Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 20 of 444
Found at i:5594104 original size:25 final size:26
Alignment explanation
Indices: 5594075--5594124 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
5594065 TTGATTGATT
* * *
5594075 ATTTTCTTGATATATTTA-ATTTGAA
1 ATTTTCTCGACATATATATATTTGAA
5594100 ATTTTCTCGACATATATATATTTGA
1 ATTTTCTCGACATATATATATTTGA
5594125 TAAGATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (26 bp):
ATTTTCTCGACATATATATATTTGAA
Found at i:5594469 original size:2 final size:2
Alignment explanation
Indices: 5594462--5594492 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5594452 TGTGTTGAAT
5594462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5594493 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5596048 original size:27 final size:27
Alignment explanation
Indices: 5595976--5596050 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
5595966 ACATATGTAC
*
5595976 ATAAAATATACACTAATATAATAATAGTT
1 ATAATATATACAC-AATATAATAATA-TT
5596005 ATAATA-ATACTAGCAATAGTAATAAT-TT
1 ATAATATATAC-A-CAATA-TAATAATATT
*
5596033 GTAATATATACACAATAT
1 ATAATATATACACAATAT
5596051 GGTATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
26 1 0.03
27 5 0.12
28 12 0.30
29 14 0.35
30 8 0.20
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (27 bp):
ATAATATATACACAATATAATAATATT
Found at i:5596110 original size:16 final size:14
Alignment explanation
Indices: 5596053--5596113 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 14
5596043 CACAATATGG
5596053 TATTTAAAATATATA
1 TATTT-AAATATATA
* *
5596068 TATATATATATATA
1 TATTTAAATATATA
*
5596082 TATGTATATATATATA
1 TAT-T-TAAATATATA
5596098 GTATTTAGAATATATA
1 -TATTTA-AATATATA
5596114 CATAAGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 11 0.29
15 6 0.16
16 18 0.47
17 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (14 bp):
TATTTAAATATATA
Found at i:5596113 original size:2 final size:2
Alignment explanation
Indices: 5596061--5596097 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5596051 GGTATTTAAA
*
5596061 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5596098 GTATTTAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5597463 original size:88 final size:83
Alignment explanation
Indices: 5597358--5598169 Score: 320
Period size: 88 Copynumber: 9.9 Consensus size: 83
5597348 AACAGACATT
** * *
5597358 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
5597423 TTGATTTTTTGAAACTTAACTTG
65 TTGATTTTTTGAAA---AAC-TG
* * * ** *
5597446 AAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGGAGGTTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
5597510 GTTGA-TTTTTGAAAAACAG
64 GTTGATTTTTTGAAAAACTG
* * * * ** *** *
5597529 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAAT
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAAT
5597590 ATGAGTTGAATTTTTTTG--AAA---
60 ATGAGTTG-A-TTTTTTGAAAAACTG
** * *
5597611 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
5597676 TTGA-TTTTTGAAAACAGAATTTG
65 TTGATTTTTTG--AA-A-AA-CTG
* * * * *
5597699 AAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
5597764 TTGATTTTTTTGAAAAA-T-
65 TTGA-TTTTTTGAAAAACTG
* *** *** * *
5597782 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
5597842 GTTGATTTTTTTG--AAA--G
64 GTTGA-TTTTTTGAAAAACTG
* * * * *
5597859 ATAGA-A-A--TTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
5597920 TTGATTTTTTG-AAAAC--
65 TTGATTTTTTGAAAAACTG
* * * ** **
5597936 --AGA-A-A--TTGAAAATACCTC-AACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTCGCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAG
*
5597993 TTGA-ATTTTG-AAAAC--
65 TTGATTTTTTGAAAAACTG
* * ** *
5598008 --AGA-A-A--TTGAAATTACCT--CAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTCGCA-CGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
5598065 TTGATTTTTTTTTGAAAGGCAGAAATTG
65 TTGA---TTTTTTG--A---A-AAACTG
* ** ** * * *
5598093 AAAAATAGAAATTGAAAATACCTCGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
5598158 TGACTTTTTTGA
66 TGA-TTTTTTGA
5598170 CAACAGAAAT
Statistics
Matches: 569, Mismatches: 93, Indels: 124
0.72 0.12 0.16
Matches are distributed among these distances:
71 1 0.00
72 62 0.11
73 34 0.06
75 17 0.03
76 14 0.02
77 52 0.09
78 6 0.01
79 59 0.10
80 12 0.02
81 36 0.06
82 10 0.02
83 14 0.02
84 38 0.07
85 12 0.02
86 2 0.00
87 21 0.04
88 118 0.21
89 1 0.00
90 13 0.02
91 11 0.02
92 35 0.06
93 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (83 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAACTG
Found at i:5597562 original size:30 final size:30
Alignment explanation
Indices: 5597526--5597587 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5597516 TTTTGAAAAA
5597526 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
5597556 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
5597586 CA
1 CA
5597588 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:5597705 original size:14 final size:14
Alignment explanation
Indices: 5597682--5597716 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5597672 TGAGTTGATT
5597682 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
5597695 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
5597709 TTTGAAAA
1 TTTGAAAA
5597717 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:5597904 original size:77 final size:75
Alignment explanation
Indices: 5597736--5598434 Score: 475
Period size: 75 Copynumber: 9.2 Consensus size: 75
5597726 ATGTGACCCG
* * * *
5597736 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTG--AAAATACCT
* *
5597801 CAGTGTGTGATCTGA
63 CA--GCGTGATCTCA
* *
5597816 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
*
5597880 GCGCGTGAGC-CA
65 --GCGTGATCTCA
* *
5597892 AGGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
**
5597956 CGTG-TCTTG
66 CGTGATCTCA
** * *
5597965 AGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
* *
5598028 CGTG-TCCCG
66 CGTGATCTCA
*
5598037 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAATAGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAA-ACAGAAATTG-AAAAT---
** * *** * *
5598102 AATTGAAAAT-ACCTCGCG
59 ACCTCAGCGTGA--TCTCA
* * * * * * * * *
5598120 TGTGATCTAAGGCTCAACTCAC-C--TCTCGCAATACGAGTTGACTTTTTTGACAACAGAAATTG
1 AG-GCTC-AA--CTCACCTCTCGCAATAT-G-AGT-TGA-TT--TTTTT--GAAAACAGAAATTG
* *
5598182 AAATTACCTCAGCGTG-TC-CTG
54 AAAATACCTCAGCGTGATCTC-A
*
5598203 AGGCTCAACTCACCTCTCGCAATATGAGTAGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTGAAAATACCTCA
* **
5598268 GCATG-TCTTG
65 GCGTGATCTCA
** *
5598278 AGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAACAGAAATTGAAAATACCTCA
* **
5598343 GCATG-TCTTG
65 GCGTGATCTCA
** * *
5598353 AGGCTCAACT-ATTTCTCGCAATAT-AGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
**
5598414 CGTG-TCTTG
66 CGTGATCTCA
5598423 AGGCTCAACTCA
1 AGGCTCAACTCA
5598435 TTTTGAACAG
Statistics
Matches: 511, Mismatches: 73, Indels: 79
0.77 0.11 0.12
Matches are distributed among these distances:
70 47 0.09
71 1 0.00
72 66 0.13
73 39 0.08
74 14 0.03
75 120 0.23
76 32 0.06
77 55 0.11
78 9 0.02
79 55 0.11
80 4 0.01
81 7 0.01
82 6 0.01
83 9 0.02
84 5 0.01
85 7 0.01
86 5 0.01
87 10 0.02
88 8 0.02
89 9 0.02
90 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
CGTGATCTCA
Found at i:5598177 original size:238 final size:238
Alignment explanation
Indices: 5597852--5598335 Score: 704
Period size: 238 Copynumber: 2.0 Consensus size: 238
5597842 GTTGATTTTT
* * *
5597852 TTGAAAGATAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
* **
5597917 AAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
66 AAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
* * *
5597982 CGCAATATGAGTTGA-ATTTTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
131 CGCAATATGAGTAGATATTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTCAA
* *
5598045 CTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAA
196 CTCACCTCTCACAATATGAGTTGA-TTTTTTTTGAAA-ACAGAAA
* * *
5598090 TTGAAAAATAGAAATTGAAAATACCTC-GCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATAC
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
* * * *
5598154 GAGTTGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
66 AAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTC
* **
5598219 TCGCAATATGAGTAGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTC
130 TCGCAATATGAGTAGA-TATTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTC
**
5598284 AACTCATTTCTCACAATATGAGTTGATTTTTTTTGAAAACAGAAA
194 AACTCACCTCTCACAATATGAGTTGATTTTTTTTGAAAACAGAAA
5598329 TTGAAAA
1 TTGAAAA
5598336 TACCTCAGCA
Statistics
Matches: 219, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
237 39 0.18
238 91 0.42
239 13 0.06
240 17 0.08
241 59 0.27
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (238 bp):
TTGAAAAATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
AAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTAGATATTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTCAA
CTCACCTCTCACAATATGAGTTGATTTTTTTTGAAAACAGAAA
Found at i:5598254 original size:164 final size:162
Alignment explanation
Indices: 5597931--5598260 Score: 484
Period size: 166 Copynumber: 2.0 Consensus size: 162
5597921 TGATTTTTTG
* * ** *
5597931 AAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGTATTAAGGCTCAACTCACCTCTCGCAATACGAGTTG
5597996 AATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
66 AATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
* **
5598061 TGAGTTGATTTTTTTTTGAAAGGCAGAAATTGA
131 TGAGTAGA-TTTTTTTTGAAAAACAGAAATTGA
* *
5598094 AAAATAGAAATTGAAAATACCTC-GCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAACGTGT-AT-TAAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
5598158 TGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
64 TGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
5598223 AATATGAGTAGA-TTTTTTTGAAAAACAGAAATTGA
127 AATATGAGTAGATTTTTTTTGAAAAACAGAAATTGA
5598258 AAA
1 AAA
5598261 TACCTCAGCA
Statistics
Matches: 150, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
162 5 0.03
163 23 0.15
164 54 0.36
166 68 0.45
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (162 bp):
AAAACAGAAATTGAAAATACCTCAACGTGTATTAAGGCTCAACTCACCTCTCGCAATACGAGTTG
AATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTAGATTTTTTTTGAAAAACAGAAATTGA
Found at i:5598318 original size:388 final size:386
Alignment explanation
Indices: 5597569--5598434 Score: 1100
Period size: 388 Copynumber: 2.2 Consensus size: 386
5597559 AAATTAAAAA
** * *
5597569 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAAAAACAGAAATTGAAAATAGCT
1 GCTCAACTCATTTCTCGCAATATGAGTTGAA---TTTTG----AAAACAGAAATTGAAATTACCT
** * * *
5597634 CAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTG
59 CAG--CGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTG
** * **
5597699 AAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAG
122 AAAAACAGAAATTGAAAATACCTCGACATGTGACCCAAGGCTCAACTCACATCTCGCAATACGAG
* * * * *
5597764 TTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACC
187 TTGACTTTTTTGAAAAACAGAAATTG-AAAAATACCTCAGCGTGT-ACCTGAAGCTCAACTCACC
* * * * *
5597829 TCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAG
250 TCTCGCAATATGAGTAGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA-CGCATGAGCCAAG
* *
5597894 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACGT
314 GCTCAACTCACCTCTCACAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACAT
5597959 GTCTTGAG
379 GTCTTGAG
5597967 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
5598032 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAA
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAA-ACAGAAATTGAAAA
* * * * *
5598097 ATAGAAATTGAAAATACCTCG-CGTGTGATCTAAGGCTCAACTCACCTCTCGCAATACGAGTTGA
126 ACAGAAATTGAAAATACCTCGACATGTGACCCAAGGCTCAACTCACATCTCGCAATACGAGTTGA
* * *
5598161 CTTTTTTG-ACAACAGAAATTG-AAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGC
191 CTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTACCTGAAGCTCAACTCACCTCTCGC
* **
5598223 AATATGAGTAGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA-GCATG-TCTTGAGGCTCAA
256 AATATGAGTAGATTTTTTTGAAAAACAGAAATTGAAAATACCTCACGCATGAGC-CAAGGCTCAA
** * *
5598286 CTCATTTCTCACAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACCTCAGCATGTCT
320 CTCACCTCTCACAATATAAGTTGA--TTTTTTGAAAACAGAAATTGAAAATACCTCAACATGTCT
5598351 TGAG
383 TGAG
5598355 GCTCAACT-ATTTCTCGCAATAT-AGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
**
5598418 TCTTGAGGCTCAACTCA
66 TCCCGAGGCTCAACTCA
5598435 TTTTGAACAG
Statistics
Matches: 416, Mismatches: 44, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
385 1 0.00
386 88 0.21
387 14 0.03
388 112 0.27
389 37 0.09
390 15 0.04
391 23 0.06
392 10 0.02
393 52 0.12
394 30 0.07
395 5 0.01
398 29 0.07
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (386 bp):
GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAAACAGA
AATTGAAAATACCTCGACATGTGACCCAAGGCTCAACTCACATCTCGCAATACGAGTTGACTTTT
TTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTACCTGAAGCTCAACTCACCTCTCGCAATAT
GAGTAGATTTTTTTGAAAAACAGAAATTGAAAATACCTCACGCATGAGCCAAGGCTCAACTCACC
TCTCACAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACATGTCTTGAG
Found at i:5598457 original size:49 final size:49
Alignment explanation
Indices: 5598391--5598486 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
5598381 GAATTTTGAA
*
5598391 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
5598440 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
5598487 CTCGCAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:5598520 original size:72 final size:72
Alignment explanation
Indices: 5598440--5598580 Score: 282
Period size: 72 Copynumber: 2.0 Consensus size: 72
5598430 ACTCATTTTG
5598440 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5598505 TTTTGAA
66 TTTTGAA
5598512 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5598577 TTTT
66 TTTT
5598581 TTTTTTTGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:5598528 original size:121 final size:119
Alignment explanation
Indices: 5598321--5598558 Score: 422
Period size: 121 Copynumber: 2.0 Consensus size: 119
5598311 TTTTTTTGAA
*
5598321 AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTATTTCTCGCAATATAGTTGAATT
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTATTTCTCGCAATATAGTTGAATT
*
5598386 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* *
5598440 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACT-ATTTCTCGCAATAT-AGTTGAA
5598505 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
64 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
5598559 CTCGCAATAT
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
119 39 0.35
120 14 0.12
121 60 0.53
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (119 bp):
AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTATTTCTCGCAATATAGTTGAATT
TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:5598646 original size:82 final size:78
Alignment explanation
Indices: 5598440--5598661 Score: 224
Period size: 72 Copynumber: 2.9 Consensus size: 78
5598430 ACTCATTTTG
* * * ** *
5598440 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
5598504 -----ATTTTGAA
66 TTTTTTTTTTGAA
* * * ** *
5598512 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGCTG-A
5598577 TTTTTTTTTTTGAA
65 TTTTTTTTTTTGAA
*
5598591 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAAATACCTCA--ACGTG-ACTCGAGGCTCAACTCACCTCTCGCAATATGAGC
5598655 TGATTTT
62 TGATTTT
5598662 GAAAAAGTAG
Statistics
Matches: 131, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
72 63 0.48
73 1 0.01
79 8 0.06
80 20 0.15
81 5 0.04
82 33 0.25
83 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (78 bp):
AACAGAAATTGAAAATACCTCAACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTTTTTTTTGAA
Found at i:5598729 original size:53 final size:55
Alignment explanation
Indices: 5598630--5598734 Score: 135
Period size: 53 Copynumber: 1.9 Consensus size: 55
5598620 GAACCGAGGC
* *
5598630 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
5598684 TCAACCCA-CTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
5598735 CAGAAATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
53 26 0.59
54 18 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:5598741 original size:13 final size:13
Alignment explanation
Indices: 5598714--5598747 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5598704 GAGTTGATTC
*
5598714 TTGAACAACATAAA
1 TTGAA-AACAGAAA
5598728 TTGAAAACAGAAA
1 TTGAAAACAGAAA
5598741 TTGAAAA
1 TTGAAAA
5598748 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:5598804 original size:139 final size:139
Alignment explanation
Indices: 5598586--5599071 Score: 886
Period size: 139 Copynumber: 3.5 Consensus size: 139
5598576 ATTTTTTTTT
5598586 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
5598650 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTCTCGCAATATGAGTTGATTCT
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTCTCGCAATATGAGTTGATTCT
*
5598715 TGAACAACATAAA
127 TGAACAACGTAAA
5598728 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5598793 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCAC-TCTCGCAATATGAGTTGATTCTTGA
5598858 ACAACGTAAA
130 ACAACGTAAA
*
5598868 TTGAAAACAGAAATT-AAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5598932 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCA-CTCTCGCAATATGAGTTGATTCTTGA
5598997 ACAACGTAAA
130 ACAACGTAAA
5599007 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5599072 TTGAAATTAA
Statistics
Matches: 337, Mismatches: 3, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
138 3 0.01
139 207 0.61
140 98 0.29
141 23 0.07
142 6 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (139 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTCTCGCAATATGAGTTGATTCTTGAA
CAACGTAAA
Found at i:5598869 original size:54 final size:54
Alignment explanation
Indices: 5598769--5598874 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
5598759 GACCTGAGGC
*
5598769 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
5598823 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5598875 CAGAAATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5599008 original size:54 final size:54
Alignment explanation
Indices: 5598908--5599013 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5598898 GACCTGAGGC
*
5598908 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5598962 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5599014 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5599138 original size:72 final size:71
Alignment explanation
Indices: 5599004--5599169 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
5598994 TGAACAACGT
* * * *
5599004 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
5599069 GAGTTG
66 GAGTTG
*
5599075 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
5599140 TGAGTTG
65 TGAGTTG
**
5599147 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
5599170 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:5599264 original size:122 final size:124
Alignment explanation
Indices: 5599044--5599290 Score: 392
Period size: 122 Copynumber: 2.0 Consensus size: 124
5599034 GCGTGACCTG
* *
5599044 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
5599109 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * * *
5599169 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* *
5599231 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
5599290 A
1 A
5599291 ATACCTCAAC
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
121 16 0.14
122 63 0.55
123 7 0.06
124 1 0.01
125 27 0.24
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:5599312 original size:71 final size:70
Alignment explanation
Indices: 5599169--5599343 Score: 228
Period size: 71 Copynumber: 2.5 Consensus size: 70
5599159 AAAAATTAAA
* * * * * *
5599169 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
5599233 CCCCG
66 CCCCG
*
5599238 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
5599303 GTCTTG
65 GCCCCG
5599309 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
5599344 CCCTTGAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
69 26 0.28
70 6 0.06
71 61 0.66
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:5609555 original size:27 final size:27
Alignment explanation
Indices: 5609483--5609557 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
5609473 ACATATGTAC
*
5609483 ATAAAATATACACTAATATAATAATAGTT
1 ATAATATATACAC-AATATAATAATA-TT
5609512 ATAATA-ATACTAGCAATAGTAATAAT-TT
1 ATAATATATAC-A-CAATA-TAATAATATT
*
5609540 GTAATATATACACAATAT
1 ATAATATATACACAATAT
5609558 GGTATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
26 1 0.03
27 5 0.12
28 12 0.30
29 14 0.35
30 8 0.20
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (27 bp):
ATAATATATACACAATATAATAATATT
Found at i:5609595 original size:25 final size:25
Alignment explanation
Indices: 5609541--5609595 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5609531 TAATAATTTG
*
5609541 TAATATATACACAATATGGTATTTA
1 TAATATATACACAATATGGTATATA
* * *
5609566 AAATATATATATATATAT-GTATATA
1 TAATATATACACA-ATATGGTATATA
5609591 TAATA
1 TAATA
5609596 GTATTTAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (25 bp):
TAATATATACACAATATGGTATATA
Found at i:5609664 original size:39 final size:39
Alignment explanation
Indices: 5609565--5609664 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
5609555 TATGGTATTT
* * * *
5609565 AAAATATATATAT-ATATATGTATATATAATAGTATTTA
1 AAAATATATACATAATATATATATATATAATAGCATTAA
* * * *
5609603 AGAATATATACATAAGAAATATATA-ACTAATGGCATTAA
1 AAAATATATACATAATATATATATATA-TAATAGCATTAA
5609642 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
5609665 AAATACCTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 12 0.24
39 37 0.76
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATATATAATAGCATTAA
Found at i:5611716 original size:29 final size:31
Alignment explanation
Indices: 5611674--5611731 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
5611664 ATCAAAATAA
*
5611674 AAAATGACTCGACTT-AATATT-TCAAACTT
1 AAAATGACTCGACTTCAAAATTATCAAACTT
* *
5611703 AAAATTACTTGACTTCAAAATTATCAAAC
1 AAAATGACTCGACTTCAAAATTATCAAAC
5611732 AAATAACTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
30 5 0.21
31 6 0.25
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (31 bp):
AAAATGACTCGACTTCAAAATTATCAAACTT
Found at i:5613084 original size:29 final size:29
Alignment explanation
Indices: 5613049--5613107 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5613039 TTCTTAACTT
*
5613049 TGGTCCTAAGCCTACACTTTAGTTATTTA
1 TGGTCCTAAGCCTAAACTTTAGTTATTTA
5613078 TGGTCCTAAGCCTAAACTTTAGTTATTTA
1 TGGTCCTAAGCCTAAACTTTAGTTATTTA
5613107 T
1 T
5613108 CTCTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (29 bp):
TGGTCCTAAGCCTAAACTTTAGTTATTTA
Found at i:5615201 original size:2 final size:2
Alignment explanation
Indices: 5615194--5615240 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5615184 TTAGGTTTAA
5615194 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5615236 AG AG A
1 AG AG A
5615241 AATATTTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5618552 original size:124 final size:124
Alignment explanation
Indices: 5618332--5618565 Score: 387
Period size: 124 Copynumber: 1.9 Consensus size: 124
5618322 GCATCAGAAA
* * *
5618332 TTATCAGTAAACTAAAAGGGATGTCATTCGTTTATTCGGGTCCAAAATTACTTCATTTCATCCAT
1 TTATCAGTAAACTAAAAGGGACGTCATTCGTTTATTCAGGTCCAAAATTACTTCATTTCATCCAA
* *
5618397 TTCTATTCATATCAACTAGCTCATGCTTTGAGAACTATTTACACATTACCATTAGCAGT
66 TTCTATTCATATCAACTAGCTCATGATTTGAGAACCATTTACACATTACCATTAGCAGT
* * *
5618456 TTATCAGTAAACTAAGAGGGCCGTCATTCGTTTATTCAGGTCTAAAATTACTTCATTTCATCCAA
1 TTATCAGTAAACTAAAAGGGACGTCATTCGTTTATTCAGGTCCAAAATTACTTCATTTCATCCAA
*
5618521 TTCTATTCATATTAACTAGCTCATGATTTGAGAACCATTTACACA
66 TTCTATTCATATCAACTAGCTCATGATTTGAGAACCATTTACACA
5618566 CGGTTTTACA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (124 bp):
TTATCAGTAAACTAAAAGGGACGTCATTCGTTTATTCAGGTCCAAAATTACTTCATTTCATCCAA
TTCTATTCATATCAACTAGCTCATGATTTGAGAACCATTTACACATTACCATTAGCAGT
Found at i:5621193 original size:16 final size:17
Alignment explanation
Indices: 5621172--5621213 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
5621162 CAAAATCATT
5621172 TTCCCAAATTC-TAAAA
1 TTCCCAAATTCGTAAAA
5621188 TTCCCAAA-TCGTAAAA
1 TTCCCAAATTCGTAAAA
5621204 TTCCCTAAAT
1 TTCCC-AAAT
5621214 CCCTAACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 18 0.78
17 3 0.13
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.31
Consensus pattern (17 bp):
TTCCCAAATTCGTAAAA
Found at i:5621270 original size:16 final size:16
Alignment explanation
Indices: 5621249--5621284 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5621239 AATCCCTAAG
* *
5621249 AATCTTCAAGTCCCTA
1 AATCTTCAAATACCTA
5621265 AATCTTCAAATACCTA
1 AATCTTCAAATACCTA
5621281 AATC
1 AATC
5621285 GATAGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.31
Consensus pattern (16 bp):
AATCTTCAAATACCTA
Found at i:5621661 original size:117 final size:117
Alignment explanation
Indices: 5621453--5621663 Score: 314
Period size: 117 Copynumber: 1.8 Consensus size: 117
5621443 TTTGATTAGT
* * *
5621453 TGGTTATTTGTGATTTACTATTGCAATTTGAGTGCGAAAATGTAGGGTTTGTTTTGTCGATTTTT
1 TGGTTAATTGTGATTTACTATTGCAATTTCAGTGCGAAAATGTAGGGTTTGTTTTGTCGATTTGT
* ** * *
5621518 GATGCGATGGTGGTCCTAATGTTGTTGATAAAACTGTTGTAAAAATTGTAGA
66 GATGAGACAGTGGTCCCAATGATGTTGATAAAACTGTTGTAAAAATTGTAGA
* * *
5621570 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCTAGAATGTAGGGTTTGTTTTGTCGATTTGT
1 TGGTTAATTGTGATTTACTATTGCAATTTCAGTGCGAAAATGTAGGGTTTGTTTTGTCGATTTGT
*
5621635 GATGAGACAGTGGTCCCGATGATGTTGAT
66 GATGAGACAGTGGTCCCAATGATGTTGAT
5621664 TTCTGTTACC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
117 82 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.43
Consensus pattern (117 bp):
TGGTTAATTGTGATTTACTATTGCAATTTCAGTGCGAAAATGTAGGGTTTGTTTTGTCGATTTGT
GATGAGACAGTGGTCCCAATGATGTTGATAAAACTGTTGTAAAAATTGTAGA
Found at i:5622367 original size:33 final size:33
Alignment explanation
Indices: 5622325--5622413 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
5622315 ATGATAAAGT
*
5622325 GGTAGAATCTGATGATGAAGGTGATCTAGAAAA
1 GGTAGAATCTGATGAGGAAGGTGATCTAGAAAA
* * * *
5622358 GGTAGAATCTGGTGAGGAGGGTGATGTAGGAAA
1 GGTAGAATCTGATGAGGAAGGTGATCTAGAAAA
* * *
5622391 GGTACAAGCTGATGGGGAAGGTG
1 GGTAGAATCTGATGAGGAAGGTG
5622414 TGTCTGCTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.33, C:0.06, G:0.40, T:0.21
Consensus pattern (33 bp):
GGTAGAATCTGATGAGGAAGGTGATCTAGAAAA
Found at i:5622591 original size:51 final size:51
Alignment explanation
Indices: 5622522--5622674 Score: 225
Period size: 51 Copynumber: 3.0 Consensus size: 51
5622512 GTTGCTGGTA
*
5622522 ATGAATATGCTAGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
1 ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
* * * *
5622573 ATGAATATGTTGGTGATTTTGCAATATCAGATAGAGTGGATAATGTTACTG
1 ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
* * * *
5622624 ATAAATATGCTGGTGACTTTGCAACATCAGATGGACTAGATAATGTTGCTG
1 ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
5622675 CTACACGTAG
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 89 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (51 bp):
ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
Found at i:5624415 original size:40 final size:40
Alignment explanation
Indices: 5624370--5624450 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5624360 CAGATGAATA
5624370 TTTGCATGAATATTATCACATTGATACCTACAAGAAAGCT
1 TTTGCATGAATATTATCACATTGATACCTACAAGAAAGCT
5624410 TTTGCATGAATATTATCACATTGATACCTACAAGAAAGCT
1 TTTGCATGAATATTATCACATTGATACCTACAAGAAAGCT
5624450 T
1 T
5624451 ACTCTTTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
TTTGCATGAATATTATCACATTGATACCTACAAGAAAGCT
Found at i:5625507 original size:22 final size:22
Alignment explanation
Indices: 5625479--5625520 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5625469 TATGCTTTTA
*
5625479 TAAAGTACATTTATCGAAATTG
1 TAAAGTACATTTATCCAAATTG
5625501 TAAAGTACATTTATCCAAAT
1 TAAAGTACATTTATCCAAAT
5625521 CATATGCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAAGTACATTTATCCAAATTG
Found at i:5626528 original size:24 final size:23
Alignment explanation
Indices: 5626481--5626524 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5626471 TGGAAAGATT
5626481 AAGGATTTCACGATTTGGTTCTA
1 AAGGATTTCACGATTTGGTTCTA
*
5626504 AAGGATTTCACGATTTTGTTC
1 AAGGATTTCACGATTTGGTTC
5626525 CTAATAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (23 bp):
AAGGATTTCACGATTTGGTTCTA
Found at i:5628227 original size:32 final size:32
Alignment explanation
Indices: 5628189--5628256 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
5628179 TTAGAGGTCG
* * * *
5628189 ATTAATACAAATCCTTGAATATATTAGGATTA
1 ATTAATACAAAGCCTCGAAAAAATTAGGATTA
*
5628221 ATTAATACAAAGCCTCGAAAAAATTAGTATTA
1 ATTAATACAAAGCCTCGAAAAAATTAGGATTA
5628253 ATTA
1 ATTA
5628257 GAAATTTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (32 bp):
ATTAATACAAAGCCTCGAAAAAATTAGGATTA
Found at i:5641322 original size:29 final size:30
Alignment explanation
Indices: 5641289--5641346 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
5641279 CCATGTGTAT
*
5641289 AATTGAACA-AAATTAAAATTCATATATCA
1 AATTGAACATAAATCAAAATTCATATATCA
5641318 AATTGAACATTAAATCAAAATTCATATAT
1 AATTGAACA-TAAATCAAAATTCATATAT
5641347 AATTTTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (30 bp):
AATTGAACATAAATCAAAATTCATATATCA
Found at i:5641350 original size:29 final size:27
Alignment explanation
Indices: 5641286--5641350 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 27
5641276 ATACCATGTG
*
5641286 TATAATTGAACAAAATTAAAATTCATA
1 TATAATTGAACAAAATCAAAATTCATA
5641313 TATCAAATTGAACATTAAATCAAAATTCATA
1 TAT--AATTGAACA--AAATCAAAATTCATA
5641344 TATAATT
1 TATAATT
5641351 TTGAGATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
29 13 0.39
31 17 0.52
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.35
Consensus pattern (27 bp):
TATAATTGAACAAAATCAAAATTCATA
Found at i:5646600 original size:2 final size:2
Alignment explanation
Indices: 5646593--5646628 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
5646583 AACAAAATAA
*
5646593 AT AT AT AT AT AT AT AT AT AT AT AT AC AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
5646629 ATTAACATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5648738 original size:3 final size:3
Alignment explanation
Indices: 5648730--5648757 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5648720 GCAAAGCCTT
5648730 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5648758 CTCTCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5665676 original size:24 final size:20
Alignment explanation
Indices: 5665645--5665694 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 20
5665635 TTTTATTAAA
*
5665645 TATTTTAAATTTATTTATACTAT
1 TATTTT-AACTTATTT-TA-TAT
5665668 TATTATTAACTTATTTTATAT
1 TATT-TTAACTTATTTTATAT
5665689 TATTTT
1 TATTTT
5665695 TAGAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.28
22 2 0.08
23 12 0.48
24 2 0.08
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTAACTTATTTTATAT
Found at i:5667772 original size:23 final size:22
Alignment explanation
Indices: 5667728--5667773 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5667718 GTCACTCAAC
5667728 TAAAACTTCATTTAAATATTTT
1 TAAAACTTCATTTAAATATTTT
* * *
5667750 TAAAGCTTCATTTTAATACTTT
1 TAAAACTTCATTTAAATATTTT
5667772 TA
1 TA
5667774 TATATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (22 bp):
TAAAACTTCATTTAAATATTTT
Found at i:5668784 original size:22 final size:22
Alignment explanation
Indices: 5668756--5668801 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5668746 ATTACAGAAC
5668756 AACAATGGCGTATCACTTAAAG
1 AACAATGGCGTATCACTTAAAG
5668778 AACAATGGCGTATCACTTAAAG
1 AACAATGGCGTATCACTTAAAG
5668800 AA
1 AA
5668802 TAAATCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (22 bp):
AACAATGGCGTATCACTTAAAG
Found at i:5672055 original size:15 final size:16
Alignment explanation
Indices: 5672035--5672067 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5672025 ATATATATTT
5672035 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
5672050 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
5672067 T
1 T
5672068 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:5672182 original size:26 final size:24
Alignment explanation
Indices: 5672143--5672192 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
5672133 ATTTATTTTA
*
5672143 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
5672167 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
5672193 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:5673340 original size:38 final size:39
Alignment explanation
Indices: 5673238--5673386 Score: 212
Period size: 39 Copynumber: 3.9 Consensus size: 39
5673228 ATAAAGTATG
* *
5673238 GTTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTA
1 GTTTTAATTAATAATAAAACAAAATAGCATGGGGAAGTA
* * *
5673277 GTTTTAATTAACAATAAAATAAAATAGTATGGGGAAGTA
1 GTTTTAATTAATAATAAAACAAAATAGCATGGGGAAGTA
*
5673316 GTTTTAATTAA-AATAAAACAAAATAGCATGGGG-AGTG
1 GTTTTAATTAATAATAAAACAAAATAGCATGGGGAAGTA
* *
5673353 GTTTTGATTAATAATAAAACAAAGTAGCATGGGG
1 GTTTTAATTAATAATAAAACAAAATAGCATGGGG
5673387 GGAGTGGAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
37 13 0.13
38 41 0.41
39 47 0.47
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (39 bp):
GTTTTAATTAATAATAAAACAAAATAGCATGGGGAAGTA
Found at i:5673369 original size:76 final size:78
Alignment explanation
Indices: 5673238--5673386 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 78
5673228 ATAAAGTATG
* *
5673238 GTTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAGTTTTAATTAACAATAAAATAAAATA
1 GTTTTAATTAATAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
*
5673303 GTATGGGGAAGTA
66 GCATGGGGAAGTA
* * * * *
5673316 GTTTTAATTAA-AATAAAACAAAATAGCATG-GGGAGTGGTTTTGATTAATAATAAAACAAAGTA
1 GTTTTAATTAATAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
5673379 GCATGGGG
66 GCATGGGG
5673387 GGAGTGGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 34 0.54
77 18 0.29
78 11 0.17
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (78 bp):
GTTTTAATTAATAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
GCATGGGGAAGTA
Found at i:5673926 original size:24 final size:24
Alignment explanation
Indices: 5673880--5673945 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
5673870 TTTATTTTTT
* **
5673880 ACATTATTATGTATATACCATGTAA
1 ACATT-TTATATATATATTATGTAA
* *
5673905 ATATTTTA-ATATTATATTATGTAT
1 ACATTTTATATA-TATATTATGTAA
5673929 ACATTTTATATATATAT
1 ACATTTTATATATATAT
5673946 CTTTTAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 2 0.06
24 24 0.73
25 7 0.21
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (24 bp):
ACATTTTATATATATATTATGTAA
Found at i:5674845 original size:12 final size:12
Alignment explanation
Indices: 5674828--5674852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5674818 TTTTTTCTTT
5674828 CGACATTAAAGA
1 CGACATTAAAGA
5674840 CGACATTAAAGA
1 CGACATTAAAGA
5674852 C
1 C
5674853 ATTTGATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (12 bp):
CGACATTAAAGA
Found at i:5676108 original size:205 final size:205
Alignment explanation
Indices: 5675735--5676448 Score: 888
Period size: 205 Copynumber: 3.5 Consensus size: 205
5675725 TATTCGGCGG
* *
5675735 GGAGCATAA-CGAAGATATAGTTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATG
1 GGAGCA-AATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATG
* *
5675799 ATTTGTCGTCTCTGTATTGTCAGAGAACGAATCAAAGTTTGGCATCTTCACTTTGATGGAGAGCA
65 ATTTGTCGTCTCTGTATTGTCAAAGAACAAATCAAAGTTTGGCATCTTCACTTTGATGGAGAGCA
* ** *
5675864 GACACATAGCAGATCTGAATTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT
130 GACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTAGCATCCT
5675929 TATGTTTACAA
195 TATGTTTACAA
* *
5675940 GGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGTTGAAACAAATCTAAGATGA
1 GGAGCAAATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATGA
* *
5676005 TTTGTCGTCTCTGTATTGTCAAAGAACAAATCGAAGTCTGGCAT-TTCCACTTTGATGGA-AGGC
66 TTTGTCGTCTCTGTATTGTCAAAGAACAAATCAAAGTTTGGCATCTT-CACTTTGATGGAGA-GC
* * ** *
5676068 AGACACATAGCAGATCTTACCTTCAGATGTTTACGCTGAAGTAGATCCAAGATGACAGATCTTAT
129 AGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATG---G-T-TTAG
***
5676133 C-TCTCTGTAT-TCGGC-A
189 CATC-CT-TATGTTTACAA
* * * ** *
5676149 GGAGTAGATCGAAGATATAACTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGA
1 GGAGCAAATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATGA
* * *
5676214 TTTTTCGTCTCTGTATTGTCAGAGAACGAATCAAAGTTTGGCATCTTCACTTTGATGGAGAGCAG
66 TTTGTCGTCTCTGTATTGTCAAAGAACAAATCAAAGTTTGGCATCTTCACTTTGATGGAGAGCAG
* * *
5676279 ACACATAGCAGATCTCGCCTTCGGATGTTTATGCTGAAGCGGATCCAAGATGGTTTAGCACCCTT
131 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTAGCATCCTT
*
5676344 ATGCTTACAA
196 ATGTTTACAA
* * * * *
5676354 GGAGCAAATCGAA-TCATAGTTCATTTGGCTTTCATGTGCTTACG-TTAAAGCAAATCTAAGATG
1 GGAGCAAATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGATGAAA-CAAATCTAAGATG
* * * *
5676417 ATTTGGCATATCTGTATTGTC-AGGAACAAATC
65 ATTTGTCGTCTCTGTATTGTCAAAGAACAAATC
5676449 GAAGAAGCAG
Statistics
Matches: 431, Mismatches: 62, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
203 14 0.03
204 66 0.15
205 174 0.40
206 1 0.00
208 1 0.00
209 162 0.38
210 10 0.02
211 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (205 bp):
GGAGCAAATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGATGAAACAAATCTAAGATGA
TTTGTCGTCTCTGTATTGTCAAAGAACAAATCAAAGTTTGGCATCTTCACTTTGATGGAGAGCAG
ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTAGCATCCTT
ATGTTTACAA
Found at i:5676622 original size:45 final size:45
Alignment explanation
Indices: 5676546--5676631 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
5676536 GAAGAAGCAA
* * *
5676546 ATTTGGCGTCGCTGTATTAGAAGGGGAGCAGATCGAAGATAATAG
1 ATTTGACGTCGCTGTAGTAGAAGGGGAGCAGATCAAAGATAATAG
* * *
5676591 ATTTGACGTCTCTGTAGTAGACGGGGGGCAGATCAAAGATA
1 ATTTGACGTCGCTGTAGTAGAAGGGGAGCAGATCAAAGATA
5676632 GCAGATATCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (45 bp):
ATTTGACGTCGCTGTAGTAGAAGGGGAGCAGATCAAAGATAATAG
Found at i:5680651 original size:210 final size:210
Alignment explanation
Indices: 5680106--5681069 Score: 1200
Period size: 210 Copynumber: 4.6 Consensus size: 210
5680096 GGGCATATCT
* * * * * *
5680106 AAGATGACAGATCTTATCTCTCTGTATTTGGCGGGGAGCATATCAAAGATATAGTTGATTTGGCT
1 AAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAAATCGAAGATATAGCTGATTTGGCT
* * *
5680171 TTCACGTGTTTACGATGAAGCAAATCTAAGATAATTTGTCGTCTCTGTATTGTCAGAGAACGAAT
66 TTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAAT
* *
5680236 CGAAGTTTGGCATCTTCACTTTGATGGATA-GCAGACACATAGCAGATCTGACCTTCAGATGTTT
131 CGAAGTCTGGCATCTTCACTTTGATGGA-AGGCAGACACATAGCAGATCTTACCTTCAGATGTTT
*
5680300 ATGCTGAAGCGGATCC
195 ATGCTGAAGCAGATCC
* ** * *
5680316 AAGATG---G-T-TTGGCATC-CT-TGTGTT-TACAAGGAACAAATCGAAGACATAGCTGATTTG
1 AAGATGACAGATCTT---ATCTCTCTGTATTCGGCAGGGAACAAATCGAAGATATAGCTGATTTG
*
5680373 GCTTTCACATGTTTAC-ATTGAAA-CAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAA
63 GCTTTCACGTGTTTACGA-T-AAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAA
5680436 CAAATCGAAGTCTGGCAT-TTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCAGA
126 CAAATCGAAGTCTGGCATCTT-CACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCAGA
* *
5680500 TGTTGACGCTGAAGCAGATCC
190 TGTTTATGCTGAAGCAGATCC
* * *
5680521 AAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAGATATAACTGATTTGGCT
1 AAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAAATCGAAGATATAGCTGATTTGGCT
*
5680586 TTCACGCGTTTACGATAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAAT
66 TTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAAT
* *
5680651 CAAAGTCTGGCAT-TTCCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCCTCAGATGTTT
131 CGAAGTCTGGCATCTT-CACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCAGATGTTT
*
5680715 ATGCTGAAGCATATCC
195 ATGCTGAAGCAGATCC
* *
5680731 AAGATGACAGATCTTATTTCTCTGTATTCGGCAGGGAACAGATCGAAGATATAGCTGATTTGGCT
1 AAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAAATCGAAGATATAGCTGATTTGGCT
* * * * *
5680796 TTCACGTATTTTCGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAAAACGAAT
66 TTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAAT
* * * * *
5680861 CAAAGTTTGGCATCTTCACTTTGATGG-AGAGCAGACACATAGCAAATCTTGCCTTCGGATGTTT
131 CGAAGTCTGGCATCTTCACTTTGATGGAAG-GCAGACACATAGCAGATCTTACCTTCAGATGTTT
5680925 ATGCTGAAGCAGATCC
195 ATGCTGAAGCAGATCC
** * ** * *
5680941 AAGATG---G-T-TTGGCATC-CT-TATGCTTACAAGGAACAAATCG-A-ATCATAGATGATTTG
1 AAGATGACAGATCTTATC-TCTCTGTATTC-GGCAGGGAACAAATCGAAGAT-ATAGCTGATTTG
* * * * *
5680997 GCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGGGAACA
63 GCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACA
5681062 AATCGAAG
128 AATCGAAG
5681070 AAGCAGATTT
Statistics
Matches: 663, Mismatches: 69, Indels: 50
0.85 0.09 0.06
Matches are distributed among these distances:
203 2 0.00
204 82 0.12
205 177 0.27
206 11 0.02
207 7 0.01
208 6 0.01
209 11 0.02
210 364 0.55
211 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (210 bp):
AAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAAATCGAAGATATAGCTGATTTGGCT
TTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAAT
CGAAGTCTGGCATCTTCACTTTGATGGAAGGCAGACACATAGCAGATCTTACCTTCAGATGTTTA
TGCTGAAGCAGATCC
Found at i:5681194 original size:44 final size:45
Alignment explanation
Indices: 5681144--5681248 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 45
5681134 AGTTTGCAAT
* * *
5681144 GAGCAGATTGAAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGG
1 GAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
* *
5681188 GAGCAGATCGAAGATAATAGATTTGGCGTCTCTGTAGTAGACGGG
1 GAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
* *
5681233 GGGCAGATCAAAGATA
1 GAGCAGATCGAAGATA
5681249 GCAGATATCG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 13 0.25
45 40 0.75
ACGTcount: A:0.31, C:0.13, G:0.32, T:0.23
Consensus pattern (45 bp):
GAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTAGTAGACGGG
Found at i:5681220 original size:45 final size:45
Alignment explanation
Indices: 5681163--5681248 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
5681153 GAAGAAGCAA
* *
5681163 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAATAG
1 ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAATAG
*
5681208 ATTTGGCGTCTCTGTAGTAGACGGGGGGCAGATCAAAGATA
1 ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATA
5681249 GCAGATATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.26
Consensus pattern (45 bp):
ATTTGGCGTCTCTGTAGTAGACGGGGAGCAGATCAAAGATAATAG
Found at i:5682579 original size:39 final size:39
Alignment explanation
Indices: 5682468--5682654 Score: 263
Period size: 38 Copynumber: 4.9 Consensus size: 39
5682458 ATAAAGTATG
* *
5682468 GTTTTAATTAATAAT-AAACAAAATAGTATGAGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAGTA
*
5682506 GTTTTAATTAACAAT-AAATAAAATAGTATGGGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAGTA
*
5682544 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAGTA
* *
5682583 GTTTTAATTAACAATAAAACAAAATAGCATGGGG-AGTG
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAGTA
* * * *
5682621 GTTTTGATTAATAATAAAACAAAGTAGCATGGGG
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGG
5682655 GGAGTGGAAT
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
38 83 0.61
39 54 0.39
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (39 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAGTA
Found at i:5682585 original size:77 final size:77
Alignment explanation
Indices: 5682468--5682654 Score: 270
Period size: 77 Copynumber: 2.4 Consensus size: 77
5682458 ATAAAGTATG
* * *
5682468 GTTTTAATTAATAAT-AAACAAAATAGTATGAGGAAGTAGTTTTAATTAACAAT-AAATAAAATA
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGGAAATAGTTTTAATTAACAATAAAACAAAATA
*
5682531 GTATGGGGAAGTA
66 GCATGGGG-AGTA
*
5682544 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATAGTTTTAATTAACAATAAAACAAAATA
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGGAAATAGTTTTAATTAACAATAAAACAAAATA
*
5682609 GCATGGGGAGTG
66 GCATGGGGAGTA
* * *
5682621 GTTTTGATTAATAATAAAACAAAGTAGCATGGGG
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGG
5682655 GGAGTGGAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
76 14 0.14
77 69 0.70
78 16 0.16
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (77 bp):
GTTTTAATTAATAATAAAACAAAATAGTATGGGGAAATAGTTTTAATTAACAATAAAACAAAATA
GCATGGGGAGTA
Found at i:5683192 original size:24 final size:24
Alignment explanation
Indices: 5683146--5683211 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
5683136 TTTATTTTTT
* **
5683146 ACATTATTATGTATATACCATGTAA
1 ACATT-TTATATATATATTATGTAA
* *
5683171 ATATTTTA-ATATTATATTATGTAT
1 ACATTTTATATA-TATATTATGTAA
5683195 ACATTTTATATATATAT
1 ACATTTTATATATATAT
5683212 CTTTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 2 0.06
24 24 0.73
25 7 0.21
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (24 bp):
ACATTTTATATATATATTATGTAA
Found at i:5683405 original size:26 final size:26
Alignment explanation
Indices: 5683374--5683429 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
5683364 GTTGTTTCTA
*
5683374 ATATTATG-A-TTATTTCTAATATGTAT
1 ATATTATGTATTTACTTC-AATAT-TAT
5683400 ATATTATGTATTTACTTCAATATTAT
1 ATATTATGTATTTACTTCAATATTAT
5683426 ATAT
1 ATAT
5683430 CGTATATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 15 0.56
27 6 0.22
28 6 0.22
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (26 bp):
ATATTATGTATTTACTTCAATATTAT
Found at i:5683411 original size:24 final size:23
Alignment explanation
Indices: 5683374--5683444 Score: 61
Period size: 26 Copynumber: 2.8 Consensus size: 23
5683364 GTTGTTTCTA
5683374 ATATTATGATTATTTCTAATATGTAT
1 ATATTATG--TATTTCTAATAT-TAT
5683400 ATATTATGTATTTACTTCAATATTAT
1 ATATTATGTATTT-C-T-AATATTAT
** *
5683426 ATATCGTATATTTCTAATA
1 ATATTATGTATTTCTAATA
5683445 CTATTACGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.10
24 6 0.15
25 2 0.05
26 22 0.56
27 5 0.13
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (23 bp):
ATATTATGTATTTCTAATATTAT
Found at i:5692551 original size:15 final size:16
Alignment explanation
Indices: 5692531--5692560 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5692521 CATATTTTGA
5692531 ATTTAAT-AATAAATC
1 ATTTAATAAATAAATC
5692546 ATTTAATAAATAAAT
1 ATTTAATAAATAAAT
5692561 TAAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTAATAAATAAATC
Found at i:5693203 original size:47 final size:47
Alignment explanation
Indices: 5693137--5693328 Score: 199
Period size: 47 Copynumber: 4.0 Consensus size: 47
5693127 ATAAAAATAG
* *
5693137 TAAAGAAGTAAGCTATTAAAGTATTCTTTGGTGAATGTGGGATTAAAA
1 TAAA-AAGTAAGCTATTAAAGTATTCTCTAGTGAATGTGGGATTAAAA
* ** *
5693185 TAAAATGTAAGCTATTAAAGTATGATCTAGT-AGATGTGGGATTAATAG
1 TAAAAAGTAAGCTATTAAAGTATTCTCTAGTGA-ATGTGGGATTAA-AA
* *
5693233 TAAAGAAGTAAGCTATTGAAGTATTCTTTAGTGAATGTGGGATTAAAA
1 TAAA-AAGTAAGCTATTAAAGTATTCTCTAGTGAATGTGGGATTAAAA
* * * * * *
5693281 TAAGAGGTGAGCTATTAGAGTATTCTCTGGTCG-ATGTGGAATTAAAA
1 TAAAAAGTAAGCTATTAAAGTATTCTCTAGT-GAATGTGGGATTAAAA
5693328 T
1 T
5693329 TAACTTTTTC
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
46 1 0.01
47 69 0.58
48 14 0.12
49 34 0.29
50 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (47 bp):
TAAAAAGTAAGCTATTAAAGTATTCTCTAGTGAATGTGGGATTAAAA
Found at i:5693255 original size:49 final size:49
Alignment explanation
Indices: 5693132--5693306 Score: 207
Period size: 47 Copynumber: 3.7 Consensus size: 49
5693122 TTTTAATAAA
*
5693132 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTGGTGAATGTGGGATT
1 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGAATGTGGGATT
* * ** *
5693181 AA-AATAAA-ATGTAAGCTATTAAAGTATGATCTAGT-AGATGTGGGATT
1 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGA-ATGTGGGATT
*
5693228 AATAGTAAAGAAGTAAGCTATTGAAGTATTCTTTAGTGAATGTGGGATT
1 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGAATGTGGGATT
* * * *
5693277 AA-AAT-AAGAGGTGAGCTATTAGAGTATTCT
1 AATAGTAAAGAAGTAAGCTATTAAAGTATTCT
5693307 CTGGTCGATG
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
46 1 0.01
47 55 0.52
48 12 0.11
49 36 0.34
50 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (49 bp):
AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGAATGTGGGATT
Found at i:5693317 original size:96 final size:96
Alignment explanation
Indices: 5693132--5693325 Score: 289
Period size: 96 Copynumber: 2.0 Consensus size: 96
5693122 TTTTAATAAA
* *
5693132 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTGGTGAATGTGGGATTAAAATAAAATGTAAGC
1 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGAATGTGGGATTAAAATAAAAGGTAAGC
*
5693197 TATTAAAGTATGATCTAGTAGATGTGGGATT
66 TATTAAAGTATGATCTAGTAGATGTGGAATT
* * *
5693228 AATAGTAAAGAAGTAAGCTATTGAAGTATTCTTTAGTGAATGTGGGATTAAAATAAGAGGTGAGC
1 AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGAATGTGGGATTAAAATAAAAGGTAAGC
* ** * *
5693293 TATTAGAGTATTCTCTGGTCGATGTGGAATT
66 TATTAAAGTATGATCTAGTAGATGTGGAATT
5693324 AA
1 AA
5693326 AATTAACTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (96 bp):
AATAGTAAAGAAGTAAGCTATTAAAGTATTCTTTAGTGAATGTGGGATTAAAATAAAAGGTAAGC
TATTAAAGTATGATCTAGTAGATGTGGAATT
Found at i:5694485 original size:2 final size:2
Alignment explanation
Indices: 5694478--5694504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5694468 ACATCTTGTA
5694478 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5694505 AAAGTTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5695736 original size:89 final size:89
Alignment explanation
Indices: 5695580--5695753 Score: 222
Period size: 89 Copynumber: 2.0 Consensus size: 89
5695570 TAATAACTTG
* ** * * *
5695580 ATACATCGACTTCTTTAATTAGATAGTTAAATATTAATGGTTTTGCCCTTAAGTCCTAAGTTTGA
1 ATACATCAACTTCTTTAATTAGATAGTTAAATATTAATAATTTTGCCATTAAGTCCTAAGATCGA
*
5695645 TTCCTCCTCTACTCACATTTGTTA
66 TTCATCCTCTACTCACATTTGTTA
* * * * * *
5695669 ATACATCAACTTCTTTGATTAGATGGTTAAATATTAATAATTTTGTCATTGAGTCTTGAGATCGA
1 ATACATCAACTTCTTTAATTAGATAGTTAAATATTAATAATTTTGCCATTAAGTCCTAAGATCGA
*
5695734 TTCATCTTCTACTCACATTT
66 TTCATCCTCTACTCACATTT
5695754 TTATTTAAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (89 bp):
ATACATCAACTTCTTTAATTAGATAGTTAAATATTAATAATTTTGCCATTAAGTCCTAAGATCGA
TTCATCCTCTACTCACATTTGTTA
Found at i:5700451 original size:31 final size:31
Alignment explanation
Indices: 5700407--5700472 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
5700397 TTTAGACACT
5700407 AAATTGAAAATTGAAGTCAAACTTAAG-TACC
1 AAATTGAAAATTGAAGTCAAA-TTAAGATACC
** *
5700438 AAATTGAGCATTGAAGTTAAATTAAGATACC
1 AAATTGAAAATTGAAGTCAAATTAAGATACC
5700469 AAAT
1 AAAT
5700473 AGCATATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (31 bp):
AAATTGAAAATTGAAGTCAAATTAAGATACC
Found at i:5703947 original size:13 final size:13
Alignment explanation
Indices: 5703925--5703958 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5703915 GATAATAGCA
*
5703925 AGATGTAAATAAT
1 AGATGAAAATAAT
5703938 AGATGAAAATAAT
1 AGATGAAAATAAT
*
5703951 AAATGAAA
1 AGATGAAA
5703959 GGGAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (13 bp):
AGATGAAAATAAT
Found at i:5707280 original size:9 final size:9
Alignment explanation
Indices: 5707239--5707288 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
5707229 TAATTTTGTT
5707239 TATATTATA
1 TATATTATA
*
5707248 TATTTTATCA
1 TATATTAT-A
*
5707258 T-TATAATA
1 TATATTATA
*
5707266 TCTATTATA
1 TATATTATA
5707275 TATATTAT-
1 TATATTATA
5707283 TATATT
1 TATATT
5707289 GAGAGAGTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
8 8 0.24
9 24 0.71
10 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATTATA
Found at i:5709570 original size:13 final size:13
Alignment explanation
Indices: 5709554--5709581 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5709544 AGAAAGGGAT
5709554 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
5709567 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
5709580 AA
1 AA
5709582 GATTACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:5710824 original size:3 final size:3
Alignment explanation
Indices: 5710816--5711092 Score: 76
Period size: 3 Copynumber: 91.7 Consensus size: 3
5710806 ATTTGCCATT
**
5710816 TTA TTA TTA AAA TTGA TTAA TTA -TA TTTA TTTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA TT-A TT-A TTA TTA T-TA T-TA TT-A TTA TTA TTA
* * * * * *
5710861 TTA TTG CTA TTA TTA TTA TTA TTA TTA TCA TTA TTT TTA TT- CTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
5710908 TTG TTA TTA TT- TCTC TTG TTG TT- TTCA TTA TTA TT- TATA TTA TTG
1 TTA TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TTA TTA T-TA TTA TTA
* * * * * *
5710953 TTA GTA CTA TTA GTA CTCT- TTA GT- TTA TTA TTA TTA TTA CTA TCTCG
1 TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA T-T-A
* * * * * *
5711000 TCA TTA TTT TCTA TTA TTG TTA TTA ATA -TA CTA TTA TTA TTC TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5711045 TTAA TGTA TTA CTA TTA TT- TT- TTA CT- TTA TTA TTA -TA TTA TTA
1 TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5711088 CTA TT
1 TTA TT
5711093 GCTATCATCA
Statistics
Matches: 201, Mismatches: 48, Indels: 50
0.67 0.16 0.17
Matches are distributed among these distances:
2 20 0.10
3 151 0.75
4 27 0.13
5 3 0.01
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5711057 original size:26 final size:24
Alignment explanation
Indices: 5711011--5711087 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
5711001 CATTATTTTC
5711011 TATTATTGTTATTAA-TA-TACTAT
1 TATTATT-TTATTAATTATTACTAT
5711034 TATTATTCTTATTAATGTATTACTAT
1 TATTATT-TTATTAAT-TATTACTAT
*
5711060 TATT-TTTTACTTTATTATTA-TAT
1 TATTATTTTA-TTAATTATTACTAT
5711083 TATTA
1 TATTA
5711088 CTATTGCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
23 21 0.45
24 8 0.17
25 8 0.17
26 10 0.21
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (24 bp):
TATTATTTTATTAATTATTACTAT
Found at i:5711110 original size:3 final size:3
Alignment explanation
Indices: 5710846--5711092 Score: 77
Period size: 3 Copynumber: 82.7 Consensus size: 3
5710836 TTATATTTAT
* * *
5710846 TTA TTAA TT- TTA TTA TTA TTG CTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
5710891 TTA TTT TTA TT- CTG TTA TTG TTA TTA TT- TCTC TTG TTG TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A
* * * * *
5710935 TTA TTA TT- TATA TTA TTG TTA GTA CTA TTA GTA CTCT- TTA GT- TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA
* * * * * *
5710980 TTA TTA TTA TTA CTA TCTCG TCA TTA TTT TCTA TTA TTG TTA TTA ATA
1 TTA TTA TTA TTA TTA T-T-A TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * *
5711028 -TA CTA TTA TTA TTC TTA TTAA TGTA TTA CTA TTA TT- TT- TTA CT-
1 TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA
*
5711071 TTA TTA TTA -TA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
5711093 GCTATCATCA
Statistics
Matches: 179, Mismatches: 43, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
2 18 0.10
3 144 0.80
4 14 0.08
5 3 0.02
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5711179 original size:3 final size:3
Alignment explanation
Indices: 5711171--5711231 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
5711161 ATATATTTAC
** *
5711171 ATT ATT ATT GCT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5711219 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
5711232 GACATAACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5711701 original size:132 final size:133
Alignment explanation
Indices: 5711452--5711719 Score: 340
Period size: 132 Copynumber: 2.0 Consensus size: 133
5711442 TTTTTTTTTA
* * * *
5711452 AAAAAATTCTTTAAAACGAAAGAGATGTTTGATATTTGGCAATCTATGGAATCGTGCCCTAACGT
1 AAAAAATTCTTTAAAACGAAAGAAATGTTCGATATTCGGCAATCTAGGGAATCGTGCCCTAACGT
* * * * * * *
5711517 GCTGGGTTGCAATTTCTCGTTTGCTCAAATTAATCAAATGTCTATTTAGAATTTCCTTCATGTTT
66 GCTGGGTGGCAATCTCTCGTTTGCGCAAAATAATCAAATATCCATTTAGAATTTCATTCATGTTT
5711582 TCT
131 TCT
* * * * * *
5711585 AAAAACTT-TTTAAAACGAAGGAAATGTTCGATGTTCGGCAATTTGGGGAATCGTGCCCTATCGT
1 AAAAAATTCTTTAAAACGAAAGAAATGTTCGATATTCGGCAATCTAGGGAATCGTGCCCTAACGT
* * * *
5711649 GCTGGGTGGCAATCTCTCGTTTGCGCAAAATAATCGAATATCCCTTTGGAATTTCATTCGTGTTT
66 GCTGGGTGGCAATCTCTCGTTTGCGCAAAATAATCAAATATCCATTTAGAATTTCATTCATGTTT
5711714 TCT
131 TCT
5711717 AAA
1 AAA
5711720 GCGAGGCAAT
Statistics
Matches: 114, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
132 107 0.94
133 7 0.06
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (133 bp):
AAAAAATTCTTTAAAACGAAAGAAATGTTCGATATTCGGCAATCTAGGGAATCGTGCCCTAACGT
GCTGGGTGGCAATCTCTCGTTTGCGCAAAATAATCAAATATCCATTTAGAATTTCATTCATGTTT
TCT
Found at i:5715215 original size:14 final size:14
Alignment explanation
Indices: 5715196--5715234 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
5715186 AGGCAAAGGT
5715196 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
5715210 AAAAAAAAGAAAAG
1 AAAAAAAAAAAAAG
5715224 AAAAGAAAAAA
1 AAAA-AAAAAA
5715235 GAAGGGGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:5715227 original size:19 final size:17
Alignment explanation
Indices: 5715196--5715234 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
5715186 AGGCAAAGGT
5715196 AAAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAAGAAA
5715213 AAAAAGAAAAGAAAAGAAA
1 AAAAA-AAAA-AAAAGAAA
5715232 AAA
1 AAA
5715235 GAAGGGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 4 0.20
19 11 0.55
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAA
Found at i:5717105 original size:66 final size:66
Alignment explanation
Indices: 5716999--5717131 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 66
5716989 TGACATTTCT
* * * *
5716999 ACATTCATAACACATCTAGTTAGGAGCATTTGATTCATTTC-AGTCATAGTATCCTAGTTATTTG
1 ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGA-TCATAGCATCCTAATCATTTG
5717063 AC
65 AC
5717065 ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
1 ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
5717130 C
66 C
5717131 A
1 A
5717132 TAAGCATAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 61 0.98
67 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (66 bp):
ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
C
Found at i:5717512 original size:66 final size:68
Alignment explanation
Indices: 5717349--5717874 Score: 684
Period size: 68 Copynumber: 7.8 Consensus size: 68
5717339 ATATCTTTTC
* * * * *
5717349 CCTGAAATGGTGTTGGAGTGGCTAAAAGTCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTATT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
5717414 -TT
66 CTT
* **
5717416 CCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTAAAGTTTCAGCAAAT-T-T
1 -CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCT
5717479 TCTT
65 TCTT
* * **
5717483 CCTGAAATGGCGTTGGAGCGGTTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCAAAT-T-TT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
*
5717546 CTC
66 CTT
* * * *
5717549 CCTGAAATGGCGTTGGAGTGGCTAAATGCCACAGCAGATCTCCTTAAAGTTTTAGTGAATCTCTT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
5717614 CTT
66 CTT
* * *
5717617 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAATTTTAGTGAATCTCTT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
*
5717682 CTC
66 CTT
* * * * * * *
5717685 CCTGAAATGGTGATGGAGCGGCTAAAATCCACAGTAGATCTCCTTGAAGTTTCAGCGGACCTCTT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
5717750 CTT
66 CTT
* * * *
5717753 CCTGAAATGACGTTGGAGCGTCTAAAAACCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
*
5717818 TTT
66 CTT
* * *
5717821 CCTGAAATGGCGTTGGAGCAGTTATAAGCCACAGCAGATCTCCTTGAAGTTTCA
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCA
5717875 ACGGAAGAAG
Statistics
Matches: 403, Mismatches: 52, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
66 116 0.29
67 4 0.01
68 283 0.70
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (68 bp):
CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
CTT
Found at i:5718122 original size:44 final size:44
Alignment explanation
Indices: 5718071--5718601 Score: 748
Period size: 44 Copynumber: 12.2 Consensus size: 44
5718061 AGTAGATCAA
5718071 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
* *
5718115 AATAGATTTGGCGTCTCTGTGTTGATAGAGAGTAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
**
5718159 AGTAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
*
5718203 AACAGATTTGGCGTCTCTGTGTTGATCGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
*
5718247 AACAGATTTGGCGTCTCTATGTTGATAGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
*
5718291 AATAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
** * *
5718335 AGTAGATTTGGCGTCTCTGTGAT--TAGAGAGCAGATTGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
* *
5718377 AACAGATTTGGCGTCTCTGTGAT--TAGAGAGCAAATCGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
* * *
5718419 AACAAATTTGGCGTCTCTGTGTTGATAGAGAGCAAATTGAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
* * *
5718463 AACAGATTTGGCGTCTCCGTGTTGATAGAGAGCAGAACGAAAAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
* * * * *
5718507 AGCAGATTTGGCATCCCTGTGCTT-ATAGGGAACAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTG-TTGATAGAGAGCAGATCGAAGAT
* * * * *
5718551 AACGGATTTGGCGTCTCTGTATTGACAGAGAGTAGATCAAAGAT
1 AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
*
5718595 AGCAGAT
1 AACAGAT
5718602 ATCGCCTTCC
Statistics
Matches: 436, Mismatches: 47, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
42 77 0.18
43 2 0.00
44 355 0.81
45 2 0.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (44 bp):
AACAGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGAT
Found at i:5720400 original size:72 final size:69
Alignment explanation
Indices: 5720318--5720477 Score: 185
Period size: 72 Copynumber: 2.3 Consensus size: 69
5720308 TTACATTTGA
* * *
5720318 TTTAAATGCTTAATGTGTTGCTGTAAAGTGCTAATTTGTTATCTTAAAAAAAATGTGTTCACTCA
1 TTTAAATGCTTAATGTGCTGCTGCAAAGGGCTAATTTGTTATCTT---AAAAATGTGTTCACTCA
*
5720383 CGTTAAT
63 CGTCAAT
* * * * * * *
5720390 TTTAGATGCTTAATTTGCTGCTGCAAAGGGCTGATTTGTTGTCTTGAAAATGTGTTCATTTACGT
1 TTTAAATGCTTAATGTGCTGCTGCAAAGGGCTAATTTGTTATCTTAAAAATGTGTTCACTCACGT
*
5720455 CCAT
66 CAAT
5720459 TTTAAATGCTTAATGTGCT
1 TTTAAATGCTTAATGTGCT
5720478 TTCCAACAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
69 36 0.49
72 38 0.51
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (69 bp):
TTTAAATGCTTAATGTGCTGCTGCAAAGGGCTAATTTGTTATCTTAAAAATGTGTTCACTCACGT
CAAT
Found at i:5721519 original size:40 final size:40
Alignment explanation
Indices: 5721464--5721777 Score: 381
Period size: 40 Copynumber: 7.9 Consensus size: 40
5721454 ATACTTGATC
5721464 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAAT
*
5721504 TGTATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCT-TCATGCTGAAAT
*
5721544 TATATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCT-AGAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCT-TCATGCTGA-AAT
*
5721584 TATATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCT-TCATGCTGAAAT
* * ** *
5721624 TATATCCGGACTT-AAGGTCCGCAGGCTTCGTGCT-AGAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGA-AAT
* *
5721663 TGTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGAAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAAT
* * *
5721703 TGTATCCGGGCTTAAAGACCCGTAGGCTTCGTGCTGGAAT
1 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAAT
** * *
5721743 TGTATCCGAACTT-AAGATCCGCAGGCTTCGTGCTG
1 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTG
5721778 GTACTATATC
Statistics
Matches: 248, Mismatches: 19, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 50 0.20
40 193 0.78
41 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (40 bp):
TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAAT
Found at i:5721788 original size:119 final size:119
Alignment explanation
Indices: 5721466--5721849 Score: 454
Period size: 119 Copynumber: 3.2 Consensus size: 119
5721456 ACTTGATCTG
* *
5721466 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAATTGTATCCGGGCTTAAAGACCCGCAGGC
1 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAATTGTATCCGGACTT-AAGATCCGCAGGC
* *
5721531 TAT-ATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCT-AGAATTA
65 T-TCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGA-AATTA
* *
5721586 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAATTATATCCGGACTTAAGGTCCGCAGGC
1 TATCCGGGCTTAAAGACCCGCAGGCT-TCATGCTGAAATTGTATCCGGACTTAAGATCCGCAGGC
* * * *
5721650 TTCGTGCTAGAATTGTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGAAATTG
65 TTCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTA
* * * *
5721705 TATCCGGGCTTAAAGACCCGTAGGCTTCGTGCTGGAATTGTATCCGAACTTAAGATCCGCAGGCT
1 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAATTGTATCCGGACTTAAGATCCGCAGGCT
* * * * ** * ** *
5721770 TCGTGCTGGTACTATATCCAGACTT-AAGGTCCGCAGGCTTCGTACTGGTACTA
66 TCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTA
* *
5721823 TATCCGGGCTTAAAGTCCCGTAGGCTT
1 TATCCGGGCTTAAAGACCCGCAGGCTT
5721850 TGTGTTGGTG
Statistics
Matches: 228, Mismatches: 31, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
118 49 0.21
119 130 0.57
120 48 0.21
121 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (119 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAATTGTATCCGGACTTAAGATCCGCAGGCT
TCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTA
Found at i:5721818 original size:39 final size:39
Alignment explanation
Indices: 5721624--5721828 Score: 169
Period size: 39 Copynumber: 5.2 Consensus size: 39
5721614 ATGCTGAAAT
* * * * *
5721624 TATATCCGGACTTAAGGTCCGCAGGCTTCGTGCTAGAAT
1 TATATCCGAACTTAAGATCCGCAGGCTTCGTGCTGGTAC
* ** * * ** *
5721663 TGTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGAAAT
1 TATATCCGAACTT-AAGATCCGCAGGCTTCGTGCTGGTAC
* ** * * * *
5721703 TGTATCCGGGCTTAAAGACCCGTAGGCTTCGTGCTGGAAT
1 TATATCCGAACTT-AAGATCCGCAGGCTTCGTGCTGGTAC
*
5721743 TGTATCCGAACTTAAGATCCGCAGGCTTCGTGCTGGTAC
1 TATATCCGAACTTAAGATCCGCAGGCTTCGTGCTGGTAC
* *
5721782 TATATCC-AGACTTAAGGTCCGCAGGCTTCGTACTGGTAC
1 TATATCCGA-ACTTAAGATCCGCAGGCTTCGTGCTGGTAC
5721821 TATATCCG
1 TATATCCG
5721829 GGCTTAAAGT
Statistics
Matches: 144, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 1 0.01
39 74 0.51
40 69 0.48
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (39 bp):
TATATCCGAACTTAAGATCCGCAGGCTTCGTGCTGGTAC
Found at i:5721835 original size:39 final size:39
Alignment explanation
Indices: 5721466--5721835 Score: 305
Period size: 40 Copynumber: 9.3 Consensus size: 39
5721456 ACTTGATCTG
* * * * *
5721466 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGAAATTG
1 TATCCGGACTT-AAGATCCGCAGGCTTCGTGCTGGAATTA
* * *
5721506 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGACTT-AAGATCCGCAGGCT-TCGTGCTGGAATTA
* * * *
5721546 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTAGAATTA
1 TATCCGGACTT-AAGATCCGCAGGCT-TCGTGCTGGAATTA
* * * *
5721586 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAATTA
1 TATCCGGACTT-AAGATCCGCAGGCT-TCGTGCTGGAATTA
* * *
5721626 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTAGAATTG
1 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTA
* * * * *
5721665 TATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGAAATTG
1 TATCCGGACTT-AAGATCCGCAGGCTTCGTGCTGGAATTA
* * * *
5721705 TATCCGGGCTTAAAGACCCGTAGGCTTCGTGCTGGAATTG
1 TATCCGGACTT-AAGATCCGCAGGCTTCGTGCTGGAATTA
* * *
5721745 TATCCGAACTTAAGATCCGCAGGCTTCGTGCTGGTACTA
1 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTA
* * * * *
5721784 TATCCAGACTTAAGGTCCGCAGGCTTCGTACTGGTACTA
1 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTA
*
5721823 TATCCGGGCTTAA
1 TATCCGGACTTAA
5721836 AGTCCCGTAG
Statistics
Matches: 293, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.00
39 99 0.34
40 192 0.66
41 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (39 bp):
TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTA
Found at i:5721848 original size:79 final size:79
Alignment explanation
Indices: 5721483--5721849 Score: 373
Period size: 79 Copynumber: 4.6 Consensus size: 79
5721473 GCTTAAAGAC
* * * * *
5721483 CCGCAGGCTTCATGCTGAAATTGTATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTAT
1 CCGCAGGCTTCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGAAATTAT
* **
5721547 ATCCGGGCTTAAAGAC
65 ATCCGGACTT-AAGGT
* * *
5721563 CCGCAGGCTAT-ATGCTAGAATTATATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAATTA
1 CCGCAGGCT-TCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGAAATTA
5721626 TATCCGGACTTAAGGT
64 TATCCGGACTTAAGGT
* * * *
5721642 CCGCAGGCTTCGTGCTAGAATTGTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGAAATTGTA
1 CCGCAGGCTTCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTATA
* **
5721707 TCCGGGCTTAAAGAC
66 TCCGGACTT-AAGGT
* * ** * ** *
5721722 CCGTAGGCTTCGTGCTGGAATTGTATCCGAACTT-AAGATCCGCAGGCTTCGTGCTGGTACTATA
1 CCGCAGGCTTCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTATA
*
5721786 TCCAGACTTAAGGT
66 TCCGGACTTAAGGT
* * * * *
5721800 CCGCAGGCTTCGTACTGGTACTATATCCGGGCTTAAAGTCCCGTAGGCTT
1 CCGCAGGCTTCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTT
5721850 TGTGTTGGTG
Statistics
Matches: 243, Mismatches: 39, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
78 32 0.13
79 110 0.45
80 100 0.41
81 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (79 bp):
CCGCAGGCTTCGTGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTATA
TCCGGACTTAAGGT
Found at i:5723196 original size:27 final size:26
Alignment explanation
Indices: 5723159--5723349 Score: 240
Period size: 27 Copynumber: 7.2 Consensus size: 26
5723149 AGCATGGCTG
* * *
5723159 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGATCAGATAATGTGGCAGAGCCA
*
5723185 CCAGATACAGATAATCGTGGCAGGGCCA
1 CCAGAT-CAGATAAT-GTGGCAGAGCCA
*
5723213 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGATCAGATA-ATGTGGCAGAGCCA
5723240 CCAGATCAGAT-ATGTGGCAGAGCCA
1 CCAGATCAGATAATGTGGCAGAGCCA
*
5723265 CCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGATCAGATA-ATGTGGCAGAGCCA
*
5723292 CCAGATCAGATATTGTGGCAGAGCCA
1 CCAGATCAGATAATGTGGCAGAGCCA
* * *
5723318 CCAGATCAGATATTTATGGCATAGCCA
1 CCAGATCAGATA-ATGTGGCAGAGCCA
5723345 CCAGA
1 CCAGA
5723350 ACGCTTCCTC
Statistics
Matches: 149, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
25 25 0.17
26 31 0.21
27 77 0.52
28 16 0.11
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (26 bp):
CCAGATCAGATAATGTGGCAGAGCCA
Found at i:5723330 original size:53 final size:53
Alignment explanation
Indices: 5723159--5723349 Score: 260
Period size: 52 Copynumber: 3.6 Consensus size: 53
5723149 AGCATGGCTG
* * * *
5723159 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGGGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGAT-ATTGTGGCAGAGCCA
5723213 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATA-TGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTGTGGCAGAGCCA
* *
5723265 CCAGATCAGATATTTGTGGCAGAGCCACCAGATCAGATATTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTGTGGCAGAGCCA
* * * *
5723318 CCAGATCAGATATTTATGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
5723350 ACGCTTCCTC
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
52 48 0.38
53 44 0.35
54 17 0.13
55 18 0.14
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (53 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTGTGGCAGAGCCA
Found at i:5724988 original size:26 final size:26
Alignment explanation
Indices: 5724952--5725061 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5724942 CATGAAATTC
5724952 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5724978 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5725004 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5725030 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5725056 TTATCA
1 TTATCA
5725062 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5729051 original size:27 final size:28
Alignment explanation
Indices: 5729014--5729151 Score: 166
Period size: 27 Copynumber: 5.2 Consensus size: 28
5729004 AGCATGGCTG
* *
5729014 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
5729040 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
5729068 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
5729095 -CA-AT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
5729120 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
5729147 CCAGA
1 CCAGA
5729152 ACGCTTCCTC
Statistics
Matches: 102, Mismatches: 4, Indels: 11
0.87 0.03 0.09
Matches are distributed among these distances:
25 21 0.21
26 9 0.09
27 55 0.54
28 17 0.17
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:5729113 original size:52 final size:54
Alignment explanation
Indices: 5729014--5729147 Score: 175
Period size: 52 Copynumber: 2.5 Consensus size: 54
5729004 AGCATGGCTG
* *
5729014 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA-CAGATACAGATAATCGTGGCAGAGCCA
* *
5729068 CCAGAACAGATATATGTGGCAGAGCCACA-AT-CAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACAGATACAGATAATCGTGGCAGAGCCA
* * *
5729120 CCAGATCAGATATTTGTGGCATAGCCAC
1 CCAGAACAGATATATGTGGCAGAGCCAC
5729148 CAGAACGCTT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 44 0.61
53 2 0.03
54 14 0.19
55 12 0.17
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACAGATACAGATAATCGTGGCAGAGCCA
Found at i:5730803 original size:26 final size:26
Alignment explanation
Indices: 5730767--5730876 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5730757 CATGAAATTC
5730767 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5730793 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5730819 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5730845 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5730871 TTATCA
1 TTATCA
5730877 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5733413 original size:3 final size:3
Alignment explanation
Indices: 5733405--5733681 Score: 76
Period size: 3 Copynumber: 91.7 Consensus size: 3
5733395 ATTTGTCATT
**
5733405 TTA TTA TTA AAA TTTA TTAA TTA -TA TTTA TTTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA T-TA TT-A TTA TTA T-TA T-TA TT-A TTA TTA TTA
* * * * * *
5733450 TTA TTG GTA TTA TTA TTA TTA TTA TTA TCA TTA TTT TTA TT- CTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
5733497 TTG TTA TTA TT- TCTC TTG TTG TT- TTCA TTA TTA TT- TATA TTA TTG
1 TTA TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TTA TTA T-TA TTA TTA
* * * * * *
5733542 TTA GTA CTA TTA GTA CTCT- TTA GT- TTA TTA TTA TTA TTA CTA TCTCG
1 TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA T-T-A
* * * * * *
5733589 TCA TTA TTT TCTA TTA TTG TTA TTA ATA -TA CTA TTA TTA TTC TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5733634 TTAA TGTA TTA CTA TTA TT- TT- TTA CT- TTA TTA TTA -TA TTA TTA
1 TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5733677 CTA TT
1 TTA TT
5733682 GCTATCATCA
Statistics
Matches: 201, Mismatches: 47, Indels: 52
0.67 0.16 0.17
Matches are distributed among these distances:
2 20 0.10
3 152 0.76
4 26 0.13
5 3 0.01
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5733422 original size:13 final size:12
Alignment explanation
Indices: 5733404--5733452 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
5733394 AATTTGTCAT
5733404 TTTATTATTAAAA
1 TTTATTATT-AAA
*
5733417 TTTATTAATTATA
1 TTTATT-ATTAAA
*
5733430 TTTATTTATTAAT
1 TTTA-TTATTAAA
5733443 TTTATTATTA
1 TTTATTATTA
5733453 TTGGTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.19
13 20 0.65
14 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTATTATTAAA
Found at i:5733436 original size:17 final size:17
Alignment explanation
Indices: 5733416--5733448 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5733406 TATTATTAAA
5733416 ATTTATTAATTATATTT
1 ATTTATTAATTATATTT
*
5733433 ATTTATTAATTTTATT
1 ATTTATTAATTATATT
5733449 ATTATTGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTATTAATTATATTT
Found at i:5733646 original size:26 final size:24
Alignment explanation
Indices: 5733600--5733676 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
5733590 CATTATTTTC
5733600 TATTATTGTTATTAA-TA-TACTAT
1 TATTATT-TTATTAATTATTACTAT
5733623 TATTATTCTTATTAATGTATTACTAT
1 TATTATT-TTATTAAT-TATTACTAT
*
5733649 TATT-TTTTACTTTATTATTA-TAT
1 TATTATTTTA-TTAATTATTACTAT
5733672 TATTA
1 TATTA
5733677 CTATTGCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
23 21 0.45
24 8 0.17
25 8 0.17
26 10 0.21
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (24 bp):
TATTATTTTATTAATTATTACTAT
Found at i:5733699 original size:3 final size:3
Alignment explanation
Indices: 5733435--5733681 Score: 77
Period size: 3 Copynumber: 82.7 Consensus size: 3
5733425 TTATATTTAT
* * *
5733435 TTA TTAA TT- TTA TTA TTA TTG GTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
5733480 TTA TTT TTA TT- CTG TTA TTG TTA TTA TT- TCTC TTG TTG TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A
* * * * *
5733524 TTA TTA TT- TATA TTA TTG TTA GTA CTA TTA GTA CTCT- TTA GT- TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA
* * * * * *
5733569 TTA TTA TTA TTA CTA TCTCG TCA TTA TTT TCTA TTA TTG TTA TTA ATA
1 TTA TTA TTA TTA TTA T-T-A TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * *
5733617 -TA CTA TTA TTA TTC TTA TTAA TGTA TTA CTA TTA TT- TT- TTA CT-
1 TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA
*
5733660 TTA TTA TTA -TA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
5733682 GCTATCATCA
Statistics
Matches: 179, Mismatches: 43, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
2 18 0.10
3 144 0.80
4 14 0.08
5 3 0.02
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5733767 original size:3 final size:3
Alignment explanation
Indices: 5733759--5733804 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
5733749 ATATATTTAC
** *
5733759 ATT ATT ATT GCT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5733805 GACATAACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5734274 original size:132 final size:132
Alignment explanation
Indices: 5734035--5734292 Score: 345
Period size: 132 Copynumber: 2.0 Consensus size: 132
5734025 AAAAAATTCA
* * * * *
5734035 TTAAAACGAAAGAGATGTTTGATATTTGGCAATCTATGGAATCGTGCCCTAACGTGCTGGGTTGC
1 TTAAAACGAAAGAAATGTTCGATATTCGGCAATCTAGGGAATCGTGCCCTAACGTGCTGGGTGGC
* * * * * *
5734100 AATTTCTCGTTTGCTCAAATTAATCAAATGTCTCTTTAGAATTTCCTTCATGTTTTCTAAAAACT
66 AATCTCTCGTTTGCGCAAAATAATCAAATATCCCTTTAGAATTTCATTCATGTTTTCTAAAAACT
5734165 TT
131 TT
* * * * *
5734167 TTAAAACGAAGGAAATGTTCGATGTTCGGCAATTTGGGGAATCGTGCCCTATCGTGCTGGGTGGC
1 TTAAAACGAAAGAAATGTTCGATATTCGGCAATCTAGGGAATCGTGCCCTAACGTGCTGGGTGGC
* * *
5734232 AATCTCTCGTTTGCGCAAAATAATCGAATATCCCTTTGGAATTTCATTCGTGTTTTCTAAA
66 AATCTCTCGTTTGCGCAAAATAATCAAATATCCCTTTAGAATTTCATTCATGTTTTCTAAA
5734293 GCGAGGCAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
132 107 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (132 bp):
TTAAAACGAAAGAAATGTTCGATATTCGGCAATCTAGGGAATCGTGCCCTAACGTGCTGGGTGGC
AATCTCTCGTTTGCGCAAAATAATCAAATATCCCTTTAGAATTTCATTCATGTTTTCTAAAAACT
TT
Found at i:5737781 original size:9 final size:9
Alignment explanation
Indices: 5737767--5737800 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
5737757 CAAAGGCAAA
5737767 AAAAAAAAG
1 AAAAAAAAG
5737776 AAAAAAAAG
1 AAAAAAAAG
5737785 AAAAGAAAAG
1 AAAA-AAAAG
5737795 AAAAAA
1 AAAAAA
5737801 GAAAGGGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:5737781 original size:10 final size:10
Alignment explanation
Indices: 5737766--5737805 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5737756 GCAAAGGCAA
5737766 AAAAAAAAAG
1 AAAAAAAAAG
5737776 -AAAAAAAAG
1 AAAAAAAAAG
*
5737785 AAAAGAAAAG
1 AAAAAAAAAG
5737795 AAAAAAGAAAG
1 AAAAAA-AAAG
5737806 GGACCCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 9 0.35
10 13 0.50
11 4 0.15
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5739666 original size:66 final size:66
Alignment explanation
Indices: 5739560--5739692 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
5739550 TGACATTTCT
* * * *
5739560 ACATTCATAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGTATCCTAGTTATTTGA
1 ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
5739625 C
66 C
5739626 ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
1 ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
5739691 C
66 C
5739692 A
1 A
5739693 TAAGCATAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (66 bp):
ACATTCACAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGA
C
Found at i:5740073 original size:66 final size:67
Alignment explanation
Indices: 5739902--5740433 Score: 714
Period size: 68 Copynumber: 7.9 Consensus size: 67
5739892 AATTACAAAT
* * *
5739902 ATCTTT-TCCCTGAAATGGTGTTGGAGCGGCTAAAAGTCACAGCAGATCTCCTTGAAGTTTCAGT
1 ATCTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGT
*
5739966 AG
66 AA
* * *
5739968 ATCTTTTTTCCCTGAAATGGCGTTGGAGCAGCTAAAAGCCACAGCAGATCTCCTTAAAGTTTCAG
1 ATCTTTCTT-CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAG
*
5740033 CAA
65 TAA
* * *
5740036 AT-TTTCTTCCTGAAATAGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGC
1 ATCTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGT
5740100 AA
66 AA
* * * *
5740102 AT-TTTCTCCCTGAAATGGCGTTGGAGCGGCTAAATGCCACACCAGATCTCCTTGAAGTTTTAGT
1 ATCTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGT
*
5740166 GA
66 AA
5740168 ATCTCTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAG
1 ATCT-TTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAG
*
5740233 TGA
65 TAA
* * *
5740236 ATCTCTTCTCCCTGAAATGGCGATGGAGCGGCTAAAAGCCACAGTAGATCTCCTTGAAGTTTCAA
1 ATCT-TTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTC-A
* *
5740301 CGGAC
64 -GTAA
* * * *
5740306 CTC-TTCTTCCTGAAATGGCGTTAGAGCGTCTAAAAACCACAGCAGATCTCCTTGAAGTTTCAGT
1 ATCTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGT
**
5740370 GG
66 AA
* *
5740372 ATCTTT-TTCCTGAAATGGCGTTGGAGCGGTTATAAGCCACAGCAGATCTCCTTGAAGTTTCA
1 ATCTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCA
5740434 ACGGAAGAAG
Statistics
Matches: 414, Mismatches: 45, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
66 175 0.42
67 10 0.02
68 225 0.54
69 1 0.00
70 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (67 bp):
ATCTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGT
AA
Found at i:5740177 original size:134 final size:135
Alignment explanation
Indices: 5739910--5740433 Score: 750
Period size: 134 Copynumber: 3.9 Consensus size: 135
5739900 ATATCTTTTC
* * *
5739910 CCTGAAATGGTGTTGGAGCGGCTAAAAGTCACAGCAGATCTCCTTGAAGTTTCAGTAGATCTTTT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTAAATC-TTT
* * * *
5739975 TTCCCTGAAATGGCGTTGGAGCAGCTAAAAGCCACAGCAGATCTCCTTAAAGTTTCAGCAAAT-T
65 CTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGCGAATCT
5740039 -TTCTT
130 CTTCTT
* * *
5740044 CCTGAAATAGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCAAAT-TTTC
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTAAATCTTTC
* * * *
5740108 TCCCTGAAATGGCGTTGGAGCGGCTAAATGCCACACCAGATCTCCTTGAAGTTTTAGTGAATCTC
66 TCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGCGAATCTC
5740173 TTCTT
131 TTCTT
*
5740178 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGAATCTCTT
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTAAATCT-TT
* * * * *
5740243 CTCCCTGAAATGGCGATGGAGCGGCTAAAAGCCACAGTAGATCTCCTTGAAGTTTCAACGGACCT
65 CTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGCGAATCT
5740308 CTTCTT
130 CTTCTT
* * * **
5740314 CCTGAAATGGCGTTAGAGCGTCTAAAAACCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTTT-
1 CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTAAATCTTTC
* * *
5740378 TTCCTGAAATGGCGTTGGAGCGGTTATAAGCCACAGCAGATCTCCTTGAAGTTTCA
66 TCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCA
5740434 ACGGAAGAAG
Statistics
Matches: 350, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
132 58 0.17
133 1 0.00
134 166 0.47
135 3 0.01
136 122 0.35
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (135 bp):
CCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTAAATCTTTC
TCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGCGAATCTC
TTCTT
Found at i:5740680 original size:44 final size:44
Alignment explanation
Indices: 5740633--5740984 Score: 444
Period size: 44 Copynumber: 8.1 Consensus size: 44
5740623 AGATTAAAAT
**
5740633 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATATT
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
**
5740677 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAGT
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
* * *
5740721 AGATTTGGCGTCTCTGTGAT--TAGAGAACAGATTGAAGATAAC
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
* *
5740763 AGATTTGGCGTCTCTGTGAT--TAGAGAGCAAATCGAAGATAAC
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
* * *
5740805 AGATTTGGCATCTCTGTGTTGATAGAGAGCAAATTGAAGATAAC
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
* **
5740849 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAAATAGT
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
* * * *
5740893 AGATTTGGCATCCCTGTGCTT-ATAGGGAACAGATCGAAGATAAC
1 AGATTTGGCGTCTCTGTG-TTGATAGAGAGCAGATCGAAGATAAC
* * * * *
5740937 GGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATAGC
1 AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
5740981 AGAT
1 AGAT
5740985 ATCGCCTTCC
Statistics
Matches: 269, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
42 75 0.28
43 2 0.01
44 190 0.71
45 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (44 bp):
AGATTTGGCGTCTCTGTGTTGATAGAGAGCAGATCGAAGATAAC
Found at i:5742742 original size:69 final size:69
Alignment explanation
Indices: 5742667--5742860 Score: 201
Period size: 72 Copynumber: 2.8 Consensus size: 69
5742657 AATTGATGAG
* * * * ** *
5742667 TTGTTATATTAAAAATGTCTTCATTTACGTTTGA-TTTAAATGCTTAATGTGTTGCTGTAAAGTG
1 TTGTTATCTTAAAAATGTGTTCATTTACG-TTAATTTTAAATGCTTAATGTGCTGCTACAAAGGG
*
5742731 CTAAT
65 ATAAT
* * *
5742736 TTGTTATCTTAAAAAAAATGTGTTCACTCACGTTAATTTTAGATGCTTAATGTGCTGCTACAAAG
1 TTGTTATCTT---AAAAATGTGTTCATTTACGTTAATTTTAAATGCTTAATGTGCTGCTACAAAG
*
5742801 GGATGAT
63 GGATAAT
* * **
5742808 TTGTTGTCTTGAAAATGTGTTCATTTACGTCCATTTTAAATGCTTAATGTGCT
1 TTGTTATCTTAAAAATGTGTTCATTTACGTTAATTTTAAATGCTTAATGTGCT
5742861 TTCCAACAAC
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
69 46 0.45
71 3 0.03
72 53 0.52
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (69 bp):
TTGTTATCTTAAAAATGTGTTCATTTACGTTAATTTTAAATGCTTAATGTGCTGCTACAAAGGGA
TAAT
Found at i:5742810 original size:72 final size:69
Alignment explanation
Indices: 5742701--5742860 Score: 176
Period size: 69 Copynumber: 2.3 Consensus size: 69
5742691 TTACGTTTGA
* ** * *
5742701 TTTAAATGCTTAATGTGTTGCTGTAAAGTGCTAATTTGTTATCTTAAAAAAAATGTGTTCACTCA
1 TTTAAATGCTTAATGTGCTGCTACAAAGGGATAATTTGTTATCTT---AAAAATGTGTTCACTCA
*
5742766 CGTTAAT
63 CGTCAAT
* * * * * *
5742773 TTTAGATGCTTAATGTGCTGCTACAAAGGGATGATTTGTTGTCTTGAAAATGTGTTCATTTACGT
1 TTTAAATGCTTAATGTGCTGCTACAAAGGGATAATTTGTTATCTTAAAAATGTGTTCACTCACGT
*
5742838 CCAT
66 CAAT
5742842 TTTAAATGCTTAATGTGCT
1 TTTAAATGCTTAATGTGCT
5742861 TTCCAACAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
69 37 0.50
72 37 0.50
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (69 bp):
TTTAAATGCTTAATGTGCTGCTACAAAGGGATAATTTGTTATCTTAAAAATGTGTTCACTCACGT
CAAT
Found at i:5743902 original size:40 final size:40
Alignment explanation
Indices: 5743849--5744219 Score: 387
Period size: 40 Copynumber: 9.4 Consensus size: 40
5743839 ACTTGATCTG
* * *
5743849 TATCAGGGCTTAAAGACCCGCAGGCTTCGTGCTGAAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
*
5743889 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGGAATTA
* * *
5743929 TATCCGGGCTTAAAGGCCCACAGGCTAT-ATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGGAATTA
* *
5743969 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGGAATTA
** ** * * *
5744009 TATCCGAACTT-AAGGTCCGCAGCCTTCGTGCTAGAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
* * *
5744048 TATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGAAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
* *
5744088 T-TCCGGGCTTAAATACCCGCAGGCTTCGTGCTGGAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
* * * *
5744127 TATCCGGACTT-AAGATCCGCAGGCTTCGTGCTGGTACTA
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
* ** * * *
5744166 TATCCGGACTT-AAGGTCCGCAGGCTTCGTACTGGTACTA
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
5744205 TATCCGGGCTTAAAG
1 TATCCGGGCTTAAAG
5744220 TCCCTTAGGC
Statistics
Matches: 288, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
38 1 0.00
39 134 0.47
40 152 0.53
41 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
Found at i:5744082 original size:79 final size:79
Alignment explanation
Indices: 5743866--5744219 Score: 387
Period size: 79 Copynumber: 4.5 Consensus size: 79
5743856 GCTTAAAGAC
* *
5743866 CCGCAGGCTTCGTGCTGAAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTATA
1 CCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGAAATTATA
* *
5743931 TCCGGGCTTAAAGGC
66 TCCGGACTT-AAGGT
* * *
5743946 CCACAGGCTAT-ATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTATATGCTGAAATTAT
1 CCGCAGGCT-TCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGAAATTAT
*
5744010 ATCCGAACTTAAGGT
65 ATCCGGACTTAAGGT
* * * * *
5744025 CCGCAGCCTTCGTGCTAGAATTGTATCCGGGCTTAAAGACCCACAGGCT-TCGTGCTGAAATTGT
1 CCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAATTAT
* *
5744089 -TCCGGGCTTAA-AT
65 ATCCGGACTTAAGGT
* * * ** *
5744102 ACCCGCAGGCTTCGTGCTGGAATTGTATCCGGACTT-AAGATCCGCAGGCT-TCGTGCTGGTACT
1 --CCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGAAATT
5744165 ATATCCGGACTTAAGGT
63 ATATCCGGACTTAAGGT
* * * *
5744182 CCGCAGGCTTCGTACTGGTACTATATCCGGGCTTAAAG
1 CCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAG
5744220 TCCCTTAGGC
Statistics
Matches: 231, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
77 1 0.00
78 63 0.27
79 100 0.43
80 66 0.29
81 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (79 bp):
CCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGAAATTATA
TCCGGACTTAAGGT
Found at i:5746144 original size:26 final size:26
Alignment explanation
Indices: 5746108--5746217 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
5746098 TATGAAATTC
5746108 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5746134 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5746160 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* * *
5746186 TTATCATGGAACATTTACCTAGCCTA
1 TTATCATGAAACATTTACCTAACCCA
5746212 TTATCA
1 TTATCA
5746218 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5747996 original size:22 final size:22
Alignment explanation
Indices: 5747971--5748017 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
5747961 TAAGGGGGGG
*
5747971 TCGATGGTATTTT-GGGGAAGAA
1 TCGATCGTATTTTAGGGG-AGAA
5747993 TCGATCGTATTTTAGGGGAGAA
1 TCGATCGTATTTTAGGGGAGAA
5748015 TCG
1 TCG
5748018 TTTGTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.32
Consensus pattern (22 bp):
TCGATCGTATTTTAGGGGAGAA
Found at i:5748759 original size:3 final size:3
Alignment explanation
Indices: 5748751--5749012 Score: 73
Period size: 3 Copynumber: 86.7 Consensus size: 3
5748741 ATTTGCCATT
**
5748751 TTA TTA TTA AAA TTGA TTAA TTA -TA TTTA TTTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA TT-A TT-A TTA TTA T-TA T-TA TT-A TTA TTA TTA
* * * * * * *
5748796 TTA TTG CTA TTA TTA TTA TTA TCA TTA TTT TTA TT- CTG TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
5748843 TTA TT- TCTC TTG TTA TT- TTCA TTA TTA TT- TATA TTA TTG TTA GTA
1 TTA TTA T-TA TTA TTA TTA TT-A TTA TTA TTA T-TA TTA TTA TTA TTA
* * * * *
5748888 CTCT- TTA GT- TTA TTA TTA TTA TTA CTA TCTCG TCA TTA TTT TCTA
1 -T-TA TTA TTA TTA TTA TTA TTA TTA TTA T-T-A TTA TTA TTA T-TA
* * * * *
5748933 TTA TTG TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA TGTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA
* *
5748979 TTA TT- TT- TTA CT- TTA TTA TTA -TA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5749013 GCTATCATCA
Statistics
Matches: 188, Mismatches: 46, Indels: 50
0.66 0.16 0.18
Matches are distributed among these distances:
2 20 0.11
3 138 0.73
4 27 0.14
5 3 0.02
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5748977 original size:26 final size:24
Alignment explanation
Indices: 5748931--5749007 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
5748921 CATTATTTTC
5748931 TATTATTGTTATTAA-TA-TACTAT
1 TATTATT-TTATTAATTATTACTAT
5748954 TATTATTCTTATTAATGTATTACTAT
1 TATTATT-TTATTAAT-TATTACTAT
*
5748980 TATT-TTTTACTTTATTATTA-TAT
1 TATTATTTTA-TTAATTATTACTAT
5749003 TATTA
1 TATTA
5749008 CTATTGCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
23 21 0.45
24 8 0.17
25 8 0.17
26 10 0.21
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (24 bp):
TATTATTTTATTAATTATTACTAT
Found at i:5749030 original size:3 final size:3
Alignment explanation
Indices: 5748781--5749012 Score: 74
Period size: 3 Copynumber: 77.7 Consensus size: 3
5748771 TTATATTTAT
* * * *
5748781 TTA TTAA TT- TTA TTA TTA TTG CTA TTA TTA TTA TTA TCA TTA TTT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
5748826 TTA TT- CTG TTA TTG TTA TTA TT- TCTC TTG TTA TT- TTCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TTA
* * * *
5748870 TT- TATA TTA TTG TTA GTA CTCT- TTA GT- TTA TTA TTA TTA TTA CTA
1 TTA T-TA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
5748915 TCTCG TCA TTA TTT TCTA TTA TTG TTA TTA ATA -TA CTA TTA TTA TTC
1 T-T-A TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5748962 TTA TTAA TGTA TTA CTA TTA TT- TT- TTA CT- TTA TTA TTA -TA TTA
1 TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5749005 TTA CTA TT
1 TTA TTA TT
5749013 GCTATCATCA
Statistics
Matches: 166, Mismatches: 41, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
2 18 0.11
3 131 0.79
4 14 0.08
5 3 0.02
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5749098 original size:3 final size:3
Alignment explanation
Indices: 5749090--5749138 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
5749080 ATATATTTAC
**
5749090 ATT ATT ATT GCT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5749138 A
1 A
5749139 GACATAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5750002 original size:30 final size:30
Alignment explanation
Indices: 5749968--5750029 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5749958 GGGGTGCTAA
5749968 CCCTTCCTCGTGCGTAACCGACTCCCGAGC
1 CCCTTCCTCGTGCGTAACCGACTCCCGAGC
5749998 CCCTTCCTCGTGCGTAACCGACTCCCGAGC
1 CCCTTCCTCGTGCGTAACCGACTCCCGAGC
5750028 CC
1 CC
5750030 TTTCTCTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.48, G:0.19, T:0.19
Consensus pattern (30 bp):
CCCTTCCTCGTGCGTAACCGACTCCCGAGC
Found at i:5750409 original size:18 final size:20
Alignment explanation
Indices: 5750370--5750409 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5750360 TAATATCATG
*
5750370 TAATACTATATCTTTTATTA
1 TAATACTATATCTTTAATTA
5750390 TAAT-CTATAT-TTTAATTA
1 TAATACTATATCTTTAATTA
5750408 TA
1 TA
5750410 GTAGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATACTATATCTTTAATTA
Done.