Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold344
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: 1758742
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 11
Found at i:201696 original size:32 final size:33
Alignment explanation
Indices: 201638--201700 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
201628 CACCCAGATA
*
201638 TATCGATACATTATGCTTTGTATCGATACATTG
1 TATCGATACATTATGCATTGTATCGATACATTG
*
201671 TATCGATACA-TATTCATTGTATCGATACAT
1 TATCGATACATTATGCATTGTATCGATACAT
201701 GGACAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (33 bp):
TATCGATACATTATGCATTGTATCGATACATTG
Found at i:201711 original size:20 final size:19
Alignment explanation
Indices: 201665--201721 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
201655 TTGTATCGAT
**
201665 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATGG
*
201684 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
201703 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
201722 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:201788 original size:33 final size:33
Alignment explanation
Indices: 201751--201815 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
201741 TATCACTGTT
201751 TGTATCGATACATGGT-ACATTATATCGATACAA
1 TGTATCGATACATGGTGA-ATTATATCGATACAA
*
201784 TGTATCGATACATGGTGAATTGTATCGATACA
1 TGTATCGATACATGGTGAATTATATCGATACA
201816 TTACTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGTGAATTATATCGATACAA
Found at i:202730 original size:20 final size:19
Alignment explanation
Indices: 202707--202779 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
202697 CACATCCATA
*
202707 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
202727 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
202746 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
202766 TGTATCGATACATG
1 TGTATCGATACATG
202780 AAACTAGTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:202847 original size:13 final size:13
Alignment explanation
Indices: 202829--202853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202819 CATGGCACAT
202829 TGTATCGATACAA
1 TGTATCGATACAA
202842 TGTATCGATACA
1 TGTATCGATACA
202854 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:202851 original size:33 final size:32
Alignment explanation
Indices: 202809--202873 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
202799 TACCACTGTT
202809 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
202842 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGA-GAATTGTATCGATACA
202874 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:211987 original size:39 final size:38
Alignment explanation
Indices: 211927--212041 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 38
211917 AGTTAACTAA
* *
211927 AATCTAAAAAATGTGACTAATGTTTGAATTTTTTATTAG
1 AATCTAAAAAATATGACTAATGTAT-AATTTTTTATTAG
* * * *
211966 AATCTAAAAAATATTAGTAATGTATAGCTTATTTATTAG
1 AATCTAAAAAATATGACTAATGTATA-ATTTTTTATTAG
* * *
212005 AATTTGAAAAATATGACTAATATATAAATTTTTTATT
1 AATCTAAAAAATATGACTAATGTAT-AATTTTTTATT
212042 GAAATTCAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.02
39 59 0.97
40 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (38 bp):
AATCTAAAAAATATGACTAATGTATAATTTTTTATTAG
Found at i:214263 original size:156 final size:156
Alignment explanation
Indices: 214024--214476 Score: 448
Period size: 157 Copynumber: 2.9 Consensus size: 156
214014 GCCCAATGAT
** * * * * * *
214024 CCTAAAGGACTTAAAAATAATTATAGATGGGATAAACCTATCTTAAATGCACACCTTC-AGCATA
1 CCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACATTCGA-CGTA
* * * *
214088 AAATCGAACCTAGTGACAACCTAGGACTCGGTTCTGAAAAAATTATGAAAATGCCCCTAAGGGAT
65 AAAGCGGACCTAGTGACAACCTAGGACTCGGTTCTGAAAAAATTATGAAAATACCCCTAGGGGAT
*
214153 ACCTTTGACTTAA-AAGTGTATAATACC
130 ACCTTTGACTTAATAA-TGCATAATACC
* * *
214180 CTTAAAGGATTTAAAAAGGATTATAAATGGGATGAACCTATCCTAAATACCCACATTCGACGTAA
1 CCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACATTCGACGTAA
* * * ** ** * *
214245 AAGCGGATCC-AGTGACAACTTAAGTCTCGAAT-TGAAAAAAAATTACAAAAATATCTCTAGGGG
66 AAGCGGA-CCTAGTGACAACCTAGGACTCGGTTCTG--AAAAAATTATGAAAATACCCCTAGGGG
* * *
214308 ATATCTTTGATTTAATAATGCCTAATACC
128 ATACCTTTGACTTAATAATGCATAATACC
* * * * *
214337 CCTAAAAGACTTAAAACGGATTATAGATGGGATGAACTTATCCTAAATACCCACATTTGGCAG-A
1 CCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACATTCGAC-GTA
* * * * * * *
214401 AAAGTGGACCTGGTGACAATCTAGGACTCAGTTCTGGAAAAATTATGCAAATACCCTTAGGGGAT
65 AAAGCGGACCTAGTGACAACCTAGGACTCGGTTCTGAAAAAATTATGAAAATACCCCTAGGGGAT
*
214466 ACCTTCGACTT
130 ACCTTTGACTT
214477 GAATGTATCA
Statistics
Matches: 234, Mismatches: 55, Indels: 16
0.77 0.18 0.05
Matches are distributed among these distances:
155 2 0.01
156 106 0.45
157 121 0.52
158 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (156 bp):
CCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACATTCGACGTAA
AAGCGGACCTAGTGACAACCTAGGACTCGGTTCTGAAAAAATTATGAAAATACCCCTAGGGGATA
CCTTTGACTTAATAATGCATAATACC
Found at i:215230 original size:12 final size:12
Alignment explanation
Indices: 215215--215254 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
215205 TACCAAACAA
215215 AAATAATATTAT
1 AAATAATATTAT
215227 AAATAATA-T-T
1 AAATAATATTAT
*
215237 AAATAATATAAT
1 AAATAATATTAT
215249 AAATAA
1 AAATAA
215255 GCTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
12 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATAATATTAT
Found at i:215260 original size:22 final size:22
Alignment explanation
Indices: 215215--215261 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
215205 TACCAAACAA
* *
215215 AAATAATATTATAAATAATATT
1 AAATAATATAATAAATAAGATT
*
215237 AAATAATATAATAAATAAGCTT
1 AAATAATATAATAAATAAGATT
215259 AAA
1 AAA
215262 AAAACTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATAATATAATAAATAAGATT
Found at i:215312 original size:21 final size:21
Alignment explanation
Indices: 215287--215332 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
215277 CTATATATCC
215287 ACATAAAACAACATAA-ATATA
1 ACATAAAACAACA-AAGATATA
*
215308 ACATAAATCAACAAAGATATA
1 ACATAAAACAACAAAGATATA
215329 ACAT
1 ACAT
215333 GATAAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.20
Consensus pattern (21 bp):
ACATAAAACAACAAAGATATA
Found at i:220783 original size:17 final size:17
Alignment explanation
Indices: 220761--220795 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
220751 TGATGAAAAG
220761 AATAAAA-TAATAATAAT
1 AATAAAATTAAT-ATAAT
220778 AATAAAATTAATATAAT
1 AATAAAATTAATATAAT
220795 A
1 A
220796 TATTAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAAATTAATATAAT
Found at i:222329 original size:35 final size:35
Alignment explanation
Indices: 222257--222329 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
222247 TAAGAAAGCA
*
222257 TAGATAGCAAACTAAAAGAAAATTGCTTAAATGTT
1 TAGATAGCAAACTAAAAGAAAATTGCTTAAATATT
* * * * *
222292 TAGATAGCAAAGTAGAAGGAAATTTCTTAAGTATT
1 TAGATAGCAAACTAAAAGAAAATTGCTTAAATATT
222327 TAG
1 TAG
222330 CGATTGGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (35 bp):
TAGATAGCAAACTAAAAGAAAATTGCTTAAATATT
Found at i:224629 original size:18 final size:17
Alignment explanation
Indices: 224595--224627 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
224585 AAGACATTGC
*
224595 TTTAATTTTCTAAAAAT
1 TTTAATTTTATAAAAAT
224612 TTTAATTTTATAAAAA
1 TTTAATTTTATAAAAA
224628 ATATTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATTTTATAAAAAT
Found at i:224634 original size:18 final size:17
Alignment explanation
Indices: 224596--224635 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
224586 AGACATTGCT
* *
224596 TTAATTTTCTAAAAATT
1 TTAATTTTATAAAAATA
224613 TTAATTTTATAAAAAATA
1 TTAATTTTAT-AAAAATA
224631 TTAAT
1 TTAAT
224636 AAAGCACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTTTATAAAAATA
Found at i:225210 original size:156 final size:156
Alignment explanation
Indices: 224949--225266 Score: 379
Period size: 156 Copynumber: 2.0 Consensus size: 156
224939 TCCTCGAAAT
* * * *
224949 CTTAAAGGACTTAAAGATGATCATAAAAAGGTGAACCTATCCTAAACGCATATATTTGGAATAAA
1 CTTAAAGCACTTAAAGATAATCATAAAAAGGTGAACCTATCCTAAACGCACACATTTGGAATAAA
* * * * * * * * * *
225014 AGCATCTTGGTGACTACTTCGAACTTGGTTCTAAGGAAAATTATCAAAATACCCTTAGGGATTAT
66 AACATATAGGTAACTACATCGAACTTGGTTCTAAGAAAAATTACCAAAATACCCTTAGAGACTAC
225079 CTTCATCTTAAAAACATCCCAGTGAC
131 CTTCATCTTAAAAACATCCCAGTGAC
* * * **
225105 CTTAAAGCACTTGAAA-ATAATCATAGAAGGGTGAACCTATCCTAAATGCACACATTTGTCATAA
1 CTTAAAGCACTT-AAAGATAATCATAAAAAGGTGAACCTATCCTAAACGCACACATTTGGAATAA
* *
225169 AAACATATAGGTAACTACATC-AGACTTGGTTTTAAGAAAAATTACCAAAATACTCTTAGAGACT
65 AAACATATAGGTAACTACATCGA-ACTTGGTTCTAAGAAAAATTACCAAAATACCCTTAGAGACT
* * *
225233 ACCTTCATCTTGAAAGCATCCTAGTGAC
129 ACCTTCATCTTAAAAACATCCCAGTGAC
*
225261 CCTAAA
1 CTTAAA
225267 AAACCAAGAA
Statistics
Matches: 135, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
155 1 0.01
156 131 0.97
157 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (156 bp):
CTTAAAGCACTTAAAGATAATCATAAAAAGGTGAACCTATCCTAAACGCACACATTTGGAATAAA
AACATATAGGTAACTACATCGAACTTGGTTCTAAGAAAAATTACCAAAATACCCTTAGAGACTAC
CTTCATCTTAAAAACATCCCAGTGAC
Found at i:227586 original size:41 final size:42
Alignment explanation
Indices: 227541--227638 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 42
227531 AAACCAGATG
* *
227541 AGTCAACAAATGAGAAGGG-TTGA-TAGGGATGGAACCATACA
1 AGTCAACAAATGAGAAGGGATTGACTA-AGATGAAACCATACA
**
227582 AGTCAAC-AA-GCTTAAGGGATTGACTAAGATGAAACCATACA
1 AGTCAACAAATG-AGAAGGGATTGACTAAGATGAAACCATACA
*
227623 AGTGAACAAATGAGAA
1 AGTCAACAAATGAGAA
227639 TGCTTGACCA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
39 1 0.02
40 7 0.16
41 30 0.67
42 6 0.13
43 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.17
Consensus pattern (42 bp):
AGTCAACAAATGAGAAGGGATTGACTAAGATGAAACCATACA
Found at i:227686 original size:40 final size:41
Alignment explanation
Indices: 227642--227751 Score: 104
Period size: 41 Copynumber: 2.7 Consensus size: 41
227632 ATGAGAATGC
* *
227642 TTGACCAGGATGAAATCAT-T-AAGTCAACAAGTTT-AAGCGG
1 TTGACCAGAATGAAACCATATGAA-TCAACAAGTTTAAAG-GG
* *
227682 TTGACTATAATGAAACCATATGAATCAACAAGTTTAAAGGG
1 TTGACCAGAATGAAACCATATGAATCAACAAGTTTAAAGGG
*
227723 TTGATC-GAGATGAAACCATACT-AATCAAC
1 TTGACCAGA-ATGAAACCATA-TGAATCAAC
227752 GAACAAGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
40 16 0.28
41 36 0.62
42 6 0.10
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (41 bp):
TTGACCAGAATGAAACCATATGAATCAACAAGTTTAAAGGG
Found at i:227712 original size:81 final size:82
Alignment explanation
Indices: 227499--227712 Score: 197
Period size: 82 Copynumber: 2.6 Consensus size: 82
227489 GGTAAGACCT
* * * ** * * *
227499 AAGTCAAGAAACTTAAGAGG-TTGACTGAGACAAAACCAGATGAGTCAACAAATGAGAAGGGTTG
1 AAGTCAACAAGCTTAAG-GGATTGACTAAGATGAAACCATATGAATCAACAAATGAGAAGGCTTG
* *
227563 ATAGGGATGGAACCATAC
65 ACAGGGATGAAACCATAC
* * *
227581 AAGTCAACAAGCTTAAGGGATTGACTAAGATGAAACCATA-CAAGTGAACAAATGAGAATGCTTG
1 AAGTCAACAAGCTTAAGGGATTGACTAAGATGAAACCATATGAA-TCAACAAATGAGAAGGCTTG
* *
227645 ACCA-GGATGAAATCAT-T
65 A-CAGGGATGAAACCATAC
*
227662 AAGTCAACAAGTTTAAGCGG-TTGACTATA-ATGAAACCATATGAATCAACAA
1 AAGTCAACAAGCTTAAG-GGATTGACTA-AGATGAAACCATATGAATCAACAA
227713 GTTTAAAGGG
Statistics
Matches: 108, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
81 43 0.40
82 64 0.59
83 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (82 bp):
AAGTCAACAAGCTTAAGGGATTGACTAAGATGAAACCATATGAATCAACAAATGAGAAGGCTTGA
CAGGGATGAAACCATAC
Found at i:227716 original size:41 final size:41
Alignment explanation
Indices: 227665--227751 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 41
227655 AATCATTAAG
*
227665 TCAACAAGTTT-AAGCGGTTGA-CTATAATGAAACCATA-TGAA
1 TCAACAAGTTTAAAG-GGTTGATCGA-AATGAAACCATACT-AA
*
227706 TCAACAAGTTTAAAGGGTTGATCGAGATGAAACCATACTAA
1 TCAACAAGTTTAAAGGGTTGATCGAAATGAAACCATACTAA
227747 TCAAC
1 TCAAC
227752 GAACAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 35 0.85
42 6 0.15
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (41 bp):
TCAACAAGTTTAAAGGGTTGATCGAAATGAAACCATACTAA
Found at i:227835 original size:41 final size:42
Alignment explanation
Indices: 227721--227849 Score: 140
Period size: 41 Copynumber: 3.1 Consensus size: 42
227711 AAGTTTAAAG
* * * * **
227721 GGTTGATCGAGATGAAACCATACTAA-TCAACGAACAAGAAA
1 GGTTGATCAAGATAAAACCATACAAAGTCAATGAATGAGAAA
* *
227762 GGTTGACCAAGACAAAACCATACAAAGT-AATGAATGAGAAA
1 GGTTGATCAAGATAAAACCATACAAAGTCAATGAATGAGAAA
*
227803 GGTTGATCAAGATAAAACTATAC-AAGTCAATGAATGA-AAA
1 GGTTGATCAAGATAAAACCATACAAAGTCAATGAATGAGAAA
227843 TGGTTGA
1 -GGTTGA
227850 CTAAGGCAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 7 0.09
41 66 0.89
42 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.19
Consensus pattern (42 bp):
GGTTGATCAAGATAAAACCATACAAAGTCAATGAATGAGAAA
Found at i:228103 original size:131 final size:131
Alignment explanation
Indices: 227889--228134 Score: 302
Period size: 131 Copynumber: 1.9 Consensus size: 131
227879 GATAAAGGCA
** *
227889 AAACCATAATAATCAACTAAGAGTGACTAGGGCAGAACCTAAGGCAAAAAAATGTTGGCCAGGAT
1 AAACCATAATAATCAACTAAGAGTGACTAGAACAGAACCTAAGGCAAAAAAATGTTGGCCAAGAT
* * * * *
227954 TAAATCATACAAACCAACTTTGGTGACCAAGGTGAGACTT-AAGTCGAAAAATGGTTGACTAGGG
66 GAAACCATACAAACCAACTTTGATAACCAAGGT-AGAATTAAAGTCGAAAAATGGTTGACTAGGG
228018 CG
130 CG
* * * *
228020 AAACCATAATAGTCAACTAA-AGGTGACTAGAATAGAACCTGAA-TCTAAAAAA-GATTGGCCAA
1 AAACCATAATAATCAACTAAGA-GTGACTAGAACAGAACCT-AAGGCAAAAAAATG-TTGGCCAA
**
228082 GATGAAACCATATGAACCAACTTTGATAACCAAGGTAGAATTAAAGTCGAAAA
63 GATGAAACCATACAAACCAACTTTGATAACCAAGGTAGAATTAAAGTCGAAAA
228135 GGGTTTGACC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
130 7 0.07
131 88 0.91
132 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (131 bp):
AAACCATAATAATCAACTAAGAGTGACTAGAACAGAACCTAAGGCAAAAAAATGTTGGCCAAGAT
GAAACCATACAAACCAACTTTGATAACCAAGGTAGAATTAAAGTCGAAAAATGGTTGACTAGGGC
G
Found at i:228143 original size:131 final size:130
Alignment explanation
Indices: 227884--228158 Score: 299
Period size: 131 Copynumber: 2.1 Consensus size: 130
227874 AGGCTGATAA
* **
227884 AGGCAAAACCATAATAATCAACTAAGAGTGACTAGGGCAGAACCTAAGGCAAAAAAATGTTGGCC
1 AGGCGAAACCATAATAATCAACTAAGAGTGACTAGAACAGAACCTAAGGCAAAAAAATGTTGGCC
* * * * * * * *
227949 AGGATTAAATCATACAAACCAACTTTGGTGACCAAGGTGAGACTTAAGTCGAAAAATGGTTGACT
66 AAGATGAAACCATACAAACCAACTTTGATAACCAAGGTGAGAATTAAGTCGAAAAAGGGTTGACC
* * * *
228014 AGGGCGAAACCATAATAGTCAACTAA-AGGTGACTAGAATAGAACCTGAA-TCTAAAAAA-GATT
1 A-GGCGAAACCATAATAATCAACTAAGA-GTGACTAGAACAGAACCT-AAGGCAAAAAAATG-TT
**
228076 GGCCAAGATGAAACCATATGAACCAACTTTGATAACCAAGGT-AGAATTAAAGTCG-AAAAGGGT
62 GGCCAAGATGAAACCATACAAACCAACTTTGATAACCAAGGTGAGAATT-AAGTCGAAAAAGGG-
228139 TTGACC
125 TTGACC
*
228145 AGGTGAAACCATAA
1 AGGCGAAACCATAA
228159 GTCAAAAAAG
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
130 26 0.21
131 93 0.77
132 2 0.02
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (130 bp):
AGGCGAAACCATAATAATCAACTAAGAGTGACTAGAACAGAACCTAAGGCAAAAAAATGTTGGCC
AAGATGAAACCATACAAACCAACTTTGATAACCAAGGTGAGAATTAAGTCGAAAAAGGGTTGACC
Found at i:228161 original size:32 final size:32
Alignment explanation
Indices: 228125--228190 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
228115 GGTAGAATTA
* * *
228125 AAGTCGAAAAGGGTTTGACCA-GGTGAAACCAT
1 AAGTCAAAAAAGG-TTGACCAGGGCGAAACCAT
*
228157 AAGTCAAAAAAGGTTGACTAGGGCGAAACCAT
1 AAGTCAAAAAAGGTTGACCAGGGCGAAACCAT
228189 AA
1 AA
228191 TAGTCAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 6 0.21
32 23 0.79
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.17
Consensus pattern (32 bp):
AAGTCAAAAAAGGTTGACCAGGGCGAAACCAT
Found at i:228315 original size:164 final size:163
Alignment explanation
Indices: 227979--228322 Score: 385
Period size: 162 Copynumber: 2.1 Consensus size: 163
227969 AACTTTGGTG
* * *
227979 ACCAAGGTGAGA-CTTAAGTCGAAAAATGGTTGACTAGGGCGAAACCATAATAGTCAACTAAAGG
1 ACCAAGGTGAAACCATAAGTCGAAAAAAGGTTGACTAGGGCGAAACCATAATAGTCAACTAAAGG
* * * ** **
228043 TGACTAGAATAGAACCTGAATCTAAAAAAGATTGGCCAAGATGAAACCATATGAACCAACTTTGA
66 TAACTAGAACAAAACCTGAATAAAAAAAAGATTGGCCAAGATGAAACCATACAAACCAACTTTGA
* * *** *
228108 TAACCAAGGTAGAATTAAAGTCGAAAAGGGTTTG
131 TAACCAAGGCAGAACTAAAGTC-AAAAGAAATTA
*
228142 ACC-AGGTGAAACCATAAGTC-AAAAAAGGTTGACTAGGGCGAAACCATAATAGTCAACTAAGGG
1 ACCAAGGTGAAACCATAAGTCGAAAAAAGGTTGACTAGGGCGAAACCATAATAGTCAACTAAAGG
* * * * *
228205 TAACTAGGACAAAACCT-AAGTAAAATAAAAGGGTTGGCCAGGCTGAAATCATACAAACCAACTT
66 TAACTAGAACAAAACCTGAA-TAAAA-AAAA-GATTGGCCAAGATGAAACCATACAAACCAACTT
*
228269 TGGTAACCAAGGCAGAACCT-AAGT-ACAAAGAAATTA
128 TGATAACCAAGGCAGAA-CTAAAGTCA-AAAGAAATTA
228305 ACCAAGGTGAAACCATAA
1 ACCAAGGTGAAACCATAA
228323 TAGTTAACCA
Statistics
Matches: 151, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
161 2 0.01
162 65 0.43
163 23 0.15
164 60 0.40
165 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (163 bp):
ACCAAGGTGAAACCATAAGTCGAAAAAAGGTTGACTAGGGCGAAACCATAATAGTCAACTAAAGG
TAACTAGAACAAAACCTGAATAAAAAAAAGATTGGCCAAGATGAAACCATACAAACCAACTTTGA
TAACCAAGGCAGAACTAAAGTCAAAAGAAATTA
Found at i:228418 original size:132 final size:130
Alignment explanation
Indices: 228151--228496 Score: 363
Period size: 132 Copynumber: 2.6 Consensus size: 130
228141 GACCAGGTGA
* * * * * * *
228151 AACCATAAGTCAAAAAAGGTTGACTAGGGCGAAACCATAATAGTCAACTAAGGGTAACTAGGACA
1 AACC-TAAGTCAAAAAA-CTTAACCAAGGCGAAACCATAATAGTAAACCAA-GGTGACTAGGACA
* * * *
228216 AAACCTAAGTAAAATAAAAGGGTTGGCCAGGCTGAAATCATACAAACCAACTTTGGTAACCAAGG
63 AAACCTAAGTAAAAAAAAAAGGTTGGCCAAGCTGAAATCATACAAACCAACTTTAGTAACCAAGG
228281 CAG
128 CAG
* *
228284 AACCTAAGTACAAAGAAA-TTAACCAAGGTGAAACCATAATAGTTAACCAATGGTGACTAGGACA
1 AACCTAAGT-CAAA-AAACTTAACCAAGGCGAAACCATAATAGTAAACCAA-GGTGACTAGGACA
* * * * * * *
228348 AAAGCTAAGTAAAAAAAAAAGGTTGGCCAAGTTGAAATCATATAAACTAATTTTAGTGA-GAAGG
63 AAACCTAAGTAAAAAAAAAAGGTTGGCCAAGCTGAAATCATACAAACCAACTTTAGTAACCAA-G
*
228412 GTAG
127 GCAG
* * * *
228416 AACCTAAGTCAAAAAAGCTTGATCAGGGCGAAACCATAATAGTAAACCAAGAGTGACTAAGACAA
1 AACCTAAGTCAAAAAA-CTTAACCAAGGCGAAACCATAATAGTAAACCAAG-GTGACTAGGACAA
*
228481 AACCTAAGTTAAAAAA
64 AACCTAAGTAAAAAAA
228497 GGTTGGTGAC
Statistics
Matches: 179, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
130 3 0.02
131 7 0.04
132 158 0.88
133 8 0.04
134 3 0.02
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (130 bp):
AACCTAAGTCAAAAAACTTAACCAAGGCGAAACCATAATAGTAAACCAAGGTGACTAGGACAAAA
CCTAAGTAAAAAAAAAAGGTTGGCCAAGCTGAAATCATACAAACCAACTTTAGTAACCAAGGCAG
Found at i:231775 original size:21 final size:23
Alignment explanation
Indices: 231724--231776 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
231714 TTTACCTTCT
* *
231724 TGATTT-TTTTTAAATATTATAA
1 TGATTTATTTGTAAACATTATAA
231746 TGATTTATTTGTAAACATTA-AA
1 TGATTTATTTGTAAACATTATAA
231768 TG-TTTATTT
1 TGATTTATTT
231777 TTACTATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 10 0.36
23 11 0.39
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (23 bp):
TGATTTATTTGTAAACATTATAA
Found at i:238090 original size:30 final size:30
Alignment explanation
Indices: 238044--238107 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
238034 GATAATTTTT
*
238044 TATTTTTATTTGTAAAAGTTAAAAATC-TA
1 TATTATTATTTGTAAAAGTTAAAAATCGTA
* *
238073 TATTATTATTATGTAAAAGTTTAACATCGTA
1 TATTATTATT-TGTAAAAGTTAAAAATCGTA
238104 TATT
1 TATT
238108 TCAACAAGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 9 0.30
30 15 0.50
31 6 0.20
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (30 bp):
TATTATTATTTGTAAAAGTTAAAAATCGTA
Found at i:238705 original size:16 final size:15
Alignment explanation
Indices: 238679--238722 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
238669 TAATTTTTTA
238679 TTATCTTTATATTATT
1 TTAT-TTTATATTATT
*
238695 TTATTTATATAATATT
1 TTATTT-TATATTATT
238711 TTATTTTATATT
1 TTATTTTATATT
238723 TTAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTATATTATT
Found at i:238714 original size:21 final size:22
Alignment explanation
Indices: 238690--238751 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
238680 TATCTTTATA
238690 TTATTTTAT-TTATATAATATT
1 TTATTTTATATTATATAATATT
*
238711 TTATTTTATATT-T-TAAT-TA
1 TTATTTTATATTATATAATATT
238730 TT-TTTTATATTATGATAATATT
1 TTATTTTATATTAT-ATAATATT
238752 ACCGAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 4 0.12
21 14 0.41
22 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATTTTATATTATATAATATT
Found at i:238752 original size:23 final size:23
Alignment explanation
Indices: 238688--238752 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 23
238678 ATTATCTTTA
238688 TATTATTTTAT-TTATATAATAT
1 TATTATTTTATATTATATAATAT
238710 T-TTATTTTATATT-T-T-A-AT
1 TATTATTTTATATTATATAATAT
238728 TATT-TTTTATATTATGATAATAT
1 TATTATTTTATATTAT-ATAATAT
238751 TA
1 TA
238753 CCGAATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
18 12 0.33
19 4 0.11
20 1 0.03
21 11 0.31
22 4 0.11
23 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTATTTTATATTATATAATAT
Found at i:239468 original size:18 final size:17
Alignment explanation
Indices: 239422--239474 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
239412 CTCTTTTTTT
239422 AAATATTATTATATTTCA
1 AAATATTATT-TATTTCA
*
239440 AAACATATATTTATTTACA
1 AAATAT-TATTTATTT-CA
239459 AAATATTATTT-TTTCA
1 AAATATTATTTATTTCA
239475 CTCATAACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 3 0.10
18 15 0.48
19 11 0.35
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATTATTTATTTCA
Found at i:240569 original size:15 final size:15
Alignment explanation
Indices: 240549--240581 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
240539 ATATGCATAT
*
240549 TTTATGTTTATGTAG
1 TTTATGTTTACGTAG
240564 TTTATGTTTACGTAG
1 TTTATGTTTACGTAG
240579 TTT
1 TTT
240582 TGATCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (15 bp):
TTTATGTTTACGTAG
Found at i:249206 original size:52 final size:52
Alignment explanation
Indices: 249128--249256 Score: 258
Period size: 52 Copynumber: 2.5 Consensus size: 52
249118 CGAAATATGA
249128 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
249180 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
249232 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
249257 AAGATCAGTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:249267 original size:52 final size:51
Alignment explanation
Indices: 249128--249276 Score: 246
Period size: 52 Copynumber: 2.9 Consensus size: 51
249118 CGAAATATGA
249128 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
249180 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
249232 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
249277 ATGTATCGAT
Statistics
Matches: 94, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
50 1 0.01
51 2 0.02
52 91 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:249283 original size:13 final size:13
Alignment explanation
Indices: 249265--249289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
249255 CAAAGATCAG
249265 TGTATCGATACAA
1 TGTATCGATACAA
249278 TGTATCGATACA
1 TGTATCGATACA
249290 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:249367 original size:33 final size:33
Alignment explanation
Indices: 249330--249396 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
249320 AGTAGCTTAA
249330 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
249363 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
249396 A
1 A
249397 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:249370 original size:13 final size:13
Alignment explanation
Indices: 249352--249376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
249342 CAAAAAAATA
249352 TGTATCGATACAT
1 TGTATCGATACAT
249365 TGTATCGATACA
1 TGTATCGATACA
249377 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:250376 original size:49 final size:49
Alignment explanation
Indices: 250323--251128 Score: 1051
Period size: 49 Copynumber: 16.6 Consensus size: 49
250313 GATGTCAACG
* *
250323 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* *
250372 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTT--AAA-GATGAAGATGCCAATA
* * * *
250424 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
250473 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * * * *
250522 TGCTGATTCCAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
250571 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * * *
250620 TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
250669 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * * *
250718 TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
250767 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * * *
250816 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
250865 TGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
250914 TGCTGATTCAATGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
*
250957 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* * *
251006 TGCTGATTCAGGGCCAGCTATATTGGGCTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
* *
251049 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAAGA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
*
251098 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTA
251129 GAAGGGTTGC
Statistics
Matches: 648, Mismatches: 94, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
43 68 0.10
44 6 0.01
45 2 0.00
46 4 0.01
47 2 0.00
48 6 0.01
49 509 0.79
50 3 0.00
51 3 0.00
52 45 0.07
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATA
Found at i:250558 original size:98 final size:98
Alignment explanation
Indices: 250323--251133 Score: 1277
Period size: 98 Copynumber: 8.4 Consensus size: 98
250313 GATGTCAACG
* * * * * * *
250323 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
* *
250388 GCGATATTGGACTTAAAAATGATGATGATGCCAATA
66 GCTACATTGGACTT--AAA-GATGATGATGCCAATA
250424 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
250489 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
250522 TGCTGATTCCAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
250587 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
250620 TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
250685 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
250718 TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
250783 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
250816 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGTTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
*
250881 GCTACATTGGACTTAAAGATGAAGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
* *
250914 TGCTGATTCAATGCCAGCGATATTGGACTT--A----AAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
*
250973 GCTACATTGGACTTAAAGATGAAGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
* * * *
251006 TGCTGATTCAGGGCCAGCTATATTGGGCTT--A----AAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
* *
251065 GCTACATTGGACTTAAAGATGAAGATGCCAAGA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
* *
251098 TGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGG
251134 GTTGCCACCG
Statistics
Matches: 681, Mismatches: 24, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
92 175 0.26
95 1 0.00
96 1 0.00
98 431 0.63
99 3 0.00
101 70 0.10
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (98 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
GCTACATTGGACTTAAAGATGATGATGCCAATA
Found at i:251172 original size:33 final size:35
Alignment explanation
Indices: 251128--251197 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
251118 TATTGGGCTT
251128 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
251162 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
251196 AG
1 AG
251198 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:251221 original size:38 final size:36
Alignment explanation
Indices: 251182--251899 Score: 587
Period size: 34 Copynumber: 21.5 Consensus size: 36
251172 CACCGACTTG
* *
251182 TGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGT
1 TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGT
*
251218 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
251253 TGTGGGCTTTAAAA-GAAAAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGA-GTGCCACGGAGT
* * * *
251289 TATGGAC--TCAAAGATGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGT
* *
251323 TATGGGC-TTAAAA--G-----GA-TGCCACAGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
251350 TGTGGGC-TTAGAA-GGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
** *
251384 TGTGGGC-TTAGGA-GGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
251418 TGTGGGCTTT-------AAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* * *
251447 CGTGGGCTTT------G--AAGGA-TGCCACAGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
251474 TGTGGGCTTTGAAAA--GAAGAAG-GTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*
251508 TGTGGGCTTTAAAGAGTGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
251545 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
*
251579 TGTGGGATTTAAAA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
251612 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
* *
251646 TGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
251683 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
*
251717 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
251754 TGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
*
251787 TGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
*
251821 TGTGGGC-TT-------AAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* * * *
251849 TGTGGAC-TT-AAAGATGAAAAA-AGTGCCACAGAAT
1 TGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGT
251883 TGTGGGCTTTAAAAGGG
1 TGTGGGCTTTAAAAGGG
251900 TGCCACGGAG
Statistics
Matches: 594, Mismatches: 39, Indels: 99
0.81 0.05 0.14
Matches are distributed among these distances:
27 46 0.08
28 26 0.04
29 27 0.05
32 2 0.00
33 64 0.11
34 234 0.39
35 62 0.10
36 65 0.11
37 68 0.11
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (36 bp):
TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
Found at i:251257 original size:71 final size:66
Alignment explanation
Indices: 251182--251946 Score: 680
Period size: 71 Copynumber: 11.6 Consensus size: 66
251172 CACCGACTTG
* * * *
251182 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTA--AAGAGAAAAAGATGCCACAGAGTTGTGGGCTTAAAA--GAAAAAG-GTGCCA
251247 CGGAGT
61 CGGAGT
* * * * * * *
251253 TGTGGGCTTTAAAAGAAAAAAAAGGTGCCACGGAGTTATGGACTCAAAGATGAAAAAAGTGCCAC
1 TGTGGGCTTT-AAAG-AGAAAAAGATGCCACAGAGTTGTGGGCTTAAA-A-GAAAAAGGTGCCAC
251318 GGAGT
62 GGAGT
* * *
251323 TATGGGC-TTAAA-AG-----GATGCCACAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAG
1 TGTGGGCTTTAAAGAGAAAAAGATGCCACAGAGTTGTGGGCTTA-AAAGAAAAAG-GTGCCACGG
251381 AGT
64 AGT
* * *
251384 TGTGGGC-TT-AGGAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT-TAA-AAAGA-GTGCCACGG
1 TGTGGGCTTTAAAGA-GAAAAAGA-TGCCACAGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACGG
251444 AGT
64 AGT
* * * *
251447 CGTGGGCTTT-----G--AAGGATGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAG
1 TGTGGGCTTTAAAGAGAAAAAGATGCCACAGAGTTGTGGGC-TT-AAAAGAAAAAGGTGCCACGG
251505 AGT
64 AGT
*
251508 TGTGGGCTTTAAAGAGTGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCA
1 TGTGGGCTTTAAAGA--GAAAAAGA-TGCCACAGAGTTGTGGGC-TTAAA-AGAAAAAGGTGCCA
251573 CGGAGT
61 CGGAGT
* * *
251579 TGTGGGATTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGG
1 TGTGGGCTTTAAAGAGAAAAAGATGCCACAGAGTTGTGGGC-TTAAA-AGAAAAAGGTGCCACGG
251643 AGT
64 AGT
251646 TGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCA
1 TGTGGGCTTT--AAAGAGAAAAAGA-TGCCACAGAGTTGTGGGC-TTAAA-AGAAAAAGGTGCCA
251711 CGGAGT
61 CGGAGT
*
251717 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCAC
1 TGTGGGCTTT--AAAGAGAAAAAGA-TGCCACAGAGTTGTGGGC-TTAAAAGAAAAAGGTGCCAC
251782 GGAGT
62 GGAGT
* * * *
251787 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT---A-AAAAGGGTGCCACGGAG
1 TGTGGGCTTTAAAGAGAAAAAGATGCCACAGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACGGAG
251848 T
66 T
* *
251849 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTAAAAG-----GGTGCCACG
1 TGTGGGCTTTAAAGA-GAAAAAGA-TGCCACAGAGTTGTGGGC-TTAAAAGAAAAAGGTGCCACG
251907 GAGT
63 GAGT
* *
251911 TGTGGGCTTT-AA-AGAAAAA-ATGCCACTGAGTCGTGG
1 TGTGGGCTTTAAAGAGAAAAAGATGCCACAGAGTTGTGG
251947 ACTTTGAGAC
Statistics
Matches: 597, Mismatches: 55, Indels: 96
0.80 0.07 0.13
Matches are distributed among these distances:
56 18 0.03
57 6 0.01
59 16 0.03
60 17 0.03
61 65 0.11
62 69 0.12
63 22 0.04
64 2 0.00
65 4 0.01
66 5 0.01
67 73 0.12
68 41 0.07
69 5 0.01
70 67 0.11
71 185 0.31
72 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (66 bp):
TGTGGGCTTTAAAGAGAAAAAGATGCCACAGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACGGAG
T
Found at i:251350 original size:61 final size:60
Alignment explanation
Indices: 251272--251393 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 60
251262 TAAAAGAAAA
* *
251272 AAAAGGTGCCACGGAGTTATGGACTCA-AAGATGAAAAA-AGTGCCACGGAGTTATGGGCTT
1 AAAAGGTGCCACAGAGTTATGGACTCAGAAG--GAAAAAGAGTGCCACAGAGTTATGGGCTT
* * * *
251332 AAAAGGATGCCACAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGG-TGCCACAGAGTTATGGACTCAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
251393 A
1 A
251394 GGAGGAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
60 12 0.23
61 38 0.72
62 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (60 bp):
AAAAGGTGCCACAGAGTTATGGACTCAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
Found at i:251534 original size:61 final size:56
Alignment explanation
Indices: 251413--251534 Score: 129
Period size: 61 Copynumber: 2.1 Consensus size: 56
251403 AGAGTGCCAC
* * ** *
251413 AGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTTGAAGGATGCCAC
1 AGAGTTGTGGGCTTTAAAAAGAGTGCCACAGAGTCGTGGGCTTTAAAGGATGAAAA
*
251469 AGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTAAA-GAGTGAAAA
1 AGAGTTGTGGGCTTT--AAA-AAG-A-GTGCCACAGAGTCGTGGGCTTTAAAGGA-TGAAAA
251530 AGAGT
1 AGAGT
251535 GCCACGGAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 15 0.28
58 3 0.06
59 3 0.06
60 3 0.06
61 30 0.56
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.23
Consensus pattern (56 bp):
AGAGTTGTGGGCTTTAAAAAGAGTGCCACAGAGTCGTGGGCTTTAAAGGATGAAAA
Found at i:251711 original size:138 final size:135
Alignment explanation
Indices: 251202--251930 Score: 742
Period size: 138 Copynumber: 5.5 Consensus size: 135
251192 AGGAAGGGAG
* * *
251202 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACAGAGTTGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
* * * * * *
251266 AGA-AAAAAAAGGTGCCACGGAGTTATGGAC-TCAAAGATGAAAAAAGTGCCACGGAGTTATGGG
63 AGAGAAAAAGA-GTGCCACGGAGTTGTGGGCTTTAAA-A-GAAAAAGGTGCCACGGAGTTGTGGG
*
251329 -CTTAAAAG--
125 ATTTAAAAGAA
* * * **
251337 ---GATGCCACAGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TTAGGA
1 AAAGGTGCCACAGAGTTGTGGGCTTTA-AAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
* * * *
251397 G-GAAAAAGAGTGCCACAGAGTTGTGGGCTTT--AA-AAAGA-GTGCCACGGAGTCGTGGGCTTT
64 GAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGATTT
251457 ----G--
129 AAAAGAA
* *
251458 -AAGGATGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTAAAG
1 AAAGG-TGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA-
*
251522 AGTGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGAT
63 AGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGAT
251587 TTAAAAGAA
127 TTAAAAGAA
*
251596 AAAGGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAGGTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA
* *
251661 GAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTT
64 GAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGATT
251726 TGAAAAGGGAA
128 T-AAAA--GAA
251737 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-
1 AAAG-GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
251801 AGAAAAAG-GTGCCACGGAGTTGTGGGC-TT---A-AAAAGGGTGCCACGGAGTTGT-GGACTTA
65 AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGATTTA
251859 AAGATGAA
130 AA-A-GAA
* *
251867 AAAAGTGCCACAGAATTGTGGGCTTTAAAAG-----GGTGCCACGGAGTTGTGGGCTTT-AAAGA
1 AAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGA
251926 -AAAAA
66 GAAAAA
251931 TGCCACTGAG
Statistics
Matches: 524, Mismatches: 38, Indels: 76
0.82 0.06 0.12
Matches are distributed among these distances:
121 1 0.00
123 9 0.02
124 77 0.15
125 19 0.04
126 3 0.01
127 30 0.06
128 1 0.00
129 43 0.08
130 22 0.04
131 35 0.07
132 61 0.12
133 3 0.01
136 1 0.00
137 5 0.01
138 130 0.25
139 19 0.04
140 4 0.01
141 37 0.07
142 24 0.05
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (135 bp):
AAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGA
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGATTTAA
AAGAA
Found at i:251768 original size:28 final size:28
Alignment explanation
Indices: 251736--251923 Score: 151
Period size: 34 Copynumber: 6.1 Consensus size: 28
251726 TGAAAAGGGA
*
251736 AAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
251764 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAG----A-GTGCCACGGAGTTGTGGGCTTT
*
251797 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTA
1 -AAAAG----A-GTGCCACGGAGTTGTGGGCTTT
* *
251831 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-----T
* * *
251864 GAAAAAAGTGCCACAGAATTGTGGGCTTT
1 -AAAAGAGTGCCACGGAGTTGTGGGCTTT
*
251893 AAAAGGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
251921 AAA
1 AAA
251924 GAAAAAATGC
Statistics
Matches: 134, Mismatches: 14, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
28 52 0.39
29 1 0.01
32 1 0.01
33 26 0.19
34 54 0.40
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (28 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTT
Found at i:251840 original size:62 final size:62
Alignment explanation
Indices: 251699--251923 Score: 283
Period size: 62 Copynumber: 3.5 Consensus size: 62
251689 CTTTAAACAG
*
251699 AAAAA-GGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACAGAGTTGTGGGC-T
251763 T
62 T
* *
251764 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCT
1 ---A-AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGGCT
251829 T
62 T
* * * *
251830 AAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTT
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGGTGCCACAGAGTTGTGGGCTT
*
251892 TAAAAGGGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTTAAA
251924 GAAAAAATGC
Statistics
Matches: 143, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
61 5 0.03
62 73 0.51
63 6 0.04
66 2 0.01
67 18 0.13
68 8 0.06
69 8 0.06
70 23 0.16
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (62 bp):
AAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTT
Found at i:251962 original size:30 final size:31
Alignment explanation
Indices: 251900--251984 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 31
251890 TTTAAAAGGG
* * *
251900 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
* *
251931 TGCCACTGAGTCGTGGACTTT-GAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
251961 TGCCACTGAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
251985 AAGGTATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 28 0.60
31 19 0.40
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
Found at i:252925 original size:1 final size:1
Alignment explanation
Indices: 252919--252950 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
252909 TGAAAAGGGG
252919 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
252951 GTGAAGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:253315 original size:1 final size:1
Alignment explanation
Indices: 253273--253302 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
253263 GCCTTTACAC
*
253273 TTTTTTTTTTTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
253303 GTGTTTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:260307 original size:13 final size:13
Alignment explanation
Indices: 260289--260313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260279 CAAAGATCAG
260289 TGTATCGATACAA
1 TGTATCGATACAA
260302 TGTATCGATACA
1 TGTATCGATACA
260314 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:260391 original size:33 final size:33
Alignment explanation
Indices: 260354--260420 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
260344 AGTAGCTTAA
260354 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
260387 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
260420 A
1 A
260421 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:260394 original size:13 final size:13
Alignment explanation
Indices: 260376--260400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260366 CAAAAAAATA
260376 TGTATCGATACAT
1 TGTATCGATACAT
260389 TGTATCGATACA
1 TGTATCGATACA
260401 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:265808 original size:20 final size:20
Alignment explanation
Indices: 265783--265836 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
265773 CTACCACTGT
*
265783 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
265803 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
265823 TTGTATCGATACAT
1 TTGTATCGATACAT
265837 TGCTTCTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:271509 original size:21 final size:20
Alignment explanation
Indices: 271475--271513 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
271465 CACATTTTTG
*
271475 TCTAAATGTATCGATACATT
1 TCTAAATATATCGATACATT
271495 TCTAGAATATATCGATACA
1 TCTA-AATATATCGATACA
271514 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATATATCGATACATT
Found at i:271653 original size:13 final size:13
Alignment explanation
Indices: 271635--271662 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
271625 GCCAAAAAAA
271635 TGTATCGATACAT
1 TGTATCGATACAT
271648 TGTATCGATACAT
1 TGTATCGATACAT
271661 TG
1 TG
271663 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:273897 original size:27 final size:27
Alignment explanation
Indices: 273863--273915 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
273853 CAAAAATTTA
273863 TTCATCGGGGACACTCCAACCCCATTC
1 TTCATCGGGGACACTCCAACCCCATTC
*
273890 TTCATCGGGGACATTCCAACCCCATT
1 TTCATCGGGGACACTCCAACCCCATT
273916 TAAACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.25
Consensus pattern (27 bp):
TTCATCGGGGACACTCCAACCCCATTC
Found at i:277995 original size:2 final size:2
Alignment explanation
Indices: 277990--278019 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
277980 TTTTTTACCT
*
277990 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
278020 CCCAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:287440 original size:13 final size:13
Alignment explanation
Indices: 287422--287447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
287412 TTTTAAGGCA
287422 ACTGTTTGTTTAT
1 ACTGTTTGTTTAT
287435 ACTGTTTGTTTAT
1 ACTGTTTGTTTAT
287448 GATGCTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
ACTGTTTGTTTAT
Found at i:290315 original size:17 final size:18
Alignment explanation
Indices: 290283--290316 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
290273 TAAATTGTGA
*
290283 TTATATGTATATTTATTT
1 TTATATGTATAATTATTT
290301 TTATAT-TATAATTATT
1 TTATATGTATAATTATT
290317 GTGATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATATGTATAATTATTT
Found at i:292805 original size:18 final size:18
Alignment explanation
Indices: 292766--292809 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
292756 AAAATTAAGT
* *
292766 AAAACATAATTTTTATTG
1 AAAATATAATTTTTATTA
292784 AAAATATAATTTTT-TATA
1 AAAATATAATTTTTAT-TA
292802 AAAATATA
1 AAAATATA
292810 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATATAATTTTTATTA
Found at i:293137 original size:15 final size:16
Alignment explanation
Indices: 293106--293173 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
293096 GAAATTATAA
*
293106 ATTTATATAATATTTT
1 ATTTATATAATAATTT
293122 ATTTAT-TAATAATTT
1 ATTTATATAATAATTT
* *
293137 ATTTTTAT-ATATTTT
1 ATTTATATAATAATTT
*
293152 A-ATATAT-AT-ATTT
1 ATTTATATAATAATTT
293165 ATATTATAT
1 AT-TTATAT
293174 TTTTATTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
13 4 0.10
14 6 0.14
15 25 0.60
16 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATATAATAATTT
Found at i:293189 original size:15 final size:16
Alignment explanation
Indices: 293171--293208 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
293161 ATTTATATTA
*
293171 TATTTTTATTTTA-AT
1 TATTTTTATGTTATAT
*
293186 TATTTTTATGTTATGT
1 TATTTTTATGTTATAT
293202 TATTTTT
1 TATTTTT
293209 TATATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TATTTTTATGTTATAT
Found at i:293344 original size:25 final size:24
Alignment explanation
Indices: 293304--293353 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
293294 TTATGTTGTA
*
293304 TTAATATTATTTTTATATTGTATT
1 TTAATATTATTTTTATATTATATT
293328 TTAATTATT-TTTCTTATATTATATT
1 TTAA-TATTATTT-TTATATTATATT
293353 T
1 T
293354 ATGTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
TTAATATTATTTTTATATTATATT
Found at i:293888 original size:2 final size:2
Alignment explanation
Indices: 293881--293907 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
293871 ATTGGATTTA
293881 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
293908 GTCAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295420 original size:46 final size:46
Alignment explanation
Indices: 295370--295459 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
295360 TAAAATTGAG
295370 TTAGTCTCTCCATGGTATAAAGTTTTAATTTAAAACTTAACCCTAC
1 TTAGTCTCTCCATGGTATAAAGTTTTAATTTAAAACTTAACCCTAC
295416 TTAGTCTCTCCATGGTATAAAGTTTTAATTTAAAACTTAACCCT
1 TTAGTCTCTCCATGGTATAAAGTTTTAATTTAAAACTTAACCCT
295460 GCTTTTTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (46 bp):
TTAGTCTCTCCATGGTATAAAGTTTTAATTTAAAACTTAACCCTAC
Found at i:300961 original size:6 final size:7
Alignment explanation
Indices: 300944--300972 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
300934 AATTTCAAAA
300944 AAAAATG
1 AAAAATG
300951 AAAAATG
1 AAAAATG
300958 AAAAATG
1 AAAAATG
300965 AAAAATG
1 AAAAATG
300972 A
1 A
300973 TAATTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:304221 original size:37 final size:39
Alignment explanation
Indices: 304171--304243 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 39
304161 TCTCAAAATT
* *
304171 AGACATTACCTAAC-TTTTAGGTTA-TTTGTCTTAACTA
1 AGACATTACCTAACTTTTTAGATCACTTTGTCTTAACTA
*
304208 AGACATTATCTAACTTTTTAGATCACTTTGTCTTAA
1 AGACATTACCTAACTTTTTAGATCACTTTGTCTTAA
304244 TTTGGACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 13 0.42
38 8 0.26
39 10 0.32
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (39 bp):
AGACATTACCTAACTTTTTAGATCACTTTGTCTTAACTA
Found at i:313733 original size:49 final size:49
Alignment explanation
Indices: 313672--313770 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
313662 AAGATGAAGC
313672 TTTAGAAAAATTCATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGT
1 TTTAGAAAAATTCATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGT
313721 TTTAGAAAAATTCATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGT
1 TTTAGAAAAATTCATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGT
313770 T
1 T
313771 ACTCCTTATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (49 bp):
TTTAGAAAAATTCATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGT
Found at i:316473 original size:13 final size:13
Alignment explanation
Indices: 316455--316494 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
316445 ACAAAGTTTT
*
316455 TTGTATGGATACA
1 TTGTATCGATACA
316468 TTGTATCGATACA
1 TTGTATCGATACA
**
316481 ACGTATCGATACA
1 TTGTATCGATACA
316494 T
1 T
316495 AGGTACTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:318370 original size:36 final size:36
Alignment explanation
Indices: 318323--318400 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
318313 ACAAAAAAGA
* *
318323 GGAGAAATATTTGCAATAAATTTTTTTTATAAAGGG
1 GGAGAAATATTTACAATAAATTTGTTTTATAAAGGG
*
318359 GGAGAAGTATTTACAATAAATTTGTTTTATAAAGGG
1 GGAGAAATATTTACAATAAATTTGTTTTATAAAGGG
318395 GGAGAA
1 GGAGAA
318401 TTTGTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (36 bp):
GGAGAAATATTTACAATAAATTTGTTTTATAAAGGG
Found at i:319719 original size:117 final size:117
Alignment explanation
Indices: 319560--319793 Score: 360
Period size: 117 Copynumber: 2.0 Consensus size: 117
319550 TACATTTCAA
*
319560 AGAGCTTTTACTGTCATTGTTATTATTCTTTGAAAGCTCATTTGTATTTCTTTTGTGCTTCTACT
1 AGAGCTTTTACTGTCATTGTTATTATTCTTTGAAAGCTCATTTGTATTTCTTTTGTGCTTATACT
* *
319625 TTCACAAACACCAACCTACTTAGAGATATTTTGAGTTTGTAAAATCTTTTTG
66 TTCACAAACACCAACCTACTTAGAGACATTTCGAGTTTGTAAAATCTTTTTG
* * * *
319677 AGAGCTTTTATTTTTATTGTTATTATTCTTTGAAAGTTCATTTGTATTTCTTTTGTGCTTATACT
1 AGAGCTTTTACTGTCATTGTTATTATTCTTTGAAAGCTCATTTGTATTTCTTTTGTGCTTATACT
** * * *
319742 TTTGCAAACACTAGCCTACTTAGAGGCATTTCGAGTTTGTAAAATCTTTTTG
66 TTCACAAACACCAACCTACTTAGAGACATTTCGAGTTTGTAAAATCTTTTTG
319794 TATTGCAAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 105 1.00
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.48
Consensus pattern (117 bp):
AGAGCTTTTACTGTCATTGTTATTATTCTTTGAAAGCTCATTTGTATTTCTTTTGTGCTTATACT
TTCACAAACACCAACCTACTTAGAGACATTTCGAGTTTGTAAAATCTTTTTG
Found at i:326136 original size:22 final size:22
Alignment explanation
Indices: 326058--326258 Score: 108
Period size: 21 Copynumber: 9.3 Consensus size: 22
326048 TTAAAAATTT
326058 TAATA-TTAATAATATACTAATAA
1 TAATATTTAATAATAT--TAATAA
*
326081 TAAT-TGATAAT-ATACTTAATAA
1 TAATAT-TTAATAATA-TTAATAA
326103 TAA-ATTT-A-AATATTAATAA
1 TAATATTTAATAATATTAATAA
*
326122 TAATATTTAATAATA-TATTAA
1 TAATATTTAATAATATTAATAA
* *
326143 AAATATTTAAATAAAATT-A-AA
1 TAATATTT-AATAATATTAATAA
* * *
326164 TATTTTTTAATAATCTTAATAA
1 TAATATTTAATAATATTAATAA
*
326186 T-ATATTTAA-ATATTTTAATAA
1 TAATATTTAATA-ATATTAATAA
*
326207 TACA-A-TT-ATAATATT-TTAA
1 TA-ATATTTAATAATATTAATAA
326226 TAATATTCTAATAAAATATTTAATAAA
1 TAATATT-TAAT--AATA-TTAAT-AA
326253 TAATAT
1 TAATAT
326259 AAAAGAGTAA
Statistics
Matches: 136, Mismatches: 17, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
18 1 0.01
19 16 0.12
20 22 0.16
21 42 0.31
22 26 0.19
23 9 0.07
24 9 0.07
25 2 0.01
26 1 0.01
27 8 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATTTAATAATATTAATAA
Found at i:326156 original size:32 final size:33
Alignment explanation
Indices: 326058--326258 Score: 116
Period size: 32 Copynumber: 6.2 Consensus size: 33
326048 TTAAAAATTT
* * *
326058 TAATA-TTAATAATATACTAATAATAATTGATAA
1 TAATATTTAATAATATATTAAAAAT-ATTAATAA
* * *
326091 T-ATACTTAATAATAAATT-TAAATATTAATAA
1 TAATATTTAATAATATATTAAAAATATTAATAA
*
326122 TAATATTTAATAATATATTAAAAATATTTA-AA
1 TAATATTTAATAATATATTAAAAATATTAATAA
* * * * * *
326154 TAAAATTAAAT-ATTTTTTAATAATCTTAATAA
1 TAATATTTAATAATATATTAAAAATATTAATAA
* * * *
326186 T-ATATTT-A-AATATTTTAATAATA-CAATTA
1 TAATATTTAATAATATATTAAAAATATTAATAA
326215 TAATATTTTAATAATAT-TCTAATAAAATATTTAATAAA
1 TAATA-TTTAATAATATAT-T-A-AAAATA-TTAAT-AA
326253 TAATAT
1 TAATAT
326259 AAAAGAGTAA
Statistics
Matches: 128, Mismatches: 25, Indels: 26
0.72 0.14 0.15
Matches are distributed among these distances:
29 5 0.04
30 16 0.12
31 28 0.22
32 37 0.29
33 26 0.20
34 1 0.01
35 5 0.04
37 4 0.03
38 6 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (33 bp):
TAATATTTAATAATATATTAAAAATATTAATAA
Found at i:326156 original size:51 final size:53
Alignment explanation
Indices: 326052--326254 Score: 154
Period size: 52 Copynumber: 3.8 Consensus size: 53
326042 TAGTATTTAA
* * * *
326052 AAATTTTAATATTAATAAT-ATA-CTAATAATA-ATTGATAATATACTTAATAAT
1 AAATTTAAATATTAATAATAATATTTAATAATATATT-A-AAAATACTTTATAAT
326104 AAATTTAAATATTAATAATAATATTTAATAATATATTAAAAATA-TTTA-AAT
1 AAATTTAAATATTAATAATAATATTTAATAATATATTAAAAATACTTTATAAT
* ** * * *
326155 AAAATTAAATATTTTTTAATAAT-CTTAATAATATATT-TAAATATTTTAATAAT
1 AAATTTAAATA-TTAATAATAATATTTAATAATATATTAAAAATACTTT-ATAAT
* *
326208 ACAA-TTATAATATT-TTAATAATATTCTAATAAAATATTTAATAAATA
1 A-AATTTA-AATATTAATAATAATATT-TAATAATATA-TTAA-AAATA
326255 ATATAAAAGA
Statistics
Matches: 125, Mismatches: 12, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
50 5 0.04
51 29 0.23
52 39 0.31
53 18 0.14
54 24 0.19
55 5 0.04
57 5 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (53 bp):
AAATTTAAATATTAATAATAATATTTAATAATATATTAAAAATACTTTATAAT
Found at i:326253 original size:11 final size:11
Alignment explanation
Indices: 326109--326254 Score: 64
Period size: 11 Copynumber: 13.5 Consensus size: 11
326099 ATAATAAATT
326109 TAAATA-TTAA
1 TAAATATTTAA
326119 TAATAATATTTAA
1 T-A-AATATTTAA
326132 T-AATATATTAA
1 TAAATAT-TTAA
326143 -AAATATTTAAA
1 TAAATATTT-AA
*
326154 TAAA-ATTAAA
1 TAAATATTTAA
* *
326164 T-ATTTTTTAA
1 TAAATATTTAA
*
326174 T-AAT-CTTAA
1 TAAATATTTAA
326183 TAATATATTTAA
1 TAA-ATATTTAA
*
326195 -ATAT-TTTAA
1 TAAATATTTAA
* *
326204 TAATACAATT-A
1 TAA-ATATTTAA
326215 T-AATATTTTAA
1 TAAATA-TTTAA
326226 T-AATATTCTAA
1 TAAATATT-TAA
326237 TAAAATATTTAA
1 T-AAATATTTAA
326249 TAAATA
1 TAAATA
326255 ATATAAAAGA
Statistics
Matches: 104, Mismatches: 13, Indels: 37
0.68 0.08 0.24
Matches are distributed among these distances:
9 13 0.12
10 27 0.26
11 36 0.35
12 17 0.16
13 11 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAATATTTAA
Found at i:327773 original size:19 final size:20
Alignment explanation
Indices: 327751--327800 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
327741 AGAAAACTGG
327751 AAAAAAAAAG-GAAAAAACA
1 AAAAAAAAAGAGAAAAAACA
*
327770 AAAAAAAAAGAGAAAAAAGA
1 AAAAAAAAAGAGAAAAAACA
*
327790 ATAAAAAAAGA
1 AAAAAAAAAGA
327801 AAGAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAAAACA
Found at i:327774 original size:20 final size:21
Alignment explanation
Indices: 327751--327808 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 21
327741 AGAAAACTGG
327751 AAAAAAAAAG-GAAAAAACA-
1 AAAAAAAAAGAGAAAAAACAT
*
327770 AAAAAAAAAGAGAAAAAAGAAT
1 AAAAAAAAAGAGAAAAAA-CAT
327792 AAAAAAAGAAAGAGAAA
1 -AAAAAA-AAAGAGAAA
327809 GAGGAGTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 10 0.30
20 7 0.21
21 1 0.03
23 6 0.18
24 9 0.27
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAGAAAAAACAT
Found at i:328423 original size:21 final size:21
Alignment explanation
Indices: 328398--328458 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 21
328388 AGAAAACTGG
*
328398 AAAAAAAAAAAGGGAAAAAAC
1 AAAAAAAAAAAGAGAAAAAAC
*
328419 -AAAAAAAAAAGAGAAAAAAGA
1 AAAAAAAAAAAGAGAAAAAA-C
328440 ATAAAAAAAGAAAGAGAAA
1 A-AAAAAAA-AAAGAGAAA
328459 GAGGAGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 18 0.53
23 7 0.21
24 9 0.26
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAGAGAAAAAAC
Found at i:328424 original size:20 final size:20
Alignment explanation
Indices: 328399--328450 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
328389 GAAAACTGGA
*
328399 AAAAAAAAAAGGGAAAAAAC
1 AAAAAAAAAAGAGAAAAAAC
*
328419 AAAAAAAAAAGAGAAAAAAG
1 AAAAAAAAAAGAGAAAAAAC
*
328439 AATAAAAAAAGA
1 AAAAAAAAAAGA
328451 AAGAGAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAGAGAAAAAAC
Found at i:331469 original size:42 final size:42
Alignment explanation
Indices: 331421--331503 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
331411 CATCCAAAGA
*
331421 ATGTTTGATAAATTTTAACTCTATCTACAAAACTTGTCATTG
1 ATGTTTGAAAAATTTTAACTCTATCTACAAAACTTGTCATTG
*
331463 ATGTTTGAAAAATTTTAACTGTATCTACAAAACTTGTCATT
1 ATGTTTGAAAAATTTTAACTCTATCTACAAAACTTGTCATT
331504 ACTTATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (42 bp):
ATGTTTGAAAAATTTTAACTCTATCTACAAAACTTGTCATTG
Found at i:337093 original size:13 final size:13
Alignment explanation
Indices: 337077--337106 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
337067 ATACATTGTT
*
337077 CATTGTATTGATA
1 CATTGTATCGATA
337090 CATTGTATCGATA
1 CATTGTATCGATA
337103 CATT
1 CATT
337107 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:337147 original size:20 final size:20
Alignment explanation
Indices: 337122--337229 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
337112 TTTACCCAGA
*
337122 TGTATCGATACATTTTACAT
1 TGTATCGATACATTCTACAT
337142 TGTATCGATACATTGCT-CAT
1 TGTATCGATACATT-CTACAT
337162 TGTATC---A-A---TACAT
1 TGTATCGATACATTCTACAT
*
337175 TATATCGATACATTGCT-CAT
1 TGTATCGATACATT-CTACAT
* * * *
337195 TGTATCAACACATTTTACAA
1 TGTATCGATACATTCTACAT
337215 TGTATCGATACATTC
1 TGTATCGATACATTC
337230 AAGCATTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
12 1 0.01
13 8 0.12
16 2 0.03
17 2 0.03
19 1 0.01
20 51 0.76
21 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCTACAT
Found at i:337175 original size:33 final size:33
Alignment explanation
Indices: 337137--337208 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
337127 CGATACATTT
*
337137 TACATTGTATCGATACATTGCTCATTGTATCAA
1 TACATTATATCGATACATTGCTCATTGTATCAA
337170 TACATTATATCGATACATTGCTCATTGTATCAA
1 TACATTATATCGATACATTGCTCATTGTATCAA
*
337203 CACATT
1 TACATT
337209 TTACAATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (33 bp):
TACATTATATCGATACATTGCTCATTGTATCAA
Found at i:339777 original size:51 final size:51
Alignment explanation
Indices: 339717--339835 Score: 186
Period size: 51 Copynumber: 2.3 Consensus size: 51
339707 TATTTCCGAA
* *
339717 GGGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
* *
339768 GGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCAATTTTTCATAATTG
1 GGGATACTCCAACCT-CGATTTTATTTCCAAAACACCAATTTTTCACAATCG
339819 GGGATACTCCAACCTCG
1 GGGATACTCCAACCTCG
339836 TTATTTCTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
50 2 0.03
51 58 0.94
52 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
Found at i:339965 original size:79 final size:78
Alignment explanation
Indices: 339767--340072 Score: 314
Period size: 79 Copynumber: 3.9 Consensus size: 78
339757 TTTCACAATC
* *
339767 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTT-CAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
* *
339832 CTCGTTA-TTTCTAA
65 CCCGTTATTTTC-GA
* ** * * * *
339846 GGGGATACTTCAACCCC-AGCCTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGA-TTTTATTTC-AAAACACCAATTTTTCATAATCGGGGATACTCCAA
339910 CCCCGTTATTTTCGA
64 CCCCGTTATTTTCGA
* * * ** *
339925 GGGGATACTCCAACCCCGATTTCATTTTCAAAATACCGATTTTT-ATAATTAGGGATACTTCAAC
1 GGGGATACTCCAACCCCGATTTTA-TTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
339989 CCTGTTATTTTCGA
65 CCCGTTATTTTCGA
* ** * * *
340003 -GGGATACTCCAACCTCGATTTTATTTCTGGAACACCAATTTTCCATAATCGGGGATACTCTAGC
1 GGGGATACTCCAACCCCGATTTTATTTC-AAAACACCAATTTTTCATAATCGGGGATACTCCAAC
340067 CCCGTT
65 CCCGTT
340073 GTTATCTCCA
Statistics
Matches: 184, Mismatches: 36, Indels: 15
0.78 0.15 0.06
Matches are distributed among these distances:
76 4 0.02
77 31 0.17
78 51 0.28
79 89 0.48
80 9 0.05
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:344047 original size:13 final size:13
Alignment explanation
Indices: 344029--344055 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
344019 ACATTATGCT
344029 TTGTATCGATACA
1 TTGTATCGATACA
344042 TTGTATCGATACA
1 TTGTATCGATACA
344055 T
1 T
344056 GTTCATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:350354 original size:20 final size:20
Alignment explanation
Indices: 350316--350355 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
350306 TTACAAATTT
350316 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
350337 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
350356 TATTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:352724 original size:13 final size:13
Alignment explanation
Indices: 352706--352732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
352696 ACATTATGCT
352706 TTGTATCGATACA
1 TTGTATCGATACA
352719 TTGTATCGATACA
1 TTGTATCGATACA
352732 T
1 T
352733 GTTCATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:352745 original size:19 final size:20
Alignment explanation
Indices: 352721--352772 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
352711 TCGATACATT
**
352721 GTATCGATACATGTTC-ATA
1 GTATCGATACATGGACAATA
*
352740 GTATCGATACATGGACAATT
1 GTATCGATACATGGACAATA
352760 GTATCGATACATG
1 GTATCGATACATG
352773 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGGACAATA
Found at i:352765 original size:20 final size:19
Alignment explanation
Indices: 352716--352772 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
352706 TTGTATCGAT
*
352716 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
352735 TCATAGTATCGATACATGG
1 ACATTGTATCGATACATGG
352754 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
352773 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:358072 original size:3 final size:3
Alignment explanation
Indices: 358064--358089 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
358054 CTTTTTCTCA
358064 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
358090 AACCTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:358272 original size:2 final size:2
Alignment explanation
Indices: 358267--358304 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
358257 CTTTATTTAC
358267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
358305 GTTGTAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:358780 original size:33 final size:33
Alignment explanation
Indices: 358707--358780 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
358697 CAACATTTTA
* ** * *
358707 AAAATAGTATTTATTATTAATACTATTAAATTG
1 AAAATAATATTTATTATTAATAAAATTAAAATC
* *
358740 AAGATAATATTTATTTTTAATAAAATTAAAATC
1 AAAATAATATTTATTATTAATAAAATTAAAATC
358773 AAAATAAT
1 AAAATAAT
358781 GAAATTTTCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (33 bp):
AAAATAATATTTATTATTAATAAAATTAAAATC
Found at i:366856 original size:13 final size:13
Alignment explanation
Indices: 366838--366863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
366828 TTTAGTTCGA
366838 ATTTTATTTTTTT
1 ATTTTATTTTTTT
366851 ATTTTATTTTTTT
1 ATTTTATTTTTTT
366864 GAGTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTATTTTTTT
Found at i:369965 original size:2 final size:2
Alignment explanation
Indices: 369960--370002 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
369950 TTTTTAAAAT
369960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
370002 T
1 T
370003 TAATATAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:374588 original size:2 final size:2
Alignment explanation
Indices: 374581--374621 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
374571 TCTAAAATGT
374581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
374622 TTTAAGGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:374977 original size:19 final size:19
Alignment explanation
Indices: 374948--374996 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
374938 TAAACATAAT
374948 TTATTAAAAAAATATT-TA
1 TTATTAAAAAAATATTATA
* *
374966 TTCTTAAAAAAATTTTATA
1 TTATTAAAAAAATATTATA
374985 TTATTAAAAAAA
1 TTATTAAAAAAA
374997 AGTTTCCTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATTAAAAAAATATTATA
Found at i:375012 original size:2 final size:2
Alignment explanation
Indices: 375007--375036 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
374997 AGTTTCCTAC
*
375007 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375037 AAACTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:391614 original size:58 final size:58
Alignment explanation
Indices: 391532--391816 Score: 283
Period size: 58 Copynumber: 4.9 Consensus size: 58
391522 ATAAAATTAT
* * * * * **
391532 CCTAAATCATGAAAAATGATTTAAATGACCTTAAAATGTATGAAATTGCATAATGAAC
1 CCTAAATCATGGAAAATAACTTAAATGACCTTAAAATGCATGAAATTGCAAAATGGTC
** * * * *
391590 TTTCAATCATGGAAAATAACTTAAATGACCTTAAAATGTATTAAATTG-AGAAATGGCC
1 CCTAAATCATGGAAAATAACTTAAATGACCTTAAAATGCATGAAATTGCA-AAATGGTC
* *
391648 CCTAAATCATAGAAGAA-AACTTAAATGACCTT-AAATGCATGAAATTACAAAATGGTC
1 CCTAAATCATGGAA-AATAACTTAAATGACCTTAAAATGCATGAAATTGCAAAATGGTC
* * *
391705 CCTAAATCA-GAGAAAATGACTTAAATGACCCTAAAATGCATGAAATTGCATAATGGTC
1 CCTAAATCATG-GAAAATAACTTAAATGACCTTAAAATGCATGAAATTGCAAAATGGTC
* * * * * *
391763 CTTAAATCATGAAAAATTACTTTAATAATCC-TAAAATGCATGAAATTACAAAAT
1 CCTAAATCATGGAAAATAACTTAAATGA-CCTTAAAATGCATGAAATTGCAAAAT
391817 AAATCCTAAA
Statistics
Matches: 189, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
56 2 0.01
57 45 0.24
58 137 0.72
59 5 0.03
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (58 bp):
CCTAAATCATGGAAAATAACTTAAATGACCTTAAAATGCATGAAATTGCAAAATGGTC
Found at i:391740 original size:115 final size:114
Alignment explanation
Indices: 391532--391826 Score: 308
Period size: 115 Copynumber: 2.5 Consensus size: 114
391522 ATAAAATTAT
* * * * ** *
391532 CCTAAATCATGAAAAATGATTTAAATGACCTTAAAATGTATGAAATTGCATAATGAACTTTCAAT
1 CCTAAATCATGAAAAAT-ACTTAAATGACCTT-AAATGCATGAAATTACAAAATGAACCCTAAAT
* * *
391597 CATGGAAAATAACTTAAATGACCTTAAAATGTATTAAATTG-AGAAATGGCC
64 CATGGAAAATAACTTAAATGACCCTAAAATGCATGAAATTGCA-AAATGGCC
**
391648 CCTAAATCATAGAAGAAA-ACTTAAATGACCTTAAATGCATGAAATTACAAAATGGTCCCTAAAT
1 CCTAAATCAT-GAA-AAATACTTAAATGACCTTAAATGCATGAAATTACAAAATGAACCCTAAAT
* * *
391712 CA-GAGAAAATGACTTAAATGACCCTAAAATGCATGAAATTGCATAATGGTC
64 CATG-GAAAATAACTTAAATGACCCTAAAATGCATGAAATTGCAAAATGGCC
* * * * * *
391763 CTTAAATCATGAAAAATTACTTTAATAATCCTAAAATGCATGAAATTACAAAATAAATCCTAAA
1 CCTAAATCATGAAAAA-TACTTAAATGA-CCTTAAATGCATGAAATTACAAAATGAACCCTAAA
391827 AGCTTCAAAC
Statistics
Matches: 149, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
113 3 0.02
114 4 0.03
115 82 0.55
116 54 0.36
117 3 0.02
118 3 0.02
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (114 bp):
CCTAAATCATGAAAAATACTTAAATGACCTTAAATGCATGAAATTACAAAATGAACCCTAAATCA
TGGAAAATAACTTAAATGACCCTAAAATGCATGAAATTGCAAAATGGCC
Found at i:391808 original size:29 final size:28
Alignment explanation
Indices: 391734--391827 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
391724 CTTAAATGAC
* **
391734 CCTAAAATGCATGAAATTGCATAATGGT
1 CCTAAAATGCATGAAATTACATAATAAT
* *
391762 CCTTAAAT-CATGAAAAATTACTTTAATAAT
1 CCTAAAATGCATG--AAATTAC-ATAATAAT
*
391792 CCTAAAATGCATGAAATTACAAAATAAAT
1 CCTAAAATGCATGAAATTACATAAT-AAT
391821 CCTAAAA
1 CCTAAAA
391828 GCTTCAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
27 4 0.08
28 10 0.19
29 23 0.43
30 12 0.23
31 4 0.08
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.29
Consensus pattern (28 bp):
CCTAAAATGCATGAAATTACATAATAAT
Found at i:392330 original size:11 final size:10
Alignment explanation
Indices: 392310--392367 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
392300 AAAAACATTA
392310 TTTTTTCCTT
1 TTTTTTCCTT
*
392320 TTTTTTCCCT
1 TTTTTTCCTT
*
392330 TTTTTTCTTGT
1 TTTTTTCCT-T
*
392341 TTTTTTTCTT
1 TTTTTTCCTT
392351 TTTTTTACCTT
1 TTTTTT-CCTT
392362 ATTTTT
1 -TTTTT
392368 GCTACTACCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 23 0.59
11 11 0.28
12 5 0.13
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:396578 original size:12 final size:12
Alignment explanation
Indices: 396558--396586 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
396548 TAAATCTAAG
396558 TTTTT-CTTTTA
1 TTTTTCCTTTTA
396569 TTTTTCCTTTTA
1 TTTTTCCTTTTA
396581 TTTTTC
1 TTTTTC
396587 AAGAGACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCCTTTTA
Found at i:399762 original size:18 final size:18
Alignment explanation
Indices: 399740--399781 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
399730 AGGAAACTAG
399740 AAAAGAAAAAGAAAA-AA
1 AAAAGAAAAAGAAAAGAA
*
399757 AGAAAGAAAAATAAAAGAA
1 A-AAAGAAAAAGAAAAGAA
399776 AAAAGA
1 AAAAGA
399782 GAGTTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGAA
Found at i:399779 original size:12 final size:11
Alignment explanation
Indices: 399738--399779 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
399728 AAAGGAAACT
*
399738 AGAAAAGAAAA
1 AGAAAAAAAAA
399749 AGAAAAAAAGAA
1 AGAAAAAAA-AA
*
399761 AGAAAAATAAA
1 AGAAAAAAAAA
399772 AGAAAAAA
1 AGAAAAAA
399780 GAGAGTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:400616 original size:58 final size:57
Alignment explanation
Indices: 400529--400726 Score: 168
Period size: 58 Copynumber: 3.4 Consensus size: 57
400519 ATTATGCATA
* * * * * * * *
400529 ATTATGCCATTTCACGTATTTTAAAGTCATAT-GAATTATTTTCCATGCTTTAAAGACT
1 ATTATGTCATTTCATGCATTTTAAGGTCAT-TCGAATAATTTGCCATGATTTAAA-ACC
* * *
400587 ATTATGTCATTTCATGCATCTTAAGGTCATTCTAGTAATTTGCCATGATTTAAAACC
1 ATTATGTCATTTCATGCATTTTAAGGTCATTCGAATAATTTGCCATGATTTAAAACC
* * * * *
400644 ATTTTGTCATTTCATGCCTTTTAAGGTCATTC-AACTAATTTGTCATGTTTTAAGGA-C
1 ATTATGTCATTTCATGCATTTTAAGGTCATTCGAA-TAATTTGCCATGATTTAA-AACC
* *
400701 ATTTATGTAATCTCATGCATTTTAAG
1 A-TTATGTCATTTCATGCATTTTAAG
400727 ACCATTTTAG
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
56 1 0.01
57 50 0.44
58 63 0.55
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (57 bp):
ATTATGTCATTTCATGCATTTTAAGGTCATTCGAATAATTTGCCATGATTTAAAACC
Found at i:400668 original size:57 final size:58
Alignment explanation
Indices: 400566--400726 Score: 173
Period size: 57 Copynumber: 2.8 Consensus size: 58
400556 CATATGAATT
* * * * *
400566 ATTTTCCATGCTTTAAAGACTATTATGTCATTTCATGCATCTTAAGGTCATTCTAGTA
1 ATTTGCCATGATTTAAAGACCATTATGTCATTTCATGCATCTTAAGGTCATTCAACTA
* * *
400624 ATTTGCCATGATTTAAA-ACCATTTTGTCATTTCATGCCTTTTAAGGTCATTCAACTA
1 ATTTGCCATGATTTAAAGACCATTATGTCATTTCATGCATCTTAAGGTCATTCAACTA
* * * * * *
400681 ATTTGTCATGTTTTAAGGA-CATTTATGTAATCTCATGCATTTTAAG
1 ATTTGCCATGATTTAAAGACCA-TTATGTCATTTCATGCATCTTAAG
400727 ACCATTTTAG
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
57 50 0.58
58 36 0.42
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (58 bp):
ATTTGCCATGATTTAAAGACCATTATGTCATTTCATGCATCTTAAGGTCATTCAACTA
Found at i:401279 original size:76 final size:76
Alignment explanation
Indices: 401183--401393 Score: 214
Period size: 76 Copynumber: 2.8 Consensus size: 76
401173 GTAAAAGTAT
* * * * *
401183 CTTAAAATTGAGTTTAGGATCATT-T-AAAGACCTTCGTGTCGAAACATATTCATTAGGGTTATT
1 CTTAAAATCGAGTCTAGGATC-TTGTGAAA-ACCTTCATGTCAAAACATATCCATTAGGGTTATT
*
401246 TTGGTAATAGCAA
64 TCGGTAATAGCAA
* *
401259 CTTAAGATCGAGTCTAGGATCTTGTGAAAACCTTCATGTCAAAACATGTCCATTAGGGTTATTTC
1 CTTAAAATCGAGTCTAGGATCTTGTGAAAACCTTCATGTCAAAACATATCCATTAGGGTTATTTC
*
401324 GGTAATAGCAC
66 GGTAATAGCAA
* * * * * * *
401335 CTTAAAAAT-AATTCTAGGAT-TATGTGAGAACTTTTATGTCAATACATATCTATTAGGGT
1 CTT-AAAATCGAGTCTAGGATCT-TGTGAAAACCTTCATGTCAAAACATATCCATTAGGGT
401394 CGTATAGGAA
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
75 3 0.03
76 103 0.91
77 7 0.06
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (76 bp):
CTTAAAATCGAGTCTAGGATCTTGTGAAAACCTTCATGTCAAAACATATCCATTAGGGTTATTTC
GGTAATAGCAA
Found at i:402918 original size:20 final size:21
Alignment explanation
Indices: 402874--402919 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
402864 TTCAACAAAT
*
402874 TGTATTGATACAATAGGGTAA
1 TGTATTGATACAATAGAGTAA
402895 TGTATTGATAC-ATA-AGTAAA
1 TGTATTGATACAATAGAGT-AA
402915 TGTAT
1 TGTAT
402920 CAATACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 11 0.48
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (21 bp):
TGTATTGATACAATAGAGTAA
Found at i:405576 original size:96 final size:97
Alignment explanation
Indices: 405430--405634 Score: 272
Period size: 96 Copynumber: 2.1 Consensus size: 97
405420 TATCCATTGG
* *
405430 GGATACTCTAACCCCATTCTTCCGAGGAAATACTCCAACCCTACTTTTAAACTCCTCAAGATTTA
1 GGATACTCCAACCCAATTCTTCCGAGGAAATACTCCAACCCTACTTTTAAACTCCTCAAGATTTA
405495 AATATTATTTTT-CTCAAATTATCATCGTCGA
66 AATATTATTTTTGCTCAAATTATCATCGTCGA
* * * * *
405526 GGATACTCCAACCTAATTCTTCCGAAGG-GATACTTCAA-CCTCGCTTTTAAACTCGTCAAGATT
1 GGATACTCCAACCCAATTCTTCCG-AGGAAATACTCCAACCCT-ACTTTTAAACTCCTCAAGATT
* * *
405589 TAAATTTTATTTTTGCTTAAATTATCATCGTCGG
64 TAAATATTATTTTTGCTCAAATTATCATCGTCGA
*
405623 GGATATTCCAAC
1 GGATACTCCAAC
405635 TTCATTCCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
95 3 0.03
96 61 0.64
97 31 0.33
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (97 bp):
GGATACTCCAACCCAATTCTTCCGAGGAAATACTCCAACCCTACTTTTAAACTCCTCAAGATTTA
AATATTATTTTTGCTCAAATTATCATCGTCGA
Found at i:412721 original size:97 final size:97
Alignment explanation
Indices: 412555--412784 Score: 289
Period size: 97 Copynumber: 2.4 Consensus size: 97
412545 AGCCAAGCTG
* * * ** * ** *
412555 GAGTATCCCCTTAGAGGAATGGGGTTAGAGTGTCCCCGATGATGACAATTTAGGTTAAAATAATA
1 GAGTATCCCCTTAGAAGAATGGGGTTGGAGTATCCCAAATGATGACAATTTAAGAAAAAATAAGA
* * *
412620 TTTAAATCTTGACAAGTTTAAAAATGGGGTTA
66 TTTAAATCTTAACAAGTTTAAAAACGAGGTTA
* * *
412652 GAGTATCCCCTTAGAAGAATGAGGTTGGAGTATCCCAAATGATGATAATTTAAGAAAAAATTAGA
1 GAGTATCCCCTTAGAAGAATGGGGTTGGAGTATCCCAAATGATGACAATTTAAGAAAAAATAAGA
* *
412717 TTTAAATCTTAACGAGTTTAAAAACGAGGTTG
66 TTTAAATCTTAACAAGTTTAAAAACGAGGTTA
* *
412749 GAGTATCCTCTCAGAAGAATGGGGTTGGAGTATCCC
1 GAGTATCCCCTTAGAAGAATGGGGTTGGAGTATCCC
412785 CGTGAATAAA
Statistics
Matches: 113, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
97 113 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (97 bp):
GAGTATCCCCTTAGAAGAATGGGGTTGGAGTATCCCAAATGATGACAATTTAAGAAAAAATAAGA
TTTAAATCTTAACAAGTTTAAAAACGAGGTTA
Found at i:415908 original size:21 final size:19
Alignment explanation
Indices: 415884--415929 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
415874 TGATGTATTG
415884 ATACCTTTTACTTAGGTATCA
1 ATACCTTTTACTT--GTATCA
*
415905 ATACCCTTTTTCTTGTATCA
1 ATA-CCTTTTACTTGTATCA
415925 ATACC
1 ATACC
415930 AACCTCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.09
20 9 0.39
21 3 0.13
22 9 0.39
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (19 bp):
ATACCTTTTACTTGTATCA
Found at i:416635 original size:22 final size:21
Alignment explanation
Indices: 416603--416651 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
416593 CCTAACTTTC
*
416603 ATTTTCAATTTATTTATTTAA
1 ATTTTCAATTTATGTATTTAA
*
416624 ATTTCTCAATTTGTGTATTTAA
1 ATTT-TCAATTTATGTATTTAA
416646 AGTTTT
1 A-TTTT
416652 TATTTGCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 17 0.71
23 3 0.12
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (21 bp):
ATTTTCAATTTATGTATTTAA
Found at i:417242 original size:17 final size:17
Alignment explanation
Indices: 417220--417255 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
417210 CCCAAGTTCG
*
417220 AAAAAATCC-AAACTTA
1 AAAAAAACCTAAACTTA
417236 AAAAAAACCTAAACTTA
1 AAAAAAACCTAAACTTA
417253 AAA
1 AAA
417256 TCCGAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAAACCTAAACTTA
Found at i:417334 original size:6 final size:6
Alignment explanation
Indices: 417323--417348 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
417313 TGTAAAGGCT
417323 AAACCC AAACCC AAACCC AAACCC AA
1 AAACCC AAACCC AAACCC AAACCC AA
417349 GATCAATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:417967 original size:16 final size:16
Alignment explanation
Indices: 417937--417969 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
417927 CTTGTAAATC
417937 AAAATATAAAGATTAA
1 AAAATATAAAGATTAA
417953 AAAATTATAAA-ATTAA
1 AAAA-TATAAAGATTAA
417969 A
1 A
417970 TTAAACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATATAAAGATTAA
Found at i:419517 original size:16 final size:16
Alignment explanation
Indices: 419493--419566 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
419483 AATCAATTTA
*
419493 AATTCAAAACAATTAAT
1 AATT-AAAATAATTAAT
*
419510 AATTAAAATAATT-TT
1 AATTAAAATAATTAAT
419525 AATTTAAAATAATTTAA-
1 AA-TTAAAATAA-TTAAT
*
419542 ATTTAAAA-AATTAAAT
1 AATTAAAATAATT-AAT
*
419558 AATTTAAAT
1 AATTAAAAT
419567 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.04
15 7 0.16
16 29 0.64
17 7 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAAATAATTAAT
Found at i:419527 original size:15 final size:16
Alignment explanation
Indices: 419512--419553 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
419502 CAATTAATAA
419512 TTAAAATAATTTTAAT
1 TTAAAATAATTTTAAT
*
419528 TTAAAATAATTTAAAT
1 TTAAAATAATTTTAAT
419544 TTAAAA-AATT
1 TTAAAATAATT
419554 AAATAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATAATTTTAAT
Done.