Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 15 of 187
Found at i:5312077 original size:2 final size:2
Alignment explanation
Indices: 5312072--5312098 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5312062 CATATATACG
5312072 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5312099 TTCAACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5334772 original size:14 final size:14
Alignment explanation
Indices: 5334741--5334779 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5334731 TTGTTTCACT
*
5334741 GAAAATGGTTTTCA
1 GAAAATGATTTTCA
**
5334755 GAAAATGATTTTTG
1 GAAAATGATTTTCA
5334769 GAAAATGATTT
1 GAAAATGATTT
5334780 ACTTTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (14 bp):
GAAAATGATTTTCA
Found at i:5344038 original size:17 final size:17
Alignment explanation
Indices: 5344016--5344048 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5344006 TTTTAATTAG
5344016 TGAATTTTGTGATTTAT
1 TGAATTTTGTGATTTAT
5344033 TGAATTTTGTGATTTA
1 TGAATTTTGTGATTTA
5344049 AAAAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (17 bp):
TGAATTTTGTGATTTAT
Found at i:5363751 original size:16 final size:17
Alignment explanation
Indices: 5363707--5363756 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
5363697 TTGAATTTTT
5363707 TTTAAAAAATCATATAAA-A
1 TTTAAAAAAT-A-A-AAATA
5363726 TTTAAAAAATAAAAATA
1 TTTAAAAAATAAAAATA
5363743 TTTAAAAATATAAA
1 TTTAAAAA-ATAAA
5363757 TAAATTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.10
17 10 0.34
18 6 0.21
19 10 0.34
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTAAAAAATAAAAATA
Found at i:5363757 original size:16 final size:17
Alignment explanation
Indices: 5363707--5363758 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
5363697 TTGAATTTTT
*
5363707 TTTAAAAAATCATATAAAA
1 TTTAAAAAAT-ATA-AATA
*
5363726 TTTAAAAAATAAAAATA
1 TTTAAAAAATATAAATA
5363743 TTT-AAAAATATAAATA
1 TTTAAAAAATATAAATA
5363759 AATTATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 12 0.40
17 6 0.20
18 2 0.07
19 10 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTAAAAAATATAAATA
Found at i:5364378 original size:21 final size:22
Alignment explanation
Indices: 5364354--5364394 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5364344 CCTATGAATT
* *
5364354 AAAAAATAACATC-AATTTATA
1 AAAAAAAAAAATCAAATTTATA
5364375 AAAAAAAAAAATCAAATTTA
1 AAAAAAAAAAATCAAATTTA
5364395 CAATATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAAAAAAATCAAATTTATA
Found at i:5365652 original size:2 final size:2
Alignment explanation
Indices: 5365645--5365680 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5365635 TTTCAAATCC
5365645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5365681 AGTTGAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5373665 original size:13 final size:14
Alignment explanation
Indices: 5373632--5373665 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5373622 TGGAGATATC
5373632 TAAACTTGGTAACT
1 TAAACTTGGTAACT
*
5373646 TATACTTGGT-ACT
1 TAAACTTGGTAACT
5373659 TAAACTT
1 TAAACTT
5373666 TTTCTTCGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (14 bp):
TAAACTTGGTAACT
Found at i:5373856 original size:12 final size:11
Alignment explanation
Indices: 5373827--5373858 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
5373817 GGAAAAAAGT
5373827 TAAAATATTTA
1 TAAAATATTTA
5373838 TAAAATATTTA
1 TAAAATATTTA
5373849 TAAAAATATT
1 T-AAAATATT
5373859 CTATGTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAAATATTTA
Found at i:5385211 original size:78 final size:79
Alignment explanation
Indices: 5385011--5385233 Score: 272
Period size: 78 Copynumber: 2.8 Consensus size: 79
5385001 TGGTTTTTTG
* * *
5385011 TATAGTGGAGTCGGAAAATGATGCAAGTCCCATATTGGTTAGGAAGGGTAAAGAGGTATTGGAAT
1 TATAGTGGAGTCGGAAAACGATGCGAGTCCCATATTGGTTAGGAAGGGCAAAGAGGTATTGGAAT
*
5385076 TTATATCTTCTACA
66 ATATATCTTCTACA
* * * * * * *
5385090 TACAATGGAGTCGGAAAACGATTGTGAGTTCCATATTGATTAGGGAGGGCAAAGAGGTCTTGGTC
1 TATAGTGGAGTCGGAAAACGA-TGCGAGTCCCATATTGGTTAGGAAGGGCAAAGAGGTATTGG--
*
5385155 AATATGT-TCTT-TA-A
63 AATATATATCTTCTACA
* *
5385169 TATAGTAGAGTTGGAAAACGATGCGAGTCCCATATTGGTTAGGAAGGGCAAAGAGGTATTGGAAT
1 TATAGTGGAGTCGGAAAACGATGCGAGTCCCATATTGGTTAGGAAGGGCAAAGAGGTATTGGAAT
5385234 TGATAAGGGA
Statistics
Matches: 120, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
76 3 0.03
78 36 0.30
79 36 0.30
80 36 0.30
81 4 0.03
82 5 0.04
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (79 bp):
TATAGTGGAGTCGGAAAACGATGCGAGTCCCATATTGGTTAGGAAGGGCAAAGAGGTATTGGAAT
ATATATCTTCTACA
Found at i:5385247 original size:26 final size:26
Alignment explanation
Indices: 5385212--5385264 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5385202 ATTGGTTAGG
*
5385212 AAGGGCAAAGAGGTATTGGAATTGAT
1 AAGGGAAAAGAGGTATTGGAATTGAT
5385238 AAGGGAAAAGAGGTATTGGAATTGAT
1 AAGGGAAAAGAGGTATTGGAATTGAT
5385264 A
1 A
5385265 TGTTTGAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.34, T:0.23
Consensus pattern (26 bp):
AAGGGAAAAGAGGTATTGGAATTGAT
Found at i:5388173 original size:78 final size:79
Alignment explanation
Indices: 5388044--5388267 Score: 262
Period size: 78 Copynumber: 2.9 Consensus size: 79
5388034 GATATGTTCT
* *
5388044 ATGGAGTC-AGAAAACGATGTGAGTTCCATATTGATTAGGAAGGGAAAAGAGGTCTTGGTTGAAA
1 ATGGAGTCGA-AAAACGATGTGAGTTCCATATTGATTAGGAAGGGCAAAGAGGTCTTGGTTGATA
*
5388108 TGTTTTTTA-ATACA
65 TGTTTTCTACATACA
* * * * *
5388122 ATGGAGTCGAAAAATGATGCGAG-TCTCATATTGGTTAGGAAGGGCAAAGAGGTATTGGAATTTA
1 ATGGAGTCGAAAAACGATGTGAGTTC-CATATTGATTAGGAAGGGCAAAGAGGTCTTGG--TTGA
*
5388186 TATG--TTCTACATAGA
63 TATGTTTTCTACATACA
* * *
5388201 ATGGAATCGAAAAACGATTTGAGTTCCATATTGATTAGGAA-GGCAAAGAGGCCTTGGTTGATAT
1 ATGGAGTCGAAAAACGATGTGAGTTCCATATTGATTAGGAAGGGCAAAGAGGTCTTGGTTGATAT
5388265 GTT
66 GTT
5388268 CATTGGAGTC
Statistics
Matches: 121, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
76 7 0.06
77 2 0.02
78 66 0.55
79 38 0.31
80 8 0.07
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (79 bp):
ATGGAGTCGAAAAACGATGTGAGTTCCATATTGATTAGGAAGGGCAAAGAGGTCTTGGTTGATAT
GTTTTCTACATACA
Found at i:5388426 original size:146 final size:146
Alignment explanation
Indices: 5388149--5388542 Score: 395
Period size: 146 Copynumber: 2.7 Consensus size: 146
5388139 TGCGAGTCTC
* * ** ** * * * *
5388149 ATATTGGTTAGGAAGGGCAAAGAGGTATTGGAATTTATATGTTCTACATAGAATGGAATCGAAAA
1 ATATTGGTTAGGAAGGACGAAGAGGTATTGGAATAGATATGTTCTATGTATAATAGAGTCAAAAA
* * * * *
5388214 ACGATTTGAGTTC-CATATTGATTAGGAAGGCAAAGAGGCCTTGGTTGATATGTTCATTGGAGTC
66 ATGATGTGA---CAAATATTGATTAGGAAGGCAAAGAGGCCTTAGTTGATATGTTCAATGGAGTC
* **
5388278 GGAAAGCGATGTAAGGT-CT
128 GGAAAGCAACAT-AGGTCCT
* *
5388297 ATATTGGTTTGGAAGTG-CGAAGAGGTATTGGACAT-GATATGTTCTATGT-TCAGTAGAGTCAA
1 ATATTGGTTAGGAAG-GACGAAGAGGTATTGGA-ATAGATATGTTCTATGTAT-AATAGAGTCAA
* * *
5388359 AAAATGATGTGACAAATATTGATTTGGAAGGCAAAGAGGTCTTAGTTGATATGTTTAATGGAGTC
63 AAAATGATGTGACAAATATTGATTAGGAAGGCAAAGAGGCCTTAGTTGATATGTTCAATGGAGTC
*
5388424 GGAAAGCAACATTGGTCCT
128 GGAAAGCAACATAGGTCCT
* *
5388443 ATATTGGTTAGGAAGGACGAAGAGGTCTTGGAATAGATATGTTCTATGTATAATGGAGTCAAAAA
1 ATATTGGTTAGGAAGGACGAAGAGGTATTGGAATAGATATGTTCTATGTATAATAGAGTCAAAAA
* *
5388508 ATTATGTGA-ATTCCATATTGATTAGGAAGGGCAAA
66 ATGATGTGACA---AATATTGATTAGGAA-GGCAAA
5388543 AAGATTTTGG
Statistics
Matches: 205, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
145 8 0.04
146 118 0.58
147 1 0.00
148 69 0.34
149 9 0.04
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (146 bp):
ATATTGGTTAGGAAGGACGAAGAGGTATTGGAATAGATATGTTCTATGTATAATAGAGTCAAAAA
ATGATGTGACAAATATTGATTAGGAAGGCAAAGAGGCCTTAGTTGATATGTTCAATGGAGTCGGA
AAGCAACATAGGTCCT
Found at i:5388553 original size:79 final size:79
Alignment explanation
Indices: 5388443--5388619 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 79
5388433 CATTGGTCCT
* * * * * * *
5388443 ATATTGGTTAGGAAGGACGAAGAGGTCTTGGAA-TAGATATGTTCTATGTATAATGGAGTCAAAA
1 ATATTGATTAGGAAGGACAAAAAGATCTTGGAATTA-ATATGTTCTATGTACAATAGAATCAAAA
*
5388507 AATTATGTGAATTCC
65 AATAATGTGAATTCC
* * * *
5388522 ATATTGATTAGGAAGGGCAAAAAGATTTTGGAATTAATATGTTTTATGTACAATAGAATCGAAAA
1 ATATTGATTAGGAAGGACAAAAAGATCTTGGAATTAATATGTTCTATGTACAATAGAATCAAAAA
* *
5388587 ATAATGTGAGTTTC
66 ATAATGTGAATTCC
5388601 ATATT-ATTAGGAAGGACAA
1 ATATTGATTAGGAAGGACAA
5388620 GAGGTCGATA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
78 13 0.16
79 67 0.82
80 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (79 bp):
ATATTGATTAGGAAGGACAAAAAGATCTTGGAATTAATATGTTCTATGTACAATAGAATCAAAAA
ATAATGTGAATTCC
Found at i:5393783 original size:18 final size:16
Alignment explanation
Indices: 5393762--5393799 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
5393752 TATAAATTAC
5393762 ATAATATATAAAAATATT
1 ATAA-ATAT-AAAATATT
5393780 AT-AATATAAAATATT
1 ATAAATATAAAATATT
5393795 ATAAA
1 ATAAA
5393800 CTTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.53
16 6 0.32
17 1 0.05
18 2 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATATAAAATATT
Found at i:5393792 original size:15 final size:16
Alignment explanation
Indices: 5393767--5393798 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5393757 ATTACATAAT
5393767 ATATAAAAATATTATA
1 ATATAAAAATATTATA
5393783 ATAT-AAAATATTATA
1 ATATAAAAATATTATA
5393798 A
1 A
5393799 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATATTATA
Found at i:5394295 original size:20 final size:21
Alignment explanation
Indices: 5394257--5394296 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5394247 TTATTACACA
* *
5394257 GGTTAGATTTTTTTTTTCTTT
1 GGTTAGATTTGTTTCTTCTTT
5394278 GGTT-GATTTGTTTCTTCTT
1 GGTTAGATTTGTTTCTTCTT
5394297 CTTCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.68
Consensus pattern (21 bp):
GGTTAGATTTGTTTCTTCTTT
Found at i:5397150 original size:17 final size:17
Alignment explanation
Indices: 5397124--5397163 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5397114 CTTAGAGGAG
*
5397124 TCAAAGGAAAAATATAC
1 TCAAAAGAAAAATATAC
* *
5397141 TCAAAAGAAACATTTAC
1 TCAAAAGAAAAATATAC
5397158 TCAAAA
1 TCAAAA
5397164 TAAGATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (17 bp):
TCAAAAGAAAAATATAC
Found at i:5412987 original size:18 final size:18
Alignment explanation
Indices: 5412966--5413026 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
5412956 TAACCCATTG
* *
5412966 TTCCTCACCTACATCTTT
1 TTCCTCACATACATCTTC
*
5412984 TTCCTCA-ATTGCATCTTC
1 TTCCTCACA-TACATCTTC
*
5413002 TTACTCACATACATCTTC
1 TTCCTCACATACATCTTC
5413020 TTCCTCA
1 TTCCTCA
5413027 TCTGCGCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 34 0.97
19 1 0.03
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.43
Consensus pattern (18 bp):
TTCCTCACATACATCTTC
Found at i:5415741 original size:22 final size:22
Alignment explanation
Indices: 5415713--5415758 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5415703 ACTTTTTTTA
*
5415713 TTTATTTTTAAAATTTTAATTT
1 TTTATTTTTAAAATTTTAAATT
*
5415735 TTTATTTTTTAAATTTTAAATT
1 TTTATTTTTAAAATTTTAAATT
5415757 TT
1 TT
5415759 AAATCCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTTTTAAAATTTTAAATT
Found at i:5416092 original size:26 final size:30
Alignment explanation
Indices: 5416034--5416091 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
5416024 AATATTATTC
*
5416034 TTATTTAATTATAATATATTTTTAAATTTT
1 TTATTTAATTATAATATATTTATAAATTTT
5416064 TTATTT-ATTA-AATATATTTAT-AATTTT
1 TTATTTAATTATAATATATTTATAAATTTT
5416091 T
1 T
5416092 ACAAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
28 10 0.37
29 4 0.15
30 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATTTAATTATAATATATTTATAAATTTT
Found at i:5416149 original size:15 final size:14
Alignment explanation
Indices: 5416121--5416159 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
5416111 ATTATATTAT
*
5416121 TTATTTTTAATATAA
1 TTATTTTT-TTATAA
5416136 TTATTCTTTTTATAA
1 TTATT-TTTTTATAA
5416151 TTATTTTTT
1 TTATTTTTT
5416160 AATTCATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 3 0.14
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTTTATAA
Found at i:5417487 original size:2 final size:2
Alignment explanation
Indices: 5417482--5417515 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5417472 TGCATATTTA
*
5417482 AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5417516 TGAGTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5421153 original size:26 final size:27
Alignment explanation
Indices: 5421123--5421175 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
5421113 AAAATGTTAA
**
5421123 AAATATTTTTTATA-TTTTATATTTTT
1 AAATATTTTAAATATTTTTATATTTTT
*
5421149 AAATATTTTAAATATTTTTTTATTTTT
1 AAATATTTTAAATATTTTTATATTTTT
5421176 GAGAAAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
AAATATTTTAAATATTTTTATATTTTT
Found at i:5421154 original size:17 final size:16
Alignment explanation
Indices: 5421125--5421158 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5421115 AATGTTAAAA
*
5421125 ATATTTTTTATATTTT
1 ATATTTTTAATATTTT
5421141 ATATTTTTAAATATTTT
1 ATATTTTT-AATATTTT
5421158 A
1 A
5421159 AATATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTTTTAATATTTT
Found at i:5421172 original size:17 final size:17
Alignment explanation
Indices: 5421123--5421174 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
5421113 AAAATGTTAA
5421123 AAATATTTTTTATATTTT
1 AAATATTTTTT-TATTTT
*
5421141 --ATATTTTTAAATATTTT
1 AAATATTTTT--TTATTTT
5421158 AAATATTTTTTTATTTT
1 AAATATTTTTTTATTTT
5421175 TGAGAAAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 8 0.29
17 12 0.43
19 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AAATATTTTTTTATTTT
Found at i:5421785 original size:15 final size:16
Alignment explanation
Indices: 5421753--5421787 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5421743 ATCCTAATAA
*
5421753 TATTTACATCTTTTAT
1 TATTTACATCTGTTAT
5421769 TATTTACAT-TGTTAT
1 TATTTACATCTGTTAT
5421784 TATT
1 TATT
5421788 GTAGCAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.63
Consensus pattern (16 bp):
TATTTACATCTGTTAT
Found at i:5423727 original size:2 final size:2
Alignment explanation
Indices: 5423720--5423749 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5423710 TCTAGTTCTA
5423720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5423750 GAGAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5425363 original size:36 final size:36
Alignment explanation
Indices: 5425316--5425506 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
5425306 GCTAAGCTAC
**
5425316 CACTTATCACTTAGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
5425352 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
5425388 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
5425430 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
5425470 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
5425506 C
1 C
5425507 TAAAGCTACC
Statistics
Matches: 138, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 99 0.72
38 3 0.02
40 3 0.02
42 3 0.02
44 2 0.01
46 28 0.20
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:5425439 original size:46 final size:46
Alignment explanation
Indices: 5425388--5425522 Score: 182
Period size: 46 Copynumber: 3.2 Consensus size: 46
5425378 ATAAGTATAG
5425388 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
5425434 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
5425470 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
5425516 CACTTAT
1 CACTTAT
5425523 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
36 28 0.37
38 2 0.03
39 1 0.01
40 3 0.04
42 3 0.04
43 1 0.01
44 2 0.03
46 35 0.47
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:5425446 original size:82 final size:82
Alignment explanation
Indices: 5425352--5425522 Score: 315
Period size: 82 Copynumber: 2.1 Consensus size: 82
5425342 ATAAGTATAG
*
5425352 CACTTATCACTTTTTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
5425417 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* *
5425434 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
5425499 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
5425516 CACTTAT
1 CACTTAT
5425523 NNNNNNNNNN
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:5425455 original size:118 final size:115
Alignment explanation
Indices: 5425273--5425506 Score: 378
Period size: 118 Copynumber: 2.0 Consensus size: 115
5425263 TACTTATGAT
5425273 CACTTATCATTTGTCCCTGATCAGATAAGTGCAGCTAAGCTACCACTTATCACTTAGTCACTTGA
1 CACTTATCATTTGTCCCTGATCAGATAAGTGCAGCTAAGCTACCACTTATCACTTAGTCACTTGA
5425338 TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* * * * *
5425388 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGCAGCT-AAGCTACCACTTATCACTTAGTCACT
* *
5425453 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
63 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
5425506 C
1 C
5425507 TAAAGCTACC
Statistics
Matches: 109, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
115 9 0.08
116 5 0.05
117 19 0.17
118 76 0.70
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (115 bp):
CACTTATCATTTGTCCCTGATCAGATAAGTGCAGCTAAGCTACCACTTATCACTTAGTCACTTGA
TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:5428973 original size:10 final size:10
Alignment explanation
Indices: 5428954--5429004 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
5428944 CTAATTTTAA
*
5428954 TATAATTTTT
1 TATAAGTTTT
5428964 TATAAGTTTT
1 TATAAGTTTT
*
5428974 TATAA-TTTC
1 TATAAGTTTT
5428983 TAT-AGTTTT
1 TATAAGTTTT
*
5428992 TAATAATTTTT
1 T-ATAAGTTTT
5429003 TA
1 TA
5429005 CGTTTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 1 0.03
9 10 0.29
10 17 0.50
11 6 0.18
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (10 bp):
TATAAGTTTT
Found at i:5429009 original size:19 final size:17
Alignment explanation
Indices: 5428954--5429015 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 17
5428944 CTAATTTTAA
5428954 TATAATTTTTTATAAGTTTT
1 TATAA-TTTTT-T-AGTTTT
*
5428974 TATAATTTCTATAGTTTT
1 TATAATTT-TTTAGTTTT
*
5428992 TAATAATTTTTTACGTTTA
1 T-ATAATTTTTTA-GTTTT
5429011 TATAA
1 TATAA
5429016 AAAAAAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 14 0.39
19 16 0.44
20 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (17 bp):
TATAATTTTTTAGTTTT
Found at i:5430422 original size:30 final size:30
Alignment explanation
Indices: 5430386--5430442 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
5430376 CAGTCATTGT
5430386 ATGTAATGGAGTAGTTTTGATGTATACAAA
1 ATGTAATGGAGTAGTTTTGATGTATACAAA
5430416 ATGTAATGGAGTAGTTTTGATGTATAC
1 ATGTAATGGAGTAGTTTTGATGTATAC
5430443 GGGCGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.39
Consensus pattern (30 bp):
ATGTAATGGAGTAGTTTTGATGTATACAAA
Found at i:5435659 original size:21 final size:21
Alignment explanation
Indices: 5435618--5435677 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
5435608 AAAACTAATT
*
5435618 TACGAAAATATTTATAATTTATA
1 TACGAAAATA--TAAAATTTATA
**
5435641 TATTAAAATATAAAATTTATA
1 TACGAAAATATAAAATTTATA
5435662 TACGAAAATATAAAAT
1 TACGAAAATATAAAAT
5435678 CCGACCAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 24 0.75
23 8 0.25
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TACGAAAATATAAAATTTATA
Found at i:5436361 original size:55 final size:55
Alignment explanation
Indices: 5436240--5436368 Score: 152
Period size: 55 Copynumber: 2.3 Consensus size: 55
5436230 GTGGGTACCG
* * * * ** *
5436240 GCCATCAATGTCCCAACACTCAAATTTTTTTTTTAAATCTGGTATAAGGGTGCTG
1 GCCATCAGTGTCCCAACACTCAAATTTTTTTCTCAAATCTGGTACAAGAATGCTA
* * *
5436295 GCCACCGGTGTCCCAGCAC-CAAATTTTTTTCCTCAAATCTGGTACAAGAATGCTA
1 GCCATCAGTGTCCCAACACTCAAATTTTTTT-CTCAAATCTGGTACAAGAATGCTA
5436350 GCCATCAGTGTCCCAACAC
1 GCCATCAGTGTCCCAACAC
5436369 ATGAAAAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 11 0.18
55 49 0.82
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (55 bp):
GCCATCAGTGTCCCAACACTCAAATTTTTTTCTCAAATCTGGTACAAGAATGCTA
Found at i:5442000 original size:2 final size:2
Alignment explanation
Indices: 5441993--5442023 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5441983 TCTCTTACAT
5441993 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 T
5442024 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5442028 original size:4 final size:4
Alignment explanation
Indices: 5442021--5442045 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5442011 TATATATATA
5442021 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
5442046 TGTTTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:5455106 original size:23 final size:22
Alignment explanation
Indices: 5455080--5455126 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
5455070 ATACTTTGAA
* *
5455080 AAATATATAAAATATTATAATAT
1 AAATATACAAAATA-TATAAAAT
*
5455103 AAATTTACAAAATATATAAAAT
1 AAATATACAAAATATATAAAAT
5455125 AA
1 AA
5455127 TTAGAACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATATACAAAATATATAAAAT
Found at i:5460756 original size:3 final size:3
Alignment explanation
Indices: 5460748--5460820 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
5460738 ATCTTCACTC
* * * * *
5460748 TCT TCT TCT TCCT CCT CCC TCT TC- TCT TCC TCA TCT TCT TCT TCT
1 TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
5460793 TCT TCT TCT TCT TCC TCGT TCT CCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT
5460821 CCTCAACTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.04
3 50 0.89
4 4 0.07
ACGTcount: A:0.01, C:0.42, G:0.01, T:0.55
Consensus pattern (3 bp):
TCT
Found at i:5469512 original size:9 final size:9
Alignment explanation
Indices: 5469494--5469533 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
5469484 TTTGGTTAAA
5469494 AATTAACCG
1 AATTAACCG
*
5469503 AATTACCCG
1 AATTAACCG
5469512 AATTAACCG
1 AATTAACCG
*
5469521 AATTAACCA
1 AATTAACCG
5469530 AATT
1 AATT
5469534 GAATCTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:5469676 original size:18 final size:18
Alignment explanation
Indices: 5469636--5469679 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5469626 AATTTTTATT
* **
5469636 ATTGAGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
5469654 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
5469672 CTTGGGTT
1 ATTGGGTT
5469680 TGGATTGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:5471264 original size:21 final size:20
Alignment explanation
Indices: 5471229--5471287 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
5471219 TTACATAAAA
5471229 AAAGAAATATAAAAAAAC-T
1 AAAGAAATATAAAAAAACTT
5471248 AAAGAATATATTAAAAAAACTT
1 AAAGAA-ATA-TAAAAAAACTT
*
5471270 AAAAAAATATAAAAAAAC
1 AAAGAAATATAAAAAAAC
5471288 CTACACAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 6 0.17
20 12 0.33
21 12 0.33
22 6 0.17
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (20 bp):
AAAGAAATATAAAAAAACTT
Found at i:5471275 original size:9 final size:10
Alignment explanation
Indices: 5471228--5471286 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
5471218 TTTACATAAA
5471228 AAAAGAAATAT
1 AAAA-AAATAT
5471239 AAAAAAACTA-
1 AAAAAAA-TAT
* *
5471249 AAGAATATATT
1 AAAAAAATA-T
5471260 AAAAAAACT-T
1 AAAAAAA-TAT
5471270 AAAAAAATAT
1 AAAAAAATAT
5471280 AAAAAAA
1 AAAAAAA
5471287 CCTACACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 11 0.28
12 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:5471278 original size:23 final size:23
Alignment explanation
Indices: 5471224--5471280 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
5471214 TAACTTTACA
* *
5471224 TAAAAAAAGAAATATAAAAAAAC
1 TAAAAAAATATATATAAAAAAAC
*
5471247 T-AAAGAATATAT-TAAAAAAAC
1 TAAAAAAATATATATAAAAAAAC
5471268 TTAAAAAAATATA
1 -TAAAAAAATATA
5471281 AAAAAACCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.32
22 9 0.32
23 10 0.36
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAAAAAATATATATAAAAAAAC
Found at i:5471310 original size:24 final size:23
Alignment explanation
Indices: 5471283--5471331 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
5471273 AAAATATAAA
*
5471283 AAAACCTACACAACCCTAAATCCT
1 AAAACCTACAAAACCCTAAA-CCT
*
5471307 AAAATCTACAAAACCCTAAACCT
1 AAAACCTACAAAACCCTAAACCT
5471330 AA
1 AA
5471332 CCGTACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAACCTACAAAACCCTAAACCT
Found at i:5474794 original size:21 final size:22
Alignment explanation
Indices: 5474750--5474794 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
5474740 ATATTAAATT
* * *
5474750 TATTTTATTTTTAGTAATTTTA
1 TATTTTATTTTCACTAAATTTA
5474772 TATTTTA-TTTCACTAAATTTA
1 TATTTTATTTTCACTAAATTTA
5474793 TA
1 TA
5474795 AACATTTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTTTATTTTCACTAAATTTA
Found at i:5474974 original size:16 final size:16
Alignment explanation
Indices: 5474953--5474997 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5474943 ATTTGGTTCG
5474953 CTGTAATATAATAGAA
1 CTGTAATATAATAGAA
*
5474969 CTGTAAT-TGAATAGAG
1 CTGTAATAT-AATAGAA
5474985 CTGTAATAGTAAT
1 CTGTAATA-TAAT
5474998 TCAATTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 20 0.80
17 3 0.12
18 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (16 bp):
CTGTAATATAATAGAA
Found at i:5475283 original size:56 final size:56
Alignment explanation
Indices: 5475168--5475296 Score: 154
Period size: 56 Copynumber: 2.3 Consensus size: 56
5475158 AATAAAATTA
* *
5475168 TTAATATAAATAATAAATAATTTAATAATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAAAATAATTATTATT-AATATAAT
* *
5475226 TTAATAAAA-AATATATAATTTAATAAAATTCTTAAAATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAAAATAATTATTATTAATAT-AAT
* *
5475282 TTACTAAAATCATAA
1 TTAATAAAATAATAA
5475297 TATATAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
55 4 0.07
56 30 0.49
57 21 0.34
58 6 0.10
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAAAATAATTATTATTAATATAAT
Found at i:5485031 original size:29 final size:31
Alignment explanation
Indices: 5484989--5485051 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
5484979 ATTCCAAAAT
5484989 TCAACTTCACATTCT-TTTTTATTGTTAA-A
1 TCAACTTCACATTCTATTTTTATTGTTAACA
* * *
5485018 TCAAGTTCCCATTCTATTTTTATTTTTAACA
1 TCAACTTCACATTCTATTTTTATTGTTAACA
5485049 TCA
1 TCA
5485052 TTTTTCAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.45
30 12 0.41
31 4 0.14
ACGTcount: A:0.27, C:0.19, G:0.03, T:0.51
Consensus pattern (31 bp):
TCAACTTCACATTCTATTTTTATTGTTAACA
Found at i:5485407 original size:96 final size:95
Alignment explanation
Indices: 5485293--5485597 Score: 388
Period size: 90 Copynumber: 3.2 Consensus size: 95
5485283 GATTTTAGGG
* * ** * *
5485293 TTTTAAGAAAAAAATTAAATAAATAAGGGTTTAGGGTTTTTTAATTAAATTAATTATAAATTTTT
1 TTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT
* *
5485358 AAAAAATAGATCAGGGTTCAGTGTTTATGGT
66 AAAAAATAGATTAGGGTT-AGTGTTTAAGGT
5485389 TTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAA--TTT
1 TTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT
** * *
5485452 AAAAAA-A-ATTA-AATTAGGGTTTAGGGT
66 AAAAAATAGATTAGGGTTAGTGTTTAAGGT
**
5485479 TTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTAA
1 TTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT
* *
5485544 AAAAAATTAGATTGGGGTTTAGTATTTAAGGT
66 AAAAAA-TAGATTAGGG-TTAGTGTTTAAGGT
*
5485576 TTTTAAGG-AAAAATCAAATAAA
1 TTTTAAGGAAAAAATTAAATAAA
5485598 ACTAGTTGTT
Statistics
Matches: 182, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
90 70 0.38
91 2 0.01
92 10 0.05
93 1 0.01
94 10 0.05
95 3 0.02
96 67 0.37
97 19 0.10
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.38
Consensus pattern (95 bp):
TTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTT
AAAAAATAGATTAGGGTTAGTGTTTAAGGT
Found at i:5485508 original size:90 final size:90
Alignment explanation
Indices: 5485286--5485565 Score: 391
Period size: 90 Copynumber: 3.1 Consensus size: 90
5485276 GTTTTTAGAT
* * ** * *
5485286 TTTAGGG-TTTTAAGAAAAAAATTAAATAAATAAGGGTTTAGGGTTTTTTAATTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
* * *
5485350 AAATTTTTAAAAAATAGATCAGGGTTCAGTG
66 AAA--TTTAAAAAA-A-ATTA-GATT-AGGG
*
5485381 TTTATGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
5485446 AAATTTAAAAAAAATTAAATTAGGG
66 AAATTTAAAAAAAATTAGATTAGGG
5485471 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
5485536 AAATTTAAAAAAAATTAGATTGGGG
66 AAATTTAAAAAAAATTAGATTAGGG
5485561 TTTAG
1 TTTAG
5485566 TATTTAAGGT
Statistics
Matches: 170, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
90 95 0.56
91 2 0.01
92 3 0.02
93 1 0.01
94 9 0.05
95 6 0.04
96 54 0.32
ACGTcount: A:0.42, C:0.01, G:0.18, T:0.38
Consensus pattern (90 bp):
TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
AAATTTAAAAAAAATTAGATTAGGG
Found at i:5499987 original size:18 final size:20
Alignment explanation
Indices: 5499967--5500003 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
5499957 ATTGGCCAAC
*
5499967 TTTATTAATTTTT-TAAACT
1 TTTAATAATTTTTATAAACT
5499986 TTTAATAATTTTTATAAA
1 TTTAATAATTTTTATAAA
5500004 AACGGTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATAATTTTTATAAACT
Found at i:5504799 original size:20 final size:21
Alignment explanation
Indices: 5504776--5504820 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5504766 AAATACTTAT
* *
5504776 AAATTATTT-AATAATTATAA
1 AAATTATTTGAAAAACTATAA
5504796 AAA-TATTTGAAAAACTATAA
1 AAATTATTTGAAAAACTATAA
5504816 AAATT
1 AAATT
5504821 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 5 0.24
20 15 0.71
21 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATTATTTGAAAAACTATAA
Found at i:5505288 original size:6 final size:6
Alignment explanation
Indices: 5505277--5505302 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5505267 TTTTGGGTTT
5505277 TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TT
5505303 TAGAGTTTTT
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:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:5505719 original size:125 final size:125
Alignment explanation
Indices: 5505497--5505779 Score: 462
Period size: 125 Copynumber: 2.3 Consensus size: 125
5505487 ATTTATTAAG
* * *
5505497 GAAATCGCTCCCACGTGGACGTG-TTTTTCATACAGTAGGTCCTGAAAAAATAATTCTGAGTTGA
1 GAAATCGCTCCCACGTGGACGTGCTTTTGC-TACAGTAGGTCCTAAAAAAATAATTCTGAGTTAA
*
5505561 CGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATAAGAAGAATTTCT
65 CGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATACTTTATAAGAAGAATTTCT
*
5505622 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTAAAAAAATAATT-TCGAGTTAA
1 GAAATCGCTCCCACGTGGACGTGCTTTTGCTACAGTAGGTCCTAAAAAAATAATTCT-GAGTTAA
* * *
5505686 CGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATATTTTATTAGAAGAATTTTT
65 CGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATACTTTATAAGAAGAATTTCT
5505747 GAAATCGCTCCCACGTGGACGTGCTTTTGCTAC
1 GAAATCGCTCCCACGTGGACGTGCTTTTGCTAC
5505780 TATAGCATGT
Statistics
Matches: 147, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
124 1 0.01
125 141 0.96
126 5 0.03
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGTGCTTTTGCTACAGTAGGTCCTAAAAAAATAATTCTGAGTTAAC
GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATACTTTATAAGAAGAATTTCT
Found at i:5510034 original size:11 final size:11
Alignment explanation
Indices: 5510006--5510042 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
5509996 TAGGGATTTA
*
5510006 AGAGGAAATTCA
1 AGAGGAAATT-G
5510018 AGAGGAAATTG
1 AGAGGAAATTG
5510029 AGAGGAAATTG
1 AGAGGAAATTG
5510040 AGA
1 AGA
5510043 AAGGATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.49, C:0.03, G:0.32, T:0.16
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:5516035 original size:16 final size:17
Alignment explanation
Indices: 5516004--5516037 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5515994 GTTAAATTGT
5516004 ATTTTATCTCTTTACTA
1 ATTTTATCTCTTTACTA
5516021 ATTTTATCT-TTTACTA
1 ATTTTATCTCTTTACTA
5516037 A
1 A
5516038 AAATTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATCTCTTTACTA
Found at i:5518341 original size:14 final size:14
Alignment explanation
Indices: 5518322--5518351 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5518312 TCAACAAAAT
*
5518322 AATTTAAAAAGGTA
1 AATTTAAAAAGCTA
5518336 AATTTAAAAAGCTA
1 AATTTAAAAAGCTA
5518350 AA
1 AA
5518352 ATTATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (14 bp):
AATTTAAAAAGCTA
Found at i:5522552 original size:47 final size:47
Alignment explanation
Indices: 5522501--5522605 Score: 153
Period size: 46 Copynumber: 2.3 Consensus size: 47
5522491 ACTGCATTGC
* * *
5522501 CAGGGAAG-TAAGGTCTGTAATTTCTTCAGTTTATTCCACTGTAATCT
1 CAGGGAAGATAAGATCTG-AAATTCTTCAGTGTATTCCACTGTAATCT
5522548 CAGGG-AGATAAGATCTGAAATTCTTCAGTGTATTCCACTGTAATCT
1 CAGGGAAGATAAGATCTGAAATTCTTCAGTGTATTCCACTGTAATCT
5522594 CAGGG-AGATAAG
1 CAGGGAAGATAAG
5522606 GCCTGATGCG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
46 41 0.76
47 13 0.24
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (47 bp):
CAGGGAAGATAAGATCTGAAATTCTTCAGTGTATTCCACTGTAATCT
Found at i:5522679 original size:44 final size:43
Alignment explanation
Indices: 5522631--5522866 Score: 163
Period size: 44 Copynumber: 5.4 Consensus size: 43
5522621 CTCTACTGTT
* * *
5522631 ACTTCAGAGAGATAATATCTGTTACTTTAATCCGCTCCACTGTA
1 ACTTCAGAGAGATAAGAT-TATTACTTTAATCCGCTCCACTGCA
* * ** * *
5522675 ACTTCAGGGAGATAAGATTATCGACTCCAATCTGTTCCACTGCA
1 ACTTCAGAGAGATAAGATTAT-TACTTTAATCCGCTCCACTGCA
* * * * * * *
5522719 ACCTCAGGGAGATAAGA-T-TTGCTATGATCCACTCTACTGCA
1 ACTTCAGAGAGATAAGATTATTACTTTAATCCGCTCCACTGCA
* *
5522760 ACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACA
1 ACTTCAGAGAGATAAGAT-TATTACTTTAATCCGCTCCACTGCA
* * * * ***
5522804 ACTTCAG-GAAGATAGGATTATCGAATTCAATTTTCTCCACTGCA
1 ACTTCAGAG-AGATAAGATTAT-TACTTTAATCCGCTCCACTGCA
* *
5522848 ACCTCAGGGAGATAAGATT
1 ACTTCAGAGAGATAAGATT
5522867 TGCTGCTTAA
Statistics
Matches: 146, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
41 28 0.19
42 1 0.01
43 8 0.05
44 108 0.74
45 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (43 bp):
ACTTCAGAGAGATAAGATTATTACTTTAATCCGCTCCACTGCA
Found at i:5522756 original size:129 final size:129
Alignment explanation
Indices: 5522615--5522870 Score: 379
Period size: 129 Copynumber: 2.0 Consensus size: 129
5522605 GGCCTGATGC
* ** * * * **
5522615 GATCTACTCTACTGTTACTTCAGAGAGATAATATCTGTTACTTTAATCCGCTCCACTGTAACTTC
1 GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTC
* *
5522680 AGGGAGATAAGATTATCGACTCCAATCTGT-TCCACTGCAACCTCAGGGAGATAAGATTTGCTAT
66 AGGAAGATAAGATTATCGAATCCAAT-TGTCTCCACTGCAACCTCAGGGAGATAAGATTTGCTAT
5522744 GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTC
1 GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTC
* * *
5522809 AGGAAGATAGGATTATCGAATTCAATTTTCTCCACTGCAACCTCAGGGAGATAAGATTTGCT
66 AGGAAGATAAGATTATCGAATCCAATTGTCTCCACTGCAACCTCAGGGAGATAAGATTTGCT
5522871 GCTTAAATCT
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
128 2 0.02
129 111 0.98
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (129 bp):
GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTC
AGGAAGATAAGATTATCGAATCCAATTGTCTCCACTGCAACCTCAGGGAGATAAGATTTGCTAT
Found at i:5523057 original size:130 final size:131
Alignment explanation
Indices: 5522895--5523210 Score: 490
Period size: 130 Copynumber: 2.4 Consensus size: 131
5522885 CCTTACGCTT
* *
5522895 GAAGATAAGATTCGCGGTCTTCGATCTGTTTCCCTACTCCTAGGGAAGATAAGATCCGTAATATT
1 GAAGATAAGATTCGCCGTCTTCGATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGTAATATT
* * *
5522960 CAACCTATCCCACTGTTGACCAGGGAGATAGGCCTAGTGACTTAAATCTGTTTCCCTACTCCT-G
66 CAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTCCTAG
5523024 G
131 G
* * *
5523025 GAAGATAAGATTCACCGTCTTCGATCTATTTCCCTACTCCTGGGGAAGATAAGATCCGTAATCTT
1 GAAGATAAGATTCGCCGTCTTCGATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGTAATATT
* *** *
5523090 CAACCTATCCCATTGCTGACCAGGGAGATAGGACTAGTTTTTTAAATTTGCTTCCCTACTCCTAG
66 CAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTCCTAG
5523155 G
131 G
* *
5523156 GAAGATAAGATTCGCCATCCTCGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
1 GAAGATAAGATTCGCCGTCTTCGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
5523211 TCGCTGCTTA
Statistics
Matches: 168, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
130 115 0.68
131 53 0.32
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (131 bp):
GAAGATAAGATTCGCCGTCTTCGATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGTAATATT
CAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTCCTAG
G
Found at i:5523206 original size:87 final size:86
Alignment explanation
Indices: 5523131--5523295 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 86
5523121 GACTAGTTTT
* * * * *
5523131 TTAAATTTGCTTCCCTACTCCTAGGGAAGATAAGATTCGCCATCCTCGATCTGTTTCCCTACTCC
1 TTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATCCGCC-GCCTAGATCTGCTTCCCTACTCC
* * *
5523196 TGGGGAAGATAAGATTCGCTGC
65 TAGGGAAGATAAGACTAGCTGC
* * *
5523218 TTAGATCTGCTTCCCTACTCCTGGGGAAGATAAGATCCGCCGCTTAGATCTGCTTCCCTACTCCT
1 TTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATCCGCCGCCTAGATCTGCTTCCCTACTCCT
5523283 AGGGAAGATAAGA
66 AGGGAAGATAAGA
5523296 TCCGCAATCT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
86 32 0.46
87 37 0.54
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (86 bp):
TTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATCCGCCGCCTAGATCTGCTTCCCTACTCCT
AGGGAAGATAAGACTAGCTGC
Found at i:5523297 original size:43 final size:43
Alignment explanation
Indices: 5523138--5523300 Score: 236
Period size: 43 Copynumber: 3.8 Consensus size: 43
5523128 TTTTTAAATT
* * * *
5523138 TGCTTCCCTACTCCTAGGGAAGATAAGATTCGCCATCCTCGATC
1 TGCTTCCCTACTCCTAGGGAAGATAAGATCCGCC-GCTTAGATC
* * * *
5523182 TGTTTCCCTACTCCTGGGGAAGATAAGATTCGCTGCTTAGATC
1 TGCTTCCCTACTCCTAGGGAAGATAAGATCCGCCGCTTAGATC
*
5523225 TGCTTCCCTACTCCTGGGGAAGATAAGATCCGCCGCTTAGATC
1 TGCTTCCCTACTCCTAGGGAAGATAAGATCCGCCGCTTAGATC
5523268 TGCTTCCCTACTCCTAGGGAAGATAAGATCCGC
1 TGCTTCCCTACTCCTAGGGAAGATAAGATCCGC
5523301 AATCTTTATT
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 78 0.72
44 31 0.28
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (43 bp):
TGCTTCCCTACTCCTAGGGAAGATAAGATCCGCCGCTTAGATC
Found at i:5531496 original size:14 final size:14
Alignment explanation
Indices: 5531477--5531506 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5531467 AAACTCACTC
5531477 TAAAAAAATTGAGA
1 TAAAAAAATTGAGA
5531491 TAAAAAAATTGAGA
1 TAAAAAAATTGAGA
5531505 TA
1 TA
5531507 GGTAGTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
TAAAAAAATTGAGA
Found at i:5535488 original size:81 final size:81
Alignment explanation
Indices: 5535348--5535510 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
5535338 TAGATATTAT
* * *
5535348 ATAACTCATTTTATTGTTAATTTTCTTACTATTTTAGAGGCATTTACTTGATAAGTTGTAGCTAT
1 ATAACTCATTTTATTGTTAATTTTCATACTATTTTAGAGGCATTTACTTGATAAATTGTAACTAT
5535413 GTTAGTGTTATTTTTA
66 GTTAGTGTTATTTTTA
* *
5535429 ATAACTCGTTTTATTGTTAATTTTCATACTATTTTAGAGGCATTTGCTTGATAAATTGTAACTAT
1 ATAACTCATTTTATTGTTAATTTTCATACTATTTTAGAGGCATTTACTTGATAAATTGTAACTAT
5535494 GTTAGTGTTATTTTTA
66 GTTAGTGTTATTTTTA
5535510 A
1 A
5535511 GTATAAAAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (81 bp):
ATAACTCATTTTATTGTTAATTTTCATACTATTTTAGAGGCATTTACTTGATAAATTGTAACTAT
GTTAGTGTTATTTTTA
Found at i:5544020 original size:15 final size:15
Alignment explanation
Indices: 5543996--5544027 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5543986 GGATCCAAAC
5543996 TTACTAGATACGACA
1 TTACTAGATACGACA
*
5544011 TTACTGGATACGACA
1 TTACTAGATACGACA
5544026 TT
1 TT
5544028 TCGTTATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (15 bp):
TTACTAGATACGACA
Found at i:5552408 original size:129 final size:129
Alignment explanation
Indices: 5552178--5552429 Score: 459
Period size: 129 Copynumber: 2.0 Consensus size: 129
5552168 GGTGACTAAC
5552178 TGATGCCAAGAATGGCATCAAATAAAGTGCCCAGGATTGCAACAATGTAAGGCATCCGCCCATGT
1 TGATGCCAAGAATGGCATCAAATAAAGTGCCCAGGATTGCAACAATGTAAGGCATCCGCCCATGT
* *
5552243 CTACGACAGCAGGCTTTGTCGTCCGACAAAGCTCCCGAGACAACACTGCTAGAACTGCCAGAAT
66 CTACGACAGCAGGCTTTGTCGTCCGACAAAGCTCCCGAGACAACACTGCCAAAACTGCCAGAAT
**
5552307 TGATGCCAAGAATGGCATCCGATAAAGTGCCCAGGATTGCAACAATGTAAGGCATCCGCCCATGT
1 TGATGCCAAGAATGGCATCAAATAAAGTGCCCAGGATTGCAACAATGTAAGGCATCCGCCCATGT
*
5552372 CTACGACAGCAGGCTTTGTCGTCCGACAAAGCTCCCGATACAACACTGCCAAAACTGC
66 CTACGACAGCAGGCTTTGTCGTCCGACAAAGCTCCCGAGACAACACTGCCAAAACTGC
5552430 GGAGCCCCAG
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 118 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (129 bp):
TGATGCCAAGAATGGCATCAAATAAAGTGCCCAGGATTGCAACAATGTAAGGCATCCGCCCATGT
CTACGACAGCAGGCTTTGTCGTCCGACAAAGCTCCCGAGACAACACTGCCAAAACTGCCAGAAT
Found at i:5553260 original size:16 final size:15
Alignment explanation
Indices: 5553239--5553268 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5553229 TCAAAAAATA
5553239 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
5553255 TATTATTTTATATT
1 TATTATTTTATATT
5553269 ATTTTAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:5553380 original size:159 final size:159
Alignment explanation
Indices: 5553198--5554362 Score: 1787
Period size: 159 Copynumber: 7.4 Consensus size: 159
5553188 TAATTTCAAT
* *
5553198 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5553263 TATATTATTTTAATACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTT-TTATATAAATTTAG
* *
5553328 T-AAATAACCCTTATTTTGGCCCTTTGTCC
130 TAAAAAAACCCTTATTTTGGCCCTTTGTTC
*
5553357 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTCTTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5553422 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTG-TTTTTTATATAAATTTAG
* *
5553487 TAAAAAAAATCATTATTTTGGCCCTTTGTTC
130 T-AAAAAAACCCTTATTTTGGCCCTTTGTTC
* * *
5553518 ATATTTTTCTTATTTTTGGATTTTATTACTTT-AAAAAATATATTATTTTCG--------TATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5553574 TATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
5553639 AAAAAAACCCCTTATTTTGGCCCTTTGTTC
131 AAAAAAA-CCCTTATTTTGGCCCTTTGTTC
* * *
5553669 GTATTTTTCTTATTTTCGGATTTTATCACTTTGAAAAAATATATTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* * *
5553734 TATATTATTTTGGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
*
5553799 AAAAAAAACCTTATTTTGGCCCTTTGTTC
131 AAAAAAACCCTTATTTTGGCCCTTTGTTC
* *
5553828 GTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTTGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* * *
5553893 TATATTATTTTAGTACATAAAGATTGAAATATATTAATTTAGTGTGTTTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
5553958 AAAAAAA-CCTTATTTTGGCCCTTTGTTC
131 AAAAAAACCCTTATTTTGGCCCTTTGTTC
* * *
5553986 GTATTTTACTTATTTTCGGATTTTATTATTTTCAAAAAATACACTA--TT--T-TTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
*
5554046 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTATGTTTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
* *
5554111 -AAAAAACTCTTATTTTGGCCCTTTATTC
131 AAAAAAACCCTTATTTTGGCCCTTTGTTC
*
5554139 GTATTTTTCTTATTTTTGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* * *
5554204 TGTATTATTTTAGTACATAATGTTTGAAATGTATTATTTTTA-TGT-TGTTTT-TATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTA-ATTTAGTGTGTTTTTTATATAAATTTAG
5554266 TAAAAAAACCCCTTATTTTGGCCCTTTGTTC
130 TAAAAAAA-CCCTTATTTTGGCCCTTTGTTC
* *
5554297 GTATTTTTCTTTTTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCAT-TTTTATTCATT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT-ATT
5554361 TT
65 TT
5554363 CGTATTTTAT
Statistics
Matches: 926, Mismatches: 57, Indels: 47
0.90 0.06 0.05
Matches are distributed among these distances:
150 7 0.01
151 68 0.07
152 74 0.08
153 133 0.14
154 1 0.00
155 2 0.00
156 14 0.02
157 19 0.02
158 186 0.20
159 274 0.30
160 94 0.10
161 54 0.06
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.53
Consensus pattern (159 bp):
GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
AAAAAAACCCTTATTTTGGCCCTTTGTTC
Found at i:5554016 original size:16 final size:17
Alignment explanation
Indices: 5553983--5554018 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5553973 TGGCCCTTTG
*
5553983 TTCGTATTTTACTTATT
1 TTCGGATTTTACTTATT
5554000 TTCGGATTTTA-TTATT
1 TTCGGATTTTACTTATT
5554016 TTC
1 TTC
5554019 AAAAAATACA
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:0.17, C:0.11, G:0.08, T:0.64
Consensus pattern (17 bp):
TTCGGATTTTACTTATT
Found at i:5554117 original size:471 final size:470
Alignment explanation
Indices: 5553198--5554362 Score: 1889
Period size: 471 Copynumber: 2.5 Consensus size: 470
5553188 TAATTTCAAT
*
5553198 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
* *
5553263 TATATTATTTTAATACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTGTT-TTATATAAATTTAG
* *
5553328 T-AAATAACCCTTATTTTGGCCCTTTGTCCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAA
130 TAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAA
* * *
5553392 AAAATATACTCTTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATT
195 AAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAAGATTGAAATATATT
5553457 AATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAAATCATTATTTTGGCCCTTTGTTCATAT
260 AATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAAATCATTATTTTGGCCCTTTGTTCATAT
* * *
5553522 TTTTCTTATTTTTGGATTTTATTACTTTAAAAAATATATTATTTTCGTATTTTATATTATTTTAG
325 TTTACTTATTTTCGGATTTTATTACTTTAAAAAATATATTATTTTAGTATTTTATATTATTTTAG
*
5553587 TACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAAACCCCTT
390 TACATAATATTTGAAATGTATTAATTTAGTATGTTTTTTATATAAATTTAGTAAAAAAA-CCCTT
*
5553652 ATTTTGGCCCTTTGTTC
454 ATTTTGGCCCTTTATTC
* *
5553669 GTATTTTTCTTATTTTCGGATTTTATCACTTTGAAAAAATATATTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
* *
5553734 TATATTATTTTGGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTGTTTTATATAAATTTAGT
* *
5553799 AAAAAAAACCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAA
131 AAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAA
*
5553864 AAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAAAGATTGAAATATATTA
196 AAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAAGATTGAAATATATTA
* *
5553929 ATTTAGTGTG-TTTTTTATATAAATTTAGT-AAAAAAA-CCTTATTTTGGCCCTTTGTTCGTATT
261 ATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAAATCATTATTTTGGCCCTTTGTTCATATT
* * *
5553991 TTACTTATTTTCGGATTTTATTATTTTCAAAAAATACACTATTTTTTTATTATTTTATATTATTT
326 TTACTTATTTTCGGATTTTATTACTTT-AAAAAAT--A-TATTATTTTAGTATTTTATATTATTT
* *
5554056 TAGTACATAATGTTTGAAATGTATTAATTTAGTATGTTTTTTATATAAATTTAGT-AAAAAACTC
387 TAGTACATAATATTTGAAATGTATTAATTTAGTATGTTTTTTATATAAATTTAGTAAAAAAACCC
5554120 TTATTTTGGCCCTTTATTC
452 TTATTTTGGCCCTTTATTC
* *
5554139 GTATTTTTCTTATTTTTGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
* *
5554204 TGTATTATTTTAGTACATAATGTTTGAAATGTATTATTTTTA-TGT-TGTTTT-TATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTA-ATTTAGTGTGTGTTTTATATAAATTTAG
*
5554266 TAAAAAAACCCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTATTACTTTCA
130 TAAAAAAA-CCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCA
*
5554331 AAAAATATACTATTTTCAT-TTTTATTCATTTT
194 AAAAATATACTATTTTCGTATTTTATT-ATTTT
5554363 CGTATTTTAT
Statistics
Matches: 646, Mismatches: 40, Indels: 18
0.92 0.06 0.03
Matches are distributed among these distances:
468 74 0.11
469 95 0.15
470 151 0.23
471 250 0.39
472 76 0.12
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.53
Consensus pattern (470 bp):
GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTGTTTTATATAAATTTAGT
AAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAA
AAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAAGATTGAAATATATTA
ATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAAATCATTATTTTGGCCCTTTGTTCATATT
TTACTTATTTTCGGATTTTATTACTTTAAAAAATATATTATTTTAGTATTTTATATTATTTTAGT
ACATAATATTTGAAATGTATTAATTTAGTATGTTTTTTATATAAATTTAGTAAAAAAACCCTTAT
TTTGGCCCTTTATTC
Found at i:5554177 original size:311 final size:315
Alignment explanation
Indices: 5553198--5554362 Score: 1729
Period size: 311 Copynumber: 3.7 Consensus size: 315
5553188 TAATTTCAAT
* *
5553198 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
5553263 TATATTATTTTAATACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTCTTATATAAATTTAG
66 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTT-TTATATAAATTTAG
* *
5553328 T-AAATAACCCTTATTTTGGCCCTTTGTCCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAA
130 TAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTC-A
* *
5553392 AAAATATACTCTTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATT
194 AAAA-ATACACTATTC-TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATT
*
5553457 AATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAAATCATTATTTTGGCCCTTTGTTC
257 AATTTAGTGTG-TTTTTTATATAAATTTAGTAAAAAAACTC-TTATTTTGGCCCTTTGTTC
* * *
5553518 ATATTTTTCTTATTTTTGGATTTTATTACTTT-AAAAAATATATTATTTTCG--------TATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
5553574 TATATTATTTTAGTACATAATA-TTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAG
* *
5553638 TAAAAAAACCCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATCACTTTGA
130 TAAAAAAA-CCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCA
* * *
5553703 AAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTTGGTACATAAAGTTTGAAATGTAT
194 AAAAATACACTA--TTC-TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTAT
*
5553768 TAATTTAGTGTGTGTTTTATATAAATTTAGTAAAAAAAAC-CTTATTTTGGCCCTTTGTTC
256 TAATTTAGTGTGTTTTTTATATAAATTTAGT-AAAAAAACTCTTATTTTGGCCCTTTGTTC
* *
5553828 GTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTTGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
5553893 TATATTATTTTAGTACATAAAGATTGAAATATATTAATTTAGTGTGTTTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
* *
5553958 AAAAAAA-CCTTATTTTGGCCCTTTGTTCGTATTTTACTTATTTTCGGATTTTATTATTTTCAAA
131 AAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAA
*
5554022 AAATACACTATT-T-TTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATT
196 AAATACACTATTCTATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATT
* *
5554085 TAGTATGTTTTTTATATAAATTTAGT-AAAAAACTCTTATTTTGGCCCTTTATTC
261 TAGTGTGTTTTTTATATAAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTC
*
5554139 GTATTTTTCTTATTTTTGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* * * *
5554204 TGTATTATTTTAGTACATAATGTTTGAAATGTATTATTTTTA-TGT-TGTTTT-TATAAATTTAG
66 TATATTATTTTAGTACATAAAGTTTGAAATGTATTA-ATTTAGTGTGTTTTTTATATAAATTTAG
*
5554266 TAAAAAAACCCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTATTACTTTCA
130 TAAAAAAA-CCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCA
* *
5554331 AAAAATATACTATTTTCATTTTTATTCATTTT
194 AAAAATACACTATTCT-A-TTTTATT-ATTTT
5554363 CGTATTTTAT
Statistics
Matches: 773, Mismatches: 47, Indels: 54
0.88 0.05 0.06
Matches are distributed among these distances:
309 19 0.02
310 79 0.10
311 279 0.36
312 198 0.26
313 1 0.00
315 9 0.01
316 5 0.01
317 61 0.08
318 1 0.00
319 91 0.12
320 30 0.04
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.53
Consensus pattern (315 bp):
GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGT
AAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAA
AAATACACTATTCTATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATT
TAGTGTGTTTTTTATATAAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTC
Found at i:5554363 original size:16 final size:17
Alignment explanation
Indices: 5554342--5554381 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5554332 AAAATATACT
5554342 ATTTTCAT-TTTTATTC
1 ATTTTCATATTTTATTC
*
5554358 ATTTTCGTATTTTATT-
1 ATTTTCATATTTTATTC
5554374 -TTTTCATA
1 ATTTTCATA
5554382 AACATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTCATATTTTATTC
Found at i:5554547 original size:30 final size:30
Alignment explanation
Indices: 5554502--5554624 Score: 154
Period size: 30 Copynumber: 4.3 Consensus size: 30
5554492 TAACAAATAA
*
5554502 ATAAAATAAAGTAATAAAACATAGAATGTAC
1 ATAACATAAA-TAATAAAACATAGAATGTAC
5554533 ATAACATAAATAATAAAACATA-AA--TA-
1 ATAACATAAATAATAAAACATAGAATGTAC
* *
5554559 AT---A-AAATAATAAGACATAGTATGTAC
1 ATAACATAAATAATAAAACATAGAATGTAC
5554585 ATAACATAAATAATAAAACATAGAATGTAC
1 ATAACATAAATAATAAAACATAGAATGTAC
5554615 ATAACATAAA
1 ATAACATAAA
5554625 AGTTAAAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
22 14 0.18
23 2 0.03
25 2 0.03
26 4 0.05
27 2 0.03
29 3 0.04
30 43 0.54
31 9 0.11
ACGTcount: A:0.62, C:0.08, G:0.07, T:0.24
Consensus pattern (30 bp):
ATAACATAAATAATAAAACATAGAATGTAC
Found at i:5554554 original size:14 final size:14
Alignment explanation
Indices: 5554507--5554564 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
5554497 AATAAATAAA
5554507 ATAAAGTAATAAAAC
1 ATAAA-TAATAAAAC
*
5554522 ATAGAAT-GTACATAAC
1 ATA-AATAATA-A-AAC
5554538 ATAAATAATAAAAC
1 ATAAATAATAAAAC
5554552 ATAAATAATAAAA
1 ATAAATAATAAAA
5554565 TAATAAGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 18 0.49
15 9 0.24
16 10 0.27
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (14 bp):
ATAAATAATAAAAC
Found at i:5554576 original size:52 final size:52
Alignment explanation
Indices: 5554506--5554606 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
5554496 AAATAAATAA
*
5554506 AATAAAGTAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
* *
5554558 AATAAAATAATAAGACATAGTATGTACATAACATAAATAATAAAACATA
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATA
5554607 GAATGTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (52 bp):
AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
Found at i:5554622 original size:16 final size:16
Alignment explanation
Indices: 5554572--5554622 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5554562 AAATAATAAG
*
5554572 ACATAGTATGTACATA
1 ACATAGAATGTACATA
*
5554588 ACATA-AATAATA-A-A
1 ACATAGAAT-GTACATA
5554602 ACATAGAATGTACATA
1 ACATAGAATGTACATA
5554618 ACATA
1 ACATA
5554623 AAAGTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (16 bp):
ACATAGAATGTACATA
Found at i:5554903 original size:13 final size:14
Alignment explanation
Indices: 5554870--5554912 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5554860 CCCTCCCTCT
*
5554870 TCTTCTTCTTCTTC
1 TCTTTTTCTTCTTC
*
5554884 TCTTTTTCTTTTTC
1 TCTTTTTCTTCTTC
5554898 -CTTTTTCTTCCTTC
1 TCTTTTTCTT-CTTC
5554912 T
1 T
5554913 GCGCCTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTTTTTCTTCTTC
Found at i:5555987 original size:16 final size:17
Alignment explanation
Indices: 5555958--5555990 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5555948 TACGAGTTGG
*
5555958 TTTTTATAATTTTTAAT
1 TTTTTATAACTTTTAAT
5555975 TTTTTA-AACTTTTAAT
1 TTTTTATAACTTTTAAT
5555991 AAATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTATAACTTTTAAT
Found at i:5556644 original size:24 final size:23
Alignment explanation
Indices: 5556596--5556659 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
5556586 TAAATTTAAA
* *
5556596 TTTTAATATTTTTATTTTTATTT
1 TTTTAATAATTTAATTTTTATTT
5556619 TTTTAATAATTTAATCTATTTA-TT
1 TTTTAATAATTTAAT-T-TTTATTT
*
5556643 TTTTAAAAATTTTAATT
1 TTTTAATAA-TTTAATT
5556660 CTGGTCTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 13 0.37
24 12 0.34
25 10 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTAATAATTTAATTTTTATTT
Found at i:5556864 original size:29 final size:30
Alignment explanation
Indices: 5556832--5556894 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
5556822 AAATAGAGCG
5556832 ACTAAATTCCTAGAA-TTA-AA-AGTACATGA
1 ACTAAATT-CTA-AATTTAGAAGAGTACATGA
5556861 ACTAAATTCTAAATTTATGAAGAGTACATGA
1 ACTAAATTCTAAATTTA-GAAGAGTACATGA
5556892 ACT
1 ACT
5556895 TGTGATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 2 0.07
28 6 0.20
29 8 0.27
30 2 0.07
31 12 0.40
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (30 bp):
ACTAAATTCTAAATTTAGAAGAGTACATGA
Found at i:5562458 original size:25 final size:25
Alignment explanation
Indices: 5562425--5562482 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 25
5562415 ACGAGCTATA
5562425 AACGGTAAGCTCCTCTGA-GCTGAAT
1 AACGGTAAGCTCCTCT-ACGCTGAAT
5562450 AACGGTAAGCTCCTCTACGCTGAAT
1 AACGGTAAGCTCCTCTACGCTGAAT
5562475 AACGGTAA
1 AACGGTAA
5562483 ACTCATACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (25 bp):
AACGGTAAGCTCCTCTACGCTGAAT
Found at i:5562496 original size:25 final size:25
Alignment explanation
Indices: 5562409--5562521 Score: 99
Period size: 25 Copynumber: 4.6 Consensus size: 25
5562399 GCACATGTAT
5562409 GCTCATACGAGCT--ATAAACGGTAA
1 GCTCATACGAGCTGAAT-AACGGTAA
*
5562433 GCTCCT-CTGAGCTGAATAACGGTAA
1 GCTCATAC-GAGCTGAATAACGGTAA
* *
5562458 GCTCCT-CTACGCTGAATAACGGTAA
1 GCTCATACGA-GCTGAATAACGGTAA
* * * *
5562483 ACTCATACGAGCTGAGTATCGATAA
1 GCTCATACGAGCTGAATAACGGTAA
*
5562508 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
5562522 GAATCGGTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
23 1 0.01
24 11 0.15
25 58 0.78
26 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:5563429 original size:22 final size:23
Alignment explanation
Indices: 5563404--5563446 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5563394 TTATCTTTAA
5563404 TTACCT-A-TTTACAAAATTACCC
1 TTACCTAACTTTA-AAAATTACCC
5563426 TTACCTAACTTTAAAAATTAC
1 TTACCTAACTTTAAAAATTAC
5563447 ACTAATGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (23 bp):
TTACCTAACTTTAAAAATTACCC
Found at i:5577240 original size:2 final size:2
Alignment explanation
Indices: 5577235--5577264 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5577225 AAGACAATAC
*
5577235 TA TA TA TT 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
5577265 ATTGGCTCCC
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:5577974 original size:15 final size:17
Alignment explanation
Indices: 5577956--5578000 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
5577946 ATCTTCAACC
5577956 TTTTTCTCTTCCA-T-T
1 TTTTTCTCTTCCACTGT
*
5577971 TTTTTCTCTTCAACTGGT
1 TTTTTCTCTTCCACT-GT
5577989 TTTTTCTCTTCC
1 TTTTTCTCTTCC
5578001 TATATGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
18 12 0.48
ACGTcount: A:0.07, C:0.27, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTTCTCTTCCACTGT
Found at i:5578372 original size:3 final size:3
Alignment explanation
Indices: 5578366--5578424 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
5578356 GCATTTTATT
* * * *
5578366 ATC ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC GTT ATC AAC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
5578414 AAC ATC ATC AT
1 ATC ATC ATC AT
5578425 ATGATATACT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:5579721 original size:24 final size:25
Alignment explanation
Indices: 5579680--5579727 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5579670 CATTGGACCA
*
5579680 AAAAAAAACACAAATACTATATTAG
1 AAAAAAAACACAAATACTAAATTAG
* *
5579705 AAAAAAAA-TCAAGTACTAAATTA
1 AAAAAAAACACAAATACTAAATTA
5579728 TATATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAAAAAACACAAATACTAAATTAG
Found at i:5581659 original size:14 final size:14
Alignment explanation
Indices: 5581625--5581665 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
5581615 ACAATAACAG
5581625 TAGACAAAGAAGAAA
1 TAGACAAA-AAGAAA
*
5581640 -AAACAAAAAGAAA
1 TAGACAAAAAGAAA
5581653 TAGAC-AAAAGAAA
1 TAGACAAAAAGAAA
5581666 ATAATGGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (14 bp):
TAGACAAAAAGAAA
Found at i:5582753 original size:3 final size:3
Alignment explanation
Indices: 5582739--5582908 Score: 74
Period size: 3 Copynumber: 55.0 Consensus size: 3
5582729 GTATATATAT
* * *
5582739 ATA ATG ATA ATA ATA ATA ACTA AGA ATA ATA ATAA ATA ATC ATA CATTA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA -A-TA
** * * * * *
5582788 ATA A-A CGA ATA ATA GTA GTA CATAA ATAA ATA AGA GTA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -AT-A AT-A ATA ATA ATA ATA ATA ATA
* * * * * * * * * **
5582835 ATA ATA GTA GTA AAA AGA GTA ATA GTA ATA ACA GTA ATA ATA GTA ACG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5582883 A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
5582909 TCAAATTTAT
Statistics
Matches: 124, Mismatches: 35, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
2 2 0.02
3 104 0.84
4 15 0.12
5 3 0.02
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:5582862 original size:36 final size:39
Alignment explanation
Indices: 5582795--5582879 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 39
5582785 TTAATAAACG
*
5582795 AATAATAGTAGTACATAAATAAATAAGAGTAACAATAAT
1 AATAATAGTAGTACATAAATAAATAAGAGTAACAACAAT
* * * * *
5582834 AATAATAGTAGTA-A-AAA-GAGTAATAGTAATAACAGT
1 AATAATAGTAGTACATAAATAAATAAGAGTAACAACAAT
5582870 AATAATAGTA
1 AATAATAGTA
5582880 ACGAAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 23 0.57
37 3 0.08
38 1 0.03
39 13 0.32
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.26
Consensus pattern (39 bp):
AATAATAGTAGTACATAAATAAATAAGAGTAACAACAAT
Found at i:5583507 original size:20 final size:20
Alignment explanation
Indices: 5583470--5583507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5583460 AAGCACTCAA
*
5583470 AAATAAAGTAAAATAAAAGT
1 AAATAAAGTAAAAAAAAAGT
5583490 AAAT-AAGTAGAAAAAAAA
1 AAATAAAGTA-AAAAAAAA
5583508 AACAAGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (20 bp):
AAATAAAGTAAAAAAAAAGT
Found at i:5589920 original size:22 final size:25
Alignment explanation
Indices: 5589877--5589922 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5589867 TCATCATCAA
*
5589877 ATAATTACACATCTATAGCAAAATC
1 ATAATTACACAACTATAGCAAAATC
5589902 ATAATTACA-AAC-ATA-CAAAAT
1 ATAATTACACAACTATAGCAAAAT
5589923 AACTAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 2 0.10
25 9 0.45
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.26
Consensus pattern (25 bp):
ATAATTACACAACTATAGCAAAATC
Found at i:5590518 original size:50 final size:50
Alignment explanation
Indices: 5590403--5590595 Score: 305
Period size: 50 Copynumber: 3.8 Consensus size: 50
5590393 GATAATAACA
* ** * *
5590403 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
5590454 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
5590504 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5590554 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5590596 TTACCCAAGT
Statistics
Matches: 132, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 98 0.74
51 34 0.26
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5590967 original size:30 final size:30
Alignment explanation
Indices: 5590932--5590989 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5590922 CCTCAACTCT
*
5590932 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTACAATTTTGCCCCTA
* *
5590962 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTGCAAAATTACAATTTTGCCCC
5590990 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCCTA
Found at i:5600912 original size:26 final size:25
Alignment explanation
Indices: 5600883--5600942 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
5600873 TTTTCTATTA
* *
5600883 TATTATTAAATTTTTTATTTAAAAAT
1 TATTATTAAATATTTAATTT-AAAAT
5600909 TATTATT--ATATTTAATTTAAAAT
1 TATTATTAAATATTTAATTTAAAAT
5600932 TATTAATTAAA
1 TATT-ATTAAA
5600943 AATAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 9 0.31
24 12 0.41
26 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTATTAAATATTTAATTTAAAAT
Found at i:5600940 original size:24 final size:23
Alignment explanation
Indices: 5600884--5600940 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
5600874 TTTCTATTAT
5600884 ATTATTAAATT-TTTTATTTAAAA
1 ATTATT-AATTATTTTATTTAAAA
5600907 ATTATT-ATTATATTTAATTT-AAA
1 ATTATTAATTAT-TTT-ATTTAAAA
5600930 ATTATTAATTA
1 ATTATTAATTA
5600941 AAAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.10
22 1 0.03
23 18 0.60
24 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTATTAATTATTTTATTTAAAA
Found at i:5600986 original size:17 final size:16
Alignment explanation
Indices: 5600966--5600997 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5600956 AGAAATTATG
5600966 ATAATTATATATTTAAA
1 ATAATTATA-ATTTAAA
5600983 ATAATTATAATTTAA
1 ATAATTATAATTTAA
5600998 TAGGAGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTATAATTTAAA
Found at i:5601610 original size:14 final size:14
Alignment explanation
Indices: 5601591--5601620 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5601581 TGATTGTTTG
*
5601591 AATCTAAATTTACT
1 AATCTAAATTAACT
5601605 AATCTAAATTAACT
1 AATCTAAATTAACT
5601619 AA
1 AA
5601621 GAACGCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
AATCTAAATTAACT
Found at i:5604449 original size:3 final size:3
Alignment explanation
Indices: 5604441--5604689 Score: 231
Period size: 3 Copynumber: 81.3 Consensus size: 3
5604431 AAACAATTAT
5604441 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
5604489 ATA ATA ATA ATAA ACA CATA TATA CTA A-A ATT TTC ATA AGTGA AT-
1 ATA ATA ATA AT-A ATA -ATA -ATA ATA ATA ATA ATA ATA A-T-A ATA
* * * *
5604534 ATAA ATA A-A A-A CATA ACA ATA ATA ACA AGA ATA TTA ATA A-A TATA
1 AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * *
5604579 CTA AGA ACA ATA GTA A-A GATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
5604624 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
5604672 ATA ACA ACTAA ATA ATA A
1 ATA ATA A-T-A ATA ATA A
5604690 AATTACTAAA
Statistics
Matches: 205, Mismatches: 26, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
2 9 0.04
3 177 0.86
4 15 0.07
5 4 0.02
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5605067 original size:36 final size:36
Alignment explanation
Indices: 5605017--5605105 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
5605007 GGGTCAGGGC
5605017 CAAAACGGCGTCGTTTTGGCACCTAACCCCTAAAGG
1 CAAAACGGCGTCGTTTTGGCACCTAACCCCTAAAGG
* **
5605053 CAAAACGGCATCGTTTTGGCACCTGTCCCCTAAAGG
1 CAAAACGGCGTCGTTTTGGCACCTAACCCCTAAAGG
5605089 CAAAACGGCGTCGTTTT
1 CAAAACGGCGTCGTTTT
5605106 AAAAAGTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (36 bp):
CAAAACGGCGTCGTTTTGGCACCTAACCCCTAAAGG
Found at i:5609584 original size:7 final size:7
Alignment explanation
Indices: 5609572--5609602 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5609562 ATTTCCCCTC
5609572 CCCATTT
1 CCCATTT
5609579 CCCATTT
1 CCCATTT
5609586 CCCATTT
1 CCCATTT
5609593 CCCATTT
1 CCCATTT
5609600 CCC
1 CCC
5609603 TAAGCCCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.48, G:0.00, T:0.39
Consensus pattern (7 bp):
CCCATTT
Found at i:5610966 original size:143 final size:143
Alignment explanation
Indices: 5610708--5611193 Score: 704
Period size: 143 Copynumber: 3.4 Consensus size: 143
5610698 CCTTGAGCTT
5610708 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA
1 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA
* * * *
5610773 GTAGACTGAAGTCAGCGAATCTTATTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATT
66 GCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATT
*
5610838 ATGGCTGATTTTA
131 ATGGCTGATCTTA
* *
5610851 TCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGA
1 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA
* * * *
5610916 GCATATTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAACAGATTAAAGCTAAAAATT
66 GCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATT
*
5610981 ATGGCGGATCTTA
131 ATGGCTGATCTTA
* * * * * *
5610994 TCTTCTTGAAGTTGCAATGGAACAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTACAGCGAA
1 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA
*** *
5611059 GCAAACTGAAGACAGCGAATCTTATTTCCCTAATGTTGCAGTGGAATAGATTAAAGCTACAAATT
66 GCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATT
5611124 ATGG-TGGATCTTA
131 ATGGCT-GATCTTA
* * ** **
5611137 TCTTCCTGAAGTTGTAGTGGAGTAGATCAAAGCCAAAAACCTTATCTCCCTGAAGTT
1 TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTT
5611194 ACAGTAGAGC
Statistics
Matches: 306, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
143 306 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (143 bp):
TCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGCAGCGGA
GCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATT
ATGGCTGATCTTA
Found at i:5611225 original size:44 final size:44
Alignment explanation
Indices: 5611177--5611281 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 44
5611167 AGCCAAAAAC
* *
5611177 CTTATCTCCCTGAAGTTAC-AGTAGAGCAGGTTGAAGCTACCAAT
1 CTTATCTCCCTAAAGTTACTA-TAGAGCAGATTGAAGCTACCAAT
* * *
5611221 CTTATCTCCCTAAAGTTACTATGGAGCAGATTGAAGTTACTAAT
1 CTTATCTCCCTAAAGTTACTATAGAGCAGATTGAAGCTACCAAT
*
5611265 CCTATCTCCCTAAAGTT
1 CTTATCTCCCTAAAGTT
5611282 GTAGTGAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTACTATAGAGCAGATTGAAGCTACCAAT
Found at i:5612242 original size:56 final size:56
Alignment explanation
Indices: 5612156--5612267 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
5612146 AGCGGTTGGC
* *
5612156 ACCGCGGCGAATCGCCGAAGCCAAAGTCGGCGAAAGGGGGCTTTGAGAGAAAAAAG
1 ACCGCGGCAAATCGCCGAAGCCAAAGTCGGCCAAAGGGGGCTTTGAGAGAAAAAAG
* *
5612212 ACCGCGGTAAATCGCCGGAGCCAAAGTCGGCCAAAGGGGGCTTTGAGAGAAAAAAG
1 ACCGCGGCAAATCGCCGAAGCCAAAGTCGGCCAAAGGGGGCTTTGAGAGAAAAAAG
5612268 GGAAGGTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.34, C:0.21, G:0.35, T:0.10
Consensus pattern (56 bp):
ACCGCGGCAAATCGCCGAAGCCAAAGTCGGCCAAAGGGGGCTTTGAGAGAAAAAAG
Found at i:5612747 original size:3 final size:3
Alignment explanation
Indices: 5612739--5612784 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
5612729 TTAATTTAAA
* *
5612739 TAT TAT TAT TAC TAT TAT TAC TAT TAT TAT T-T T-T TACT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
5612783 TA
1 TA
5612785 CCATACTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5613396 original size:46 final size:46
Alignment explanation
Indices: 5613329--5613505 Score: 327
Period size: 46 Copynumber: 3.8 Consensus size: 46
5613319 ACATTGTTAT
* *
5613329 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
5613375 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
5613421 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
5613467 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTAC
5613506 GTTCCACACT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 128 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:5615541 original size:15 final size:15
Alignment explanation
Indices: 5615521--5615550 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5615511 ATCCATTTTC
5615521 CTTAGTTTCTAGATT
1 CTTAGTTTCTAGATT
5615536 CTTAGTTTCTAGATT
1 CTTAGTTTCTAGATT
5615551 ATTCCACCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
CTTAGTTTCTAGATT
Found at i:5621732 original size:24 final size:25
Alignment explanation
Indices: 5621691--5621738 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5621681 CATTGGACCA
*
5621691 AAAAAAAACACAAATACTATATTAG
1 AAAAAAAACACAAATACTAAATTAG
* *
5621716 AAAAAAAA-TCAAGTACTAAATTA
1 AAAAAAAACACAAATACTAAATTA
5621739 TATATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAAAAAACACAAATACTAAATTAG
Found at i:5624191 original size:3 final size:3
Alignment explanation
Indices: 5624183--5624328 Score: 186
Period size: 3 Copynumber: 48.7 Consensus size: 3
5624173 TATTTTTAAC
* * * *
5624183 ATT ATT ATT TTT AAT ATT TTT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5624231 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
5624279 ATC ATCT -TT ACT ATT ATT ATT AAT ATT AAT ATT ATT ATT ATT ATC
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5624324 ATT AT
1 ATT AT
5624329 ATTTCTATGT
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
2 1 0.01
3 120 0.99
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5624551 original size:14 final size:15
Alignment explanation
Indices: 5624534--5624562 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5624524 ACGTATTAAA
5624534 ATATGTATAT-TTTT
1 ATATGTATATATTTT
5624548 ATATGTATATATTTT
1 ATATGTATATATTTT
5624563 TCATCTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
ATATGTATATATTTT
Found at i:5624807 original size:3 final size:3
Alignment explanation
Indices: 5624799--5624827 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5624789 AGTAATTTTG
5624799 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5624828 GTTACTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5625847 original size:18 final size:18
Alignment explanation
Indices: 5625826--5625871 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
5625816 TCATATGTCC
5625826 ATTTTTATGT-TTTAGTTT
1 ATTTTTATGTATTTA-TTT
*
5625844 ATTTTTATTTATTTATTT
1 ATTTTTATGTATTTATTT
5625862 ATTTGTTATG
1 ATTT-TTATG
5625872 ATATATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (18 bp):
ATTTTTATGTATTTATTT
Found at i:5629838 original size:22 final size:21
Alignment explanation
Indices: 5629762--5629836 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 21
5629752 AAAATCAAAG
* *
5629762 TCAAAATGAAAATGAAAAAAA
1 TCAAAATCAAAAAGAAAAAAA
*
5629783 TCAAAAATCAAAAATAAAAAAA
1 TC-AAAATCAAAAAGAAAAAAA
* **
5629805 ACAAAAAGAAGAAAGAAAAAAA
1 TCAAAATCAA-AAAGAAAAAAA
5629827 TCAAAATCAA
1 TCAAAATCAA
5629837 GATCAAAATA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
21 8 0.19
22 34 0.81
ACGTcount: A:0.75, C:0.08, G:0.07, T:0.11
Consensus pattern (21 bp):
TCAAAATCAAAAAGAAAAAAA
Found at i:5629868 original size:18 final size:18
Alignment explanation
Indices: 5629842--5629879 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
5629832 ATCAAGATCA
5629842 AAATAAAAATGAGAAAAAG
1 AAATAAAAATGA-AAAAAG
5629861 AAATAAAAATGAAAAAAG
1 AAATAAAAATGAAAAAAG
5629879 A
1 A
5629880 GAAATCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (18 bp):
AAATAAAAATGAAAAAAG
Found at i:5630536 original size:87 final size:87
Alignment explanation
Indices: 5630426--5630723 Score: 223
Period size: 87 Copynumber: 3.4 Consensus size: 87
5630416 TTGAAGCAAG
** * *
5630426 AGATCTTATCTCAT-TG-AGATTACAGTGGAGCAGATCCAAGACA-CAATCCTATCTCTCTGGGA
1 AGATCTTATCTC-TCTGAAG-TTACAGCAGAGCAGATCCAAG-CAGCAATCATATCTCCCTGGGA
5630488 TTACAGTGGAGCGGATTAAAATAAA
63 TTACAGTGGAGCGGATTAAAATAAA
* * * *
5630513 AGATCTTATCTCTCTGAAGTTACAGCAGAGTAGAT-C--GCATCAGGTCTTATCTCCCTGAGG-T
1 AGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCCAAGCAGCA-ATCATATCTCCCTG-GGAT
** ** ***
5630574 TACAGTGGAGTAGACCGAAGAATTTC
64 TACAGTGGAGCGGA-TTAA-AATAAA
* * * * ** * **
5630600 AGATCTTATCTCCCTGAGGTTATAGCGGAGCAGATTGAAGCTAGTAATCATATCTCCCTGATATT
1 AGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCCAAGC-AGCAATCATATCTCCCTGGGATT
*
5630665 ACAGTGAAGCGGATTAAAATAAA
65 ACAGTGGAGCGGATTAAAATAAA
* * *
5630688 AGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATC
1 AGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATC
5630724 GCATCAGGTC
Statistics
Matches: 160, Mismatches: 39, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
83 2 0.01
84 3 0.02
85 24 0.15
86 6 0.04
87 60 0.38
88 35 0.22
89 2 0.01
90 26 0.16
91 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (87 bp):
AGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCCAAGCAGCAATCATATCTCCCTGGGATTA
CAGTGGAGCGGATTAAAATAAA
Found at i:5630668 original size:218 final size:218
Alignment explanation
Indices: 5630177--5630670 Score: 810
Period size: 218 Copynumber: 2.3 Consensus size: 218
5630167 AGCACGATAA
* *
5630177 CTGAGGTTACAGTAGAGCAGATTGAAGCAAGAGATCTTATCTCCTTGAGATTACAGTGGAGCAGA
1 CTGAGGTTATAGTGGAGCAGATTGAAGCAAGAGATCTTATCTCCTTGAGATTACAGTGGAGCAGA
* *
5630242 TCCAAGACATAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAAGTTCTTATCTC
66 TCCAAGACACAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTC
*
5630307 TCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAGTGGAGTAAACC
131 TCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAGTGGAGTAAACC
*
5630372 GAATAATTTCAGATCTTATCTCC
196 GAAGAATTTCAGATCTTATCTCC
* *
5630395 CTGAGGTCATAGTGGAGCAGATTGAAGCAAGAGATCTTATCTCATTGAGATTACAGTGGAGCAGA
1 CTGAGGTTATAGTGGAGCAGATTGAAGCAAGAGATCTTATCTCCTTGAGATTACAGTGGAGCAGA
* **
5630460 TCCAAGACACAATCCTATCTCTCTGGGATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTC
66 TCCAAGACACAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTC
* *
5630525 TCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACC
131 TCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAGTGGAGTAAACC
5630590 GAAGAATTTCAGATCTTATCTCC
196 GAAGAATTTCAGATCTTATCTCC
* * * * *
5630613 CTGAGGTTATAGCGGAGCAGATTGAAGCTAGTA-ATCATATCTCCCTGATATTACAGTG
1 CTGAGGTTATAGTGGAGCAGATTGAAGCAAG-AGATCTTATCTCCTTGAGATTACAGTG
5630671 AAGCGGATTA
Statistics
Matches: 255, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
218 254 1.00
219 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (218 bp):
CTGAGGTTATAGTGGAGCAGATTGAAGCAAGAGATCTTATCTCCTTGAGATTACAGTGGAGCAGA
TCCAAGACACAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTC
TCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAGTGGAGTAAACC
GAAGAATTTCAGATCTTATCTCC
Done.