Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 183 of 297
Found at i:61760122 original size:93 final size:94
Alignment explanation
Indices: 61759956--61760177 Score: 236
Period size: 93 Copynumber: 2.4 Consensus size: 94
61759946 ACTTTATGGG
* * * * * *
61759956 AGCCAGTATAAAATCATGTCTAGGACATGGCATCGGCATTGAGATGAGAGTTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGATGAGAGTCACTGTAAGACATG
* * * * *
61760021 TTTGGGACAT-GCATTGGCCTCGAGACGTA
66 TCTAGGACATGGCA-TCGACTCGAGACATA
* * *
61760050 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGAGATGATAGTCACTGTAAGATCA
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCAT-CGAGATGAGAGTCACTGTAAGA-CA
* * *
61760112 TGTCTAGGACATGGCATCGACTTGAGATATG
64 TGTCTAGGACATGGCATCGACTCGAGACATA
61760143 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
61760178 TCACCTTACC
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
91 1 0.01
92 26 0.25
93 46 0.44
94 26 0.25
95 6 0.06
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGATGAGAGTCACTGTAAGACATG
TCTAGGACATGGCATCGACTCGAGACATA
Found at i:61760169 original size:140 final size:140
Alignment explanation
Indices: 61759914--61760171 Score: 333
Period size: 140 Copynumber: 1.8 Consensus size: 140
61759904 TATGTGAGCC
*** * *
61759914 AGTGTAAAACATGTCTGGGACATGCATCGGTAACTTTATGGGAGCCAGTATAAAATCATGTCTAG
1 AGTGTAAAACATGTCTGGGACATGCATCGGTAACGAGATGAGAGCCACTATAAAATCATGTCTAG
* ** * *
61759979 GACATGGCATCGGCATTGAGATGAGAGTTAGTGTAAGACATGTTTGGGACATGCATTGGCCTCGA
66 GACATGGCATCGACATTGAGATGAGAGCCAGTGTAAGACATGTCTAGGACATGCATTGGCCTCGA
61760044 GACGTAAGCT
131 GACGTAAGCT
* * * * *
61760054 AGTGTAAGACATGTCTGGGACATGCATCGGCT-ACGAGATGATAGTCACTGTAAGATCATGTCTA
1 AGTGTAAAACATGTCTGGGACATGCATCGG-TAACGAGATGAGAGCCACTATAAAATCATGTCTA
61760118 GGACATGGCATCGAC-TTGAGAT-ATGAGCCAGTGTAAGACCATGTCTAGGACATG
65 GGACATGGCATCGACATTGAGATGA-GAGCCAGTGTAAGA-CATGTCTAGGACATG
61760172 GCATCGTCAC
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
138 1 0.01
139 19 0.19
140 79 0.79
141 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (140 bp):
AGTGTAAAACATGTCTGGGACATGCATCGGTAACGAGATGAGAGCCACTATAAAATCATGTCTAG
GACATGGCATCGACATTGAGATGAGAGCCAGTGTAAGACATGTCTAGGACATGCATTGGCCTCGA
GACGTAAGCT
Found at i:61761108 original size:28 final size:28
Alignment explanation
Indices: 61761069--61761131 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
61761059 GACACGGGCT
61761069 AGGG-CACGGGCGTGTCGTGGCCGTGTG
1 AGGGACACGGGCGTGTCGTGGCCGTGTG
61761096 AGGGACACGGGCGTGTCGTGGCCGTGTG
1 AGGGACACGGGCGTGTCGTGGCCGTGTG
61761124 AGGGACAC
1 AGGGACAC
61761132 AAGCCAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.11
28 31 0.89
ACGTcount: A:0.13, C:0.22, G:0.49, T:0.16
Consensus pattern (28 bp):
AGGGACACGGGCGTGTCGTGGCCGTGTG
Found at i:61763903 original size:42 final size:41
Alignment explanation
Indices: 61763826--61763964 Score: 127
Period size: 42 Copynumber: 3.2 Consensus size: 41
61763816 TCTTATATGT
* *
61763826 AATCAAATATCGATGCCACTGTCCCAAATAGGGTCTTACACGA
1 AATCAAATAT-GATGCCA-TGTCCCAAACATGGTCTTACACGA
*
61763869 AATCAAATATGATGCCGATGTCCCAAACATGGTCTTACACATA
1 AATCAAATATGATGCC-ATGTCCCAAACATGGTCTTACAC-GA
** * * *
61763912 AATCTCAAAT-TGATGCCAACATTCCAAACGTGGTCTTACATGA
1 AA--TCAAATATGATGCC-ATGTCCCAAACATGGTCTTACACGA
*
61763955 AATCACATAT
1 AATCAAATAT
61763965 AGGAATCCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
41 5 0.06
42 27 0.34
43 17 0.21
44 25 0.31
45 6 0.08
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (41 bp):
AATCAAATATGATGCCATGTCCCAAACATGGTCTTACACGA
Found at i:61764581 original size:32 final size:32
Alignment explanation
Indices: 61764540--61764606 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
61764530 AAACATAGTA
61764540 ATCTAACACATATCTTTCATTTTTCATCAACT
1 ATCTAACACATATCTTTCATTTTTCATCAACT
61764572 ATCTAACACATATCTTTCATTTTTCATCAACT
1 ATCTAACACATATCTTTCATTTTTCATCAACT
61764604 ATC
1 ATC
61764607 ATCACAAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.43
Consensus pattern (32 bp):
ATCTAACACATATCTTTCATTTTTCATCAACT
Found at i:61771118 original size:43 final size:44
Alignment explanation
Indices: 61771051--61771222 Score: 160
Period size: 43 Copynumber: 4.0 Consensus size: 44
61771041 AGCTCATACA
*
61771051 ATGCCAAC-GTCCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACTGTCCCAGACATGGTCTTACACGTAATCAAATATCG
*
61771094 ATGCC-ACTGTCCCAGACA-GTGTCTTACACGAAATCAAATA-CG
1 ATGCCAACTGTCCCAGACATG-GTCTTACACGTAATCAAATATCG
* * *
61771136 ATGCCGA-TGTTCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAACTGTCCCAGACATGGTCTTACACGT-AATC-AAATATCG
* * * * * * *
61771180 ATGCCAAC-ATCCCATACGTAGTCTTGCACGAAATCACATATCG
1 ATGCCAACTGTCCCAGACATGGTCTTACACGTAATCAAATATCG
61771223 GGATCCTATG
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 31 0.30
43 48 0.46
44 26 0.25
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACATGGTCTTACACGTAATCAAATATCG
Found at i:61774667 original size:3 final size:3
Alignment explanation
Indices: 61774659--61774694 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
61774649 AATTAATGTT
61774659 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
61774695 GCATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61778089 original size:3 final size:3
Alignment explanation
Indices: 61778081--61778123 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
61778071 ACTTGTTAAC
61778081 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
61778124 TAGAAAGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:61778199 original size:6 final size:6
Alignment explanation
Indices: 61778188--61778214 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
61778178 TGAAGTGTGC
61778188 GGATAT GGATAT GGATAT GGATAT GGA
1 GGATAT GGATAT GGATAT GGATAT GGA
61778215 CATTGAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (6 bp):
GGATAT
Found at i:61782240 original size:46 final size:45
Alignment explanation
Indices: 61782152--61782270 Score: 148
Period size: 46 Copynumber: 2.6 Consensus size: 45
61782142 TAGGCTATTT
* * *
61782152 TTTGTGTAAGTTCAACCCTAACGGTGAATAGGCACTATTATCCGA
1 TTTGTGTAGGTTCAACCTTAACGGTGAATAGACACTATTATCCGA
* * *
61782197 TTTGTGTAGGTTCAACTTTAATGGGTGAATAGACACTGTTATCCGA
1 TTTGTGTAGGTTCAACCTTAA-CGGTGAATAGACACTATTATCCGA
**
61782243 TTCATGTAGGTTCAACCTTAACGAGTGA
1 TTTGTGTAGGTTCAACCTTAACG-GTGA
61782271 CCAGACAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 19 0.31
46 43 0.69
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (45 bp):
TTTGTGTAGGTTCAACCTTAACGGTGAATAGACACTATTATCCGA
Found at i:61783810 original size:7 final size:7
Alignment explanation
Indices: 61783798--61783832 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
61783788 ATAATAATGC
61783798 TGATAAA
1 TGATAAA
61783805 TGATAAA
1 TGATAAA
61783812 TGATAAA
1 TGATAAA
61783819 TGATAAA
1 TGATAAA
61783826 TGATAAA
1 TGATAAA
61783833 AATGTTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
TGATAAA
Found at i:61785000 original size:26 final size:26
Alignment explanation
Indices: 61784971--61785078 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
61784961 TGGTACAAAT
61784971 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
61784997 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61785023 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
61785049 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61785075 TGAT
1 TGAT
61785079 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:61802052 original size:23 final size:22
Alignment explanation
Indices: 61802026--61802174 Score: 102
Period size: 23 Copynumber: 6.4 Consensus size: 22
61802016 CAGCTCGTAT
*
61802026 GAGCTTACTAATTCAGCTCATAA
1 GAGCTTACTGATTCAGCTCA-AA
* * * **
61802049 GAGCTTATTGTTTCATCTCATTG
1 GAGCTTACTGATTCAGCTCA-AA
*
61802072 GAGCTTATTGATTCAGCTCGAAA
1 GAGCTTACTGATTCAGCTC-AAA
*
61802095 GAACTTACTG-TTCAGCTCAATA
1 GAGCTTACTGATTCAGCTCAA-A
* *
61802117 GAGCTTATTGTTTTCAGCTCAATA
1 GAGCTTACTG-ATTCAGCTCAA-A
*
61802141 GAGCTTACTGTTTATCAGCTCAAGA
1 GAGCTTACTG-AT-TCAGCTCAA-A
61802166 GGAGCTTAC
1 -GAGCTTAC
61802175 CGACCATGAC
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.02
22 17 0.16
23 42 0.40
24 25 0.24
25 10 0.10
26 8 0.08
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (22 bp):
GAGCTTACTGATTCAGCTCAAA
Found at i:61802109 original size:22 final size:22
Alignment explanation
Indices: 61802026--61802152 Score: 105
Period size: 23 Copynumber: 5.5 Consensus size: 22
61802016 CAGCTCGTAT
*
61802026 GAGCTTACTAATTCAGCTC-ATAA
1 GAGCTTACT-GTTCAGCTCAAT-A
* * * *
61802049 GAGCTTATTGTTTCATCTCATTG
1 GAGCTTACTG-TTCAGCTCAATA
*
61802072 GAGCTTATTGATTCAGCTCGAA-A
1 GAGCTTACTG-TTCAGCTC-AATA
*
61802095 GAACTTACTGTTCAGCTCAATA
1 GAGCTTACTGTTCAGCTCAATA
*
61802117 GAGCTTATTGTTTTCAGCTCAATA
1 GAGCTTACTG--TTCAGCTCAATA
61802141 GAGCTTACTGTT
1 GAGCTTACTGTT
61802153 TATCAGCTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
21 2 0.02
22 19 0.23
23 40 0.48
24 23 0.27
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:61802133 original size:46 final size:44
Alignment explanation
Indices: 61802026--61802152 Score: 137
Period size: 46 Copynumber: 2.8 Consensus size: 44
61802016 CAGCTCGTAT
* * * * * *
61802026 GAGCTTACTAATTCAGCTCATAAGAGCTTATTGTTTCATCTCATTG
1 GAGCTTATTGATTCAGCTCA-AAGAGCTTACTG-TTCAGCTCAATA
*
61802072 GAGCTTATTGATTCAGCTCGAAAGAACTTACTGTTCAGCTCAATA
1 GAGCTTATTGATTCAGCTC-AAAGAGCTTACTGTTCAGCTCAATA
*
61802117 GAGCTTATTGTTTTCAGCTCAATAGAGCTTACTGTT
1 GAGCTTATTG-ATTCAGCTCAA-AGAGCTTACTGTT
61802153 TATCAGCTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
45 21 0.30
46 47 0.68
47 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (44 bp):
GAGCTTATTGATTCAGCTCAAAGAGCTTACTGTTCAGCTCAATA
Found at i:61802636 original size:32 final size:32
Alignment explanation
Indices: 61802595--61802658 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
61802585 CGCATATAAG
* *
61802595 CCCATTAGTGTGCAAGATACAGAATATTCAAT
1 CCCATTAGTGTGAAAGATACAGAATATCCAAT
61802627 CCCATTAGTGTGAAAGATACAGAATATCCAAT
1 CCCATTAGTGTGAAAGATACAGAATATCCAAT
61802659 GTTATTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (32 bp):
CCCATTAGTGTGAAAGATACAGAATATCCAAT
Found at i:61809782 original size:46 final size:45
Alignment explanation
Indices: 61809694--61809812 Score: 148
Period size: 46 Copynumber: 2.6 Consensus size: 45
61809684 TAGGCTATTT
* * *
61809694 TTTGTGTAAGTTCAACCCTAACGGTGAATAGGCACTATTATCCGA
1 TTTGTGTAGGTTCAACCTTAACGGTGAATAGACACTATTATCCGA
* * *
61809739 TTTGTGTAGGTTCAACTTTAATGGGTGAATAGACACTGTTATCCGA
1 TTTGTGTAGGTTCAACCTTAA-CGGTGAATAGACACTATTATCCGA
**
61809785 TTCATGTAGGTTCAACCTTAACGAGTGA
1 TTTGTGTAGGTTCAACCTTAACG-GTGA
61809813 CCAGACAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 19 0.31
46 43 0.69
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (45 bp):
TTTGTGTAGGTTCAACCTTAACGGTGAATAGACACTATTATCCGA
Found at i:61811352 original size:7 final size:7
Alignment explanation
Indices: 61811340--61811374 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
61811330 ATAATAATGC
61811340 TGATAAA
1 TGATAAA
61811347 TGATAAA
1 TGATAAA
61811354 TGATAAA
1 TGATAAA
61811361 TGATAAA
1 TGATAAA
61811368 TGATAAA
1 TGATAAA
61811375 AATGTTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
TGATAAA
Found at i:61812542 original size:26 final size:26
Alignment explanation
Indices: 61812513--61812568 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
61812503 TGGTACAAAT
61812513 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
61812539 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61812565 TGAT
1 TGAT
61812569 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:61814428 original size:46 final size:46
Alignment explanation
Indices: 61814361--61814449 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
61814351 GTCTCCCCAA
*
61814361 ATGGGCTTGTATATGTTATTGATGTTGCATGTATTTTGAAATGGGG
1 ATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGG
61814407 ATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATG
1 ATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATG
61814450 AGCCTACGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (46 bp):
ATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGG
Found at i:61814470 original size:46 final size:44
Alignment explanation
Indices: 61814371--61814471 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 44
61814361 ATGGGCTTGT
* *
61814371 ATATGTTATTGATGTTGCATGTATTTTGAAATGGGGATGGGCTTGC
1 ATATGTTATTGATGTTGCATGTATTTTGAAATGGCGACGGGC-T-C
*
61814417 ATATGTTATTGATGTTGCATGTATTTTGAAATGAGCCTACGGGC-C
1 ATATGTTATTGATGTTGCATGTATTTTGAAATG-G-CGACGGGCTC
61814462 ATACTGTTAT
1 ATA-TGTTAT
61814472 CTGAATAAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
45 4 0.08
46 39 0.80
47 1 0.02
48 5 0.10
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.41
Consensus pattern (44 bp):
ATATGTTATTGATGTTGCATGTATTTTGAAATGGCGACGGGCTC
Found at i:61818587 original size:40 final size:40
Alignment explanation
Indices: 61818539--61818744 Score: 299
Period size: 40 Copynumber: 5.2 Consensus size: 40
61818529 GGACTAAGAT
* *
61818539 CCGAAGGCATTTGTGCTAGTGATTATATCCGAGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
61818579 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
61818619 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
61818659 CCAAAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* * * * *
61818699 CCGAAGGCATTCGTACGAGTTG-CTATATCC-GGCTAAATT
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
61818738 CCGAAGG
1 CCGAAGG
61818745 TACTTGGGTT
Statistics
Matches: 154, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 14 0.09
40 138 0.90
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:61826476 original size:40 final size:40
Alignment explanation
Indices: 61826045--61826455 Score: 786
Period size: 40 Copynumber: 10.3 Consensus size: 40
61826035 GGACTAAGAT
61826045 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826085 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826125 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826165 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826205 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826245 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826285 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826325 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
*
61826365 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
* * *
61826405 CCAAAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
61826445 CCGAAGGCATT
1 CCGAAGGCATT
61826456 CGTACGAGTT
Statistics
Matches: 367, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 367 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
Found at i:61837371 original size:26 final size:26
Alignment explanation
Indices: 61837342--61837449 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
61837332 TGGTACAAAT
61837342 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
61837368 TGATAATAGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61837394 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
61837420 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61837446 TGAT
1 TGAT
61837450 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:61847348 original size:23 final size:22
Alignment explanation
Indices: 61847312--61847361 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
61847302 CGGCCTGCAG
* * *
61847312 CACGGGTGTGTCT-TAGGGTCA
1 CACGGGCGTGTCTCTTGGATCA
61847333 CACGGGCGTGTCTCTTGGATCA
1 CACGGGCGTGTCTCTTGGATCA
61847355 CACGGGC
1 CACGGGC
61847362 ATGTGAGCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.14, C:0.26, G:0.36, T:0.24
Consensus pattern (22 bp):
CACGGGCGTGTCTCTTGGATCA
Found at i:61849616 original size:38 final size:39
Alignment explanation
Indices: 61849564--61849643 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
61849554 TACTTTTTGT
* * *
61849564 TTGGCATGCTTCGGG-TGAATCAGCTCTTATGAGCTTCTG
1 TTGGCAAGCTTCGGGAAGAAT-AGCTCTTATAAGCTTCTG
* *
61849603 TTGGCAAG-TTCGGGAAGACTAGGTCTTATAAGCTTCTG
1 TTGGCAAGCTTCGGGAAGAATAGCTCTTATAAGCTTCTG
61849641 TTG
1 TTG
61849644 ATGATGTACT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (39 bp):
TTGGCAAGCTTCGGGAAGAATAGCTCTTATAAGCTTCTG
Found at i:61855280 original size:16 final size:18
Alignment explanation
Indices: 61855261--61855293 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
61855251 CATACTAGAT
61855261 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
61855277 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
61855294 GTGGCGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:61855835 original size:45 final size:45
Alignment explanation
Indices: 61855768--61855899 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 45
61855758 TTTTATCAAA
* * *
61855768 TCACCGGCAT-TTAGCCTTCTAGGCTCGAAGGCCCGAATAGTATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
61855812 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
61855857 TCACCGGCATCATAGCCTGCTAGGCTTAAAGGCCCGAATAGTA
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
61855900 CTGTACGATA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 10 0.12
45 72 0.88
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (45 bp):
TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:61867116 original size:32 final size:32
Alignment explanation
Indices: 61867075--61867138 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
61867065 TGGAAATAAC
* *
61867075 ATTGGATATTCTGTATCTTTCACACTAATGGG
1 ATTGAATATTCTGTATCTTGCACACTAATGGG
61867107 ATTGAATATTCTGTATCTTGCACACTAATGGG
1 ATTGAATATTCTGTATCTTGCACACTAATGGG
61867139 CTTATATGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (32 bp):
ATTGAATATTCTGTATCTTGCACACTAATGGG
Found at i:61867602 original size:25 final size:24
Alignment explanation
Indices: 61867559--61867696 Score: 117
Period size: 23 Copynumber: 5.8 Consensus size: 24
61867549 GTCATGGTCG
*
61867559 GTAAGCTCCTCTTGAGCTGATAAACA
1 GTAAGCT-CTATTGAGCTGA-AAACA
61867585 GTAAGCTCTATTGAGCTGAAAACA
1 GTAAGCTCTATTGAGCTGAAAACA
*
61867609 ATAAGCTCTATTGAGCTG--AACA
1 GTAAGCTCTATTGAGCTGAAAACA
* *
61867631 GTAAGTTCT-TTCGAGCTG-AATCA
1 GTAAGCTCTATT-GAGCTGAAAACA
* * * *
61867654 ATAAGCTCCAATGAGATG-AAACA
1 GTAAGCTCTATTGAGCTGAAAACA
*
61867677 ATAAGCTCT-TATGAGCTGAA
1 GTAAGCTCTAT-TGAGCTGAA
61867697 TTAGTAAGCT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.02
22 17 0.18
23 32 0.34
24 24 0.26
25 11 0.12
26 7 0.08
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (24 bp):
GTAAGCTCTATTGAGCTGAAAACA
Found at i:61867647 original size:46 final size:46
Alignment explanation
Indices: 61867580--61867696 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
61867570 TTGAGCTGAT
* * *
61867580 AAACAGTAAGCTCTATTGAGCTGAAAACAATAAGCTCTATTGAGCTG
1 AAACAGTAAGCTCT-TTGAGCTGAAAACAATAAGCTCCAATGAGATG
* *
61867627 -AACAGTAAGTTCTTTCGAGCTG-AATCAATAAGCTCCAATGAGATG
1 AAACAGTAAGCTCTTT-GAGCTGAAAACAATAAGCTCCAATGAGATG
*
61867672 AAACAATAAGCTCTTATGAGCTGAA
1 AAACAGTAAGCTCTT-TGAGCTGAA
61867697 TTAGTAAGCT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
45 21 0.36
46 36 0.61
47 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (46 bp):
AAACAGTAAGCTCTTTGAGCTGAAAACAATAAGCTCCAATGAGATG
Found at i:61867673 original size:23 final size:23
Alignment explanation
Indices: 61867647--61867707 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
61867637 TCTTTCGAGC
61867647 TGAATCAATAAGCTCCAATGAGA
1 TGAATCAATAAGCTCCAATGAGA
* ** *
61867670 TGAAACAATAAGCTCTTATGAGC
1 TGAATCAATAAGCTCCAATGAGA
* *
61867693 TGAATTAGTAAGCTC
1 TGAATCAATAAGCTC
61867708 ATACGAGCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (23 bp):
TGAATCAATAAGCTCCAATGAGA
Found at i:61867715 original size:69 final size:69
Alignment explanation
Indices: 61867586--61867717 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 69
61867576 TGATAAACAG
* * * * * *
61867586 TAAGCTCTATTGAGCTGAAAACAATAAGCTCTATTGAGCTGAACAGTAAGTTCTTTCGAGCTGAA
1 TAAGCTCCAATGAGATGAAAACAATAAGCTCTATTGAGCTGAACAGTAAGCTCATACGAGCTGAA
61867651 TCAA
66 TCAA
*
61867655 TAAGCTCCAATGAGATG-AAACAATAAGCTCT-TATGAGCTGAATTAGTAAGCTCATACGAGCTG
1 TAAGCTCCAATGAGATGAAAACAATAAGCTCTAT-TGAGCTGAA-CAGTAAGCTCATACGAGCTG
61867718 TGGTGAGTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 1 0.02
68 23 0.43
69 30 0.56
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (69 bp):
TAAGCTCCAATGAGATGAAAACAATAAGCTCTATTGAGCTGAACAGTAAGCTCATACGAGCTGAA
TCAA
Found at i:61874829 original size:40 final size:40
Alignment explanation
Indices: 61874770--61875135 Score: 476
Period size: 40 Copynumber: 9.2 Consensus size: 40
61874760 NNNNNNNNNC
*
61874770 CCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGT
*
61874810 CCCAAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGT
* *
61874850 CCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATA-TCTGGGCTAAGT
* *
61874890 CCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATA-TCTGGGCTAAGT
* *
61874930 CCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATA-TCTGGGCTAAGT
* *
61874970 CCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATA-TCTGGGCTAAGT
* * *
61875010 CCCGAAGGCATTTGTGCAAGTTACTATATCCGGACTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGT
*
61875050 CCCGAAGGCATTT-TGCGAGTTACTATATCCGGGCTAAGT
1 CCCGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGT
* * *
61875089 CCCGAAGGCATTTGAGCGAG-TAGCTATATC-CGGCTAAAT
1 CCCGAAGGCATTTGTGCGAGTTA-CTATATCTGGGCTAAGT
*
61875128 CCTGAAGG
1 CCCGAAGG
61875136 TACTTGGTTT
Statistics
Matches: 307, Mismatches: 15, Indels: 9
0.93 0.05 0.03
Matches are distributed among these distances:
39 54 0.18
40 252 0.82
41 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCCGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGT
Found at i:61874983 original size:120 final size:120
Alignment explanation
Indices: 61874770--61875102 Score: 546
Period size: 120 Copynumber: 2.8 Consensus size: 120
61874760 NNNNNNNNNC
* *
61874770 CCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACT
1 CCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
61874835 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGT
66 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGT
* * * * *
61874890 CCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAC
1 CCCGAAGGCATTTGTGCAAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
61874954 TA-ATTCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGT
65 TATA-TCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGT
*
61875010 CCCGAAGGCATTTGTGCAAGTTACTATATCCGGACTAAGTCCCGAAGGCATTT-TGCGAGTTACT
1 CCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
61875074 ATATCCGGGCTAAGTCCCGAAGGCATTTG
66 ATATCTGGGCTAAGTCCCGAAGGCATTTG
61875103 AGCGAGTAGC
Statistics
Matches: 196, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
119 37 0.19
120 158 0.81
121 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (120 bp):
CCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGT
Found at i:61882110 original size:22 final size:22
Alignment explanation
Indices: 61882085--61882127 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
61882075 AGTAAAAGTA
61882085 TTATGGTGAAGTTATAATATTG
1 TTATGGTGAAGTTATAATATTG
61882107 TTATGGTGAAGTTATAATATT
1 TTATGGTGAAGTTATAATATT
61882128 AAGAAGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (22 bp):
TTATGGTGAAGTTATAATATTG
Found at i:61883853 original size:39 final size:39
Alignment explanation
Indices: 61883786--61884008 Score: 322
Period size: 39 Copynumber: 5.7 Consensus size: 39
61883776 ACAAAGCATG
* * *
61883786 CGGGACTTTAAGCCCGGATATAATACCAGCA-GAAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
61883826 CGGGACTTTAGCCCGGATATAACACCAGGACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
61883866 CGGGCCTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
61883905 CGGGACTTAGCCCGAATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
61883944 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
61883983 CGGGACTTAGCCTGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
61884009 TTATAAAGTC
Statistics
Matches: 167, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 146 0.87
40 21 0.13
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:61884114 original size:28 final size:28
Alignment explanation
Indices: 61884081--61884162 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
61884071 ATTTAATCAT
* *
61884081 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
61884109 TCAATATCTCGCACATTAAGTGCCATTT
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
61884137 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
61884163 ATTTGATTGC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:61889857 original size:28 final size:28
Alignment explanation
Indices: 61889825--61889889 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
61889815 ATTTACTAGA
*
61889825 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
61889853 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
61889881 ATACCCCTA
1 ATACCCCTA
61889890 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:61890041 original size:28 final size:28
Alignment explanation
Indices: 61890005--61890085 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
61889995 CTAATGGCTA
*
61890005 TGCCACAAATAATCTGTTCTGGTGGCCC
1 TGCCACAAATAATCTGTTCTGGTGGCAC
* *
61890033 TGCTACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAATAATCTGTTCTGGTGGCAC
61890061 TGCCACAAA-ATATCTGTATCTGGTG
1 TGCCACAAATA-ATCTGT-TCTGGTG
61890086 ACTCTGTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 39 0.85
29 7 0.15
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAATAATCTGTTCTGGTGGCAC
Found at i:61890578 original size:19 final size:19
Alignment explanation
Indices: 61890544--61890584 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
61890534 GGCCTTTTAA
* *
61890544 TTATTTTTATGGTTTTGTT
1 TTATTTTTATGATTTTATT
*
61890563 TTATTTTTATTATTTTATT
1 TTATTTTTATGATTTTATT
61890582 TTA
1 TTA
61890585 CTATGATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (19 bp):
TTATTTTTATGATTTTATT
Found at i:61897748 original size:28 final size:28
Alignment explanation
Indices: 61897716--61897780 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
61897706 ATTTACTAGA
*
61897716 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
61897744 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
*
61897772 ATAACCCTA
1 ATACCCCTA
61897781 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:61897918 original size:28 final size:27
Alignment explanation
Indices: 61897886--61897976 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 27
61897876 CGGAAGCGTC
*
61897886 CTGGTGGATATGCCACAAATAATCTGTT
1 CTGGTGGA-CTGCCACAAATAATCTGTT
* *
61897914 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGG-ACTGCCACAAATAATCTGTT
61897942 CTGGTGGCACTGCCACAAA-ATATCTGTAT
1 CTGGTGG-ACTGCCACAAATA-ATCTGT-T
61897971 CTGGTG
1 CTGGTG
61897977 ACTCTGCCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
28 48 0.87
29 7 0.13
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
CTGGTGGACTGCCACAAATAATCTGTT
Found at i:61897974 original size:29 final size:28
Alignment explanation
Indices: 61897896--61897987 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
61897886 CTGGTGGATA
*
61897896 TGCCAC-AAATAATCTGTTCTGGTGGCCC
1 TGCCACAAAAT-ATCTGTTCTGGTGGCAC
*
61897924 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
* *
61897952 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGGCAC
61897981 TGCCACA
1 TGCCACA
61897988 TTTTCTGTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
28 38 0.67
29 19 0.33
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGGCAC
Found at i:61898001 original size:56 final size:55
Alignment explanation
Indices: 61897896--61898001 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 55
61897886 CTGGTGGATA
*
61897896 TGCCACAAATAATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAATAATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTTCTGGTGGCAC
* *
61897952 TGCCACAAA-ATATCTGTATCTGGTGACTCTGCCAC-ATTTTCTGTATCTGG
1 TGCCACAAATA-ATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-TCTGG
61898002 CAGCCATGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
55 9 0.20
56 20 0.45
57 15 0.34
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (55 bp):
TGCCACAAATAATCTGTTCTGGTGACCCTGCCACAATTATCTGTTCTGGTGGCAC
Found at i:61898469 original size:19 final size:19
Alignment explanation
Indices: 61898435--61898475 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
61898425 GGCCTTTTAA
* *
61898435 TTATTTTTATGGTTTTGTT
1 TTATTTTTATGATTTTATT
*
61898454 TTATTTTTATTATTTTATT
1 TTATTTTTATGATTTTATT
61898473 TTA
1 TTA
61898476 CTATGATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (19 bp):
TTATTTTTATGATTTTATT
Found at i:61901207 original size:39 final size:39
Alignment explanation
Indices: 61901099--61901398 Score: 433
Period size: 39 Copynumber: 7.7 Consensus size: 39
61901089 ACAAAGCATG
* * *
61901099 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
61901139 C-AGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
61901178 CGGGGCTTAGCCCGGATATTACACTAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
61901217 CGGGACTTAGCCCGGATATAACACCAGGACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
61901256 TGGGACTTAGCCCGGATATACCACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
61901295 CGGGACTTAGCCCGGATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
61901334 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
61901373 CGGGACTTAGCCCAGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
61901399 TTATAAAGTC
Statistics
Matches: 235, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
38 21 0.09
39 211 0.90
40 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:61901505 original size:28 final size:28
Alignment explanation
Indices: 61901471--61901543 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
61901461 ATTTAATCAT
*
61901471 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGTCATTC
* * *
61901499 TCAATATCTCGCACATTAAGTGTCATTT
1 TCAATATTTCGCACACTAAGTGTCATTC
*
61901527 TCAATATTTCGTACACT
1 TCAATATTTCGCACACT
61901544 GAGTACCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGTCATTC
Found at i:61903031 original size:44 final size:45
Alignment explanation
Indices: 61902982--61903076 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
61902972 TTACACCTCT
* *
61902982 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
61903026 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
61903071 ATTACA
1 ATTACA
61903077 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:61903076 original size:16 final size:16
Alignment explanation
Indices: 61903057--61903124 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
61903047 GATTTGCTAT
* *
61903057 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
61903073 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61903089 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61903105 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61903121 TACA
1 TACA
61903125 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:61907014 original size:32 final size:31
Alignment explanation
Indices: 61906934--61907021 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 31
61906924 ATTGTCAATC
*
61906934 ATTTCAATATCCAACAAGCTTAAAACATAATA
1 ATTTCAATATCCAACAA-ATTAAAACATAATA
* ** * *
61906966 AATTCAATATGTAACAAATTCAAGACATATTA
1 ATTTCAATATCCAACAAATT-AAAACATAATA
* *
61906998 ATTTCAAAATCCAACAAACTAAAA
1 ATTTCAATATCCAACAAATTAAAA
61907022 TTTCAATATC
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
31 5 0.12
32 38 0.88
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.27
Consensus pattern (31 bp):
ATTTCAATATCCAACAAATTAAAACATAATA
Found at i:61912057 original size:305 final size:305
Alignment explanation
Indices: 61911506--61912116 Score: 1213
Period size: 305 Copynumber: 2.0 Consensus size: 305
61911496 AGAAGGAGAT
61911506 GGAAAATGTCTTACTGAAAAGAAATCGGTAAGACTTTTTCCCCAAATTGCAAGTCATTTTACCCA
1 GGAAAATGTCTTACTGAAAAGAAATCGGTAAGACTTTTTCCCCAAATTGCAAGTCATTTTACCCA
61911571 TGTCTTGGAAAACATTTTCCAAATGTAAAATGTTTTCAAGCTTCCAAACACAGTAAAACCAGGAA
66 TGTCTTGGAAAACATTTTCCAAATGTAAAATGTTTTCAAGCTTCCAAACACAGTAAAACCAGGAA
61911636 AATATTTTTCGGAAATTGTTTTCCTAGCTTCCAAATGGACCTTAAATTCACAGCAAAACAAGGCA
131 AATATTTTTCGGAAATTGTTTTCCTAGCTTCCAAATGGACCTTAAATTCACAGCAAAACAAGGCA
61911701 TTTGACACAACCATACATATATCAATTCAAAATGCATCTACAACCTCAAAATAAAACATAAAAAA
196 TTTGACACAACCATACATATATCAATTCAAAATGCATCTACAACCTCAAAATAAAACATAAAAAA
61911766 TATTTGAATTTGTAGCTCAAAGCATCATCAATATTTCCAAACCAA
261 TATTTGAATTTGTAGCTCAAAGCATCATCAATATTTCCAAACCAA
61911811 GGAAAATGTCTTACTGAAAAGAAATCGGTAAGACTTTTTCCCCAAATTGCAAGTCATTTTACCCA
1 GGAAAATGTCTTACTGAAAAGAAATCGGTAAGACTTTTTCCCCAAATTGCAAGTCATTTTACCCA
61911876 TGTCTTGGAAAACATTTTCCAAATGTAAAATGTTTTCAAGCTTCCAAACACAGTAAAACCAGGAA
66 TGTCTTGGAAAACATTTTCCAAATGTAAAATGTTTTCAAGCTTCCAAACACAGTAAAACCAGGAA
61911941 AATATTTTTCGGAAATTGTTTTCCTAGCTTCCAAATGGACCTTAAATTCACAGCAAAACAAGGCA
131 AATATTTTTCGGAAATTGTTTTCCTAGCTTCCAAATGGACCTTAAATTCACAGCAAAACAAGGCA
61912006 TTTGACACAACCATACATATATCAATTCAAAATGCATCTACAACCTCAAAATAAAACATAAAAAA
196 TTTGACACAACCATACATATATCAATTCAAAATGCATCTACAACCTCAAAATAAAACATAAAAAA
*
61912071 TATTTGACTTTGTAGCTCAAAGCATCATCAATATTTCCAAACCAA
261 TATTTGAATTTGTAGCTCAAAGCATCATCAATATTTCCAAACCAA
61912116 G
1 G
61912117 ATAACCCAAT
Statistics
Matches: 305, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
305 305 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (305 bp):
GGAAAATGTCTTACTGAAAAGAAATCGGTAAGACTTTTTCCCCAAATTGCAAGTCATTTTACCCA
TGTCTTGGAAAACATTTTCCAAATGTAAAATGTTTTCAAGCTTCCAAACACAGTAAAACCAGGAA
AATATTTTTCGGAAATTGTTTTCCTAGCTTCCAAATGGACCTTAAATTCACAGCAAAACAAGGCA
TTTGACACAACCATACATATATCAATTCAAAATGCATCTACAACCTCAAAATAAAACATAAAAAA
TATTTGAATTTGTAGCTCAAAGCATCATCAATATTTCCAAACCAA
Found at i:61915844 original size:26 final size:26
Alignment explanation
Indices: 61915807--61915864 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
61915797 TGATACAAAT
61915807 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
61915833 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
61915859 TGATAA
1 TGATAA
61915865 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:61921741 original size:95 final size:95
Alignment explanation
Indices: 61921578--61921766 Score: 369
Period size: 95 Copynumber: 2.0 Consensus size: 95
61921568 GCGGTGAAGA
61921578 AGCAACTCTATTTTCAATTTTTGCACTGGCTTGAGGAGGCGACTCTGTATTAATCTGATGCTCTA
1 AGCAACTCTATTTTCAATTTTTGCACTGGCTTGAGGAGGCGACTCTGTATTAATCTGATGCTCTA
61921643 CCTGCTTTTGATTTTCTTTATTGGAAGAGG
66 CCTGCTTTTGATTTTCTTTATTGGAAGAGG
*
61921673 AGCAACTCTATTTTCAATTTTTGCACTGGCTTGAGGAGTCGACTCTGTATTAATCTGATGCTCTA
1 AGCAACTCTATTTTCAATTTTTGCACTGGCTTGAGGAGGCGACTCTGTATTAATCTGATGCTCTA
61921738 CCTGCTTTTGATTTTCTTTATTGGAAGAG
66 CCTGCTTTTGATTTTCTTTATTGGAAGAG
61921767 TCTTTAAGAG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (95 bp):
AGCAACTCTATTTTCAATTTTTGCACTGGCTTGAGGAGGCGACTCTGTATTAATCTGATGCTCTA
CCTGCTTTTGATTTTCTTTATTGGAAGAGG
Found at i:61924725 original size:41 final size:40
Alignment explanation
Indices: 61924598--61924742 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
61924588 CTCGCACAAG
* * * * *
61924598 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
*
61924638 GCCTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
61924678 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
61924719 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
61924743 CTTTCGAGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 57 0.63
41 27 0.30
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:61928089 original size:47 final size:47
Alignment explanation
Indices: 61928035--61928164 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 47
61928025 GGATAATTGT
*
61928035 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCC
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATAGCC
* * * *
61928082 GATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCC
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATAGCC
* * * *
61928129 AACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAG
61928165 TCCCGAAGGG
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.28
Consensus pattern (47 bp):
GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATAGCC
Found at i:61932264 original size:16 final size:17
Alignment explanation
Indices: 61932239--61932275 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
61932229 AATTTTATGG
61932239 AATTCAAAA-TTAAA-A
1 AATTCAAAATTTAAATA
61932254 AATTACAAAATTTAAATA
1 AATT-CAAAATTTAAATA
61932272 AATT
1 AATT
61932276 TAAATGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 5 0.26
17 5 0.26
18 5 0.26
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTCAAAATTTAAATA
Found at i:61932748 original size:13 final size:14
Alignment explanation
Indices: 61932724--61932754 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
61932714 AGAAAAGTAA
61932724 AATATATTTTTTAT
1 AATATATTTTTTAT
61932738 AATAT-TTTTTTAT
1 AATATATTTTTTAT
61932751 AATA
1 AATA
61932755 AAGCAGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATATATTTTTTAT
Found at i:61933194 original size:16 final size:16
Alignment explanation
Indices: 61933175--61933207 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
61933165 CAACTCTTGT
*
61933175 TTAGAACAGTTGTTGC
1 TTAGAACAATTGTTGC
61933191 TTAGAACAATTGTTGC
1 TTAGAACAATTGTTGC
61933207 T
1 T
61933208 CGGGGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (16 bp):
TTAGAACAATTGTTGC
Found at i:61940912 original size:27 final size:24
Alignment explanation
Indices: 61940868--61940955 Score: 61
Period size: 27 Copynumber: 3.3 Consensus size: 24
61940858 ACCAAAGTAC
* *
61940868 CCTCGATTTATAGAATTATCGTTTTA
1 CCTCGATTTACA-AATTA-CATTTTA
61940894 CGCTCGATTTACAACATTACCATTTTA
1 C-CTCGATTTACAA-ATTA-CATTTTA
*
61940921 CCCTC-AGTTTACAAAATTACCTTTTA
1 -CCTCGA-TTTAC-AAATTACATTTTA
61940947 CCTTCGATT
1 CC-TCGATT
61940956 GTGAAATTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
25 2 0.04
26 13 0.25
27 33 0.65
28 3 0.06
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (24 bp):
CCTCGATTTACAAATTACATTTTA
Found at i:61941063 original size:27 final size:27
Alignment explanation
Indices: 61940987--61941063 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
61940977 TATAGGATAG
** *
61940987 AATTACCAAAATACTACTGGTTTGAGA
1 AATTACCAAAATACCCCTGATTTGAGA
* *
61941014 AATTACCGAAATA-CCCTCAATTTGTA-A
1 AATTACCAAAATACCCCT-GATTTG-AGA
61941041 AATTACCAAAATACCCCTGATTT
1 AATTACCAAAATACCCCTGATTT
61941064 ACAAGATTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
26 2 0.05
27 33 0.82
28 5 0.12
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGAGA
Found at i:61941128 original size:27 final size:26
Alignment explanation
Indices: 61941092--61941147 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
61941082 CCTTGACTTT
*
61941092 TTTAAAAATTA-TAGGAATACCATTGG
1 TTTAAAAATTACT-GAAATACCATTGG
*
61941118 TTTACAAAATTACTGAAATACCCTTGG
1 TTTA-AAAATTACTGAAATACCATTGG
61941145 TTT
1 TTT
61941148 GTAGATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTACTGAAATACCATTGG
Found at i:61942081 original size:25 final size:24
Alignment explanation
Indices: 61942047--61942116 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
61942037 AGGAAGTGCT
61942047 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTCTGCCCCAGTTTACC
*
61942071 GAAAAGGGCTCTGCCCCAGTTTATC
1 -AAAAGGGCTCTGCCCCAGTTTACC
*
61942096 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTCTGCCCCAGTT
61942117 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTCTGCCCCAGTTTACC
Found at i:61942129 original size:24 final size:24
Alignment explanation
Indices: 61942046--61942129 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
61942036 GAGGAAGTGC
*
61942046 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTCTGCCCCAGTTTA-T
*
61942071 GAAAAGGGCTCTGCCCCAGTTTAT
1 TAAAAGGGCTCTGCCCCAGTTTAT
* *
61942095 CAGAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTCTGCCCCAGTTTAT
61942119 TAAAAGAGGCT
1 TAAAAG-GGCT
61942130 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
TAAAAGGGCTCTGCCCCAGTTTAT
Found at i:61942323 original size:42 final size:42
Alignment explanation
Indices: 61942264--61942355 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
61942254 TAGTCTCCCC
* ** *
61942264 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61942306 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61942348 AAATGGGC
1 AAATGGGC
61942356 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:61942458 original size:29 final size:29
Alignment explanation
Indices: 61942410--61942482 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
61942400 TGATTTATGA
* *
61942410 AAAGGCTTCGGTCCAGTAACCGTTAAACG
1 AAAGGCTTCGGCCCAATAACCGTTAAACG
61942439 AAAGGCTTCGGCCCAATAACCGTTAAACG
1 AAAGGCTTCGGCCCAATAACCGTTAAACG
*
61942468 AAAGGCTTTGGCCCA
1 AAAGGCTTCGGCCCA
61942483 GTATATGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (29 bp):
AAAGGCTTCGGCCCAATAACCGTTAAACG
Found at i:61947298 original size:12 final size:13
Alignment explanation
Indices: 61947272--61947300 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
61947262 GTTTTTCTTT
61947272 TTTTGAAATAGGG
1 TTTTGAAATAGGG
61947285 TTTTGAAA-AGGG
1 TTTTGAAATAGGG
61947297 TTTT
1 TTTT
61947301 TCTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (13 bp):
TTTTGAAATAGGG
Found at i:61947712 original size:55 final size:55
Alignment explanation
Indices: 61947563--61947712 Score: 180
Period size: 55 Copynumber: 2.7 Consensus size: 55
61947553 CTTATGACTC
* *
61947563 ACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTT
1 ACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCC-TTGCCTTATAGAAACTT
* * * * * *
61947618 ATCAATGCCATGTCTTGACATGGCCTTACATGATTTCCTTGCC-T-TAGAAACCTT
1 ACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAAA-CTT
61947672 ACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 ACCAA-TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
61947713 AAACCCTAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
53 5 0.06
54 8 0.10
55 63 0.81
56 2 0.03
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (55 bp):
ACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAAACTT
Found at i:61954335 original size:20 final size:20
Alignment explanation
Indices: 61954310--61954350 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
61954300 CTTGGTGTTG
61954310 ATCAATAGAAGACAATTTGA
1 ATCAATAGAAGACAATTTGA
61954330 ATCAATAGAAGACAATTTGA
1 ATCAATAGAAGACAATTTGA
61954350 A
1 A
61954351 CTTTAGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (20 bp):
ATCAATAGAAGACAATTTGA
Found at i:61969521 original size:47 final size:47
Alignment explanation
Indices: 61969431--61969521 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
61969421 GGAGGGAAGC
* *
61969431 CAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTTTAAAAAAAAGGT
1 CAAAGTGAAAACCCGCAAAGGGCACTTTGAGACTTCAAAAAAAAGGT
* *
61969478 CAAAGTGAAAATCCGCAAAGGGCACTTTGATAC-TCAAATAAAAA
1 CAAAGTGAAAACCCGCAAAGGGCACTTTGAGACTTCAAA-AAAAA
61969522 TGGAAAGGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 4 0.10
47 35 0.90
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (47 bp):
CAAAGTGAAAACCCGCAAAGGGCACTTTGAGACTTCAAAAAAAAGGT
Found at i:61970978 original size:180 final size:180
Alignment explanation
Indices: 61970676--61972013 Score: 1618
Period size: 180 Copynumber: 7.5 Consensus size: 180
61970666 ATTGGTCAAG
* * ** *
61970676 ATTGAAGATCTTATCTCCCTGAAGTTGCAGTGGAATAGATCTTTACAGATGGTGAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* *
61970741 CATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAA
66 CATGTATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
* * *
61970806 GTTGAAGAATGAGTCTTATCTTTCTGAGGTAGCAAGGAAGTAAACTGAGA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * * *
61970856 ATTGAAGATTTTATCTCCTTGAAGTTGCAGCAGAGCAGATCTTCGCAGATGGTAAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* * * *
61970921 CATGAATCAGTAATGGAGAAGATTTTACCACCAAGCCTTATCTCTCTGAAGTAGCAAGAGAGTAG
66 CATGTATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
* *
61970986 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGTAAGGAAACAGACTGAGA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* *
61971036 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAAATCTTCACAGATGGTGAATCTTATCTT
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* * *
61971101 CATGAATTAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTTTGAGGTAGCAAGAGAGCAG
66 CATGTATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
61971166 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * * **
61971216 ATTGAAGATTTTATCTCCTTGAAGTTACAGCAGAGCAGATCTTCGTAGATGGTGAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* *
61971281 CATGAATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTACCAAGAGAGCAG
66 CATGTATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
* * * * *
61971346 GTTTATGAATGAGTCTTATCTTCCTGAGGTAGTAAGGAAGCAGACTAAAA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * ** * *
61971396 ATTAAAGATCTTATCTCCCTG-AGATTGCAGTAGAGCAGATCTTCGCAGATGGTGAATCTTATTT
1 ATTGAAGATTTTATCTCCCTGAAG-TTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
* * *
61971460 CCATGTATCAGGCAATAGAGTAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGC
65 CCATGTATCA-GTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGC
* * * *
61971525 ATGTTTATGAATGAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAGA
129 AGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * *
61971577 ATTAAAGATCTTATCTCCCT-AAGATTACAGCGGAGCAGATCTTCACAGATGGCT-AATCTTATC
1 ATTGAAGATTTTATCTCCCTGAAG-TTGCAGCGGAGCAGATCTTCACAGATGG-TGAATCTTATC
** * * ** * * *
61971640 TCCATGTATTGGCT-A-GGAAGTAGATTTAAGCC-TTAAGCCTCATCTCTCTGAAGTAACAAGAG
64 TCCATGTATCAG-TAATGG-AGCAGATTTTA-CCACCAAGCCTTATCTCTCTGAGGTAGCAAGAG
* * * *
61971702 AGTAGGTTGAAG---GAGTCTGATCTTCCTGAGGTAGCAAGGAAGCAAATTGAGA
126 AGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * * **
61971754 ATTGAAG-TTTTATCTCCCTGAAGTCGCAGCGGAGTAGATCTTCACAGGTGGTGAATCTTAAATC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
** * ** * * *
61971818 CATGTATTGGCAATGGAGCAGATTTTACGTCC-AGCCTCATCTCTCTGAGGTAACAAGGGAGCAG
66 CATGTATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
* *
61971882 GTTGAAGAATGAG-----TCTTCCTGAGGTAGCAAGAAAGCAGACTGAGG
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
* * * ** * * * * * *
61971927 GTTGAGGATCTTATCTCCCCAAAGTGGCAGTGGAACAGA--TTGA-AAATGGTGAATTTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
* *
61971989 CATGTATC-GACAATAGAGCAGATTT
66 CATGTATCAG-TAATGGAGCAGATTT
61972014 AATTTAATCT
Statistics
Matches: 1015, Mismatches: 126, Indels: 43
0.86 0.11 0.04
Matches are distributed among these distances:
170 1 0.00
171 35 0.03
172 3 0.00
173 33 0.03
174 24 0.02
175 38 0.04
176 64 0.06
177 47 0.05
178 3 0.00
179 3 0.00
180 600 0.59
181 163 0.16
182 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (180 bp):
ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCTC
CATGTATCAGTAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
Found at i:61973553 original size:11 final size:10
Alignment explanation
Indices: 61973537--61973564 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
61973527 TAAATATTTA
61973537 TTTTTTTTGT
1 TTTTTTTTGT
61973547 TTTTTTTTGT
1 TTTTTTTTGT
61973557 TTTTTTTT
1 TTTTTTTT
61973565 CATTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:61977891 original size:16 final size:16
Alignment explanation
Indices: 61977872--61977902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61977862 CTTCTTCACT
61977872 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
61977888 TACTTACTTACTTAA
1 TACTCACTTACTTAA
61977903 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:61977908 original size:20 final size:20
Alignment explanation
Indices: 61977869--61977908 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
61977859 AAACTTCTTC
* *
61977869 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
61977889 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
61977909 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:61978284 original size:55 final size:53
Alignment explanation
Indices: 61978094--61978348 Score: 245
Period size: 55 Copynumber: 4.8 Consensus size: 53
61978084 ACACGGGTAC
* * * * *
61978094 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA---T-CCTT-TTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAG-AA
* *
61978143 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAA
* * *
61978196 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AA
* * * * *
61978251 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAA
*
61978304 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
61978349 AAACCCTAAT
Statistics
Matches: 172, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
49 35 0.20
52 2 0.01
53 47 0.27
54 14 0.08
55 72 0.42
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAA
Found at i:61978285 original size:108 final size:110
Alignment explanation
Indices: 61978141--61978341 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
61978131 ATCCTTTTGA
* *
61978141 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
61978204 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
61978249 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
61978314 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
61978342 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 28 0.33
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:61983330 original size:33 final size:33
Alignment explanation
Indices: 61983288--61983350 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
61983278 GTCTGGAGGA
*
61983288 TCATTAATAACAAAGATACATTGTGTTTTATGC
1 TCATTAATAACAAAGATACACTGTGTTTTATGC
61983321 TCATTAATAACAAAGATACACTGTGTTTTA
1 TCATTAATAACAAAGATACACTGTGTTTTA
61983351 AAGTTTTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (33 bp):
TCATTAATAACAAAGATACACTGTGTTTTATGC
Found at i:61986093 original size:42 final size:42
Alignment explanation
Indices: 61986047--61986142 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
61986037 ACAATTCTAT
**
61986047 TGAGCTTCTGTAT-AACCCTTATGGGTTTCCGTTTAGCTTTTA
1 TGAGCTTCTGT-TCAACCCTTATGGGTTTCCGTTTAGCACTTA
* *
61986089 TGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTA
1 TGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTTAGCACTTA
*
61986131 TGTGCTTCTGTT
1 TGAGCTTCTGTT
61986143 TAGTCTTCGG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.45
Consensus pattern (42 bp):
TGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTTAGCACTTA
Found at i:61986130 original size:21 final size:21
Alignment explanation
Indices: 61986064--61986145 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
61986054 CTGTATAACC
* *
61986064 CTTATGGGTTTCCGTTTAGCT
1 CTTATGGGCTTCCGTTTAGCA
* * * * *
61986085 TTTATGAGCTTCCGTTCAACC
1 CTTATGGGCTTCCGTTTAGCA
* *
61986106 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGCTTCCGTTTAGCA
* *
61986127 CTTATGTGCTTCTGTTTAG
1 CTTATGGGCTTCCGTTTAG
61986146 TCTTCGGGCT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (21 bp):
CTTATGGGCTTCCGTTTAGCA
Found at i:61989981 original size:23 final size:24
Alignment explanation
Indices: 61989931--61989985 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
61989921 GTTAGAAATT
61989931 TTTTATTTTAATCTATTTATTTGA
1 TTTTATTTTAATCTATTTATTTGA
61989955 -TTTATTTTAAAT-TCATTT-TTT-A
1 TTTTATTTT-AATCT-ATTTATTTGA
61989977 TTTTATTTT
1 TTTTATTTT
61989986 TTAATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 1 0.04
23 20 0.71
24 7 0.25
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTATTTTAATCTATTTATTTGA
Found at i:61989995 original size:23 final size:24
Alignment explanation
Indices: 61989928--61989997 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
61989918 TGAGTTAGAA
61989928 ATTTT-TTATTTTAATCTATTTATTTG
1 ATTTTATT-TTTTAAT-TATTT-TTTG
*
61989954 A-TTTA-TTTTAAATTCATTTTTT-
1 ATTTTATTTTTTAATT-ATTTTTTG
61989976 ATTTTATTTTTTAATTATTTTT
1 ATTTTATTTTTTAATTATTTTT
61989998 ATTCGTTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
22 1 0.03
23 14 0.37
24 18 0.47
25 4 0.11
26 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (24 bp):
ATTTTATTTTTTAATTATTTTTTG
Found at i:61991561 original size:18 final size:19
Alignment explanation
Indices: 61991530--61991571 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
61991520 AAAATCACAA
61991530 AAAAACAAAGAAAAAAT-AT
1 AAAAAC-AAGAAAAAATCAT
*
61991549 AAAAACTA-AAAAAATCAT
1 AAAAACAAGAAAAAATCAT
61991567 AAAAA
1 AAAAA
61991572 GGGGAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAAACAAGAAAAAATCAT
Found at i:61991672 original size:27 final size:27
Alignment explanation
Indices: 61991615--61991679 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 27
61991605 TGCAATATAC
61991615 ATAATTTTAAAAAAATTATAAAAATTTCA
1 ATAATTTTAAAAAAATTATAAAAA--TCA
61991644 ATAATTATTAAAAAAATT-TAAAACA-CA
1 ATAATT-TTAAAAAAATTATAAAA-ATCA
61991671 ATAATTTTA
1 ATAATTTTA
61991680 TAAACATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
26 3 0.09
27 8 0.24
29 11 0.32
30 12 0.35
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAATTTTAAAAAAATTATAAAAATCA
Found at i:61995888 original size:17 final size:18
Alignment explanation
Indices: 61995874--61995908 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61995864 CCATAATTTC
61995874 TATTAAAT-TATAATTAT
1 TATTAAATGTATAATTAT
*
61995891 TTTTAAATGTATAATTAT
1 TATTAAATGTATAATTAT
61995909 CACAACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTAAATGTATAATTAT
Found at i:61996089 original size:3 final size:3
Alignment explanation
Indices: 61996081--61996110 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
61996071 AGGCAGATAG
61996081 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
61996111 TTTGATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:62008377 original size:27 final size:27
Alignment explanation
Indices: 62008346--62008523 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
62008336 TAAATTGTAC
62008346 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
62008373 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
62008399 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
62008427 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
62008455 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
62008482 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
62008509 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
62008524 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:62008460 original size:82 final size:81
Alignment explanation
Indices: 62008347--62008502 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
62008337 AAATTGTACA
* *
62008347 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
62008411 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
62008428 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
62008493 TGCGAGTTGA
65 TGCGAATTGA
62008503 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:62008514 original size:82 final size:81
Alignment explanation
Indices: 62008343--62008523 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
62008333 GATTAAATTG
* *
62008343 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
62008408 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
62008424 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
62008488 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
62008506 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
62008524 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:62024108 original size:13 final size:13
Alignment explanation
Indices: 62024090--62024122 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
62024080 GGTTGTTTAT
62024090 TAAACTAATTAAC
1 TAAACTAATTAAC
62024103 TAAACTAATTAAC
1 TAAACTAATTAAC
62024116 T-AACTAA
1 TAAACTAA
62024123 ACTAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:62032101 original size:21 final size:21
Alignment explanation
Indices: 62032076--62032149 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
62032066 GTTGTTGAGA
*
62032076 AGGAAGTTGCTACTGTAGAAG
1 AGGAAGTTGCTACTGAAGAAG
* * **
62032097 AGGAAGTTGTTTCCAAAGAAG
1 AGGAAGTTGCTACTGAAGAAG
* *
62032118 AGGAAGTTGTTGCTGAAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
62032139 AAGAAGTTGCT
1 AGGAAGTTGCT
62032150 GAAAATAAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.24
Consensus pattern (21 bp):
AGGAAGTTGCTACTGAAGAAG
Found at i:62032623 original size:16 final size:16
Alignment explanation
Indices: 62032604--62032636 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
62032594 GATAAGTATA
62032604 TATTGCCATTACATTT
1 TATTGCCATTACATTT
*
62032620 TATTGTCATTACATTT
1 TATTGCCATTACATTT
62032636 T
1 T
62032637 CATGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (16 bp):
TATTGCCATTACATTT
Found at i:62040088 original size:15 final size:15
Alignment explanation
Indices: 62040068--62040099 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62040058 ACCGAGCTCA
62040068 AACCATAGTCTAGCC
1 AACCATAGTCTAGCC
62040083 AACCATAGTCTAGCC
1 AACCATAGTCTAGCC
62040098 AA
1 AA
62040100 ACCAAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (15 bp):
AACCATAGTCTAGCC
Found at i:62048213 original size:15 final size:15
Alignment explanation
Indices: 62048193--62048224 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62048183 ACCGAGCTCA
62048193 AACCATAGTCTAGCC
1 AACCATAGTCTAGCC
62048208 AACCATAGTCTAGCC
1 AACCATAGTCTAGCC
62048223 AA
1 AA
62048225 ACCAAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (15 bp):
AACCATAGTCTAGCC
Found at i:62057057 original size:11 final size:13
Alignment explanation
Indices: 62057029--62057062 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
62057019 TCGTGTCCTT
62057029 CACACGGCTGAGA
1 CACACGGCTGAGA
*
62057042 CACACGGCTGAAA
1 CACACGGCTGAGA
62057055 CACACGGC
1 CACACGGC
62057063 CGTGTCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.35, G:0.26, T:0.06
Consensus pattern (13 bp):
CACACGGCTGAGA
Found at i:62058599 original size:13 final size:13
Alignment explanation
Indices: 62058581--62058605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62058571 GTTAGTGATT
62058581 TTGATGATTTTTC
1 TTGATGATTTTTC
62058594 TTGATGATTTTT
1 TTGATGATTTTT
62058606 GCATTTTTAG
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:62059363 original size:47 final size:47
Alignment explanation
Indices: 62059297--62059418 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 47
62059287 ATTGTGTGCT
*
62059297 AGTGTAAGACATGTTTGGGACATGCATCAACCACATT-ACGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAACCACATTGACGAGAGCC
* ** * *
62059343 AGTGTAAGAACATGTCTGGGACATG--TCATCGGCATTGAGATGAGAGCT
1 AGTGTAAG-ACATGTCTGGGACATGCATCAACCACATT--GACGAGAGCC
62059391 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
62059419 GGCCTCGACA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
45 8 0.12
46 8 0.12
47 31 0.48
48 15 0.23
49 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCAACCACATTGACGAGAGCC
Found at i:62059442 original size:46 final size:47
Alignment explanation
Indices: 62059297--62059561 Score: 181
Period size: 46 Copynumber: 5.6 Consensus size: 47
62059287 ATTGTGTGCT
* ** * * *
62059297 AGTGTAAGACATGTTTGGGACATGCATCAACCAC-ATTACG-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-CATGTAGAGCC
* * * *
62059343 AGTGTAAGAACATGTCTGGGACATGTCATCGGCATTGAGATG-AGAGCT
1 AGTGTAAG-ACATGTCTGGGACATG-CATCGGCCTCGACATGTAGAGCC
62059391 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGTAGAGCC
** * * *
62059437 AGTGTAAGACATGT-TCGGGACATGCATAAG-CTACAAAATGT---GTC
1 AGTGTAAGACATGTCT-GGGACATGCATCGGCCT-CGACATGTAGAGCC
* * * * *
62059481 AGTGTAAGACCATGTCTGGGACTTGGCGTAGGCAC-GGACATGTGAGAGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCGACATGT-AGAGCC
62059531 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
62059562 ACTTGATAGA
Statistics
Matches: 177, Mismatches: 27, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
44 11 0.06
45 14 0.08
46 67 0.38
47 32 0.18
48 21 0.12
49 1 0.01
50 31 0.18
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGTAGAGCC
Found at i:62069867 original size:27 final size:28
Alignment explanation
Indices: 62069812--62069880 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
62069802 NNNNNNNNNN
62069812 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
62069840 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
62069867 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
62069881 GACTTAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:62069891 original size:27 final size:27
Alignment explanation
Indices: 62069812--62069893 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
62069802 NNNNNNNNNN
* *
62069812 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTGAATATATA
* *
62069840 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTGAATATATA
*
62069867 GCACTGAGTGTGCGGACTT-AATATATA
1 GCACTAAGTGTGC-GACTTGAATATATA
62069894 CTTTTGAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.61
28 19 0.39
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTGAATATATA
Found at i:62072326 original size:27 final size:27
Alignment explanation
Indices: 62072264--62072341 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
62072254 GGGCATATTC
62072264 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
62072291 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
* *
62072318 GTCTTTTTACC-TAATAGGGGTATT
1 GTCATTTTACCAT-ACAGGGGTATT
62072342 TTAGTCACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:62072639 original size:27 final size:27
Alignment explanation
Indices: 62072359--62072815 Score: 233
Period size: 27 Copynumber: 16.8 Consensus size: 27
62072349 CTTCACCCAA
* * * * *
62072359 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAT
* ** *
62072386 CAAGGGTATTTCAGTAAATTTTGTAAAC
1 CAAGGGTATTTTAGT-AATTTTACAAAT
* *
62072414 CAATGGTATTTCTA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTACAAA-T
* **
62072443 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTACAAAT
* * *
62072470 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
** ** * *
62072497 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAT
*
62072524 CAAGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTAGTAATTTTACAAAT
* *
62072550 CTAGGGGTATTTTGGTAATTTTACAAA-
1 C-AAGGGTATTTTAGTAATTTTACAAAT
* *
62072577 CTAAGGGTATTTTGGTAATTTTACAAAC
1 C-AAGGGTATTTTAGTAATTTTACAAAT
* **
62072605 CAATGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
* *** * **
62072632 CGAGGGTAAAATAGTAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
*** * **
62072659 CAAGGGTAAAATAGTAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
* ***** **
62072686 CGAGGGTAAAACGGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAAT
** * * *
62072713 CGGGGGTACTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTAGTAATTTTACAAAT
62072740 CGAA-GGTATTTTAGTAATTTTACAAAT
1 C-AAGGGTATTTTAGTAATTTTACAAAT
* * *
62072767 CGAGGGTATTTCAGTATTTTTACAAA-
1 CAAGGGTATTTTAGTAATTTTACAAAT
**
62072793 CTAAGGGTATTTCGGTAATTTTA
1 C-AAGGGTATTTTAGTAATTTTA
62072816 GTAAACTAAA
Statistics
Matches: 352, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
26 4 0.01
27 299 0.85
28 33 0.09
29 16 0.05
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTACAAAT
Found at i:62072639 original size:81 final size:81
Alignment explanation
Indices: 62072443--62072637 Score: 268
Period size: 81 Copynumber: 2.4 Consensus size: 81
62072433 TTTAGAAAGT
* * *
62072443 CAAGGGTATTTCTGTAACTTTGTAAAT-TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATT
1 CAAGGGTATTT-TGTAATTTTGTAAATCTAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATT
62072507 TCGGTAATTTCACAAAC
65 TCGGTAATTTCACAAAC
**
62072524 CAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATT
1 CAAGGGTATTTT-GTAATTTTGTAAATCTAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATT
* *
62072588 TTGGTAATTTTACAAAC
65 TCGGTAATTTCACAAAC
* *
62072605 CAATGGTATTTTAGTAATTTTGTAAATCGAGGG
1 CAAGGGTATTTT-GTAATTTTGTAAATCTAGGG
62072638 TAAAATAGTA
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 93 0.94
82 5 0.05
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (81 bp):
CAAGGGTATTTTGTAATTTTGTAAATCTAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
CGGTAATTTCACAAAC
Found at i:62072829 original size:27 final size:27
Alignment explanation
Indices: 62072726--62072830 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
62072716 GGGTACTTTG
* * *
62072726 GTAATTTTACAAGTCGAAG-GTATTTTA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
62072753 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
62072780 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
62072807 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
62072831 CTAAACAGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.03
27 54 0.84
28 8 0.12
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:62079105 original size:16 final size:16
Alignment explanation
Indices: 62079086--62079169 Score: 78
Period size: 16 Copynumber: 5.1 Consensus size: 16
62079076 ACGTTAACAA
62079086 TAAATTTTTAAAAATT
1 TAAATTTTTAAAAATT
* *
62079102 TAAAATATTAAAATATT
1 TAAATTTTTAAAA-ATT
* * *
62079119 TATACTTTTTAATTATTT
1 TA-AATTTTTAA-AAATT
**
62079137 TAAATTTTTAAATTTT
1 TAAATTTTTAAAAATT
62079153 TAAATTTTTAAAAATT
1 TAAATTTTTAAAAATT
62079169 T
1 T
62079170 TAAAATTAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
16 29 0.55
17 13 0.25
18 10 0.19
19 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTTTTAAAAATT
Found at i:62079152 original size:7 final size:8
Alignment explanation
Indices: 62079086--62079164 Score: 68
Period size: 8 Copynumber: 9.5 Consensus size: 8
62079076 ACGTTAACAA
62079086 TAAATTTT
1 TAAATTTT
*
62079094 TAAAAATTT
1 T-AAATTTT
* *
62079103 AAAATATT
1 TAAATTTT
* *
62079111 AAAATATT
1 TAAATTTT
*
62079119 TATACTTTT
1 TA-AATTTT
*
62079128 TAATTATTT
1 TAAAT-TTT
62079137 TAAATTTT
1 TAAATTTT
62079145 TAAATTTT
1 TAAATTTT
62079153 TAAATTTT
1 TAAATTTT
62079161 TAAA
1 TAAA
62079165 AATTTTAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
8 40 0.68
9 19 0.32
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (8 bp):
TAAATTTT
Found at i:62079174 original size:8 final size:8
Alignment explanation
Indices: 62079086--62079176 Score: 65
Period size: 8 Copynumber: 10.9 Consensus size: 8
62079076 ACGTTAACAA
*
62079086 TAAATTTT
1 TAAAATTT
*
62079094 TAAAAATT
1 TAAAATTT
*
62079102 TAAAATAT
1 TAAAATTT
62079110 TAAAATATT
1 TAAAAT-TT
**
62079119 TATACTTTT
1 TA-AAATTT
*
62079128 TAATTATTT
1 TAA-AATTT
*
62079137 TAAATTTT
1 TAAAATTT
*
62079145 TAAATTTT
1 TAAAATTT
*
62079153 TAAATTTT
1 TAAAATTT
62079161 TAAAAATTT
1 T-AAAATTT
62079170 TAAAATT
1 TAAAATT
62079177 AATTAATTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
8 45 0.67
9 20 0.30
10 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (8 bp):
TAAAATTT
Found at i:62079241 original size:20 final size:20
Alignment explanation
Indices: 62079212--62079258 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
62079202 GTGTATGCCA
*
62079212 CATCAGTAAGTTAACTTTTC
1 CATCAATAAGTTAACTTTTC
62079232 CATCAATAAGTTAACTTTTC
1 CATCAATAAGTTAACTTTTC
62079252 CATCAAT
1 CATCAAT
62079259 TTTGGGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (20 bp):
CATCAATAAGTTAACTTTTC
Found at i:62082586 original size:20 final size:20
Alignment explanation
Indices: 62082552--62082606 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
62082542 ATCCTGAACC
* *
62082552 TTAAGGTTCAAGGTTC-AAGG
1 TTAAGGTTTAGGGTTCGAA-G
*
62082572 TTAAGGTTTAGGGTTCGAAT
1 TTAAGGTTTAGGGTTCGAAG
*
62082592 TTAAGGTTTGGGGTT
1 TTAAGGTTTAGGGTT
62082607 TAAGATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.24, C:0.05, G:0.33, T:0.38
Consensus pattern (20 bp):
TTAAGGTTTAGGGTTCGAAG
Found at i:62085281 original size:70 final size:70
Alignment explanation
Indices: 62085183--62085315 Score: 153
Period size: 70 Copynumber: 1.9 Consensus size: 70
62085173 AATATTGGAT
* * * * * * *
62085183 GCAATAGTAAGACATATTATATTCTTAAA-AAGAGATGTAAATTTAAA-CATTAGAAATAATATT
1 GCAATAATAAGACACATTACATTATTAAAGAA-AAATGTAAATTCAAACCA-TAAAAATAATATT
62085246 GTTGAAA
64 GTTGAAA
* *
62085253 GCAATAATAAGATACATTACATTATTAAAGAAAAATGTAAGTTCAAACCATAAAAATAATATT
1 GCAATAATAAGACACATTACATTATTAAAGAAAAATGTAAATTCAAACCATAAAAATAATATT
62085316 ATTAGAAGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
70 48 0.92
71 4 0.08
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.31
Consensus pattern (70 bp):
GCAATAATAAGACACATTACATTATTAAAGAAAAATGTAAATTCAAACCATAAAAATAATATTGT
TGAAA
Found at i:62086251 original size:26 final size:26
Alignment explanation
Indices: 62086182--62086251 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
62086172 TTTGTCGTTG
* *
62086182 AATAATTGACATAAAAATCAACAATTC
1 AATAATTTACAT-ACAATCAACAATTC
* * * *
62086209 AAAAATTTATATGCAATCATCAATTC
1 AATAATTTACATACAATCAACAATTC
62086235 AATAATTTACATACAAT
1 AATAATTTACATACAAT
62086252 AAATTAGTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
26 25 0.74
27 9 0.26
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAATTTACATACAATCAACAATTC
Found at i:62088467 original size:26 final size:25
Alignment explanation
Indices: 62088397--62088467 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
62088387 ATCAATTTTT
*
62088397 TATTTTAATTTAATAATAATATAAAAA
1 TATTATAATTT-ATAA-AATATAAAAA
*
62088424 TATTATAATTTATGAAAATTTAAAAA
1 TATTATAATTTAT-AAAATATAAAAA
62088450 TA-TATAAATTTACTAAAA
1 TATTAT-AATTTA-TAAAA
62088468 AGCATGTCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.08
26 23 0.59
27 13 0.33
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (25 bp):
TATTATAATTTATAAAATATAAAAA
Found at i:62091411 original size:38 final size:38
Alignment explanation
Indices: 62091366--62091450 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
62091356 CATCCAACCT
62091366 TACACTCCATGTGGGGATATAATCAACCCACCCATCCC
1 TACACTCCATGTGGGGATATAATCAACCCACCCATCCC
* *
62091404 TACACTCCATGTGGTGATATAATCAACCCACCCATCTC
1 TACACTCCATGTGGGGATATAATCAACCCACCCATCCC
62091442 TACACTCCA
1 TACACTCCA
62091451 AAAAGTACCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.24
Consensus pattern (38 bp):
TACACTCCATGTGGGGATATAATCAACCCACCCATCCC
Found at i:62092751 original size:38 final size:38
Alignment explanation
Indices: 62092700--62092776 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
62092690 ATATGGACTC
62092700 GTATGAGCATGGGTACTATTCGGCCTAACATGGGTGTT
1 GTATGAGCATGGGTACTATTCGGCCTAACATGGGTGTT
62092738 GTATGAGCATGGGTACTATTCGGCCTAACATGGGTGTT
1 GTATGAGCATGGGTACTATTCGGCCTAACATGGGTGTT
62092776 G
1 G
62092777 AGAAATTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (38 bp):
GTATGAGCATGGGTACTATTCGGCCTAACATGGGTGTT
Found at i:62094417 original size:49 final size:50
Alignment explanation
Indices: 62094361--62094460 Score: 175
Period size: 49 Copynumber: 2.0 Consensus size: 50
62094351 AGCAAGGTTC
62094361 GGCCTTGAATGAGTATAGATAAAACATAT-AATGGTATGTTCATTATCAT
1 GGCCTTGAATGAGTATAGATAAAACATATGAATGGTATGTTCATTATCAT
* *
62094410 GGCCTTGAATGAGTATAGATAAAACGTATGTATGGTATGTTCATTATCAT
1 GGCCTTGAATGAGTATAGATAAAACATATGAATGGTATGTTCATTATCAT
62094460 G
1 G
62094461 TGATGGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 28 0.58
50 20 0.42
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (50 bp):
GGCCTTGAATGAGTATAGATAAAACATATGAATGGTATGTTCATTATCAT
Found at i:62141104 original size:23 final size:24
Alignment explanation
Indices: 62141072--62141116 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
62141062 TTGAACTACT
62141072 TTTTATTTTTTTTAGATT-TTAAAA
1 TTTTATTTTTTTTA-ATTATTAAAA
62141096 TTTTA-TTTTTTTAATTATTAA
1 TTTTATTTTTTTTAATTATTAA
62141117 TTTTGGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 12 0.60
24 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTATTTTTTTTAATTATTAAAA
Found at i:62145571 original size:29 final size:29
Alignment explanation
Indices: 62145538--62145621 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
62145528 GAAAACCCAT
62145538 TGGAAAAATTGTAAAATATGGAAAAATAG
1 TGGAAAAATTGTAAAATATGGAAAAATAG
** *
62145567 TGGAAAAATTGTAAAACCTGGAAAACTAG
1 TGGAAAAATTGTAAAATATGGAAAAATAG
* * *
62145596 TTGCAAAATTGTAAAATTTGGAAAAA
1 TGGAAAAATTGTAAAATATGGAAAAA
62145622 CTATGGCAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (29 bp):
TGGAAAAATTGTAAAATATGGAAAAATAG
Found at i:62151434 original size:19 final size:19
Alignment explanation
Indices: 62151410--62151447 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
62151400 AAAACCTTAT
62151410 TTTGATGAGATTGATAGCA
1 TTTGATGAGATTGATAGCA
*
62151429 TTTGATGAGATTTATAGCA
1 TTTGATGAGATTGATAGCA
62151448 GGAATTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (19 bp):
TTTGATGAGATTGATAGCA
Found at i:62158791 original size:32 final size:33
Alignment explanation
Indices: 62158755--62158823 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
62158745 AAGAAAGATA
*
62158755 AATTCTAA-TAGAATTTGAAAAGGAGTAGTTTG
1 AATTCTAATTAGAATTTGAAAAGGAGTAATTTG
* * *
62158787 AATTCTAATTAGGATTTTAAAAGGATTAATTTG
1 AATTCTAATTAGAATTTGAAAAGGAGTAATTTG
62158820 AATT
1 AATT
62158824 TCAAATTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (33 bp):
AATTCTAATTAGAATTTGAAAAGGAGTAATTTG
Found at i:62160803 original size:37 final size:40
Alignment explanation
Indices: 62160710--62160848 Score: 119
Period size: 40 Copynumber: 3.5 Consensus size: 40
62160700 GCACACTAGT
*
62160710 TTGGCACCCAGTG-CTTCATCGGATAATTCGAAGTAATAAG
1 TTGGCACCCAGTGTC-TCATCGGATAAATCGAAGTAATAAG
* *
62160750 TTGACACCCAGTGTCTCATCGGCTAAAT-GAAAGT-A-AA-
1 TTGGCACCCAGTGTCTCATCGGATAAATCG-AAGTAATAAG
* * * *
62160787 TTGGCACCCAGTGTCTCATTGAATTAATCCAAAGTAAT-AG
1 TTGGCACCCAGTGTCTCATCGGATAAAT-CGAAGTAATAAG
* *
62160827 ATTGACACCCTGTGTCTCATCG
1 -TTGGCACCCAGTGTCTCATCG
62160849 ACTTGAGGTC
Statistics
Matches: 79, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
37 23 0.29
38 6 0.08
39 4 0.05
40 27 0.34
41 19 0.24
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (40 bp):
TTGGCACCCAGTGTCTCATCGGATAAATCGAAGTAATAAG
Found at i:62161423 original size:28 final size:28
Alignment explanation
Indices: 62161380--62161433 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
62161370 TTACTTAAAT
* *
62161380 CCCTAAATTTCAAAATTTCACCATTTAGG
1 CCCTAAATCTCAAAATTT-ACAATTTAGG
62161409 CCCTAAA-CTCAAAATTTACAATTTA
1 CCCTAAATCTCAAAATTTACAATTTA
62161434 TTCTACAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 9 0.39
29 7 0.30
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (28 bp):
CCCTAAATCTCAAAATTTACAATTTAGG
Done.