Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 173 of 297
Found at i:58283419 original size:44 final size:43
Alignment explanation
Indices: 58283339--58283440 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
58283329 ATCCGATTGT
* * *
58283339 GTTATCGTGTAAGACCACGTCTGAGACGTTGGCATCG-ACTTATGA
1 GTTA-CGTGTAAGACCACGTCTGAGACATCGACATCGTA-TT-TGA
* *
58283384 GTTACGTGTAAGACCAGGTCTGGGACATCGACATCGTATTTGA
1 GTTACGTGTAAGACCACGTCTGAGACATCGACATCGTATTTGA
*
58283427 -TTTCGTGTAAGACC
1 GTTACGTGTAAGACC
58283441 CTATGTGGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 13 0.26
43 3 0.06
44 29 0.58
45 5 0.10
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (43 bp):
GTTACGTGTAAGACCACGTCTGAGACATCGACATCGTATTTGA
Found at i:58283504 original size:43 final size:43
Alignment explanation
Indices: 58283339--58283502 Score: 147
Period size: 43 Copynumber: 3.8 Consensus size: 43
58283329 ATCCGATTGT
* *
58283339 GTTATCGTGTAAGACCACGTCTGAGACGTTGGCATCGACT-TATG
1 GTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTG
* * * *
58283383 AGTTACGTGTAAGACCAGGTCTGGGACATCGACATCG-TATTTG
1 -GTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTG
* * * * *
58283426 ATTTCGTGTAAGACC-CTATGTGGGACAG-TGGCATTGATATTTG
1 GTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTG
*
58283469 GTTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
58283503 TGTATGAGCT
Statistics
Matches: 93, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
42 27 0.29
43 34 0.37
44 28 0.30
45 4 0.04
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTG
Found at i:58292630 original size:29 final size:29
Alignment explanation
Indices: 58292570--58292649 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
58292560 AGTTTGCCAC
* * *
58292570 AAGGCATTCATTTAACAGAGATAGCTAGA
1 AAGGCTTTCATATAACAGAGATAGCTAAA
58292599 AAGGCTTTCATATAACAGAGATCA-CTAAA
1 AAGGCTTTCATATAACAGAGAT-AGCTAAA
* * *
58292628 AAGCCTTTCTTATAACAAAGAT
1 AAGGCTTTCATATAACAGAGAT
58292650 TGCCACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
29 43 0.98
30 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGGCTTTCATATAACAGAGATAGCTAAA
Found at i:58293827 original size:20 final size:19
Alignment explanation
Indices: 58293802--58293863 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
58293792 CCAATACATT
58293802 TCACATAGCATATATTGAGC
1 TCACATAGCATATATTGA-C
** *
58293822 TCACATCTCATACATT---
1 TCACATAGCATATATTGAC
58293838 TCACATAGCATATATTGAAC
1 TCACATAGCATATATTG-AC
58293858 TCACAT
1 TCACAT
58293864 CTCATACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 13 0.41
20 19 0.59
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (19 bp):
TCACATAGCATATATTGAC
Found at i:58293842 original size:36 final size:36
Alignment explanation
Indices: 58293795--58293875 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
58293785 TCACTAGCCA
*
58293795 ATACATTTCACATAGCATATATTGAGCTCACATCTC
1 ATACATTTCACATAGCATATATTGAACTCACATCTC
58293831 ATACATTTCACATAGCATATATTGAACTCACATCTC
1 ATACATTTCACATAGCATATATTGAACTCACATCTC
*
58293867 ATACTTTTC
1 ATACATTTC
58293876 TCATCTAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (36 bp):
ATACATTTCACATAGCATATATTGAACTCACATCTC
Found at i:58294259 original size:140 final size:140
Alignment explanation
Indices: 58294018--58294276 Score: 333
Period size: 140 Copynumber: 1.8 Consensus size: 140
58294008 AGGCTAAGAC
* **
58294018 CATGTCCCAGACATGGTCTTACATTAGCTCTCACATATCCGTGCCGATGCCATATCCCAGACAGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATATCCCAGACAGG
** *
58294083 GTCTTACACTGACACATCTTGTAGCTGATGCATGTCCTAGACATGTCTTACACTGGCTTATGTCA
65 GTCTTACACTGACACATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCA
58294148 CGAGGTTGATA
130 CGAGGTTGATA
* * * * *
58294159 CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGTCGATGCCATCTCCCAGACATGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATATCCCAGACAGGG
* * * * *
58294222 TCTTACGCTGGCTCTTATAATGTGGCTTATGCATGTCCCAGACATGTCTTACACT
66 TCTTACACTGACAC--ATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACT
58294277 AGCACACAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
138 37 0.37
140 49 0.49
141 14 0.14
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATATCCCAGACAGGG
TCTTACACTGACACATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCAC
GAGGTTGATA
Found at i:58295795 original size:20 final size:19
Alignment explanation
Indices: 58295770--58295831 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
58295760 CCAATACATT
58295770 TCACATAGCATATATTGAGC
1 TCACATAGCATATATTGA-C
** *
58295790 TCACATCTCATACATT---
1 TCACATAGCATATATTGAC
58295806 TCACATAGCATATATTGAAC
1 TCACATAGCATATATTG-AC
58295826 TCACAT
1 TCACAT
58295832 CTCATACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 13 0.41
20 19 0.59
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (19 bp):
TCACATAGCATATATTGAC
Found at i:58295810 original size:36 final size:36
Alignment explanation
Indices: 58295763--58295843 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
58295753 TCACTAGCCA
*
58295763 ATACATTTCACATAGCATATATTGAGCTCACATCTC
1 ATACATTTCACATAGCATATATTGAACTCACATCTC
58295799 ATACATTTCACATAGCATATATTGAACTCACATCTC
1 ATACATTTCACATAGCATATATTGAACTCACATCTC
*
58295835 ATACTTTTC
1 ATACATTTC
58295844 TCATCTAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (36 bp):
ATACATTTCACATAGCATATATTGAACTCACATCTC
Found at i:58296227 original size:140 final size:140
Alignment explanation
Indices: 58295986--58296244 Score: 333
Period size: 140 Copynumber: 1.8 Consensus size: 140
58295976 AGGCTAAGAC
* **
58295986 CATGTCCCAGACATGGTCTTACATTAGCTCTCACATATCCGTGCCGATGCCATATCCCAGACAGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATATCCCAGACAGG
** *
58296051 GTCTTACACTGACACATCTTGTAGCTGATGCATGTCCTAGACATGTCTTACACTGGCTTATGTCA
65 GTCTTACACTGACACATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCA
58296116 CGAGGTTGATA
130 CGAGGTTGATA
* * * * *
58296127 CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGTCGATGCCATCTCCCAGACATGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATATCCCAGACAGGG
* * * * *
58296190 TCTTACGCTGGCTCTTATAATGTGGCTTATGCATGTCCCAGACATGTCTTACACT
66 TCTTACACTGACAC--ATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACT
58296245 AGCACACAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
138 37 0.37
140 49 0.49
141 14 0.14
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATATCCCAGACAGGG
TCTTACACTGACACATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACTGGCTTATGTCAC
GAGGTTGATA
Found at i:58302443 original size:27 final size:27
Alignment explanation
Indices: 58302413--58302616 Score: 203
Period size: 27 Copynumber: 7.6 Consensus size: 27
58302403 CCTTAATCGA
*
58302413 TAAAATGACTATTTTACCCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* **
58302440 TAAAATAACTATTTTGCCCTTACAAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* * * *
58302467 TGAAATGATTGTTTTGCCCTTAGGAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* * * * * *
58302494 TAAAAGGATTGTTTTACCTTTATGATG
1 TAAAATGACTATTTTGCCCTTATGAGG
*
58302521 TAAAATGACTGTTTTGCCCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* * *
58302548 TAAAATGACTGTTTCGCCCTTATAAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* *
58302575 TAAAATGACTATTTTTCCCTT-TTATGG
1 TAAAATGACTATTTTGCCCTTATGA-GG
*
58302602 TAAGATGACTATTTT
1 TAAAATGACTATTTT
58302617 ACCCCTATAT
Statistics
Matches: 148, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 2 0.01
27 146 0.99
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGAGG
Found at i:58302973 original size:30 final size:30
Alignment explanation
Indices: 58302937--58302994 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
58302927 AGACTAGCAT
*
58302937 ACTGTTTACCGTTACTGCACTATTTACTAC
1 ACTGTTTACCGTTACTACACTATTTACTAC
* *
58302967 ACTGTTTACTGTTACTACACTGTTTACT
1 ACTGTTTACCGTTACTACACTATTTACT
58302995 GTTACTGCAA
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:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (30 bp):
ACTGTTTACCGTTACTACACTATTTACTAC
Found at i:58302981 original size:18 final size:18
Alignment explanation
Indices: 58302960--58303000 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
58302950 ACTGCACTAT
58302960 TTACTACACTGTTTACTG
1 TTACTACACTGTTTACTG
58302978 TTACTACACTGTTTACTG
1 TTACTACACTGTTTACTG
58302996 TTACT
1 TTACT
58303001 GCAATGGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (18 bp):
TTACTACACTGTTTACTG
Found at i:58305976 original size:21 final size:21
Alignment explanation
Indices: 58305950--58306002 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
58305940 CTACTCACTA
58305950 TGTTGCAACATCGACCTTCCG
1 TGTTGCAACATCGACCTTCCG
58305971 TGTTGCAACATCGACCTTCCG
1 TGTTGCAACATCGACCTTCCG
58305992 TGTTGCAACAT
1 TGTTGCAACAT
58306003 TATGGTCAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTTGCAACATCGACCTTCCG
Found at i:58312238 original size:30 final size:30
Alignment explanation
Indices: 58312204--58312264 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
58312194 TCCTTAACTC
58312204 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
58312234 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
58312264 A
1 A
58312265 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:58317898 original size:138 final size:137
Alignment explanation
Indices: 58317717--58318415 Score: 699
Period size: 140 Copynumber: 5.1 Consensus size: 137
58317707 GAGAACATAG
* * * * * * *
58317717 ATATAATTAATATATGATTTTGTTTCATACAATATATTAATTGTCTATATTTTATCAATTTTATT
1 ATATAATTAATATATAAATTTGATTAATACAAAATATTAATTGTATATATTTTACCAA-TTTATT
* *
58317782 AATATAAGA-AATTATATTAATTAATTCTGGTCAAGATATAAAAAACATGGAAATTAATATTCTT
65 AATATAA-ACAATTATATTAATTAATTCTGGTCAAAATATAAAAAACATAGAAATTAATATTCTT
58317846 TTGGACAA-A
129 TTGGA-AAGA
*
58317855 ATATGATTAATATATAAATTTGATTAATACAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATAAATTTGATTAATACAAAATATTAATTGTATATATTTTACC-AATTTATT
* * *
58317920 AATATAAACAATTATATTAATTAATT-TCGGTCAAAATATAAAAGACAT-GAAA--ATTATTATT
65 AATATAAACAATTATATTAATTAATTCT-GGTCAAAATATAAAAAACATAGAAATTAATATTCTT
58317981 TTGGAAAGA
129 TTGGAAAGA
* * * * * * *
58317990 ATATAATTAATATATGAATTTGATTCAA-ACTAAATATTAGTTGTAGATATTTTATCGAAATTGT
1 ATATAATTAATATATAAATTTGATT-AATACAAAATATTAATTGTATATATTTTA-CCAATTTAT
* * ** *
58318054 TGATATAAACAATTATATTAATTAATTTCAAT-TTTGAAATA-AAAGAA-ATAGAAATTAATATT
64 TAATATAAACAATTATATTAATTAA-TTC--TGGTCAAAATATAAAAAACATAGAAATTAATATT
* *
58318116 GTTTTGGAAATA
126 CTTTTGGAAAGA
* * * *
58318128 ATATAATTAATATATATGAATTTGATTCAA-ACTAAATATTAGTTGTAGATATTTTACCGAAATT
1 ATATAATTAATATATA--AATTTGATT-AATACAAAATATTAATTGTATATATTTTACC-AATTT
* * * ** * *
58318192 GTTAATATAAACAATTATATTAATTAATTTCAGTTTTGACATA-AAAGAA-ATAGAAATTAATAT
62 ATTAATATAAACAATTATATTAATTAA-TTCTG-GTCAAAATATAAAAAACATAGAAATTAATAT
* *
58318255 TGTTTTGGAAATA
125 TCTTTTGGAAAGA
*
58318268 ATATAATTAATATATATGAATTTGAATT-ATACAAAATATTAATTGTATATATTTTACAGAATTT
1 ATATAATTAATATATA--AATTTG-ATTAATACAAAATATTAATTGTATATATTTTAC-CAATTT
* * *
58318332 ATTAATATAAA-AAGTTATATTAATTAATTCCGGTCAAAATATAAAAGACATTGAAATTAATATT
62 ATTAATATAAACAA-TTATATTAATTAATTCTGGTCAAAATATAAAAAACATAGAAATTAATATT
*
58318396 CTTCTGGAAAGA
126 CTTTTGGAAAGA
58318408 ATATAATT
1 ATATAATT
58318416 CTTCTTTTTC
Statistics
Matches: 486, Mismatches: 51, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
134 2 0.00
135 90 0.19
136 13 0.03
137 12 0.02
138 131 0.27
139 15 0.03
140 220 0.45
141 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (137 bp):
ATATAATTAATATATAAATTTGATTAATACAAAATATTAATTGTATATATTTTACCAATTTATTA
ATATAAACAATTATATTAATTAATTCTGGTCAAAATATAAAAAACATAGAAATTAATATTCTTTT
GGAAAGA
Found at i:58318221 original size:71 final size:71
Alignment explanation
Indices: 58318006--58318221 Score: 182
Period size: 71 Copynumber: 3.1 Consensus size: 71
58317996 TTAATATATG
*
58318006 AATTTGATTCAAACTAAATATTAGTTGTAGATATTTTATCGAAATTGTTGATATAAACAATTATA
1 AATTTGATTCAAACTAAATATTAGTTGTAGATATTTTATCGAAATTGTTAATATAAACAATTATA
58318071 TTAATT
66 TTAATT
* * * * * * * *
58318077 AATTTCAATTTTGAAA-TAAAAGAAATAGAAAT-TA-ATATTGTTTTGGAAA----TAATATAAT
1 AATTT-GA--TTCAAACT-AAA-TATTAG--TTGTAGATATT-TTATCGAAATTGTTAATATAAA
* *
58318135 TAA-TATA-T-ATG
58 CAATTATATTAATT
*
58318146 AATTTGATTCAAACTAAATATTAGTTGTAGATATTTTACCGAAATTGTTAATATAAACAATTATA
1 AATTTGATTCAAACTAAATATTAGTTGTAGATATTTTATCGAAATTGTTAATATAAACAATTATA
58318211 TTAATT
66 TTAATT
58318217 AATTT
1 AATTT
58318222 CAGTTTTGAC
Statistics
Matches: 105, Mismatches: 22, Indels: 36
0.64 0.13 0.22
Matches are distributed among these distances:
63 1 0.01
64 8 0.08
65 9 0.09
66 8 0.08
67 1 0.01
68 11 0.10
69 11 0.10
70 2 0.02
71 16 0.15
72 10 0.10
73 1 0.01
74 8 0.08
75 9 0.09
76 9 0.09
77 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (71 bp):
AATTTGATTCAAACTAAATATTAGTTGTAGATATTTTATCGAAATTGTTAATATAAACAATTATA
TTAATT
Found at i:58336113 original size:124 final size:124
Alignment explanation
Indices: 58335948--58336197 Score: 358
Period size: 124 Copynumber: 2.0 Consensus size: 124
58335938 CATGAAAATT
* * *
58335948 AATATTCTTTTAGAAAAAGATATAATTAATAGATGAATTTGATTAATAAAAAATATTAATTGTAT
1 AATATTCTTTTAGAAAAAGATATAACTAATAGAGGAATTTGATTAATAAAAAATACTAATTGTAT
* *
58336013 ATATTTTACCGAATTTATTAATATAAATAGTTATATTAATCAATTTTGGTCAAAATATA
66 ATATTTTACCAAATTTATTAATATAAACAGTTATATTAATCAATTTTGGTCAAAATATA
* * * *
58336072 AATATTCTTTTGGAAAAA-ATATAACTAATATAGGAATTTTGATTCATACAAAATACTAATTGTA
1 AATATTCTTTTAGAAAAAGATATAACTAATAGAGGAA-TTTGATTAATAAAAAATACTAATTGTA
* * * * *
58336136 TATTTTTTACTAAATTTATTCATATAAACAGTTATATTAATTAATTTTGGTTAAAATATA
65 TATATTTTACCAAATTTATTAATATAAACAGTTATATTAATCAATTTTGGTCAAAATATA
58336196 AA
1 AA
58336198 AGACATGAAA
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 15 0.14
124 96 0.86
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (124 bp):
AATATTCTTTTAGAAAAAGATATAACTAATAGAGGAATTTGATTAATAAAAAATACTAATTGTAT
ATATTTTACCAAATTTATTAATATAAACAGTTATATTAATCAATTTTGGTCAAAATATA
Found at i:58336460 original size:140 final size:138
Alignment explanation
Indices: 58336072--58336514 Score: 661
Period size: 140 Copynumber: 3.2 Consensus size: 138
58336062 TCAAAATATA
* * * *
58336072 AATATTCTTTTGGAAAAAATATAACTAATATAGGAATTTTGATTCATACAAAATACTAATTGTAT
1 AATATTCTTTTGGAAAGAATATAATTAATATATGAA-TTTGATTCATACAAAATATTAATTGTAT
* * * * *
58336137 ATTTTTTACTAAATTTATTCATATAAACAGTTATATTAATTAATTTTGGTTAAAATATAAAAGAC
65 ATATTTTACTGAATTTATTAATATAAACAGTTATATTAATTAATTTTGATTAAAATATAAAAGAT
* *
58336202 ATGAAAAAT
130 ATGGAAATT
*
58336211 AATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAGTTGTATA
1 AATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATA
* *
58336276 TATTTTACTGAACTTATTAATATAAACAGTTATATTAATTAATTTTGATTAAAATATAAAATATA
66 TATTTTACTGAATTTATTAATATAAACAGTTATATTAATTAATTTTGATTAAAATATAAAAGATA
58336341 TGGAAATT
131 TGGAAATT
* *
58336349 AATATTCTTTTGGAAATAATATAATTAATATATATGAATTTGATTCATAAAAAATATTAATTGTA
1 AATATTCTTTTGGAAAGAATATAATT-A-ATATATGAATTTGATTCATACAAAATATTAATTGTA
* ** *
58336414 TATATTTTACTGAATTTATTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGA
64 TATATTTTACTGAATTTATTAATATAAACAGTTATATTAATTAATTTTGATTAAAATATAAAAGA
58336479 TATGGAAATT
129 TATGGAAATT
* *
58336489 AATATTTTTTTGAAAAGAATATAATT
1 AATATTCTTTTGGAAAGAATATAATT
58336515 CATTTTTCTA
Statistics
Matches: 276, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
138 116 0.42
139 34 0.12
140 126 0.46
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (138 bp):
AATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATA
TATTTTACTGAATTTATTAATATAAACAGTTATATTAATTAATTTTGATTAAAATATAAAAGATA
TGGAAATT
Found at i:58344336 original size:46 final size:46
Alignment explanation
Indices: 58344269--58344443 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
58344259 TGTAACCCGC
* * * *
58344269 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
58344315 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
58344361 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
58344407 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
58344444 TGCTCAACCA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:58352431 original size:5 final size:6
Alignment explanation
Indices: 58352418--58352464 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
58352408 ATAATTTAAT
58352418 AAATAA AAATAA AAATCTAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAA
58352465 ACATATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:58352465 original size:20 final size:20
Alignment explanation
Indices: 58352418--58352458 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
58352408 ATAATTTAAT
**
58352418 AAATAAAAATAAAAATCTAA
1 AAATAAAAATAAAAATAAAA
58352438 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
58352458 A
1 A
58352459 TAAAAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:58352498 original size:9 final size:9
Alignment explanation
Indices: 58352484--58352532 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
58352474 TTTATACAAA
*
58352484 TAATTCAGT
1 TAATTCGGT
58352493 TAATTCGGT
1 TAATTCGGT
*
58352502 TAATTC-GA
1 TAATTCGGT
58352510 TAATTCGGT
1 TAATTCGGT
58352519 TAATTCGGT
1 TAATTCGGT
58352528 TAATT
1 TAATT
58352533 TTATACTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
8 7 0.19
9 29 0.81
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (9 bp):
TAATTCGGT
Found at i:58352513 original size:26 final size:26
Alignment explanation
Indices: 58352483--58352532 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
58352473 TTTTATACAA
58352483 ATAATTCAGTTAATTCGGTTAATTCG
1 ATAATTCAGTTAATTCGGTTAATTCG
*
58352509 ATAATTCGGTTAATTCGGTTAATT
1 ATAATTCAGTTAATTCGGTTAATT
58352533 TTATACTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (26 bp):
ATAATTCAGTTAATTCGGTTAATTCG
Found at i:58352515 original size:17 final size:17
Alignment explanation
Indices: 58352493--58352525 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
58352483 ATAATTCAGT
58352493 TAATTCGGTTAATTCGA
1 TAATTCGGTTAATTCGA
58352510 TAATTCGGTTAATTCG
1 TAATTCGGTTAATTCG
58352526 GTTAATTTTA
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:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (17 bp):
TAATTCGGTTAATTCGA
Found at i:58385706 original size:50 final size:50
Alignment explanation
Indices: 58385644--58385747 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
58385634 ATCACCTAGG
*
58385644 AAAA-GATGTTTCACACATATCCAACTTTCATATTCCTCCATAATCCATC
1 AAAATGATGTTTCACACATATCCAACTTTCATATTCCTCAATAATCCATC
58385693 AAAATGATGTTTCACACATATCCAACTTTCATATTCCTCAATAATCCATC
1 AAAATGATGTTTCACACATATCCAACTTTCATATTCCTCAATAATCCATC
58385743 AAAAT
1 AAAAT
58385748 ACAAGTAACT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 4 0.08
50 49 0.92
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (50 bp):
AAAATGATGTTTCACACATATCCAACTTTCATATTCCTCAATAATCCATC
Found at i:58391827 original size:29 final size:29
Alignment explanation
Indices: 58391795--58391900 Score: 167
Period size: 29 Copynumber: 3.7 Consensus size: 29
58391785 AATCATATTC
58391795 ATATGGCCCATTAGGCCCAAATCACCTGA
1 ATATGGCCCATTAGGCCCAAATCACCTGA
58391824 ATATGGCCCATTAGGCCCAAATCACCTGA
1 ATATGGCCCATTAGGCCCAAATCACCTGA
* **
58391853 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACCTGA
* *
58391882 GTATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
58391901 GTCACATTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACCTGA
Found at i:58396345 original size:28 final size:29
Alignment explanation
Indices: 58396313--58396427 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
58396303 TACCTGTATC
* *
58396313 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* **
58396341 TGGCCCATTAGGCCCAAATCACCTGAATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
58396370 TGGCCTATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
58396399 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
58396427 T
1 T
58396428 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 26 0.36
29 47 0.64
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:58396410 original size:58 final size:57
Alignment explanation
Indices: 58396304--58396414 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
58396294 AAATTCACAT
* * *
58396304 ACCTGTATCTGGCCCATTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGAATATGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
58396361 ACCTGAATATGGCCTATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGAATATGGCCCATTAAGCCC-AATCACATTCATATGGCCCATTAGGCCCA
58396415 GTCACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 20 0.43
58 26 0.57
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (57 bp):
ACCTGAATATGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:58398934 original size:47 final size:46
Alignment explanation
Indices: 58398878--58399051 Score: 140
Period size: 47 Copynumber: 3.7 Consensus size: 46
58398868 ATCTCATGTT
*
58398878 GATGCCATGTCCTAGACATGGTCTGACACTAACTATCATATCGTAGCC
1 GATGCCATGTCCTAGACAT-GTCTGACACTAGCTATCATAT-GTAGCC
* * * * *
58398926 GATG-CATGTCCCAAACATGTCTGACACTAGC-ACTCGTCTTGATA-CT
1 GATGCCATGTCCTAGACATGTCTGACACTAGCTA-TCAT-ATG-TAGCC
* * * *
58398972 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTGGTC
1 GATGCCATGTCCTAGACAT-GTCTGACACTAGCTATCAT-ATGTAGCC
* * *
58399020 AATG-CATGTCCAAGACATGTCTTACACTAGCT
1 GATGCCATGTCCTAGACATGTCTGACACTAGCT
58399052 CACAATAACC
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
45 1 0.01
46 35 0.35
47 41 0.41
48 24 0.24
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (46 bp):
GATGCCATGTCCTAGACATGTCTGACACTAGCTATCATATGTAGCC
Found at i:58399001 original size:94 final size:94
Alignment explanation
Indices: 58398877--58399050 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 94
58398867 TATCTCATGT
*
58398877 TGATGCCATGTCCTAGACATGGTCTGACACTAACTATCAT-ATCGTAGCCGATGCATGTCCCAA-
1 TGATGCCATGTCCTAGACATGGTCTGACACTAACTATCATAAT-GTAGCCAATGCATGT-CCAAG
58398940 ACATGTCTGACACTAGCACTCGTCTTGATAC
64 ACATGTCTGACACTAGCACTCGTCTTGATAC
* * * * *
58398971 TGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTGGTCAATGCATGTCCAAGAC
1 TGATGCCATGTCCTAGACATGGTCTGACACTAACTATCATAATGTAGCCAATGCATGTCCAAGAC
*
58399036 ATGTCTTACACTAGC
66 ATGTCTGACACTAGC
58399051 TCACAATAAC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
93 4 0.06
94 65 0.92
95 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (94 bp):
TGATGCCATGTCCTAGACATGGTCTGACACTAACTATCATAATGTAGCCAATGCATGTCCAAGAC
ATGTCTGACACTAGCACTCGTCTTGATAC
Found at i:58416054 original size:47 final size:48
Alignment explanation
Indices: 58415980--58416156 Score: 222
Period size: 47 Copynumber: 3.8 Consensus size: 48
58415970 AGTAAGGTGC
58415980 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTC-AAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCGAAGT
* *
58416027 CGATGCCATGTCCCAGACATGGCCTTACACTGACT-ATCATCTCGTAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCG-AAGT
* * * *
58416076 -GATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TAGTCTCGATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATA-TCTCGAAGT
*
58416121 CGATACCATGTCCCAGACATGGTCTTACACTGGCTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
58416157 TCATAATGTG
Statistics
Matches: 111, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
45 3 0.03
46 21 0.19
47 66 0.59
48 17 0.15
49 4 0.04
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCGAAGT
Found at i:58416148 original size:94 final size:92
Alignment explanation
Indices: 58415981--58416200 Score: 248
Period size: 94 Copynumber: 2.3 Consensus size: 92
58415971 GTAAGGTGCC
* * * *
58415981 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCACATATCTCAAGCCGATACCATGTCCCAGACA
*
58416046 TGGCCTTACACTGACTATCAT-CTCGTAAGT-
64 TGGCCTTACACTGACTATCATAAT-GT--GTA
*
58416076 GATGCATGTCCCAGACATGTCTTACACTAGCAC-TAGTCTCGATGCCGATACCATGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACATA-TCTC-AAGCCGATACCATGTCCCAGACA
* * *
58416140 TGGTCTTACACTGGCTCTCATAATGTGTA
64 TGGCCTTACACTGACTATCATAATGTGTA
* *
58416169 CGATGCATGTCCCCGACATGTGTTACACTAGC
1 -GATGCATGTCCCAGACATGTCTTACACTAGC
58416201 TCACAATAAC
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
92 4 0.04
93 17 0.16
94 83 0.76
95 5 0.05
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACATATCTCAAGCCGATACCATGTCCCAGACATG
GCCTTACACTGACTATCATAATGTGTA
Found at i:58416178 original size:47 final size:47
Alignment explanation
Indices: 58415980--58416202 Score: 178
Period size: 47 Copynumber: 4.7 Consensus size: 47
58415970 AGTAAGGTGC
58415980 CGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCATATC-TCAAGT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGT--AGT
* * * *
58416027 CGATGCCATGTCCCAGACATGGCCTTACACTGACTATCATCTCGTAAGT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGT-AGT
* * * *
58416076 -GATGCATGTCCCAGACAT-GTCTTACACTAGCACT-AGTCTCG-ATGC
1 CGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCA-TATCGTA-GT
*
58416121 CGATACCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GT-GT
1 CGAT-GCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCGTAGT
* * *
58416168 ACGATGCATGTCCCCGACAT-GTGTTACACTAGCTC
1 -CGATGCATGTCCCAGACATGGTCTTACACTGGCTC
58416203 ACAATAACCC
Statistics
Matches: 145, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 32 0.22
47 73 0.50
48 24 0.17
49 12 0.08
50 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGTAGT
Found at i:58419754 original size:14 final size:14
Alignment explanation
Indices: 58419735--58419762 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58419725 CTAGGCTCGA
58419735 AAAATGAAATTCTT
1 AAAATGAAATTCTT
58419749 AAAATGAAATTCTT
1 AAAATGAAATTCTT
58419763 GAAGTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAAATGAAATTCTT
Found at i:58422354 original size:4 final size:4
Alignment explanation
Indices: 58422347--58422386 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
58422337 TACATAACAC
58422347 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
58422387 GGTAATAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:58423527 original size:22 final size:21
Alignment explanation
Indices: 58423501--58423546 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
58423491 CTTCCTTTAT
* *
58423501 AATTATCATATATATTAATTAA
1 AATTATAAAATATATTAA-TAA
*
58423523 AATTATAAAATATCTTAATAA
1 AATTATAAAATATATTAATAA
58423544 AAT
1 AAT
58423547 ATTAATTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTATAAAATATATTAATAA
Found at i:58425926 original size:25 final size:25
Alignment explanation
Indices: 58425885--58425946 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
58425875 CAGGCCCATT
* *
58425885 TTCACAGCTTGTGTGAGCATTCTGA
1 TTCACAGCTCGTATGAGCATTCTGA
* *
58425910 TTCGCAGCTCGTATGAGCATTTTGA
1 TTCACAGCTCGTATGAGCATTCTGA
58425935 TTCACAGCTCGT
1 TTCACAGCTCGT
58425947 GTGAACATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (25 bp):
TTCACAGCTCGTATGAGCATTCTGA
Found at i:58427219 original size:17 final size:17
Alignment explanation
Indices: 58427193--58427239 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
58427183 ATCTGACAAA
58427193 GCCCGATCAATGATAAT
1 GCCCGATCAATGATAAT
*
58427210 GCCTGATCAATGATAAT
1 GCCCGATCAATGATAAT
*
58427227 GCCCGATAAATGA
1 GCCCGATCAATGA
58427240 GAAATGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (17 bp):
GCCCGATCAATGATAAT
Found at i:58427504 original size:44 final size:44
Alignment explanation
Indices: 58427436--58427549 Score: 156
Period size: 44 Copynumber: 2.6 Consensus size: 44
58427426 TGTTGCTGAT
* * * * * * *
58427436 AGGATTTAGCTCGAACGAGCAATCCTATTTACCTCATTACAGAA
1 AGGATTTAGCCCGGACGGGTAATCCTACTGACCTCATGACAGAA
58427480 AGGATTTAGCCCGGACGGGTAATCCTACTGACCTCATGACAGAA
1 AGGATTTAGCCCGGACGGGTAATCCTACTGACCTCATGACAGAA
*
58427524 AGGATTTAGCCCAGACGGGTAATCCT
1 AGGATTTAGCCCGGACGGGTAATCCT
58427550 GATATAAGTC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (44 bp):
AGGATTTAGCCCGGACGGGTAATCCTACTGACCTCATGACAGAA
Found at i:58428559 original size:30 final size:30
Alignment explanation
Indices: 58428524--58428580 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
58428514 TTTACGAGCC
58428524 TAGGGGCAAAAA-TGTAATTTTGACAAAGTT
1 TAGGGG-AAAAATTGTAATTTTGACAAAGTT
*
58428554 TAGGGGAAAAATTGTAATTTTGCCAAA
1 TAGGGGAAAAATTGTAATTTTGACAAA
58428581 ATATGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAATTGTAATTTTGACAAAGTT
Found at i:58435927 original size:20 final size:20
Alignment explanation
Indices: 58435900--58435967 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
58435890 ATGCGATCAC
58435900 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
58435920 ATACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
* *
58435940 ACATGCCCATGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
58435960 ACACGCCC
1 ACACGCCC
58435968 ATGTACTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.13, C:0.31, G:0.35, T:0.21
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGGG
Found at i:58440083 original size:10 final size:10
Alignment explanation
Indices: 58440068--58440102 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
58440058 TTATGTATTC
58440068 TAATTAAATT
1 TAATTAAATT
58440078 TAATTAAATAT
1 TAATTAAAT-T
*
58440089 TAAATAAATT
1 TAATTAAATT
58440099 TAAT
1 TAAT
58440103 ACATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TAATTAAATT
Found at i:58440314 original size:16 final size:17
Alignment explanation
Indices: 58440293--58440330 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
58440283 TACCAACGAA
58440293 AATTTATAGTTGTTTC-
1 AATTTATAGTTGTTTCG
58440309 AATTTATAGTTGTTTCG
1 AATTTATAGTTGTTTCG
58440326 AATTT
1 AATTT
58440331 CGAAATGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (17 bp):
AATTTATAGTTGTTTCG
Found at i:58440516 original size:21 final size:20
Alignment explanation
Indices: 58440479--58440520 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
58440469 TTACATTCAA
58440479 TACTCATTTAATATTAAAAT
1 TACTCATTTAATATTAAAAT
* * *
58440499 TACTTATTTTATATTTAAAT
1 TACTCATTTAATATTAAAAT
58440519 TA
1 TA
58440521 TTTTTAACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TACTCATTTAATATTAAAAT
Found at i:58441184 original size:4 final size:4
Alignment explanation
Indices: 58441175--58441227 Score: 88
Period size: 4 Copynumber: 13.2 Consensus size: 4
58441165 TGGGATTGGA
* *
58441175 ACAT ACAT ACGT ACAT ACAT ACAT ACAT AAAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58441223 ACAT A
1 ACAT A
58441228 TGTATGTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:58441668 original size:2 final size:2
Alignment explanation
Indices: 58441661--58441699 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
58441651 CAAATGCATA
58441661 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
58441700 AACCTAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58469616 original size:79 final size:81
Alignment explanation
Indices: 58469480--58469664 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
58469470 TTGAATGATG
*
58469480 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
58469544 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
58469559 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
58469621 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
58469639 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
58469665 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:58469678 original size:40 final size:40
Alignment explanation
Indices: 58469481--58469664 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
58469471 TGAATGATGT
* * * *
58469481 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
58469521 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
58469561 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
58469599 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
58469640 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
58469665 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:58469686 original size:79 final size:79
Alignment explanation
Indices: 58469533--58469697 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
58469523 GGACTAAGAT
* **
58469533 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
58469598 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
58469612 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
58469675 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
58469691 CCGAAGG
1 CCGAAGG
58469698 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:58474294 original size:40 final size:39
Alignment explanation
Indices: 58474232--58474490 Score: 351
Period size: 40 Copynumber: 6.5 Consensus size: 39
58474222 AAGCCAAGTA
* * *
58474232 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCAC-AATG
*
58474271 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCA-CAATG
58474311 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCA-CAATG
* *
58474351 CCTTCGAGACTTTGCCCGGATATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAA-TG
* *
58474391 CCTTCGGGACTTAGGCCGGATATAGTAACTCACACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAA-TG
* *
58474431 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
58474471 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAGCCCGGA
58474491 ACTAGTCACT
Statistics
Matches: 200, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
39 15 0.08
40 182 0.91
41 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATG
Found at i:58480862 original size:40 final size:40
Alignment explanation
Indices: 58480818--58481081 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
58480808 GCTCCTCGTT
* *
58480818 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
58480858 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
58480898 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
58480938 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
58480978 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
58481017 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
58481058 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58481082 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:58488877 original size:40 final size:40
Alignment explanation
Indices: 58488833--58489094 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
58488823 GCTCCTCGTT
* *
58488833 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
58488873 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
58488913 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
58488952 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
58488991 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
58489030 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
58489071 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58489095 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:58490394 original size:11 final size:11
Alignment explanation
Indices: 58490378--58490402 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58490368 CCTCACTAGG
58490378 CCAACATGTTC
1 CCAACATGTTC
58490389 CCAACATGTTC
1 CCAACATGTTC
58490400 CCA
1 CCA
58490403 CCCATAGCAT
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:0.28, C:0.40, G:0.08, T:0.24
Consensus pattern (11 bp):
CCAACATGTTC
Found at i:58494440 original size:11 final size:11
Alignment explanation
Indices: 58494424--58494466 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
58494414 AAGTAATTTT
58494424 TCAATTCAATC
1 TCAATTCAATC
*
58494435 TCAATTCTAATTTT
1 TCAATTC-AA--TC
58494449 TCAATTCAATC
1 TCAATTCAATC
58494460 TCAATTC
1 TCAATTC
58494467 TAACCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 15 0.56
12 2 0.07
13 2 0.07
14 8 0.30
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (11 bp):
TCAATTCAATC
Found at i:58494481 original size:30 final size:25
Alignment explanation
Indices: 58494417--58494469 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
58494407 TCTAGTTAAG
58494417 TAATTTTTCAATTCAATCTCAATTC
1 TAATTTTTCAATTCAATCTCAATTC
58494442 TAATTTTTCAATTCAATCTCAATTC
1 TAATTTTTCAATTCAATCTCAATTC
58494467 TAA
1 TAA
58494470 CCTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (25 bp):
TAATTTTTCAATTCAATCTCAATTC
Found at i:58507060 original size:46 final size:46
Alignment explanation
Indices: 58506993--58507301 Score: 449
Period size: 46 Copynumber: 6.7 Consensus size: 46
58506983 TCATCCAGAN
58506993 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
58507039 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
* *
58507085 GTGTAAGACCATGGTTGAAAGATACCATGGCGACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
*
58507131 GTGTAAGACCATGATTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
* ***
58507177 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-TATGAAAT
** * * *
58507224 GAATAAGACCATGGTTGAATGATACCATGGCAACATGACA-GAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAAT
* * * *
58507270 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
58507302 TCATGTCGAA
Statistics
Matches: 240, Mismatches: 21, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
45 1 0.00
46 200 0.83
47 39 0.16
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
Found at i:58511586 original size:46 final size:46
Alignment explanation
Indices: 58511519--58511610 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
58511509 GATATACACA
*
58511519 TTACCAAACGTATTCACAAACTTCTAGCCTATACATGCCATACTTC
1 TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
58511565 TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
1 TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
58511611 AATATATACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.30
Consensus pattern (46 bp):
TTACCAAACATATTCACAAACTTCTAGCCTATACATGCCATACTTC
Found at i:58514667 original size:43 final size:43
Alignment explanation
Indices: 58514601--58514756 Score: 131
Period size: 43 Copynumber: 3.6 Consensus size: 43
58514591 AGCTCGTACA
*
58514601 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
*** *
58514644 ATGCC-ACTGTCCCAGACAGGGTCTTACACAAAATCATATAT-G
1 ATGCCAAC-GTCCCAGACAGGGTCTTACATGTAATCAAATATCG
* * * * * * *
58514686 ATGTCGATGTCCCAAATATGGTCTTACATGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGT-AATCA-AATATCG
*
58514730 ATGCCAACGTCCTAGAC-GTGGTCTTAC
1 ATGCCAACGTCCCAGACAG-GGTCTTAC
58514757 GCGAAAACAC
Statistics
Matches: 85, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
42 24 0.28
43 40 0.47
44 21 0.25
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
Found at i:58518242 original size:24 final size:24
Alignment explanation
Indices: 58518214--58518260 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
58518204 ACACATATTC
*
58518214 AATTCAATC-AATACAAATTCAATA
1 AATTC-ATCAAATACAAAATCAATA
58518238 AATTCATCAAATACAAAATCAAT
1 AATTCATCAAATACAAAATCAAT
58518261 CCATTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (24 bp):
AATTCATCAAATACAAAATCAATA
Found at i:58524475 original size:28 final size:28
Alignment explanation
Indices: 58524443--58524508 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
58524433 ACAGTGCATG
*
58524443 CAGTAACAGTCTGGGCCTTAGCCCT-ATA
1 CAGTAACAGTCTGGGCCTAAG-CCTAATA
* *
58524471 CAGTAATAGTGTGGGCCTAAGCCTAATA
1 CAGTAACAGTCTGGGCCTAAGCCTAATA
*
58524499 CAGTATCAGT
1 CAGTAACAGT
58524509 ACAATGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (28 bp):
CAGTAACAGTCTGGGCCTAAGCCTAATA
Found at i:58524694 original size:27 final size:27
Alignment explanation
Indices: 58524664--58524723 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
58524654 AGTTGCCAGA
*
58524664 AACAGTAAATGTGGCAAAGCCACCAAT
1 AACAGTAAATGTGACAAAGCCACCAAT
** * *
58524691 AACAGTGGATGTGACATAGTCACCAAT
1 AACAGTAAATGTGACAAAGCCACCAAT
58524718 -ACAGTA
1 AACAGTA
58524724 CTTCCTCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
AACAGTAAATGTGACAAAGCCACCAAT
Found at i:58529980 original size:20 final size:19
Alignment explanation
Indices: 58529957--58530000 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
58529947 TTGGCTCGTT
58529957 ATGGGCCACGT-TGGGCCACA
1 ATGGGCC-CGTGTGGGCC-CA
58529977 ATGGG-CCGTGTGGGCCCA
1 ATGGGCCCGTGTGGGCCCA
58529995 ATGGGC
1 ATGGGC
58530001 TCGCTGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (19 bp):
ATGGGCCCGTGTGGGCCCA
Found at i:58530314 original size:27 final size:27
Alignment explanation
Indices: 58530240--58530314 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
58530230 CCCCAAAATA
* * *
58530240 GGTAAAATGACCATAATACCACTGTAG
1 GGTAAAATGACGATAATACCCCTATAG
* *
58530267 GGTAAAATGATTG-TAATACCCCTATAT
1 GGTAAAATGA-CGATAATACCCCTATAG
*
58530294 GGTAAAATGACGATTATACCC
1 GGTAAAATGACGATAATACCC
58530315 TTATGTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (27 bp):
GGTAAAATGACGATAATACCCCTATAG
Found at i:58530490 original size:27 final size:26
Alignment explanation
Indices: 58530441--58530492 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
58530431 TGGAGGAAGT
*
58530441 ACTATACTGGTGACTATGTCACATTC
1 ACTATACTGGTGACTATGCCACATTC
* *
58530467 ACTATTACTGGTGGCTTTGCCACATT
1 ACTA-TACTGGTGACTATGCCACATT
58530493 TACTGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (26 bp):
ACTATACTGGTGACTATGCCACATTC
Found at i:58530700 original size:28 final size:28
Alignment explanation
Indices: 58530655--58530752 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 28
58530645 ATTACACTGT
* * * * *
58530655 ACTGATACTGTATTGGGCTTAGGCCCAC
1 ACTGTTACTATATAGGGCTAAGGCCCAA
58530683 ACTGTTACTATATAGGGCTAAGGCCCAA
1 ACTGTTACTATATAGGGCTAAGGCCCAA
* * *
58530711 ACTGTACTAATACTGAATAGGGCTCAGGCCCAG
1 ACTGT--TACTA-T--ATAGGGCTAAGGCCCAA
58530744 ACTGTTACT
1 ACTGTTACT
58530753 GCATGTACTG
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 28 0.50
30 4 0.07
31 4 0.07
33 20 0.36
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (28 bp):
ACTGTTACTATATAGGGCTAAGGCCCAA
Found at i:58538993 original size:40 final size:40
Alignment explanation
Indices: 58538938--58539114 Score: 322
Period size: 40 Copynumber: 4.5 Consensus size: 40
58538928 NNNNNNNNNN
58538938 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
58538978 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
58539018 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
58539058 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
58539098 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
58539115 ATACTTGGGT
Statistics
Matches: 135, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
38 1 0.01
39 13 0.10
40 121 0.90
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:58542731 original size:19 final size:19
Alignment explanation
Indices: 58542707--58542744 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
58542697 TGGACCACGT
58542707 TGGGCCAAAATGGGC-CATG
1 TGGGCC-AAATGGGCTCATG
*
58542726 TGGGCCCAATGGGCTCATG
1 TGGGCCAAATGGGCTCATG
58542745 GGACCCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (19 bp):
TGGGCCAAATGGGCTCATG
Found at i:58543012 original size:26 final size:27
Alignment explanation
Indices: 58542980--58543043 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
58542970 CCTTAAAATA
58542980 GGTAAAATGACCAT-ATACTCC-TATAG
1 GGTAAAATGACCATAATAC-CCTTATAG
* * *
58543006 GGTAAAATGACCGTAATACCCTTGTAT
1 GGTAAAATGACCATAATACCCTTATAG
58543033 GGTAAAATGAC
1 GGTAAAATGAC
58543044 GATTATGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.45
27 18 0.55
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
GGTAAAATGACCATAATACCCTTATAG
Found at i:58543423 original size:33 final size:30
Alignment explanation
Indices: 58543386--58543485 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 30
58543376 TAATTGCATT
*
58543386 ACACTGTACTGATATTGTATTGGGCTTAGGCCC
1 ACACTGTACTGATA-T-TA-TGGGCTAAGGCCC
58543419 ACACTGTTACT-ATA-TA-GGGCTAAGGCCC
1 ACACTG-TACTGATATTATGGGCTAAGGCCC
* *
58543447 AGACTGTACTGTTACTATATAGGGCTAAGGCCC
1 ACACTGTACTGATA-T-TAT-GGGCTAAGGCCC
58543480 ACACTG
1 ACACTG
58543486 CACTATTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
27 4 0.07
28 18 0.32
30 2 0.04
31 2 0.04
33 26 0.46
34 4 0.07
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (30 bp):
ACACTGTACTGATATTATGGGCTAAGGCCC
Found at i:58543439 original size:28 final size:28
Alignment explanation
Indices: 58543407--58543485 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 28
58543397 ATATTGTATT
*
58543407 GGGCTTAGGCCCACACTGTTACTATATA
1 GGGCTAAGGCCCACACTGTTACTATATA
58543435 GGGCTAAGGCCCAGACTGTACTGTTACTATATA
1 GGGCTAAGGCCC--AC---ACTGTTACTATATA
58543468 GGGCTAAGGCCCACACTG
1 GGGCTAAGGCCCACACTG
58543486 CACTATTTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
28 15 0.33
30 2 0.04
31 2 0.04
33 26 0.58
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (28 bp):
GGGCTAAGGCCCACACTGTTACTATATA
Found at i:58545492 original size:44 final size:41
Alignment explanation
Indices: 58545444--58545560 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 41
58545434 GTCTGGGATG
58545444 TTGGCATCGACTTATGATTTACGTGTAAGA-CTATGTCAGGGACA
1 TTGGCATCGA-TT-TGATTT-CGTGTAAGACCT-TGTCAGGGACA
* *
58545488 TTGGCATCGTATTTGATTTTGTGTAAGACCTTGTCTGGGACA
1 TTGGCATCG-ATTTGATTTCGTGTAAGACCTTGTCAGGGACA
* * *
58545530 GTGGCATCGATATTTGATTACATGTAAGACC
1 TTGGCATCG--ATTTGATTTCGTGTAAGACC
58545561 ACGTCTGGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
42 26 0.41
43 26 0.41
44 11 0.17
45 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGGCATCGATTTGATTTCGTGTAAGACCTTGTCAGGGACA
Found at i:58545528 original size:42 final size:42
Alignment explanation
Indices: 58545418--58545576 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 42
58545408 TGGTATGTAT
* **
58545418 TTTCATGTAAGACCACGTCTGGGATGTTGGCATCG-ACTTATGA
1 TTTCGTGTAAGACCACGTCTGGGACATTGGCATCGTA-TT-TGA
* * *
58545461 TTTACGTGTAAGACTATGTCAGGGACATTGGCATCGTATTTGA
1 TTT-CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGA
* ** *
58545504 TTTTGTGTAAGACCTTGTCTGGGACAGTGGCATCGATATTTGA
1 TTTCGTGTAAGACCACGTCTGGGACATTGGCATCG-TATTTGA
* * *
58545547 TTACATGTAAGACCACGTCTGGGACGTTGG
1 TTTCGTGTAAGACCACGTCTGGGACATTGG
58545577 GATTGTACAA
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 27 0.28
43 39 0.41
44 28 0.29
45 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
TTTCGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGA
Found at i:58548062 original size:25 final size:25
Alignment explanation
Indices: 58548041--58548133 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
58548031 GTTCCAACCA
*
58548041 ATAACTCGTATGAGCATACCAATTT
1 ATAACTCGTATGAGCATACCAATCT
* **
58548066 ATAGCTCGT-TAGAGCATACTGATCT
1 ATAACTCGTAT-GAGCATACCAATCT
*
58548091 ATAACTCGTATGAGCATACCGAT-T
1 ATAACTCGTATGAGCATACCAATCT
*
58548115 ACAACTCGTAT-ATGCATAC
1 ATAACTCGTATGA-GCATAC
58548134 ATGTACATGA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 18 0.31
25 38 0.66
26 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (25 bp):
ATAACTCGTATGAGCATACCAATCT
Found at i:58555384 original size:51 final size:51
Alignment explanation
Indices: 58555307--58555505 Score: 301
Period size: 51 Copynumber: 3.9 Consensus size: 51
58555297 CGGATACACG
* * *
58555307 GTGGCCTTCACATAGCACCACCCTTGTAG-CCAAAACTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAA
58555358 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* * * *
58555409 GTGGCCTTCACATAGAACCACACTTGGGCCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
58555460 GTGGCCTTCCCATAGTACCACTCTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
58555506 CTAAGGTTCA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 1 0.01
51 133 0.99
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:58555585 original size:52 final size:52
Alignment explanation
Indices: 58555529--58555646 Score: 200
Period size: 52 Copynumber: 2.3 Consensus size: 52
58555519 GGAAAATTTC
58555529 TCACTTAGCACAATGCAATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACAATGCAATGGACTTATTTCACTTAGATGCCATGGACTTATT
* * * *
58555581 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGTCATGGTCTTATT
1 TCACTTAGCACAATGCAATGGACTTATTTCACTTAGATGCCATGGACTTATT
58555633 TCACTTAGCACAAT
1 TCACTTAGCACAAT
58555647 TTCGTATCCT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TCACTTAGCACAATGCAATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:58555606 original size:28 final size:27
Alignment explanation
Indices: 58555529--58555644 Score: 145
Period size: 24 Copynumber: 4.4 Consensus size: 27
58555519 GGAAAATTTC
*
58555529 TCACTTAGCACAATGCAATGGACTTATT
1 TCACTTAGCAC-ATGCCATGGACTTATT
58555557 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
58555581 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
* *
58555609 TCACTTAG---ATGTCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
58555633 TCACTTAGCACA
1 TCACTTAGCACA
58555645 ATTTCGTATC
Statistics
Matches: 78, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
24 44 0.56
25 1 0.01
27 2 0.03
28 31 0.40
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:58559297 original size:24 final size:26
Alignment explanation
Indices: 58559270--58559318 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
58559260 AGTTCATGCA
58559270 ATATTAAAGC-ATTTAA-ATACAATT
1 ATATTAAAGCTATTTAACATACAATT
58559294 ATATTAAAGCTTATTTAACATACAA
1 ATATTAAAGC-TATTTAACATACAA
58559319 ACTTACCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
ATATTAAAGCTATTTAACATACAATT
Found at i:58561725 original size:25 final size:25
Alignment explanation
Indices: 58561697--58561779 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
58561687 TCATGTACAT
58561697 GTATGCTCACACGAGCTGTAGATCA
1 GTATGCTCACACGAGCTGTAGATCA
* * * * *
58561722 GTATGCTCTCATGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTAGATCA
* *
58561747 GTATACTTACACGAGCTGTAGATCA
1 GTATGCTCACACGAGCTGTAGATCA
58561772 GTATGCTC
1 GTATGCTC
58561780 TTGCGAGCTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAGATCA
Found at i:58561809 original size:50 final size:50
Alignment explanation
Indices: 58561697--58561811 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
58561687 TCATGTACAT
*
58561697 GTATGCTCACACGAGCTGTAGATCAGTATGCTCTCATGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTAGATCAGTATGCTCTCACGAGCTATAAATCG
* * ** * *
58561747 GTATACTTACACGAGCTGTAGATCAGTATGCTCTTGCGAGCTATATATTG
1 GTATGCTCACACGAGCTGTAGATCAGTATGCTCTCACGAGCTATAAATCG
*
58561797 GTATGGTCACACGAG
1 GTATGCTCACACGAG
58561812 TTATGGGTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (50 bp):
GTATGCTCACACGAGCTGTAGATCAGTATGCTCTCACGAGCTATAAATCG
Found at i:58563652 original size:22 final size:22
Alignment explanation
Indices: 58563627--58563670 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
58563617 GGGAGAAATC
58563627 TATACGTACCAGAATAAAATGT
1 TATACGTACCAGAATAAAATGT
58563649 TATACGTACCAGAATAAAATGT
1 TATACGTACCAGAATAAAATGT
58563671 GCAGACTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (22 bp):
TATACGTACCAGAATAAAATGT
Found at i:58571563 original size:24 final size:24
Alignment explanation
Indices: 58571536--58571587 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
58571526 AGCTAGTTGA
*
58571536 ATTGTACAGTGTTGAGGTTGTTAG
1 ATTGTACAGTGCTGAGGTTGTTAG
58571560 ATTGTACAGTGCTGAGGTTGTTAG
1 ATTGTACAGTGCTGAGGTTGTTAG
58571584 ATTG
1 ATTG
58571588 CACGGGGTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.06, G:0.33, T:0.40
Consensus pattern (24 bp):
ATTGTACAGTGCTGAGGTTGTTAG
Found at i:58574653 original size:15 final size:17
Alignment explanation
Indices: 58574623--58574654 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
58574613 TTGATACTTG
58574623 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
58574640 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
58574655 AATAATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Found at i:58576417 original size:15 final size:15
Alignment explanation
Indices: 58576394--58576424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58576384 TAGGTCGTTG
58576394 AGCACGAATTGGATT
1 AGCACGAATTGGATT
*
58576409 AGCATGAATTGGATT
1 AGCACGAATTGGATT
58576424 A
1 A
58576425 ATACTCGGTG
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:0.10, G:0.26, T:0.29
Consensus pattern (15 bp):
AGCACGAATTGGATT
Found at i:58588391 original size:20 final size:20
Alignment explanation
Indices: 58588366--58588405 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
58588356 TAAAAAGATA
58588366 GTTATTACTAGTACTTTTGG
1 GTTATTACTAGTACTTTTGG
58588386 GTTATTACTAGTACTTTTGG
1 GTTATTACTAGTACTTTTGG
58588406 TTCCCTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (20 bp):
GTTATTACTAGTACTTTTGG
Found at i:58604239 original size:19 final size:19
Alignment explanation
Indices: 58604215--58604259 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
58604205 AAATGAATCG
58604215 GTAACTCAGGTAATGCTCC
1 GTAACTCAGGTAATGCTCC
58604234 GTAACTCAGGTAATGCTCC
1 GTAACTCAGGTAATGCTCC
58604253 GTAACTC
1 GTAACTC
58604260 TATTCCGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (19 bp):
GTAACTCAGGTAATGCTCC
Found at i:58605100 original size:2 final size:2
Alignment explanation
Indices: 58605075--58605119 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
58605065 TCTAACTAAA
* * *
58605075 AC AC AA AC AC AA AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
58605117 AC A
1 AC A
58605120 AAAAAAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:58606866 original size:114 final size:114
Alignment explanation
Indices: 58606678--58606935 Score: 317
Period size: 114 Copynumber: 2.3 Consensus size: 114
58606668 GAGGAGCGAA
* *
58606678 GAAAGTGAAAGAATTCATG-C--TGATAATGATAGTAAGGATAGGCAGAGAGAAAAACGTCCTAG
1 GAAAGAGAAAGAATTCATGACGGTGATAATGATAGTAAGGATAGGCAGAGAGAAAAACGTCCAAG
* **
58606740 ATCCTCTGATGAAGAAGATGGCAAGCATTCCTATAGAGATAGAAGGGGT
66 ATCCTCTGATGAAGAAGATGACAAGCATTCCTATAGAGATAGAAGGCAT
* * * * **
58606789 GAAAGAGAGAGAATTCATGACGGTGATGATGATGGTAAGGATAGGCGGAGAGAAGAAGGGT-CAA
1 GAAAGAGAAAGAATTCATGACGGTGATAATGATAGTAAGGATAGGCAGAGAGAA-AAACGTCCAA
* * * *
58606853 GATCTTCTGATGAAGAAGATGACAAGCCTTCCTTTAGGGATAGAAGGCAT
65 GATCCTCTGATGAAGAAGATGACAAGCATTCCTATAGAGATAGAAGGCAT
* * *
58606903 GAAAGAGATAGAATTCGTGACGGTGAAAATGAT
1 GAAAGAGAAAGAATTCATGACGGTGATAATGAT
58606936 TCCAAGGCTA
Statistics
Matches: 124, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
111 17 0.14
112 1 0.01
114 102 0.82
115 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (114 bp):
GAAAGAGAAAGAATTCATGACGGTGATAATGATAGTAAGGATAGGCAGAGAGAAAAACGTCCAAG
ATCCTCTGATGAAGAAGATGACAAGCATTCCTATAGAGATAGAAGGCAT
Found at i:58617190 original size:43 final size:40
Alignment explanation
Indices: 58617143--58617240 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
58617133 GCCATATCCT
* *
58617143 AGATATGGTCTTACATGCGATCACATACCGATGCCACTGTCCC
1 AGATATGGTCTTACATG-AATCACATA-CGATGCCA-AGTCCC
* *
58617186 AGATAGGGTCTTACATGAATCATATACGATGCCAAGTCCC
1 AGATATGGTCTTACATGAATCACATACGATGCCAAGTCCC
* *
58617226 AGACATAGTCTTACA
1 AGATATGGTCTTACA
58617241 CATTTTCTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 17 0.35
41 8 0.17
42 7 0.15
43 16 0.33
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (40 bp):
AGATATGGTCTTACATGAATCACATACGATGCCAAGTCCC
Found at i:58621574 original size:11 final size:10
Alignment explanation
Indices: 58621544--58621582 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
58621534 ACATGAGAGC
58621544 CTTTCTTTTT
1 CTTTCTTTTT
*
58621554 TTTTCTTTTT
1 CTTTCTTTTT
58621564 CTTTCTCTTTT
1 CTTTCT-TTTT
58621575 CTTT-TTTT
1 CTTTCTTTT
58621583 CATCATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.12
10 15 0.58
11 8 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:58623105 original size:24 final size:23
Alignment explanation
Indices: 58623077--58623121 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
58623067 ACAGCTCTAC
*
58623077 ATGAGCGTCCTGATATAGGCTCTT
1 ATGAGCGTCCTGACAT-GGCTCTT
*
58623101 ATGAGCTTCCTGACATGGCTC
1 ATGAGCGTCCTGACATGGCTC
58623122 GCTTGCACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
ATGAGCGTCCTGACATGGCTCTT
Found at i:58628866 original size:5 final size:5
Alignment explanation
Indices: 58628856--58628925 Score: 52
Period size: 5 Copynumber: 12.8 Consensus size: 5
58628846 TTTTTCTCGT
**
58628856 TTTTC TTTTC TTTTTC ATTTTC TTTTC TTTT- TTCAC ATTCATTC TTTTC
1 TTTTC TTTTC -TTTTC -TTTTC TTTTC TTTTC TTTTC -TT--TTC TTTTC
58628905 TTTTTC ATTTTC TTTTC TTTT
1 -TTTTC -TTTTC TTTTC TTTT
58628926 TTTCACATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 2 0.04
5 26 0.49
6 22 0.42
7 2 0.04
8 1 0.02
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:58628878 original size:17 final size:17
Alignment explanation
Indices: 58628856--58628926 Score: 97
Period size: 17 Copynumber: 3.9 Consensus size: 17
58628846 TTTTTCTCGT
58628856 TTTTCTTTTCTTTTTCA
1 TTTTCTTTTCTTTTTCA
58628873 TTTTCTTTTCTTTTTTCACA
1 TTTTCTTTTC-TTTTT--CA
58628893 TTCATTCTTTTCTTTTTCA
1 TT--TTCTTTTCTTTTTCA
58628912 TTTTCTTTTCTTTTT
1 TTTTCTTTTCTTTTT
58628927 TTCACATTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
17 23 0.47
18 5 0.10
19 4 0.08
20 4 0.08
21 5 0.10
22 8 0.16
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTCA
Found at i:58628901 original size:39 final size:40
Alignment explanation
Indices: 58628858--58628950 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
58628848 TTTCTCGTTT
58628858 TTCTTTTCTTTTTCATTTTCTTTTC-TTTTTTCACATTCA
1 TTCTTTTCTTTTTCATTTTCTTTTCTTTTTTTCACATTCA
58628897 TTCTTTTCTTTTTCATTTTCTTTTCTTTTTTTCACATTCA
1 TTCTTTTCTTTTTCATTTTCTTTTCTTTTTTTCACATTCA
*
58628937 TTCTTTTTTTTTTC
1 TTCTTTTCTTTTTC
58628951 TCTCAATTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 25 0.48
40 27 0.52
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (40 bp):
TTCTTTTCTTTTTCATTTTCTTTTCTTTTTTTCACATTCA
Found at i:58628943 original size:17 final size:18
Alignment explanation
Indices: 58628883--58628946 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
58628873 TTTTCTTTTC
58628883 TTTTTTCACATTCATTCTTT
1 TTTTTTCACATTCATTC--T
** *
58628903 TCTTTTTCATTTTCTTTTCT
1 T-TTTTTCACATTC-ATTCT
58628923 TTTTTTCACATTCATTCT
1 TTTTTTCACATTCATTCT
58628941 TTTTTT
1 TTTTTT
58628947 TTTCTCTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 10 0.28
19 10 0.28
20 3 0.08
21 10 0.28
22 3 0.08
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTCACATTCATTCT
Found at i:58628944 original size:19 final size:19
Alignment explanation
Indices: 58628883--58628947 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
58628873 TTTTCTTTTC
58628883 TTTTTTCACATTCATTCTTT
1 TTTTTTCACATTCATTC-TT
** *
58628903 TCTTTTTCATTTTC-TTTTCT
1 T-TTTTTCACATTCATTCT-T
58628923 TTTTTTCACATTCATTCTT
1 TTTTTTCACATTCATTCTT
58628942 TTTTTT
1 TTTTTT
58628948 TTCTCTCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 18 0.50
20 8 0.22
21 10 0.28
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTCACATTCATTCTT
Found at i:58630490 original size:13 final size:13
Alignment explanation
Indices: 58630472--58630497 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58630462 AAATTACAAC
58630472 AGACACACGCTCG
1 AGACACACGCTCG
58630485 AGACACACGCTCG
1 AGACACACGCTCG
58630498 TGTGCTCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (13 bp):
AGACACACGCTCG
Found at i:58631877 original size:29 final size:29
Alignment explanation
Indices: 58631816--58631905 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
58631806 CACATACCTG
*
58631816 TATATGGCCCACTAGGCCC-AATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
58631844 TATATGACCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * * *
58631873 TATATGGCTCATCAGACCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
58631902 TATA
1 TATA
58631906 GTCATGCTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 17 0.31
29 37 0.69
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:58640281 original size:43 final size:43
Alignment explanation
Indices: 58640199--58640281 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
58640189 TGAGGTATGT
* * *
58640199 AGCATCCAAGCTCGTTGAGAGGTCCGAGTTTATTATGGATGCG
1 AGCATCCAAGCTCGCTGAGAGGTCCGAGTTCATGATGGATGCG
* * * *
58640242 AGCATCCGAGCTCGCTGAGTGGTCTGAGTTCATGGTGGAT
1 AGCATCCAAGCTCGCTGAGAGGTCCGAGTTCATGATGGAT
58640282 ACGATTTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (43 bp):
AGCATCCAAGCTCGCTGAGAGGTCCGAGTTCATGATGGATGCG
Found at i:58642059 original size:21 final size:21
Alignment explanation
Indices: 58642035--58642075 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58642025 AAAATATAAA
58642035 TTACAACTCATAAATATTTTT
1 TTACAACTCATAAATATTTTT
* * *
58642056 TTACAATTTATAATTATTTT
1 TTACAACTCATAAATATTTT
58642076 ATCAAATCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (21 bp):
TTACAACTCATAAATATTTTT
Found at i:58642790 original size:48 final size:47
Alignment explanation
Indices: 58642701--58642877 Score: 277
Period size: 48 Copynumber: 3.7 Consensus size: 47
58642691 CATAGGGTAT
58642701 AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTC
58642748 AATGCCGA-GCCATGTCCCAGACATGTGTTTTACACTAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCCAGACA--TGTTTTACACTAGCTCTCGTCTC
*
58642796 AATGCCGA-GCCATGTCCCAGACATGTTTTACACTAGCTGTCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTC
* * *
58642842 AATGCCGATGACATGCCCCAGACATGGTCTTACACT
1 AATGCCGATGCCATGTCCCAGACAT-GTTTTACACT
58642878 GACTATCGAA
Statistics
Matches: 122, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
46 45 0.37
47 22 0.18
48 55 0.45
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (47 bp):
AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTC
Found at i:58642820 original size:94 final size:95
Alignment explanation
Indices: 58642701--58642877 Score: 295
Period size: 94 Copynumber: 1.9 Consensus size: 95
58642691 CATAGGGTAT
* *
58642701 AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTCAATGCCGA-GCCATGTCC
1 AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTCAATGCCGATGACATGCCC
*
58642765 CAGACATGTGTTTTACACTAGCTCTCGTCTC
66 CAGACATG-GTCTTACACTAGCTCTCGTCTC
*
58642796 AATGCCGA-GCCATGTCCCAGACATGTTTTACACTAGCTGTCGTCTCAATGCCGATGACATGCCC
1 AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTCAATGCCGATGACATGCCC
58642860 CAGACATGGTCTTACACT
66 CAGACATGGTCTTACACT
58642878 GACTATCGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
94 54 0.70
95 23 0.30
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (95 bp):
AATGCCGATGCCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTCAATGCCGATGACATGCCC
CAGACATGGTCTTACACTAGCTCTCGTCTC
Found at i:58642964 original size:46 final size:46
Alignment explanation
Indices: 58642901--58643014 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 46
58642891 GAGGTTGACA
* * **
58642901 CCATGTCCCAGACATGGTCTTACGCTCTCACATATCCGT-GCCGATG
1 CCATGTCTCAGACATGGTCTTACACTAACACATAT-CGTAGCCGATG
*
58642947 CCATGTCTCAGACATGGTCTTACACTAACACATCTCGTAGCCGATG
1 CCATGTCTCAGACATGGTCTTACACTAACACATATCGTAGCCGATG
58642993 -CATGT-TCTAGACAT-GTCTTACA
1 CCATGTCTC-AGACATGGTCTTACA
58643015 TTAGCTATTG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
44 10 0.16
45 14 0.23
46 37 0.61
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (46 bp):
CCATGTCTCAGACATGGTCTTACACTAACACATATCGTAGCCGATG
Found at i:58645917 original size:42 final size:37
Alignment explanation
Indices: 58645837--58645913 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
58645827 AGGCCTTGTA
58645837 ACTTGTCCCGATCTCGGGTACGGGTAAGGGGTGTTAC
1 ACTTGTCCCGATCTCGGGTACGGGTAAGGGGTGTTAC
58645874 ACTT-TCCCGATCTCGGGTACGGGTAAGGGGTGTTAC
1 ACTTGTCCCGATCTCGGGTACGGGTAAGGGGTGTTAC
58645910 ACTT
1 ACTT
58645914 ACACATGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.90
37 4 0.10
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (37 bp):
ACTTGTCCCGATCTCGGGTACGGGTAAGGGGTGTTAC
Found at i:58660872 original size:3 final size:3
Alignment explanation
Indices: 58660864--58660912 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
58660854 CGGGAAGCTA
*
58660864 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TAG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
58660912 T
1 T
58660913 AGGTCTTCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.02, C:0.00, G:0.63, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:58675747 original size:28 final size:28
Alignment explanation
Indices: 58675474--58675747 Score: 214
Period size: 28 Copynumber: 9.8 Consensus size: 28
58675464 ATTTCGTAGA
* * *
58675474 TCGCCATAAAGGCTTCCCTATCTATAGAT
1 TCGCCACAAAGGCTTCCCTTTTTATAG-T
* * * *
58675503 T-GCAACAAAGTCTTTCCTTCTTATAGAT
1 TCGCCACAAAGGCTTCCCTTTTTATAG-T
* * * * *
58675531 T-TCCAGAAATGCTTCCTTTTTTATAAT
1 TCGCCACAAAGGCTTCCCTTTTTATAGT
** * *
58675558 TTTCCACAAAAGCTTCCCTTTTCATAG-
1 TCGCCACAAAGGCTTCCCTTTTTATAGT
* *
58675585 TCGCCAAAAAGGCTTTCCTTTTTATAGT
1 TCGCCACAAAGGCTTCCCTTTTTATAGT
* * * *
58675613 TCACCACTAAGGCTTCACTTTTCATAGAT
1 TCGCCACAAAGGCTTCCCTTTTTATAG-T
*
58675642 T-GCCACAAAGACTTCCCTTTTTATAGT
1 TCGCCACAAAGGCTTCCCTTTTTATAGT
* * *
58675669 TTGCCATAAAGGCTTCCCTTTTCATAGT
1 TCGCCACAAAGGCTTCCCTTTTTATAGT
* ***
58675697 TTGTTGCAAAGGCTTCCCTTTTTATAGT
1 TCGCCACAAAGGCTTCCCTTTTTATAGT
*
58675725 TCGCAACAAAGGCTTCCCTTTTT
1 TCGCCACAAAGGCTTCCCTTTTT
58675748 TTAACGTCTT
Statistics
Matches: 191, Mismatches: 50, Indels: 9
0.76 0.20 0.04
Matches are distributed among these distances:
27 25 0.13
28 163 0.85
29 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (28 bp):
TCGCCACAAAGGCTTCCCTTTTTATAGT
Found at i:58690322 original size:213 final size:213
Alignment explanation
Indices: 58689951--58690366 Score: 733
Period size: 213 Copynumber: 2.0 Consensus size: 213
58689941 TTATCAATCT
*
58689951 TGTATTCAATTTCACATCAATAGCATGTACACAATTCATACATACAATATTCAATTTAAGCATAT
1 TGTATTCAATTTCACATCAATAGCATGTAAACAATTCATACATACAATATTCAATTTAAGCATAT
* * *
58690016 AAATAAACACAATTTAGTTACACGAACTTACCTCAATACTTGTTCTTATACGAAAATCTACTAAT
66 AAATAAACACAATTTAATTACACGAACTTACATCAATACTTGTTCGTATACGAAAATCTACTAAT
58690081 CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGAATCTATATAAATGAAT
131 CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGAATCTATATAAATGAAT
58690146 TTAATCATGAATTTATCA
196 TTAATCATGAATTTATCA
*
58690164 TGTATTCAATTTCACATCAATAGCATTTAAACAATTCATACATACAATATTCAATTTAAGCATAT
1 TGTATTCAATTTCACATCAATAGCATGTAAACAATTCATACATACAATATTCAATTTAAGCATAT
* * *
58690229 AAATAAACACGATTTAATTACACGAACTTACATCAATATTTGTTCGTATACGAAAATCTACTACT
66 AAATAAACACAATTTAATTACACGAACTTACATCAATACTTGTTCGTATACGAAAATCTACTAAT
* * *
58690294 CAGAAACTTTTTGTTTTCCTCGATCCAATTTCGTATTTGGTCTTTTCGGATCTATATAAATGAAT
131 CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGAATCTATATAAATGAAT
58690359 TTAATCAT
196 TTAATCAT
58690367 CAATATATTA
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
213 192 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (213 bp):
TGTATTCAATTTCACATCAATAGCATGTAAACAATTCATACATACAATATTCAATTTAAGCATAT
AAATAAACACAATTTAATTACACGAACTTACATCAATACTTGTTCGTATACGAAAATCTACTAAT
CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGAATCTATATAAATGAAT
TTAATCATGAATTTATCA
Found at i:58692627 original size:213 final size:213
Alignment explanation
Indices: 58692256--58692671 Score: 715
Period size: 213 Copynumber: 2.0 Consensus size: 213
58692246 TTATCGATCT
** *
58692256 TGTATTCAATTTCACATCAATAGCATGTACCCAATTCATACATACAATATTCAATTTAAGCATAT
1 TGTATTCAATTTCACATCAATAGCATGTAAACAACTCATACATACAATATTCAATTTAAGCATAT
* * * *
58692321 AAATAAACACAATTTAGTTACATAAAGTTACCTCAATACTTGTTCTTATACGAAAATCTACTAAT
66 AAATAAACACAATTTAGTTACACAAACTTACCTCAATACTTGTTCGTATACGAAAATCAACTAAT
*
58692386 CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGGATTTATATAAATGAAT
131 CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGGATCTATATAAATGAAT
58692451 TTAATCATGAATTTATCA
196 TTAATCATGAATTTATCA
*
58692469 TGTATTCAATTTCACATCAATAGCATTTAAACAACTCATACATACAATATTCAATTTAAGCATAT
1 TGTATTCAATTTCACATCAATAGCATGTAAACAACTCATACATACAATATTCAATTTAAGCATAT
* *
58692534 AAATAAACACGATTTAGTTACACGAACTTACCTCAATACTTGTTCGTATACGAAAATCAACTAAT
66 AAATAAACACAATTTAGTTACACAAACTTACCTCAATACTTGTTCGTATACGAAAATCAACTAAT
* *
58692599 CAGAAACTTTTTGTTTTCCTCGATCCAATTCCGTATTTGGTCTTTTCGGATCTATGTAAATGAAT
131 CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGGATCTATATAAATGAAT
58692664 TTAATCAT
196 TTAATCAT
58692672 CAATATATTA
Statistics
Matches: 190, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
213 190 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (213 bp):
TGTATTCAATTTCACATCAATAGCATGTAAACAACTCATACATACAATATTCAATTTAAGCATAT
AAATAAACACAATTTAGTTACACAAACTTACCTCAATACTTGTTCGTATACGAAAATCAACTAAT
CAGAAACTTTTTGTTTTCCTCAATCCAATTCCGTATTTGGTCTTTTCGGATCTATATAAATGAAT
TTAATCATGAATTTATCA
Found at i:58701566 original size:13 final size:13
Alignment explanation
Indices: 58701548--58701573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58701538 TTTTTCGACC
58701548 CGGGTGTGGGGTA
1 CGGGTGTGGGGTA
58701561 CGGGTGTGGGGTA
1 CGGGTGTGGGGTA
58701574 TGCTAGACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.62, T:0.23
Consensus pattern (13 bp):
CGGGTGTGGGGTA
Found at i:58702702 original size:25 final size:25
Alignment explanation
Indices: 58702619--58702736 Score: 119
Period size: 25 Copynumber: 4.6 Consensus size: 25
58702609 TGAACTCTAG
* *
58702619 CTCAAGGCCTGATAATTAAACACCGA
1 CTCAAAGCCTGCTAA-TAAACACCGA
* * *
58702645 CTCACAGCCTGCTAGATAAATCACTGG
1 CTCAAAGCCTGCTA-ATAAA-CACCGA
* * *
58702672 CTCAAAGTCTACTAATAAATACCGA
1 CTCAAAGCCTGCTAATAAACACCGA
*
58702697 CTCAAAGCCTGCTAATATACACCGA
1 CTCAAAGCCTGCTAATAAACACCGA
*
58702722 CTTAAAGCCTGCTAA
1 CTCAAAGCCTGCTAA
58702737 GCAATCACAT
Statistics
Matches: 74, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
25 38 0.51
26 20 0.27
27 16 0.22
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (25 bp):
CTCAAAGCCTGCTAATAAACACCGA
Found at i:58708615 original size:28 final size:28
Alignment explanation
Indices: 58708573--58708803 Score: 148
Period size: 28 Copynumber: 8.3 Consensus size: 28
58708563 TTCTCCGTAA
* *
58708573 CATAGACCTCCATAAAGGCTTCTATTTT
1 CATAGATCACCATAAAGGCTTCTATTTT
* *
58708601 -AGTAGATCACTATAAAGGCTTCTCTTTT
1 CA-TAGATCACCATAAAGGCTTCTATTTT
** **
58708629 CATAGATTGCCATAAAGGCTTCCCTTTT
1 CATAGATCACCATAAAGGCTTCTATTTT
* * * * **
58708657 TATAGTTCACCACAAAGGTTTCCCTTTT
1 CATAGATCACCATAAAGGCTTCTATTTT
* **
58708685 CATAGAT-AGTC-TCAAAGGCTTCCCTTTT
1 CATAGATCA-CCAT-AAAGGCTTCTATTTT
* ** *
58708713 CATAGATCGA-CACAAAGGCTTCCCTCTT
1 CATAGATC-ACCATAAAGGCTTCTATTTT
* *
58708741 -ATAGTTCACCATAAAGGCTTCTCTTTT
1 CATAGATCACCATAAAGGCTTCTATTTT
* * **
58708768 CATATATCACCACAAAGGCTTCCCTTTT
1 CATAGATCACCATAAAGGCTTCTATTTT
58708796 CATAGATC
1 CATAGATC
58708804 GCTACAAACA
Statistics
Matches: 164, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
26 1 0.01
27 23 0.14
28 138 0.84
29 1 0.01
30 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (28 bp):
CATAGATCACCATAAAGGCTTCTATTTT
Found at i:58708810 original size:28 final size:28
Alignment explanation
Indices: 58708614--58708969 Score: 333
Period size: 28 Copynumber: 12.6 Consensus size: 28
58708604 AGATCACTAT
* * *
58708614 AAAGGCTTCTCTTTTCATAGATTGCCAT
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
* * *
58708642 AAAGGCTTCCCTTTTTATAGTTCACCAC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
* * * *
58708670 AAAGGTTTCCCTTTTCATAGATAGTCTC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
*
58708698 AAAGGCTTCCCTTTTCATAGATCGACAC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
* * * *
58708726 AAAGGCTTCCCTCTT-ATAGTTCACCAT
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
* * *
58708753 AAAGGCTTCTCTTTTCATATATCACCAC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
58708781 AAAGGCTTCCCTTTTCATAGATCGCTACAAAC
1 AAAGGCTTCCCTTTTCATAGATCGC--C--AC
* * * *
58708813 AAAGGATTTCTTTTTCACA-ATTCGCCAC
1 AAAGGCTTCCCTTTTCATAGA-TCGCCAC
* *
58708841 AAAGGCTT-CCTTTGTCAGAAATCGCCAC
1 AAAGGCTTCCCTTT-TCATAGATCGCCAC
** *
58708869 AAAGGCTTCCCTTTTTTTAGTTCGCCAC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
*
58708897 AAAGGCTTCTCTTTTCATAGATCGCCAC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
* * * *
58708925 AAAGGCTT-CATTTTTATAGTTTGCCAC
1 AAAGGCTTCCCTTTTCATAGATCGCCAC
*
58708952 AAAAGCTTCCCTTTTCAT
1 AAAGGCTTCCCTTTTCAT
58708970 GCTTCTCTTT
Statistics
Matches: 264, Mismatches: 54, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
27 46 0.17
28 188 0.71
29 6 0.02
30 2 0.01
31 1 0.00
32 21 0.08
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (28 bp):
AAAGGCTTCCCTTTTCATAGATCGCCAC
Found at i:58709010 original size:28 final size:28
Alignment explanation
Indices: 58708970--58709033 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
58708960 CCCTTTTCAT
* * *
58708970 GCTTCTCTTTTTATAGTTTGCCACAAAG
1 GCTTCCCTCTTTATAGTTCGCCACAAAG
58708998 GCTTCCCTCTTTATAGTTCGCCACAAAG
1 GCTTCCCTCTTTATAGTTCGCCACAAAG
58709026 GCTTCCCT
1 GCTTCCCT
58709034 TTTTCTAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (28 bp):
GCTTCCCTCTTTATAGTTCGCCACAAAG
Found at i:58714274 original size:10 final size:10
Alignment explanation
Indices: 58714261--58714289 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
58714251 AAAAAACTTA
58714261 AAAATATTTC
1 AAAATATTTC
58714271 AAAATATTTC
1 AAAATATTTC
58714281 AAAATATTT
1 AAAATATTT
58714290 TTCGTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATATTTC
Found at i:58726537 original size:20 final size:21
Alignment explanation
Indices: 58726512--58726553 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
58726502 AATATGCTGT
*
58726512 AAAATGAAAG-TTTTTGATAG
1 AAAATGAAAGATTATTGATAG
58726532 AAAATGAAAGATTATTGATAG
1 AAAATGAAAGATTATTGATAG
58726553 A
1 A
58726554 TAAACCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (21 bp):
AAAATGAAAGATTATTGATAG
Found at i:58727083 original size:32 final size:32
Alignment explanation
Indices: 58727041--58727149 Score: 121
Period size: 32 Copynumber: 3.3 Consensus size: 32
58727031 AAATGATACA
*
58727041 ACTTGAAAAGGTTAGGTACACTTTGTGTGTAC
1 ACTTGAAAAGGTTAGGTATACTTTGTGTGTAC
* *
58727073 ACTTGGAAAGGTTAGGTATACTTTGTGTATAC
1 ACTTGAAAAGGTTAGGTATACTTTGTGTGTAC
** *
58727105 -CATATGAAAAGGAAAGGTATACTTTGTGAGTACC
1 AC-T-TGAAAAGGTTAGGTATACTTTGTGTGTA-C
*
58727139 ACTTGGAAAGG
1 ACTTGAAAAGG
58727150 AATGTACGCC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.02
32 30 0.47
33 30 0.47
34 2 0.03
35 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (32 bp):
ACTTGAAAAGGTTAGGTATACTTTGTGTGTAC
Found at i:58727149 original size:33 final size:33
Alignment explanation
Indices: 58727054--58727151 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 33
58727044 TGAAAAGGTT
* * **
58727054 AGGTACACTTTGTGTGTA-CACTTGGAAAGGTT
1 AGGTATACTTTGTGAGTACCACTTGGAAAGGAA
*
58727086 AGGTATACTTTGTGTA-TACCA-TATGAAAAGGAA
1 AGGTATACTTTGTG-AGTACCACT-TGGAAAGGAA
58727119 AGGTATACTTTGTGAGTACCACTTGGAAAGGAA
1 AGGTATACTTTGTGAGTACCACTTGGAAAGGAA
58727152 TGTACGCCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
32 17 0.31
33 37 0.67
34 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.31
Consensus pattern (33 bp):
AGGTATACTTTGTGAGTACCACTTGGAAAGGAA
Found at i:58737913 original size:21 final size:21
Alignment explanation
Indices: 58737889--58737929 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58737879 CATTATAATA
*
58737889 AGCCTACGAGGTATTAAAACG
1 AGCCTACGAGGCATTAAAACG
* *
58737910 AGCCTATGAGGCCTTAAAAC
1 AGCCTACGAGGCATTAAAAC
58737930 TAGTTTAGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (21 bp):
AGCCTACGAGGCATTAAAACG
Found at i:58738808 original size:38 final size:37
Alignment explanation
Indices: 58738766--58738869 Score: 97
Period size: 38 Copynumber: 2.8 Consensus size: 37
58738756 ATGAATCGTT
*
58738766 ACACCAATACGAAGCCTGCTAGGCATCAAGCCCGATAA
1 ACACCAATA-GAAGCCTGCTAGGCATCAAGACCGATAA
* * *
58738804 ACACCTACA-ATAAGCCTACTAGGCATCAAGATCGATAA
1 ACACC-A-ATAGAAGCCTGCTAGGCATCAAGACCGATAA
*
58738842 ACATCGGAAT-GAAGCCTGCTAGGC-TCAA
1 ACA-C-CAATAGAAGCCTGCTAGGCATCAA
58738870 AGTCTAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
37 4 0.07
38 45 0.83
39 4 0.07
40 1 0.02
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (37 bp):
ACACCAATAGAAGCCTGCTAGGCATCAAGACCGATAA
Found at i:58738916 original size:39 final size:39
Alignment explanation
Indices: 58738853--58738962 Score: 166
Period size: 39 Copynumber: 2.8 Consensus size: 39
58738843 CATCGGAATG
* * *
58738853 AAGCCTGCTAGGCTCAAAGTCTAATAAGTCTCCGGCACA
1 AAGCCTGTTAGGCTCAAAGCCTAATAAGTCACCGGCACA
* *
58738892 AAGCTTGTTAGGCTCAAAGCCTAATAAGTCACCGGCACG
1 AAGCCTGTTAGGCTCAAAGCCTAATAAGTCACCGGCACA
*
58738931 AAGCCTGTTAGGCTCAAAGCCTGATAAGTCAC
1 AAGCCTGTTAGGCTCAAAGCCTAATAAGTCAC
58738963 TGAACAAGGC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (39 bp):
AAGCCTGTTAGGCTCAAAGCCTAATAAGTCACCGGCACA
Found at i:58738984 original size:38 final size:39
Alignment explanation
Indices: 58738846--58738985 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 39
58738836 CGATAAACAT
* * * *
58738846 CGGAATGAAGCCTGCTAGGCTCAAAGTCTAATAAGTCTC
1 CGGAACGAAGCCTGCCAGGCTCAAAGCCTAATAAGTCAC
* * * **
58738885 CGGCACAAAGCTTGTTAGGCTCAAAGCCTAATAAGTCAC
1 CGGAACGAAGCCTGCCAGGCTCAAAGCCTAATAAGTCAC
* ** *
58738924 CGGCACGAAGCCTGTTAGGCTCAAAGCCTGATAAGTCA-
1 CGGAACGAAGCCTGCCAGGCTCAAAGCCTAATAAGTCAC
*
58738962 CTGAAC-AAGGCCTGCCAGGCTCAA
1 CGGAACGAA-GCCTGCCAGGCTCAA
58738986 GCTCCGATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
37 2 0.02
38 17 0.20
39 67 0.78
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (39 bp):
CGGAACGAAGCCTGCCAGGCTCAAAGCCTAATAAGTCAC
Done.