Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009568.1 Hibiscus syriacus cultivar Beakdansim tig00116927_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 696633
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:570073 original size:28 final size:28
Alignment explanation
Indices: 570042--570117 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
570032 AGATTGAGAA
570042 ACATACATCAACTCATACATACATATAT
1 ACATACATCAACTCATACATACATATAT
570070 ACATACATCAACTCATACATACATATAT
1 ACATACATCAACTCATACATACATATAT
*
570098 ACATACATCAACACATACAT
1 ACATACATCAACTCATACAT
570118 GCATGTTACA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (28 bp):
ACATACATCAACTCATACATACATATAT
Found at i:570117 original size:4 final size:4
Alignment explanation
Indices: 570055--570105 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
570045 TACATCAACT
* *
570055 CATA CATA CATA TATA CATA CAT- CA-A C-T- CATA CATA CATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
570099 CATA CAT
1 CATA CAT
570106 CAACACATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 1 0.03
3 4 0.10
4 34 0.87
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:570722 original size:105 final size:104
Alignment explanation
Indices: 570530--570773 Score: 275
Period size: 105 Copynumber: 2.4 Consensus size: 104
570520 GACAACTTTC
* *
570530 TCTTTAAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGAT
1 TCTTTAAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGAT
570595 TCACTAAAAACAAAATTAATCTCACCTTAGATTGTTATT
66 TCACTAAAAACAAAATTAATCTCACCTTAGATTGTTATT
* * *
570634 TCTTTCAAAACAAATTTCGTCTCGTTTGAGACCTTTTCCCTTTGAGAT-CAAAATTTCGAATTTG
1 TCTTT-AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATAC-AAATTTCGAATTTG
* * * * *
570698 TTTCAC-ATTAAACAAAGTTGATCTCA-CTTGAGATCG-T-TT
64 ATTCACTA-AAAACAAAATTAATCTCACCTT-AGATTGTTATT
** * *
570737 TCTCAAAAACAAACTT-TGTCTCGCTTGAGACAATTTC
1 TCTTTAAAACAAA-TTGCGTCTCGCTTGAGACATTTTC
570774 TCTAAAAACA
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
102 25 0.21
103 7 0.06
104 11 0.09
105 76 0.64
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (104 bp):
TCTTTAAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGAT
TCACTAAAAACAAAATTAATCTCACCTTAGATTGTTATT
Found at i:570764 original size:36 final size:34
Alignment explanation
Indices: 570719--570837 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 34
570709 ACAAAGTTGA
*
570719 TCTCACTTGAGATCGTTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTTCTCAAAAACAAATTTTG
* *
570755 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC-TTTTCTC-AAAAACAAATTTTG
* * * *
570791 TCTCATTTGAGACTATATCT-TAAAGCAAATTTTG
1 TCTCACTTGAGACT-TTTCTCAAAAACAAATTTTG
*
570825 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
570838 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 23 0.33
35 7 0.10
36 39 0.57
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTCACTTGAGACTTTTCTCAAAAACAAATTTTG
Found at i:570825 original size:34 final size:36
Alignment explanation
Indices: 570737--570838 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
570727 GAGATCGTTT
* *
570737 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
570772 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
570808 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
570839 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:570986 original size:29 final size:29
Alignment explanation
Indices: 570944--571054 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 29
570934 TTTCTCTTGA
570944 AAAAATCTTTGAGTTTATTCATTTTGAAT
1 AAAAATCTTTGAGTTTATTCATTTTGAAT
* * *
570973 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTATTCATTTTGAAT
*
571002 AAATATCTTTGAGTTGT-TTC-TTTTG---
1 AAAAATCTTTGAGTT-TATTCATTTTGAAT
* *
571027 AAAAATCTTTGAGTCTATTTATTTTGAA
1 AAAAATCTTTGAGTTTATTCATTTTGAA
571055 ACAAAGTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
24 1 0.01
25 15 0.22
26 5 0.07
28 5 0.07
29 42 0.61
30 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTATTCATTTTGAAT
Found at i:571129 original size:52 final size:53
Alignment explanation
Indices: 571051--571153 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
571041 CTATTTATTT
571051 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAGCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
* *
571103 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAG
571154 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 36 0.75
53 12 0.25
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
Found at i:571173 original size:140 final size:140
Alignment explanation
Indices: 570997--571783 Score: 1461
Period size: 140 Copynumber: 5.6 Consensus size: 140
570987 TTGTTCCTTT
570997 TGAATAAATATCTTTGAG-TTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAG
1 TGAA-AAA-ATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAG
571061 TTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTT
64 TTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTT
571126 GAGACAATTTTG
129 GAGACAATTTTG
571138 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
1 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
571203 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
66 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
571268 GACAATTTTG
131 GACAATTTTG
571278 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
1 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
571343 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
66 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
571408 GACAATTTTG
131 GACAATTTTG
571418 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
1 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
571483 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
66 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
571548 GACAATTTTG
131 GACAATTTTG
571558 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
1 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
571623 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
66 TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
571688 GACAATTTTG
131 GACAATTTTG
* * * * * **
571698 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAATCTGTTTCTCTTAAAATGAA-TT
1 TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
* *
571762 TTGTATCTCTTGAGACAGTTTC
66 TTGTCTCTCTTGAGACAATTTC
571784 TCTTGAAGTA
Statistics
Matches: 636, Mismatches: 9, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
139 31 0.05
140 601 0.94
141 4 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (140 bp):
TGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTT
TTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTTGA
GACAATTTTG
Found at i:571191 original size:26 final size:26
Alignment explanation
Indices: 571141--571195 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
571131 AATTTTGTGA
* *
571141 AAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAATCTTTGAGATTATTTATTTTG
571167 AAAAATCTTTGAG-TCTATTTATTTTG
1 AAAAATCTTTGAGAT-TATTTATTTTG
571193 AAA
1 AAA
571196 CAAAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAATCTTTGAGATTATTTATTTTG
Found at i:571269 original size:52 final size:53
Alignment explanation
Indices: 571191--571293 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
571181 CTATTTATTT
571191 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAGCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
* *
571243 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAG
571294 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 36 0.75
53 12 0.25
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
Found at i:571331 original size:26 final size:26
Alignment explanation
Indices: 571281--571335 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
571271 AATTTTGTGA
* *
571281 AAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAATCTTTGAGATTATTTATTTTG
571307 AAAAATCTTTGAG-TCTATTTATTTTG
1 AAAAATCTTTGAGAT-TATTTATTTTG
571333 AAA
1 AAA
571336 CAAAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAATCTTTGAGATTATTTATTTTG
Found at i:571409 original size:52 final size:53
Alignment explanation
Indices: 571331--571433 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
571321 CTATTTATTT
571331 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAGCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
* *
571383 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAG
571434 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 36 0.75
53 12 0.25
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
Found at i:571471 original size:26 final size:26
Alignment explanation
Indices: 571421--571475 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
571411 AATTTTGTGA
* *
571421 AAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAATCTTTGAGATTATTTATTTTG
571447 AAAAATCTTTGAG-TCTATTTATTTTG
1 AAAAATCTTTGAGAT-TATTTATTTTG
571473 AAA
1 AAA
571476 CAAAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAATCTTTGAGATTATTTATTTTG
Found at i:571549 original size:52 final size:53
Alignment explanation
Indices: 571471--571573 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
571461 CTATTTATTT
571471 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAGCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
* *
571523 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAG
571574 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 36 0.75
53 12 0.25
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
Found at i:571611 original size:26 final size:26
Alignment explanation
Indices: 571561--571615 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
571551 AATTTTGTGA
* *
571561 AAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAATCTTTGAGATTATTTATTTTG
571587 AAAAATCTTTGAG-TCTATTTATTTTG
1 AAAAATCTTTGAGAT-TATTTATTTTG
571613 AAA
1 AAA
571616 CAAAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAATCTTTGAGATTATTTATTTTG
Found at i:571689 original size:52 final size:53
Alignment explanation
Indices: 571611--571713 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
571601 CTATTTATTT
571611 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAGCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
* *
571663 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAG
571714 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 36 0.75
53 12 0.25
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
Found at i:571730 original size:25 final size:25
Alignment explanation
Indices: 571701--571755 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
571691 AATTTTGTGA
*
571701 AAAAATCTTTGAGAT-TGTTTCTTTT
1 AAAAATCTTTGA-ATCTGTTTCTCTT
571726 GAAAAATCTTTGAATCTGTTTCTCTT
1 -AAAAATCTTTGAATCTGTTTCTCTT
571752 AAAA
1 AAAA
571756 TGAATTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (25 bp):
AAAAATCTTTGAATCTGTTTCTCTT
Found at i:571835 original size:89 final size:87
Alignment explanation
Indices: 571673--571842 Score: 220
Period size: 89 Copynumber: 1.9 Consensus size: 87
571663 TGAAACAAAG
*
571673 TTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
1 TTTTGTATCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
571738 AATCTGTTTCTCTTAAAATGAA
66 AATCTGTTTCTCTTAAAATGAA
* * *
571760 TTTTGTATCTCTTGAGACAGTTTCTCTTGAAGTAAATCTTTGA-ATATG-TTCATTTTG-AAAAT
1 TTTTGTATCTCTTGAGACAATTT-T-GTGAA-AAAATCTTTGAGAT-TGTTTC-TTTTGAAAAAT
* *
571822 CTTTGAGTTTGTTTCTCTTAA
61 CTTTGAATCTGTTTCTCTTAA
571843 CAAAATCATC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
87 21 0.29
88 1 0.01
89 33 0.46
90 17 0.24
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (87 bp):
TTTTGTATCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
AATCTGTTTCTCTTAAAATGAA
Found at i:571988 original size:120 final size:118
Alignment explanation
Indices: 571849--572071 Score: 263
Period size: 120 Copynumber: 1.9 Consensus size: 118
571839 TTAACAAAAT
* * *
571849 CATCTTCGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTCGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
571912 ACTAACTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
64 A--AAC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* * ** **
571969 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTCGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * * *
572034 TCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 ACTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
572072 TTGAGACAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
117 21 0.24
118 13 0.15
119 7 0.08
120 42 0.48
121 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (118 bp):
CATCTTCGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
ACTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:572096 original size:63 final size:63
Alignment explanation
Indices: 571970--572095 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
571960 GATGTGATCC
* *
571970 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
* * *
572033 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTT-GAGACAACTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
572095 A
1 A
572096 AACATCTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 20 0.34
63 38 0.66
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
Found at i:572328 original size:129 final size:127
Alignment explanation
Indices: 571969--572328 Score: 318
Period size: 129 Copynumber: 2.8 Consensus size: 127
571959 AGATGTGATC
* * * *
571969 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTG-A-AAA
1 CATCTTTGAGTTTGTTTCTATTGAAAC-AAATTTTATCACTTAAA-ACAGTTTCTTTTGAAGAAA
* * *
572032 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAGACAACTTCTTTTGAAAAAAA
64 AATC--TGAGTCTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAAACAACTTCTCTTGAAAAAAA
572097 A
127 A
* * * * * * * * * **
572098 CATCTTTGAGATCGTTTCTATTAAAACAAATTCTATCTCACATGAGACAGTTTCCTTTCAATGTC
1 CATCTTTGAGTTTGTTTCTATTGAAACAAATT-T-TATCACTTAAAACAGTTTCTTTTGAA-GAA
** * * **
572163 CTATTTGAGTC-GTTTCCTTTGAAAC-GAATTTTGTCTCTTGAAACATTTTCTCTT-AAAACAAG
63 AAATCTGAGTCTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAAACAACTTCTCTTGAAAA-AA-
*
572225 AT
126 AA
* * * *
572227 CATCTTTGAGTTTGTTTCTCTGGAAACAAGGTTTTATCGCTTAAAACAGTTTCTTTTGAAGAAAA
1 CATCTTTGAGTTTGTTTCTATTGAAACAA-ATTTTATCACTTAAAACAGTTTCTTTTGAAGAAAA
572292 ATCTGAGTCTGTTT-CTTTGGAAACAAAATTTTGTCTC
65 ATCTGAGTCTGTTTCCTTT-GAAACAAAATTTTGTCTC
572329 ACTAAGATAC
Statistics
Matches: 176, Mismatches: 44, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
127 17 0.10
128 59 0.34
129 84 0.48
130 14 0.08
132 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (127 bp):
CATCTTTGAGTTTGTTTCTATTGAAACAAATTTTATCACTTAAAACAGTTTCTTTTGAAGAAAAA
TCTGAGTCTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAAACAACTTCTCTTGAAAAAAAA
Found at i:572510 original size:36 final size:34
Alignment explanation
Indices: 572459--572554 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 34
572449 TTTGAGAAAA
* * * *
572459 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTACC
1 ATCTTTGAATCTGTTTCTTT-GAAACAAAA-TAAAC
*
572495 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAATCTGTTT-CTTTGAAACAAAATAAAC
572530 ATCTTTGAGATC-GTTTCTCTTGAAA
1 ATCTTTGA-ATCTGTTTCT-TTGAAA
572555 TGAATTTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 21 0.41
36 26 0.51
37 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
ATCTTTGAATCTGTTTCTTTGAAACAAAATAAAC
Found at i:572546 original size:35 final size:36
Alignment explanation
Indices: 572480--572554 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
572470 TGTTTCTTTG
* *
572480 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
572516 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
572551 GAAA
1 GAAA
572555 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:572757 original size:28 final size:28
Alignment explanation
Indices: 572726--572787 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
572716 AAAAAATATC
572726 ATCTTTGGGTTTATTT-TTCTTGAAACAA
1 ATCTTTGGGTTTATTTCTT-TTGAAACAA
*
572754 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGGGTTTATTTCTTTTGAAACAA
572782 ATCTTT
1 ATCTTT
572788 AATTTGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.52
Consensus pattern (28 bp):
ATCTTTGGGTTTATTTCTTTTGAAACAA
Found at i:572797 original size:28 final size:28
Alignment explanation
Indices: 572743--572807 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
572733 GGTTTATTTT
**
572743 TCTTGAAACAAATCTTTGGGTTTGTTTC
1 TCTTGAAACAAATCTTTGAATTTGTTTC
*
572771 TTTTGAAACAAATCTTT-AATTTGGTTTC
1 TCTTGAAACAAATCTTTGAATTT-GTTTC
572799 TCTTGAAAC
1 TCTTGAAAC
572808 CATAACTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (28 bp):
TCTTGAAACAAATCTTTGAATTTGTTTC
Found at i:572899 original size:46 final size:42
Alignment explanation
Indices: 572832--573245 Score: 301
Period size: 40 Copynumber: 9.5 Consensus size: 42
572822 TAACCAGCCA
* *
572832 TCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGTCG
1 TCCTCATCACGTAGGAACCGTGTCATC-CCT--AGAT-GCCAGACG
* *
572878 TCCTCATCACGTAGGAACCGTGTCATCCCTCGA--CCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAGATGCCAGACG
* * * *
572918 TCCCCATCACGTAGGAGCTGTGTCA-CCCTTAGATAGCCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCCC-TAGAT-GCCAGACG
* * *
572961 TCCTCATCACGTAGGAACCGTGTTATCACTTAAAGATGGCCAGTCG
1 TCCTCATCACGTAGGAACCGTGTCATC-CCT--AGAT-GCCAGACG
* *
573007 TCCTCATCACGTAGGAACCGTGTCATCCCTCGA--CCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAGATGCCAGACG
* * *
573047 TCCCCATCACGTAGGAGCCGTGTCA-CCCTTAGATAGCCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCCC-TAGAT-GCCAGACG
*
573090 TCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAAC-
1 TCCTCATCACGTAGGAACCGTGTCAT----C--CCT--AGATG-CCAG-ACG
* * * * *
573141 TCTTCATCACGTATGAGCAGTGTCATCCCCT-GA--CCAGACC
1 TCCTCATCACGTAGGAACCGTGTCAT-CCCTAGATGCCAGACG
* * *
573181 TCCTCATCACGTAGGAGCCGTGTCAT-CCTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAGAT-GCCAGACG
*
573223 TCCTCATCACGTAGGAATCGTGT
1 TCCTCATCACGTAGGAACCGTGT
573246 TATCACTCCT
Statistics
Matches: 297, Mismatches: 43, Indels: 60
0.74 0.11 0.15
Matches are distributed among these distances:
38 3 0.01
39 10 0.03
40 88 0.30
42 26 0.09
43 59 0.20
44 2 0.01
45 6 0.02
46 66 0.22
48 3 0.01
49 1 0.00
50 3 0.01
51 29 0.10
52 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (42 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTAGATGCCAGACG
Found at i:573048 original size:129 final size:129
Alignment explanation
Indices: 572818--573251 Score: 658
Period size: 129 Copynumber: 3.3 Consensus size: 129
572808 CATAACTCCA
*
572818 TAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGTCGTCCTC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGTCGTCCTC
*
572883 ATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCTGTGTCACCCT
66 ATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCCT
* *
572947 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACTTAAAGATGGCCAGTCGTCCTC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGTCGTCCTC
573012 ATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCCT
66 ATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCCT
* * *
573076 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAAC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT----C-ACCTAAAGATGGCCAG-TC
* * * * *
573141 -TCTTCATCACGTATGAGCAGTGTCATCCC-CTGACCAGACCTCCTCATCACGTAGGAGCCGTGT
60 GTCCTCATCACGTAGGAACCGTGTCATCCCTC-GACCAGACCTCCCCATCACGTAGGAGCCGTGT
*
573204 CATCC-
124 CACCCT
*
573209 TAGATAACCAGCCGTCCTCATCACGTAGGAATCGTGTTATCAC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAC
573252 TCCTCCTAAA
Statistics
Matches: 283, Mismatches: 15, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
128 2 0.01
129 166 0.59
133 40 0.14
134 74 0.26
135 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (129 bp):
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGTCGTCCTC
ATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCCT
Found at i:573100 original size:83 final size:84
Alignment explanation
Indices: 572818--573112 Score: 273
Period size: 83 Copynumber: 3.4 Consensus size: 84
572808 CATAACTCCA
* * * *
572818 TAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGTCGTCCTC
1 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CCT--AGA--GCCAG-CCTCCTC
572883 ATCACGTAGGAACCGTGTCATCCC-
60 ATCACGTAGGAACCGTGTCATCCCT
* * * *
572907 TCG--A-CCAGACC-TCCCCATCACGTAGGAGCTGTGTCA-CCCTTAGATAGCCAGCCGTCCTCA
1 TAGATAGCCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCCC-TAG--AGCCAGCC-TCCTCA
* *
572967 TCACGTAGGAACCGTGTTATCACT
61 TCACGTAGGAACCGTGTCATCCCT
* * * *
572991 TAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGA-CCAGACCTCCCCATC
1 T--AGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGAGCCAG-CCTCCTCATC
*
573055 ACGTAGGAGCCGTGTCA-CCCT
63 ACGTAGGAACCGTGTCATCCCT
573076 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGT
1 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGT
573113 TATCGCCCTA
Statistics
Matches: 171, Mismatches: 21, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
82 1 0.01
83 68 0.40
84 3 0.02
85 7 0.04
86 52 0.30
87 6 0.04
88 1 0.01
89 30 0.18
90 3 0.02
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.22
Consensus pattern (84 bp):
TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGAGCCAGCCTCCTCATCACG
TAGGAACCGTGTCATCCCT
Found at i:573271 original size:133 final size:131
Alignment explanation
Indices: 572818--573339 Score: 646
Period size: 129 Copynumber: 4.0 Consensus size: 131
572808 CATAACTCCA
* *
572818 TAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCA--CCTAAAGATGGCCAGTCGTCC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACTCCTAAAGATGGCCAGACGTCC
* *
572881 TCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCTGTGTCACCC
66 TCATCACGTAGGAACAGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCC
572946 T
131 T
* *
572947 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACT--TAAAGATGGCCAGTCGTCC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACTCCTAAAGATGGCCAGACGTCC
*
573010 TCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCC
66 TCATCACGTAGGAACAGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCC
573075 T
131 T
* * *
573076 TAGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAAC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT--CACT-CCTAAAGATGGCCAG-AC
* * * *
573141 -TCTTCATCACGTATGAGCAGTGTCATCCC-CTGACCAGACCTCCTCATCACGTAGGAGCCGTGT
62 GTCCTCATCACGTAGGAACAGTGTCATCCCTC-GACCAGACCTCCCCATCACGTAGGAGCCGTGT
*
573204 CATCC-
126 CACCCT
* *
573209 TAGATAACCAGCCGTCCTCATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAAC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA---CTCCTAAAGATGGCCAG-AC
* * * * * * ** * * * *
573274 -TCTTCATCATGTATGAGCAGTGTCATCCCTTGATCAGATTTCCTCATCATGTAGGAACCTTGTC
62 GTCCTCATCACGTAGGAACAGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTC
573338 AC
127 AC
573340 TTTTAGACGA
Statistics
Matches: 355, Mismatches: 25, Indels: 22
0.88 0.06 0.05
Matches are distributed among these distances:
129 164 0.46
131 4 0.01
133 112 0.32
134 74 0.21
135 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (131 bp):
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACTCCTAAAGATGGCCAGACGTCC
TCATCACGTAGGAACAGTGTCATCCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCACCC
T
Found at i:573554 original size:9 final size:10
Alignment explanation
Indices: 573536--573596 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 10
573526 GTCTTTTTTA
573536 TATTATTTAAT
1 TATTA-TTAAT
573547 T-TTATTAAT
1 TATTATTAAT
573556 TATTATT-AT
1 TATTATTAAT
573565 TATTATTATTAT
1 TATTATTA--AT
573577 TATTATTAAAT
1 TATTATT-AAT
573588 TATATATTA
1 TAT-TATTA
573597 CAAATTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 15 0.34
10 8 0.18
11 7 0.16
12 13 0.30
13 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:573560 original size:3 final size:3
Alignment explanation
Indices: 573536--573584 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
573526 GTCTTTTTTA
*
573536 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
573580 TAT TA
1 TAT TA
573585 AATTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:584021 original size:23 final size:23
Alignment explanation
Indices: 583989--584037 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
583979 GTTTACATGC
*
583989 ATGACATGTTTCCATCTATTTTT
1 ATGACATGTTTCCATCTATCTTT
* *
584012 ATGACGTGTTTCTATCTATCTTT
1 ATGACATGTTTCCATCTATCTTT
584035 ATG
1 ATG
584038 TCACGTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.51
Consensus pattern (23 bp):
ATGACATGTTTCCATCTATCTTT
Found at i:584045 original size:23 final size:23
Alignment explanation
Indices: 583989--584045 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
583979 GTTTACATGC
* *
583989 ATGACATGTTTCCATCTATTTTT
1 ATGACACGTTTCCATCTATCTTT
** *
584012 ATGACGTGTTTCTATCTATCTTT
1 ATGACACGTTTCCATCTATCTTT
*
584035 ATGTCACGTTT
1 ATGACACGTTT
584046 TCTTATTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (23 bp):
ATGACACGTTTCCATCTATCTTT
Found at i:584346 original size:14 final size:14
Alignment explanation
Indices: 584329--584355 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
584319 TTTGTATCTA
584329 TCTTTGTTCGAGTT
1 TCTTTGTTCGAGTT
584343 TCTTTGTTCGAGT
1 TCTTTGTTCGAGT
584356 CTAATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.22, T:0.56
Consensus pattern (14 bp):
TCTTTGTTCGAGTT
Found at i:590906 original size:21 final size:21
Alignment explanation
Indices: 590882--590986 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 21
590872 GCAAATTCGC
590882 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** **
590903 GTTGAAAATCATGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
590923 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** *
590944 GTTGAAAATCGCGTTACGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
590964 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
590985 GT
1 GT
590987 CTACAGTTGT
Statistics
Matches: 57, Mismatches: 25, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:590933 original size:41 final size:41
Alignment explanation
Indices: 590886--590986 Score: 175
Period size: 41 Copynumber: 2.5 Consensus size: 41
590876 ATTCGCGTTG
* *
590886 CATTTCGCGTTGCGATAGTTGAAAATCATGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCACGTTACGATTTTC
*
590927 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCACGTTACGATTTTC
590968 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
590987 CTACAGTTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCACGTTACGATTTTC
Found at i:590940 original size:20 final size:20
Alignment explanation
Indices: 590915--591036 Score: 79
Period size: 20 Copynumber: 6.0 Consensus size: 20
590905 TGAAAATCAT
*
590915 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCAATTCGC
* ** *
590935 GTTGCGATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCAATTCGC
* *
590956 GTTACGATTTTCCATTTCGC
1 GTTGCGATTTTCCAATTCGC
* * *
590976 GTTGCGATAGTCTACAGTT-GTC
1 GTTGCGAT--TTTCCAATTCG-C
590998 GTTGCGATTTTCCAAATT--C
1 GTTGCGATTTTCC-AATTCGC
591017 GTTGCGATTTTCCAAATTCG
1 GTTGCGATTTTCC-AATTCG
591037 TTTCGATAGT
Statistics
Matches: 77, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
19 19 0.25
20 25 0.32
21 18 0.23
22 15 0.19
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTTCCAATTCGC
Found at i:591020 original size:19 final size:19
Alignment explanation
Indices: 590996--591080 Score: 98
Period size: 19 Copynumber: 4.3 Consensus size: 19
590986 TCTACAGTTG
590996 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
591015 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
591034 TCGTTTCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
591055 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
591075 TCGTTG
1 TCGTTG
591081 TGATAGTCTA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 34 0.64
20 5 0.09
21 5 0.09
22 9 0.17
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:591049 original size:60 final size:61
Alignment explanation
Indices: 590975--591145 Score: 240
Period size: 60 Copynumber: 2.8 Consensus size: 61
590965 TTCCATTTCG
* **
590975 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATTTTCCA-AATT
1 CGTTTCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCATAATT
* * *
591035 CGTTTCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGTGATAGTCTATAGTT
1 CGTTTCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCATAATT
591096 -GTTGTTGCGATAGTCTACAGTTGTCGTTGCGATTTT-CAAATTCGTTGCGA
1 CG-T-TT-CGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGA
591146 AAATTCGTTG
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
60 52 0.52
61 4 0.04
62 15 0.15
63 29 0.29
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (61 bp):
CGTTTCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCATAATT
Found at i:591060 original size:41 final size:41
Alignment explanation
Indices: 591015--591106 Score: 150
Period size: 41 Copynumber: 2.2 Consensus size: 41
591005 TTTTCCAAAT
591015 TCGTTGCGATTTTCCAAATTCGTT-TCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGT-GATAGTCTACAGTTG
*
591056 TCGTTGCGATTTTCCAAATTCGTTGTGATAGTCTATAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGTGATAGTCTACAGTTG
*
591097 TTGTTGCGAT
1 TCGTTGCGAT
591107 AGTCTACAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 47 0.98
42 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.43
Consensus pattern (41 bp):
TCGTTGCGATTTTCCAAATTCGTTGTGATAGTCTACAGTTG
Found at i:591099 original size:19 final size:21
Alignment explanation
Indices: 591082--591128 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
591072 AATTCGTTGT
*
591082 GATAGTCTATAGTTGTTGTTGC
1 GATAGTCTACAGTTGTTGTT-C
*
591104 GATAGTCTACAGTTGTCGTTGC
1 GATAGTCTACAGTTGTTGTT-C
591126 GAT
1 GAT
591129 TTTCAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (21 bp):
GATAGTCTACAGTTGTTGTTC
Found at i:591279 original size:5 final size:6
Alignment explanation
Indices: 591243--591276 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
591233 ACGTATGACA
591243 ACGACC ACGACC ACGACC ACGACC -CGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
591277 CGAGACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:591784 original size:5 final size:5
Alignment explanation
Indices: 591776--591838 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
591766 GTCTCGTCTT
* * * * * *
591776 GGGTC GGGTC GGGTC GGGTC GTGTC GTGTC GTGTC GTGTC GTGTC GTGTC
1 GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC
591826 GTGGTC GTGGTC G
1 G-GGTC G-GGTC G
591839 TGGTAATACG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
5 45 0.82
6 10 0.18
ACGTcount: A:0.00, C:0.19, G:0.49, T:0.32
Consensus pattern (5 bp):
GGGTC
Found at i:591962 original size:19 final size:20
Alignment explanation
Indices: 591938--591985 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
591928 CAACGAATTT
591938 TCGCAACGAATTTGG-AAAA
1 TCGCAACGAATTTGGAAAAA
591957 TCGCAACGAATTTGGAAAAA
1 TCGCAACGAATTTGGAAAAA
591977 TCGCAACGA
1 TCGCAACGA
591986 CAACTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGAATTTGGAAAAA
Found at i:592204 original size:2 final size:2
Alignment explanation
Indices: 592197--592221 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
592187 ATTTAATCAT
592197 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
592222 TTAAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:594184 original size:28 final size:28
Alignment explanation
Indices: 594145--594222 Score: 77
Period size: 34 Copynumber: 2.6 Consensus size: 28
594135 CTAAAATGCC
*
594145 CTTCTTTTCCCCCTTTACCTCTGCGTAT
1 CTTCTTCTCCCCCTTTACCTCTGCGTAT
*
594173 CTTCTTCTCCCCCCTTGAGCTTGCCTCTGCGTAT
1 CTTCTTCT-CCCCC-T----TTACCTCTGCGTAT
594207 CTTCTTCT-CCCCTTTA
1 CTTCTTCTCCCCCTTTA
594223 GCTTGCCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
27 2 0.05
28 7 0.17
29 5 0.12
30 1 0.02
31 1 0.02
32 4 0.10
34 21 0.51
ACGTcount: A:0.06, C:0.41, G:0.09, T:0.44
Consensus pattern (28 bp):
CTTCTTCTCCCCCTTTACCTCTGCGTAT
Found at i:594226 original size:32 final size:33
Alignment explanation
Indices: 594162--594235 Score: 114
Period size: 32 Copynumber: 2.2 Consensus size: 33
594152 TCCCCCTTTA
594162 CCTCTGCGTATCTTCTTCTCCCCCCTTGAGCTTG
1 CCTCTGCGTATCTTCTTCT-CCCCCTTGAGCTTG
*
594196 CCTCTGCGTATCTTCTTCT-CCCCTTTAGCTTG
1 CCTCTGCGTATCTTCTTCTCCCCCTTGAGCTTG
*
594228 CCTTTGCG
1 CCTCTGCG
594236 AAAAATTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 19 0.50
34 19 0.50
ACGTcount: A:0.05, C:0.39, G:0.15, T:0.41
Consensus pattern (33 bp):
CCTCTGCGTATCTTCTTCTCCCCCTTGAGCTTG
Found at i:594284 original size:16 final size:16
Alignment explanation
Indices: 594263--594297 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
594253 CTAGTAAGAG
*
594263 TTCTTCTCTTCTCCCT
1 TTCTTCTCCTCTCCCT
594279 TTCTTCTCCTCTCCCT
1 TTCTTCTCCTCTCCCT
594295 TTC
1 TTC
594298 GTTGACCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (16 bp):
TTCTTCTCCTCTCCCT
Found at i:594452 original size:24 final size:24
Alignment explanation
Indices: 594420--594495 Score: 152
Period size: 24 Copynumber: 3.2 Consensus size: 24
594410 TGTGCCGGAG
594420 CGTCTGCTCTGGCATCCGCGACGA
1 CGTCTGCTCTGGCATCCGCGACGA
594444 CGTCTGCTCTGGCATCCGCGACGA
1 CGTCTGCTCTGGCATCCGCGACGA
594468 CGTCTGCTCTGGCATCCGCGACGA
1 CGTCTGCTCTGGCATCCGCGACGA
594492 CGTC
1 CGTC
594496 GTCGGCTGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (24 bp):
CGTCTGCTCTGGCATCCGCGACGA
Found at i:598510 original size:22 final size:22
Alignment explanation
Indices: 598482--598533 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
598472 AAAATTTTAT
598482 GATATAAATATATTTCAAGCAA
1 GATATAAATATATTTCAAGCAA
*
598504 GATATAAATATATTTCTAGCAA
1 GATATAAATATATTTCAAGCAA
*
598526 GACATAAA
1 GATATAAA
598534 CGTACAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (22 bp):
GATATAAATATATTTCAAGCAA
Found at i:601525 original size:105 final size:104
Alignment explanation
Indices: 601331--601528 Score: 256
Period size: 105 Copynumber: 1.9 Consensus size: 104
601321 TTAATTCCAG
* *
601331 GTCAAAAGAGAATGAAGGCTCTGAAATGGATGTCGCTGGTGATAGTGATTACAATGGAGGAGGTT
1 GTCAAAAGAGAATGAAGGCTCTGAAATGGATGTAGCTGCTGATAGTGATTACAATGGAGGAGGTT
**
601396 TAGCTAATAGCAGTGCCATGGCCAATGTTCTTGATTTCAC
66 TAGCTAATAG-AGTGCCAACGCCAATGTTCTTGATTTCAC
* * * * *
601436 GTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTTCTGATGGTGATTGCAATGGA-GATGGT
1 GTCAAAAGAGAATGAAGGCTCTGAAATGGATGTAGCTGCTGATAGTGATTACAATGGAGGA-GGT
*
601500 TTAGCTAAT-GATGGTGCTAACGCCAATGT
65 TTAGCTAATAGA--GTGCCAACGCCAATGT
601529 GTCTGATCCC
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
103 1 0.01
104 3 0.04
105 76 0.95
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.28
Consensus pattern (104 bp):
GTCAAAAGAGAATGAAGGCTCTGAAATGGATGTAGCTGCTGATAGTGATTACAATGGAGGAGGTT
TAGCTAATAGAGTGCCAACGCCAATGTTCTTGATTTCAC
Found at i:601613 original size:225 final size:225
Alignment explanation
Indices: 601194--601623 Score: 515
Period size: 225 Copynumber: 1.9 Consensus size: 225
601184 TGTCGAAGTG
* * * *
601194 AATGTTCTCGATTTCAGGTCAAAAGGGAAAGAGGAGTCTGAAACGGCTGTAGCTGATGGTTGTGA
1 AATGTTCTCGATTTCACGTCAAAAGAGAAAGAGGAGTCTGAAACGGCTGTAGCTGATGATGGTGA
* * **
601259 TTGCAATGGAGACGATTTAGCTAATGATGGTGCTAAGGCCACTGTGTCTAAAGTCAATGATATTA
66 TTGCAATGGAGACGATTTAGCTAATGATGGTGCTAACGCCAATGTGTCTAAACCCAATGATATTA
* * * * * * *
601324 ATTCCAGGTCAAAAGAGAATGAAGGCTCTGAAATGGATGTCGCTGGTGATAGTGATTACAATGGA
131 ATTCCAGGTCAAAAGAGAACGAAGGCCCTGAAAAGGATCTAGCTGATGATAGCGATTACAATGGA
* *
601389 GGAGGTTTAGCTAATAGCAGTGCCATGGCC
196 GAAGGCTTAGCTAATAGCAGTGCCATGGCC
* * * **
601419 AATGTTCTTGATTTCACGTCAAAAGAGAATGAGG-GCTCTGAAATGGCTGTAGCTTCTGATGGTG
1 AATGTTCTCGATTTCACGTCAAAAGAGAAAGAGGAG-TCTGAAACGGCTGTAGCTGATGATGGTG
* * * * * *
601483 ATTGCAATGGAGATGGTTTAGCTAATGATGGTGCTAACGCCAATGTGTCTGATCCCAGTG-TTTT
65 ATTGCAATGGAGACGATTTAGCTAATGATGGTGCTAACGCCAATGTGTCTAAACCCAATGATATT
* * * * *
601547 CGATTTCAGGTCAAAAGAGAACG-AGAGCCCTGAAAAGGCTCTAGCTGATGATGGCGATTGCAAT
130 -AATTCCAGGTCAAAAGAGAACGAAG-GCCCTGAAAAGGATCTAGCTGATGATAGCGATTACAAT
601611 GGAGAAGGCTTAG
193 GGAGAAGGCTTAG
601624 TTACTGATAG
Statistics
Matches: 169, Mismatches: 33, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
224 6 0.04
225 163 0.96
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (225 bp):
AATGTTCTCGATTTCACGTCAAAAGAGAAAGAGGAGTCTGAAACGGCTGTAGCTGATGATGGTGA
TTGCAATGGAGACGATTTAGCTAATGATGGTGCTAACGCCAATGTGTCTAAACCCAATGATATTA
ATTCCAGGTCAAAAGAGAACGAAGGCCCTGAAAAGGATCTAGCTGATGATAGCGATTACAATGGA
GAAGGCTTAGCTAATAGCAGTGCCATGGCC
Found at i:601879 original size:239 final size:240
Alignment explanation
Indices: 601436--601968 Score: 597
Period size: 239 Copynumber: 2.2 Consensus size: 240
601426 TTGATTTCAC
* ** * *
601436 GTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTTCTGATGGTGATTGCAATGGAGATGGTT
1 GTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAAATGCTT
* * * * * * * *
601501 TAGCTAATGATGGTGCTAACGCCAATGTGTCTGATCCCAGTGTTTTCGATTTCAGGTCAAAAGAG
66 TAGCCAATGATAGTGCCAACGCCAACGTCTCTGATACCAATGTTTTCGATTCCAGGTCAAAAGAG
* * * * * *
601566 AACGAGAGCCCTGAAAAGGCTCTAGCTGATGATGGCGATTGCAATGGAGAAGGCTTAGTTACTGA
131 AACGAGAGCCCTGAAAAGACTCTAGCTGATCATGACAATTGCAATGGAGAAGGCTTAGCTAATGA
* * *
601631 TAGTGCTAAGGCAACCGTCTCTGAAGCCAATATTATCTATTCCAG
196 GAGTGCTAAGGCAACCGTCTCTGAAGCCAATATTATCGATCCCAG
* *
601676 GTCAAAAGAGAATG-GAGACTCTGAAATGGCTTTAGCTGATGATGGTGATTGCACTGGAAATGCT
1 GTCAAAAGAGAATGAG-GACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAAATGCT
* * * * *
601740 TTAGCCGATGATAGTGCCGAGGCCAGCGTCTCTGA-AGCAATGTTATT-GATTCCAGGTCAAAAG
65 TTAGCCAATGATAGTGCCAACGCCAACGTCTCTGATACCAATGTT-TTCGATTCCAGGTCAAAAG
* * * * * * *
601803 AG-ACTGAGGGCTCTGAAATGATTGTAGCTGATCATGACAATTGCAATGGAGATGGTTTAGCTAA
129 AGAAC-GAGAGCCCTGAAAAGACTCTAGCTGATCATGACAATTGCAATGGAGAAGGCTTAGCTAA
* * * * * * *
601867 TGAGATTGCTAAGGCCACTGTCTCTGAAGCCAATGTTCTGGATCCCGG
193 TGAGAGTGCTAAGGCAACCGTCTCTGAAGCCAATATTATCGATCCCAG
** *
601915 GTTGAGAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAA
1 GTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAA
601969 ACGAGATGGT
Statistics
Matches: 241, Mismatches: 48, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
238 2 0.01
239 155 0.64
240 84 0.35
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (240 bp):
GTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAAATGCTT
TAGCCAATGATAGTGCCAACGCCAACGTCTCTGATACCAATGTTTTCGATTCCAGGTCAAAAGAG
AACGAGAGCCCTGAAAAGACTCTAGCTGATCATGACAATTGCAATGGAGAAGGCTTAGCTAATGA
GAGTGCTAAGGCAACCGTCTCTGAAGCCAATATTATCGATCCCAG
Found at i:601975 original size:120 final size:120
Alignment explanation
Indices: 601416--601989 Score: 555
Period size: 120 Copynumber: 4.8 Consensus size: 120
601406 CAGTGCCATG
* * * * * **
601416 GCCAATGTTCTTGATTTCACGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTTCTGATGG
1 GCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
* * * *
601481 TGATTGCAATGGAGATGGTTTAGCTAATGATG-GTGCTAACGCCAATGTGTCTGAT
66 TGATTGCAATGGAGATGGTTTAGCTAATGA-GAGTGCTAAGGCCACTGTCTCTGAA
* * * * * * * *
601536 CCCAGTGTTTTCGATTTCAGGTCAAAAGAGAACGA-GAGCCCTGAAAAGGCTCTAGCTGATGATG
1 GCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGA-CTCTGAAATGGCTGTAGCTGATGATG
* * * * * * * *
601600 GCGATTGCAATGGAGAAGGCTTAGTTACTGATAGTGCTAAGGCAACCGTCTCTGAA
65 GTGATTGCAATGGAGATGGTTTAGCTAATGAGAGTGCTAAGGCCACTGTCTCTGAA
* * *
601656 GCCAATATTATCTATTCCAGGTCAAAAGAGAATG-GAGACTCTGAAATGGCTTTAGCTGATGATG
1 GCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAG-GACTCTGAAATGGCTGTAGCTGATGATG
* * * ** * **
601720 GTGATTGCACTGGAAATGCTTTAGCCGATGATAGTGCCGAGGCCAGC-GTCTCTGAA
65 GTGATTGCAATGGAGATGGTTTAGCTAATGAGAGTGCTAAGGCCA-CTGTCTCTGAA
* * * ** * *
601776 G-CAATGTTATTGATTCCAGGTCAAAAGAGACTGAGGGCTCTGAAATGATTGTAGCTGATCATGA
1 GCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
** *
601840 CAATTGCAATGGAGATGGTTTAGCTAATGAGATTGCTAAGGCCACTGTCTCTGAA
66 TGATTGCAATGGAGATGGTTTAGCTAATGAGAGTGCTAAGGCCACTGTCTCTGAA
* * * * ** *
601895 GCCAATGTTCTGGATCCCGGGTTGAGAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
1 GCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
** *
601960 TGATTGCAAACGAGATGGTTTAGCTGATGA
66 TGATTGCAATGGAGATGGTTTAGCTAATGA
601990 TGGTGATTGC
Statistics
Matches: 360, Mismatches: 86, Indels: 16
0.78 0.19 0.03
Matches are distributed among these distances:
118 1 0.00
119 95 0.26
120 261 0.73
121 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (120 bp):
GCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGATGG
TGATTGCAATGGAGATGGTTTAGCTAATGAGAGTGCTAAGGCCACTGTCTCTGAA
Found at i:601978 original size:18 final size:18
Alignment explanation
Indices: 601955--602011 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
601945 TGTAGCTGAT
601955 GATGGTGATTGCAAACGA
1 GATGGTGATTGCAAACGA
*
601973 GATGGT--TTAGC---TGA
1 GATGGTGATT-GCAAACGA
601987 TGATGGTGATTGCAAACGA
1 -GATGGTGATTGCAAACGA
602006 GATGGT
1 GATGGT
602012 TTAGCTGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 2 0.07
15 6 0.20
16 4 0.13
17 4 0.13
18 12 0.40
19 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (18 bp):
GATGGTGATTGCAAACGA
Found at i:601989 original size:33 final size:33
Alignment explanation
Indices: 601947--602056 Score: 193
Period size: 33 Copynumber: 3.3 Consensus size: 33
601937 GAAATGGCTG
601947 TAGCTGATGATGGTGATTGCAAACGAGATGGTT
1 TAGCTGATGATGGTGATTGCAAACGAGATGGTT
601980 TAGCTGATGATGGTGATTGCAAACGAGATGGTT
1 TAGCTGATGATGGTGATTGCAAACGAGATGGTT
* *
602013 TAGCTGATGATGGCGATTGCAATCGAGATGGTT
1 TAGCTGATGATGGTGATTGCAAACGAGATGGTT
*
602046 TAGGTGATGAT
1 TAGCTGATGAT
602057 ATTGCTAAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (33 bp):
TAGCTGATGATGGTGATTGCAAACGAGATGGTT
Found at i:602168 original size:186 final size:186
Alignment explanation
Indices: 601827--602169 Score: 420
Period size: 186 Copynumber: 1.8 Consensus size: 186
601817 GAAATGATTG
*
601827 TAGCTGATCATGACAATTGCAATGGAGATGGTTTAGCTAATGAGATTGCTAAGGCCACTGTCTCT
1 TAGCTGATCATGACAATTGCAATCGAGATGGTTTAGCTAATGAGATTGCTAAGGCCACTGTCTCT
* * * ** * * **
601892 GAAGCCAATGTTCTGGATCCCGGGTTGAGAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATGA
66 GAAGCCAATGTTATCGATCCCGAGTCAAAAGAGAATGAGGACTCTCAAATGGCCATAGCTGATGA
** *
601957 TGGTGATTGCAAACGAGATGGTTTAGCTGATGATGGTGATTGCAAACGAGATGGTT
131 TGCAGATTGCAAACGAGACGGTTTAGCTGATGATGGTGATTGCAAACGAGATGGTT
* * * * * * *
602013 TAGCTGATGATGGCGATTGCAATCGAGATGGTTTAGGTGATGATATTGCTAAGGCTACTGTCTCT
1 TAGCTGATCATGACAATTGCAATCGAGATGGTTTAGCTAATGAGATTGCTAAGGCCACTGTCTCT
* * ** *
602078 GAAGCCAATGTTATCTATTCCGAGTCAAAAGAGAATGAGGGTTCTCAAATGGCCATAGCTGATGG
66 GAAGCCAATGTTATCGATCCCGAGTCAAAAGAGAATGAGGACTCTCAAATGGCCATAGCTGATGA
*
602143 TGACAG-TTGCTATA-GAGACGGTTTAGC
131 TG-CAGATTGC-AAACGAGACGGTTTAGC
602170 AAATGATAGT
Statistics
Matches: 129, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
186 126 0.98
187 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (186 bp):
TAGCTGATCATGACAATTGCAATCGAGATGGTTTAGCTAATGAGATTGCTAAGGCCACTGTCTCT
GAAGCCAATGTTATCGATCCCGAGTCAAAAGAGAATGAGGACTCTCAAATGGCCATAGCTGATGA
TGCAGATTGCAAACGAGACGGTTTAGCTGATGATGGTGATTGCAAACGAGATGGTT
Found at i:614520 original size:35 final size:34
Alignment explanation
Indices: 614467--614568 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 34
614457 AATGTGAATA
* * *
614467 AAGTAGAACAGAATGAAGCATTGCACTTTCGATTC
1 AAGTAGAACGGGAGGAAGCATT-CACTTTCGATTC
614502 AAGTAGAACGGGAGGAAGCA-T-ACTTTCGATTC
1 AAGTAGAACGGGAGGAAGCATTCACTTTCGATTC
* * * *
614534 AAGTACAACGGGAGAAAGCATCACACTTTTGATTC
1 AAGTAGAACGGGAGGAAGCAT-TCACTTTCGATTC
614569 TCATCTAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
32 29 0.51
34 1 0.02
35 27 0.47
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (34 bp):
AAGTAGAACGGGAGGAAGCATTCACTTTCGATTC
Found at i:614532 original size:32 final size:32
Alignment explanation
Indices: 614491--614554 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
614481 GAAGCATTGC
* *
614491 ACTTTCGATTCAAGTAGAACGGGAGGAAGCAT
1 ACTTTCGATTCAAGTACAACGGGAGAAAGCAT
614523 ACTTTCGATTCAAGTACAACGGGAGAAAGCAT
1 ACTTTCGATTCAAGTACAACGGGAGAAAGCAT
614555 CACACTTTTG
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:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (32 bp):
ACTTTCGATTCAAGTACAACGGGAGAAAGCAT
Found at i:614604 original size:42 final size:42
Alignment explanation
Indices: 614534--614652 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
614524 CTTTCGATTC
* * * * * *
614534 AAGTACAACGGGAGAAAGCATCACACTTTTGATTCTCATCTA
1 AAGTAGAACGGAAGGAAGCATAAAACTTTCGATTCTCATCTA
* *
614576 AAGTAGAACGGAAGGAGGCATAAAACTTTCGATTCTCTTCTA
1 AAGTAGAACGGAAGGAAGCATAAAACTTTCGATTCTCATCTA
***
614618 AAGTAGAACGGAAGGAAGCATCGTACTTTCGATTC
1 AAGTAGAACGGAAGGAAGCATAAAACTTTCGATTC
614653 AATTAGAACG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (42 bp):
AAGTAGAACGGAAGGAAGCATAAAACTTTCGATTCTCATCTA
Found at i:619279 original size:8 final size:8
Alignment explanation
Indices: 619266--619306 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
619256 CTCATTTTCA
619266 GAGAATTT
1 GAGAATTT
619274 GAGAATTT
1 GAGAATTT
*
619282 -AGAGTTT
1 GAGAATTT
*
619289 GGGAATTT
1 GAGAATTT
619297 GAGAATTT
1 GAGAATTT
619305 GA
1 GA
619307 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:619615 original size:128 final size:128
Alignment explanation
Indices: 619387--620120 Score: 1299
Period size: 128 Copynumber: 5.7 Consensus size: 128
619377 ACTATTCACA
* * *
619387 TGAAGGCGCGTTCCCAGGGGCACGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
619452 TTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTCTCAAGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
619515 TGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
619580 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGTCT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
619643 TGAAGACGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
619707 TTATGTCACTCATGTCCCTCGGGGTCATTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
619770 TGAAGGCGCGTTCCCGGGGGCTCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
619835 TTATGTAACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
619898 TGAAGGCGCGTTCCCGGGGGCGCGTCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
** * *
619963 TTATGTCACTCATGTCCCTCGGAAATACTATTCATATCATTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
620026 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
620091 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
620121 GATGGATTGT
Statistics
Matches: 575, Mismatches: 30, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
127 123 0.21
128 452 0.79
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:619860 original size:255 final size:255
Alignment explanation
Indices: 619387--620120 Score: 1290
Period size: 255 Copynumber: 2.9 Consensus size: 255
619377 ACTATTCACA
**
619387 TGAAGGCGCGTTCCCAGGGGCACGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCC-GGGGGGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
619452 TTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTG
65 TTATGTCACTCATGTCCCTCGGGGTCACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
*
619517 AAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
130 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
619582 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGTCT
195 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
619643 TGAAGACGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
619708 TATGTCACTCATGTCCCTCGGGGTCATTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGA
66 TATGTCACTCATGTCCCTCGGGGTCACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGA
*
619773 AGGCGCGTTCCCGGGGGCTCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
131 AGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
*
619838 TGTAACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
196 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
619898 TGAAGGCGCGTTCCCGGGGGCGCGTCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGG-GCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
** *
619963 TTATGTCACTCATGTCCCTCGGAAAT-ACTATTCATATCATTACCTATTATTTCTCAGGGGACTT
65 TTATGTCACTCATGTCCCTCGG-GGTCACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
620027 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
129 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
620092 TATGTCACTCATGTCCCTCGGGGACACTA
194 TATGTCACTCATGTCCCTCGGGGACACTA
620121 GATGGATTGT
Statistics
Matches: 455, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
255 248 0.55
256 206 0.45
257 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (255 bp):
TGAAGGCGCGTTCCCGGGGGGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGTCACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGA
AGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:620562 original size:34 final size:34
Alignment explanation
Indices: 620524--620624 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
620514 AAATTTAATG
*
620524 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
620558 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
620592 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
620625 AACATTTATC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:621171 original size:21 final size:21
Alignment explanation
Indices: 621141--621255 Score: 146
Period size: 21 Copynumber: 5.5 Consensus size: 21
621131 TATGGTATAA
*
621141 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
621162 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
621183 AACCCTACGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
621204 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
621225 AACCCTGCGGGCTCGAAATGT
1 AACCCTGCGGGCTAGGAATGT
621246 AACCCTGCGG
1 AACCCTGCGG
621256 AGATGGCATA
Statistics
Matches: 83, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
20 7 0.08
21 69 0.83
22 7 0.08
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:621204 original size:42 final size:42
Alignment explanation
Indices: 621141--621249 Score: 168
Period size: 42 Copynumber: 2.6 Consensus size: 42
621131 TATGGTATAA
*
621141 AACCCTGCGGGCT-AGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCA-GAATGTAACCTGGCGGGCTAGGAATGT
*
621183 AACCCTACGGGCTCAGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCAGAATGTAACCTGGCGGGCTAGGAATGT
621225 AACCCTGCGGGCTC-GAAATGTAACC
1 AACCCTGCGGGCTCAG-AATGTAACC
621250 CTGCGGAGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
41 1 0.02
42 60 0.97
43 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTCAGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:623071 original size:20 final size:20
Alignment explanation
Indices: 623018--623071 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 20
623008 AATTCTAAAT
* *
623018 AAATAATAATTATATAAATA
1 AAATAATATTTATATAAAAA
**
623038 TTAT-AT-TTTA-ATAAAAA
1 AAATAATATTTATATAAAAA
623055 AAATAATATTTATATAA
1 AAATAATATTTATATAA
623072 TTATATTAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
17 8 0.32
18 5 0.20
19 6 0.24
20 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATATTTATATAAAAA
Found at i:623081 original size:32 final size:35
Alignment explanation
Indices: 623018--623094 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 35
623008 AATTCTAAAT
623018 AAATAATAATTATATAAATATTATATTTTAATAAAAA
1 AAATAAT-ATTATATAAATATTATA-TTTAATAAAAA
* *
623055 AAATAATATT-TATATA-ATTATA-TTAATATAAA
1 AAATAATATTATATAAATATTATATTTAATAAAAA
*
623087 ATATAATA
1 AAATAATA
623095 ACTATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 16 0.43
34 6 0.16
35 5 0.14
36 3 0.08
37 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
AAATAATATTATATAAATATTATATTTAATAAAAA
Found at i:640893 original size:26 final size:25
Alignment explanation
Indices: 640854--640914 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
640844 GAGACCCGAC
* *
640854 CCGACTCGACCAAAATAAGGTTGTA
1 CCGACCCGACCAAAACAAGGTTGTA
* *
640879 TCCGACCCGATCAAAACAAGGTTTTA
1 -CCGACCCGACCAAAACAAGGTTGTA
640905 CCGACCCGAC
1 CCGACCCGAC
640915 TCGACCCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (25 bp):
CCGACCCGACCAAAACAAGGTTGTA
Found at i:641120 original size:22 final size:23
Alignment explanation
Indices: 641079--641121 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
641069 TATATATATT
*
641079 TTTCGGGTCGGGTTCGGATTTAG
1 TTTCGGGTAGGGTTCGGATTTAG
641102 TTTCGGGTAGGG-TCGGATTT
1 TTTCGGGTAGGGTTCGGATTT
641122 TTTCACCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.09, C:0.12, G:0.40, T:0.40
Consensus pattern (23 bp):
TTTCGGGTAGGGTTCGGATTTAG
Found at i:645878 original size:36 final size:36
Alignment explanation
Indices: 645825--645896 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
645815 TGGCAACCAA
*
645825 CTTTGGAAAATGTTTTTTCAAAGTTTGATAAATATTT
1 CTTTGAAAAATGTTTTTTCAAAGTTTGATAAA-ATTT
*
645862 CTTTGAAAAATG-TTTTTCAAAGTTTGGTAAAATTT
1 CTTTGAAAAATGTTTTTTCAAAGTTTGATAAAATTT
645897 TGGTAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 4 0.12
36 18 0.55
37 11 0.33
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTTCAAAGTTTGATAAAATTT
Found at i:646346 original size:16 final size:16
Alignment explanation
Indices: 646325--646358 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
646315 TTACTATTCA
*
646325 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
646341 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
646357 CG
1 CG
646359 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:662002 original size:24 final size:24
Alignment explanation
Indices: 661951--662002 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
661941 TAATATTTTA
* * *
661951 AAATCTTTATAAATTATGATGATC
1 AAATCTTTAAAAATTAAGAAGATC
661975 AAATCTTTAAAAATTAAAGAAGAT-
1 AAATCTTTAAAAATT-AAGAAGATC
661999 AAAT
1 AAAT
662003 TAATTTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (24 bp):
AAATCTTTAAAAATTAAGAAGATC
Found at i:663114 original size:15 final size:18
Alignment explanation
Indices: 663078--663115 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
663068 AAAAGAACAA
663078 TAAAAAACATTGACTAAT
1 TAAAAAACATTGACTAAT
663096 TAAAAAA-ATTGA-T-AT
1 TAAAAAACATTGACTAAT
663111 TAAAA
1 TAAAA
663116 TTGATAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 1 0.05
17 5 0.25
18 7 0.35
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAAAAACATTGACTAAT
Found at i:665717 original size:27 final size:27
Alignment explanation
Indices: 665663--665717 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
665653 GAGTTTTTAA
*
665663 AAAAAAATTAAATTAATAAAATATTAC
1 AAAAAAATTAAATTAATAAAATAATAC
* *
665690 AAAATAATTAAA-TAATTAAATGAATAC
1 AAAAAAATTAAATTAATAAAAT-AATAC
665717 A
1 A
665718 TCGATGACGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAAAAATTAAATTAATAAAATAATAC
Found at i:668724 original size:14 final size:15
Alignment explanation
Indices: 668690--668727 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
668680 ACATTTACGT
* *
668690 TTTAATTATTATAAT
1 TTTATTTATTATAAG
668705 TTTATTTATT-TAAG
1 TTTATTTATTATAAG
668719 TTTATTTAT
1 TTTATTTAT
668728 ACGCACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTATTTATTATAAG
Found at i:668936 original size:41 final size:42
Alignment explanation
Indices: 668841--668999 Score: 137
Period size: 41 Copynumber: 3.6 Consensus size: 42
668831 CTTTAGTATA
* *
668841 TATTTTTATTTTTTTAGA-TTATATATATATATTGT-T-TTTT
1 TATTTTTATTTTATTATATTTATATATATATATT-TATATTTT
* *
668881 TATTATCAGTTTTATTA-ATTTATATATATATATTTACTATTTT
1 TATTTTTA-TTTTATTATATTTATATATATATATTTA-TATTTT
* *
668924 TATTTTTATTTATTTATTTTATTTAATATATATATATATATTATTTT
1 TATTTTTA--T-TTTATTATATTT-ATATATATATATTTA-TATTTT
*
668971 TACTTTTTATTATTATTTTATTTATATAT
1 TA-TTTTTATT-TTATTATATTTATATAT
669000 TTTTTCTTCT
Statistics
Matches: 99, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
40 8 0.08
41 22 0.22
42 1 0.01
43 10 0.10
44 1 0.01
45 13 0.13
46 16 0.16
47 22 0.22
48 6 0.06
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (42 bp):
TATTTTTATTTTATTATATTTATATATATATATTTATATTTT
Found at i:668954 original size:47 final size:45
Alignment explanation
Indices: 668898--668999 Score: 152
Period size: 47 Copynumber: 2.2 Consensus size: 45
668888 AGTTTTATTA
*
668898 ATTTATATATATATATTTACTATTTTTA-TTTTTATTTATTTATTTT
1 ATTTATATATATATATATACTATTTTTACTTTTTA-TTA-TTATTTT
*
668944 ATTTAATATATATATATATATTATTTTTACTTTTTATTATTATTTT
1 ATTT-ATATATATATATATACTATTTTTACTTTTTATTATTATTTT
668990 ATTTATATAT
1 ATTTATATAT
669000 TTTTTCTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
45 6 0.12
46 15 0.29
47 25 0.48
48 6 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (45 bp):
ATTTATATATATATATATACTATTTTTACTTTTTATTATTATTTT
Found at i:668991 original size:11 final size:13
Alignment explanation
Indices: 668907--669002 Score: 64
Period size: 13 Copynumber: 7.8 Consensus size: 13
668897 AATTTATATA
668907 TATATATTTACTATT
1 TATATATTT--TATT
*
668922 TTTAT-TTTTATT
1 TATATATTTTATT
*
668934 TATTTATTTTATT
1 TATATATTTTATT
* *
668947 TA-ATA-TATATA
1 TATATATTTTATT
668958 TATATATTATT-TT
1 TATATATT-TTATT
*
668971 TA-CT-TTTTA-T
1 TATATATTTTATT
668981 TAT-TATTTTATT
1 TATATATTTTATT
668993 TATATATTTT
1 TATATATTTT
669003 TTCTTCTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
10 6 0.10
11 13 0.21
12 17 0.27
13 19 0.30
14 4 0.06
15 4 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATATTTTATT
Found at i:668991 original size:24 final size:23
Alignment explanation
Indices: 668918--669065 Score: 72
Period size: 23 Copynumber: 6.3 Consensus size: 23
668908 ATATATTTAC
668918 TATTTTTATTTTTATTTATTTATTT
1 TATTTTTATTTTTA-TTA-TTATTT
* * * *
668943 TA-TTTAATATATA-TATATATAT
1 TATTTTTATTTTTATTAT-TATTT
668965 TATTTTTACTTTTTATTATTATTT
1 TATTTTTA-TTTTTATTATTATTT
* * *
668989 TATTTATATATTTT-TTCTTCTTT
1 TATTTTTAT-TTTTATTATTATTT
* * *
669012 T-TCTTTATTTTTTTTTATTTTTT
1 TATTTTTA-TTTTTATTATTATTT
** *
669035 TACATTTA-TTTTACTTACTATTT
1 TATTTTTATTTTTA-TTATTATTT
*
669058 TATCTTTA
1 TATTTTTA
669066 CTTTCTTTAT
Statistics
Matches: 92, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
21 1 0.01
22 20 0.22
23 35 0.38
24 31 0.34
25 5 0.05
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTTTATTTTTATTATTATTT
Found at i:668997 original size:35 final size:34
Alignment explanation
Indices: 668958--669029 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
668948 AATATATATA
668958 TATATATTATTTT-TACTTTTT-ATTATTATTTTATT
1 TATATATT-TTTTCTACTTTTTCATTATT-TTTT-TT
* *
668993 TATATATTTTTTCTTCTTTTTCTTTATTTTTTTT
1 TATATATTTTTTCTACTTTTTCATTATTTTTTTT
669027 TAT
1 TAT
669030 TTTTTTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 9 0.27
35 19 0.58
36 5 0.15
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (34 bp):
TATATATTTTTTCTACTTTTTCATTATTTTTTTT
Found at i:669004 original size:33 final size:33
Alignment explanation
Indices: 668958--669037 Score: 78
Period size: 33 Copynumber: 2.4 Consensus size: 33
668948 AATATATATA
668958 TATATATTATTTTTACTT-TTTATT-ATTATTTTATT
1 TATATA-T-TTTTTACTTCTTT-TTCATTATTTT-TT
*
668993 TATATATTTTTT-CTTCTTTTTCTTTATTTTTT
1 TATATATTTTTTACTTCTTTTTCATTATTTTTT
*
669025 TTTAT-TTTTTTAC
1 TATATATTTTTTAC
669038 ATTTATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
31 6 0.15
32 12 0.30
33 15 0.38
34 1 0.03
35 6 0.15
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (33 bp):
TATATATTTTTTACTTCTTTTTCATTATTTTTT
Found at i:673205 original size:32 final size:32
Alignment explanation
Indices: 673169--673288 Score: 152
Period size: 32 Copynumber: 3.8 Consensus size: 32
673159 GGAACAATAA
*
673169 GGGCATCTTTGAAGATTCAACATCAAATATTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
* * * *
673201 GGGCATTTTTTTAGATTTAACATCAAATGTTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
* *
673233 GGGCATTTTTTTAGATTCAACATCAAATATTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
*
673265 GGGCATCTTTG-GGAATTCAACATC
1 GGGCATCTTTGTAG-ATTCAACATC
673289 CTGATGCAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 1 0.01
32 76 0.99
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (32 bp):
GGGCATCTTTGTAGATTCAACATCAAATATTG
Found at i:674531 original size:87 final size:87
Alignment explanation
Indices: 674337--674495 Score: 266
Period size: 87 Copynumber: 1.8 Consensus size: 87
674327 GACAGTTTCT
*
674337 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
674402 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
* * *
674424 CTTGAAACATAAACATTGAAAATATTTCCCTTGAAATAAATTTTATCTC-ACTTGGGGTAGTTTC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGA-TTGAGATAGTTTC
674488 CCTTGAAA
65 CCTTGAAA
674496 TTTTTTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
86 1 0.01
87 66 0.99
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACGAAATTTTGTCTCC
Found at i:674540 original size:101 final size:102
Alignment explanation
Indices: 674424--674662 Score: 345
Period size: 101 Copynumber: 2.4 Consensus size: 102
674414 TTTTGTCTCC
* * *
674424 CTTGAAACATAAACATTGAAAATATTTCCCTTGAAATAAATTTTATCTCACTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCACTTGAGATAGTTTCC
****
674489 CTTGAAA-TTTTTTTTGTCTCCCTTGAGACAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* * * *
674525 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCACTTGAGATAGTTTCC
*
674590 CTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
674627 CTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
674663 CACAAAATAT
Statistics
Matches: 122, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 65 0.53
102 57 0.47
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCACTTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:674610 original size:37 final size:37
Alignment explanation
Indices: 674563--674635 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
674553 CTTTGAAATT
*
674563 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
*
674600 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
674636 TAAACCTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:674755 original size:37 final size:37
Alignment explanation
Indices: 674700--674802 Score: 163
Period size: 36 Copynumber: 2.8 Consensus size: 37
674690 AAAACGAGTT
674700 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* * * *
674737 TTGAGACGGTTTCGCTTGAAAC-AAATTTTGTCTCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
674773 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
674803 TGAATATCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 32 0.55
37 26 0.45
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:674870 original size:102 final size:102
Alignment explanation
Indices: 674714--674899 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 102
674704 GACAGTTTCC
* * * *
674714 CTTGAAACAAAATCTTGTCTCTCTTGAGACGGTTTCGCTTGAAACAAATTTTGTCTCTTTTGAGA
1 CTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCGCTTAAAACAAATTTTGTCTCTCTTGAGA
674779 CAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTTT
66 CAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTTT
** *
674816 CTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAGTTTCTTTTAAAACTAAGTTTTGTCTCTCTTGA
1 CTTGAAACAAAATCTT-GTCTCCCTTGAGACAGTTTCGCTTAAAAC-AAATTTTGTCTCTCTTGA
**
674879 GACAGTTTCTTTTGAAACAAA
64 GACAGTTTCCCTTGAAACAAA
674900 TTTTGTCCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
100 2 0.03
101 28 0.38
102 43 0.59
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (102 bp):
CTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCGCTTAAAACAAATTTTGTCTCTCTTGAGA
CAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTTT
Found at i:674912 original size:36 final size:36
Alignment explanation
Indices: 674817--674933 Score: 164
Period size: 36 Copynumber: 3.2 Consensus size: 36
674807 TATCTTTTTC
*
674817 TTGAAACAAATTTCGTCTCC-CTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTC-CCTCTTGAGACAGTTTCTT
* * *
674853 TTAAAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGAAAC-AAATTTTGTCCCTCTTGAGACAGTTTCTT
*
674890 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTT
674926 TTGAAACA
1 TTGAAACA
674934 CAAAAAAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
36 41 0.58
37 30 0.42
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTT
Found at i:676162 original size:2 final size:2
Alignment explanation
Indices: 676157--676193 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
676147 TTTTTTAGAT
*
676157 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
676194 TATTTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:676169 original size:10 final size:10
Alignment explanation
Indices: 676156--676198 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
676146 TTTTTTTAGA
676156 TTATATATAT
1 TTATATATAT
676166 TTATATATAT
1 TTATATATAT
*
676176 ATATATATAT
1 TTATATATAT
*
676186 ATATATATTAT
1 TTATATA-TAT
676197 TT
1 TT
676199 TTACTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 26 0.87
11 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATATAT
Found at i:676218 original size:9 final size:9
Alignment explanation
Indices: 676191--676281 Score: 59
Period size: 8 Copynumber: 10.1 Consensus size: 9
676181 TATATATATA
676191 TATTATTTT
1 TATTATTTT
*
676200 TACTTTTTTT
1 TA-TTATTTT
676210 TATTA-TTT
1 TATTATTTT
676218 TATTTATTTGT
1 TA-TTATTT-T
676229 T-TTATTTAT
1 TATTATTT-T
676238 ATATT-TTTT
1 -TATTATTTT
* *
676247 TCTTTTTCTT
1 TATTATT-TT
676257 TATT-TTTT
1 TATTATTTT
676265 TATT-TTTT
1 TATTATTTT
676273 TA-TATTTT
1 TATTATTTT
676281 T
1 T
676282 TACTTACTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
7 1 0.01
8 25 0.37
9 19 0.28
10 19 0.28
11 4 0.06
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (9 bp):
TATTATTTT
Found at i:676258 original size:26 final size:24
Alignment explanation
Indices: 676203--676294 Score: 78
Period size: 26 Copynumber: 3.7 Consensus size: 24
676193 TTATTTTTAC
*
676203 TTTTTTTTATTATTTTATTTATTTG
1 TTTTATTTATTATTTT-TTTATTTG
* *
676228 TTTTATTTATATATTTTTTTCTTTT
1 TTTTATTTAT-TATTTTTTTATTTG
*
676253 TCTTTATTTTTTTATTTTTTTATATT-
1 T-TTTA-TTTATTATTTTTTTAT-TTG
* *
676279 TTTTACTTACTATTTT
1 TTTTATTTATTATTTT
676295 ATCTTTACTT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
24 8 0.15
25 20 0.36
26 21 0.38
27 6 0.11
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTATTTATTATTTTTTTATTTG
Found at i:676278 original size:18 final size:18
Alignment explanation
Indices: 676191--676282 Score: 75
Period size: 18 Copynumber: 5.0 Consensus size: 18
676181 TATATATATA
676191 TATTATTTTTACT-TTTTTT
1 TATT-TTTTTA-TATTTTTT
*
676210 TATTATTTTAT-TTATTTGT
1 TATTTTTTTATATT-TTT-T
*
676229 T-TTATTTATATATTTTTT
1 TATT-TTTTTATATTTTTT
*
676247 TCTTTTTCTT-TATTTTTT
1 TATTTTT-TTATATTTTTT
676265 TATTTTTTTATATTTTTT
1 TATTTTTTTATATTTTTT
676283 ACTTACTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
17 5 0.08
18 37 0.61
19 17 0.28
20 2 0.03
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (18 bp):
TATTTTTTTATATTTTTT
Found at i:676282 original size:9 final size:8
Alignment explanation
Indices: 676206--676283 Score: 75
Period size: 9 Copynumber: 9.0 Consensus size: 8
676196 TTTTTACTTT
676206 TTTTTATTA
1 TTTTT-TTA
676215 TTTTATTTA
1 TTTT-TTTA
676224 TTTGTTTTA
1 TTT-TTTTA
* *
676233 TTTATATA
1 TTTTTTTA
*
676241 TTTTTTTCT
1 TTTTTTT-A
676250 TTTTCTTTA
1 TTTT-TTTA
676259 TTTTTTTA
1 TTTTTTTA
676267 TTTTTTTA
1 TTTTTTTA
676275 TATTTTTTA
1 T-TTTTTTA
676284 CTTACTATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
8 21 0.36
9 32 0.55
10 5 0.09
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Done.