Alignment explanation
Indices: 1163683--1163711 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1163673 ATTATTCTTT
1163683 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
1163712 GTAATTATCT
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:1163689 original size:22 final size:21
Alignment explanation
Indices: 1163628--1163693 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
1163618 TAAATCTTTA
*
1163628 ATTATTTTTTTATTTAGTATATT
1 ATTA-TTTTTTATATA-TATATT
*
1163651 ATGT-TTTATTATCATATATATT
1 AT-TATTTTTTAT-ATATATATT
1163673 ATTATTCTTTTATATATATAT
1 ATTATT-TTTTATATATATAT
1163694 ATATATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.03
22 25 0.69
23 9 0.25
24 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTATTTTTTATATATATATT
Found at i:1171725 original size:2 final size:2
Alignment explanation
Indices: 1171718--1171747 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1171708 TGCACAATTA
1171718 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
1171748 GTCATCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1171990 original size:21 final size:21
Alignment explanation
Indices: 1171957--1172033 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
1171947 ATATATTCCA
* * *
1171957 AAGGACTAAATATGTGTCCCG
1 AAGGACCACATATATGTCCCG
* * *
1171978 AAGAACCACATATATGTTCCA
1 AAGGACCACATATATGTCCCG
** *
1171999 AAGGATTACATATATATCCCG
1 AAGGACCACATATATGTCCCG
1172020 AAGGACCACATATA
1 AAGGACCACATATA
1172034 ACCCTCGACT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATGTCCCG
Found at i:1172001 original size:42 final size:42
Alignment explanation
Indices: 1171945--1172033 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
1171935 AGGATCACAT
* *
1171945 ATATATATTCCAAAGGACTAAATATGTGTCCCGAAGAACCAC
1 ATATATATTCCAAAGGACTAAATATATATCCCGAAGAACCAC
* * * *
1171987 ATATATGTTCCAAAGGATTACATATATATCCCGAAGGACCAC
1 ATATATATTCCAAAGGACTAAATATATATCCCGAAGAACCAC
1172029 ATATA
1 ATATA
1172034 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (42 bp):
ATATATATTCCAAAGGACTAAATATATATCCCGAAGAACCAC
Found at i:1174413 original size:20 final size:20
Alignment explanation
Indices: 1174385--1174432 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1174375 ATCTGACTCA
*
1174385 AAATTCTGATAACTCAATAT
1 AAATACTGATAACTCAATAT
1174405 AAATACTGATAACTCAATAT
1 AAATACTGATAACTCAATAT
1174425 AAATACTG
1 AAATACTG
1174433 GATACCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATACTGATAACTCAATAT
Found at i:1174872 original size:7 final size:7
Alignment explanation
Indices: 1174848--1174881 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1174838 TAAAAACATG
1174848 ATTTCTA
1 ATTTCTA
* *
1174855 ATTTTTG
1 ATTTCTA
1174862 ATTTCTA
1 ATTTCTA
1174869 ATTTCTA
1 ATTTCTA
1174876 ATTTCT
1 ATTTCT
1174882 GATACAAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (7 bp):
ATTTCTA
Found at i:1177240 original size:12 final size:12
Alignment explanation
Indices: 1177225--1177271 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
1177215 CCGGTTTTTT
*
1177225 AACCGGATAAAA
1 AACCGGTTAAAA
1177237 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
1177252 AACCGGTTAAAA
1 AACCGGTTAAAA
1177264 AACCGGTT
1 AACCGGTT
1177272 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:1178154 original size:21 final size:21
Alignment explanation
Indices: 1178130--1178169 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1178120 TTTATTTTAT
1178130 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1178151 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1178170 AACTTGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1178222 original size:33 final size:32
Alignment explanation
Indices: 1178164--1178306 Score: 154
Period size: 33 Copynumber: 4.6 Consensus size: 32
1178154 TTTGTTTCAA
*
1178164 TTATCGAACTTGAAGATTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1178196 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
* * *
1178229 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
* *
1178261 TTAT-G---TTG-AGTTAATTAAGTATTTCAAT
1 TTATCGAACTTGAAGTT-TTTAAGTATTTGAAT
*
1178289 TTATCGAACTTGAGGTTT
1 TTATCGAACTTGAAGTTT
1178307 GATGCTTTCT
Statistics
Matches: 93, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
26 3 0.03
27 14 0.15
28 6 0.06
29 1 0.01
32 18 0.19
33 51 0.55
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:1178710 original size:15 final size:15
Alignment explanation
Indices: 1178685--1178740 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1178675 ATCTGGAATA
*
1178685 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1178700 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1178715 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1178732 TTAAAACCG
1 TTAAAACCG
1178741 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1178749 original size:21 final size:18
Alignment explanation
Indices: 1178704--1178737 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1178694 GTTTTTTTAT
1178704 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1178721 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1178738 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1178857 original size:15 final size:17
Alignment explanation
Indices: 1178831--1178862 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1178821 TTCTATGGGA
1178831 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1178847 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1178863 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1184977 original size:117 final size:117
Alignment explanation
Indices: 1184771--1185001 Score: 365
Period size: 117 Copynumber: 2.0 Consensus size: 117
1184761 TTTAGCTTTG
* * *
1184771 CCTTCTGAATTTCGGCTAATGTTTCCTTTCTGATCACTCGGAATTTGTTCCAGTCTTAATGGAGT
1 CCTTCTGAATTTCGGCTAATGTTGCCTTTCTGATCACTCAGAATTTGTTCCAGTCTTAATGGAGA
* * * *
1184836 ATGACTCTTTTCAGTAGCACTAACAGTGTCAACCGTCAGACCTAAAGCATTT
66 ATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTAAAGCATTT
*
1184888 CCTTCTGAATTTCGGCTATTGTTGCCTTTCTGATCACTCAG-ATGTTGTTCCAGTCTTAATGGAG
1 CCTTCTGAATTTCGGCTAATGTTGCCTTTCTGATCACTCAGAAT-TTGTTCCAGTCTTAATGGAG
*
1184952 AATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTGAAGCA
65 AATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTAAAGCA
1185002 CCAGTTTCCA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 2 0.02
117 102 0.98
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (117 bp):
CCTTCTGAATTTCGGCTAATGTTGCCTTTCTGATCACTCAGAATTTGTTCCAGTCTTAATGGAGA
ATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTAAAGCATTT
Found at i:1186421 original size:15 final size:17
Alignment explanation
Indices: 1186401--1186437 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1186391 TGAAACACGT
1186401 CAAAGAAA-AATT-ATC
1 CAAAGAAAGAATTAATC
*
1186416 CAAAGAAAGCATTAATC
1 CAAAGAAAGAATTAATC
1186433 CAAAG
1 CAAAG
1186438 GTCAAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (17 bp):
CAAAGAAAGAATTAATC
Found at i:1186568 original size:20 final size:18
Alignment explanation
Indices: 1186530--1186570 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1186520 CGACAGGTAC
*
1186530 AAAAAAAAAAAGAGATAG
1 AAAAAAAAAAAGACATAG
1186548 AAAAAAAAAAAGAACAGTAG
1 AAAAAAAAAAAG-ACA-TAG
1186568 AAA
1 AAA
1186571 GATAGAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 2 0.10
20 6 0.30
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAGACATAG
Found at i:1187173 original size:17 final size:17
Alignment explanation
Indices: 1187131--1187171 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1187121 TATTTTGAAT
*
1187131 TTATTTTAAATGGTATA
1 TTATTTTAAATGGTACA
1187148 TTATTTTAAATGGTACA
1 TTATTTTAAATGGTACA
1187165 TATATTT
1 T-TATTT
1187172 AATTTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (17 bp):
TTATTTTAAATGGTACA
Found at i:1187679 original size:2 final size:2
Alignment explanation
Indices: 1187672--1187708 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1187662 TATGTAATTA
1187672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1187709 TTTTTATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1189442 original size:35 final size:36
Alignment explanation
Indices: 1189324--1189465 Score: 214
Period size: 36 Copynumber: 4.0 Consensus size: 36
1189314 AAAGTTGAAC
* * *
1189324 ACTTAAATCAAAAGTGTCGATGCCTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCG
1189360 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCG
* *
1189396 ACTTGAATCGAAAGTGCCGATGCTTCTTTCCGTTC-
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCG
* *
1189431 ACTTGAATCGAAAGTGTTGATGCTTCCTTTCGTTC
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC
1189466 TTCTTGTTCA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 31 0.32
36 66 0.68
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCG
Found at i:1189453 original size:71 final size:72
Alignment explanation
Indices: 1189324--1189465 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 72
1189314 AAAGTTGAAC
*
1189324 ACTTAAATCAAAAGTGTCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTT
1 ACTTAAATCAAAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTT
1189389 CCGTTCG
66 CCGTTCG
* * * * *
1189396 ACTTGAATCGAAAGTGCCGATGCTTCTTTCCGTTC-ACTTGAATCGAAAGTGTTGATGCTTCCTT
1 ACTTAAATCAAAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTT
*
1189460 TCGTTC
66 CCGTTC
1189466 TTCTTGTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 33 0.52
72 30 0.48
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (72 bp):
ACTTAAATCAAAAGTGCCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTT
CCGTTCG
Found at i:1193886 original size:22 final size:22
Alignment explanation
Indices: 1193861--1193953 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
1193851 AAAATCATGG
*
1193861 AAGTGCCTTTGCACTAATACTA
1 AAGTGCCTTTGCACTAATACAA
* **
1193883 AAGTGCCTTTTCACTAATATTA
1 AAGTGCCTTTGCACTAATACAA
** **
1193905 AAGTGCCTCAGCACTGGTACAA
1 AAGTGCCTTTGCACTAATACAA
* * *
1193927 AAGTGCATTCGCACTGATACAA
1 AAGTGCCTTTGCACTAATACAA
1193949 AAGTG
1 AAGTG
1193954 GCGTAACACT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTGCCTTTGCACTAATACAA
Found at i:1194257 original size:18 final size:19
Alignment explanation
Indices: 1194215--1194261 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1194205 AGCCTGTCAC
*
1194215 TATCGATACTGGTCTTAGGG
1 TATCGATACTGGCCTTA-GG
*
1194235 TATCGATATTGGCCTTA-G
1 TATCGATACTGGCCTTAGG
1194253 TATCGATAC
1 TATCGATAC
1194262 CAATTTTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (19 bp):
TATCGATACTGGCCTTAGG
Found at i:1194812 original size:2 final size:2
Alignment explanation
Indices: 1194807--1194856 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1194797 CTATATAACA
1194807 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
1194849 AT AT AT AT
1 AT AT AT AT
1194857 TCGAATATGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1197767 original size:31 final size:31
Alignment explanation
Indices: 1197729--1197851 Score: 203
Period size: 31 Copynumber: 4.0 Consensus size: 31
1197719 CCCGAAGGAC
* * *
1197729 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1197760 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1197791 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1197822 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1197852 CCCTCGACCC
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1208801 original size:68 final size:68
Alignment explanation
Indices: 1208713--1208982 Score: 320
Period size: 68 Copynumber: 4.0 Consensus size: 68
1208703 TTAGGAATTT
* * *
1208713 TTTATGGTAAACTACTTATTTGGTCACTTATATATTATCTAGTTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1208778 TTA
66 TTA
* * * *
1208781 TTTAGAGTAAACTACATATTTAGTCACATATATATTATCTAATTTATGTTTTGG-CGACTCGATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTC-ACTCGATT
1208845 ATTA
65 ATTA
* * ** *
1208849 TTTAGGGTAAACTACCTATTTGATCACTTATATATTATCTAATATAAT-TCAT-AT-A-T--ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
1208908 TTTA
65 ATTA
* * **
1208912 TTTAGGGTAAGCTACCTATTTGGTAACTTATATATTATCTAATTTATGTTTTGGTCACTTTATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1208977 TTA
66 TTA
1208980 TTT
1 TTT
1208983 TTTTCAAAAT
Statistics
Matches: 169, Mismatches: 24, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
62 3 0.02
63 48 0.28
64 1 0.01
65 2 0.01
66 2 0.01
67 1 0.01
68 109 0.64
69 3 0.02
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:1210493 original size:215 final size:215
Alignment explanation
Indices: 1209807--1210710 Score: 1449
Period size: 215 Copynumber: 4.3 Consensus size: 215
1209797 ATTTAAGAAT
* *
1209807 TAAATTGAACAAATATGAAATTACAAATAAAAATGTAAATAAAGTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
1209872 GGATCAAATCGATATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAAT-ACAAAAAGTACTAAATTATAC
* * *
1209937 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTTTGGATCAATTTTA-A
130 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
1210001 TGCAAATAAAATTTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
* * * *
1210022 TACATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAAAACACGCATTGACGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * **
1210087 GGATCAAATCGAAATAATTTTAAATTGTAAAGTTGGAATTAATACAAAAAACACTAAATTATACC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACC
1210152 CATTTAAAAAGTTATGGGCCAATTAAAAAATAG-----A--AATAAGTATGGGTCAATTTCAGAT
131 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
1210210 GCAAATAAAATTTGGAGGAC
196 GCAAATAAAATTTGGAGGAC
*
1210230 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGTG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1210295 GGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAATACAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTT-AAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATAC
*
1210359 TCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
130 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
1210424 TGCAAATAAAATTTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
1210445 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1210510 GGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAATACAAAAAGTACTAAA-T-TAC
66 GGATCAAATCGAAATAATTTT-AAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATAC
* * * *
1210572 TCATTTAAAAAGTT-TGGGCCAATT-AAAAATAGAAATAAATAATACGTATGGGTCAATTTCAAA
130 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
* *
1210635 AGGAAATAAAATTTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
*
1210656 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1210711 AAGGGATCAA
Statistics
Matches: 645, Mismatches: 35, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
207 18 0.03
208 168 0.26
209 6 0.01
211 109 0.17
212 10 0.02
213 18 0.03
214 52 0.08
215 264 0.41
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (215 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACC
CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
GCAAATAAAATTTGGAGGAC
Found at i:1210568 original size:423 final size:423
Alignment explanation
Indices: 1209807--1210710 Score: 1453
Period size: 423 Copynumber: 2.1 Consensus size: 423
1209797 ATTTAAGAAT
* *
1209807 TAAATTGAACAAATATGAAATTACAAATAAAAATGTAAATAAAGTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
1209872 GGATCAAATCGATATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATAC
* *
1209937 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTTTGGATCAATTTTAAT
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAAT
*
1210002 GCAAATAAAATTTGGAGGACTACATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
196 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
* *
1210067 AAAAAACACGCATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGGAATTAATAC
261 AAAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGAAATTAATAC
1210132 AAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAG-AAAT-A-A-GT
326 AAAAAACACTAAA-T-TACCCATTTAAAAAGTT-TGGGCCAATT-AAAAATAGAAAATAATACGT
* *
1210193 ATGGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
387 ATGGGTCAATTTCAAAAGCAAATAAAATTTGGAGGAC
*
1210230 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGTG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
1210295 GGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAAT-ACAAAAAGTACTAAATTATA
66 GGATCAAATCGAAATAATTTT-AAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATA
* *
1210358 CTCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCA-
1210423 ATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAA
194 ATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAA
* * * *
1210488 TTAAACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAA
259 TTAAAAAACACACATTGACGAGGGATCAAATCGAAATAATTTT-AAATTGTAAAGTTGAAATTAA
** *
1210552 TACAAAAAGTACTAAATTACTCATTTAAAAAGTTTGGGCCAATTAAAAATAGAAATAAATAATAC
323 TACAAAAAACACTAAATTACCCATTTAAAAAGTTTGGGCCAATTAAAAATAG--A-AAATAATAC
*
1210617 GTATGGGTCAATTTCAAAAGGAAATAAAATTTGGAGGAC
385 GTATGGGTCAATTTCAAAAGCAAATAAAATTTGGAGGAC
*
1210656 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1210711 AAGGGATCAA
Statistics
Matches: 447, Mismatches: 24, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
419 8 0.02
420 10 0.02
421 16 0.04
422 79 0.18
423 232 0.52
424 11 0.02
425 1 0.00
426 90 0.20
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (423 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAAT
GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
AAAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGAAATTAATAC
AAAAAACACTAAATTACCCATTTAAAAAGTTTGGGCCAATTAAAAATAGAAAATAATACGTATGG
GTCAATTTCAAAAGCAAATAAAATTTGGAGGAC
Found at i:1210798 original size:2 final size:2
Alignment explanation
Indices: 1210791--1210902 Score: 63
Period size: 2 Copynumber: 56.5 Consensus size: 2
1210781 AAAACAATTA
* * * *
1210791 AT AT AT AT AT AT A- AT AT AA ACT AG AT AGT TT AT AT AT AA AGT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T
* * *
1210833 AT AT GT AT -T AT AT AT AT AT AT AT AT AA ACT AT AT A- AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
1210874 AT AT AT AT GT -T AT GT AT AA AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1210903 CCATGTATAA
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
1 5 0.06
2 73 0.89
3 4 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1210874 original size:28 final size:30
Alignment explanation
Indices: 1210821--1210881 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1210811 CTAGATAGTT
* *
1210821 TATATATAAAGTATATGTATTATATATATA
1 TATATATAAACTATATGAATTATATATATA
1210851 TATATATAAACTATAT-AATT-TATATATA
1 TATATATAAACTATATGAATTATATATATA
1210879 TAT
1 TAT
1210882 GTTATGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.38
29 3 0.10
30 15 0.52
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
TATATATAAACTATATGAATTATATATATA
Found at i:1210891 original size:24 final size:25
Alignment explanation
Indices: 1210819--1210911 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 25
1210809 AACTAGATAG
* *
1210819 TTTATATATA-AAGTATATGTATTA
1 TTTATATATATATGTATATGTATAA
* * * *
1210843 TATATATATATATATAAACTATATAA
1 TTTATATATATATGTATA-TGTATAA
1210869 TTTATATATATATGT-TATGTATAA
1 TTTATATATATATGTATATGTATAA
* *
1210893 ATTATATATACCATGTATA
1 TTTATATATA-TATGTATA
1210912 AACTATAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
24 24 0.45
25 9 0.17
26 20 0.38
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTTATATATATATGTATATGTATAA
Found at i:1210908 original size:20 final size:19
Alignment explanation
Indices: 1210885--1210922 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1210875 TATATATGTT
*
1210885 ATGTATAAATTATATATACC
1 ATGTATAAACTATA-ATACC
1210905 ATGTATAAACTATAATAC
1 ATGTATAAACTATAATAC
1210923 TATATAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
ATGTATAAACTATAATACC
Found at i:1211014 original size:20 final size:19
Alignment explanation
Indices: 1210988--1211048 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
1210978 CAGTTCATAT
*
1210988 ATATAGTGTATAAATATAA
1 ATATAGTATATAAATATAA
*
1211007 ACTATAGTTTATAAAAGTATAA
1 A-TATAGTATAT-AAA-TATAA
*
1211029 AAATA-TATATAAATATAA
1 ATATAGTATATAAATATAA
1211047 AT
1 AT
1211049 TCTAGTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.17
19 4 0.11
20 13 0.37
21 6 0.17
22 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATAGTATATAAATATAA
Found at i:1211118 original size:19 final size:18
Alignment explanation
Indices: 1211094--1211169 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 18
1211084 CTAAACCATA
1211094 TATATAGTTCATATGTAAC
1 TATATAGTTCATAT-TAAC
1211113 TATATA--T-ATA-T-A-
1 TATATAGTTCATATTAAC
*
1211125 TATATAGTTTATATTAATC
1 TATATAGTTCATATTAA-C
*
1211144 TATATAGTTTACATATGAAC
1 TATATAG-TT-CATATTAAC
1211164 TATATA
1 TATATA
1211170 TATATATACT
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
12 6 0.13
13 1 0.02
14 2 0.04
15 3 0.07
16 4 0.09
17 2 0.04
19 13 0.28
20 9 0.20
21 6 0.13
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATAGTTCATATTAAC
Found at i:1211126 original size:31 final size:31
Alignment explanation
Indices: 1211091--1211149 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1211081 ACCCTAAACC
1211091 ATATATATAGTTCATATGTAA-CTATATATAT
1 ATATATATAGTTCATAT-TAATCTATATATAT
*
1211122 ATATATATAGTTTATATTAATCTATATA
1 ATATATATAGTTCATATTAATCTATATA
1211150 GTTTACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
ATATATATAGTTCATATTAATCTATATATAT
Found at i:1211148 original size:52 final size:52
Alignment explanation
Indices: 1211094--1211406 Score: 185
Period size: 51 Copynumber: 5.7 Consensus size: 52
1211084 CTAAACCATA
*
1211094 TATATAG-TT-CATATGTAACTATATATATATATA-TATAGTTTATATTAATC
1 TATATAGTTTACATATG-AACTATATATATATATACTATAGTTGATATTAATC
*
1211144 TATATAGTTTACATATGAACTATATATATATATACTATAGTTGATATTTATATA
1 TATATAGTTTACATATGAACTATATATATATATACTATAGTTGATA-TTA-ATC
* * * * * *
1211198 TGAACTATAGTTTACATATAAACTATATAGTTTATATAGTAATTATATTTTACATATAAAC
1 T--A-TATAGTTTACATATGAACTATATA---TATATA-T-ACTATAGTTGATAT-TAATC
* * * *
1211259 TATAGTTGATATTTACATATGAACTATATTTTACATATAAACTATA--T-ATA-TAAAC
1 TATA--T-A-GTTTACATATGAACTATA---TATATATATACTATAGTTGATATTAATC
* *
1211314 TATATAGTTTACATATGAACTATATATATATA-A-TATAGTTAATATTTATATA
1 TATATAGTTTACATATGAACTATATATATATATACTATAGTTGATA-TTA-ATC
* * *
1211366 TGAACTATAGTTTACATTTAAACTATATAGTTTATATACTA
1 T--A-TATAGTTTACATATGAACTATATA-TATATATACTA
1211407 ACTATAGTTT
Statistics
Matches: 208, Mismatches: 22, Indels: 58
0.72 0.08 0.20
Matches are distributed among these distances:
46 4 0.02
47 1 0.00
48 8 0.04
49 3 0.01
50 7 0.03
51 38 0.18
52 19 0.09
53 4 0.02
54 4 0.02
55 31 0.15
56 6 0.03
57 26 0.12
58 5 0.02
59 1 0.00
60 12 0.06
61 5 0.02
62 32 0.15
65 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (52 bp):
TATATAGTTTACATATGAACTATATATATATATACTATAGTTGATATTAATC
Found at i:1211168 original size:20 final size:20
Alignment explanation
Indices: 1211125--1211457 Score: 137
Period size: 18 Copynumber: 17.9 Consensus size: 20
1211115 TATATATATA
*
1211125 TATATAGTTT--ATATTAATC
1 TATATAGTTTACATATGAA-C
1211144 TATATAGTTTACATATGAAC
1 TATATAGTTTACATATGAAC
* * *
1211164 TATATA-TATATATACT-ATAG
1 TATATAGTTTACATA-TGA-AC
*
1211184 T-TGATA-TTTATATATGAAC
1 TAT-ATAGTTTACATATGAAC
*
1211203 --TATAGTTTACATATAAAC
1 TATATAGTTTACATATGAAC
*
1211221 TATATAGTTTATATA-GTAA-
1 TATATAGTTTACATATG-AAC
* *
1211240 T-TATATTTTACATATAAAC
1 TATATAGTTTACATATGAAC
*
1211259 TATAGTTGATATTTACATATGAAC
1 TATA--T-A-GTTTACATATGAAC
*
1211283 TATAT--TTTACATATAAAC
1 TATATAGTTTACATATGAAC
1211301 TATATA---T--ATA--AAC
1 TATATAGTTTACATATGAAC
1211314 TATATAGTTTACATATGAAC
1 TATATAGTTTACATATGAAC
**
1211334 TATATA-TATATA-ATAT-AGT
1 TATATAGT-T-TACATATGAAC
*
1211353 TA-ATA-TTTATATATGAAC
1 TATATAGTTTACATATGAAC
* *
1211371 --TATAGTTTACATTTAAAC
1 TATATAGTTTACATATGAAC
*
1211389 TATATAGTTTATATACT-AAC
1 TATATAGTTTACATA-TGAAC
*
1211409 --TATAGTTTACATATTAAC
1 TATATAGTTTACATATGAAC
1211427 TATATA---T--ATA--AAC
1 TATATAGTTTACATATGAAC
1211440 TATATAGTTTACATATGA
1 TATATAGTTTACATATGA
1211458 CCAATATATA
Statistics
Matches: 244, Mismatches: 26, Indels: 87
0.68 0.07 0.24
Matches are distributed among these distances:
13 18 0.07
15 6 0.02
16 4 0.02
17 14 0.06
18 78 0.32
19 26 0.11
20 70 0.29
21 9 0.04
22 2 0.01
23 1 0.00
24 16 0.07
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (20 bp):
TATATAGTTTACATATGAAC
Found at i:1211190 original size:22 final size:23
Alignment explanation
Indices: 1211164--1211209 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1211154 ACATATGAAC
1211164 TATATATATATATACTATAGTTGA
1 TATATATATATA-ACTATAGTTGA
*
1211188 TATTTATATATGAACTATAGTT
1 TATATATATAT-AACTATAGTT
1211210 TACATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (23 bp):
TATATATATATAACTATAGTTGA
Found at i:1211299 original size:42 final size:42
Alignment explanation
Indices: 1211151--1211304 Score: 180
Period size: 42 Copynumber: 3.8 Consensus size: 42
1211141 ATCTATATAG
* *
1211151 TTTACATATGAACTATA---TATATATATACTATAGTTGATA
1 TTTACATATGAACTATATTTTACATATAAACTATAGTTGATA
* * *
1211190 TTTATATATGAACTATAGTTTACATATAAACTATA--T-A-G
1 TTTACATATGAACTATATTTTACATATAAACTATAGTTGATA
* *
1211228 TTTATATA-GTAATTATATTTTACATATAAACTATAGTTGATA
1 TTTACATATG-AACTATATTTTACATATAAACTATAGTTGATA
1211270 TTTACATATGAACTATATTTTACATATAAACTATA
1 TTTACATATGAACTATATTTTACATATAAACTATA
1211305 TATATAAACT
Statistics
Matches: 97, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
37 1 0.01
38 31 0.32
39 17 0.18
40 2 0.02
41 1 0.01
42 44 0.45
43 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (42 bp):
TTTACATATGAACTATATTTTACATATAAACTATAGTTGATA
Found at i:1211311 original size:13 final size:13
Alignment explanation
Indices: 1211293--1211319 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1211283 TATATTTTAC
1211293 ATATAAACTATAT
1 ATATAAACTATAT
1211306 ATATAAACTATAT
1 ATATAAACTATAT
1211319 A
1 A
1211320 GTTTACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:1211328 original size:33 final size:31
Alignment explanation
Indices: 1211275--1211343 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 31
1211265 TGATATTTAC
*
1211275 ATATGAACTATATTTTACATATAAACTATAT
1 ATATAAACTATATTTTACATATAAACTATAT
*
1211306 ATATAAACTATATAGTTTACATATGAACTATAT
1 ATATAAACTATAT--TTTACATATAAACTATAT
1211339 ATATA
1 ATATA
1211344 TAATATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 12 0.35
33 22 0.65
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
ATATAAACTATATTTTACATATAAACTATAT
Found at i:1211384 original size:24 final size:22
Alignment explanation
Indices: 1211338--1211385 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
1211328 ATGAACTATA
*
1211338 TATATATAATATAGTTAATATT
1 TATATATAATATAGTTAACATT
*
1211360 TATATATGAACTATAGTTTACATT
1 TATATAT-AA-TATAGTTAACATT
1211384 TA
1 TA
1211386 AACTATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
24 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (22 bp):
TATATATAATATAGTTAACATT
Found at i:1211410 original size:38 final size:38
Alignment explanation
Indices: 1211306--1211432 Score: 129
Period size: 38 Copynumber: 3.4 Consensus size: 38
1211296 TAAACTATAT
* * * *
1211306 ATATAAACTATATAGTTTACATATGAACTATA-TATAT
1 ATATTAACTATATAGTTTATATATGAACTATAGTTTAC
* *
1211343 ATAATATAGT-TAATA-TTTATATATGAACTATAGTTTAC
1 ATATTA-ACTAT-ATAGTTTATATATGAACTATAGTTTAC
1211381 AT-TTAAACTATATAGTTTATATACT-AACTATAGTTTAC
1 ATATT-AACTATATAGTTTATATA-TGAACTATAGTTTAC
1211419 ATATTAACTATATA
1 ATATTAACTATATA
1211433 TATAAACTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
37 27 0.36
38 44 0.59
39 3 0.04
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATTAACTATATAGTTTATATATGAACTATAGTTTAC
Found at i:1211446 original size:33 final size:35
Alignment explanation
Indices: 1211368--1211469 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 35
1211358 TTTATATATG
*
1211368 AACTATAGTTTACAT-TTAAACTATATAGTTTATATACT
1 AACTATAGTTTACATATT-AACTATATA---TATAAACT
1211406 AACTATAGTTTACATATTAACTATATATATAAACT
1 AACTATAGTTTACATATTAACTATATATATAAACT
* * *
1211441 -A-TATAGTTTACATATGACCAATATATATA
1 AACTATAGTTTACATATTAACTATATATATA
1211470 TAGTTTATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
33 25 0.42
34 1 0.02
35 7 0.12
38 24 0.41
39 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (35 bp):
AACTATAGTTTACATATTAACTATATATATAAACT
Found at i:1211536 original size:27 final size:27
Alignment explanation
Indices: 1211506--1211563 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1211496 ATTTATATAA
*
1211506 TATACACTATA-AATATAAACTATAGTT
1 TATA-ACTATACAATACAAACTATAGTT
** *
1211533 TATATTTATACAATACATACTATAGTT
1 TATAACTATACAATACAAACTATAGTT
1211560 TATA
1 TATA
1211564 TTTATATACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (27 bp):
TATAACTATACAATACAAACTATAGTT
Found at i:1211572 original size:20 final size:21
Alignment explanation
Indices: 1211549--1211596 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1211539 TATACAATAC
1211549 ATACTATAGT-TTATAT-TTAT
1 ATACTATA-TATTATATATTAT
1211569 ATACTATATATTATATATTAT
1 ATACTATATATTATATATTAT
1211590 ATA-TATA
1 ATACTATA
1211597 CTATATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
ATACTATATATTATATATTAT
Found at i:1211576 original size:7 final size:6
Alignment explanation
Indices: 1211560--1211790 Score: 52
Period size: 7 Copynumber: 37.3 Consensus size: 6
1211550 TACTATAGTT
*
1211560 TATATT TATATA CTATATA T-TATA TAT-TA TATATA TACTATA TAGTATA
1 TATATA TATATA -TATATA TATATA TATATA TATATA TA-TATA TA-TATA
* * * * * * *
1211609 -ATTTA CATATGA -ACTATA TATAAA AACCATA TAAACTA TATACTA TAGTTTA
1 TATATA TATAT-A TA-TATA TATATA TA-TATA TATA-TA TATA-TA TA-TATA
* * * *
1211661 TATTTA TATACTA TATA-A AATA-A TTTATA CTATA-A TATATA TAAACTA
1 TATATA TATA-TA TATATA TATATA TATATA -TATATA TATATA TATA-TA
* * * * *
1211709 TATA-A TACATA TAAACTA TATGGTA TATATA AACTATA CAT-TA TATATA
1 TATATA TATATA TATA-TA TAT-ATA TATATA TA-TATA TATATA TATATA
* *
1211758 TTTCAT- TAGTATA TATAAA CTATATA T-TATA TA
1 TAT-ATA TA-TATA TATATA -TATATA TATATA TA
1211791 GTTCATTAGT
Statistics
Matches: 168, Mismatches: 31, Indels: 52
0.67 0.12 0.21
Matches are distributed among these distances:
5 37 0.22
6 54 0.32
7 76 0.45
8 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:1211583 original size:27 final size:25
Alignment explanation
Indices: 1211519--1211703 Score: 103
Period size: 27 Copynumber: 7.2 Consensus size: 25
1211509 ACACTATAAA
* *
1211519 TATAAACTATAGTTTATATTTATAC
1 TATATACTATAGTTTATATATATAC
*
1211544 AATACATACTATAGTTTATATTTATATAC
1 --TATATACTATAGTTTATA--TATATAC
*
1211573 TATATATTATA-TATTATATATATAC
1 TATATACTATAGT-TTATATATATAC
* * *
1211598 TATATAGTATAATTTACATATGA-AC
1 TATATACTATAGTTTATATAT-ATAC
* ****
1211623 TATATA-TAAAAACCATATA-A-AC
1 TATATACTATAGTTTATATATATAC
1211645 TATATACTATAGTTTATATTTATATAC
1 TATATACTATAGTTTATA--TATATAC
** *
1211672 TATATAAAATAATTTATACTATAATA-
1 TATATACTATAGTTTATA-TAT-ATAC
1211698 TATATA
1 TATATA
1211704 AACTATATAA
Statistics
Matches: 126, Mismatches: 21, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
22 9 0.07
23 6 0.05
24 8 0.06
25 34 0.27
26 13 0.10
27 50 0.40
29 6 0.05
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (25 bp):
TATATACTATAGTTTATATATATAC
Found at i:1211604 original size:47 final size:48
Alignment explanation
Indices: 1211519--1211677 Score: 125
Period size: 47 Copynumber: 3.3 Consensus size: 48
1211509 ACACTATAAA
* *
1211519 TATAAACTATAGT-TTATAT-TTATACA-ATACATACTATAGTTTATATT
1 TATATACTATA-TATTATATATTATAAATATAC-TACTATAGTTTATATT
* *
1211566 TATATACTATATATTATATATTATATATATACTA-TATAGTATA-ATT
1 TATATACTATATATTATATATTATAAATATACTACTATAGTTTATATT
* * *
1211612 TACATATGAACTATATA-TAAAAACCATATAAACTATA-TACTATAGTTTATATT
1 T--ATAT--ACTATATATTATATA--TTATAAA-TATACTACTATAGTTTATATT
1211665 TATATACTATATA
1 TATATACTATATA
1211678 AAATAATTTA
Statistics
Matches: 92, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
46 5 0.05
47 24 0.26
48 12 0.13
49 16 0.17
50 8 0.09
51 11 0.12
52 12 0.13
53 4 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (48 bp):
TATATACTATATATTATATATTATAAATATACTACTATAGTTTATATT
Found at i:1211714 original size:18 final size:18
Alignment explanation
Indices: 1211691--1211873 Score: 125
Period size: 18 Copynumber: 10.6 Consensus size: 18
1211681 TAATTTATAC
*
1211691 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
* *
1211709 TATAATACATATAAACTA
1 TATAGTATATATAAACTA
*
1211727 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
* * **
1211745 TACATTATATAT-ATTTCA
1 TATAGTATATATAAACT-A
1211763 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
**
1211780 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
*
1211796 T-TAGTATATATAAACTC
1 TATAGTATATATAAACTA
*
1211813 TATAGTATATGTAAACTA
1 TATAGTATATATAAACTA
* **
1211831 TATA-T-TAT-TTAGTTCA
1 TATAGTATATATAAACT-A
*
1211847 T-TAGTATATATAACCTA
1 TATAGTATATATAAACTA
1211864 TATAGTATAT
1 TATAGTATAT
1211874 TGTATATACA
Statistics
Matches: 126, Mismatches: 26, Indels: 26
0.71 0.15 0.15
Matches are distributed among these distances:
15 9 0.07
16 14 0.11
17 25 0.20
18 78 0.62
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:1211789 original size:33 final size:33
Alignment explanation
Indices: 1211731--1211822 Score: 130
Period size: 33 Copynumber: 2.7 Consensus size: 33
1211721 AAACTATATG
* *
1211731 GTATATATAAACTATACATTATATATATTTCATTA
1 GTATATATAAACTATATA-T-TATATAGTTCATTA
1211766 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* *
1211799 GTATATATAAACTCTATAGTATAT
1 GTATATATAAACTATATATTATAT
1211823 GTAAACTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 35 0.66
34 1 0.02
35 17 0.32
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (33 bp):
GTATATATAAACTATATATTATATAGTTCATTA
Found at i:1211807 original size:2 final size:2
Alignment explanation
Indices: 1211560--1211790 Score: 52
Period size: 2 Copynumber: 112.0 Consensus size: 2
1211550 TACTATAGTT
*
1211560 TA TA TT TA TA TA CTA TA TA T- TA TA TA T- TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
1211602 TA GTA TA -A TT TA CA TA TGA -A CTA TA TA TA AA AA CCA TA TA AA
1 TA -TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA -TA TA TA TA
* * * *
1211644 CTA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA -A AA TA -A TT
1 -TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
1211686 TA TA CTA TA -A TA TA TA TA AA CTA TA TA -A TA CA TA TA AA CTA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * * *
1211727 TA TGG TA TA TA TA AA CTA TA CA T- TA TA TA TA TT TCA T- TA GTA
1 TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA TA -TA
*
1211769 TA TA TA AA CTA TA TA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA
1211791 GTTCATTAGT
Statistics
Matches: 166, Mismatches: 34, Indels: 58
0.64 0.13 0.22
Matches are distributed among these distances:
1 11 0.07
2 130 0.78
3 25 0.15
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1211819 original size:51 final size:51
Alignment explanation
Indices: 1211764--1212035 Score: 294
Period size: 58 Copynumber: 5.0 Consensus size: 51
1211754 TATATTTCAT
*
1211764 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTCTA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATA
* * *
1211815 TAGTATATGTAAACTATATATTATTTAGTTCATTAGTATATATAACCTATA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATA
* * *
1211866 TAGTATATTGTATATACAAACTATATATTATATAGTGCATTGGTATATATAACCTATA
1 TAG--TA---TATAT--AAACTATATATTATATAGTTCATTAGTATATATAAACTATA
* *
1211924 TAATATATGGCATATACAAACTATATATTAAATAGTTCATTAGTATATATAAACTATA
1 T-A-GTAT---ATAT--AAACTATATATTATATAGTTCATTAGTATATATAAACTATA
* *
1211982 TAGTATATATAAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTATA
1 TAGTATATATAAACTATATATT-ATATAGTTCATTAGTATA-TATAAACTATA
1212034 TA
1 TA
1212036 TTAATTTATT
Statistics
Matches: 191, Mismatches: 16, Indels: 27
0.82 0.07 0.12
Matches are distributed among these distances:
51 77 0.40
52 13 0.07
53 6 0.03
55 1 0.01
56 7 0.04
57 1 0.01
58 85 0.45
59 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (51 bp):
TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATA
Found at i:1211912 original size:109 final size:112
Alignment explanation
Indices: 1211766--1211989 Score: 310
Period size: 109 Copynumber: 2.0 Consensus size: 112
1211756 TATTTCATTA
* * * *
1211766 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTCTATAGTATAT-G-T-AAA
1 GTATATACAAACTATATATTATATAGTGCATTAGTATATATAAACTATATAATATATGGATAAAA
** *
1211828 CTATATATTATTTAGTTCATTAGTATATATAACCTATATAGTATATT
66 CTATATATTAAATAGTTCATTAGTATATATAAACTATATAGTATATT
* *
1211875 GTATATACAAACTATATATTATATAGTGCATTGGTATATATAACCTATATAATATATGGCATATA
1 GTATATACAAACTATATATTATATAGTGCATTAGTATATATAAACTATATAATATATGG---ATA
1211940 CAAACTATATATTAAATAGTTCATTAGTATATATAAACTATATAGTATAT
63 -AAACTATATATTAAATAGTTCATTAGTATATATAAACTATATAGTATAT
1211990 ATAAACTATA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
109 51 0.52
110 1 0.01
114 1 0.01
116 46 0.46
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (112 bp):
GTATATACAAACTATATATTATATAGTGCATTAGTATATATAAACTATATAATATATGGATAAAA
CTATATATTAAATAGTTCATTAGTATATATAAACTATATAGTATATT
Found at i:1211987 original size:18 final size:18
Alignment explanation
Indices: 1211964--1212001 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1211954 AATAGTTCAT
1211964 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
1211982 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
1212000 TA
1 TA
1212002 TTGAAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:1211990 original size:109 final size:105
Alignment explanation
Indices: 1211764--1212035 Score: 309
Period size: 109 Copynumber: 2.5 Consensus size: 105
1211754 TATATTTCAT
* * *
1211764 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTCTATAGTATATGTAAAC
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAATATATGTAAAC
**
1211829 TATATATTATTTAGTTCATTAGTATATATAACCTATATAGTA
66 TATATATTAAATAGTTCATTAGTATATATAA-C-ATATAGTA
* * *
1211871 TATTGTATATACAAACTATATATTATATAGTGCATTGGTATATATAACCTATATAATATATGGCA
1 TA--GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAATATAT-G--
*
1211936 TATACAAACTATATATTAAATAGTTCATTAGTATATATAA-A-CTA-TA
61 --T--AAACTATATATTAAATAGTTCATTAGTATATATAACATATAGTA
*
1211982 TAGTATATATAAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTATATA
1 TAGTATATATAAACTATATATT-ATATAGTTCATTAGTATA-TATAACCTATATA
1212036 TTAATTTATT
Statistics
Matches: 141, Mismatches: 13, Indels: 19
0.82 0.08 0.11
Matches are distributed among these distances:
107 2 0.01
109 83 0.59
110 15 0.11
111 4 0.03
112 2 0.01
113 1 0.01
114 1 0.01
116 33 0.23
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (105 bp):
TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAATATATGTAAAC
TATATATTAAATAGTTCATTAGTATATATAACATATAGTA
Found at i:1212660 original size:124 final size:122
Alignment explanation
Indices: 1212439--1212774 Score: 485
Period size: 124 Copynumber: 2.7 Consensus size: 122
1212429 AAAATCAACC
* * *
1212439 GTGTTCTTCATTTATTCATCCCAGTTCTTCCCCAAAACCCTCGTTTGGTCTTCAAAAACACCAAA
1 GTGTTCTTCATTTGTTCAT-CCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACC-AA
* *
1212504 ACCAAAACATTTTCGTGTTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCTTAT
64 ACCAAACCA-TTTCGTGTTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATAT
1212564 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAA-CCTCCTTTGATCTTCAAAAACACCTAAA
1 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACC-AAA
* * * * *
1212628 CACAAACCATTTCGTGTTTTTTTTCAGTTCAAACACCCAAATTTTCTTCGGTGTTCATCT
65 C-CAAACCATTTCGTGTTTTTTTTC-GATCAAACACCCAAATATTCATCCGTGTTCATAT
* *
1212688 GTGTTCTTCATTAGTTCATCCTAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACATCAAA
1 GTGTTCTTCATTTGTTCATCC-AGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACCAAA
1212753 CCCAAACCATTTCGTGTTTTTT
65 -CCAAACCATTTCGTGTTTTTT
1212775 CGTTTAAACA
Statistics
Matches: 193, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
123 42 0.22
124 71 0.37
125 56 0.29
126 24 0.12
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.38
Consensus pattern (122 bp):
GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACCAAAC
CAAACCATTTCGTGTTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATAT
Found at i:1212927 original size:34 final size:33
Alignment explanation
Indices: 1212888--1212953 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
1212878 CCAAAACCCA
*
1212888 AACTATTCATCTTCTCTAACCCCTAACTCTAAAT
1 AACTATTCATCTTCCCTAACCCCTAACT-TAAAT
1212922 AACTATTCATCTTCCCTAACCCCTAACTTAAA
1 AACTATTCATCTTCCCTAACCCCTAACTTAAA
1212954 CCCAAACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (33 bp):
AACTATTCATCTTCCCTAACCCCTAACTTAAAT
Found at i:1212962 original size:6 final size:6
Alignment explanation
Indices: 1212951--1213105 Score: 77
Period size: 6 Copynumber: 26.5 Consensus size: 6
1212941 CCCCTAACTT
* * * * ** *
1212951 AAACCC AAACCC AAACCT AAACCC TAA-TC GAACAT AAATCC AAA-CC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * * * * * * *
1212997 GAACCG AAATCC AATCCG AAACCC AAACCT AAACCT AAATCCT AAA-CC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAA-CCC AAACCC
* * * *
1213045 AAACCC CAACCT AAACCC AAACCC AAA-CC GAACTC AAACCC AAA-CC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* *
1213091 GAACCT AAACCC AAA
1 AAACCC AAACCC AAA
1213106 TTGAACCCAA
Statistics
Matches: 108, Mismatches: 35, Indels: 12
0.70 0.23 0.08
Matches are distributed among these distances:
5 19 0.18
6 83 0.77
7 6 0.06
ACGTcount: A:0.48, C:0.39, G:0.04, T:0.09
Consensus pattern (6 bp):
AAACCC
Found at i:1213059 original size:17 final size:18
Alignment explanation
Indices: 1212950--1213160 Score: 110
Period size: 17 Copynumber: 12.0 Consensus size: 18
1212940 ACCCCTAACT
1212950 TAAACCCAAACCCAAACC
1 TAAACCCAAACCCAAACC
* * * *
1212968 TAAACCCTAA-TCGAACA
1 TAAACCCAAACCCAAACC
* *
1212985 TAAATCCAAA-CCGAACC
1 TAAACCCAAACCCAAACC
* * * *
1213002 GAAATCCAATCCGAAACC
1 TAAACCCAAACCCAAACC
* * *
1213020 CAAACCTAAACCTAAATCC
1 TAAACCCAAACCCAAA-CC
*
1213039 TAAA-CCAAACCCCAACC
1 TAAACCCAAACCCAAACC
1213056 TAAACCCAAACCCAAACC
1 TAAACCCAAACCCAAACC
* *
1213074 -GAACTCAAACCCAAACC
1 TAAACCCAAACCCAAACC
* * *
1213091 -GAACCTAAACCCAAA-T
1 TAAACCCAAACCCAAACC
* ***
1213107 TGAACCCAAACTTGAACC
1 TAAACCCAAACCCAAACC
* * * *
1213125 TAAATCCTAACCAAAACT
1 TAAACCCAAACCCAAACC
* *
1213143 TGAACCCAAACCCTAACC
1 TAAACCCAAACCCAAACC
1213161 AGAATCGAAC
Statistics
Matches: 143, Mismatches: 45, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
17 70 0.49
18 68 0.48
19 5 0.03
ACGTcount: A:0.46, C:0.37, G:0.04, T:0.12
Consensus pattern (18 bp):
TAAACCCAAACCCAAACC
Found at i:1213123 original size:12 final size:12
Alignment explanation
Indices: 1213098--1213153 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1213088 ACCGAACCTA
1213098 AACCCAAA-TTG
1 AACCCAAACTTG
1213109 AACCCAAACTTG
1 AACCCAAACTTG
* *
1213121 AACCTAAATCCT-
1 AACCCAAA-CTTG
*
1213133 AACCAAAACTTG
1 AACCCAAACTTG
1213145 AACCCAAAC
1 AACCCAAAC
1213154 CCTAACCAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.27
12 25 0.68
13 2 0.05
ACGTcount: A:0.46, C:0.32, G:0.05, T:0.16
Consensus pattern (12 bp):
AACCCAAACTTG
Found at i:1213141 original size:24 final size:24
Alignment explanation
Indices: 1213109--1213175 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1213099 ACCCAAATTG
* * *
1213109 AACCCAAACTTGAACCTAAATCCT
1 AACCAAAACTTGAACCCAAACCCT
1213133 AACCAAAACTTGAACCCAAACCCT
1 AACCAAAACTTGAACCCAAACCCT
* *
1213157 AACCAGAA-TCGAACCCAAA
1 AACCAAAACTTGAACCCAAA
1213176 ATATTCGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
23 10 0.26
24 28 0.74
ACGTcount: A:0.46, C:0.34, G:0.06, T:0.13
Consensus pattern (24 bp):
AACCAAAACTTGAACCCAAACCCT
Found at i:1213411 original size:2 final size:2
Alignment explanation
Indices: 1213404--1213428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1213394 CTTGATATTT
1213404 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 T
1213429 TGGTTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1213464 original size:31 final size:31
Alignment explanation
Indices: 1213429--1213902 Score: 718
Period size: 31 Copynumber: 15.3 Consensus size: 31
1213419 ATATATATAT
1213429 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1213460 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
*
1213491 TGGTTTATTGCTGTTGATGTAAATGATATAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
*
1213522 TGGTTTATTACTGTTGATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* *
1213553 TGGTTTATTGTTGTTGATGTAAATGATATA-
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* *
1213583 AGGTTTATTGCTGTTGATGTAAATGATGTAT
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* *
1213614 TGGTTTATTACTGTTGATGTAAATGATATAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
*
1213645 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
*
1213676 TGGTTTATTGCTATTGATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* * *
1213707 TGGTTTACTGCTGTTGATATAAATGATGTAT
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* *
1213738 TGGTTTATTGTTGTTGATGTAAATAATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* *
1213769 TGGTTTATTGTTGTTGATGTAAATGATATAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
*
1213800 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* *
1213831 TGGTTTATTGCCGTTAATGTAAATGATGTAC
1 TGGTTTATTGCTGTTGATGTAAATGATGTAC
* * *
1213862 TAGTTTATAT-TTGTTGATGTAAATGATATAC
1 TGGTTTAT-TGCTGTTGATGTAAATGATGTAC
1213893 TGGTTTATTG
1 TGGTTTATTG
1213903 TTGTAATGTA
Statistics
Matches: 401, Mismatches: 39, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
30 28 0.07
31 372 0.93
32 1 0.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (31 bp):
TGGTTTATTGCTGTTGATGTAAATGATGTAC
Found at i:1216281 original size:20 final size:20
Alignment explanation
Indices: 1216231--1216291 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1216221 TGCTTGATTC
* *
1216231 TGCTTGATTATGTTTTATAT
1 TGCTTGATTCTGTTTGATAT
*
1216251 TGTTTGATTCTGTTTGATAT
1 TGCTTGATTCTGTTTGATAT
* **
1216271 TGCTTGCTTCTACTTGATAT
1 TGCTTGATTCTGTTTGATAT
1216291 T
1 T
1216292 TGTAAGGGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.57
Consensus pattern (20 bp):
TGCTTGATTCTGTTTGATAT
Found at i:1221473 original size:40 final size:39
Alignment explanation
Indices: 1221305--1221473 Score: 155
Period size: 39 Copynumber: 4.3 Consensus size: 39
1221295 AAATCCGAAC
* *
1221305 TTATTTCCTTTTGTAAAATAGGAAAATAAA-CTTAATAAT
1 TTATTTCCTTTTCTAAAATAGGAAAATAAATC-CAATAAT
*
1221344 TTATTT-CATTTCATAAAATAGGAAAATAAATCCAA-AGAT
1 TTATTTCCTTTTC-TAAAATAGGAAAATAAATCCAATA-AT
* * * * * **
1221383 TTATTTTCTTATATAAAATAGGAAACTAAATTCAACGAT
1 TTATTTCCTTTTCTAAAATAGGAAAATAAATCCAATAAT
* * *
1221422 TTGTTTCCCTTTTCCAAAATAGGAAAATAAATCCGATAAT
1 TTATTT-CCTTTTCTAAAATAGGAAAATAAATCCAATAAT
1221462 TTATTTACCTTT
1 TTATTT-CCTTT
1221474 AAAAGATAGA
Statistics
Matches: 103, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
38 5 0.05
39 60 0.58
40 38 0.37
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (39 bp):
TTATTTCCTTTTCTAAAATAGGAAAATAAATCCAATAAT
Found at i:1221771 original size:58 final size:58
Alignment explanation
Indices: 1221537--1221862 Score: 310
Period size: 58 Copynumber: 5.7 Consensus size: 58
1221527 GATTCCTGAA
* * *
1221537 AAAATAAATTTAACAATTTA-TTTCCTTTAACAAA-ATAGAATCATTTAAGATTCTCAA-
1 AAAATAAATTCAACAATCTATTTTCC-TT-ACAAAGTTAGAATCATTTAAGATTCTCAAG
* * * ** *
1221594 AAGAATAATTTAAATAAT-TATTAGCTTTTACACAA--TAGAATCATTTAAGATTCTCAAG
1 AA-AATAAATTCAACAATCTATTTTC-CTTACA-AAGTTAGAATCATTTAAGATTCTCAAG
* * ** ** * ** *
1221652 AAAATAAATTTAATAATAGATTTT--TTA-ACGGATAGAATCATCCATGATTCTCAAG
1 AAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAG
* *
1221707 AAAATAAATTCGACAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAG
1 AAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAG
* * *
1221765 GAAATAAATTCAACAATCTATTTTCCTTACAAAATTAGAATCATTTAAGATTCTTAAG
1 AAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAG
* *
1221823 AAAATAAATTCAACAATCTATTTTCCTTGCGAAGTTAGAA
1 AAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAA
1221863 CCAACGCAAG
Statistics
Matches: 222, Mismatches: 36, Indels: 21
0.80 0.13 0.08
Matches are distributed among these distances:
54 1 0.00
55 42 0.19
57 45 0.20
58 134 0.60
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (58 bp):
AAAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAG
Found at i:1226844 original size:18 final size:21
Alignment explanation
Indices: 1226802--1226844 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
1226792 GTTTCACTTA
1226802 ATCTTCTCCTCTTTCTTTTCT
1 ATCTTCTCCTCTTTCTTTTCT
1226823 -TCTTCT-C-CTTTCTTTT-T
1 ATCTTCTCCTCTTTCTTTTCT
1226840 ATCTT
1 ATCTT
1226845 GCATGCGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 13 0.62
19 1 0.05
20 6 0.29
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (21 bp):
ATCTTCTCCTCTTTCTTTTCT
Found at i:1233385 original size:19 final size:19
Alignment explanation
Indices: 1233342--1233378 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1233332 AGTGATAAAA
1233342 TAATAATAAAATAAAAATT
1 TAATAATAAAATAAAAATT
* *
1233361 TAATAATTAAATTAAAAT
1 TAATAATAAAATAAAAAT
1233379 ATTATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAATAAAATAAAAATT
Found at i:1237980 original size:20 final size:20
Alignment explanation
Indices: 1237955--1238025 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
1237945 TTGGATGAAC
* * *
1237955 TAGTATTGAGATCAATCCCT
1 TAGTATCGATATCGATCCCT
*
1237975 TAGTATCGATATCGAT-CCG
1 TAGTATCGATATCGATCCCT
1237994 TAGTATCGATATCGATCCCT
1 TAGTATCGATATCGATCCCT
1238014 TAGTATCGATAT
1 TAGTATCGATAT
1238026 TGAGGGTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
19 18 0.40
20 27 0.60
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
TAGTATCGATATCGATCCCT
Found at i:1238133 original size:21 final size:21
Alignment explanation
Indices: 1238109--1238171 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1238099 TATCCATATT
1238109 GGATAAACTGGAATTCATACC
1 GGATAAACTGGAATTCATACC
** * *
1238130 GGAT-AAGGGGCATCCATACC
1 GGATAAACTGGAATTCATACC
*
1238150 GGATAAACTGGTATTCATACC
1 GGATAAACTGGAATTCATACC
1238171 G
1 G
1238172 AAGATTGGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (21 bp):
GGATAAACTGGAATTCATACC
Found at i:1238186 original size:41 final size:41
Alignment explanation
Indices: 1238099--1238186 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
1238089 GAATGAGTGA
** * *
1238099 TATCCATATTGGATAAACTGGAATTCATACCGGATAAGGGG
1 TATCCATACCGGATAAACTGGAATTCATACCGAAGAAGGGG
* * **
1238140 CATCCATACCGGATAAACTGGTATTCATACCGAAGATTGGG
1 TATCCATACCGGATAAACTGGAATTCATACCGAAGAAGGGG
1238181 TATCCA
1 TATCCA
1238187 CACCCAATAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (41 bp):
TATCCATACCGGATAAACTGGAATTCATACCGAAGAAGGGG
Found at i:1244871 original size:92 final size:93
Alignment explanation
Indices: 1244711--1244882 Score: 222
Period size: 92 Copynumber: 1.9 Consensus size: 93
1244701 GAATGGATCA
* * *
1244711 ATCCTTTTGAAAAAGGATCAATCCTATGCACAACATAAAGTTTGGGATCGATCATTTTGGTCAAG
1 ATCCTTTTGAAAAAGGATCAATCCTATGCACAACAAAAACTTTAGGATCGATCATTTTGGTCAAG
1244776 GGATCGATT-TTTTTGCCTGAGGGATTG
66 GGATCGATTCTTTTTGCCTGAGGGATTG
* * * *** **
1244803 ATCCTTTTGAAAAGGGATCGATCCTTTGCTGGACAAAAACTTTAGGATCGATCCA-TTTGGTCGG
1 ATCCTTTTGAAAAAGGATCAATCCTATGCACAACAAAAACTTTAGGATCGAT-CATTTTGGTCAA
1244867 GGGATCGATTCTTTTT
65 GGGATCGATTCTTTTT
1244883 CTGGGAATGA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
92 60 0.90
93 7 0.10
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (93 bp):
ATCCTTTTGAAAAAGGATCAATCCTATGCACAACAAAAACTTTAGGATCGATCATTTTGGTCAAG
GGATCGATTCTTTTTGCCTGAGGGATTG
Found at i:1249673 original size:69 final size:69
Alignment explanation
Indices: 1249562--1249701 Score: 244
Period size: 69 Copynumber: 2.0 Consensus size: 69
1249552 AGTGAATCCT
*
1249562 TCCTTGCTTCTTCCTTCAGCAACAAATGCATCCCCAACTTGAACTCTCCCGTATTCGATCAAAAC
1 TCCTTGCTTCTTCCTTCAGCAACAAATGCATCCCCAACTTGAACTCTCCCATATTCGATCAAAAC
*
1249627 GGCA
66 GCCA
* *
1249631 TCCTTGCTTCTTCCTTTAGCAACAAATGCATCCCCAACTTGAACTCTCCCATATTCGATCGAAAC
1 TCCTTGCTTCTTCCTTCAGCAACAAATGCATCCCCAACTTGAACTCTCCCATATTCGATCAAAAC
1249696 GCCA
66 GCCA
1249700 TC
1 TC
1249702 ATCAAATCTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.26, C:0.35, G:0.11, T:0.29
Consensus pattern (69 bp):
TCCTTGCTTCTTCCTTCAGCAACAAATGCATCCCCAACTTGAACTCTCCCATATTCGATCAAAAC
GCCA
Found at i:1253054 original size:57 final size:58
Alignment explanation
Indices: 1252940--1253093 Score: 193
Period size: 57 Copynumber: 2.6 Consensus size: 58
1252930 TTTAATTTAG
* * *
1252940 TCTCCAAAATTTTGTACATTTCAATAACATCTCTAAAATATGACCCTCGTTCCATATTGC
1 TCTCC-AAACTTTGAACATTTCAATAACATC-CCAAAATATGACCCTCGTTCCATATTGC
* * * * * *
1253000 TCTCCAAGCTTTGAACATTTCGATAAAATCCCAAAATATG-CCCTCTTTCTATATTGG
1 TCTCCAAACTTTGAACATTTCAATAACATCCCAAAATATGACCCTCGTTCCATATTGC
1253057 TCTCCAAACTTTGAACATTTCAATAACATCCCCAAAA
1 TCTCCAAACTTTGAACATTTCAATAACAT-CCCAAAA
1253094 ATCATTCAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 40 0.49
58 16 0.20
59 20 0.25
60 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (58 bp):
TCTCCAAACTTTGAACATTTCAATAACATCCCAAAATATGACCCTCGTTCCATATTGC
Found at i:1256962 original size:21 final size:21
Alignment explanation
Indices: 1256929--1256972 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1256919 CAACTACGCA
*
1256929 TTTAGTATATAAACTATCAAT
1 TTTAGTACATAAACTATCAAT
* * *
1256950 TTTAGTACCTAAATTTTCAAT
1 TTTAGTACATAAACTATCAAT
1256971 TT
1 TT
1256973 AAAAAAACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTAGTACATAAACTATCAAT
Found at i:1257765 original size:20 final size:19
Alignment explanation
Indices: 1257742--1257787 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1257732 CGATATAATA
1257742 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1257762 GGTATTAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
1257782 GATAAA
1 GGTAAA
1257788 GCACTATCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1258865 original size:4 final size:4
Alignment explanation
Indices: 1258856--1258992 Score: 265
Period size: 4 Copynumber: 34.2 Consensus size: 4
1258846 TAAGAGATTG
1258856 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1258904 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
1258952 GTAT GTAT GTAT GTAT ATAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1258993 AAAGGACAAT
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 131 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:1260093 original size:201 final size:201
Alignment explanation
Indices: 1259859--1261204 Score: 2386
Period size: 201 Copynumber: 6.7 Consensus size: 201
1259849 AGGTAAATTT
*
1259859 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* * *
1259924 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATTGATATTTTTTTAATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
1259989 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
1260054 AAAAAG
196 AAAAAG
* *
1260060 TATCGATCCCAGAAATATATGTATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* * *
1260125 TATAAATATACCAGTTTTATGAGAGAATATGTCTACAATATGTATCGACACTTTTTTGATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
* * *
1260190 GTCGATACTTTTGGTCCAGAATGAATTCCAAAAAGGGTGCAATCATAAAGTGTCAATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
1260255 AAAAAG
196 AAAAAG
1260261 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
1260326 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
* *
1260391 GTTGATACTTTTGGTCCAGAATGAATGTCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
1260456 AAAAAG
196 AAAAAG
* *
1260462 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAAGTAAATTTTCAATGTAACCAG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
*
1260527 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTTTATTTTG
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACAC-TTTTTTAATTTTG
1260592 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
130 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
1260657 TAAAAAG
195 TAAAAAG
* * *
1260664 TATCGATCCCAGAAACATATTCATCCATAAGTATAATGTAATAGATAAATTTTCAATGTAACCAG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* *
1260729 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTAT
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
* *
1260794 GTCGATACTTTTGGTTCAGAATGAATACCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
*
1260859 AAAATG
196 AAAAAG
1260865 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* * * *
1260930 TATAAATATACCAGTTTTATGAGAGAATGTGTCTACAATATGTATCGACACTTTTTTGATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
1260995 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
1261060 AAAAAG
196 AAAAAG
* *
1261066 TATCGATCCCAGAAACATATGCATCCATAAGTGTATTGTAATAGGTAAATTTTCAATGTAACCGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* *
1261131 TATAAATATACCGGTTTTATGAGAGAATATGTATACAACATGTATCGACACGTTTTTAATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
1261196 GTCGATACT
131 GTCGATACT
1261205 AATTTAAATA
Statistics
Matches: 1088, Mismatches: 56, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
201 894 0.82
202 194 0.18
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (201 bp):
TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGT
GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
AAAAAG
Found at i:1261006 original size:604 final size:604
Alignment explanation
Indices: 1259859--1261204 Score: 2401
Period size: 604 Copynumber: 2.2 Consensus size: 604
1259849 AGGTAAATTT
*
1259859 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* *
1259924 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATTGATA-TTTTTTTAATTTTG
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTTAATTTTG
1259988 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
131 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
* *
1260053 TAAAAAGTATCGATCCCAGAAATATATGTATCCATAAGTATAATGTAATAGGTAAATTTTCAATG
196 TAAAAAGTATCGATCCCAGAAACATATGTATCCATAAGTATAATGTAATAGATAAATTTTCAATG
* * * *
1260118 TAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACAATATGTATCGACACTTTTTTG
261 TAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTA
* * *
1260183 ATTTTGTGTCGATACTTTTGGTCCAGAATGAATTCCAAAAAGGGTGCAATCATAAAGTGTCAATA
326 ATTTTATGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACCATAAAGTGTCAATA
1260248 CATTTATAAAAAGTATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTT
391 CATTTATAAAAAGTATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTT
*
1260313 TCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACT
456 TCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACAACATGTATCGACACT
* *
1260378 TTTTTAATTTTGTGTTGATACTTTTGGTCCAGAATGAATGTCAAAAAGGGTGCAACCATAAAGTG
521 TTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTG
1260443 TCGATACATTTATAAAAAG
586 TCGATACATTTATAAAAAG
* *
1260462 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAAGTAAATTTTCAATGTAACCAG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
*
1260527 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTTTATTTTG
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTTAATTTTG
1260592 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
131 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
1260657 TAAAAAGTATCGATCCCAGAAACATAT-TCATCCATAAGTATAATGTAATAGATAAATTTTCAAT
196 TAAAAAGTATCGATCCCAGAAACATATGT-ATCCATAAGTATAATGTAATAGATAAATTTTCAAT
*
1260721 GTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTT
260 GTAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTT
* *
1260786 AATTTTATGTCGATACTTTTGGTTCAGAATGAATACCAAAAAGGGTGCAACCATAAAGTGTCGAT
325 AATTTTATGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACCATAAAGTGTCAAT
*
1260851 ACATTTATAAAATGTATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATT
390 ACATTTATAAAAAGTATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATT
* *
1260916 TTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATGTGTCTACAATATGTATCGACAC
455 TTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACAACATGTATCGACAC
*
1260981 TTTTTTGATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGT
520 TTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGT
1261046 GTCGATACATTTATAAAAAG
585 GTCGATACATTTATAAAAAG
* *
1261066 TATCGATCCCAGAAACATATGCATCCATAAGTGTATTGTAATAGGTAAATTTTCAATGTAACCGG
1 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
* *
1261131 TATAAATATACCGGTTTTATGAGAGAATATGTATACAACATGTATCGACAC-GTTTTTAATTTTG
66 TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTTAATTTTG
1261195 TGTCGATACT
131 TGTCGATACT
1261205 AATTTAAATA
Statistics
Matches: 709, Mismatches: 32, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
603 132 0.19
604 577 0.81
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (604 bp):
TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGG
TATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTTAATTTTG
TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
TAAAAAGTATCGATCCCAGAAACATATGTATCCATAAGTATAATGTAATAGATAAATTTTCAATG
TAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTA
ATTTTATGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACCATAAAGTGTCAATA
CATTTATAAAAAGTATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTT
TCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATATGTCTACAACATGTATCGACACT
TTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTG
TCGATACATTTATAAAAAG
Done.