Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 23 of 131
Found at i:5579458 original size:53 final size:51
Alignment explanation
Indices: 5579371--5579525 Score: 165
Period size: 52 Copynumber: 3.0 Consensus size: 51
5579361 GGACAAGAAG
*
5579371 ACTTGAAAAAAAAAATTTTAAGAGAAAGAGGATTCTTAATAGGTAAGTTTA
1 ACTTGAAAAAAAAAATTTTAAAAGAAAGAGGATTCTTAATAGGTAAGTTTA
* *
5579422 ACTTGCAAAAAAAATAATTTTAAAAGGAAATA-GATTCTTAATAGGTAAGTTTG
1 ACTTG-AAAAAAAA-AATTTTAAAA-GAAAGAGGATTCTTAATAGGTAAGTTTA
* **
5579475 A-TTTATAAGAAAAAAATTTTAAGATTAAAG-GGATTCTTAAT-GGATAAGTTT
1 ACTTGA-AA-AAAAAAATTTTAA-AAGAAAGAGGATTCTTAATAGG-TAAGTTT
5579526 GTATGGTTAT
Statistics
Matches: 89, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
51 8 0.09
52 40 0.45
53 36 0.40
54 5 0.06
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (51 bp):
ACTTGAAAAAAAAAATTTTAAAAGAAAGAGGATTCTTAATAGGTAAGTTTA
Found at i:5579515 original size:52 final size:51
Alignment explanation
Indices: 5579376--5579526 Score: 169
Period size: 53 Copynumber: 2.9 Consensus size: 51
5579366 AGAAGACTTG
* *
5579376 AAAAAAAAAATTTTAAGAGAAAGAGGATTCTTAATAGGTAAGTTTAACTTGC
1 AAAAAAAAAATTTTAAGAGAAAG-GGATTCTTAATAGGTAAGTTTGACTTAC
* ** * *
5579428 AAAAAAAATAATTTTAAAAGGAAATAGATTCTTAATAGGTAAGTTTGATTTAT
1 AAAAAAAA-AATTTTAAGA-GAAAGGGATTCTTAATAGGTAAGTTTGACTTAC
* *
5579481 AAGAAAAAAATTTTAAGATTAAAGGGATTCTTAAT-GGATAAGTTTG
1 AAAAAAAAAATTTTAAGA-GAAAGGGATTCTTAATAGG-TAAGTTTG
5579527 TATGGTTATA
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 2 0.02
52 38 0.46
53 39 0.47
54 4 0.05
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (51 bp):
AAAAAAAAAATTTTAAGAGAAAGGGATTCTTAATAGGTAAGTTTGACTTAC
Found at i:5580079 original size:190 final size:186
Alignment explanation
Indices: 5579756--5580127 Score: 564
Period size: 190 Copynumber: 2.0 Consensus size: 186
5579746 GTACACAAGA
* *
5579756 GTTTGGGTTTGTATTTGTTTGGGTTAAGAATACTACATAGGACTAAAAGAAATTAAGAGTGTTAA
1 GTTTGGGTTTGTATTTGTTTGAGTTAAGAATACTACATAGGACTAAAAGAAATTAAAAGTGTTAA
* * *
5579821 GTATTGATTGTTGAGTGTAGTTGATGATTTAATGTATGTTTGTAATTCTCTGCAACTAGTGGATC
66 GTATTGATTGTTGAGTGTAGTTGATGATTTAATATATGTTTGTAATTCTCTACAACTAGTGAATC
* * *
5579886 TTGTTTCTCATCTGTGGACGTAGGTTGATTGGACCGAACCACGTTAAATTGTGTTT
131 TTGTTTCTCATCCGTGAACGTAGGTTGATTGGACCGAAACACGTTAAATTGTGTTT
* * * * *
5579942 GTTTGGGTTTGTGTTTGTTTGAGTTGAGAATACTATATAGGACTAAAAGAGATTAAAAATGTCTT
1 GTTTGGGTTTGTATTTGTTTGAGTTAAGAATACTACATAGGACTAAAAGAAATT-AAAA-GT-GT
* *
5580007 ATAAGTATTGATTGTTGAGTGTAGTTGATGATTTGATATTTGTTTGTAATTCTCTACAACTAGTG
63 -TAAGTATTGATTGTTGAGTGTAGTTGATGATTTAATATATGTTTGTAATTCTCTACAACTAGTG
*
5580072 AATCTTGTTTCTCATCCGTGAACGTAGGTTGATTGGATCGAAACACGTTAAATTGT
127 AATCTTGTTTCTCATCCGTGAACGTAGGTTGATTGGACCGAAACACGTTAAATTGT
5580128 TATCTCTTGT
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
186 49 0.30
187 3 0.02
188 2 0.01
189 1 0.01
190 111 0.67
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.41
Consensus pattern (186 bp):
GTTTGGGTTTGTATTTGTTTGAGTTAAGAATACTACATAGGACTAAAAGAAATTAAAAGTGTTAA
GTATTGATTGTTGAGTGTAGTTGATGATTTAATATATGTTTGTAATTCTCTACAACTAGTGAATC
TTGTTTCTCATCCGTGAACGTAGGTTGATTGGACCGAAACACGTTAAATTGTGTTT
Found at i:5581881 original size:23 final size:23
Alignment explanation
Indices: 5581839--5581883 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5581829 GTTTGATAAA
5581839 AATTTGATTGATCAACAAAAAAT
1 AATTTGATTGATCAACAAAAAAT
* *
5581862 AATTT-ATTGATTAACGAAAAAT
1 AATTTGATTGATCAACAAAAAAT
5581884 GAGACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
AATTTGATTGATCAACAAAAAAT
Found at i:5582078 original size:31 final size:32
Alignment explanation
Indices: 5582016--5582085 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
5582006 ATATTATATT
* *
5582016 ATAATATATTAATAATAATATTATATGAATAA
1 ATAATATACTAATAATAATAATATATGAATAA
* *
5582048 ATAATATACTATTAAT-ATAATATATTAATAA
1 ATAATATACTAATAATAATAATATATGAATAA
5582079 ATAATAT
1 ATAATAT
5582086 TTTAATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
ATAATATACTAATAATAATAATATATGAATAA
Found at i:5582099 original size:15 final size:15
Alignment explanation
Indices: 5582016--5582091 Score: 82
Period size: 15 Copynumber: 4.9 Consensus size: 15
5582006 ATATTATATT
5582016 ATAATATATTAAT-A
1 ATAATATATTAATAA
5582030 ATAATATTATATGAATAA
1 ATAATA-TAT-T-AATAA
* *
5582048 ATAATATACTATTAA
1 ATAATATATTAATAA
5582063 TATAATATATTAATAA
1 -ATAATATATTAATAA
*
5582079 ATAATATTTTAAT
1 ATAATATATTAAT
5582092 TATTAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
14 6 0.12
15 19 0.37
16 15 0.29
17 5 0.10
18 7 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
ATAATATATTAATAA
Found at i:5582211 original size:16 final size:16
Alignment explanation
Indices: 5582158--5582227 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
5582148 TAACATAACA
5582158 TTTTAATATTAAATATTAT
1 TTTTAATATT-AATA--AT
* * *
5582177 TATTAAAATATAATTAT
1 TTTTAATAT-TAATAAT
5582194 TTTTAATATTAATAA-
1 TTTTAATATTAATAAT
*
5582209 TTTTAATAATAAATAAT
1 TTTTAAT-ATTAATAAT
5582226 TT
1 TT
5582228 AATATATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
15 7 0.17
16 12 0.29
17 11 0.27
19 10 0.24
20 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAATATTAATAAT
Found at i:5582212 original size:15 final size:15
Alignment explanation
Indices: 5582157--5582232 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 15
5582147 TTAACATAAC
5582157 ATTTTAATATTAAATA
1 ATTTTAATATT-AATA
*
5582173 TTATTATTAAAATATAATTA
1 --ATT-TTAATAT-TAA-TA
*
5582193 TTTTTAATATTAATA
1 ATTTTAATATTAATA
*
5582208 ATTTTAATAATAAATA
1 ATTTTAAT-ATTAATA
5582224 A-TTTAATAT
1 ATTTTAATAT
5582233 ATTTTAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 15 0.31
16 10 0.20
17 6 0.12
18 5 0.10
19 8 0.16
20 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTTAATATTAATA
Found at i:5582225 original size:25 final size:24
Alignment explanation
Indices: 5582197--5582266 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 24
5582187 TAATTATTTT
5582197 TAATATTAATAATTTTAATAATAAA
1 TAAT-TTAATAATTTTAATAATAAA
5582222 TAATTTAATATATTTTAATAATAAA
1 TAATTTAATA-ATTTTAATAATAAA
5582247 TAATTTTTAAT-ATTTTAATA
1 TAA--TTTAATAATTTTAATA
5582267 GTTATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.14
25 30 0.71
27 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTTAATAATTTTAATAATAAA
Found at i:5582258 original size:10 final size:9
Alignment explanation
Indices: 5582197--5582266 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
5582187 TAATTATTTT
*
5582197 TAATATTAA
1 TAATTTTAA
5582206 TAATTTTAA
1 TAATTTTAA
*
5582215 TAA--TAAA
1 TAATTTTAA
5582222 TAA-TTTAA
1 TAATTTTAA
5582230 TATATTTTAA
1 TA-ATTTTAA
*
5582240 TAA--TAAA
1 TAATTTTAA
5582247 TAATTTTTAA
1 TAA-TTTTAA
5582257 T-ATTTTAA
1 TAATTTTAA
5582265 TA
1 TA
5582267 GTTATATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
7 12 0.24
8 12 0.24
9 14 0.29
10 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATTTTAA
Found at i:5582418 original size:15 final size:14
Alignment explanation
Indices: 5582383--5582417 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5582373 AAAATGTAAA
5582383 CATTTTTCAAAAAT
1 CATTTTTCAAAAAT
5582397 CATTTTTCAAAAAT
1 CATTTTTCAAAAAT
5582411 CATTTTT
1 CATTTTT
5582418 TACATAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (14 bp):
CATTTTTCAAAAAT
Found at i:5588617 original size:22 final size:24
Alignment explanation
Indices: 5588585--5588628 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5588575 TATATATAAA
*
5588585 TTTATTTAAAT-ATAT-TAAAATT
1 TTTATTAAAATAATATATAAAATT
5588607 TTTATTAAAATAATATATAAAA
1 TTTATTAAAATAATATATAAAA
5588629 AATTAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATTAAAATAATATATAAAATT
Found at i:5589825 original size:10 final size:10
Alignment explanation
Indices: 5589810--5589857 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
5589800 TTAAATATGT
5589810 AAAATTTTAA
1 AAAATTTTAA
5589820 AAAATTTTAA
1 AAAATTTTAA
* *
5589830 TATATTTTAA
1 AAAATTTTAA
5589840 ATAAATCTTTTAA
1 A-AAA--TTTTAA
5589853 AAAAT
1 AAAAT
5589858 AAATTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 19 0.61
11 2 0.06
12 3 0.10
13 7 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:5589950 original size:15 final size:17
Alignment explanation
Indices: 5589913--5589948 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5589903 ATTATAAATA
*
5589913 ATATTTTTAATTTTTAT
1 ATATTATTAATTTTTAT
5589930 ATATTATTAATTTTTAT
1 ATATTATTAATTTTTAT
5589947 AT
1 AT
5589949 TAAATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATTAATTTTTAT
Found at i:5590584 original size:30 final size:30
Alignment explanation
Indices: 5590481--5590591 Score: 77
Period size: 30 Copynumber: 3.8 Consensus size: 30
5590471 TGATTTGTGT
* * * *
5590481 ATTTAAATT-ATA-TAAAATATTAATTTTT
1 ATTTATATTGATATTAAAATATAAATTATA
* * *
5590509 A-TTATATTTCATATGAAAATATATATTATA
1 ATTTATA-TTGATATTAAAATATAAATTATA
*
5590539 ATTTATGTTGATATTAAAATATAAATTATA
1 ATTTATATTGATATTAAAATATAAATTATA
* * *
5590569 TATTTTTATT-TTATTAAATTATA
1 -ATTTATATTGATATTAAAATATA
5590592 TATAATTTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
27 4 0.06
28 3 0.05
29 3 0.05
30 43 0.67
31 11 0.17
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTATATTGATATTAAAATATAAATTATA
Found at i:5591193 original size:22 final size:22
Alignment explanation
Indices: 5591150--5591204 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
5591140 GCCACATATA
5591150 TATATATATTTATATTAAAATTTT
1 TATATAT-TTTATATT-AAATTTT
5591174 TATATATTTTAATATT-AATTTT
1 TATATATTTT-ATATTAAATTTT
* *
5591196 AATAAATTT
1 TATATATTT
5591205 AAAAGATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.46
23 3 0.11
24 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATATTTTATATTAAATTTT
Found at i:5592316 original size:11 final size:11
Alignment explanation
Indices: 5592300--5592333 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5592290 GTACGTTTAG
5592300 TTTATATTATT
1 TTTATATTATT
5592311 TTTATATTATAT
1 TTTATATTAT-T
*
5592323 TTTAGATTATT
1 TTTATATTATT
5592334 CGATCTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTATATTATT
Found at i:5592736 original size:15 final size:15
Alignment explanation
Indices: 5592718--5592747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5592708 ATTTCAGTCA
*
5592718 TTTTAATTTTAAAAT
1 TTTTAATTTCAAAAT
5592733 TTTTAATTTCAAAAT
1 TTTTAATTTCAAAAT
5592748 CAAATCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAATTTCAAAAT
Found at i:5593958 original size:15 final size:15
Alignment explanation
Indices: 5593934--5593964 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5593924 ATATTAAATC
5593934 AACATCTTTCTTTAA
1 AACATCTTTCTTTAA
*
5593949 AACATTTTTCTTTAA
1 AACATCTTTCTTTAA
5593964 A
1 A
5593965 TTGAAGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (15 bp):
AACATCTTTCTTTAA
Found at i:5599171 original size:13 final size:14
Alignment explanation
Indices: 5599153--5599182 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5599143 CATGTATTTA
5599153 AAATAATT-TTAAT
1 AAATAATTATTAAT
5599166 AAATAATTATTAAT
1 AAATAATTATTAAT
5599180 AAA
1 AAA
5599183 ATTTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATAATTATTAAT
Found at i:5625084 original size:25 final size:25
Alignment explanation
Indices: 5625056--5625109 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5625046 CAGCAATGTG
* *
5625056 TTCAGAAACATCATTCAACAAACTA
1 TTCAGAAACACCATTCAACAAACCA
* *
5625081 TTCAGAAATACCATTCAGCAAACCA
1 TTCAGAAACACCATTCAACAAACCA
5625106 TTCA
1 TTCA
5625110 ATATACCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (25 bp):
TTCAGAAACACCATTCAACAAACCA
Found at i:5625107 original size:12 final size:12
Alignment explanation
Indices: 5625028--5625109 Score: 58
Period size: 12 Copynumber: 6.7 Consensus size: 12
5625018 GTATAGAAAC
5625028 ACCATTCAGCAA
1 ACCATTCAGCAA
*
5625040 ACCAATCAGCAA
1 ACCATTCAGCAA
****
5625052 TGTGTTCAG-AA
1 ACCATTCAGCAA
*
5625063 ACATCATTCAACAA
1 AC--CATTCAGCAA
* *
5625077 ACTATTCAGAAA
1 ACCATTCAGCAA
5625089 TACCATTCAGCAA
1 -ACCATTCAGCAA
5625102 ACCATTCA
1 ACCATTCA
5625110 ATATACCATT
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
11 2 0.04
12 30 0.60
13 14 0.28
14 4 0.08
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.22
Consensus pattern (12 bp):
ACCATTCAGCAA
Found at i:5625133 original size:24 final size:24
Alignment explanation
Indices: 5625067--5625122 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
5625057 TCAGAAACAT
* * *
5625067 CATTCAACAAACTATTCAGAAATAC
1 CATTCAGCAAACCATTCA-ATATAC
5625092 CATTCAGCAAACCATTCAATATAC
1 CATTCAGCAAACCATTCAATATAC
5625116 CATTCAG
1 CATTCAG
5625123 TGTACCATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (24 bp):
CATTCAGCAAACCATTCAATATAC
Found at i:5625179 original size:12 final size:12
Alignment explanation
Indices: 5625088--5625179 Score: 67
Period size: 12 Copynumber: 7.3 Consensus size: 12
5625078 CTATTCAGAA
5625088 ATACCATTCAGC
1 ATACCATTCAGC
* **
5625100 AAACCATTCAAT
1 ATACCATTCAGC
*
5625112 ATACCATTCAGT
1 ATACCATTCAGC
*
5625124 GTACCATTCAGC
1 ATACCATTCAGC
* *
5625136 ATACTAATATCATAC
1 ATAC-CAT-TCA-GC
*
5625151 AATACCATTCAGT
1 -ATACCATTCAGC
*
5625164 ATACCATTTAGC
1 ATACCATTCAGC
5625176 ATAC
1 ATAC
5625180 TAATATCATA
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
12 46 0.75
13 2 0.03
14 6 0.10
15 3 0.05
16 4 0.07
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (12 bp):
ATACCATTCAGC
Found at i:5625201 original size:40 final size:40
Alignment explanation
Indices: 5625112--5625194 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
5625102 ACCATTCAAT
*
5625112 ATACCATTCAGTGTACCATTCAGCATACTAATATCATACA
1 ATACCATTCAGTATACCATTCAGCATACTAATATCATACA
*
5625152 ATACCATTCAGTATACCATTTAGCATACTAATATCATACA
1 ATACCATTCAGTATACCATTCAGCATACTAATATCATACA
5625192 ATA
1 ATA
5625195 TTATTCAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (40 bp):
ATACCATTCAGTATACCATTCAGCATACTAATATCATACA
Found at i:5625233 original size:25 final size:24
Alignment explanation
Indices: 5625205--5625259 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
5625195 TTATTCAACA
* *
5625205 ATACCATTCAACAAATCATTTAGC
1 ATACCATTCAACAAACCATTCAGC
* * *
5625229 GATACTATTTAGCAAACCATTCAGC
1 -ATACCATTCAACAAACCATTCAGC
5625254 ATACCA
1 ATACCA
5625260 ATATTATACA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.27
Consensus pattern (24 bp):
ATACCATTCAACAAACCATTCAGC
Found at i:5625276 original size:28 final size:28
Alignment explanation
Indices: 5625244--5625457 Score: 104
Period size: 28 Copynumber: 7.6 Consensus size: 28
5625234 TATTTAGCAA
* * *
5625244 ACCATTCAGCATACCAATATTATACAAT
1 ACCATTCAACAAACCAATATCATACAAT
** *
5625272 ACCATTCAACAAAATAATATCATATAAT
1 ACCATTCAACAAACCAATATCATACAAT
* * * *
5625300 ACCATTCAACAAACCAATCGGTAATGTGTTAAAAAAC
1 ACCATTCAACAAACCAA----T-A----TCATACAAT
* * *
5625337 ACCATTCAACAAACC-AT-TTAGA-AAC
1 ACCATTCAACAAACCAATATCATACAAT
*
5625362 ACCATTCAACAAA-C--TAT-TTAGCAA-
1 ACCATTCAACAAACCAATATCATA-CAAT
* *
5625386 ACCATTCAATATACCAATATCATACAAT
1 ACCATTCAACAAACCAATATCATACAAT
* *
5625414 ACCATTCAACAAAACAATATCACACAAT
1 ACCATTCAACAAACCAATATCATACAAT
5625442 ACCATT-AAGCAAACCA
1 ACCATTCAA-CAAACCA
5625458 TAATATTTAA
Statistics
Matches: 145, Mismatches: 23, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
23 2 0.01
24 13 0.09
25 19 0.13
26 4 0.03
27 8 0.06
28 75 0.52
32 2 0.01
33 1 0.01
36 1 0.01
37 20 0.14
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (28 bp):
ACCATTCAACAAACCAATATCATACAAT
Found at i:5625353 original size:142 final size:143
Alignment explanation
Indices: 5625197--5625457 Score: 368
Period size: 142 Copynumber: 1.8 Consensus size: 143
5625187 ATACAATATT
* * * * *
5625197 ATTCAACAATACCATTCA-ACAA-ATCATTTAGCGATACTATTTAGCAAACCATTCAGCATACCA
1 ATTCAACAATACCATTCAGA-AACACCATTCAAC-AAACTATTTAGCAAACCATTCAACATACCA
* * * *
5625260 ATATTATACAATACCATTCAACAAAATAATATCATATAATACCATTCAA-CAAACCAATCGGTAA
64 ATATCATACAATACCATTCAACAAAACAATATCACACAATACCATT-AAGCAAACCAATCGGTAA
5625324 TGTGTTAAAAAACACC
128 TGTGTTAAAAAACACC
* *
5625340 ATTCAACAA-ACCATTTAGAAACACCATTCAACAAACTATTTAGCAAACCATTCAATATACCAAT
1 ATTCAACAATACCATTCAGAAACACCATTCAACAAACTATTTAGCAAACCATTCAACATACCAAT
5625404 ATCATACAATACCATTCAACAAAACAATATCACACAATACCATTAAGCAAACCA
66 ATCATACAATACCATTCAACAAAACAATATCACACAATACCATTAAGCAAACCA
5625458 TAATATTTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
141 2 0.02
142 85 0.82
143 17 0.16
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (143 bp):
ATTCAACAATACCATTCAGAAACACCATTCAACAAACTATTTAGCAAACCATTCAACATACCAAT
ATCATACAATACCATTCAACAAAACAATATCACACAATACCATTAAGCAAACCAATCGGTAATGT
GTTAAAAAACACC
Found at i:5625361 original size:25 final size:25
Alignment explanation
Indices: 5625333--5625394 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
5625323 ATGTGTTAAA
5625333 AAACACCATTCAACAAACCATTTAG
1 AAACACCATTCAACAAACCATTTAG
*
5625358 AAACACCATTCAACAAACTATTTAG
1 AAACACCATTCAACAAACCATTTAG
*
5625383 CAA-ACCATTCAA
1 AAACACCATTCAA
5625395 TATACCAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 9 0.26
25 26 0.74
ACGTcount: A:0.48, C:0.27, G:0.03, T:0.21
Consensus pattern (25 bp):
AAACACCATTCAACAAACCATTTAG
Found at i:5625845 original size:21 final size:21
Alignment explanation
Indices: 5625821--5625865 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5625811 GAATATAAAA
*
5625821 TTATTAGTGAAGGTATTTTTT
1 TTATTAGTAAAGGTATTTTTT
5625842 TTATTAGTAAAGGTATTTTTT
1 TTATTAGTAAAGGTATTTTTT
5625863 TTA
1 TTA
5625866 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.58
Consensus pattern (21 bp):
TTATTAGTAAAGGTATTTTTT
Found at i:5627011 original size:239 final size:239
Alignment explanation
Indices: 5626384--5627032 Score: 754
Period size: 244 Copynumber: 2.7 Consensus size: 239
5626374 TTTTTTTGGG
* ** * * *
5626384 ATTATTAAAGGCGTATTTTGCAAAAAATGCCTTCAATAAATTATTTTAAAAAATTAGAATGAATT
1 ATTATTGAAGGCGTATAATGCCAAAAA-GTCTTCAATAAATT-TTTTCAAAAATTAGAATGAATT
* * * ** *
5626449 AGTGAAGGCATTTTTTTAGAATAAACGCCTTCAATAATGTCTTTAAAATTTTAGTAGTAGAATAT
64 AGTGAAGAC-TTTTTCTAGAATAAACACCTTCAATAATCCCTTTAAAATTTTAGTAGTAAAATAT
* * * *
5626514 TGAAGGTATTTTTTACTAAAAGACACCCTGAATAATCCCAACCGTATAATTTTTAAAAAGAAATT
128 TGAAGGTATTTTCTACTAAAAGACACCTTTAATAATCCCAA-C--ACAATTTTTAAAAAGAAATT
** * ** *
5626579 ATTAAAGGTGTTTTGTTCTAAAAAAATACTTTCATTAATTCTATACAAAA
190 ATTAAAGGCATTTTGTTCTAAAAAAATACCTTCAAGAATTCTACACAAAA
* * *
5626629 ATTATTGAATGCGTATAATG-CAAAAAATACATTCAATAAATTTCTTCAAAAATTAGAATGAATT
1 ATTATTGAAGGCGTATAATGCCAAAAAGT-C-TTCAATAAATTTTTTCAAAAATTAGAATGAATT
5626693 AGTGAATGTA-TTTTTCTAGAATAAACACCTTCAATAATCTCC-TTAAAATTTTAGTAGTAAAAT
64 AGTGAA-G-ACTTTTTCTAGAATAAACACCTTCAATAATC-CCTTTAAAATTTTAGTAGTAAAAT
* * *
5626756 ATTGAAGGTGTTTTCTACTAGAAGACACCTTTAATAATCTCAA-ACAATTTTT-AAAAGTAAATT
126 ATTGAAGGTATTTTCTACTAAAAGACACCTTTAATAATCCCAACACAATTTTTAAAAAG-AAATT
* * *
5626819 ATTGAATGCATTTT-TTCTCAAAAAATACCTTCAAGAATTCTACACAAAA
190 ATTAAAGGCATTTTGTTCTAAAAAAATACCTTCAAGAATTCTACACAAAA
5626868 ATTATTGAAGGCGTATAATGCCAAAAACGTCTTCAAATAAATTTTTTCAAAAATTAGAATGAATT
1 ATTATTGAAGGCGTATAATGCCAAAAA-GTCTTC-AATAAATTTTTTCAAAAATTAGAATGAATT
* * * * * *
5626933 AGTGAAGACGTTTTCCTAAAATAAATACCTTCAATAA-CCCTTTAAAATTTTATTAATATAATAT
64 AGTGAAGAC-TTTTTCTAGAATAAACACCTTCAATAATCCCTTTAAAATTTTAGTAGTAAAATAT
** *
5626997 TGAAGACATTTTCTACTAAAAGACGCCTTTAATAAT
128 TGAAGGTATTTTCTACTAAAAGACACCTTTAATAAT
5627033 TCTATAAACA
Statistics
Matches: 347, Mismatches: 45, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
238 3 0.01
239 110 0.32
240 89 0.26
241 1 0.00
244 115 0.33
245 29 0.08
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (239 bp):
ATTATTGAAGGCGTATAATGCCAAAAAGTCTTCAATAAATTTTTTCAAAAATTAGAATGAATTAG
TGAAGACTTTTTCTAGAATAAACACCTTCAATAATCCCTTTAAAATTTTAGTAGTAAAATATTGA
AGGTATTTTCTACTAAAAGACACCTTTAATAATCCCAACACAATTTTTAAAAAGAAATTATTAAA
GGCATTTTGTTCTAAAAAAATACCTTCAAGAATTCTACACAAAA
Found at i:5629445 original size:3 final size:3
Alignment explanation
Indices: 5629430--5629488 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
5629420 AGATGCTTTC
* * * *
5629430 ATT ATT GTT ATT ATT ATT ATT ACT ATT TTT CTTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
5629476 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
5629489 CTACTACTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5629493 original size:3 final size:3
Alignment explanation
Indices: 5629487--5629518 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5629477 TTATTATTAT
*
5629487 TAC TAC TAC TAC TAC TAC TAC TAC TAT TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
5629519 TTATTATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
TAC
Found at i:5629523 original size:9 final size:9
Alignment explanation
Indices: 5629437--5629524 Score: 70
Period size: 9 Copynumber: 9.7 Consensus size: 9
5629427 TTCATTATTG
*
5629437 TTATTATTA
1 TTATTACTA
5629446 TTATTACTA
1 TTATTACTA
*
5629455 TT-TTTCTTTA
1 TTATTAC--TA
*
5629465 TTATTATTA
1 TTATTACTA
*
5629474 TTATTATTA
1 TTATTACTA
5629483 TTATTACTA
1 TTATTACTA
* *
5629492 CTACTACTA
1 TTATTACTA
* *
5629501 CTACTACTA
1 TTATTACTA
*
5629510 CTATTACTA
1 TTATTACTA
5629519 TTATTA
1 TTATTA
5629525 TCTTTATTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
8 3 0.04
9 58 0.87
10 4 0.06
11 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (9 bp):
TTATTACTA
Found at i:5629733 original size:65 final size:65
Alignment explanation
Indices: 5629658--5629790 Score: 266
Period size: 65 Copynumber: 2.0 Consensus size: 65
5629648 AACTGCTAAA
5629658 ATTTTGGCCCTAAAATCTGGTCTGGATAGAATACAATCCCAGAAATTAAGCTTGGGATTGATTCT
1 ATTTTGGCCCTAAAATCTGGTCTGGATAGAATACAATCCCAGAAATTAAGCTTGGGATTGATTCT
5629723 ATTTTGGCCCTAAAATCTGGTCTGGATAGAATACAATCCCAGAAATTAAGCTTGGGATTGATTCT
1 ATTTTGGCCCTAAAATCTGGTCTGGATAGAATACAATCCCAGAAATTAAGCTTGGGATTGATTCT
5629788 ATT
1 ATT
5629791 CATTTTTTGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (65 bp):
ATTTTGGCCCTAAAATCTGGTCTGGATAGAATACAATCCCAGAAATTAAGCTTGGGATTGATTCT
Found at i:5629977 original size:124 final size:124
Alignment explanation
Indices: 5629757--5630003 Score: 494
Period size: 124 Copynumber: 2.0 Consensus size: 124
5629747 GATAGAATAC
5629757 AATCCCAGAAATTAAGCTTGGGATTGATTCTATTCATTTTTTGAATTGATCTTAAGCTGCCTATA
1 AATCCCAGAAATTAAGCTTGGGATTGATTCTATTCATTTTTTGAATTGATCTTAAGCTGCCTATA
5629822 AATTAGACTAATTTTACAAAACAAGAACACATAGAGAGACACACAAAAAATAGAAAAAT
66 AATTAGACTAATTTTACAAAACAAGAACACATAGAGAGACACACAAAAAATAGAAAAAT
5629881 AATCCCAGAAATTAAGCTTGGGATTGATTCTATTCATTTTTTGAATTGATCTTAAGCTGCCTATA
1 AATCCCAGAAATTAAGCTTGGGATTGATTCTATTCATTTTTTGAATTGATCTTAAGCTGCCTATA
5629946 AATTAGACTAATTTTACAAAACAAGAACACATAGAGAGACACACAAAAAATAGAAAAA
66 AATTAGACTAATTTTACAAAACAAGAACACATAGAGAGACACACAAAAAATAGAAAAA
5630004 AAATTGTTAG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (124 bp):
AATCCCAGAAATTAAGCTTGGGATTGATTCTATTCATTTTTTGAATTGATCTTAAGCTGCCTATA
AATTAGACTAATTTTACAAAACAAGAACACATAGAGAGACACACAAAAAATAGAAAAAT
Found at i:5631502 original size:11 final size:11
Alignment explanation
Indices: 5631486--5631510 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5631476 TCTTAACTGT
5631486 TATGTTTTCCC
1 TATGTTTTCCC
5631497 TATGTTTTCCC
1 TATGTTTTCCC
5631508 TAT
1 TAT
5631511 ATTGAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (11 bp):
TATGTTTTCCC
Found at i:5641977 original size:119 final size:119
Alignment explanation
Indices: 5641771--5642278 Score: 587
Period size: 119 Copynumber: 4.3 Consensus size: 119
5641761 TTCTGTCCTT
* * * * ** * * *
5641771 ATCATTTATTTTTGACCTTGACTCAGTCCTAGTTGTCTCA-TTTGACTTGTGGTTTTATCTCGAT
1 ATCATTTATTCTCGACCTTGACTCAATCCTGGTCATTTTATTTTGACTTGTGATTTTATCTCGAT
* * * * *
5641835 CGCTGGATCTTGGCTCAGTCCAGATCATTTTTTATGATTCGTGGTTTCATCCCG
66 CACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCA
* * *
5641889 ATCATTGATTCTCGACCTTGACTCGATCCTGGTCATTTTATTTTGACTTGTGATTTTGTCTCTG-
1 ATCATTTATTCTCGACCTTGACTCAATCCTGGTCATTTTATTTTGACTTGTGATTTTATCTC-GA
* *
5641953 TCACTTGATCTTGGCTTAATCCAGATCATTT-TTCATGATTCGT-GTTTCTGTCCCA
65 TCACTTGATCTTGGCTTAGTCCAGATCATTTCTT-ATGATTCGTGGTTTC-ATCCCA
* * *
5642008 ATCATTTATTCTCGACCTTGACTCGATCCTGGTCACTTTATTTTGACTTGTGATTTCATCTCCG-
1 ATCATTTATTCTCGACCTTGACTCAATCCTGGTCATTTTATTTTGACTTGTGATTTTATCT-CGA
* * * * *
5642072 TCACTTGATCTTGGCTTAGTACGGATCATTTCTTATGATTTGTGGTTCCAT-TCA
65 TCACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCA
* * *
5642126 GATCATTTATTCTCGACCTTGACTCAATCCTGGTCGTTTTATTTTGACTTGTGATTTTGTTTCGA
1 -ATCATTTATTCTCGACCTTGACTCAATCCTGGTCATTTTATTTTGACTTGTGATTTTATCTCGA
* * * *
5642191 TCACTTGATCTTGGCTTAGTTCAGATCATTGCTTACGATTCGTGGTTTCATCTCA
65 TCACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCA
* * **
5642246 ATCATTTATTTTTGACCTCAACTCAATCCTGGT
1 ATCATTTATTCTCGACCTTGACTCAATCCTGGT
5642279 TGCCTCTTTT
Statistics
Matches: 335, Mismatches: 45, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
118 41 0.12
119 283 0.84
120 11 0.03
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (119 bp):
ATCATTTATTCTCGACCTTGACTCAATCCTGGTCATTTTATTTTGACTTGTGATTTTATCTCGAT
CACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCA
Found at i:5642590 original size:3 final size:3
Alignment explanation
Indices: 5642575--5642640 Score: 82
Period size: 3 Copynumber: 22.7 Consensus size: 3
5642565 AAATGCTTTC
* * *
5642575 ATT ATT GTT ATT ATT ATT ATT ACT ATT TTT ATT -TT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5642621 ATT ATT ATT ACT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
5642641 CTTTATTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5642616 original size:22 final size:22
Alignment explanation
Indices: 5642588--5642654 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
5642578 ATTGTTATTA
*
5642588 TTATTATTACTATTTTTATTTT
1 TTATTATTACTATTATTATTTT
* *
5642610 TTATTATTATTATTATTA-TTA
1 TTATTATTACTATTATTATTTT
* *
5642631 CTATTATTATCT-TTATTTTTTT
1 TTATTATTA-CTATTATTATTTT
5642653 TT
1 TT
5642655 GTTTCATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATTATTACTATTATTATTTT
Found at i:5642646 original size:9 final size:10
Alignment explanation
Indices: 5642582--5642647 Score: 60
Period size: 9 Copynumber: 7.5 Consensus size: 10
5642572 TTCATTATTG
5642582 TTATTAT-TA
1 TTATTATCTA
5642591 TTATTA-CTA
1 TTATTATCTA
*
5642600 TTTTTAT-T-
1 TTATTATCTA
5642608 TT-TTAT-TA
1 TTATTATCTA
5642616 TTATTAT-TA
1 TTATTATCTA
5642625 TTATTA-CTA
1 TTATTATCTA
5642634 TTATTATCT-
1 TTATTATCTA
5642643 TTATT
1 TTATT
5642648 TTTTTTTGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
7 5 0.10
8 4 0.08
9 39 0.78
10 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATCTA
Found at i:5643494 original size:20 final size:20
Alignment explanation
Indices: 5643469--5643506 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5643459 TTAGTAAGCC
*
5643469 AAGATTCGTGCATCAACCCG
1 AAGATTCGTGCACCAACCCG
5643489 AAGATTCGTGCACCAACC
1 AAGATTCGTGCACCAACC
5643507 TACGTCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (20 bp):
AAGATTCGTGCACCAACCCG
Found at i:5643551 original size:10 final size:10
Alignment explanation
Indices: 5643534--5643589 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
5643524 CAATCGTTGG
5643534 TTTTTTTTT-
1 TTTTTTTTTA
*
5643543 TTATTTTTTA
1 TTTTTTTTTA
5643553 TTTTTTTTTA
1 TTTTTTTTTA
*
5643563 CCTTTTTTTTCA
1 --TTTTTTTTTA
* *
5643575 TTATTTTCTA
1 TTTTTTTTTA
5643585 TTTTT
1 TTTTT
5643590 ATAAAAAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 8 0.22
10 20 0.54
12 9 0.24
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:5643568 original size:17 final size:16
Alignment explanation
Indices: 5643534--5643572 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
5643524 CAATCGTTGG
**
5643534 TTTTTTTTTTTATTTT
1 TTTTTTTTTTTACCTT
5643550 TTATTTTTTTTTACCTT
1 TT-TTTTTTTTTACCTT
5643567 TTTTTT
1 TTTTTT
5643573 CATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTTTACCTT
Found at i:5644321 original size:21 final size:21
Alignment explanation
Indices: 5644296--5644339 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5644286 CATATTACGT
5644296 AAGTTAGTGATAC-TGATATTC
1 AAGTTAGTGAT-CTTGATATTC
*
5644317 AAGTTGGTGATCTTGATATTC
1 AAGTTAGTGATCTTGATATTC
5644338 AA
1 AA
5644340 AATAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (21 bp):
AAGTTAGTGATCTTGATATTC
Found at i:5648010 original size:140 final size:140
Alignment explanation
Indices: 5647754--5648010 Score: 336
Period size: 140 Copynumber: 1.8 Consensus size: 140
5647744 AATTAACAGT
* * *
5647754 TATTGTTCTATTTTAATAGTTTTGATAGTTTCAATACATGATATTAAACTTATCGAAAGTATTAA
1 TATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTATCGAAAGTATTAA
* * *
5647819 ACTTAGTTGCCACGGTTGATATGTATGAAAAAGTTATTGTTTACATTTATTTAGGTAAAAATACA
66 ACTTAGTTGCCACGGTTGATATATATGAAAAAGTTATCGTTTACATCTATTTAGGTAAAAATACA
5647884 AATTTGAGGC
131 AATTTGAGGC
* * ** *
5647894 TATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACTTGATATTAAACTTGTC-CCATTAATTA
1 TATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTATCGAAAGT-ATTA
* * * * * **
5647958 AACTTGGTTTCTACGGTTGATATATGTGAAAAAGTTGTCGTTTGTATCTATTT
65 AACTTAGTTGCCACGGTTGATATATATGAAAAAGTTATCGTTTACATCTATTT
5648011 GGGACTATTT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
139 2 0.02
140 96 0.98
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTGTTCTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTATCGAAAGTATTAA
ACTTAGTTGCCACGGTTGATATATATGAAAAAGTTATCGTTTACATCTATTTAGGTAAAAATACA
AATTTGAGGC
Found at i:5650142 original size:31 final size:32
Alignment explanation
Indices: 5650107--5650167 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5650097 TAGGATTTCA
* *
5650107 AATTTAAC-AACTCTAGATCTAACCGTTCAAG
1 AATTTAACAAACTCTAGATCAAACCATTCAAG
* *
5650138 AATTTTACAAATTCTAGATCAAACCATTCA
1 AATTTAACAAACTCTAGATCAAACCATTCA
5650168 TTTGCATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (32 bp):
AATTTAACAAACTCTAGATCAAACCATTCAAG
Found at i:5653477 original size:18 final size:19
Alignment explanation
Indices: 5653451--5653501 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
5653441 CTCTTTTTTG
5653451 TTTTT-ATTTTTATTCCAA
1 TTTTTAATTTTTATTCCAA
* *
5653469 -TTTTAATTTTAATTCTAA
1 TTTTTAATTTTTATTCCAA
5653487 TTTTTAATTTTTATT
1 TTTTTAATTTTTATT
5653502 ATTATCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 13 0.46
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAATTTTTATTCCAA
Found at i:5653818 original size:3 final size:3
Alignment explanation
Indices: 5653812--5653844 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5653802 CGTCGTCGTC
5653812 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5653845 TGTGCTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5654255 original size:159 final size:158
Alignment explanation
Indices: 5654064--5654402 Score: 405
Period size: 159 Copynumber: 2.1 Consensus size: 158
5654054 GAACAAATTT
* * ** ***
5654064 TATGCTTTATATTTTAAAATTTTATTTATTATAGAATTTTAACTAAAAAAAATTATTTGGACCTA
1 TATGATTTATATTTT-ATATTTTATTTATTATAGAATTCCAACTAAAAAAAATTATCCAGACCTA
* * * *
5654129 TCCCATTTTAAACCAAA-CAAATGGGAGG-TAAAGGAGAAATATATAATGCAACAACTTCACAAT
65 TCCCATTTTAAACCAAACCAAA-AGAAGGCAAAAGG-GAAATATA-AATACAACAACTTCACAAT
* * * **
5654192 CA-AGGTCTTTATGTCATGGCTGTTGGTGTTTA
127 CATA-GTCCTCACGTCATGGCTGTTAATGTTTA
* *
5654224 TATGATTTATATTTTATATTTTATTTATTATAGAATTCCAACTAATAAAAATTATCCAGATCTAT
1 TATGATTTATATTTTATATTTTATTTATTATAGAATTCCAACTAAAAAAAATTATCCAGACCTAT
*
5654289 CGCATTTTAAACCAAACCAAAAGAAGGCAAAAGGGAAATATAAATACAACAACTTCACAATCATA
66 CCCATTTTAAACCAAACCAAAAGAAGGCAAAAGGGAAATATAAATACAACAACTTCACAATCATA
*
5654354 GTCCTCACGTCATGGCTTTTAATGTTTA
131 GTCCTCACGTCATGGCTGTTAATGTTTA
*
5654382 TATGATGTTATTATTATATAT
1 TATGAT-TTA-TATTTTATAT
5654403 GTAAATATAT
Statistics
Matches: 153, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
158 48 0.31
159 73 0.48
160 32 0.21
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (158 bp):
TATGATTTATATTTTATATTTTATTTATTATAGAATTCCAACTAAAAAAAATTATCCAGACCTAT
CCCATTTTAAACCAAACCAAAAGAAGGCAAAAGGGAAATATAAATACAACAACTTCACAATCATA
GTCCTCACGTCATGGCTGTTAATGTTTA
Found at i:5656003 original size:16 final size:16
Alignment explanation
Indices: 5655982--5656041 Score: 79
Period size: 16 Copynumber: 3.7 Consensus size: 16
5655972 ATTTTTTAAT
5655982 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
5655998 TATTTA--TACATTTATA
1 TATTTATTTA-ATTT-TA
5656014 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
5656030 TATTTATATTAA
1 TATTTAT-TTAA
5656042 AAATATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.05
15 4 0.10
16 23 0.59
17 8 0.21
18 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATTTAATTTTA
Found at i:5656073 original size:19 final size:19
Alignment explanation
Indices: 5656031--5656074 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5656021 TTAATTTTAT
*
5656031 ATTTATATTAAAAATATTA
1 ATTTATATTAAAAATAATA
*
5656050 TTTTATA-TATAAAATAATA
1 ATTTATATTA-AAAATAATA
5656069 ATTTAT
1 ATTTAT
5656075 TAATTTTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATATTAAAAATAATA
Found at i:5659088 original size:18 final size:19
Alignment explanation
Indices: 5659067--5659113 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5659057 TTTGTCAATT
*
5659067 TTTTAATTAAAATTT-TTA
1 TTTTAATTAAAATTTGATA
* *
5659085 TTTTTATTATAATTTGATA
1 TTTTAATTAAAATTTGATA
5659104 TTCTTAATTA
1 TT-TTAATTA
5659114 TATTAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAATTAAAATTTGATA
Found at i:5659090 original size:19 final size:20
Alignment explanation
Indices: 5659066--5659113 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
5659056 GTTTGTCAAT
*
5659066 TTTTTAATTAAAATTT-TTA
1 TTTTTAATTAAAATTTGATA
*
5659085 TTTTT-ATTATAATTTGATA
1 TTTTTAATTAAAATTTGATA
*
5659104 TTCTTAATTA
1 TTTTTAATTA
5659114 TATTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 11 0.46
20 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTAATTAAAATTTGATA
Found at i:5661223 original size:3 final size:3
Alignment explanation
Indices: 5661215--5661239 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5661205 AGAGAGAATT
5661215 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
5661240 CCAACCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5666838 original size:14 final size:15
Alignment explanation
Indices: 5666809--5666842 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5666799 ATTAATTATG
5666809 AAAATTAAATATATA
1 AAAATTAAATATATA
*
5666824 AAAATTACATA-ATA
1 AAAATTAAATATATA
5666838 AAAAT
1 AAAAT
5666843 GTATTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTAAATATATA
Found at i:5669679 original size:21 final size:20
Alignment explanation
Indices: 5669654--5669692 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5669644 TTTTTTTATA
5669654 TTTAAAAATTAAAAATTATTT
1 TTTAAAAATT-AAAATTATTT
**
5669675 TTTAATTATTAAAATTAT
1 TTTAAAAATTAAAATTAT
5669693 AAATTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAAATTAAAATTATTT
Found at i:5669700 original size:28 final size:27
Alignment explanation
Indices: 5669645--5669697 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5669635 TTTCACTCAT
5669645 TTTTTTATATTTAAAAATTAAAAATTA
1 TTTTTTATATTTAAAAATTAAAAATTA
* *
5669672 TTTTTTA-ATTATTAAAATTATAAATT
1 TTTTTTATATT-TAAAAATTAAAAATT
5669698 TATATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTTTATATTTAAAAATTAAAAATTA
Found at i:5670519 original size:24 final size:24
Alignment explanation
Indices: 5670489--5670547 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
5670479 TAAAATTAAA
5670489 TTTTATTTTTTTA-ACATCTAAAAT
1 TTTTATTTTTTTATA-ATCTAAAAT
* *
5670513 TTTTATTTTTTTATATTTTAAAAT
1 TTTTATTTTTTTATAATCTAAAAT
5670537 TATTTATTTTT
1 T-TTTATTTTT
5670548 AACATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATTTTTTTATAATCTAAAAT
Found at i:5670547 original size:16 final size:17
Alignment explanation
Indices: 5670522--5670554 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5670512 TTTTTATTTT
5670522 TTTATATTTTAAAATTA
1 TTTATATTTTAAAATTA
*
5670539 TTTAT-TTTTAACATTA
1 TTTATATTTTAAAATTA
5670555 AAAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATATTTTAAAATTA
Found at i:5670558 original size:23 final size:23
Alignment explanation
Indices: 5670490--5670562 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 23
5670480 AAAATTAAAT
5670490 TTTATTTTTTTAACATCTAAAATT-
1 TTTA-TTTTTTAACAT-TAAAATTA
**
5670514 TTTATTTTTTTATATTTTAAAATTA
1 TTTA-TTTTTTA-ACATTAAAATTA
5670539 TTTA-TTTTTAACATTAAAAATTA
1 TTTATTTTTTAACATT-AAAATTA
5670562 T
1 T
5670563 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.07
23 14 0.33
24 19 0.45
25 6 0.14
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATTTTTTAACATTAAAATTA
Found at i:5681216 original size:20 final size:20
Alignment explanation
Indices: 5681175--5681216 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5681165 TAGGCGTTCG
**
5681175 TTGGAGTTTGTTGTATTTTC
1 TTGGAGTTTGTTGTATGATC
5681195 TTGGAGTTTGTATGTA-GATC
1 TTGGAGTTTGT-TGTATGATC
5681215 TT
1 TT
5681217 TTGGCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.14, C:0.05, G:0.26, T:0.55
Consensus pattern (20 bp):
TTGGAGTTTGTTGTATGATC
Found at i:5684271 original size:22 final size:22
Alignment explanation
Indices: 5684245--5684314 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
5684235 ATTTGTTTTA
5684245 TTGGTCTTGACATCTAGTCTTT
1 TTGGTCTTGACATCTAGTCTTT
* *
5684267 TTGGT-TATGACAAGCT-GT-TTAA
1 TTGGTCT-TGAC-ATCTAGTCTT-T
*
5684289 TT-GTCTTGACATCTAGTCCTT
1 TTGGTCTTGACATCTAGTCTTT
5684310 TTGGT
1 TTGGT
5684315 TGTTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 17 0.47
23 3 0.08
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (22 bp):
TTGGTCTTGACATCTAGTCTTT
Found at i:5700184 original size:20 final size:20
Alignment explanation
Indices: 5700143--5700184 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5700133 TAGGCGTTCG
**
5700143 TTGGAGTTTGTTGTATTTTC
1 TTGGAGTTTGTTGTATGATC
5700163 TTGGAGTTTGTATGTA-GATC
1 TTGGAGTTTGT-TGTATGATC
5700183 TT
1 TT
5700185 TTGGCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.14, C:0.05, G:0.26, T:0.55
Consensus pattern (20 bp):
TTGGAGTTTGTTGTATGATC
Found at i:5703237 original size:22 final size:22
Alignment explanation
Indices: 5703212--5703281 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
5703202 ATCTGTTTTA
5703212 TTGGTCTTGACATCTAGTCTTT
1 TTGGTCTTGACATCTAGTCTTT
* *
5703234 TTGGT-TATGACAAGCT-GT-TTAA
1 TTGGTCT-TGAC-ATCTAGTCTT-T
*
5703256 TT-GTCTTGACATCTAGTCCTT
1 TTGGTCTTGACATCTAGTCTTT
5703277 TTGGT
1 TTGGT
5703282 TGTTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 17 0.47
23 3 0.08
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (22 bp):
TTGGTCTTGACATCTAGTCTTT
Found at i:5703271 original size:43 final size:44
Alignment explanation
Indices: 5703195--5703282 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 44
5703185 GTGTCCTATG
* * *
5703195 TATGACAATCTGTTTTATTGGTCTTGACATCTAGTCTTTTTGGT
1 TATGACAAGCTGTTTAATTGGTCTTGACATCTAGTCCTTTTGGT
5703239 TATGACAAGCTGTTTAATT-GTCTTGACATCTAGTCCTTTTGGT
1 TATGACAAGCTGTTTAATTGGTCTTGACATCTAGTCCTTTTGGT
5703282 T
1 T
5703283 GTTTAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 24 0.59
44 17 0.41
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (44 bp):
TATGACAAGCTGTTTAATTGGTCTTGACATCTAGTCCTTTTGGT
Found at i:5706027 original size:2 final size:2
Alignment explanation
Indices: 5706022--5706056 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5706012 CGAGCGCGTG
5706022 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
5706057 GAATACAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5709444 original size:29 final size:29
Alignment explanation
Indices: 5709411--5709468 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5709401 TTGAATGTCG
*
5709411 TTACAAAAGCTAATTTATCAAATCATAAA
1 TTACAAAAGCCAATTTATCAAATCATAAA
5709440 TTACAAAAGCCAATTTATCAAATCATAAA
1 TTACAAAAGCCAATTTATCAAATCATAAA
5709469 CCAAAGTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (29 bp):
TTACAAAAGCCAATTTATCAAATCATAAA
Found at i:5717321 original size:255 final size:257
Alignment explanation
Indices: 5716861--5717380 Score: 884
Period size: 255 Copynumber: 2.0 Consensus size: 257
5716851 CTTCAGCAGA
* *
5716861 AAAATTATAAAAAGAAAATGGAAAATAGAAAGTAAAAATGAATACTTACATGATTTTGACATGGG
1 AAAATTATAAAAAAAAAATGGAAAATAGAAAGTAAAAATGAATACTT--ATCATTTTGACATGGG
5716926 AGATTTTCGTCGCAACGCGATATCGAGGAACGTGAACAGCACGCTTAAGAAAATGAAGCAGTCCA
64 AGATTTTCGTCGCAACGCGATATCGAGGAACGTGAACAGCACGCTTAAGAAAATGAAGCAGTCCA
* **
5716991 ATTGCAAAGGCCCAAAGCGGAACTCTGATTTCCCTCTTCCAAAGAAAAGCCCTAAATCCACAGTT
129 ATTGCAAAGGCCCAAAGCCGAAAACTGATTTCCCTCTTCCAAAGAAAAGCCCTAAATCCACAGTT
* * *
5717056 TGACCATTGGGCTTTGATGTCGTCTCTGAAAAAAATATTATTTTTCCTCGACTTCAACCAAAAAC
194 TGAACATTGGGCTTTGACGTCATCTCTGAAAAAAA-ATTATTTTTCCTCGACTTCAACCAAAAAC
*
5717121 AAAATTATAAAAAAAAAATGGAAAATAGAAAG-CAAAATGAATACTT-TCATTTTGACATGGGAG
1 AAAATTATAAAAAAAAAATGGAAAATAGAAAGTAAAAATGAATACTTATCATTTTGACATGGGAG
* *
5717184 ATTTTCGTCGCAACGCGATATTGAGGAACGTGAACGGCACGCTTAA-AAAATGAAGCAGTCCAAT
66 ATTTTCGTCGCAACGCGATATCGAGGAACGTGAACAGCACGCTTAAGAAAATGAAGCAGTCCAAT
5717248 TGCAAAGGCCCAAAGCCGAAAACTGATTTCCCTCTTCCAAAGAAAAGCCCTAAATCCACAGTTTG
131 TGCAAAGGCCCAAAGCCGAAAACTGATTTCCCTCTTCCAAAGAAAAGCCCTAAATCCACAGTTTG
*
5717313 AACATTGGGCTTTGACGTCATCTCTGAAAAAAAATTATTTTTCCTCGACTTCAACGAAAAAC
196 AACATTGGGCTTTGACGTCATCTCTGAAAAAAAATTATTTTTCCTCGACTTCAACCAAAAAC
5717375 AAAATT
1 AAAATT
5717381 CTCATTGTTA
Statistics
Matches: 248, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
254 34 0.14
255 110 0.44
256 60 0.24
259 13 0.05
260 31 0.12
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (257 bp):
AAAATTATAAAAAAAAAATGGAAAATAGAAAGTAAAAATGAATACTTATCATTTTGACATGGGAG
ATTTTCGTCGCAACGCGATATCGAGGAACGTGAACAGCACGCTTAAGAAAATGAAGCAGTCCAAT
TGCAAAGGCCCAAAGCCGAAAACTGATTTCCCTCTTCCAAAGAAAAGCCCTAAATCCACAGTTTG
AACATTGGGCTTTGACGTCATCTCTGAAAAAAAATTATTTTTCCTCGACTTCAACCAAAAAC
Found at i:5717597 original size:14 final size:15
Alignment explanation
Indices: 5717578--5717607 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5717568 GTATTACACA
5717578 TGATATG-ATATAAT
1 TGATATGTATATAAT
5717592 TGATATGTATATAAT
1 TGATATGTATATAAT
5717607 T
1 T
5717608 AATCAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TGATATGTATATAAT
Found at i:5717656 original size:19 final size:19
Alignment explanation
Indices: 5717624--5717661 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5717614 TTTAAACATT
5717624 ACATAAATAAACATGAATA
1 ACATAAATAAACATGAATA
* *
5717643 ACATAGATATACATGAATA
1 ACATAAATAAACATGAATA
5717662 CAAATTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (19 bp):
ACATAAATAAACATGAATA
Found at i:5717691 original size:148 final size:146
Alignment explanation
Indices: 5717507--5717806 Score: 492
Period size: 148 Copynumber: 2.0 Consensus size: 146
5717497 TAAAACATGA
5717507 ACATAATACAAATTATAAATATATTTAAATCTTAAATATGAATATGATATTTTTATTATAAGTAT
1 ACATAATACAAATTATAAATATATTTAAATCTTAAATATGAATATGATATTTTTATTATAAGTAT
** * * *
5717572 TACACATGATATGATATAATTGATATGTATATAATTAATCAATTTAAACATTACATAAATAAACA
66 TACACATGATACAATAAAATTGATACGTATATAATTAATCAATTTAAACATAACATAAATAAACA
*
5717637 TGAATAACATAGATAT
131 TGAATAACACAGATAT
*
5717653 ACATGAATACAAATTATAAAATATGTTTAAATCTTAAATATGAATATGATATTTTTATTATAAGT
1 ACAT-AATACAAATTAT-AAATATATTTAAATCTTAAATATGAATATGATATTTTTATTATAAGT
* *
5717718 ATTACACATGATACAATAAAATTGATACGTGTATAATTAATCTATTTAAACATAACATAAATAAA
64 ATTACACATGATACAATAAAATTGATACGTATATAATTAATCAATTTAAACATAACATAAATAAA
5717783 CATGAATAACACAGATAT
129 CATGAATAACACAGATAT
*
5717801 ATATAA
1 ACATAA
5717807 ATAATACGAA
Statistics
Matches: 142, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
146 4 0.03
147 14 0.10
148 124 0.87
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.37
Consensus pattern (146 bp):
ACATAATACAAATTATAAATATATTTAAATCTTAAATATGAATATGATATTTTTATTATAAGTAT
TACACATGATACAATAAAATTGATACGTATATAATTAATCAATTTAAACATAACATAAATAAACA
TGAATAACACAGATAT
Found at i:5718312 original size:9 final size:9
Alignment explanation
Indices: 5718300--5718343 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
5718290 TATAAAAAAT
5718300 ATGTTAAAC
1 ATGTTAAAC
*
5718309 ATGTTAAAT
1 ATGTTAAAC
*
5718318 ATGTTAAAA
1 ATGTTAAAC
*
5718327 ATATTAAAC
1 ATGTTAAAC
5718336 ATGTTAAA
1 ATGTTAAA
5718344 TATATATTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (9 bp):
ATGTTAAAC
Found at i:5718316 original size:27 final size:25
Alignment explanation
Indices: 5718286--5718347 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 25
5718276 TAAATTAAAA
5718286 TAAATATAAAAAATATGTTAAACATGT
1 TAAATATAAAAAATA--TTAAACATGT
*
5718313 TAAATATGTTAAAAATATTAAACATGT
1 TAAATA--TAAAAAATATTAAACATGT
5718340 TAAATATA
1 TAAATATA
5718348 TATTCGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
27 22 0.71
29 8 0.26
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (25 bp):
TAAATATAAAAAATATTAAACATGT
Found at i:5718317 original size:18 final size:18
Alignment explanation
Indices: 5718296--5718348 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
5718286 TAAATATAAA
* *
5718296 AAATATGTTAAACATGTT
1 AAATATGTTAAAAATATT
5718314 AAATATGTTAAAAATATT
1 AAATATGTTAAAAATATT
* *
5718332 AAACATGTTAAATATAT
1 AAATATGTTAAAAATAT
5718349 ATTCGTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (18 bp):
AAATATGTTAAAAATATT
Found at i:5725845 original size:18 final size:20
Alignment explanation
Indices: 5725802--5725845 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
5725792 TAAATTAAAA
*
5725802 AATAAATTTTAAATTTATTT
1 AATAAATTTTAAATTTATAT
*
5725822 ATTAAA-TTT-AATTTATAT
1 AATAAATTTTAAATTTATAT
5725840 AATAAA
1 AATAAA
5725846 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAAATTTTAAATTTATAT
Found at i:5730999 original size:2 final size:2
Alignment explanation
Indices: 5730992--5731020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5730982 TTCAAAGGGT
5730992 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 T
5731021 TTTATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5739823 original size:19 final size:20
Alignment explanation
Indices: 5739782--5739823 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
5739772 AGTTTTTTAT
* *
5739782 TTTTATTTTATATATTTAGA
1 TTTTATTTTATAAATATAGA
*
5739802 TTTT-TTTTATAAATATATA
1 TTTTATTTTATAAATATAGA
5739821 TTT
1 TTT
5739824 ATGAACATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATTTTATAAATATAGA
Found at i:5752568 original size:30 final size:31
Alignment explanation
Indices: 5752510--5752577 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
5752500 GAATAGTCCT
* * *
5752510 AATTTTTTTTAATTTTAGGATATTTAAATTTTA
1 AATTTTTTTTAATATT--GATATCTAAATTATA
5752543 AATTTTTTTTAATATT-ATATCTAAATTATA
1 AATTTTTTTTAATATTGATATCTAAATTATA
5752573 AATTT
1 AATTT
5752578 ACTAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.53
33 15 0.47
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (31 bp):
AATTTTTTTTAATATTGATATCTAAATTATA
Found at i:5753406 original size:23 final size:25
Alignment explanation
Indices: 5753363--5753410 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
5753353 GGTAAATAGG
5753363 TTTTAATAATATACTTGTTATTATTA
1 TTTTAATAATATAC-TGTTATTATTA
5753389 TTTTAATAATATA-T-TTATTATT
1 TTTTAATAATATACTGTTATTATT
5753411 GTTAATTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 1 0.05
26 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTAATAATATACTGTTATTATTA
Found at i:5753638 original size:29 final size:29
Alignment explanation
Indices: 5753599--5753676 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
5753589 AATTAATAAA
*
5753599 TTTATAATTTAAATATCACATTAAAAATT
1 TTTATAATTTAAATATCAAATTAAAAATT
* * *
5753628 TTTAAAATTTAAGTATCAAATTAAACATT
1 TTTATAATTTAAATATCAAATTAAAAATT
*
5753657 TCATTATAATTTAAAAATCA
1 T--TTATAATTTAAATATCA
5753677 TTAATCATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 26 0.65
31 14 0.35
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (29 bp):
TTTATAATTTAAATATCAAATTAAAAATT
Found at i:5775752 original size:29 final size:29
Alignment explanation
Indices: 5775710--5775766 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5775700 TTATTTTTTA
5775710 TTATTATACAATAAATTAAA-AAATAAATC
1 TTATTATACAATAAA-TAAATAAATAAATC
* *
5775739 TTATTGTATAATAAATAAATAAATAAAT
1 TTATTATACAATAAATAAATAAATAAAT
5775767 TTTAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (29 bp):
TTATTATACAATAAATAAATAAATAAATC
Found at i:5779453 original size:30 final size:30
Alignment explanation
Indices: 5779417--5779484 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5779407 CGAAATTAAT
* * *
5779417 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATTATTATATAAATATAAATAATTA
* *
5779447 AAAATATCATTATATAAATATATATAATTA
1 AAAATATTATTATATAAATATAAATAATTA
5779477 AAAA-ATTA
1 AAAATATTA
5779485 AAAAATTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (30 bp):
AAAATATTATTATATAAATATAAATAATTA
Found at i:5781001 original size:12 final size:11
Alignment explanation
Indices: 5780959--5781008 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 11
5780949 TGAATATTTC
5780959 AAAAATAAATGA
1 AAAAATAAAT-A
*
5780971 TAAAAATAAGTA
1 -AAAAATAAATA
5780983 AACAAATAAACTA
1 AA-AAATAAA-TA
5780996 AAAAATAAATA
1 AAAAATAAATA
5781007 AA
1 AA
5781009 TGAAAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 6 0.18
12 14 0.42
13 13 0.39
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:5782039 original size:13 final size:13
Alignment explanation
Indices: 5782021--5782045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5782011 ACCAAAATAT
5782021 TAAAATAAATAAA
1 TAAAATAAATAAA
5782034 TAAAATAAATAA
1 TAAAATAAATAA
5782046 GTAAGTAAAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:5782465 original size:17 final size:18
Alignment explanation
Indices: 5782446--5782494 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5782436 GGATTTCAGG
* *
5782446 TTTGCAATAATTTTTAGT
1 TTTGCAAGAATTTTTAGA
*
5782464 TTTGTAAGAATTTTTAGA
1 TTTGCAAGAATTTTTAGA
*
5782482 TTTGTAAGAATTT
1 TTTGCAAGAATTT
5782495 AGATTCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (18 bp):
TTTGCAAGAATTTTTAGA
Found at i:5782475 original size:18 final size:18
Alignment explanation
Indices: 5782454--5782494 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
5782444 GGTTTGCAAT
*
5782454 AATTTTTAGTTTTGTAAG
1 AATTTTTAGATTTGTAAG
5782472 AATTTTTAGATTTGTAAG
1 AATTTTTAGATTTGTAAG
5782490 AATTT
1 AATTT
5782495 AGATTCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (18 bp):
AATTTTTAGATTTGTAAG
Found at i:5782497 original size:16 final size:17
Alignment explanation
Indices: 5782457--5782499 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5782447 TTGCAATAAT
*
5782457 TTTTAGTTTTGTAAGAA
1 TTTTAGATTTGTAAGAA
5782474 TTTTTAGATTTGTAAGAA
1 -TTTTAGATTTGTAAGAA
5782492 -TTTAGATT
1 TTTTAGATT
5782500 CTCAAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 8 0.33
18 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (17 bp):
TTTTAGATTTGTAAGAA
Found at i:5782602 original size:17 final size:17
Alignment explanation
Indices: 5782568--5782624 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
5782558 TCAAATTCAA
*
5782568 AAGAATTT--GATTCAC
1 AAGAATTTAAGATTTAC
* *
5782583 AAGAATTTTAGATTTGC
1 AAGAATTTAAGATTTAC
**
5782600 AAGAATGAAAGATTTAC
1 AAGAATTTAAGATTTAC
5782617 AAGAATTT
1 AAGAATTT
5782625 GATTATCAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 8 0.25
17 24 0.75
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (17 bp):
AAGAATTTAAGATTTAC
Found at i:5782748 original size:23 final size:21
Alignment explanation
Indices: 5782704--5782750 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
5782694 ATTGCAAGGC
*
5782704 TCAAATCTAACATTTAAAGAT
1 TCAAATCTAAAATTTAAAGAT
*
5782725 TCAAATTCTAAAATTCTGAAGAT
1 TCAAA-TCTAAAATT-TAAAGAT
5782748 TCA
1 TCA
5782751 CACCCAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (21 bp):
TCAAATCTAAAATTTAAAGAT
Found at i:5783098 original size:23 final size:23
Alignment explanation
Indices: 5783045--5783087 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5783035 CAAAACTTCT
*
5783045 CATTAAAAAACTTTAGAGATTCA
1 CATTAAAAAACTTCAGAGATTCA
*
5783068 CATAAAAAAACTTCA-AGATT
1 CATTAAAAAACTTCAGAGATT
5783088 ACCATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (23 bp):
CATTAAAAAACTTCAGAGATTCA
Found at i:5784310 original size:7 final size:7
Alignment explanation
Indices: 5784289--5784337 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
5784279 AATTTGACTC
5784289 TTTTT-T
1 TTTTTAT
*
5784295 TTTTCAT
1 TTTTTAT
5784302 TTTTTATT
1 TTTTTA-T
5784310 TTTTTACTT
1 TTTTTA--T
5784319 TTTTTAT
1 TTTTTAT
5784326 TTTTTAT
1 TTTTTAT
5784333 TTTTT
1 TTTTT
5784338 TCACTTCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 4 0.11
7 19 0.50
8 7 0.18
9 8 0.21
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:5784327 original size:24 final size:26
Alignment explanation
Indices: 5784292--5784343 Score: 90
Period size: 24 Copynumber: 2.1 Consensus size: 26
5784282 TTGACTCTTT
5784292 TTTTTTTCATTTTTTATTTTTTT-AC
1 TTTTTTTCATTTTTTATTTTTTTCAC
5784317 TTTTTTT-ATTTTTTATTTTTTTCAC
1 TTTTTTTCATTTTTTATTTTTTTCAC
5784342 TT
1 TT
5784344 CATCCATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTTCATTTTTTATTTTTTTCAC
Found at i:5784337 original size:17 final size:17
Alignment explanation
Indices: 5784291--5784338 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
5784281 TTTGACTCTT
* *
5784291 TTTTTTTTCATTTTTTA
1 TTTTTTTACTTTTTTTA
5784308 TTTTTTTACTTTTTTTA
1 TTTTTTTACTTTTTTTA
5784325 -TTTTTTA-TTTTTTT
1 TTTTTTTACTTTTTTT
5784339 CACTTCATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
17 15 0.52
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTACTTTTTTTA
Found at i:5784338 original size:8 final size:8
Alignment explanation
Indices: 5784292--5784338 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
5784282 TTGACTCTTT
5784292 TTTTTTTCA
1 TTTTTTT-A
5784301 -TTTTTTA
1 TTTTTTTA
5784308 TTTTTTTA
1 TTTTTTTA
5784316 CTTTTTTTA
1 -TTTTTTTA
5784325 -TTTTTTA
1 TTTTTTTA
5784332 TTTTTTT
1 TTTTTTT
5784339 CACTTCATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 8 0.23
8 19 0.54
9 8 0.23
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:5795120 original size:15 final size:15
Alignment explanation
Indices: 5795085--5795128 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
5795075 CTTTTGTTCT
5795085 TGATACATTTGAGATGGA
1 TGATACATTT--GA-GGA
*
5795103 TGATATATTTGAGGA
1 TGATACATTTGAGGA
5795118 TGATACATTTG
1 TGATACATTTG
5795129 TCGTGGGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 2 0.08
18 9 0.38
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.39
Consensus pattern (15 bp):
TGATACATTTGAGGA
Found at i:5795180 original size:18 final size:18
Alignment explanation
Indices: 5795085--5795190 Score: 60
Period size: 18 Copynumber: 6.1 Consensus size: 18
5795075 CTTTTGTTCT
*
5795085 TGATACATTTGAGATGGA
1 TGATACATTTGAGGTGGA
*
5795103 TGATATATTTGA---GGA
1 TGATACATTTGAGGTGGA
** *
5795118 TGATACATTTGTCGTGGG
1 TGATACATTTGAGGTGGA
* * **
5795136 GGATATATTT-ATGGTAAA
1 TGATACATTTGA-GGTGGA
* *
5795154 GGATTCATTTGAGGTGGA
1 TGATACATTTGAGGTGGA
5795172 TGATACATTT-ATGGTGGA
1 TGATACATTTGA-GGTGGA
5795190 T
1 T
5795191 AATAACCATA
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
15 13 0.20
17 1 0.02
18 50 0.77
19 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.38
Consensus pattern (18 bp):
TGATACATTTGAGGTGGA
Found at i:5797738 original size:42 final size:43
Alignment explanation
Indices: 5797691--5797775 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
5797681 TTGAAGATTA
5797691 GAGGTTTGAGATTTTGATTTT-AGGGTTTCGA-CTTTAGGGTTT
1 GAGGTTTGAGATTTTGATTTTGA-GGTTTCGAGCTTTAGGGTTT
* *
5797733 GAGGTTTGAGATTTTGATTTTGAGGTTTGGAGGTTTAGGGTTT
1 GAGGTTTGAGATTTTGATTTTGAGGTTTCGAGCTTTAGGGTTT
5797776 CGATTTTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
42 28 0.72
43 11 0.28
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.47
Consensus pattern (43 bp):
GAGGTTTGAGATTTTGATTTTGAGGTTTCGAGCTTTAGGGTTT
Found at i:5797754 original size:21 final size:21
Alignment explanation
Indices: 5797691--5797761 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
5797681 TTGAAGATTA
5797691 GAGGTTTGAGATTTTGATTTT
1 GAGGTTTGAGATTTTGATTTT
* * **
5797712 -AGGGTTTCGA-CTTTAGGGTTT
1 GA-GGTTT-GAGATTTTGATTTT
5797733 GAGGTTTGAGATTTTGATTTT
1 GAGGTTTGAGATTTTGATTTT
5797754 GAGGTTTG
1 GAGGTTTG
5797762 GAGGTTTAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 32 0.84
22 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.32, T:0.48
Consensus pattern (21 bp):
GAGGTTTGAGATTTTGATTTT
Found at i:5797780 original size:29 final size:29
Alignment explanation
Indices: 5797709--5797791 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
5797699 AGATTTTGAT
*
5797709 TTTAGGGTTTCGACTTTAGGGTTT-GAGG
1 TTTAGGGTTTCGATTTTAGGGTTTGGAGG
* *
5797737 TTT-GAGATTTTGATTTT-GAGGTTTGGAGG
1 TTTAG-GGTTTCGATTTTAG-GGTTTGGAGG
5797766 TTTAGGGTTTCGATTTTAGGGTTTGG
1 TTTAGGGTTTCGATTTTAGGGTTTGG
5797792 GATTTTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
27 2 0.04
28 17 0.38
29 24 0.53
30 2 0.04
ACGTcount: A:0.14, C:0.04, G:0.35, T:0.47
Consensus pattern (29 bp):
TTTAGGGTTTCGATTTTAGGGTTTGGAGG
Found at i:5797798 original size:15 final size:14
Alignment explanation
Indices: 5797706--5797789 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 14
5797696 TTGAGATTTT
5797706 GATTTTAGGGTTTC
1 GATTTTAGGGTTTC
*
5797720 GACTTTAGGGTTT-
1 GATTTTAGGGTTTC
* * *
5797733 GAGGTTT-GAGATTTT
1 GA-TTTTAG-GGTTTC
*
5797748 GATTTT-GAGGTTTG
1 GATTTTAG-GGTTTC
*
5797762 GAGGTTTAGGGTTTC
1 GA-TTTTAGGGTTTC
5797777 GATTTTAGGGTTT
1 GATTTTAGGGTTT
5797790 GGGATTTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
13 3 0.05
14 40 0.71
15 12 0.21
16 1 0.02
ACGTcount: A:0.15, C:0.04, G:0.33, T:0.48
Consensus pattern (14 bp):
GATTTTAGGGTTTC
Found at i:5797798 original size:29 final size:29
Alignment explanation
Indices: 5797706--5797798 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
5797696 TTGAGATTTT
*
5797706 GATTTTAGGGTTTCGACTTTAGGGTTTGAG
1 GATTTTAGGGTTTCGATTTTAGGGTTTG-G
* * *
5797736 G-TTTGA-GATTTTGATTTT-GAGGTTT-G
1 GATTTTAGGGTTTCGATTTTAG-GGTTTGG
*
5797762 GAGGTTTAGGGTTTCGATTTTAGGGTTTGG
1 GA-TTTTAGGGTTTCGATTTTAGGGTTTGG
5797792 GATTTTA
1 GATTTTA
5797799 ATTTTTAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 17 0.35
29 23 0.48
30 5 0.10
ACGTcount: A:0.16, C:0.03, G:0.33, T:0.47
Consensus pattern (29 bp):
GATTTTAGGGTTTCGATTTTAGGGTTTGG
Found at i:5799326 original size:24 final size:24
Alignment explanation
Indices: 5799299--5799353 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
5799289 TCTTTCTTTT
5799299 TTTTAAAAAAATAATT-TTTATTAA
1 TTTTAAAAAAATAATTATTT-TTAA
* * *
5799323 TTTTTAATAATTAATTGATTTTTAA
1 TTTTAAAAAAATAATT-ATTTTTAA
5799348 TTTTAA
1 TTTTAA
5799354 TTAAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 13 0.52
25 9 0.36
26 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTAAAAAAATAATTATTTTTAA
Found at i:5799330 original size:17 final size:17
Alignment explanation
Indices: 5799310--5799357 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
5799300 TTTAAAAAAA
*
5799310 TAATTTTTATTAATTTT
1 TAATTTTAATTAATTTT
* *
5799327 TAATAATTAATTGATTTT
1 TAAT-TTTAATTAATTTT
5799345 TAATTTTAATTAA
1 TAATTTTAATTAA
5799358 ATTAATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTTTAATTAATTTT
Found at i:5799843 original size:105 final size:105
Alignment explanation
Indices: 5799712--5800102 Score: 436
Period size: 105 Copynumber: 3.7 Consensus size: 105
5799702 AACAAGATAG
* * * *
5799712 GATTGAACCGTGAGGCAAGAAAAATAAAGAGACTAG-GATTAGACCGCAAGTCAGAGAAATAATA
1 GATTAAACCGT-AGTCAAGAAAAATAAAGAGACTAGAGATTAAACCGTAAGTCAGAGAAATAATA
5799776 AAGATCAGGATTAAACCATGACTTAAAAGTAAAGAGATCGA
65 AAGATCAGGATTAAACCATGACTTAAAAGTAAAGAGATCGA
* * * *
5799817 GATTAAACCGTGAGTCAAGAAAAATAAAGAGA-TTGAGATTAAATCGTAAGTTAGAGAAATAGTA
1 GATTAAACCGT-AGTCAAGAAAAATAAAGAGACTAGAGATTAAACCGTAAGTCAGAGAAATAATA
* * * * *
5799881 AATATC-GAGATTAAACCACGACTTAAAAGTAAAAAGATTGG
65 AAGATCAG-GATTAAACCATGACTTAAAAGTAAAGAGATCGA
* ** * * *
5799922 GATTGAATTGTAGGTCAAGAAAAATAAAGAGACTA-ATATTAAACCGTAAGTTAGAGAAA-AAAA
1 GATTAAACCGTA-GTCAAGAAAAATAAAGAGACTAGAGATTAAACCGTAAGTCAGAGAAATAATA
* * *
5799985 AAGATCAGGATTAAATCATGACTTAAAAGTAAAGATATCAA
65 AAGATCAGGATTAAACCATGACTTAAAAGTAAAGAGATCGA
* * * * *
5800026 GATTAAACCGCTAATCAA-AAAAATAAAGAGAC-CGAGATTAAATCATAAGTCAGAGAAATAGTA
1 GATTAAACCG-TAGTCAAGAAAAATAAAGAGACTAGAGATTAAACCGTAAGTCAGAGAAATAATA
*
5800089 AAGATCGGGATTAA
65 AAGATCAGGATTAA
5800103 CCCGCGAGTC
Statistics
Matches: 237, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
103 34 0.14
104 63 0.27
105 139 0.59
106 1 0.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.21
Consensus pattern (105 bp):
GATTAAACCGTAGTCAAGAAAAATAAAGAGACTAGAGATTAAACCGTAAGTCAGAGAAATAATAA
AGATCAGGATTAAACCATGACTTAAAAGTAAAGAGATCGA
Found at i:5799849 original size:36 final size:37
Alignment explanation
Indices: 5799710--5799859 Score: 120
Period size: 36 Copynumber: 4.2 Consensus size: 37
5799700 ATAACAAGAT
* * *
5799710 AGGATTGAACCGTGAGGCAAGAAAAATAAAGAGA-CT
1 AGGATTAAACCGTGAGTCAAGAAAAATAAAGAGATCG
* **
5799746 AGGATTAGACCGCAAGTCAGAGAAATAAT-AA-AGATC-
1 AGGATTAAACCGTGAGTCA-AGAAA-AATAAAGAGATCG
* ** *
5799782 AGGATTAAACCATGA--C-TTAAAAGTAAAGAGATCG
1 AGGATTAAACCGTGAGTCAAGAAAAATAAAGAGATCG
*
5799816 A-GATTAAACCGTGAGTCAAGAAAAATAAAGAGATTG
1 AGGATTAAACCGTGAGTCAAGAAAAATAAAGAGATCG
5799852 A-GATTAAA
1 AGGATTAAA
5799860 TCGTAAGTTA
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
31 2 0.02
32 5 0.06
33 17 0.19
34 2 0.02
35 1 0.01
36 50 0.57
37 8 0.09
38 3 0.03
ACGTcount: A:0.49, C:0.11, G:0.23, T:0.18
Consensus pattern (37 bp):
AGGATTAAACCGTGAGTCAAGAAAAATAAAGAGATCG
Found at i:5800569 original size:108 final size:108
Alignment explanation
Indices: 5800031--5801122 Score: 900
Period size: 108 Copynumber: 10.1 Consensus size: 108
5800021 ATCAAGATTA
* * * * *
5800031 AACCGCTAA-TCAAAAAAAT-AAAGAGACCGAGATTAAATCATAAGTCAGAGAA--ATAGTAAA-
1 AACCGC-AAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCA-AAAACTATAG-AAAT
* * * ** *
5800091 GATCGGGATTAACCCGCGAGTCAAAGATTAAAAATGACTGGGACTA
63 GATCGAGATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
*** * * ** * **
5800137 AATAACAAATCAAAACAATAAAAGTA-ACTGATATTAAATCGTAAGTCAAAAAACTATAGAAATG
1 AACCGCAAGTCAAAAAAATAAAAG-AGACTGGGATTAAACCACAAGTC-AAAAACTATAGAAATG
* * * * * * *
5800201 A-CTGGGATTGAACCACGAGTCAAAGATTAACGACGATTAGGATTG
64 ATC-GAGATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
* * *
5800246 AACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAATCAGGAAAACTATAAAAATG
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCA--AAAACTATAGAAATG
* *
5800311 ATCG-GAATTGAACCACGAGTCAAAGATTAACGATGACTGTGG-CTG
64 ATCGAG-ATTAAACCACGAGTCAAAGATTAATGATGACTG-GGACTG
* * * * *
5800356 AATCGCAAGTCAAAAAAATAAAAGAGACTGTGATTAAATCGCAAGTCAAGAAAATTATAGAAATG
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTC-A-AAAACTATAGAAATG
* * * * * **
5800421 ATCGGGATTAAACCACAAGCCAAATATTGATGACAACTGGGACTG
64 ATCGAGATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
* * * ** *
5800466 AATCGCAAGTCAGAAAGATAAAAGAGACTGACATTAAACCACAAGTCAAAAATTATAGAAATGAT
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGAT
** * *
5800531 CGAGATTAAACCATAAG-CTAAATATTAACGATGACTGGGACTG
66 CGAGATTAAACCACGAGTC-AAAGATTAATGATGACTGGGACTG
* * * **
5800574 AACCGTAAGTCAGAAAGATAAAAGAGACTGGGATTAAACCGTAAGTCAAAAACTATAGAAATGAC
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGA-
* * * *
5800639 CCG-GATTGAACCATGAGTCAAAGATTAATGATGACTAGGG-CTA
65 TCGAGATTAAACCACGAGTCAAAGATTAATGATGACT-GGGACTG
* * * * ** * *
5800682 AACCGTAAGTTAGAAAAATAAAAGAGACTGGGACTAAACCGTAAGTCGAAAACTATAAAAATGAT
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGAT
* * *
5800747 C-AGAATTAAACCACGAGCCAAATATTAATGATAACTGGGACTG
66 CGAG-ATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
* * * * * * * ** *
5800790 AACCACAAGTTAGAGAAATAAAAGAGATTGAGATTAAATCACAAGTTGAAAACTACAGAAATGAT
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGAT
* * * ** *
5800855 TGGGATTGAACCACGAGTCAAAGATTAATGACAACTGGGGCTG
66 CGAGATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
* * * ** *
5800898 AACCGTAAGTCAAAAAAATAAAAGAGA-TTGAATTAAACCGTAAGTCAAAAACTATAAAAATGA-
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGAT
* * * * *
5800961 CCAGGATTGAACCATGAGTCAAAGATTAATGATGATTGGGGCTG
66 CGA-GATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
* * * *
5801005 AACCACAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAATAAAAAACTATAGAAATAAT
1 AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGAT
* * * * * * *
5801070 TGAGATTAAATCATGAGCCAAATATTAACGATGATTGGGACTG
66 CGAGATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
*
5801113 AACCGTAAGT
1 AACCGCAAGT
5801123 TAGAGAAATA
Statistics
Matches: 809, Mismatches: 149, Indels: 54
0.80 0.15 0.05
Matches are distributed among these distances:
105 2 0.00
106 12 0.01
107 118 0.15
108 413 0.51
109 83 0.10
110 176 0.22
111 5 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (108 bp):
AACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAGTCAAAAACTATAGAAATGAT
CGAGATTAAACCACGAGTCAAAGATTAATGATGACTGGGACTG
Found at i:5800614 original size:36 final size:36
Alignment explanation
Indices: 5800472--5800732 Score: 126
Period size: 37 Copynumber: 7.3 Consensus size: 36
5800462 ACTGAATCGC
** **
5800472 AAGTCAGAAAGATAAAAGAGACTGACATTAAACCAC
1 AAGTCAGAAAGATAAAAGAGACTGGGATTAAACCGT
* * * * *
5800508 AAGTCAAAAATTATAGAAA-TGA-TCGAGATTAAACCAT
1 AAGTCAGAAA-GATA-AAAGAGACT-GGGATTAAACCGT
* * * * * *
5800545 AAG-C-TAAATATTAACGATGACTGGGACTGAACCGT
1 AAGTCAGAAAGATAAAAGA-GACTGGGATTAAACCGT
5800580 AAGTCAGAAAGATAAAAGAGACTGGGATTAAACCGT
1 AAGTCAGAAAGATAAAAGAGACTGGGATTAAACCGT
* * * ** * *
5800616 AAGTCAAAAACTATAGAAA-TGACCCGGATTGAACCAT
1 AAGTCAGAAA-GATA-AAAGAGACTGGGATTAAACCGT
* * * *
5800653 GAGTC--AAAGATTAATGATGACTAGGG-CTAAACCGT
1 AAGTCAGAAAGATAAAAGA-GACT-GGGATTAAACCGT
* * *
5800688 AAGTTAGAAAAATAAAAGAGACTGGGACTAAACCGT
1 AAGTCAGAAAGATAAAAGAGACTGGGATTAAACCGT
5800724 AAGTC-GAAA
1 AAGTCAGAAA
5800733 ACTATAAAAA
Statistics
Matches: 167, Mismatches: 42, Indels: 33
0.69 0.17 0.14
Matches are distributed among these distances:
33 4 0.02
34 5 0.03
35 39 0.23
36 56 0.34
37 57 0.34
38 6 0.04
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.19
Consensus pattern (36 bp):
AAGTCAGAAAGATAAAAGAGACTGGGATTAAACCGT
Found at i:5800759 original size:216 final size:216
Alignment explanation
Indices: 5800098--5801142 Score: 1001
Period size: 216 Copynumber: 4.8 Consensus size: 216
5800088 AAAGATCGGG
* * ** * ** * *
5800098 ATTAACCCGCGAGTCAAAGATTAAAAATGACTGGGACTAAATAACAAATCAAAACAATAAAAGTA
1 ATTAAACCACGAGTCAAAGATTAACGATGACTGGGACTGAACCACAAGTCAAAAAAATAAAAG-A
** *
5800163 -ACTGATATTAAATCGTAAGTCAAAAAACTATAGAAATGACTGGGATTGAACCACGAGTCAAAGA
65 GACTGGGATTAAATCGCAAGTC-AAAAACTATAGAAATGACTGGGATTGAACCACGAGTCAAAGA
* * ** * *
5800227 TTAACGACGATTAGGATTGAACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAAT
129 TTAATGACGACTAGGGCTGAACCGTAAGTCAGAAAAATAAAAGAGACTGGGATTAAACCACAAGT
*
5800292 CAGGAAAACTATAAAAATGATCGGA
194 CA--AAAACTATAAAAATGATCAGA
* * *
5800317 ATTGAACCACGAGTCAAAGATTAACGATGACTGTGG-CTGAATCGCAAGTCAAAAAAATAAAAGA
1 ATTAAACCACGAGTCAAAGATTAACGATGACTG-GGACTGAACCACAAGTCAAAAAAATAAAAGA
* * * * *
5800381 GACTGTGATTAAATCGCAAGTCAAGAAAATTATAGAAATGA-TCGGGATTAAACCACAAGCCAAA
65 GACTGGGATTAAATCGCAAGTC-A-AAAACTATAGAAATGACT-GGGATTGAACCACGAGTCAAA
* * * * * * **
5800445 TATTGATGACAACT-GGGACTGAATCGCAAGTCAGAAAGATAAAAGAGACTGACATTAAACCACA
127 GATTAATGACGACTAGGG-CTGAACCGTAAGTCAGAAAAATAAAAGAGACTGGGATTAAACCACA
* *
5800509 AGTCAAAAATTATAGAAATGATC-GA
191 AGTCAAAAACTATAAAAATGATCAGA
** * ** * *
5800534 GATTAAACCATAAG-CTAAATATTAACGATGACTGGGACTGAACCGTAAGTCAGAAAGATAAAAG
1 -ATTAAACCACGAGTC-AAAGATTAACGATGACTGGGACTGAACCACAAGTCAAAAAAATAAAAG
* * ** *
5800598 AGACTGGGATTAAACCGTAAGTCAAAAACTATAGAAATGACCCGGATTGAACCATGAGTCAAAGA
64 AGACTGGGATTAAATCGCAAGTCAAAAACTATAGAAATGACTGGGATTGAACCACGAGTCAAAGA
* * * * **
5800663 TTAATGATGACTAGGGCTAAACCGTAAGTTAGAAAAATAAAAGAGACTGGGACTAAACCGTAAGT
129 TTAATGACGACTAGGGCTGAACCGTAAGTCAGAAAAATAAAAGAGACTGGGATTAAACCACAAGT
*
5800728 CGAAAACTATAAAAATGATCAGA
194 CAAAAACTATAAAAATGATCAGA
* * * * * * *
5800751 ATTAAACCACGAGCCAAATATTAATGATAACTGGGACTGAACCACAAGTTAGAGAAATAAAAGAG
1 ATTAAACCACGAGTCAAAGATTAACGATGACTGGGACTGAACCACAAGTCAAAAAAATAAAAGAG
* * * ** * *
5800816 ATTGAGATTAAATCACAAGTTGAAAACTACAGAAATGATTGGGATTGAACCACGAGTCAAAGATT
66 ACTGGGATTAAATCGCAAGTCAAAAACTATAGAAATGACTGGGATTGAACCACGAGTCAAAGATT
* * * * * **
5800881 AATGACAACTGGGGCTGAACCGTAAGTCAAAAAAATAAAAGAGA-TTGAATTAAACCGTAAGTCA
131 AATGACGACTAGGGCTGAACCGTAAGTCAGAAAAATAAAAGAGACTGGGATTAAACCACAAGTCA
* *
5800945 AAAACTATAAAAATGACCAGG
196 AAAACTATAAAAATGATCAGA
* * * * *
5800966 ATTGAACCATGAGTCAAAGATTAATGATGATTGGGGCTGAACCACAAGTCAAAAAAATAAAAGAG
1 ATTAAACCACGAGTCAAAGATTAACGATGACTGGGACTGAACCACAAGTCAAAAAAATAAAAGAG
* * * * * * * * * * * *
5801031 ACTGGGATTAAACCACAAATAAAAAACTATAGAAATAATTGAGATTAAATCATGAGCCAAATATT
66 ACTGGGATTAAATCGCAAGTCAAAAACTATAGAAATGACTGGGATTGAACCACGAGTCAAAGATT
* * * * *
5801096 AACGATGA-TTGGGACTGAACCGTAAGTTAGAGAAATAAATA-AGACTG
131 AATGACGACTAGGG-CTGAACCGTAAGTCAGAAAAATAAA-AGAGACTG
5801143 AGCTGTGAGT
Statistics
Matches: 678, Mismatches: 133, Indels: 33
0.80 0.16 0.04
Matches are distributed among these distances:
214 4 0.01
215 171 0.25
216 244 0.36
217 12 0.02
218 87 0.13
219 73 0.11
220 87 0.13
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (216 bp):
ATTAAACCACGAGTCAAAGATTAACGATGACTGGGACTGAACCACAAGTCAAAAAAATAAAAGAG
ACTGGGATTAAATCGCAAGTCAAAAACTATAGAAATGACTGGGATTGAACCACGAGTCAAAGATT
AATGACGACTAGGGCTGAACCGTAAGTCAGAAAAATAAAAGAGACTGGGATTAAACCACAAGTCA
AAAACTATAAAAATGATCAGA
Found at i:5801060 original size:323 final size:323
Alignment explanation
Indices: 5800153--5801143 Score: 1184
Period size: 323 Copynumber: 3.0 Consensus size: 323
5800143 AAATCAAAAC
* * ** *
5800153 AATAAAAGTA-ACTGATATTAAATCGTAAGTCAAAAAACTATAGAAATGACTGGGATTGAACCAC
1 AATAAAAG-AGACTGACATTAAACCACAAGTC-AAAAACTATAGAAATGATTGGGATTGAACCAC
* * *
5800217 GAGTCAAAGATTAACGACGATTAGGATTGAACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTA
64 GAGTCAAAGATTAACGACGACTGGGACTGAACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTA
** * * * *
5800282 AACCACAAATCAGGAAAACTATAAAAATGATCGGAATTGAACCACGAGTCAAAGATTAACGATGA
129 AACCGTAAGTCA--AAAACTATAAAAATGACCGG-ATTGAACCATGAGTCAAAGATTAATGATGA
* * * * *
5800347 CTGTGGCTGAATCGCAAGTCAAAAAAATAAAAGAGACTGTGATTAAATCGCAAGTCAAGAAAATT
191 CTGGGGCTGAACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCGCAAGT-AA-AAAACT
* * * * * * *
5800412 ATAGAAATGATCGGGATTAAACCACAAGCCAAATATTGATGACAACTGGGACTGAATCGCAAGTC
254 ATAGAAATGATCAGAATTAAACCACGAGCCAAATATTAATGATAACTGGGACTGAACCGCAAGTT
5800477 AGA-A
319 AGAGA
* * * * **
5800481 AGATAAAAGAGACTGACATTAAACCACAAGTCAAAAATTATAGAAATGATCGAGATTAAACCATA
1 A-ATAAAAGAGACTGACATTAAACCACAAGTCAAAAACTATAGAAATGATTGGGATTGAACCACG
* * * *
5800546 AG-CTAAATATTAACGATGACTGGGACTGAACCGTAAGTCAGAAAGATAAAAGAGACTGGGATTA
65 AGTC-AAAGATTAACGACGACTGGGACTGAACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTA
*
5800610 AACCGTAAGTCAAAAACTATAGAAATGACCCGGATTGAACCATGAGTCAAAGATTAATGATGACT
129 AACCGTAAGTCAAAAACTATAAAAATGA-CCGGATTGAACCATGAGTCAAAGATTAATGATGACT
* * * * * * * ** *
5800675 AGGGCTAAACCGTAAGTTAGAAAAATAAAAGAGACTGGGACTAAACCGTAAGTCGAAAACTATAA
193 GGGGCTGAACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCGCAAGTAAAAAACTATAG
*
5800740 AAATGATCAGAATTAAACCACGAGCCAAATATTAATGATAACTGGGACTGAACCACAAGTTAGAG
258 AAATGATCAGAATTAAACCACGAGCCAAATATTAATGATAACTGGGACTGAACCGCAAGTTAGAG
5800805 A
323 A
* * * ** *
5800806 AATAAAAGAGATTGAGATTAAATCACAAGTTGAAAACTACAGAAATGATTGGGATTGAACCACGA
1 AATAAAAGAGACTGACATTAAACCACAAGTCAAAAACTATAGAAATGATTGGGATTGAACCACGA
* * * * *
5800871 GTCAAAGATTAATGACAACTGGGGCTGAACCGTAAGTCAAAAAAATAAAAGAGA-TTGAATTAAA
66 GTCAAAGATTAACGACGACTGGGACTGAACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTAAA
*
5800935 CCGTAAGTCAAAAACTATAAAAATGACCAGGATTGAACCATGAGTCAAAGATTAATGATGATTGG
131 CCGTAAGTCAAAAACTATAAAAATGACC-GGATTGAACCATGAGTCAAAGATTAATGATGACTGG
* * *
5801000 GGCTGAACCACAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCACAAATAAAAAACTATAGAA
195 GGCTGAACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCGCAAGTAAAAAACTATAGAA
* * * * * * * *
5801065 ATAAT-TGAGATTAAATCATGAGCCAAATATTAACGATGATTGGGACTGAACCGTAAGTTAGAGA
260 ATGATCAGA-ATTAAACCACGAGCCAAATATTAATGATAACTGGGACTGAACCGCAAGTTAGAGA
5801129 AATAAATA-AGACTGA
1 AATAAA-AGAGACTGA
5801144 GCTGTGAGTT
Statistics
Matches: 560, Mismatches: 94, Indels: 23
0.83 0.14 0.03
Matches are distributed among these distances:
322 4 0.01
323 184 0.33
324 162 0.29
325 3 0.01
326 87 0.16
327 4 0.01
328 92 0.16
329 24 0.04
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (323 bp):
AATAAAAGAGACTGACATTAAACCACAAGTCAAAAACTATAGAAATGATTGGGATTGAACCACGA
GTCAAAGATTAACGACGACTGGGACTGAACCGTAAGTCAAAAAAATAAAAGAGACTGGGATTAAA
CCGTAAGTCAAAAACTATAAAAATGACCGGATTGAACCATGAGTCAAAGATTAATGATGACTGGG
GCTGAACCGCAAGTCAAAAAAATAAAAGAGACTGGGATTAAACCGCAAGTAAAAAACTATAGAAA
TGATCAGAATTAAACCACGAGCCAAATATTAATGATAACTGGGACTGAACCGCAAGTTAGAGA
Found at i:5809607 original size:35 final size:36
Alignment explanation
Indices: 5809540--5809625 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
5809530 TGGCATCTTA
* *
5809540 AAAATATATAAATTAATATCTTGAAATCTTAAA-AAT
1 AAAATTTAT-AATTAATATCTTAAAATCTTAAATAAT
* *
5809576 AAAATTTATAATTTATATCTTAAAATTTTAAATAAT
1 AAAATTTATAATTAATATCTTAAAATCTTAAATAAT
5809612 ATATAATTT-TAATT
1 A-A-AATTTATAATT
5809626 CAATTTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
35 20 0.47
36 12 0.28
37 6 0.14
38 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (36 bp):
AAAATTTATAATTAATATCTTAAAATCTTAAATAAT
Found at i:5809950 original size:16 final size:15
Alignment explanation
Indices: 5809929--5809979 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
5809919 TAACTAGTTT
5809929 ATATAATATTTAATTA
1 ATATAATATTT-ATTA
5809945 ATATAAT-TTTATTA
1 ATATAATATTTATTA
*
5809959 TATATATTATTTATTA
1 -ATATAATATTTATTA
5809975 A-ATAA
1 ATATAA
5809980 AAATATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 7 0.23
15 10 0.32
16 14 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATAATATTTATTA
Found at i:5810247 original size:31 final size:30
Alignment explanation
Indices: 5810209--5810270 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
5810199 ATATAAAATT
5810209 TAAAATTTTA-ATATAAAAATTATACATTTTA
1 TAAAATTTTAGATAT--AAATTATACATTTTA
* *
5810240 TAAAATTTTAGATGTAAATTATATATTTTA
1 TAAAATTTTAGATATAAATTATACATTTTA
5810270 T
1 T
5810271 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 15 0.54
31 10 0.36
32 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAAATTTTAGATATAAATTATACATTTTA
Found at i:5811061 original size:63 final size:62
Alignment explanation
Indices: 5810942--5811128 Score: 173
Period size: 62 Copynumber: 3.0 Consensus size: 62
5810932 AAAAAATATT
* * * * * **
5810942 AAAGATTATTTAAGATATTTTTTAT-TGAAAAACACCTTAAATAATCTCTTTTATTTTTTTAAA
1 AAAGATTATTT-AGGTATTTTTTGTCT-AAAAATATCTTAAATAATCACTTAAATTTTTTTAAA
* *
5811005 AAAGATTATTTAGGGATTTTTTGTCTAAAAATATCTTAAATAATCACTTAAAATTTTTT-AA
1 AAAGATTATTTAGGTATTTTTTGTCTAAAAATATCTTAAATAATCACTTAAATTTTTTTAAA
** * * * *
5811066 AGGGTATTATTTTAGGTA-TTTTTGACTAAAAATATTTTAAATAATACATTTCAATTTTTTTAA
1 AAAG-ATTA-TTTAGGTATTTTTTGTCTAAAAATATCTTAAATAAT-CACTTAAATTTTTTTAA
5811129 TCGTATTAGT
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
61 4 0.04
62 66 0.65
63 31 0.30
64 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.47
Consensus pattern (62 bp):
AAAGATTATTTAGGTATTTTTTGTCTAAAAATATCTTAAATAATCACTTAAATTTTTTTAAA
Found at i:5811135 original size:62 final size:61
Alignment explanation
Indices: 5811009--5811159 Score: 151
Period size: 62 Copynumber: 2.4 Consensus size: 61
5810999 TTTAAAAAAG
* * *
5811009 ATTATTTAGGGATTTTTTGTCTAAAAATATCTTAAATAATCACTTAAAATTTTTTAAAGGGT
1 ATTATTTAGGTA-TTTTTGACTAAAAATATCTTAAATAATCACTTAAAATTTTTTAAAGCGT
* ** * *
5811071 ATTATTTTAGGTATTTTTGACTAAAAATATTTTAAATAAT-ACATTTCAATTTTTTTAATCGT
1 ATTA-TTTAGGTATTTTTGACTAAAAATATCTTAAATAATCAC-TTAAAATTTTTTAAAGCGT
* * * *
5811133 ATTAGTTAAAGTGTTTTTAACTAAAAA
1 ATTA-TTTAGGTATTTTTGACTAAAAA
5811160 CGCCTTAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 2 0.03
62 65 0.88
63 7 0.09
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (61 bp):
ATTATTTAGGTATTTTTGACTAAAAATATCTTAAATAATCACTTAAAATTTTTTAAAGCGT
Found at i:5811417 original size:63 final size:64
Alignment explanation
Indices: 5811295--5811415 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 64
5811285 ATGCTTTAAT
* * *
5811295 TTTTTTGAAGGAGATTATTTAATGAGTTTTTGATCTAAAAATACTTTAAATTATCTTTTAAAAA
1 TTTTTTGAAGGAGATTATTTAAAGAGTTTTTGATCAAAAAATACTTTAAATAATCTTTTAAAAA
* *
5811359 TTTTTT-AAGG-GCATTATTTAAAGTGTTTTTGAT-AAAAAATA-TCTTAAATAATTTTTT
1 TTTTTTGAAGGAG-ATTATTTAAAGAGTTTTTGATCAAAAAATACT-TTAAATAATCTTTT
5811416 TATTATTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 1 0.02
62 20 0.40
63 23 0.46
64 6 0.12
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (64 bp):
TTTTTTGAAGGAGATTATTTAAAGAGTTTTTGATCAAAAAATACTTTAAATAATCTTTTAAAAA
Found at i:5812282 original size:15 final size:14
Alignment explanation
Indices: 5812263--5812297 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5812253 TTAATAAATT
*
5812263 AATAATTAATTTTA
1 AATAATTAATCTTA
5812277 ACATAATTAATCTTA
1 A-ATAATTAATCTTA
5812292 AATAAT
1 AATAAT
5812298 AATAGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAATTAATCTTA
Found at i:5812335 original size:26 final size:28
Alignment explanation
Indices: 5812306--5812387 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
5812296 ATAATAGATA
*
5812306 AATAATTTTTTAATAT-TATATTA-ATT
1 AATAATTTTTTAATATAAATATTATATT
* *
5812332 AATAAATTTATAATATAAATATTATATT
1 AATAATTTTTTAATATAAATATTATATT
*
5812360 AA-AATTTTTTAAATTTAAATATTATATT
1 AATAATTTTTT-AATATAAATATTATATT
5812388 TAATTTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.30
27 12 0.26
28 21 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATAATTTTTTAATATAAATATTATATT
Found at i:5812775 original size:18 final size:18
Alignment explanation
Indices: 5812749--5812803 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
5812739 ATTAATACAC
*
5812749 GTTTGACATATTTTATAT
1 GTTTAACATATTTTATAT
* * *
5812767 GTTTAACATCTTTAACAT
1 GTTTAACATATTTTATAT
*
5812785 ATTTAACATATTTTTATAT
1 GTTTAACATA-TTTTATAT
5812804 TTATTTTAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (18 bp):
GTTTAACATATTTTATAT
Found at i:5812782 original size:9 final size:9
Alignment explanation
Indices: 5812754--5812797 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
5812744 TACACGTTTG
*
5812754 ACATATTTT
1 ACATATTTA
* *
5812763 ATATGTTTA
1 ACATATTTA
*
5812772 ACATCTTTA
1 ACATATTTA
5812781 ACATATTTA
1 ACATATTTA
5812790 ACATATTT
1 ACATATTT
5812798 TTATATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (9 bp):
ACATATTTA
Done.