Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 34 of 279
Found at i:11529745 original size:173 final size:169
Alignment explanation
Indices: 11529452--11529851 Score: 430
Period size: 173 Copynumber: 2.3 Consensus size: 169
11529442 ACGTGAGCCA
* * * * * *
11529452 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGAAATATGAGTTGACTTTTGAAAAATATAAA-T-AAAAAC--TAA--
* * * *
11529517 GAAATTACCTCAGCTTATGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGG
60 -AAA-TGCCTCAGCATGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGG
* **
11529580 AAGAAACAGAAATTGAAAAATG-AAATTTTGAAAATACCTCAGCATGTGGCCC-G
122 AA-AAACAGAAACTG-AAAA-GCAAA-AATGAAAATACCTCAGC--GT-GCCCTG
* * *
11529633 AGGCTCAACTCATCTTTCGAAATATGAGTTGACTTTTGAAAAGTATAAATAAAAACTAAAAATGC
1 AGGCTCAACTCACCTCTCGAAATATGAGTTGACTTTTGAAAAATATAAATAAAAACTAAAAATGC
* *
11529698 CTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGA
66 CTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAGA
* *
11529763 GACTGAAAAGCAAAAATGAAAATTCCTCAGCGTGCCCTG
131 AACTGAAAAGCAAAAATGAAAATACCTCAGCGTGCCCTG
* *
11529802 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAAT
1 AGGCTCAACTCACCTCTCGAAATATGAGTTGACTTTTGAAAAATATAAAT
11529852 TGAAAAACAG
Statistics
Matches: 192, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
168 4 0.02
169 48 0.25
171 15 0.08
172 7 0.04
173 53 0.28
174 13 0.07
177 2 0.01
179 6 0.03
180 1 0.01
181 43 0.22
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (169 bp):
AGGCTCAACTCACCTCTCGAAATATGAGTTGACTTTTGAAAAATATAAATAAAAACTAAAAATGC
CTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAGA
AACTGAAAAGCAAAAATGAAAATACCTCAGCGTGCCCTG
Found at i:11529856 original size:14 final size:14
Alignment explanation
Indices: 11529837--11529871 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11529827 GAGTTGATTT
* *
11529837 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
11529851 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
11529865 TTGAAAA
1 TTGAAAA
11529872 TACTTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:11529898 original size:87 final size:86
Alignment explanation
Indices: 11529452--11529938 Score: 427
Period size: 87 Copynumber: 5.6 Consensus size: 86
11529442 ACGTGAGCCA
* * * *
11529452 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAACTGAAAAACA-AAAAT
* * *
11529517 GAAATTACCTCAGCTTATGACCTG
65 GAAAATACCTCAGCGTA--CCCTG
* * *
11529541 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAACAGAAATTGAAAAATGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAA-AAATAGAAACTGAAAAA-CAAA-
** *
11529606 TTTGAAAATACCTCAGCATGTGGCCC-G
62 AATGAAAATACCTCAGC--GT-ACCCTG
* * * * * *
11529633 AGGCTCAACTCATCTTTCGAAATATGAGTTGACTTTTGAAAAGTATAAA-T-AAAAACTAAAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAACTGAAAAAC-AAAAAT
* *
11529696 G------CCTCAGCATGTGAGCC-A
65 GAAAATACCTCAGC--GT-ACCCTG
** * *
11529714 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAGACTGAAAAGCAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAAACTGAAAAACAAAAA
* *
11529779 TGAAAATTCCTCAGCGTGCCCTG
64 TGAAAATACCTCAGCGTACCCTG
* * *
11529802 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAACTGAAAAACA-AAAAT
* *
11529867 GAAAATACTTCAGCGTATCCTG
65 GAAAATACCTCAGCGTACCCTG
* ** *
11529889 AGGTTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAATAAAAAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAAC
11529939 ATCAAAATAC
Statistics
Matches: 329, Mismatches: 49, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
81 43 0.13
83 13 0.04
84 8 0.02
85 5 0.02
86 21 0.06
87 71 0.22
88 42 0.13
89 37 0.11
90 16 0.05
91 20 0.06
92 50 0.15
93 2 0.01
94 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (86 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAACTGAAAAACAAAAATG
AAAATACCTCAGCGTACCCTG
Found at i:11530047 original size:64 final size:64
Alignment explanation
Indices: 11529973--11530099 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
11529963 TGGTGGAGCT
*
11529973 CAGGTGTCTTTTCCTTTGATTCAGTACGGCTATCATCACATTTTCTTGCTATATTGGAGTACCC
1 CAGGTGTCTTTTCCTTTGATTCAGTACGACTATCATCACATTTTCTTGCTATATTGGAGTACCC
11530037 CAGGTGTCTTTTCCTTTGATTCAGTACGACTATCATCACATTTTCTTGCTATATTGGAGTACC
1 CAGGTGTCTTTTCCTTTGATTCAGTACGACTATCATCACATTTTCTTGCTATATTGGAGTACC
11530100 TGTATATGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.41
Consensus pattern (64 bp):
CAGGTGTCTTTTCCTTTGATTCAGTACGACTATCATCACATTTTCTTGCTATATTGGAGTACCC
Found at i:11536296 original size:59 final size:59
Alignment explanation
Indices: 11536215--11536332 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
11536205 GTCGGCGCTA
*
11536215 TACGGGAAACCTGACGATTGATTGCCAGAGGCACATATTTCTCCTCTATCGGCCTCTTT
1 TACGAGAAACCTGACGATTGATTGCCAGAGGCACATATTTCTCCTCTATCGGCCTCTTT
* *
11536274 TACGAGAAACCTGAGGATTGATTGTCAGAGGCACATATTTCTCCTCTATCGGCCTCTTT
1 TACGAGAAACCTGACGATTGATTGCCAGAGGCACATATTTCTCCTCTATCGGCCTCTTT
11536333 GCCTTTATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.31
Consensus pattern (59 bp):
TACGAGAAACCTGACGATTGATTGCCAGAGGCACATATTTCTCCTCTATCGGCCTCTTT
Found at i:11537820 original size:84 final size:84
Alignment explanation
Indices: 11537710--11537885 Score: 327
Period size: 84 Copynumber: 2.1 Consensus size: 84
11537700 GGGCACCAAA
* *
11537710 TTGAG-CTCTTTGGCACTCAATGCAGAGAAGGCTTCAGTACCCTCTATTGCTTTAAGTCTTTCCT
1 TTGAGCCTTTTTGGCACTCAATGCAGAGAAGGCTTCAGTACCCTCTATTGCTTTAAGCCTTTCCT
11537774 CTAAGCTCCTATACTTCTC
66 CTAAGCTCCTATACTTCTC
11537793 TTGAGCCTTTTTGGCACTCAATGCAGAGAAGGCTTCAGTACCCTCTATTGCTTTAAGCCTTTCCT
1 TTGAGCCTTTTTGGCACTCAATGCAGAGAAGGCTTCAGTACCCTCTATTGCTTTAAGCCTTTCCT
11537858 CTAAGCTCCTATACTTCTC
66 CTAAGCTCCTATACTTCTC
11537877 TTGAGCCTT
1 TTGAGCCTT
11537886 GTGATCACCG
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 5 0.06
84 85 0.94
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (84 bp):
TTGAGCCTTTTTGGCACTCAATGCAGAGAAGGCTTCAGTACCCTCTATTGCTTTAAGCCTTTCCT
CTAAGCTCCTATACTTCTC
Found at i:11539336 original size:86 final size:86
Alignment explanation
Indices: 11539237--11539407 Score: 324
Period size: 86 Copynumber: 2.0 Consensus size: 86
11539227 AATCTGAACG
*
11539237 TTGATCTTCAACTGGTAATTTTCTTCTTACAGAGCACTGAGGTCCCTTGATATCTTGGTCTTTTC
1 TTGATCTTCAACTGGTAATTTTCTTCTTACAGAGCACTGAGGTCCCTTGACATCTTGGTCTTTTC
11539302 GTATTCAAACTCTTGTCTTGA
66 GTATTCAAACTCTTGTCTTGA
*
11539323 TTGATCTTCAACTGGTAATTTTCTTCTTGCAGAGCACTGAGGTCCCTTGACATCTTGGTCTTTTC
1 TTGATCTTCAACTGGTAATTTTCTTCTTACAGAGCACTGAGGTCCCTTGACATCTTGGTCTTTTC
11539388 GTATTCAAACTCTTGTCTTG
66 GTATTCAAACTCTTGTCTTG
11539408 CCACTTCTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.43
Consensus pattern (86 bp):
TTGATCTTCAACTGGTAATTTTCTTCTTACAGAGCACTGAGGTCCCTTGACATCTTGGTCTTTTC
GTATTCAAACTCTTGTCTTGA
Found at i:11541850 original size:22 final size:21
Alignment explanation
Indices: 11541821--11541867 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
11541811 ACACATACAT
*
11541821 AATATATACGTATTATATATA
1 AATATATACGTATAATATATA
* *
11541842 AATACTATATGTATAATATATT
1 AATA-TATACGTATAATATATA
11541864 AATA
1 AATA
11541868 GAAACATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
AATATATACGTATAATATATA
Found at i:11542111 original size:13 final size:15
Alignment explanation
Indices: 11542087--11542123 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
11542077 AAAATATAAT
*
11542087 AATAACATTAATA-A
1 AATAATATTAATACA
11542101 AAT-ATATTAATACA
1 AATAATATTAATACA
11542115 AATAATATT
1 AATAATATT
11542124 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 8 0.40
14 7 0.35
15 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATTAATACA
Found at i:11542120 original size:22 final size:22
Alignment explanation
Indices: 11542077--11542121 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11542067 TAGAATACCA
*
11542077 AAAATATAATAATAACATTAAT
1 AAAATATAATAATAACAATAAT
*
11542099 AAAATATATTAAT-ACAAATAAT
1 AAAATATAATAATAAC-AATAAT
11542121 A
1 A
11542122 TTGAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATATAATAATAACAATAAT
Found at i:11546177 original size:13 final size:13
Alignment explanation
Indices: 11546159--11546183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11546149 CCCGGGGGAC
11546159 ACATGACCGTGTA
1 ACATGACCGTGTA
11546172 ACATGACCGTGT
1 ACATGACCGTGT
11546184 GTTGCACATG
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
ACATGACCGTGTA
Found at i:11546418 original size:23 final size:22
Alignment explanation
Indices: 11546388--11546431 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
11546378 TCTCAATTCA
*
11546388 TAAATAAATTCATACCAAAACT
1 TAAATAAAATCATACCAAAACT
*
11546410 TAAACTAAAATCATACCTAAAC
1 TAAA-TAAAATCATACCAAAAC
11546432 ATACGATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAATCATACCAAAACT
Found at i:11557166 original size:23 final size:23
Alignment explanation
Indices: 11557138--11557183 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11557128 GCTATGTTTA
11557138 TAGTGTAAACCGAGTTCAAAATT
1 TAGTGTAAACCGAGTTCAAAATT
11557161 TAGTGTAAACCGAGTTCAAAATT
1 TAGTGTAAACCGAGTTCAAAATT
11557184 CTCTCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (23 bp):
TAGTGTAAACCGAGTTCAAAATT
Found at i:11562290 original size:51 final size:49
Alignment explanation
Indices: 11562208--11562349 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 49
11562198 CGAAACACCA
* * * * * * *
11562208 TTTGTAGACAAGCTACGACTGATTTGTAGATAAATTGCCACTGATAACACT
1 TTTGTGGACAAGCCACCACTAATTTGCAGATATACTGCCACTGATAA-A-T
* *
11562259 TTTGTGGACAAGCCACCACTAATATGCAGATATACTACCACTGATAAAT
1 TTTGTGGACAAGCCACCACTAATTTGCAGATATACTGCCACTGATAAAT
* *
11562308 TTTGTGGACAAGCCACCACAAATTTGCAAATATACTGCCACT
1 TTTGTGGACAAGCCACCACTAATTTGCAGATATACTGCCACT
11562350 ACTTCCACCT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 39 0.50
50 1 0.01
51 38 0.49
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (49 bp):
TTTGTGGACAAGCCACCACTAATTTGCAGATATACTGCCACTGATAAAT
Found at i:11562507 original size:20 final size:18
Alignment explanation
Indices: 11562464--11562507 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
11562454 AAATCACATA
11562464 TCACATGATAAACACTTT
1 TCACATGATAAACACTTT
* *
11562482 TAACATGTTAAACATGCTTT
1 TCACATGATAAACA--CTTT
11562502 TCACAT
1 TCACAT
11562508 TAGGTAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (18 bp):
TCACATGATAAACACTTT
Found at i:11565381 original size:49 final size:49
Alignment explanation
Indices: 11565308--11565427 Score: 143
Period size: 49 Copynumber: 2.4 Consensus size: 49
11565298 CTGACGCCAG
* * *
11565308 GTCCCAGGCATGGTCTTACACTGGCTTTCATATAGCGAG-GCCGATGACAT
1 GTCCCAGACA-GGTCTTACACTGGCTCTCATATAGC-AGTGCCAATGACAT
* * * * *
11565358 GTCCCAGACAGGTCTTACCCTGGCTCTCATCTATCAGTGTCAATGTCAT
1 GTCCCAGACAGGTCTTACACTGGCTCTCATATAGCAGTGCCAATGACAT
11565407 GTCCCAGACAGGTCTTACACT
1 GTCCCAGACAGGTCTTACACT
11565428 AACACACCAC
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
48 2 0.03
49 49 0.82
50 9 0.15
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (49 bp):
GTCCCAGACAGGTCTTACACTGGCTCTCATATAGCAGTGCCAATGACAT
Found at i:11565560 original size:94 final size:94
Alignment explanation
Indices: 11565448--11565662 Score: 218
Period size: 94 Copynumber: 2.3 Consensus size: 94
11565438 AAGCTGACAC
* ** ** *
11565448 CATGTCCCAAACGGGTCTTACACTAGCTTGTATATCACGAAGCCGATGTATGTCCC-GAACATGT
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAAGCCGATGCATGTCCCAG-ACATGT
* * * *
11565512 CCTGCACTAGCTCTCGTCTCAATGTC-GATG
65 CCTACACTAACTCTCATCT-AATGGCTGATG
* * * * * *
11565542 CATGTCCTAGACATGTCTTACTCTGGCTTAAATATCTCGAGGTCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAAGCCGATGCATGTCCCAGACATGTC
* * **
11565607 TTACACTAACTCTCATGTTGTGGCTGATG
66 CTACACTAACTCTCATCTAATGGCTGATG
11565636 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
11565663 ACACATATCA
Statistics
Matches: 96, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
93 3 0.03
94 92 0.96
95 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAAGCCGATGCATGTCCCAGACATGTC
CTACACTAACTCTCATCTAATGGCTGATG
Found at i:11567179 original size:49 final size:49
Alignment explanation
Indices: 11567106--11567293 Score: 241
Period size: 49 Copynumber: 3.8 Consensus size: 49
11567096 TAGCCGAAGC
* *
11567106 TATCTGGTACGCATAGTAGCCTGCACTTATTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * *
11567155 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * *
11567206 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * *
11567255 TATCCGGTACACGTAGTAGCTTGCACTTAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
11567294 CGTGACCTCA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 75 0.64
50 2 0.02
51 40 0.34
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:11567225 original size:100 final size:100
Alignment explanation
Indices: 11567111--11567298 Score: 340
Period size: 100 Copynumber: 1.9 Consensus size: 100
11567101 GAAGCTATCT
* *
11567111 GGTACGCATAGTAGCCTGCACTTATTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
11567176 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* *
11567211 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
11567276 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
11567299 CCTCACAATA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:11576291 original size:49 final size:49
Alignment explanation
Indices: 11576190--11576315 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 49
11576180 AGATGCCGAC
* *
11576190 GCCATGTCCCAGACATGGTCTTACACTGCCTTTCATATAGCGAGGCTGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGCCTCTCATATAGCGAGGCTAAT
* * *
11576240 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCG-GTG-TCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGCCTCTCATATAGCGAG-GCT-AAT
* *
11576289 GCCATATCCCAGACAAGTCTTACACTG
1 GCCATGTCCCAGACAGGTCTTACACTG
11576316 ACACACCACA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
48 2 0.03
49 50 0.75
50 15 0.22
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGCCTCTCATATAGCGAGGCTAAT
Found at i:11576484 original size:94 final size:94
Alignment explanation
Indices: 11576379--11577295 Score: 1746
Period size: 94 Copynumber: 9.8 Consensus size: 94
11576369 TCGTGAGCCT
11576379 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11576444 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
*
11576473 GATGCATGTCCCAGACATGTCTTACACTGGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11576538 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11576567 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11576632 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11576661 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11576726 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11576755 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11576820 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11576849 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11576914 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11576943 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11577008 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11577037 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11577102 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
11577131 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
11577196 TCTTACTCTGGCTTAAATATTTCGAGGGC
66 TCTTACTCTGGCTTAAATATTTCGAGGGC
* * * * ** *
11577225 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATGT-TGTGGCTGATGCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAAT-GCCGATGCATGTCCCAGACAT
11577289 GTCTTAC
65 GTCTTAC
11577296 ACTCATACAC
Statistics
Matches: 813, Mismatches: 9, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
93 1 0.00
94 812 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (94 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAATGCCGATGCATGTCCCAGACATG
TCTTACTCTGGCTTAAATATTTCGAGGGC
Found at i:11586687 original size:28 final size:28
Alignment explanation
Indices: 11586612--11586688 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
11586602 TATATATGTA
* * *
11586612 TATGGAACTTAGTGTTCAAAATATTAAG
1 TATGGAACTTAGTGTACGAGATATTAAG
* * * *
11586640 AATGGAACTTGGTGTGCGAGATATTGAG
1 TATGGAACTTAGTGTACGAGATATTAAG
*
11586668 TATGGCACTTAGTGTACGAGA
1 TATGGAACTTAGTGTACGAGA
11586689 CATCGAAGAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.31
Consensus pattern (28 bp):
TATGGAACTTAGTGTACGAGATATTAAG
Found at i:11599513 original size:46 final size:45
Alignment explanation
Indices: 11599463--11599637 Score: 179
Period size: 46 Copynumber: 3.8 Consensus size: 45
11599453 ACAACTATTA
*
11599463 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACGTCACGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTT-CATCACGAG
* * * *
11599509 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TTCATCACGAG
* * * * * *
11599555 GTCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCATCACGAG
* * *
11599603 GCTGATGCATGTTCTAGACATGTCTTACACTAGCT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
11599638 CACATAAGTG
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
46 57 0.55
47 27 0.26
48 20 0.19
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCATCACGAG
Found at i:11601116 original size:6 final size:6
Alignment explanation
Indices: 11601094--11601152 Score: 75
Period size: 6 Copynumber: 9.8 Consensus size: 6
11601084 TAGTGCTTGG
* * *
11601094 ATCTAC TTCTA- ATTCTAC GTCTAC ATCTAC ATCTAC ATCTAC GTCTAC
1 ATCTAC ATCTAC A-TCTAC ATCTAC ATCTAC ATCTAC ATCTAC ATCTAC
11601142 ATCTAC ATCTA
1 ATCTAC ATCTA
11601153 TAGCTATGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.29, C:0.31, G:0.03, T:0.37
Consensus pattern (6 bp):
ATCTAC
Found at i:11604914 original size:19 final size:20
Alignment explanation
Indices: 11604876--11604914 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11604866 CCTTTCAAAT
*
11604876 TCTTCCATTTTCATCCTCTC
1 TCTTACATTTTCATCCTCTC
11604896 TCTTACATTTTCA-CCTCTC
1 TCTTACATTTTCATCCTCTC
11604915 CTCCATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.13, C:0.38, G:0.00, T:0.49
Consensus pattern (20 bp):
TCTTACATTTTCATCCTCTC
Found at i:11608238 original size:14 final size:14
Alignment explanation
Indices: 11608219--11608247 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11608209 GATGAATCCA
11608219 AATCATATCCACAT
1 AATCATATCCACAT
11608233 AATCATATCCACAT
1 AATCATATCCACAT
11608247 A
1 A
11608248 CCCATATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCATATCCACAT
Found at i:11608253 original size:14 final size:14
Alignment explanation
Indices: 11608222--11608255 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11608212 GAATCCAAAT
*
11608222 CATATCCACATAAT
1 CATATCCACATAAC
*
11608236 CATATCCACATACC
1 CATATCCACATAAC
11608250 CATATC
1 CATATC
11608256 TGAATATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (14 bp):
CATATCCACATAAC
Found at i:11612597 original size:14 final size:15
Alignment explanation
Indices: 11612578--11612609 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
11612568 TTTCACTAAG
11612578 AATAATTTTT-AGAA
1 AATAATTTTTAAGAA
11612592 AATAATTTTTAAGAA
1 AATAATTTTTAAGAA
11612607 AAT
1 AAT
11612610 TTATTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
AATAATTTTTAAGAA
Found at i:11612610 original size:12 final size:13
Alignment explanation
Indices: 11612574--11612611 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
11612564 TTTATTTCAC
11612574 TAAGAATAATTTT
1 TAAGAATAATTTT
*
11612587 TAGAAAATAATTTT
1 TA-AGAATAATTTT
11612601 TAAGAA-AATTT
1 TAAGAATAATTT
11612612 ATTTAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 5 0.23
14 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (13 bp):
TAAGAATAATTTT
Found at i:11613166 original size:22 final size:21
Alignment explanation
Indices: 11613141--11613204 Score: 56
Period size: 24 Copynumber: 2.8 Consensus size: 21
11613131 CTCTAATGCA
11613141 AACATTAAAATAATATTAGTAT
1 AACATTAAAATAATATTA-TAT
*
11613163 AACATTATAAAAAAATTATTATAT
1 AACA-T-TAAAATAA-TATTATAT
*
11613187 ATTCAATTAAAATAATAT
1 A-AC-ATTAAAATAATAT
11613205 AAATATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 4 0.12
23 4 0.12
24 18 0.53
25 7 0.21
26 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
AACATTAAAATAATATTATAT
Found at i:11618559 original size:14 final size:16
Alignment explanation
Indices: 11618531--11618563 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
11618521 AATTTAAAAT
11618531 ATAAATATATATTTAG
1 ATAAATATATATTTAG
11618547 ATAAATAT-T-TTTAG
1 ATAAATATATATTTAG
11618561 ATA
1 ATA
11618564 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATAAATATATATTTAG
Found at i:11619875 original size:20 final size:20
Alignment explanation
Indices: 11619815--11619880 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 20
11619805 ATATATATAT
* * *
11619815 AAATT-TTTGGAATTTTTAT
1 AAATTATTTTGAATTTTAAA
* *
11619834 AAA-TATCTTGAA-TTTCAA
1 AAATTATTTTGAATTTTAAA
11619852 AAATTATTTTGAATTTTAAA
1 AAATTATTTTGAATTTTAAA
11619872 AAATTATTT
1 AAATTATTT
11619881 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.21
19 16 0.42
20 14 0.37
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (20 bp):
AAATTATTTTGAATTTTAAA
Found at i:11619888 original size:20 final size:20
Alignment explanation
Indices: 11619850--11619887 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11619840 CTTGAATTTC
*
11619850 AAAAATTATTTTGAATTTTA
1 AAAAATTATTTTAAATTTTA
11619870 AAAAATTA-TTTAAATTTT
1 AAAAATTATTTTAAATTTT
11619888 TTTGTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAAAATTATTTTAAATTTTA
Found at i:11620791 original size:39 final size:40
Alignment explanation
Indices: 11620730--11620824 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 40
11620720 TGTTAAAAAC
* *
11620730 ATTTTGTAACCAAATA-CTAAAATTACTATTGGAAACCCA
1 ATTTTATAACCAAATATCTAAAATTACTACTGGAAACCCA
* * ** *
11620769 TTTTTATAATCAAATATC-AAAATTTTTACTGGAAACTCA
1 ATTTTATAACCAAATATCTAAAATTACTACTGGAAACCCA
*
11620808 ACTTTATAACCAAATAT
1 ATTTTATAACCAAATAT
11620825 TTTGTAAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
39 44 0.98
40 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (40 bp):
ATTTTATAACCAAATATCTAAAATTACTACTGGAAACCCA
Found at i:11621299 original size:16 final size:16
Alignment explanation
Indices: 11621259--11621303 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
11621249 TACATATTAT
11621259 ATAAAACA-TATTTTA
1 ATAAAACATTATTTTA
* *
11621274 AAAAATACATTTTTTTA
1 ATAAA-ACATTATTTTA
11621291 ATAAAACATTATT
1 ATAAAACATTATT
11621304 CGCTTATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 10 0.42
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAACATTATTTTA
Found at i:11621397 original size:20 final size:20
Alignment explanation
Indices: 11621372--11621411 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11621362 AAATCAATTG
11621372 AATCGATTTTGAAAATTGAT
1 AATCGATTTTGAAAATTGAT
11621392 AATCGATTTTGAAAATTGAT
1 AATCGATTTTGAAAATTGAT
11621412 GGTTCAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
AATCGATTTTGAAAATTGAT
Found at i:11623946 original size:48 final size:46
Alignment explanation
Indices: 11623891--11624047 Score: 131
Period size: 48 Copynumber: 3.3 Consensus size: 46
11623881 TTCAGATATG
*
11623891 GTCTTACACTGGCTCTCACACATCCGTGTCGATGCATGTCCCAGACAT
1 GTCTTACACTGGCTCTCACA-ATCAGTG-CGATGCATGTCCCAGACAT
* *** *
11623939 GTCTTACACTGGCACTC-GTTTCAATGCAGATGCCATGTCCCAGACAT
1 GTCTTACACTGGCTCTCACAATCAGTGC-GATG-CATGTCCCAGACAT
* * * *
11623986 GGTCTTACACTGGCTTTCATAAT-A-TGGCCGATGCATGTCTCAAACAT
1 -GTCTTACACTGGCTCTCACAATCAGT-G-CGATGCATGTCCCAGACAT
*
11624033 GTCTTACACTAGCTC
1 GTCTTACACTGGCTC
11624048 ACATAACAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
45 1 0.01
46 21 0.24
47 27 0.31
48 37 0.42
49 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
GTCTTACACTGGCTCTCACAATCAGTGCGATGCATGTCCCAGACAT
Found at i:11625890 original size:23 final size:22
Alignment explanation
Indices: 11625860--11625903 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
11625850 TTGCGAAAAG
11625860 ATAATATCTCATAATAATATCAT
1 ATAATATCTCATAATAA-ATCAT
*
11625883 ATAATATCTCATTATAAATCA
1 ATAATATCTCATAATAAATCA
11625904 AATTGCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATCTCATAATAAATCAT
Found at i:11658572 original size:36 final size:35
Alignment explanation
Indices: 11658519--11658647 Score: 156
Period size: 36 Copynumber: 3.6 Consensus size: 35
11658509 GTACATCGAA
*
11658519 AATCCAACC-AAAGCACACCAGATGCTCATAAGAGCT
1 AATCCATCCGAAA-CACACCA-ATGCTCATAAGAGCT
*
11658555 AATCCATCCGAAACACACCAAATGCTCATAAAAGCT
1 AATCCATCCGAAACACACC-AATGCTCATAAGAGCT
11658591 AATCCATCCGAAACACACCAATGGCTC-TGAAGAGCT
1 AATCCATCCGAAACACACCAAT-GCTCAT-AAGAGCT
*
11658627 AGTCCAAT-CGAAACACACCAA
1 AATCC-ATCCGAAACACACCAA
11658648 AATAGAGAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
35 4 0.05
36 74 0.88
37 6 0.07
ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15
Consensus pattern (35 bp):
AATCCATCCGAAACACACCAATGCTCATAAGAGCT
Found at i:11665142 original size:30 final size:30
Alignment explanation
Indices: 11665107--11665166 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
11665097 CAAGAAAACT
*
11665107 GAATAAAGAAATTCAAG-ATAGAGAAACCCA
1 GAATAAAGAAA-TCAAGAATAAAGAAACCCA
*
11665137 GAATAAAGAAATCCAGAATAAAGAAACCCA
1 GAATAAAGAAATCAAGAATAAAGAAACCCA
11665167 AGATACGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (30 bp):
GAATAAAGAAATCAAGAATAAAGAAACCCA
Found at i:11665146 original size:15 final size:15
Alignment explanation
Indices: 11665128--11665166 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
11665118 TTCAAGATAG
11665128 AGAAACCCAGAATAA
1 AGAAACCCAGAATAA
*
11665143 AGAAATCCAGAATAA
1 AGAAACCCAGAATAA
11665158 AGAAACCCA
1 AGAAACCCA
11665167 AGATACGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.59, C:0.21, G:0.13, T:0.08
Consensus pattern (15 bp):
AGAAACCCAGAATAA
Found at i:11671754 original size:12 final size:12
Alignment explanation
Indices: 11671724--11671755 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
11671714 CACTTATAAT
11671724 TGCACCAAAACA
1 TGCACCAAAACA
11671736 -G-ACCAAAACA
1 TGCACCAAAACA
11671746 TGCACCAAAA
1 TGCACCAAAA
11671756 TGTTAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.50
11 2 0.11
12 7 0.39
ACGTcount: A:0.53, C:0.31, G:0.09, T:0.06
Consensus pattern (12 bp):
TGCACCAAAACA
Found at i:11683476 original size:27 final size:27
Alignment explanation
Indices: 11683446--11684228 Score: 1566
Period size: 27 Copynumber: 29.0 Consensus size: 27
11683436 TTAAATGCTA
11683446 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683473 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683500 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683527 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683554 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683581 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683608 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683635 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683662 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683689 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683716 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683743 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683770 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683797 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683824 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683851 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683878 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683905 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683932 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683959 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11683986 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684013 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684040 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684067 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684094 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684121 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684148 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684175 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684202 ATTAAATAAAAGATGAAAAGAAACTAT
1 ATTAAATAAAAGATGAAAAGAAACTAT
11684229 CATCTTTTTC
Statistics
Matches: 756, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 756 1.00
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (27 bp):
ATTAAATAAAAGATGAAAAGAAACTAT
Found at i:11692736 original size:32 final size:32
Alignment explanation
Indices: 11692700--11692806 Score: 91
Period size: 32 Copynumber: 3.5 Consensus size: 32
11692690 ATGATCATTT
11692700 TTAAAAGTTAATTAAGTAATTTGATAATTAAG
1 TTAAAAGTTAATTAAGTAATTTGATAATTAAG
* * **
11692732 TTAAATGTTAATTAAATAA-AAGATGAA--AAG
1 TTAAAAGTTAATTAAGTAATTTGAT-AATTAAG
* *
11692762 ---AAACTATCATTAAGTAATTTGATAATTAAG
1 TTAAAAGT-TAATTAAGTAATTTGATAATTAAG
*
11692792 TTAAATGTTAATTAA
1 TTAAAAGTTAATTAA
11692807 ATAAAAGATG
Statistics
Matches: 54, Mismatches: 13, Indels: 16
0.65 0.16 0.19
Matches are distributed among these distances:
27 3 0.06
28 11 0.20
29 3 0.06
30 6 0.11
31 3 0.06
32 25 0.46
33 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (32 bp):
TTAAAAGTTAATTAAGTAATTTGATAATTAAG
Found at i:11692743 original size:16 final size:16
Alignment explanation
Indices: 11692700--11692746 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
11692690 ATGATCATTT
*
11692700 TTAAAAGTTAATTAAG
1 TTAAATGTTAATTAAG
* *
11692716 -TAATTTGATAATTAAG
1 TTAA-ATGTTAATTAAG
11692732 TTAAATGTTAATTAA
1 TTAAATGTTAATTAA
11692747 ATAAAAGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (16 bp):
TTAAATGTTAATTAAG
Found at i:11692775 original size:60 final size:60
Alignment explanation
Indices: 11692710--11692831 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
11692700 TTAAAAGTTA
11692710 ATTAAGTAATTTGATAATTAAGTTAAATGTTAATTAAATAAAAGATGAAAAGAAACTATC
1 ATTAAGTAATTTGATAATTAAGTTAAATGTTAATTAAATAAAAGATGAAAAGAAACTATC
11692770 ATTAAGTAATTTGATAATTAAGTTAAATGTTAATTAAATAAAAGATGAAAAGAAACTATC
1 ATTAAGTAATTTGATAATTAAGTTAAATGTTAATTAAATAAAAGATGAAAAGAAACTATC
11692830 AT
1 AT
11692832 CTTTTTCATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (60 bp):
ATTAAGTAATTTGATAATTAAGTTAAATGTTAATTAAATAAAAGATGAAAAGAAACTATC
Found at i:11709112 original size:14 final size:14
Alignment explanation
Indices: 11709093--11709131 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11709083 CTAAAAAAAT
11709093 AAATCATTTTCCAG
1 AAATCATTTTCCAG
**
11709107 AAATCATTTTCTGG
1 AAATCATTTTCCAG
*
11709121 AAGTCATTTTC
1 AAATCATTTTC
11709132 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:11712205 original size:45 final size:44
Alignment explanation
Indices: 11712153--11712359 Score: 161
Period size: 45 Copynumber: 4.6 Consensus size: 44
11712143 CATTCCTAAA
* *
11712153 GTAATGCCATAGTGTCTTCCAACTATGGTATTGATT-GT-TACCGAT
1 GTAATGCCATAGT-TCTTTCAACTATGGTATT-ATTCGTAT-CAGAT
* *
11712198 GTGATGCCATAGTATCTTTCAACTATGGTCTTATTCGTATCAGAT
1 GTAATGCCATAGT-TCTTTCAACTATGGTATTATTCGTATCAGAT
* * * * * * *
11712243 TTAATGCCATAGTTCTTTCAACTATGGTTTTATACATTTCTGGT
1 GTAATGCCATAGTTCTTTCAACTATGGTATTATTCGTATCAGAT
* * * * * *
11712287 TTAGTGTCATAGTATCTTTCAACCATGGTTTTATTCAT-TCCAG-T
1 GTAATGCCATAGT-TCTTTCAACTATGGTATTATTCGTAT-CAGAT
*
11712331 TTAATGCCATAGTATCTTTCAACTATGGT
1 GTAATGCCATAGT-TCTTTCAACTATGGT
11712360 CTTTCTCATT
Statistics
Matches: 137, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
44 67 0.49
45 69 0.50
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (44 bp):
GTAATGCCATAGTTCTTTCAACTATGGTATTATTCGTATCAGAT
Found at i:11712298 original size:44 final size:45
Alignment explanation
Indices: 11712201--11712397 Score: 222
Period size: 44 Copynumber: 4.4 Consensus size: 45
11712191 TACCGATGTG
* * * *
11712201 ATGCCATAGTATCTTTCAACTATGGTCTTATTCGTATCAGATTTA
1 ATGCCATAGTATCTTTCAACTATGGTTTTATTCATTTCAGGTTTA
* *
11712246 ATGCCATAGT-TCTTTCAACTATGGTTTTATACATTTCTGGTTTA
1 ATGCCATAGTATCTTTCAACTATGGTTTTATTCATTTCAGGTTTA
* * * *
11712290 GTGTCATAGTATCTTTCAACCATGGTTTTATTCATTCCA-GTTTA
1 ATGCCATAGTATCTTTCAACTATGGTTTTATTCATTTCAGGTTTA
* **
11712334 ATGCCATAGTATCTTTCAACTATGGTCTTT-CTCATTTCAGGTAAA
1 ATGCCATAGTATCTTTCAACTATGGT-TTTATTCATTTCAGGTTTA
*
11712379 ATGCCA-CGATATCTTTCAA
1 ATGCCATAG-TATCTTTCAA
11712398 TCATGGTCAT
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
44 72 0.56
45 56 0.44
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (45 bp):
ATGCCATAGTATCTTTCAACTATGGTTTTATTCATTTCAGGTTTA
Found at i:11712392 original size:89 final size:89
Alignment explanation
Indices: 11712201--11712405 Score: 238
Period size: 89 Copynumber: 2.3 Consensus size: 89
11712191 TACCGATGTG
* * *
11712201 ATGCCATAGTATCTTTCAACTATGGTCTTATTCGTATCAGATTTAATGCCATAGTTCTTTCAACT
1 ATGCCAGAGTATCTTTCAACCATGGTCTTATTCATATCAGATTTAATGCCATAGTTCTTTCAACT
* **
11712266 ATGGTTTTATACATTTCTGGTTTA
66 ATGGTTTTATACATTTCAGGTAAA
* * * *
11712290 GTGTCATAGTATCTTTCAACCATGGTTTTATTCAT-TCCAG-TTTAATGCCATAGTATCTTTCAA
1 ATGCCAGAGTATCTTTCAACCATGGTCTTATTCATAT-CAGATTTAATGCCATAGT-TCTTTCAA
*
11712353 CTATGGTCTTTCT-CATTTCAGGTAAA
64 CTATGGT-TTTATACATTTCAGGTAAA
*
11712379 ATGCCACGA-TATCTTTCAATCATGGTC
1 ATGCCA-GAGTATCTTTCAACCATGGTC
11712406 ATTTTCGTTT
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
88 15 0.15
89 78 0.80
90 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (89 bp):
ATGCCAGAGTATCTTTCAACCATGGTCTTATTCATATCAGATTTAATGCCATAGTTCTTTCAACT
ATGGTTTTATACATTTCAGGTAAA
Found at i:11712952 original size:22 final size:23
Alignment explanation
Indices: 11712927--11712969 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11712917 TGACATGTTG
11712927 AATTTTAATTAATTTT-ATAAAA
1 AATTTTAATTAATTTTGATAAAA
*
11712949 AATTTTGATTAATTTTGATAA
1 AATTTTAATTAATTTTGATAA
11712970 TTTTCGACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
AATTTTAATTAATTTTGATAAAA
Found at i:11728310 original size:6 final size:6
Alignment explanation
Indices: 11728300--11728399 Score: 73
Period size: 6 Copynumber: 16.7 Consensus size: 6
11728290 AAGTATATTC
* * *
11728300 ATATAT GTATAT ATAT-T CATATAT GTATAT ATATAT -TCATAT ATGTAT
1 ATATAT ATATAT ATATAT -ATATAT ATATAT ATATAT AT-ATAT ATATAT
* * * *
11728348 ATACAT -TCATAT ATATAT GTATAT ATAT-T CATATAT GTATGT ATATAT
1 ATATAT AT-ATAT ATATAT ATATAT ATATAT -ATATAT ATATAT ATATAT
11728396 ATAT
1 ATAT
11728400 GAACACTTGA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
5 4 0.06
6 64 0.89
7 4 0.06
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:11728330 original size:20 final size:20
Alignment explanation
Indices: 11728293--11728395 Score: 133
Period size: 18 Copynumber: 5.2 Consensus size: 20
11728283 GACGAGAAAG
11728293 TATATTCATATATG--TATA
1 TATATTCATATATGTATATA
11728311 TATATTCATATATGTATATA
1 TATATTCATATATGTATATA
11728331 TATATTCATATATG--TATA
1 TATATTCATATATGTATATA
* *
11728349 TACATTCATATATATATGTATA
1 TATATTCATATATGTA--TATA
*
11728371 TATATTCATATATGTATGTA
1 TATATTCATATATGTATATA
11728391 TATAT
1 TATAT
11728396 ATATGAACAC
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
18 30 0.41
20 26 0.35
22 18 0.24
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
TATATTCATATATGTATATA
Found at i:11728335 original size:22 final size:19
Alignment explanation
Indices: 11728293--11728395 Score: 120
Period size: 20 Copynumber: 5.3 Consensus size: 19
11728283 GACGAGAAAG
11728293 TATATTCATATATG-TATA
1 TATATTCATATATGTTATA
11728311 TATATTCATATATGTATATA
1 TATATTCATATATGT-TATA
11728331 TATATTCATATATG-TATA
1 TATATTCATATATGTTATA
* *
11728349 TACATTCATATATATATGTATA
1 TATATTC--ATATATGT-TATA
*
11728371 TATATTCATATATGTATGTA
1 TATATTCATATATGT-TATA
11728391 TATAT
1 TATAT
11728396 ATATGAACAC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
18 24 0.33
20 39 0.53
22 10 0.14
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (19 bp):
TATATTCATATATGTTATA
Found at i:11728340 original size:38 final size:39
Alignment explanation
Indices: 11728293--11728400 Score: 159
Period size: 38 Copynumber: 2.8 Consensus size: 39
11728283 GACGAGAAAG
11728293 TATATTCATATATGTATATATATTCATATATGTA-TATA
1 TATATTCATATATGTATATATATTCATATATGTAGTATA
* *
11728331 TATATTCATATATGTATATACATTCATATATATATGTATA
1 TATATTCATATATGTATATATATTCATATATGTA-GTATA
*
11728371 TATATTCATATATGTATGTATA-T-ATATATG
1 TATATTCATATATGTATATATATTCATATATG
11728401 AACACTTGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
38 38 0.60
39 1 0.02
40 24 0.38
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (39 bp):
TATATTCATATATGTATATATATTCATATATGTAGTATA
Found at i:11728396 original size:22 final size:22
Alignment explanation
Indices: 11728303--11728397 Score: 130
Period size: 22 Copynumber: 4.6 Consensus size: 22
11728293 TATATTCATA
11728303 TATGTATATATATTCATATATG
1 TATGTATATATATTCATATATG
11728325 TA--TATATATATTC--ATA--
1 TATGTATATATATTCATATATG
* *
11728341 TATGTATATACATTCATATATA
1 TATGTATATATATTCATATATG
11728363 TATGTATATATATTCATATATG
1 TATGTATATATATTCATATATG
11728385 TATGTATATATAT
1 TATGTATATATAT
11728398 ATGAACACTT
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.03
18 13 0.20
20 14 0.22
22 35 0.55
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (22 bp):
TATGTATATATATTCATATATG
Found at i:11731293 original size:3 final size:3
Alignment explanation
Indices: 11731285--11731310 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11731275 TAAAGGTCCC
11731285 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
11731311 TCCCACAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11732586 original size:14 final size:13
Alignment explanation
Indices: 11732569--11732626 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
11732559 GCTCGTGAAA
11732569 AAAAAAGAGAAAAG
1 AAAAAAGA-AAAAG
*
11732583 AAAAGAAAAAAAAG
1 AAAA-AAGAAAAAG
*
11732597 AAAAATGAAACAAG
1 AAAAAAGAAA-AAG
11732611 AAAAAAGAAAAA-
1 AAAAAAGAAAAAG
11732623 AAAA
1 AAAA
11732627 GAGAGCATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 4 0.11
13 6 0.16
14 25 0.66
15 3 0.08
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:11732591 original size:21 final size:20
Alignment explanation
Indices: 11732567--11732628 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
11732557 ATGCTCGTGA
11732567 AAAAAAAAGAGAAAAGAAAAG
1 AAAAAAAAGA-AAAAGAAAAG
11732588 AAAAAAAAGAAAAATGAAACA-
1 AAAAAAAAGAAAAA-GAAA-AG
*
11732609 AGAAAAAAGAAAAA-AAAAG
1 AAAAAAAAGAAAAAGAAAAG
11732628 A
1 A
11732629 GAGCATAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 4 0.11
21 27 0.73
22 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAGAAAAG
Found at i:11742043 original size:39 final size:39
Alignment explanation
Indices: 11742000--11742086 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
11741990 CCGGCAATTA
*
11742000 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
11742039 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
11742078 GCCTGCTAG
1 GCCTGCTAG
11742087 ACATTAAGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.21
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
Found at i:11758596 original size:15 final size:15
Alignment explanation
Indices: 11758572--11758635 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
11758562 GCATAGTATC
*
11758572 TTATCTTGGATTTCT
1 TTATCCTGGATTTCT
*
11758587 TTATCCTGGATCTCT
1 TTATCCTGGATTTCT
* *
11758602 TTATTCTGGGTTTCT
1 TTATCCTGGATTTCT
* *
11758617 CTATCTTGGATTTCT
1 TTATCCTGGATTTCT
11758632 TTAT
1 TTAT
11758636 TCGGTTTTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.56
Consensus pattern (15 bp):
TTATCCTGGATTTCT
Found at i:11765131 original size:39 final size:39
Alignment explanation
Indices: 11765065--11765191 Score: 175
Period size: 39 Copynumber: 3.2 Consensus size: 39
11765055 ATATTTGATG
*
11765065 TATATCC-GAGCTTAAAGGTCCGTAGGCTATGTGCTGGAAT
1 TATATCCGGA-CTT-AAGGTCCGCAGGCTATGTGCTGGAAT
11765105 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
11765144 TATATCTGGACTTAAGGTCCGCGGGCTATGTGCTAGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
11765183 TATGTCCGG
1 TATATCCGG
11765192 GCTAAAGTCC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 67 0.85
40 10 0.13
41 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:11767962 original size:15 final size:15
Alignment explanation
Indices: 11767932--11768010 Score: 86
Period size: 15 Copynumber: 5.3 Consensus size: 15
11767922 GCATAGTATC
* *
11767932 TTATCTTGGGTTTCT
1 TTATCCTGGATTTCT
*
11767947 TTATCCTGGATCTCT
1 TTATCCTGGATTTCT
*
11767962 TTATTCTGGATTTCT
1 TTATCCTGGATTTCT
* *
11767977 TTATTCTGGGTTTCT
1 TTATCCTGGATTTCT
* *
11767992 CTATCTTGGATTTCT
1 TTATCCTGGATTTCT
11768007 TTAT
1 TTAT
11768011 TTGGTTTTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.57
Consensus pattern (15 bp):
TTATCCTGGATTTCT
Found at i:11768011 original size:30 final size:30
Alignment explanation
Indices: 11767933--11768020 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
11767923 CATAGTATCT
* * * *
11767933 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
11767963 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
11767993 TATCTTGGATTTCTTTATT-TGGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
11768021 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.18
30 40 0.80
31 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.58
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:11768019 original size:14 final size:15
Alignment explanation
Indices: 11767942--11768021 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
11767932 TTATCTTGGG
*
11767942 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
11767957 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
11767972 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
11767987 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
11768002 TTTCTTTATT-TGGT
1 TTTCTTTATTCTGGA
11768016 TTTCTT
1 TTTCTT
11768022 GTTATCTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 11 0.20
15 43 0.78
16 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:11776631 original size:40 final size:41
Alignment explanation
Indices: 11776594--11776699 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 41
11776584 TGAGGAATTG
*
11776594 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATGT
1 TATCCGGGCTTAAAGACCCGCAGGCTATCATGCTGGAATGC
* *
11776634 TATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTAGAATGC
1 TATCCGGGCTTAAAGACCCGCAGGCTATCATGCTGGAATGC
*
11776674 TATCCGGGC-TAGAGACCCGCAGGCTA
1 TATCCGGGCTTAAAGACCCGCAGGCTA
11776700 CGAGCTAGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 16 0.27
40 44 0.73
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (41 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATCATGCTGGAATGC
Found at i:11776707 original size:39 final size:40
Alignment explanation
Indices: 11776594--11776737 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 40
11776584 TGAGGAATTG
* * *
11776594 TATCCGGGCTTAAAGACCCGCAGGCTA-TATGCTGGAATGT
1 TATCCGGGCTTAAAGACCCGCAGGCTACGA-GCTAGAATGC
* *
11776634 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTAGAATGC
1 TATCCGGGCTTAAAGACCCGCAGGCTACGAGCTAGAATGC
* *
11776674 TATCCGGGC-TAGAGACCCGCAGGCTACGAGCTAGTAT--
1 TATCCGGGCTTAAAGACCCGCAGGCTACGAGCTAGAATGC
* **
11776711 TATACCGGGTTTAAATTCCCGCAGGCT
1 TAT-CCGGGCTTAAAGACCCGCAGGCT
11776738 GGTGCTAGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
37 3 0.03
38 5 0.06
39 37 0.42
40 43 0.49
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTACGAGCTAGAATGC
Found at i:11778744 original size:7 final size:7
Alignment explanation
Indices: 11778711--11778746 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
11778701 CCCGGTCCCA
11778711 GTCTC-G
1 GTCTCGG
*
11778717 GTCTCGA
1 GTCTCGG
11778724 GTCTCGG
1 GTCTCGG
11778731 GTCTCGG
1 GTCTCGG
11778738 GTCTCGG
1 GTCTCGG
11778745 GT
1 GT
11778747 AAAGGGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.03, C:0.28, G:0.39, T:0.31
Consensus pattern (7 bp):
GTCTCGG
Found at i:11780216 original size:23 final size:23
Alignment explanation
Indices: 11780181--11780224 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
11780171 ATACTATAAA
*
11780181 ACATTTAACCACA-AAGTTAACAT
1 ACATTCAACCACATAA-TTAACAT
*
11780204 ACATTCAATCACATAATTAAC
1 ACATTCAACCACATAATTAAC
11780225 CATAAACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (23 bp):
ACATTCAACCACATAATTAACAT
Found at i:11787164 original size:27 final size:27
Alignment explanation
Indices: 11787053--11787361 Score: 308
Period size: 27 Copynumber: 11.6 Consensus size: 27
11787043 TTAGTTTACC
* *
11787053 AAATTACTGAAATACCC-CCAGTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
11787079 AAATTAC-CAAAGTACCC-CGGTTTATA
1 AAATTACTGAAA-TACCCTCGATTTGTA
* *
11787105 AAATTACCGAAATACCGTCGA-TTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
11787131 AAATTACTGAAATACCCTAGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
11787158 AAATTACCGAAATACCCTC-AGTTTGAA
1 AAATTACTGAAATACCCTCGA-TTTGTA
*
11787185 AAATTACTTAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
11787212 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * * * *
11787239 AAATCAC-CAAAGTACCCCCAATTTATA
1 AAATTACTGAAA-TACCCTCGATTTGTA
** *
11787266 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
11787293 AAATTACCGAAATACCCTC-AGTTTGCA
1 AAATTACTGAAATACCCTCGA-TTTGTA
*
11787320 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
11787347 AAATTACTAAAATAC
1 AAATTACTGAAATAC
11787362 TCCTGTAAGA
Statistics
Matches: 236, Mismatches: 37, Indels: 19
0.81 0.13 0.07
Matches are distributed among these distances:
25 3 0.01
26 55 0.23
27 172 0.73
28 6 0.03
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:11787403 original size:27 final size:27
Alignment explanation
Indices: 11787373--11787515 Score: 196
Period size: 27 Copynumber: 5.3 Consensus size: 27
11787363 CCTGTAAGAT
*
11787373 AGAATTATCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* * *
11787400 AGAATTATCGTTTTACCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
*
11787427 AGAATTACTATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* * *
11787454 AGAATTACCGTCTTACCCTTGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
11787481 AGAATTACCATTTTACCCTCAATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
11787508 AAAATTAC
1 AGAATTAC
11787516 TGAAATACCT
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 101 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (27 bp):
AGAATTACCATTTTACCCTCGATTTAC
Found at i:11787524 original size:27 final size:27
Alignment explanation
Indices: 11787475--11787633 Score: 95
Period size: 27 Copynumber: 5.9 Consensus size: 27
11787465 CTTACCCTTG
* ***
11787475 ATTTACAGAATTACCATTTTACCCTCA
1 ATTTACAAAATTACCAAAATACCCTCA
** * **
11787502 ATTTACAAAATTACTGAAATACCTTTG
1 ATTTACAAAATTACCAAAATACCCTCA
* *
11787529 GTTTACAAAATTACCAAAATACCCTCG
1 ATTTACAAAATTACCAAAATACCCTCA
** * **
11787556 ATCAATAAAATTACCAAAATACCCTTG
1 ATTTACAAAATTACCAAAATACCCTCA
* **
11787583 GTTTGTAAAATTACCAAAATACCC-CTA
1 ATTTACAAAATTACCAAAATACCCTC-A
** * *
11787610 ATTTGTAAAATTATCGAAATACCC
1 ATTTACAAAATTACCAAAATACCC
11787634 CTGTAGGGTA
Statistics
Matches: 103, Mismatches: 28, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (27 bp):
ATTTACAAAATTACCAAAATACCCTCA
Found at i:11787534 original size:81 final size:81
Alignment explanation
Indices: 11787385--11787543 Score: 194
Period size: 81 Copynumber: 2.0 Consensus size: 81
11787375 AATTATCATT
* * * * * **
11787385 TTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTCGAT
1 TTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACTATAATACCCTCGAT
*
11787450 TTACAGAATTACCGTC
66 TTACAAAATTACCGTC
* * * *
11787466 TTACCCTTGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACTGA-AATACCTTTGG
1 TTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACT-ATAATACCCTCGA
11787530 TTTACAAAATTACC
65 TTTACAAAATTACC
11787544 AAAATACCCT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
81 64 0.98
82 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (81 bp):
TTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACTATAATACCCTCGAT
TTACAAAATTACCGTC
Found at i:11787552 original size:54 final size:54
Alignment explanation
Indices: 11787078--11787633 Score: 205
Period size: 54 Copynumber: 10.3 Consensus size: 54
11787068 CCCCAGTTGT
* * * * *
11787078 AAAATTACC-AAAGTACCC-CGGTTTATAAAATTACCGAAATACCGTCGATTGT--
1 AAAATTACCGAAA-TACCCTTGGTTTACAAAATTACCAAAATACCCTCAATT-TAC
* * * ** * *
11787130 AAAATTACTGAAATACCCTAGATTTGTAAAATTACCGAAATACCCTCAGTTTGA-
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTT-AC
** * * ** * * * **
11787184 AAAATTACTTAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
* **** * * * * **
11787238 AAAATCACC-AAAGTACCCCCAATTTATAAAATTACCCAAATATCCTCGATTTGT
1 AAAATTACCGAAA-TACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
** * * * **
11787292 AAAATTACCGAAATACCCTCAGTTTGCAAAATTACTAAAATACCCTCGATTTGT
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
** * * * *** *
11787346 AAAATTACTAAAATACTCC-T-G-TAAGATAGAATTATCATTTTACCCTCGATTTAC
1 AAAATTACCGAAATAC-CCTTGGTTTACA-A-AATTACCAAAATACCCTCAATTTAC
* * *** * * * * * *** *
11787400 AGAATTATCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTAC
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
* *** * * ***
11787454 AGAATTACCGTCTTACCCTTGATTTACAGAATTACCATTTTACCCTCAATTTAC
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
* * * ** *
11787508 AAAATTACTGAAATACCTTTGGTTTACAAAATTACCAAAATACCCTCGATCAAT
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
* ** **
11787562 AAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC-CTAATTTGT
1 AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTC-AATTTAC
*
11787616 AAAATTATCGAAATACCC
1 AAAATTACCGAAATACCC
11787634 CTGTAGGGTA
Statistics
Matches: 399, Mismatches: 91, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
52 16 0.04
53 37 0.09
54 338 0.85
55 5 0.01
56 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.32
Consensus pattern (54 bp):
AAAATTACCGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATTTAC
Found at i:11787552 original size:81 final size:81
Alignment explanation
Indices: 11787170--11787557 Score: 193
Period size: 81 Copynumber: 4.8 Consensus size: 81
11787160 ATTACCGAAA
* ** *
11787170 TACCCTCAGTTTGA-AAAATTACT-TAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGA
1 TACCCTCAATTT-ACAAAATTACTAT-AATACCCTCGATTTACAAAATTACCAAAATACCCTCGA
* ***
11787233 CTTGTA-A-AATCACCAAAG
64 -TT-TACAGAATTACCATTT
* * * * ** *
11787251 TACCCCCAATTTATAAAATTACCCA-AATATCCTCGATTTGTAAAATTACCGAAATACCCTC-AG
1 TACCCTCAATTTACAAAATTA-CTATAATACCCTCGATTTACAAAATTACCAAAATACCCTCGA-
* * * ***
11787314 TTTGCAAAATTACTAAAA
64 TTTACAGAATTACCATTT
* ** * * * * ***
11787332 TACCCTCGATTTGTAAAATTACTAAAATACTCCT-G--TAAGATAGAATTATCATTTTACCCTCG
1 TACCCTCAATTTACAAAATTACTATAATAC-CCTCGATTTACA-A-AATTACCAAAATACCCTCG
* *
11787394 ATTTACAGAATTATCGTTT
63 ATTTACAGAATTACCATTT
* * * ** * **** *
11787413 TACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTCTTACCCTTGATT
1 TACCCTCAATTTACAAAATTACTATAATACCCTCGATTTACAAAATTACCAAAATACCCTCGATT
11787478 TACAGAATTACCATTT
66 TACAGAATTACCATTT
* * *
11787494 TACCCTCAATTTACAAAATTACTGA-AATACCTTTGGTTTACAAAATTACCAAAATACCCTCGAT
1 TACCCTCAATTTACAAAATTACT-ATAATACCCTCGATTTACAAAATTACCAAAATACCCTCGAT
11787558 CAATAAAATT
Statistics
Matches: 233, Mismatches: 60, Indels: 28
0.73 0.19 0.09
Matches are distributed among these distances:
79 3 0.01
80 11 0.05
81 210 0.90
82 6 0.03
83 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (81 bp):
TACCCTCAATTTACAAAATTACTATAATACCCTCGATTTACAAAATTACCAAAATACCCTCGATT
TACAGAATTACCATTT
Found at i:11787634 original size:27 final size:26
Alignment explanation
Indices: 11787535--11787637 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 26
11787525 TTTGGTTTAC
***
11787535 AAAATTACCAAAATA-CCCTCGATCAAT
1 AAAATTACCAAAATACCCCT-G-TTTGT
*
11787562 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
*
11787589 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
* *
11787616 AAAATTATCGAAATACCCCTGT
1 AAAATTACCAAAATACCCCTGT
11787638 AGGGTAGAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.02
27 59 0.92
28 4 0.06
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (26 bp):
AAAATTACCAAAATACCCCTGTTTGT
Found at i:11787648 original size:27 final size:27
Alignment explanation
Indices: 11787618--11787945 Score: 448
Period size: 27 Copynumber: 12.3 Consensus size: 27
11787608 TAATTTGTAA
*
11787618 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
11787645 AATTATCGAAATACCCCTG-AGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
11787671 AATTACCGGAATACCCCTGTAGGGGAT
1 AATTACCGAAATACCCCTGTAGGGTAG
*
11787698 AATTACCGGAATACCCCTGTAGGGTA-
1 AATTACCGAAATACCCCTGTAGGGTAG
*
11787724 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
11787751 AATTATCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
11787778 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
11787805 AATTACCGAAATATCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
11787832 AATTATCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
11787859 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
11787886 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
11787913 AATTACC-AAGATA-CCTTGTGGGGTAA
1 AATTACCGAA-ATACCCCTGTAGGGTAG
11787939 AATTACC
1 AATTACC
11787946 ATTTTGCCCT
Statistics
Matches: 274, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
26 68 0.25
27 206 0.75
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:11787649 original size:81 final size:79
Alignment explanation
Indices: 11787564--11787927 Score: 383
Period size: 81 Copynumber: 4.5 Consensus size: 79
11787554 CGATCAATAA
* * * * * ** * *
11787564 AATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTA-ATTTGTAAAATTATCGAA
1 AATTACCGAAATACCCCTGG--GGTAGAATTACCGAAATACCCCTATA-GGGTAGAATTACCGAA
11787628 ATACCCCTGTAGGGTAG
63 ATACCCCTGTAGGGTAG
* * * * * *
11787645 AATTATCGAAATACCCCTGAGGGTAGAATTACCGGAATACCCCTGTAGGGGATAATTACCGGAAT
1 AATTACCGAAATACCCCTG-GGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAAT
11787710 ACCCCTGTAGGGTA-
65 ACCCCTGTAGGGTAG
* *
11787724 AATTACCGGAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAATTACCGAAA
1 AATTACCGAAATACCCCTG--GGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAA
11787789 TACCCCTGTAGGGTAG
64 TACCCCTGTAGGGTAG
* * * * *
11787805 AATTACCGAAATATCCCTGTAGGGTAGAATTATCGTAATACCCCTGTAGGGTAGAATTATCGAAA
1 AATTACCGAAATACCCCTG--GGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAA
11787870 TACCCCTGTAGGGTAG
64 TACCCCTGTAGGGTAG
** *
11787886 AATTACTAAAATACCCCTGTAGGGTGGAATTACC-AAGATACC
1 AATTACCGAAATACCCCTG--GGGTAGAATTACCGAA-ATACC
11787928 TTGTGGGGTA
Statistics
Matches: 245, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
79 17 0.07
80 100 0.41
81 127 0.52
82 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (79 bp):
AATTACCGAAATACCCCTGGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAATA
CCCCTGTAGGGTAG
Found at i:11788405 original size:22 final size:22
Alignment explanation
Indices: 11788372--11788436 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
11788362 TTAAAGCCTT
* * *
11788372 CTGATTATGGCTTTGTGTCAAC
1 CTGACTATGGCTCTGTGCCAAC
11788394 CT-ACATATGGCTCTGTGCCAAC
1 CTGAC-TATGGCTCTGTGCCAAC
*
11788416 CTGACTATGGCTGTGTGCCAA
1 CTGACTATGGCTCTGTGCCAA
11788437 ACGTATTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.92
23 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
CTGACTATGGCTCTGTGCCAAC
Found at i:11788631 original size:26 final size:27
Alignment explanation
Indices: 11788595--11788668 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
11788585 ATTCTGTTAA
* *
11788595 GTGGCTTTGCCACATTATCTGT-TCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
11788621 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
* *
11788648 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
11788669 ATAACTGAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 20 0.47
27 23 0.53
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:11788843 original size:6 final size:6
Alignment explanation
Indices: 11788828--11788905 Score: 70
Period size: 6 Copynumber: 12.8 Consensus size: 6
11788818 ATTCTGTTAC
* * * *
11788828 CTGATA CTGATC CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
*
11788877 CTGATT CTGATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGA-TT CTGAT
11788906 AATGTTTCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 3 0.05
6 51 0.86
7 4 0.07
8 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:11788844 original size:12 final size:12
Alignment explanation
Indices: 11788816--11788887 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
11788806 TTATGATTTT
*
11788816 TGATTCTGTTACC
1 TGATTCTGAT-CC
*
11788829 TGATACTGATCC
1 TGATTCTGATCC
* *
11788841 TGATTTTGATTC
1 TGATTCTGATCC
*
11788853 TG-TTACCTGATAC
1 TGATT--CTGATCC
*
11788866 TGATTCTGATTC
1 TGATTCTGATCC
11788878 TGATTCTGAT
1 TGATTCTGAT
11788888 TTTGATTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
11 2 0.04
12 29 0.60
13 15 0.31
14 2 0.04
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.46
Consensus pattern (12 bp):
TGATTCTGATCC
Found at i:11788850 original size:31 final size:31
Alignment explanation
Indices: 11788813--11788885 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
11788803 ACATTATGAT
11788813 TTTTGATTCTGTTACCTGATACTGATCCTGA
1 TTTTGATTCTGTTACCTGATACTGATCCTGA
*
11788844 TTTTGATTCTGTTACCTGATACTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATCCTGA
*
11788875 TTCTGATTCTG
1 TTTTGATTCTG
11788886 ATTTTGATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (31 bp):
TTTTGATTCTGTTACCTGATACTGATCCTGA
Found at i:11802827 original size:30 final size:31
Alignment explanation
Indices: 11802787--11802844 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
11802777 CCAAAATCAT
*
11802787 TTTTTACAAAATTACATTTTTGCCCCTAAAC
1 TTTTTACAAAATTACACTTTTGCCCCTAAAC
11802818 TTTTT-CAAAATTACACTTTTGCCCCTA
1 TTTTTACAAAATTACACTTTTGCCCCTA
11802845 GGCTTGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.43
Consensus pattern (31 bp):
TTTTTACAAAATTACACTTTTGCCCCTAAAC
Found at i:11809753 original size:41 final size:41
Alignment explanation
Indices: 11809656--11809753 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
11809646 ATCAATGGGT
*
11809656 CTACTCACACAAGCTAAAGGTCATGACAAAGCTACAAGGTG
1 CTACTCACACAAGCTGAAGGTCATGACAAAGCTACAAGGTG
* * * *
11809697 TTGCTCACACAAGCTGACGGTCATGACGAAGCTACACA-GTG
1 CTACTCACACAAGCTGAAGGTCATGACAAAGCTACA-AGGTG
11809738 CTACTCACACAAGCTG
1 CTACTCACACAAGCTG
11809754 GCGAGAATCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (41 bp):
CTACTCACACAAGCTGAAGGTCATGACAAAGCTACAAGGTG
Found at i:11811657 original size:26 final size:26
Alignment explanation
Indices: 11811621--11811673 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11811611 TTTGAGTATG
11811621 ACTCTAATAAGTACTTTTAAACATTA
1 ACTCTAATAAGTACTTTTAAACATTA
11811647 ACTCTAATAAGTACTTTTAAACATTA
1 ACTCTAATAAGTACTTTTAAACATTA
11811673 A
1 A
11811674 ATACATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (26 bp):
ACTCTAATAAGTACTTTTAAACATTA
Found at i:11816754 original size:22 final size:24
Alignment explanation
Indices: 11816706--11816763 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
11816696 GTTATTTATA
* **
11816706 TATAATATATATGGATTTTGGTGT
1 TATAATATATATGGAGTGGGGTGT
11816730 TATAATATATAT-GAGTGGGGT-T
1 TATAATATATATGGAGTGGGGTGT
11816752 TATAATATATAT
1 TATAATATATAT
11816764 CTACGTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 13 0.42
23 6 0.19
24 12 0.39
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (24 bp):
TATAATATATATGGAGTGGGGTGT
Found at i:11816793 original size:32 final size:33
Alignment explanation
Indices: 11816752--11816827 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
11816742 GAGTGGGGTT
11816752 TATAATATATATCTACGTGCATGGGTATTATA-
1 TATAATATATATCTACGTGCATGGGTATTATAG
* ** *
11816784 TATAATATATATTTGGGTGCATGGGTGTTATATG
1 TATAATATATATCTACGTGCATGGGTATTATA-G
11816818 TATAATATAT
1 TATAATATAT
11816828 CTGCGTGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 28 0.74
34 10 0.26
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (33 bp):
TATAATATATATCTACGTGCATGGGTATTATAG
Found at i:11821112 original size:34 final size:34
Alignment explanation
Indices: 11821047--11821112 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
11821037 GTTATGAGGA
* * *
11821047 GTATGAACTGTTATTTTTCATGAATTTTTATTCG
1 GTATGAACTGATATTTTTCATGAACTGTTATTCG
11821081 GTATGAACTGATATTTTGT-ATGAACTGTTATT
1 GTATGAACTGATATTTT-TCATGAACTGTTATT
11821113 TTTCATGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.50
Consensus pattern (34 bp):
GTATGAACTGATATTTTTCATGAACTGTTATTCG
Found at i:11821113 original size:17 final size:17
Alignment explanation
Indices: 11821047--11821114 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
11821037 GTTATGAGGA
11821047 GTATGAACTGTTATTTT
1 GTATGAACTGTTATTTT
* * **
11821064 -TCATGAATTTTTATTCG
1 GT-ATGAACTGTTATTTT
*
11821081 GTATGAACTGATATTTT
1 GTATGAACTGTTATTTT
11821098 GTATGAACTGTTATTTT
1 GTATGAACTGTTATTTT
11821115 TCATGAGCTG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
16 1 0.03
17 37 0.95
18 1 0.03
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.51
Consensus pattern (17 bp):
GTATGAACTGTTATTTT
Found at i:11821120 original size:17 final size:16
Alignment explanation
Indices: 11821048--11821130 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 16
11821038 TTATGAGGAG
11821048 TATGAACTGTTATTTT
1 TATGAACTGTTATTTT
* * **
11821064 TCATGAATTTTTATTCGG
1 T-ATGAACTGTTATT-TT
*
11821082 TATGAACTGATATTTT
1 TATGAACTGTTATTTT
11821098 GTATGAACTGTTATTTT
1 -TATGAACTGTTATTTT
* *
11821115 TCATGAGCTGTCATTT
1 T-ATGAACTGTTATTT
11821131 GATAAGAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
16 2 0.04
17 48 0.94
18 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.51
Consensus pattern (16 bp):
TATGAACTGTTATTTT
Found at i:11821147 original size:51 final size:51
Alignment explanation
Indices: 11821047--11821147 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
11821037 GTTATGAGGA
* * * * *
11821047 GTATGAACTGTTATTTTTCATGAATTTTTATTCGGTATGAACTGATATTTT
1 GTATGAACTGTTATTTTTCATGAACTGTCATTCGATAAGAACTGATATTTT
* * * *
11821098 GTATGAACTGTTATTTTTCATGAGCTGTCATTTGATAAGAATTGTTATTT
1 GTATGAACTGTTATTTTTCATGAACTGTCATTCGATAAGAACTGATATTT
11821148 CATATGAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.50
Consensus pattern (51 bp):
GTATGAACTGTTATTTTTCATGAACTGTCATTCGATAAGAACTGATATTTT
Found at i:11825516 original size:27 final size:26
Alignment explanation
Indices: 11825486--11825662 Score: 158
Period size: 27 Copynumber: 6.5 Consensus size: 26
11825476 AAATTGTACA
* *
11825486 GCACTAAGGGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* *
11825513 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
* *
11825540 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
11825567 GCACTAAGTGTGCGAGTTTGACTATGTG
1 GCACTAAGTGTGCGA--TTGACTATGTG
* * *
11825595 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGA-TTGACTATGTG
* * *
11825622 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGA-TTGACTATGTG
*
11825649 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
11825663 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 101 0.78
28 27 0.21
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:11825600 original size:82 final size:81
Alignment explanation
Indices: 11825486--11825641 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
11825476 AAATTGTACA
* *
11825486 GCACTAAGGGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGGGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
11825550 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* * ** *
11825567 GCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGGGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
11825632 TGCGAGTTGA
65 TGCGAATTGA
11825642 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 14 0.22
82 50 0.77
83 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:11825653 original size:82 final size:81
Alignment explanation
Indices: 11825482--11825662 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
11825472 GATTAAATTG
* * *
11825482 TACAGCACTAAGGGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
11825547 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
11825563 TGCGGCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
11825627 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
11825645 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
11825663 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:11825673 original size:27 final size:27
Alignment explanation
Indices: 11825620--11825673 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
11825610 TTTGATTACG
* * *
11825620 TAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGAGCTCAATATA
* *
11825647 TAGCACTGAGTGTGCGGGCTCAATATA
1 TAGCACTAAGTGTGCGAGCTCAATATA
11825674 CATTCGTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGAGCTCAATATA
Found at i:11828350 original size:53 final size:54
Alignment explanation
Indices: 11828281--11828487 Score: 186
Period size: 53 Copynumber: 3.8 Consensus size: 54
11828271 TTCCTTTTTA
* * * *
11828281 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
11828334 AACTCACCATTGCCATGCCTT-AGCATGGTCTTACATGGGAT-CTTCGCCTTATCG
1 AACTTACCAATGCCATGCCTTGA-CATGGTCTTACATGGTATCCTT-GCCTTATAG
* * * * * * * *
11828388 TAATTTATCAATGTCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
11828443 AACTTACCAATCCCATGCCTTGGCATGGTTTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
11828488 AAACCCTAAT
Statistics
Matches: 121, Mismatches: 27, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
52 4 0.03
53 41 0.34
54 36 0.30
55 36 0.30
56 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:11833841 original size:46 final size:46
Alignment explanation
Indices: 11833791--11834059 Score: 307
Period size: 46 Copynumber: 5.8 Consensus size: 46
11833781 TGGTTGAGCA
*
11833791 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
11833837 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
* *
11833882 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
11833930 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
* *
11833975 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* *
11834023 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11834060 GCGGGTTACA
Statistics
Matches: 188, Mismatches: 21, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
43 11 0.06
45 8 0.04
46 93 0.49
47 58 0.31
48 8 0.04
50 10 0.05
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
Found at i:11833947 original size:93 final size:93
Alignment explanation
Indices: 11833788--11834051 Score: 492
Period size: 93 Copynumber: 2.8 Consensus size: 93
11833778 GGATGGTTGA
*
11833788 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
11833853 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
11833881 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
11833946 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
11833974 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
11834039 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
11834052 ACTTATGGGC
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11837047 original size:14 final size:15
Alignment explanation
Indices: 11836998--11837047 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
11836988 CATATCTTGG
* *
11836998 TTTCTTTATCCTGCA
1 TTTCTTTATTCTGGA
*
11837013 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
11837028 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
11837042 TTTCTT
1 TTTCTT
11837048 GTTATCTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.10, C:0.20, G:0.10, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:11852970 original size:23 final size:23
Alignment explanation
Indices: 11852921--11852970 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
11852911 TGCCAATTCA
* * **
11852921 TATAGCCAAATTCATTAACAAGT
1 TATAACCAAAATCATTAACAACC
*
11852944 TATAACCAAAATCATTATCAACC
1 TATAACCAAAATCATTAACAACC
11852967 TATA
1 TATA
11852971 TTCAAAATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (23 bp):
TATAACCAAAATCATTAACAACC
Found at i:11853515 original size:29 final size:28
Alignment explanation
Indices: 11853464--11853518 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
11853454 CTCCGAAGTA
* *
11853464 CTGATATCATGTCCCGAAGCCAAATCAG
1 CTGATATCATGGCCCAAAGCCAAATCAG
*
11853492 CTGATATGCATGGCCCAAATCCAAATC
1 CTGATAT-CATGGCCCAAAGCCAAATC
11853519 GGTATAACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (28 bp):
CTGATATCATGGCCCAAAGCCAAATCAG
Found at i:11854453 original size:24 final size:25
Alignment explanation
Indices: 11854409--11854461 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
11854399 TGTTTTATTT
11854409 AATTAACCTTTAATTACTAATGACAA
1 AATTAACCTTTAATTACTAAT-ACAA
* *
11854435 AATTAACC-TT-ATTATTAATTCAA
1 AATTAACCTTTAATTACTAATACAA
11854458 AATT
1 AATT
11854462 TCAATTATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 8 0.32
25 2 0.08
26 8 0.32
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (25 bp):
AATTAACCTTTAATTACTAATACAA
Found at i:11857337 original size:25 final size:25
Alignment explanation
Indices: 11857281--11857338 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11857271 ACTCGAGCTG
* *
11857281 TAGATCGGTATGCTCTCACAAGCTA
1 TAGATCGGTATGCTCACACAAGATA
*
11857306 TAAATCGGTATGCTCACACAAGATA
1 TAGATCGGTATGCTCACACAAGATA
*
11857331 TGGATCGG
1 TAGATCGG
11857339 AACATAGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (25 bp):
TAGATCGGTATGCTCACACAAGATA
Found at i:11861424 original size:23 final size:23
Alignment explanation
Indices: 11861364--11861425 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
11861354 GGTTATGCCT
* *
11861364 CACACACCCGTGTGAAGGCAAAG
1 CACACGCCCGTGTGCAGGCAAAG
* *
11861387 CACATGCCCATGTGCAGGCAAAG
1 CACACGCCCGTGTGCAGGCAAAG
11861410 CACACGCCCGTGTGCA
1 CACACGCCCGTGTGCA
11861426 CACCCGTGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (23 bp):
CACACGCCCGTGTGCAGGCAAAG
Found at i:11863564 original size:21 final size:21
Alignment explanation
Indices: 11863540--11863582 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11863530 AGACACTGTC
11863540 TAAGAGTACATTTGTCATAAT
1 TAAGAGTACATTTGTCATAAT
11863561 TAAGAGTACATTTGTCATAAT
1 TAAGAGTACATTTGTCATAAT
11863582 T
1 T
11863583 TGTCAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (21 bp):
TAAGAGTACATTTGTCATAAT
Found at i:11872134 original size:13 final size:13
Alignment explanation
Indices: 11872116--11872145 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11872106 CTGGACTTCC
11872116 TCACACGGACGTG
1 TCACACGGACGTG
*
11872129 TCACACGGCCGTG
1 TCACACGGACGTG
11872142 TCAC
1 TCAC
11872146 TTTGGCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (13 bp):
TCACACGGACGTG
Found at i:11880822 original size:42 final size:42
Alignment explanation
Indices: 11880742--11880942 Score: 138
Period size: 42 Copynumber: 4.6 Consensus size: 42
11880732 AATAAGATGC
* * * * * ** *
11880742 CAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCACAT
1 CAATGCTATATCCCAGATATGGTCTTACACGAAATCTCATAT
* * * *
11880784 CGATGCCATATCCCAGATATGGTCTTATAC-AAATTCTCATTT
1 CAATGCTATATCCCAGATATGGTCTTACACGAAA-TCTCATAT
* * **
11880826 CAACGCTATGTCCCAGACGTGGTCTTACACGAAATCTCATAT
1 CAATGCTATATCCCAGATATGGTCTTACACGAAATCTCATAT
*
11880868 CAACT-CTATATCCCAGATATGGTCTTACATGATAA-CTCATACTGAT
1 CAA-TGCTATATCCCAGATATGGTCTTACACGA-AATCTC--A-T-AT
*
11880914 GCCAATGCCATATCCCAGATATGGTCTTA
1 --CAATGCTATATCCCAGATATGGTCTTA
11880943 TATGGGATCT
Statistics
Matches: 124, Mismatches: 24, Indels: 16
0.76 0.15 0.10
Matches are distributed among these distances:
41 1 0.01
42 89 0.72
43 5 0.04
44 1 0.01
45 1 0.01
46 2 0.02
47 1 0.01
48 24 0.19
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (42 bp):
CAATGCTATATCCCAGATATGGTCTTACACGAAATCTCATAT
Found at i:11887935 original size:19 final size:19
Alignment explanation
Indices: 11887911--11887950 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
11887901 AATCACATCT
11887911 ATGCTTTATATAGCATTTC
1 ATGCTTTATATAGCATTTC
11887930 ATGCTTTATATAGCATTTC
1 ATGCTTTATATAGCATTTC
11887949 AT
1 AT
11887951 CTTCAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (19 bp):
ATGCTTTATATAGCATTTC
Found at i:11888297 original size:48 final size:48
Alignment explanation
Indices: 11888226--11888323 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
11888216 TAAACCACCA
*
11888226 AATTGCACTACAGTTTGTAACATCTAGAACATTACCGGTTTCAACTCG
1 AATTGCACTACAGTTTGTAACATCTAAAACATTACCGGTTTCAACTCG
* * *
11888274 AATTGCCCTACAGTTTGTAACATCTAAAACATTACTGGTTTTAACTCG
1 AATTGCACTACAGTTTGTAACATCTAAAACATTACCGGTTTCAACTCG
11888322 AA
1 AA
11888324 CTACTGAGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (48 bp):
AATTGCACTACAGTTTGTAACATCTAAAACATTACCGGTTTCAACTCG
Found at i:11899289 original size:12 final size:12
Alignment explanation
Indices: 11899272--11899310 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11899262 AACGACCTCC
11899272 ACCCCCTATTGT
1 ACCCCCTATTGT
* *
11899284 ACCCCCTGTTAT
1 ACCCCCTATTGT
*
11899296 ACCACCTATTGT
1 ACCCCCTATTGT
11899308 ACC
1 ACC
11899311 TTCGGTTGCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.21, C:0.41, G:0.08, T:0.31
Consensus pattern (12 bp):
ACCCCCTATTGT
Found at i:11914412 original size:28 final size:28
Alignment explanation
Indices: 11914387--11914479 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
11914377 AAAAATATAC
11914387 ATATATGATGGATACTACTATTATATCG
1 ATATATGATGGATACTACTATTATATCG
* * ** *
11914415 ATATATTTAATAGGATTAGTTAAAAATATA-C-
1 ATATA--TGAT-GGA-TA-CTACTATTATATCG
11914446 ATATATGATGGATACTACTATTATATCG
1 ATATATGATGGATACTACTATTATATCG
11914474 ATATAT
1 ATATAT
11914480 TTAATTGAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
26 7 0.15
27 3 0.06
28 14 0.29
29 3 0.06
30 3 0.06
31 8 0.17
32 3 0.06
33 7 0.15
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (28 bp):
ATATATGATGGATACTACTATTATATCG
Found at i:11914434 original size:59 final size:59
Alignment explanation
Indices: 11914365--11914484 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
11914355 TGATAAAGAC
11914365 ATAGGATTAGTTAAAAATATACATATATGATGGATACTACTATTATATCGATATATTTA
1 ATAGGATTAGTTAAAAATATACATATATGATGGATACTACTATTATATCGATATATTTA
11914424 ATAGGATTAGTTAAAAATATACATATATGATGGATACTACTATTATATCGATATATTTA
1 ATAGGATTAGTTAAAAATATACATATATGATGGATACTACTATTATATCGATATATTTA
11914483 AT
1 AT
11914485 TGAATCGTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (59 bp):
ATAGGATTAGTTAAAAATATACATATATGATGGATACTACTATTATATCGATATATTTA
Found at i:11915751 original size:31 final size:31
Alignment explanation
Indices: 11915714--11915820 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
11915704 TCAACTAGAT
*
11915714 TTAAGGGTTTATTTAAATAAGTCATTATAGC
1 TTAAGGGTTTATTTAAATAAGACATTATAGC
* ** * **
11915745 TCAAGGGTTTATTTAGGTAA-AAAAAATA-C
1 TTAAGGGTTTATTTAAATAAGACATTATAGC
* * *
11915774 TATAAAGGCTTATTTAAATAAGCCATTATAGC
1 T-TAAGGGTTTATTTAAATAAGACATTATAGC
11915806 TTAAGGGTTTATTTA
1 TTAAGGGTTTATTTA
11915821 GGTAAAAGAA
Statistics
Matches: 55, Mismatches: 18, Indels: 6
0.70 0.23 0.08
Matches are distributed among these distances:
29 2 0.04
30 18 0.33
31 33 0.60
32 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (31 bp):
TTAAGGGTTTATTTAAATAAGACATTATAGC
Found at i:11915817 original size:61 final size:60
Alignment explanation
Indices: 11915722--11915854 Score: 203
Period size: 61 Copynumber: 2.2 Consensus size: 60
11915712 ATTTAAGGGT
* *
11915722 TTATTTAAATAAGTCATTATAGCTCAAGGGTTTATTTAGGTAAAAAAAATACTATAAAGGC
1 TTATTTAAATAAGCCATTATAGCTCAAGGGTTTATTTAGGT-AAAAAAATACTATAAAAGC
* * * *
11915783 TTATTTAAATAAGCCATTATAGCTTAAGGGTTTATTTAGGTAAAAGAATATTATAAAAGT
1 TTATTTAAATAAGCCATTATAGCTCAAGGGTTTATTTAGGTAAAAAAATACTATAAAAGC
11915843 TTATTTAAATAA
1 TTATTTAAATAA
11915855 TTTAGTATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
60 27 0.41
61 39 0.59
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.38
Consensus pattern (60 bp):
TTATTTAAATAAGCCATTATAGCTCAAGGGTTTATTTAGGTAAAAAAATACTATAAAAGC
Found at i:11916710 original size:26 final size:26
Alignment explanation
Indices: 11916681--11916736 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
11916671 TGGTACAAAT
11916681 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
11916707 TGATAATGGTTTAGTTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11916733 TGAT
1 TGAT
11916737 GGGCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.39
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11920173 original size:24 final size:25
Alignment explanation
Indices: 11920146--11920200 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
11920136 TTAGCTAAAA
*
11920146 TGTGTTGTAT-ATTTGATGCATATT
1 TGTGTTGTATAATTTCATGCATATT
* * *
11920170 TGTGGTATATAATTTCATGCATTTT
1 TGTGTTGTATAATTTCATGCATATT
11920195 TG-GTTG
1 TGTGTTG
11920201 AAATTAGAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (25 bp):
TGTGTTGTATAATTTCATGCATATT
Found at i:11920353 original size:36 final size:36
Alignment explanation
Indices: 11920306--11920375 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
11920296 TCATTTATGA
*
11920306 CATTTTTTAATTAACTAAAGTGTATAAAA-TAGTTAC
1 CATTTTTTAATTAACTAAAATGTA-AAAAGTAGTTAC
*
11920342 CATTTTTTAATTCACTAAAATGTAAAAAGTAGTT
1 CATTTTTTAATTAACTAAAATGTAAAAAGTAGTT
11920376 GCCAATGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (36 bp):
CATTTTTTAATTAACTAAAATGTAAAAAGTAGTTAC
Found at i:11921592 original size:25 final size:25
Alignment explanation
Indices: 11921564--11921619 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
11921554 CACAACAGAA
*
11921564 CAGAACAAGACAAAACCAAA-CAAAG
1 CAGAACAAAAC-AAACCAAACCAAAG
* *
11921589 CAGAACAAAACAAATCAAACCAGAG
1 CAGAACAAAACAAACCAAACCAAAG
11921614 CAGAAC
1 CAGAAC
11921620 CGAACAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.61, C:0.25, G:0.12, T:0.02
Consensus pattern (25 bp):
CAGAACAAAACAAACCAAACCAAAG
Found at i:11921596 original size:20 final size:20
Alignment explanation
Indices: 11921573--11921627 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
11921563 ACAGAACAAG
*
11921573 ACAAAACCAAACAAAGCAGA
1 ACAAAACCAAACAAACCAGA
11921593 ACAAAA-CAAATCAAACCAGA
1 ACAAAACCAAA-CAAACCAGA
* * *
11921613 GCAGAACCGAACAAA
1 ACAAAACCAAACAAA
11921628 ATAGTACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.62, C:0.25, G:0.11, T:0.02
Consensus pattern (20 bp):
ACAAAACCAAACAAACCAGA
Done.