Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 7 of 235
Found at i:1761041 original size:14 final size:14
Alignment explanation
Indices: 1761022--1761049 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1761012 TTTTTTTTAC
1761022 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1761036 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1761050 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1761409 original size:74 final size:76
Alignment explanation
Indices: 1761289--1761463 Score: 246
Period size: 74 Copynumber: 2.3 Consensus size: 76
1761279 NNNNNNNNNA
* **
1761289 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAAT
1761354 ATGAGTTG-AT
66 ATGAGTTGAAT
* * * *
1761364 TTTTTTGACA-ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAAT
1761428 ATGAGTTGAAT
66 ATGAGTTGAAT
* * *
1761439 TTTTTTGAAAAATATAAATTGAAAA
1 TTTTTTGAAAGACAAAAATTGAAAA
1761464 GCAGAAATTG
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 56 0.64
75 20 0.23
76 11 0.13
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (76 bp):
TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGAAT
Found at i:1761550 original size:73 final size:73
Alignment explanation
Indices: 1761457--1761609 Score: 238
Period size: 73 Copynumber: 2.1 Consensus size: 73
1761447 AAAATATAAA
1761457 TTGAAAAGCAGAAATTGAAATTACCTCAACGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAGCAGAAATTGAAATTACCTCAACGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATG
1761521 AGTTGATTT
65 AGTTGATTT
* ** *
1761530 TTGACAAA-CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATG
1 TTGA-AAAGCAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1761594 AGTTGATTT
65 AGTTGATTT
1761603 TTGAAAA
1 TTGAAAA
1761610 ATAGGTTGAA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
72 3 0.04
73 66 0.89
74 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (73 bp):
TTGAAAAGCAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:1761598 original size:163 final size:158
Alignment explanation
Indices: 1761293--1762571 Score: 892
Period size: 158 Copynumber: 8.0 Consensus size: 158
1761283 NNNNNATTTT
* * * **
1761293 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAA-ACAGAAATTG-AAATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
1761358 GTTGATTTTTTTGAC-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
64 GTTGA-TTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
1761422 CGCAATATGAGTTGAATTTTTTTGAAAAATATAAA
128 CGCAATATGAGTTG-A--TTTTTGAAAAA-ATAAA
*
1761457 TTGAAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAA-CAGAAATTGAAA-TACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
* **
1761522 GTTGA-TTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTC
64 GTTGATTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
* **
1761586 GTAATATGAGTTGATTTTTG-AAAAATAGG
129 GCAATATGAGTTGATTTTTGAAAAAATAAA
* * * * **
1761615 TTGAAACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAA-ACAGAAATTGA-AATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
* *
1761680 GTTGA-TTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTC
64 GTTGATTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
1761744 GCAATATGAGTTGATTTTTGAAAAACATAAA
129 GCAATATGAGTTGATTTTTGAAAAA-ATAAA
* **
1761775 TTG--AACAGAAATTGAAACTACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAA-TACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * **
1761838 TTGAGATTTTTTTGA-AAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTT
65 TT--GA-TTTTTTGACAA-ACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCT
*
1761902 CTCGCAATATGAGTTGATTTTT-------T--T
126 CTCGCAATATGAGTTGATTTTTGAAAAAATAAA
* * * *
1761926 TTGACAA-AGAAAATTGAAATTACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTTGCAATATG
1 TTGAAAACAG-AAATTGAAA-TACCTCAACATG-CCTTGAGGCTCAACTCACCTCTCGCAATATG
* * *
1761989 AGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTACCTCAACGTG-CCTTG
63 AGTTG-A-TTTTTTG----------A---CAAA-CAGAAATTGAAAATACCTCAGCGTGTCC-TG
1762053 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG---------A
111 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAATAAA
* * * ** *
1762092 ---CAAACAGAAATTGAAATTACCTCAGCGTGTCC-TGAGGCTCAACTCATTTCTCGTAATATGA
1 TTGAAAACAGAAATTGAAA-TACCTCAACATG-CCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * * * *
1762153 GTTGATTTTTGAAAAATAGGTTGA-AACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTC
64 GTTGA--TTT------T---TTGACAA-ACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTC
* *
1762217 AATTCACCTCTCACAAT-TGAGTTGATTTTTG---------A
117 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAATAAA
***
1762249 ---AAAACAGAAATTGAAAATACCTCAGTGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAACAGAAATTG-AAATACCTCAACATG-CCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * * * *
1762310 GTTGA-CTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCTTGAGGCTCA
64 GTTGATTTTTTG----AC----A---AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
** * *
1762374 ACTCATTTCTTGCAATATGAGTTGATTTTT-------T--T
118 ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAATAAA
* * * **
1762406 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAA-ACAGAAATTG-AAATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
* *
1762471 GTTGATTTTTTTTAC-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
64 GTTGA-TTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
1762535 CGCAATATGAGTTGAATTTTTTTGAAAAATATAAA
128 CGCAATATGAGTTG-A--TTTTTGAAAAA-ATAAA
1762570 TT
1 TT
1762572 NNNNNNNNNN
Statistics
Matches: 926, Mismatches: 106, Indels: 166
0.77 0.09 0.14
Matches are distributed among these distances:
145 3 0.00
148 1 0.00
149 1 0.00
151 60 0.06
152 12 0.01
153 51 0.06
154 8 0.01
156 42 0.05
157 135 0.15
158 184 0.20
159 18 0.02
160 18 0.02
161 124 0.13
162 13 0.01
163 128 0.14
164 62 0.07
165 2 0.00
166 60 0.06
169 1 0.00
172 3 0.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (158 bp):
TTGAAAACAGAAATTGAAATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTTTTGAAAAAATAAA
Found at i:1761743 original size:73 final size:74
Alignment explanation
Indices: 1761457--1762563 Score: 519
Period size: 77 Copynumber: 14.1 Consensus size: 74
1761447 AAAATATAAA
* * *
1761457 TTGAAAAGCAGAAATTGAAATTACCTCAACGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATG
1761521 AGTTGA-TTT
65 AGTTGATTTT
* * ** *
1761530 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1761595 GTTGA-TTT
66 GTTGATTTT
* *** * * * * * * *
1761603 TTGAAAAATAGGTTGAAACACAAAAATTGACAATACATC-AG--C-GTGCCCCGAGGCTCAACTC
1 TTGAAAAACA----GAAA-TTGAAAA-T-AC-CT-CAGCGTGTCCTGAGGCTC-A-ACTC-AC-C
*
1761664 ACCTCTCGCAATATGAGTTGA-TTT
53 -T--CTCGCAATATGAGTTGATTTT
*
1761688 TTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1761753 GTTGA-TTT
66 GTTGATTTT
* * * * **
1761761 TTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCTTGAGGCTCAACTCATTTC
1 TTG--------AAA---AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
1761826 TCGCAATATGAGTTGAGATTTTT
55 TCGCAATATGAGTT--GA-TTTT
* * * * **
1761849 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1761914 GTTGATTTTTTT
66 GTTGA---TTTT
* * * *
1761926 TTGACAAAGA-AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1761990 GTTGAATTTTT
66 GTTG-A-TTTT
* * * ** *** * * * *
1762001 TTGAAAAATATAAATTG-AAA-AGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTG----T-CCT-GA-G-G-C-TCA-ACTCACCTC
*
1762064 ACCTCTCGCAATATGAGTTGA-TTT
55 T-----CGCAATATGAGTTGATTTT
* * ** *
1762088 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1762153 GTTGA-TTT
66 GTTGATTTT
* *** * * * * * * *
1762161 TTGAAAAATAGGTTGAAACACAAAAATTGACAATACATC-AG--C-GTGCCCCGAGGCTCAATTC
1 TTGAAAAACA----GAAA-TTGAAAA-T-AC-CT-CAGCGTGTCCTGAGGCTC-A-ACTC-A--C
** *
1762222 ACCTCTCACA-ATTGAGTTGA-TTT
52 CTCTCGCA-ATA-TGAGTTGATTTT
*
1762245 TTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
1762310 GTTGA-CTT
66 GTTGATTTT
* * * * **
1762318 TTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCTTGAGGCTCAACTCATTTC
1 TTG--------AAA---AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
*
1762383 TTGCAATATGAGTTGATTTTTTT
55 TCGCAATATGAGTTGA---TTTT
* * * * **
1762406 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1762471 GTTGATTTT
66 GTTGATTTT
** * *
1762480 TTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1762545 GTTGAATTTTT
66 GTTG-A-TTTT
1762556 TTGAAAAA
1 TTGAAAAA
1762564 TATAAATTNN
Statistics
Matches: 789, Mismatches: 149, Indels: 189
0.70 0.13 0.17
Matches are distributed among these distances:
73 134 0.17
74 77 0.10
75 20 0.03
76 73 0.09
77 147 0.19
78 29 0.04
79 22 0.03
80 30 0.04
81 18 0.02
82 8 0.01
83 7 0.01
84 137 0.17
85 36 0.05
86 2 0.00
87 17 0.02
88 13 0.02
89 6 0.01
90 13 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTT
Found at i:1762430 original size:557 final size:557
Alignment explanation
Indices: 1761289--1762571 Score: 2457
Period size: 558 Copynumber: 2.3 Consensus size: 557
1761279 NNNNNNNNNA
1761289 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1761354 ATGAGTTGA-TTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
66 ATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
1761418 CTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTACCT
131 CTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTACCT
1761483 CAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGA
196 CAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGA
1761548 AATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTGAAAAATA
261 AATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTGAAAAATA
*
1761613 GGTTGAAACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATAT
326 GGTTGAAACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAATAT
1761678 GAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCT
391 GAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCT
*
1761743 CGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCT
456 CGCAATATGAGTTGACTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCT
1761808 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAGAT
521 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAGAT
1761845 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1761910 ATGAGTTGATTTTTTTTTGACAA-AGAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC
66 ATGAGTTGA-TTTTTTTTGACAACAG-AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC
*
1761974 ACCTCTTGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTAC
129 ACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTAC
1762039 CTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATT
194 CTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATT
1762104 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTGAAAAA
259 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTGAAAAA
*
1762169 TAGGTTGAAACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTCAATTCACCTCTCACAAT
324 TAGGTTGAAACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAAT
1762234 -TGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCT
389 ATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCT
1762298 CTCGCAATATGAGTTGACTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGT
454 CTCGCAATATGAGTTGACTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGT
* **
1762363 CTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGATTT
519 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAGAT
1762402 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1 TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
1762467 ATGAGTTGATTTTTTTT-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
66 ATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
1762531 CTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATT
131 CTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATT
1762572 NNNNNNNNNN
Statistics
Matches: 715, Mismatches: 8, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
555 84 0.12
556 84 0.12
557 240 0.34
558 307 0.43
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (557 bp):
TTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
ATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
CTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTACCT
CAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGA
AATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTGAAAAATA
GGTTGAAACACAAAAATTGACAATACATCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAATAT
GAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGACTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCT
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAGAT
Found at i:1762523 original size:74 final size:75
Alignment explanation
Indices: 1762335--1762562 Score: 332
Period size: 74 Copynumber: 3.0 Consensus size: 75
1762325 ACATAAATTG
* * *
1762335 AACAGAAATTGAAACTACCTCAACATGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
1762400 TTTTTTTTGAA
65 TTTTTTTTGAA
*
1762411 AGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 A-ACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
*
1762476 TTTTTTTT-AC
65 TTTTTTTTGAA
* * * ** *
1762486 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1762551 TTTTTTTGAA
66 TTTTTTTGAA
1762561 AA
1 AA
1762563 ATATAAATTN
Statistics
Matches: 137, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
74 64 0.47
75 5 0.04
76 9 0.07
77 59 0.43
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (75 bp):
AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
TTTTTTTGAA
Found at i:1762544 original size:235 final size:224
Alignment explanation
Indices: 1761290--1762554 Score: 854
Period size: 237 Copynumber: 5.3 Consensus size: 224
1761280 NNNNNNNNAT
* * * * * **
1761290 TTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATA
1 TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
* * * * **
1761355 TGAGTTGATTTTTTTGAC-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACC
66 TGAGTTGA--ATTTTGACAAACAGAAATTGAAACTACCTCAACATGTCCTGAGGCTCAACTCATT
* * * *
1761419 TCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAA-AGCAGAAATTGAAATTACCT
129 TCTCGCAATATGAGTTG-A---TTTT------TAT-AGTTGAAACA-CAAAAATTGAAAATACAT
* * ** *
1761483 CAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
182 CAGCATGCCCCGAGGCTCAACTCACCTCTCACAAT-TGAGTTGA
* ** *
1761527 TTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATA
1 TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
* * * * * * * *
1761592 TGAGTTGATTTTTGAAAAATAGGTTGAAACACAAAAATTGACAA-TACATCAGCGTGCCCCGAGG
66 TGAGTTGAATTTTG------A-----CAA-ACAGAAATTGA-AACTACCTCAACATGTCCTGAGG
** * * *
1761656 CTCAACTCACCTCTCGCAATATGAGTTGA---TT-T--TTGAAAAACAGAAATTGAAAATACCTC
118 CTCAACTCATTTCTCGCAATATGAGTTGATTTTTATAGTTGAAACACAAAAATTGAAAATACATC
** * * *
1761715 AGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
183 AGCATGCCCCGAGGCTCAACTCACCTCTCACAAT-TGAGTTGA
* * * * *
1761758 TTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCTTGAGGCTCAACTCAT
1 TTTTTG--------AAA---AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
* * * * *
1761823 TTCTCGCAATATGAGTTGAGATTTTTTTGA-AAGACAAAAATTGAAAATACCTCAGCATGTCTTG
55 CTCTCGCAATATGAGTTGA-A---TTTTGACAA-ACAGAAATTGAAACTACCTCAACATGTCCTG
* * *
1761887 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT-T-TTTGACAA-A-GAAAATTGAAATTA
115 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTATAGTTGA-AACACAAAAATTGAAAATA
* * * * **
1761948 CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAA
179 CATCAGCATGCCCCGAGGCTCAACTCACCTCTCACAAT-TGAGTTG-A
*
1761996 TTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTACCTCAACGTG-CCTTGAGGCTCA
1 --TTTTTG----------A---AAAA-CAGAAATTGAAATTACCTCAGCGTGTCC-TGAGGCTCA
* * * *
1762060 ACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCT
49 ACTCACCTCTCGCAATATGAGTTGAATTTTGACAAACAGAAATTGAAACTACCTCAACATGTCCT
*
1762125 GAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTGAAAAATAGGTTGAAACACAAAAATTG
114 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT-----ATA-GTTGAAACACAAAAATTG
* * *
1762190 ACAATACATCAGCGTGCCCCGAGGCTCAATTCACCTCTCACAATTGAGTTGA
173 AAAATACATCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATTGAGTTGA
* *
1762242 TTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
* *
1762307 TGAGTTGACTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACATGTCTTGAGGCT
66 TGAGTTGAATTTTG----AC----A---AACAGAAATTGAAACTACCTCAACATGTCCTGAGGCT
* * * *
1762372 CAACTCATTTCTTGCAATATGAGTTGATTTTT-T-TTTGAAAGACAAAAATTGAAAATACCTCAG
120 CAACTCATTTCTCGCAATATGAGTTGATTTTTATAGTTGAAACACAAAAATTGAAAATACATCAG
* ** ** *
1762435 CATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
185 CATGCCCCGAGGCTCAACTCACCTCTCACAAT-TGAGTTGA
** *
1762476 TTTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 -TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1762541 ATGAGTTGAATTTT
65 ATGAGTTGAATTTT
1762555 TTTGAAAAAT
Statistics
Matches: 868, Mismatches: 89, Indels: 144
0.79 0.08 0.13
Matches are distributed among these distances:
230 61 0.07
231 75 0.09
232 1 0.00
233 52 0.06
234 67 0.08
235 80 0.09
237 124 0.14
238 7 0.01
239 73 0.08
240 9 0.01
241 65 0.07
242 68 0.08
243 55 0.06
244 6 0.01
245 3 0.00
246 8 0.01
247 14 0.02
248 98 0.11
249 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (224 bp):
TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGAATTTTGACAAACAGAAATTGAAACTACCTCAACATGTCCTGAGGCTCAACTCATTTC
TCGCAATATGAGTTGATTTTTATAGTTGAAACACAAAAATTGAAAATACATCAGCATGCCCCGAG
GCTCAACTCACCTCTCACAATTGAGTTGA
Found at i:1773317 original size:12 final size:12
Alignment explanation
Indices: 1773300--1773330 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1773290 TATGCAATAA
*
1773300 ATGAATGGATGC
1 ATGAATGAATGC
1773312 ATGAATGAATGC
1 ATGAATGAATGC
1773324 ATGAATG
1 ATGAATG
1773331 TCAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (12 bp):
ATGAATGAATGC
Found at i:1780479 original size:12 final size:12
Alignment explanation
Indices: 1780462--1780487 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1780452 GAAATTAAGC
1780462 TTTTAGTGGCGT
1 TTTTAGTGGCGT
1780474 TTTTAGTGGCGT
1 TTTTAGTGGCGT
1780486 TT
1 TT
1780488 GGACTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.31, T:0.54
Consensus pattern (12 bp):
TTTTAGTGGCGT
Found at i:1800855 original size:30 final size:29
Alignment explanation
Indices: 1800819--1800883 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 29
1800809 AAACGGAAGT
1800819 TTTGGCACTAAGTGTGCGATTTAAAATAGC
1 TTTGGCACTAAGTGTGCGATTT-AAATAGC
* *
1800849 TTTGGCACTAAGTGTGTGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAATAGC
1800878 TTTGGC
1 TTTGGC
1800884 TACTTGAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAAATAGC
Found at i:1801673 original size:37 final size:37
Alignment explanation
Indices: 1801623--1801704 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
1801613 TAAGGTTTAT
1801623 AAGTATGTAAATGGTTGATAATATTATGGCATGAATG
1 AAGTATGTAAATGGTTGATAATATTATGGCATGAATG
1801660 AAGTATGTAAATGGTTGATAATATTATGGCATGAATG
1 AAGTATGTAAATGGTTGATAATATTATGGCATGAATG
1801697 AAGTATGT
1 AAGTATGT
1801705 TTTAGCTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (37 bp):
AAGTATGTAAATGGTTGATAATATTATGGCATGAATG
Found at i:1808975 original size:49 final size:48
Alignment explanation
Indices: 1808919--1809099 Score: 229
Period size: 49 Copynumber: 3.7 Consensus size: 48
1808909 TTGGTACGCA
**
1808919 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA-G
* * *
1808968 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTAGCA-
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTA-CAG
* * *
1809018 TAGTAGTCTGCACTTAGTACTTCAAATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA-G
*
1809067 TAGTAGCCTGCACTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC
1809100 TCACAGTAGA
Statistics
Matches: 113, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
47 2 0.02
48 9 0.08
49 62 0.55
50 30 0.27
51 8 0.07
52 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAG
Found at i:1809087 original size:99 final size:100
Alignment explanation
Indices: 1808911--1809097 Score: 313
Period size: 99 Copynumber: 1.9 Consensus size: 100
1808901 AAAGCTATTT
* *
1808911 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTAGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACAAATGCGACCAATTATCCAGTACACGTAGTAGCC
1808976 TGCACTTAGTACTACACATGTGATCGAAGTTATCG
66 TGCACTTAGTACTACACATGTGATCGAAGTTATCG
* * * *
1809011 GGTA-GCATAGTAGTCTGCACTTAGTACTTCAAATGCGACCAATTATCCGGTACATGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACAAATGCGACCAATTATCCAGTACACGTAGTAGCC
1809075 TGCACTTAGTACTACACATGTGA
66 TGCACTTAGTACTACACATGTGA
1809098 CCTCACAGTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 77 0.95
100 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACAAATGCGACCAATTATCCAGTACACGTAGTAGCC
TGCACTTAGTACTACACATGTGATCGAAGTTATCG
Found at i:1811186 original size:26 final size:26
Alignment explanation
Indices: 1811157--1811213 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1811147 ACCTGTAGGA
1811157 GATAGTTCTTGAGTATGACTGAGGGT
1 GATAGTTCTTGAGTATGACTGAGGGT
*
1811183 GATAGTTCTTGAGTTTGACTGAGGGT
1 GATAGTTCTTGAGTATGACTGAGGGT
1811209 GATAG
1 GATAG
1811214 ATTAATGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (26 bp):
GATAGTTCTTGAGTATGACTGAGGGT
Found at i:1822742 original size:47 final size:48
Alignment explanation
Indices: 1822688--1822781 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 48
1822678 TGAGAATTAG
1822688 TTGTAAGTGAATAATTAGATGAACGAAATC-ATTTTTAGGCAAAAATT
1 TTGTAAGTGAATAATTAGATGAACGAAATCAATTTTTAGGCAAAAATT
*
1822735 TTGTAAGTGAATAATTAGATGAACGAAATCAATTTTTTGGCAAAAAT
1 TTGTAAGTGAATAATTAGATGAACGAAATCAATTTTTAGGCAAAAAT
1822782 ATTAAGTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 30 0.67
48 15 0.33
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (48 bp):
TTGTAAGTGAATAATTAGATGAACGAAATCAATTTTTAGGCAAAAATT
Found at i:1824748 original size:26 final size:26
Alignment explanation
Indices: 1824718--1824770 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1824708 ATTGTGAATG
1824718 AATGGTGAACTTTACTTATTAACTAT
1 AATGGTGAACTTTACTTATTAACTAT
*
1824744 AATGGTGAGCTTTACTTATTAACTAT
1 AATGGTGAACTTTACTTATTAACTAT
1824770 A
1 A
1824771 CGAGGTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (26 bp):
AATGGTGAACTTTACTTATTAACTAT
Found at i:1846145 original size:14 final size:13
Alignment explanation
Indices: 1846126--1846158 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1846116 ATAATGCAAT
1846126 TTACCATAATCTCA
1 TTACCATAAT-TCA
1846140 TTACCATAATTCA
1 TTACCATAATTCA
1846153 TT-CCAT
1 TTACCAT
1846159 CACAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 5 0.26
14 10 0.53
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (13 bp):
TTACCATAATTCA
Found at i:1857532 original size:30 final size:30
Alignment explanation
Indices: 1857489--1857545 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1857479 TGTGCCCTTC
* * *
1857489 CACACAGGTTGGACACATGCCCATGTGAGG
1 CACACAGGCTGGACACACGACCATGTGAGG
*
1857519 CACACGGGCTGGACACACGACCATGTG
1 CACACAGGCTGGACACACGACCATGTG
1857546 CCAGCTCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (30 bp):
CACACAGGCTGGACACACGACCATGTGAGG
Found at i:1873546 original size:24 final size:24
Alignment explanation
Indices: 1873519--1873570 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1873509 TTAGTAAGTC
*
1873519 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1873543 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1873567 AAAT
1 AAAT
1873571 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1875517 original size:24 final size:24
Alignment explanation
Indices: 1875490--1875541 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1875480 TTAGTAAGTC
*
1875490 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1875514 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1875538 AAAT
1 AAAT
1875542 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1884970 original size:60 final size:60
Alignment explanation
Indices: 1884877--1884996 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
1884867 AAAAGAAAGG
1884877 TGACTGTATTGAAAGAAGGGTGTCCTTTGGAAGGATTGTGTGTTTATTCTTAATATGTTC
1 TGACTGTATTGAAAGAAGGGTGTCCTTTGGAAGGATTGTGTGTTTATTCTTAATATGTTC
1884937 TGACTGTATTGAAAGAAGGGTGTCCTTTGGAAGGATTGTGTGTTTATTCTTAATATGTTC
1 TGACTGTATTGAAAGAAGGGTGTCCTTTGGAAGGATTGTGTGTTTATTCTTAATATGTTC
1884997 ATTGTACTCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (60 bp):
TGACTGTATTGAAAGAAGGGTGTCCTTTGGAAGGATTGTGTGTTTATTCTTAATATGTTC
Found at i:1886980 original size:22 final size:23
Alignment explanation
Indices: 1886940--1886986 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1886930 CACGTTAGCG
1886940 AACAAATATATAAAAAT-AAATA
1 AACAAATATATAAAAATAAAATA
* * *
1886962 AACAAATATTTATATATAAAATA
1 AACAAATATATAAAAATAAAATA
1886985 AA
1 AA
1886987 ATATAAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AACAAATATATAAAAATAAAATA
Found at i:1888688 original size:31 final size:31
Alignment explanation
Indices: 1888622--1888690 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
1888612 TAAAAAGTGT
**
1888622 TAATTAAGCTTAAGTTTAATTAATTATAAGT
1 TAATTAAGCTTAAGTTTAATTAATTATAAAC
1888653 TAATTAAG-TTAA-TTATAATTAATTAATAAAC
1 TAATTAAGCTTAAGTT-TAATTAATT-ATAAAC
1888684 TAATTAA
1 TAATTAA
1888691 AATGTATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 13 0.38
31 19 0.56
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (31 bp):
TAATTAAGCTTAAGTTTAATTAATTATAAAC
Found at i:1889808 original size:21 final size:24
Alignment explanation
Indices: 1889773--1889817 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1889763 ATTTAACGTG
*
1889773 AAAAAACTCATCCAA-ATAGATAA
1 AAAAAACTCATCCAACAAAGATAA
1889796 AAAAAAC-CA-CCAACAAAGATAA
1 AAAAAACTCATCCAACAAAGATAA
1889818 TTTTACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.64, C:0.20, G:0.04, T:0.11
Consensus pattern (24 bp):
AAAAAACTCATCCAACAAAGATAA
Found at i:1890034 original size:24 final size:24
Alignment explanation
Indices: 1890007--1890058 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1889997 TTCGTAGGTC
* *
1890007 AAATAGATCATGCTAATAAATGCT
1 AAATAGATCATACTAATAAATACT
* *
1890031 AAATATATTATACTAATAAATACT
1 AAATAGATCATACTAATAAATACT
1890055 AAAT
1 AAAT
1890059 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAGATCATACTAATAAATACT
Found at i:1898552 original size:43 final size:43
Alignment explanation
Indices: 1898490--1898651 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 43
1898480 GTACAATGTC
* * *
1898490 ATGTCCCAGATATGGTCTTACATGTTATTACATATCGATGCCA
1 ATGTCCCAGACATGGTCTTACACGTAATTACATATCGATGCCA
* * * * *
1898533 CTGTCCCAGACAGGGTCTTACACGAAATTGA-TTAACGATGCCA
1 ATGTCCCAGACATGGTCTTACACGTAATT-ACATATCGATGCCA
* * *
1898576 ATGTCCTAGACATGGTCTTACACGTAATCACA-ATACAATGCCA
1 ATGTCCCAGACATGGTCTTACACGTAATTACATAT-CGATGCCA
* * *
1898619 ATGTCCTAGACATGGTCCTACATGTAATTACAT
1 ATGTCCCAGACATGGTCTTACACGTAATTACAT
1898652 CTCGGTAACC
Statistics
Matches: 96, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
42 2 0.02
43 93 0.97
44 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (43 bp):
ATGTCCCAGACATGGTCTTACACGTAATTACATATCGATGCCA
Found at i:1898768 original size:21 final size:21
Alignment explanation
Indices: 1898743--1898785 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1898733 CGATTCTTGC
1898743 TTGTATTTACTTGTTCAACAT
1 TTGTATTTACTTGTTCAACAT
1898764 TTGTATTTACTTGTTCAACAT
1 TTGTATTTACTTGTTCAACAT
1898785 T
1 T
1898786 CATAGTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (21 bp):
TTGTATTTACTTGTTCAACAT
Found at i:1911707 original size:3 final size:3
Alignment explanation
Indices: 1911647--1911693 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1911637 TACTTAAGTA
*
1911647 AAT ATAT AAT -AT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1911692 AA
1 AA
1911694 AGTAAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1911708 original size:9 final size:8
Alignment explanation
Indices: 1911647--1911707 Score: 54
Period size: 9 Copynumber: 7.2 Consensus size: 8
1911637 TACTTAAGTA
1911647 AATAT-AT
1 AATATAAT
*
1911654 AATATTAT
1 AATATAAT
1911662 AATAATAAT
1 AAT-ATAAT
1911671 AATAATAAT
1 AAT-ATAAT
1911680 AATAATAAT
1 AAT-ATAAT
1911689 AATA-AAGT
1 AATATAA-T
1911697 AAATATAAT
1 -AATATAAT
1911706 AA
1 AA
1911708 AACAAATAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
7 7 0.15
8 9 0.19
9 30 0.62
10 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (8 bp):
AATATAAT
Found at i:1919644 original size:16 final size:14
Alignment explanation
Indices: 1919604--1919665 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
1919594 ATTTTAACGG
*
1919604 AATTAGAATTATGTT
1 AATTAAAATTAT-TT
*
1919619 AA-AAAAATTATTT
1 AATTAAAATTATTT
*
1919632 AATTAGGAAATTAATT
1 AATTA--AAATTATTT
1919648 AATTAAAATTAATTT
1 AATTAAAATT-ATTT
1919663 AAT
1 AAT
1919666 ATATTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
13 4 0.11
14 13 0.34
15 8 0.21
16 13 0.34
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
AATTAAAATTATTT
Found at i:1924779 original size:44 final size:45
Alignment explanation
Indices: 1924714--1924804 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1924704 ACCTCTATTC
* * *
1924714 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1924758 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1924803 CA
1 CA
1924805 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1924806 original size:16 final size:16
Alignment explanation
Indices: 1924785--1924820 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1924775 GATTAGCTAT
1924785 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1924801 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1924817 TACA
1 TACA
1924821 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1926062 original size:24 final size:25
Alignment explanation
Indices: 1926017--1926080 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
1926007 TTTTTTTAAC
* *
1926017 TTATTATTTTAATATATTATTTTGTT
1 TTATTTTTTTAA-ATATCATTTTGTT
1926043 TTATTTTTTTAAATA-CATTTTGTT
1 TTATTTTTTTAAATATCATTTTGTT
*
1926067 TTATTTTTTAAAAT
1 TTATTTTTTTAAAT
1926081 TTTCTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 21 0.60
25 3 0.09
26 11 0.31
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (25 bp):
TTATTTTTTTAAATATCATTTTGTT
Found at i:1927121 original size:23 final size:23
Alignment explanation
Indices: 1927091--1927137 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1927081 CTTTGGACGT
1927091 AGTGAGGGTGCTAACCCTTCCTC
1 AGTGAGGGTGCTAACCCTTCCTC
1927114 AGTGAGGGTGCTAACCCTTCCTC
1 AGTGAGGGTGCTAACCCTTCCTC
1927137 A
1 A
1927138 TACGTAACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (23 bp):
AGTGAGGGTGCTAACCCTTCCTC
Found at i:1929854 original size:9 final size:9
Alignment explanation
Indices: 1929830--1929882 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
1929820 ATAAATTATT
1929830 TTTTTATAA
1 TTTTTATAA
* *
1929839 ATATTATAA
1 TTTTTATAA
*
1929848 TTTTTATGA
1 TTTTTATAA
1929857 TTTTTAATTAA
1 TTTTT-A-TAA
1929868 TTTTTAATAA
1 TTTTT-ATAA
1929878 TTTTT
1 TTTTT
1929883 TTTATAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 18 0.50
10 9 0.25
11 9 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1929872 original size:11 final size:10
Alignment explanation
Indices: 1929844--1929882 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1929834 TATAAATATT
1929844 ATAATTTTT-
1 ATAATTTTTA
*
1929853 ATGATTTTTA
1 ATAATTTTTA
1929863 ATTAATTTTTA
1 A-TAATTTTTA
1929874 ATAATTTTT
1 ATAATTTTT
1929883 TTTATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 9 0.35
11 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:1929898 original size:21 final size:21
Alignment explanation
Indices: 1929842--1929906 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1929832 TTTATAAATA
* *
1929842 TTATAATTTTTATGATTTTTA
1 TTATAATTTTTATAATTTTTT
*
1929863 AT-TAATTTTTAATAATTTTTT
1 TTATAATTTTT-ATAATTTTTT
* *
1929884 TTATAAATTTTATAATTCTTT
1 TTATAATTTTTATAATTTTTT
1929905 TT
1 TT
1929907 GTGCTTTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 8 0.22
21 21 0.58
22 7 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATAATTTTTATAATTTTTT
Found at i:1934694 original size:15 final size:15
Alignment explanation
Indices: 1934661--1934700 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1934651 TGTGCTTGAT
*
1934661 TTAGGGTTTT-AGGG
1 TTAGGGTTTTAAGAG
1934675 TTAGGGTTTTAAGAG
1 TTAGGGTTTTAAGAG
1934690 TTAGGGTTTTA
1 TTAGGGTTTTA
1934701 TTGTGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (15 bp):
TTAGGGTTTTAAGAG
Found at i:1935050 original size:126 final size:126
Alignment explanation
Indices: 1934822--1935243 Score: 564
Period size: 126 Copynumber: 3.4 Consensus size: 126
1934812 TAATTAAATT
* * *
1934822 AGGATGCACTATCAGCAAAATTACTAAAAAAAACTCCCACGTTGACGCTCTTTTGCTACAGTAGT
1 AGGATGCACTATAAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTCTTTTGCTACAGTAGT
* *
1934887 ATCTGAAAAAATAATTTTGAGAAGACA-TTTCTAAACAAATAGTGTCCAAAATGCTTCAAGC
66 ATCTGAAAAAATAATTTTGAGAAGA-AGTTTCTGAACAAATAGTGTCCAAAAAGCTTCAAGC
* * * ** * * *
1934948 ATGATGCACTGTAAGCAAAATTATTGAAAAAAGTTCCCACATGGACGCTCTTTTGCTAGAATAGT
1 AGGATGCACTATAAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTCTTTTGCTACAGTAGT
*
1935013 ATCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTATCCAAAACA-CTTCAAGC
66 ATCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCCAAAA-AGCTTCAAGC
* *
1935074 AGGATGCACTATCAA-CAAAATTACTGAAAAAAACTCCCACGTGGATGCTTTTTTGCTACAGTAG
1 AGGATGCACTAT-AAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTCTTTTGCTACAGTAG
* * * *
1935138 TATCTGAAAAAGTAATTTTGAGAAGACGTTTTTGAACAAATATTGTCCAAAAAGCTTCAAGC
65 TATCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCCAAAAAGCTTCAAGC
* * * * *
1935200 AGGATGCACTGTCAGTAAAATTAC-GTAAAAAGCTCCCACGTGGA
1 AGGATGCACTATAAGCAAAATTACTGAAAAAAACTCCCACGTGGA
1935244 TCCACTTCAA
Statistics
Matches: 257, Mismatches: 34, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
125 21 0.08
126 234 0.91
127 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (126 bp):
AGGATGCACTATAAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTCTTTTGCTACAGTAGT
ATCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCCAAAAAGCTTCAAGC
Found at i:1937875 original size:24 final size:24
Alignment explanation
Indices: 1937829--1937875 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1937819 ATGAATGCAG
* *
1937829 AGGTGTTTGTATCACCTATGGCGA
1 AGGTGTTTGAATCACCTAAGGCGA
1937853 AGGTGTTTGAATC-CCATAAGGCG
1 AGGTGTTTGAATCACC-TAAGGCG
1937876 GTGGGGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (24 bp):
AGGTGTTTGAATCACCTAAGGCGA
Found at i:1939878 original size:9 final size:10
Alignment explanation
Indices: 1939841--1939891 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
1939831 TAAAGAAAGC
*
1939841 TTTGAGAAAA
1 TTTGAGAGAA
*
1939851 TATGAGAGAAA
1 TTTGAGAG-AA
1939862 TTTGAGAGAA
1 TTTGAGAGAA
1939872 TTTAGAGAGAA
1 TTT-GAGAGAA
1939883 TTATGAGAG
1 TT-TGAGAG
1939892 GACTTTCGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 11 0.31
11 23 0.66
12 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:1939882 original size:22 final size:20
Alignment explanation
Indices: 1939841--1939891 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
1939831 TAAAGAAAGC
*
1939841 TTTGAGAAAATATGAGAGAAA
1 TTTGAGAGAATATGAGAG-AA
*
1939862 TTTGAGAGAATTTAGAGAGAA
1 TTTGAGAGAATAT-GAGAGAA
1939883 TTATGAGAG
1 TT-TGAGAG
1939892 GACTTTCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (20 bp):
TTTGAGAGAATATGAGAGAA
Found at i:1943079 original size:27 final size:30
Alignment explanation
Indices: 1943049--1943112 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
1943039 ATAATTTTTT
*
1943049 AATAATTTTAATGATTTTT-AA-TTT-AAA
1 AATAATTTTAATAATTTTTAAATTTTAAAA
* *
1943076 AATAGTTTTTATAATTTTTAAATTTTAAAA
1 AATAATTTTAATAATTTTTAAATTTTAAAA
1943106 AATAATT
1 AATAATT
1943113 AAATGCTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.53
28 2 0.07
29 3 0.10
30 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
AATAATTTTAATAATTTTTAAATTTTAAAA
Found at i:1946911 original size:15 final size:15
Alignment explanation
Indices: 1946871--1946915 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
1946861 TATTAATATT
*
1946871 ATTAAATTTATATAAA
1 ATTAAATTTATA-ATA
1946887 ATTAAA--TATAATA
1 ATTAAATTTATAATA
1946900 ATTAAATTTATAATA
1 ATTAAATTTATAATA
1946915 A
1 A
1946916 ACTTTTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.31
14 4 0.15
15 8 0.31
16 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAATTTATAATA
Found at i:1948328 original size:46 final size:46
Alignment explanation
Indices: 1948258--1948531 Score: 397
Period size: 46 Copynumber: 6.0 Consensus size: 46
1948248 TTTGACATGA
* * * * * * *
1948258 TGCCATAGTGTCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
1948304 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
1948350 TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
1948396 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
1948442 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1948488 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1948532 AGAGCACACT
Statistics
Matches: 212, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 208 0.98
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:1955109 original size:16 final size:17
Alignment explanation
Indices: 1955084--1955122 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1955074 CTATTTTAAG
1955084 TTTA-TTTTAATT-TTA
1 TTTATTTTTAATTATTA
1955099 TTTATTTTTAATTATTA
1 TTTATTTTTAATTATTA
1955116 -TTATTTT
1 TTTATTTT
1955123 GGATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 15 0.68
17 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTTAATTATTA
Found at i:1955134 original size:17 final size:17
Alignment explanation
Indices: 1955085--1955140 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
1955075 TATTTTAAGT
1955085 TTATTTT-AATTTTAT-
1 TTATTTTGAATTTTATA
* *
1955100 TTATTTTTAATTAT-TA
1 TTATTTTGAATTTTATA
*
1955116 TTATTTTGGATTTTATA
1 TTATTTTGAATTTTATA
1955133 TTAATTTT
1 TT-ATTTT
1955141 CTTAAGCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 8 0.24
16 16 0.48
17 4 0.12
18 5 0.15
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (17 bp):
TTATTTTGAATTTTATA
Found at i:1961784 original size:20 final size:19
Alignment explanation
Indices: 1961728--1961784 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1961718 CCCACATATA
* * *
1961728 CCAAAACCCAAAATCAAAC
1 CCAATACCCAAAACCTAAC
*
1961747 CCAATACCCAAATCCTAAC
1 CCAATACCCAAAACCTAAC
* *
1961766 CCATTTACCCAAAAGCTAA
1 CCA-ATACCCAAAACCTAA
1961785 AATAACCCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.47, C:0.37, G:0.02, T:0.14
Consensus pattern (19 bp):
CCAATACCCAAAACCTAAC
Found at i:1965204 original size:16 final size:15
Alignment explanation
Indices: 1965179--1965226 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1965169 CTATTTTAAG
1965179 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
1965194 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
1965211 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
1965226 T
1 T
1965227 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:1966163 original size:7 final size:7
Alignment explanation
Indices: 1966153--1966177 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1966143 TTATTTCATC
1966153 TTTTACT
1 TTTTACT
1966160 TTTTACT
1 TTTTACT
1966167 TTTTACT
1 TTTTACT
1966174 TTTT
1 TTTT
1966178 CTTGTGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTACT
Found at i:1966164 original size:19 final size:19
Alignment explanation
Indices: 1966117--1966156 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1966107 TATTTTGTTA
1966117 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1966136 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1966155 TT
1 TT
1966157 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:1977456 original size:28 final size:28
Alignment explanation
Indices: 1977415--1977470 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1977405 TGGGAGTGGA
*
1977415 AACTTACCAGACTTGAATACCATACATC
1 AACTTACCAAACTTGAATACCATACATC
1977443 AACTTACCAAACTTGAATACCATACATC
1 AACTTACCAAACTTGAATACCATACATC
1977471 GAAAAGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.29, G:0.05, T:0.25
Consensus pattern (28 bp):
AACTTACCAAACTTGAATACCATACATC
Found at i:1986846 original size:10 final size:10
Alignment explanation
Indices: 1986831--1986856 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1986821 TGTCAACTTG
1986831 TATCGACTCA
1 TATCGACTCA
1986841 TATCGACTCA
1 TATCGACTCA
1986851 TATCGA
1 TATCGA
1986857 TAGTGTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (10 bp):
TATCGACTCA
Found at i:1989823 original size:40 final size:39
Alignment explanation
Indices: 1989743--1989854 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 39
1989733 TATCAATAAA
1989743 CTGAAGCTATTT-CAGTATCGCACACTTAGTGCCTCATATAG
1 CTGAAGCTATTTCCA--ATCGCACACTTAGTG-CTCATATAG
*
1989784 CTGAAGTTA-TTCCAATTCGCACACTTAGTGCT-ATTTATAG
1 CTGAAGCTATTTCCAA-TCGCACACTTAGTGCTCA--TATAG
* *
1989824 CTGAAGCTATTTCGAATCGTACACTTAGTGC
1 CTGAAGCTATTTCCAATCGCACACTTAGTGC
1989855 CGAACATAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
38 1 0.02
39 3 0.05
40 43 0.69
41 15 0.24
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (39 bp):
CTGAAGCTATTTCCAATCGCACACTTAGTGCTCATATAG
Found at i:1991988 original size:29 final size:30
Alignment explanation
Indices: 1991929--1991986 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1991919 TCCGAGCCTT
*
1991929 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1991959 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1991987 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1992216 original size:13 final size:13
Alignment explanation
Indices: 1992198--1992229 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1992188 TTTCCAGCAA
1992198 TTATGAATTTATT
1 TTATGAATTTATT
1992211 TTATGAATTTATT
1 TTATGAATTTATT
*
1992224 TGATGA
1 TTATGA
1992230 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1992404 original size:50 final size:50
Alignment explanation
Indices: 1992324--1992559 Score: 411
Period size: 50 Copynumber: 4.7 Consensus size: 50
1992314 ATTTGGGTAA
*
1992324 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1992374 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1992424 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
*
1992474 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1992524 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1992560 TTTGGCATGT
Statistics
Matches: 180, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
49 1 0.01
50 148 0.82
51 31 0.17
ACGTcount: A:0.27, C:0.25, G:0.31, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1992511 original size:26 final size:26
Alignment explanation
Indices: 1992482--1992559 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
1992472 CGAGAGGTCC
1992482 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
* ** * **
1992508 CATG--GGCACCATCAC-GAGAACATCC
1 CATGTAAG-ACCATGTCTG-GGACATGG
1992533 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
1992559 C
1 C
1992560 TTTGGCATGT
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
24 2 0.06
25 15 0.43
26 16 0.46
27 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (26 bp):
CATGTAAGACCATGTCTGGGACATGG
Found at i:1999576 original size:29 final size:30
Alignment explanation
Indices: 1999517--1999574 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1999507 TCCGAGCCTT
*
1999517 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1999547 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1999575 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1999804 original size:13 final size:13
Alignment explanation
Indices: 1999786--1999817 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1999776 TTTCCAGCAA
1999786 TTATGAATTTATT
1 TTATGAATTTATT
1999799 TTATGAATTTATT
1 TTATGAATTTATT
*
1999812 TGATGA
1 TTATGA
1999818 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1999992 original size:50 final size:50
Alignment explanation
Indices: 1999912--2000096 Score: 361
Period size: 50 Copynumber: 3.7 Consensus size: 50
1999902 ATTTGGGTAA
*
1999912 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1999962 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
2000012 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
2000062 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
2000097 TTTGGCATGT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2008788 original size:126 final size:126
Alignment explanation
Indices: 2008583--2008923 Score: 488
Period size: 126 Copynumber: 2.7 Consensus size: 126
2008573 AAGATATTTA
* * * * * * * * *
2008583 ATTATTTGGTCCAAC-GAAAAATCGAAACCCAACATGTTAAGGTACAATTTCTCGGATTTCCAAA
1 ATTATTTGGACAAACAG-AAAATTGAATCCCAGCACGTTAAGGCACGATTTCTCGAATTTCCAAA
*
2008647 CATAGAACATTGCCTTATTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATAATTG
65 CATAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATAATTG
* *
2008709 GTTATTTGGACAAACAGAAAATTGAATCCCAGCACGTTAAGGCACGATTTCTCGAATTTCTAAAC
1 ATTATTTGGACAAACAGAAAATTGAATCCCAGCACGTTAAGGCACGATTTCTCGAATTTCCAAAC
* * * *
2008774 ATAGAACATTGCCTTGTTTTAAAGTTTTGAAAACACGGACGAAATTTTAAAGGGGTATTTG
66 ATAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATAATTG
*
2008835 ATTATTTGGACAAACAGAAAATTGAATCCCAGCACGTTAGGGCACGATTTCTCGAATTTCCAAAC
1 ATTATTTGGACAAACAGAAAATTGAATCCCAGCACGTTAAGGCACGATTTCTCGAATTTCCAAAC
2008900 ATCA-AACATTGCCTTTGTTTTGAA
66 AT-AGAACATTGCC-TTGTTTTGAA
2008924 AAATTTTCGA
Statistics
Matches: 192, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
126 181 0.94
127 11 0.06
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (126 bp):
ATTATTTGGACAAACAGAAAATTGAATCCCAGCACGTTAAGGCACGATTTCTCGAATTTCCAAAC
ATAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATAATTG
Found at i:2014163 original size:36 final size:36
Alignment explanation
Indices: 2014116--2014189 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
2014106 TTAAAAAGAG
2014116 TTAGGATTTTTGGTCATTTGACTACTTTCGCTTATT
1 TTAGGATTTTTGGTCATTTGACTACTTTCGCTTATT
2014152 TTAGGATTTTTGGTCATTTGACTACTTTCGCTTATT
1 TTAGGATTTTTGGTCATTTGACTACTTTCGCTTATT
2014188 TT
1 TT
2014190 GCTTTCTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (36 bp):
TTAGGATTTTTGGTCATTTGACTACTTTCGCTTATT
Found at i:2014188 original size:18 final size:18
Alignment explanation
Indices: 2014131--2014188 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
2014121 ATTTTTGGTC
2014131 ATTTGACTACTTTCGCTT
1 ATTTGACTACTTTCGCTT
* ** * * * *
2014149 ATTTTAGGATTTTTGGTC
1 ATTTGACTACTTTCGCTT
2014167 ATTTGACTACTTTCGCTT
1 ATTTGACTACTTTCGCTT
2014185 ATTT
1 ATTT
2014189 TGCTTTCTTT
Statistics
Matches: 26, Mismatches: 14, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.16, G:0.14, T:0.53
Consensus pattern (18 bp):
ATTTGACTACTTTCGCTT
Found at i:2019753 original size:42 final size:42
Alignment explanation
Indices: 2019673--2019756 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2019663 CCGACAACAA
2019673 GTAAAAATTTCTCCTAACGAATACAGTTGGATCCGAACTCGG
1 GTAAAAATTTCTCCTAACGAATACAGTTGGATCCGAACTCGG
2019715 GTAAAAATTTCTCCTAACGAATACAGTTGGATCCGAACTCGG
1 GTAAAAATTTCTCCTAACGAATACAGTTGGATCCGAACTCGG
2019757 AACCAGATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
GTAAAAATTTCTCCTAACGAATACAGTTGGATCCGAACTCGG
Found at i:2021043 original size:18 final size:18
Alignment explanation
Indices: 2021011--2021056 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2021001 GTATTAAGCG
*
2021011 TTCAATTTAA-ATTAGTT
1 TTCAATTTAATTTTAGTT
*
2021028 TTTAATTTAATTTTAGTT
1 TTCAATTTAATTTTAGTT
2021046 TTCAATTTAAT
1 TTCAATTTAAT
2021057 AAAAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
TTCAATTTAATTTTAGTT
Found at i:2021663 original size:27 final size:30
Alignment explanation
Indices: 2021611--2021686 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 30
2021601 CGATATACTA
* * *
2021611 AATTCATATATTACTAATACATAAAA-AAT
1 AATTAATATATAACTATTACATAAAATAAT
2021640 -A-TAATATATAACTATTAC-TGAAAATAAT
1 AATTAATATATAACTATTACAT-AAAATAAT
* *
2021668 AATTCACATATAACTATTA
1 AATTAATATATAACTATTA
2021687 TTATAACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 18 0.47
28 4 0.11
29 1 0.03
30 14 0.37
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.36
Consensus pattern (30 bp):
AATTAATATATAACTATTACATAAAATAAT
Found at i:2022493 original size:24 final size:26
Alignment explanation
Indices: 2022439--2022494 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
2022429 ATTTTCATTG
*
2022439 TATAAAAATAAAATGACTTATTACAT
1 TATAAAAATAAAATGACTTATAACAT
*
2022465 T-TAAAAATAAAAT-ATTTATAAC-T
1 TATAAAAATAAAATGACTTATAACAT
2022488 TATAAAA
1 TATAAAA
2022495 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 12 0.44
25 12 0.44
26 1 0.04
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (26 bp):
TATAAAAATAAAATGACTTATAACAT
Found at i:2024474 original size:60 final size:60
Alignment explanation
Indices: 2024401--2024520 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
2024391 AATCCTTTTA
* *
2024401 CTTTTAATTCTAAAAATTTAATATTTTTACTAATTTATTTTAATGATTAAAGTCCAATTG
1 CTTTTAATTCTAAAAAATTAATATTTTTACTAATTTAATTTAATGATTAAAGTCCAATTG
2024461 CTTTTAATTCTAAAAAATTAATATTTTTACTAATTTAATTTAATGATTAAAGTCCAATTG
1 CTTTTAATTCTAAAAAATTAATATTTTTACTAATTTAATTTAATGATTAAAGTCCAATTG
2024521 ATAATGTTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.48
Consensus pattern (60 bp):
CTTTTAATTCTAAAAAATTAATATTTTTACTAATTTAATTTAATGATTAAAGTCCAATTG
Found at i:2025259 original size:13 final size:13
Alignment explanation
Indices: 2025238--2025269 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2025228 ATTATAAATC
*
2025238 TTTAAAAAAATAA
1 TTTATAAAAATAA
2025251 TTTATAAAAATAA
1 TTTATAAAAATAA
2025264 TTTATA
1 TTTATA
2025270 TGTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTATAAAAATAA
Found at i:2029135 original size:2 final size:2
Alignment explanation
Indices: 2029128--2029152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2029118 TCATGGTACT
2029128 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2029153 GATATGTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2030011 original size:20 final size:21
Alignment explanation
Indices: 2029986--2030030 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2029976 TGCCAAATTC
2029986 ACAAATG-AAAAA-TATATATA
1 ACAAATGAAAAAATTA-ATATA
*
2030006 ACAAATTAAAAAATTAATATA
1 ACAAATGAAAAAATTAATATA
2030027 ACAA
1 ACAA
2030031 CAAAAAGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 14 0.64
22 2 0.09
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
ACAAATGAAAAAATTAATATA
Found at i:2032065 original size:13 final size:14
Alignment explanation
Indices: 2032049--2032084 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2032039 CAATCTCATA
2032049 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
2032062 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
2032075 TCTC-ATTTCA
1 TCTCAATTTCA
2032085 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:2032074 original size:18 final size:19
Alignment explanation
Indices: 2032036--2032076 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
2032026 TGGTTCATGT
2032036 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
2032055 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
2032073 TTTC
1 TTTC
2032077 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:2032266 original size:39 final size:38
Alignment explanation
Indices: 2032199--2032333 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
2032189 ACCAATATGG
* * *
2032199 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
2032238 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
2032276 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
2032317 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
2032334 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:2032599 original size:18 final size:19
Alignment explanation
Indices: 2032573--2032611 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2032563 TTTCAATTCA
2032573 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
2032592 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
2032610 AT
1 AT
2032612 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:2033937 original size:5 final size:5
Alignment explanation
Indices: 2033927--2033983 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
2033917 TTACTTATTT
* *
2033927 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
2033975 ATAT- ATATA
1 ATATA ATATA
2033984 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:2033943 original size:12 final size:12
Alignment explanation
Indices: 2033926--2033981 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
2033916 TTTACTTATT
2033926 TATATAATATAA
1 TATATAATATAA
2033938 TATATAATATAATA
1 TATATAATAT-A-A
2033952 TACTATAATATAA
1 TA-TATAATATAA
*
2033965 TA-ATAATTTAA
1 TATATAATATAA
2033976 TATATA
1 TATATA
2033982 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:2037128 original size:24 final size:24
Alignment explanation
Indices: 2037096--2037147 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2037086 TTTAGGAACA
2037096 CTTTTGTAATGCTTGCATGTCCTC
1 CTTTTGTAATGCTTGCATGTCCTC
2037120 CTTTTGTAATGCTTGCATGTCCTC
1 CTTTTGTAATGCTTGCATGTCCTC
2037144 CTTT
1 CTTT
2037148 CCACCCTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.48
Consensus pattern (24 bp):
CTTTTGTAATGCTTGCATGTCCTC
Found at i:2045853 original size:19 final size:19
Alignment explanation
Indices: 2045831--2045881 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2045821 TAAAAAATTG
2045831 AAAATTATATAAAG-TATAT
1 AAAATTATATAAAGAT-TAT
*
2045850 AAAATTATAAAAAGATTAT
1 AAAATTATATAAAGATTAT
2045869 AAATATATATATA
1 AAA-AT-TATATA
2045882 TAAAAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 19 0.70
20 3 0.11
21 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATTATATAAAGATTAT
Found at i:2049957 original size:28 final size:27
Alignment explanation
Indices: 2049909--2049987 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
2049899 ATTTATTCTT
* *
2049909 TTTAAACG-GTTTTGTATATTATTTAG
1 TTTAAACGTTTTTTATATATTATTTAG
* * *
2049935 TTTAGACTTCTTTTTATATATTATTTAT
1 TTTAAACGT-TTTTTATATATTATTTAG
*
2049963 TTTAAACGTTTTTCATATATTATTT
1 TTTAAACGTTTTTTATATATTATTT
2049988 TAAGTTGTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 6 0.14
27 15 0.35
28 22 0.51
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (27 bp):
TTTAAACGTTTTTTATATATTATTTAG
Found at i:2050031 original size:26 final size:26
Alignment explanation
Indices: 2049908--2050108 Score: 130
Period size: 26 Copynumber: 7.9 Consensus size: 26
2049898 CATTTATTCT
** *
2049908 TTTTAAACGGTTTTGTATATTATTTA
1 TTTTAAATTGTTTTATATATTATTTA
* * *
2049934 GTTTAGACTTCTTTTTATATATTATTTA
1 TTTTA-AATT-GTTTTATATATTATTTA
*
2049962 TTTTAAA-CGTTTT-TCATA-TA-TTA
1 TTTTAAATTGTTTTAT-ATATTATTTA
* * * *
2049985 TTTTAAGTTGTCTTATGTATTATTTG
1 TTTTAAATTGTTTTATATATTATTTA
* *
2050011 TTTTAAATTGCTTTGTATATTATTCT-
1 TTTTAAATTGTTTTATATATTATT-TA
* *
2050037 TCTT-AATTGTTTTACATATTATTTA
1 TTTTAAATTGTTTTATATATTATTTA
* *
2050062 TCTTAAATTG-TTT-TATACTATTTA
1 TTTTAAATTGTTTTATATATTATTTA
* * *
2050086 CTTCAAACTGTTTTATATATTAT
1 TTTTAAATTGTTTTATATATTAT
2050109 GTTGTTTTGC
Statistics
Matches: 132, Mismatches: 31, Indels: 24
0.71 0.17 0.13
Matches are distributed among these distances:
23 9 0.07
24 25 0.19
25 36 0.27
26 40 0.30
27 3 0.02
28 19 0.14
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (26 bp):
TTTTAAATTGTTTTATATATTATTTA
Found at i:2050097 original size:24 final size:23
Alignment explanation
Indices: 2050056--2050106 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2050046 TTTTACATAT
*
2050056 TATTTATCTTAAATTGTTTTATA
1 TATTTATCTTAAACTGTTTTATA
2050079 CTATTTA-CTTCAAACTGTTTTATA
1 -TATTTATCTT-AAACTGTTTTATA
2050103 TATT
1 TATT
2050107 ATGTTGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTTATCTTAAACTGTTTTATA
Found at i:2062207 original size:44 final size:45
Alignment explanation
Indices: 2062159--2062556 Score: 180
Period size: 45 Copynumber: 8.6 Consensus size: 45
2062149 CTTACCTACT
* *
2062159 TGAAGTTGCAGTAGAGCAGATTGAAGCCA-CAAGTCTTATCCCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * * * * * *
2062203 TGAAGTTACAGCGAAGCAGACTAAAGACAGCGAA-TCTTATTTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGC-AAGTCTTATCTCCC
* * *
2062248 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAA-TCTTATCTTCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGC--C-----A--GC-AAGTCTTATCTCCC
* * * *
2062302 TGAAGTTG-AGTGAAGCAGATTGAAGCCA-CCAGCCTTATCTTCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * * * ** * * * *
2062345 TGAAATTGCAGCGGAGTAGACTGAAGATACCAAATCTCATGTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * * *
2062390 TGAAGTTGCAGTTGAACAGATTGAAGCTACAAGTCACAATCATTGTCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGC--C-AG-CA-AGTC-TTATCTCCC
* * * * *
2062441 TGAAGTTGCAGTAGAGCAAATTGAAGCCATC-AGCCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* * *** * * *
2062485 TGAAGTTGCAGTGGAGCAGGTTAAAATTACCAATTTTTATCT-CC
1 TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
* *
2062529 TCGAAGTTCCAGTGGAGTAGATTGAAGC
1 T-GAAGTTGCAGTGGAGCAGATTGAAGC
2062557 TACAAATCTC
Statistics
Matches: 259, Mismatches: 73, Indels: 43
0.69 0.19 0.11
Matches are distributed among these distances:
42 1 0.00
43 18 0.07
44 68 0.26
45 89 0.34
46 3 0.01
47 2 0.01
48 2 0.01
49 3 0.01
50 4 0.02
51 31 0.12
52 1 0.00
53 15 0.06
54 22 0.08
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGCCAGCAAGTCTTATCTCCC
Found at i:2062366 original size:142 final size:142
Alignment explanation
Indices: 2062137--2062503 Score: 413
Period size: 142 Copynumber: 2.6 Consensus size: 142
2062127 GAATTAAATC
* * * * * *
2062137 ATCATGGTGAATCTTACCTACTTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAGTCTTATCCCC
1 ATCATGGCGAATCTTATCTACCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTAT-CTC
* * * * * *
2062202 CTGAAGTTACAGCGAAGCAGACTAAAGACAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAG
65 CTGAAGTTGCAGCGGAGCAGACTAAAGACACCAAATCTCATGTCCCTGAAGTTGCAGTGGAACAG
2062267 ATTAAAGCTACAA
130 ATTAAAGCTACAA
* *
2062280 ATTATGGCGAATCTTATCTTCCTGAAGTTG-AGT-GAAGCAGATTGAAGCCACCAGCCTTATCTT
1 ATCATGGCGAATCTTATCTACCTGAAGTTGCAGTAG-AGCAGATTGAAGCCACCAGCCTTATC-T
* * * * *
2062343 CCTGAAATTGCAGCGGAGTAGACTGAAGATACCAAATCTCATGTCCCTGAAGTTGCAGTTGAACA
64 CCTGAAGTTGCAGCGGAGCAGACTAAAGACACCAAATCTCATGTCCCTGAAGTTGCAGTGGAACA
*
2062408 GATTGAAGCTACAA
129 GATTAAAGCTACAA
* * * * *
2062422 GTCA---C-AATCATTGTCTCCCTGAAGTTGCAGTAGAGCAAATTGAAGCCATCAGCCTTATCTC
1 ATCATGGCGAATC-TTATCTACCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTC
*
2062483 TCTGAAGTTGCAGTGGAGCAG
65 -CTGAAGTTGCAGCGGAGCAG
2062504 GTTAAAATTA
Statistics
Matches: 189, Mismatches: 29, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
138 4 0.02
139 18 0.10
140 44 0.23
141 3 0.02
142 95 0.50
143 25 0.13
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (142 bp):
ATCATGGCGAATCTTATCTACCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCC
TGAAGTTGCAGCGGAGCAGACTAAAGACACCAAATCTCATGTCCCTGAAGTTGCAGTGGAACAGA
TTAAAGCTACAA
Found at i:2064123 original size:26 final size:28
Alignment explanation
Indices: 2064094--2064154 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2064084 ATTTATTATT
*
2064094 TTTAAAC-T-GTTTTGTATATTATTTAG
1 TTTAAACTTCGTTTTATATATTATTTAG
* * *
2064120 TTTAGACTTCTTTTTATATATTATTTAT
1 TTTAAACTTCGTTTTATATATTATTTAG
2064148 TTTAAAC
1 TTTAAAC
2064155 ATTTTTCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 6 0.21
27 1 0.04
28 21 0.75
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTAAACTTCGTTTTATATATTATTTAG
Found at i:2064270 original size:24 final size:23
Alignment explanation
Indices: 2064241--2064291 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2064231 TTTTACATAT
2064241 TATTTATCTT-AAACCGTTTTATA
1 TATTTA-CTTCAAACCGTTTTATA
*
2064264 CTATTTACTTCAAACTGTTTTATA
1 -TATTTACTTCAAACCGTTTTATA
2064288 TATT
1 TATT
2064292 ATGTTGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTACTTCAAACCGTTTTATA
Found at i:2065609 original size:28 final size:28
Alignment explanation
Indices: 2065566--2065621 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2065556 CAATCACTCA
*
2065566 ACTTTCGAAAACTGACAAAACAGTCATT
1 ACTTTCGAAAACTGACAAAACAATCATT
*
2065594 ACTTTCGAAAAGTGACAAAACAATCATT
1 ACTTTCGAAAACTGACAAAACAATCATT
2065622 TTTATCGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.25
Consensus pattern (28 bp):
ACTTTCGAAAACTGACAAAACAATCATT
Found at i:2066886 original size:21 final size:21
Alignment explanation
Indices: 2066862--2066906 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2066852 TCTTGGGGCA
* * *
2066862 GCAACTTTTTGGTGAGTTGGG
1 GCAACTTGTTGATAAGTTGGG
2066883 GCAACTTGTTGATAAGTTGGG
1 GCAACTTGTTGATAAGTTGGG
2066904 GCA
1 GCA
2066907 GTTTGTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.36, T:0.33
Consensus pattern (21 bp):
GCAACTTGTTGATAAGTTGGG
Found at i:2066912 original size:21 final size:21
Alignment explanation
Indices: 2066876--2066935 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2066866 CTTTTTGGTG
*
2066876 AGTTGGGGCAACTTGTTGA-TA
1 AGTTGGGGCAGCTTGTT-ACTA
* *
2066897 AGTTGGGGCAGTTTGTTACTG
1 AGTTGGGGCAGCTTGTTACTA
*
2066918 AGTTGGGGCAGCCTGTTA
1 AGTTGGGGCAGCTTGTTA
2066936 AGTTGGGGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (21 bp):
AGTTGGGGCAGCTTGTTACTA
Found at i:2066941 original size:18 final size:18
Alignment explanation
Indices: 2066895--2066943 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
2066885 AACTTGTTGA
**
2066895 TAAGTTGGGGCAGTTTGT
1 TAAGTTGGGGCAGCCTGT
2066913 TACTGAGTTGGGGCAGCCTGT
1 TA---AGTTGGGGCAGCCTGT
2066934 TAAGTTGGGG
1 TAAGTTGGGG
2066944 TATTTTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.38
21 16 0.62
ACGTcount: A:0.16, C:0.10, G:0.41, T:0.33
Consensus pattern (18 bp):
TAAGTTGGGGCAGCCTGT
Found at i:2067912 original size:85 final size:85
Alignment explanation
Indices: 2067764--2067919 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
2067754 ACAATCACTG
* * * *
2067764 CATGCATATTAAAAAAAACAGTCATACACATACACACACATCTAAAAAATAGCCACTGCATGCAT
1 CATGCATATTAAAAAAAACAGTCATACACATACACACACACCTAAAAAACAGCCAATGAATGCAT
2067829 ATTAAAAAAATAGACAACAA
66 ATTAAAAAAATAGACAACAA
* * * *
2067849 CATGTATATT-AAAAAAA-AGTTATACACATACATACACACACCTAAAAAGCAGTCAATGAATGC
1 CATGCATATTAAAAAAAACAGTCATACACATAC--ACACACACCTAAAAAACAGCCAATGAATGC
2067912 ATATTAAA
64 ATATTAAA
2067920 TAGTCATACA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 13 0.21
84 7 0.11
85 41 0.67
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (85 bp):
CATGCATATTAAAAAAAACAGTCATACACATACACACACACCTAAAAAACAGCCAATGAATGCAT
ATTAAAAAAATAGACAACAA
Found at i:2067956 original size:63 final size:66
Alignment explanation
Indices: 2067878--2068049 Score: 235
Period size: 63 Copynumber: 2.6 Consensus size: 66
2067868 TTATACACAT
* * *
2067878 ACATACACACACCTAAAAAGCAGTCAATGAATGCATATTAAATAGTCATACACACCAA-AA-AT-
1 ACATACACACCCCTAAAAAACAGTCACTGAATGCATATTAAATAGTCATACACACCAACAACATA
2067940 C
66 C
* * *
2067941 ATATACACACCCCTAAAAAATAGTCACT-AGATGCATATTAAATAGTCATACACACTAACAATCA
1 ACATACACACCCCTAAAAAACAGTCACTGA-ATGCATATTAAATAGTCATACACACCAACAA-CA
2068005 TAC
64 TAC
*
2068008 ACATACACACCCCTAAAAAACAGTCACTGTATGCATATTAAA
1 ACATACACACCCCTAAAAAACAGTCACTGAATGCATATTAAA
2068050 AAGTAGTCAA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 50 0.53
64 2 0.02
66 2 0.02
67 39 0.41
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (66 bp):
ACATACACACCCCTAAAAAACAGTCACTGAATGCATATTAAATAGTCATACACACCAACAACATA
C
Found at i:2070738 original size:39 final size:39
Alignment explanation
Indices: 2070684--2070892 Score: 337
Period size: 39 Copynumber: 5.4 Consensus size: 39
2070674 GCATCGGTCC
*
2070684 TGTCCAGATATATTTCCAGCATATAGCCTGCGGACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
* *
2070723 TGTCCGGATATATTTCCAGCATATAGCTTGCGAACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
* *
2070762 TGTCCGGGTATATTCCCAGCATATAGCCTGCGGACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
* *
2070801 TGTCCGGATATATTTCCAGCATATAGCTTGCGAACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
* *
2070840 TGTCCGGGTATATTCCCAGCATATAGCCTGCGGACCTCA
1 TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
2070879 TGTCCGGATATATT
1 TGTCCGGATATATT
2070893 CCCAATATCA
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 154 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (39 bp):
TGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTCA
Found at i:2070813 original size:78 final size:78
Alignment explanation
Indices: 2070692--2070892 Score: 393
Period size: 78 Copynumber: 2.6 Consensus size: 78
2070682 CCTGTCCAGA
*
2070692 TATATTTCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATATAGCTTGCGAA
1 TATATTCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATATAGCTTGCGAA
2070757 CCTCATGTCCGGG
66 CCTCATGTCCGGG
2070770 TATATTCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATATAGCTTGCGAA
1 TATATTCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATATAGCTTGCGAA
2070835 CCTCATGTCCGGG
66 CCTCATGTCCGGG
2070848 TATATTCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATT
1 TATATTCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATT
2070893 CCCAATATCA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 122 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (78 bp):
TATATTCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATATAGCTTGCGAA
CCTCATGTCCGGG
Found at i:2073223 original size:9 final size:9
Alignment explanation
Indices: 2073202--2073245 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 9
2073192 TTGTTTTTAA
2073202 TATTTATTTT
1 TATTTA-TTT
2073212 TATTTATTT
1 TATTTATTT
2073221 TATTTATTT
1 TATTTATTT
2073230 TATTTTATTT
1 TA-TTTATTT
2073240 CTATTT
1 -TATTT
2073246 TTGGAAACGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.44
10 16 0.50
11 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTATTT
Found at i:2073224 original size:5 final size:5
Alignment explanation
Indices: 2073204--2073246 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
2073194 GTTTTTAATA
2073204 TTTAT TTT-T ATTTAT TTTA- TTTAT TTTAT TTTAT TTCTAT TTT
1 TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTT
2073247 TGGAAACGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 5 0.15
5 23 0.68
6 6 0.18
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:2075066 original size:25 final size:25
Alignment explanation
Indices: 2075037--2075088 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2075027 AAAAATAATT
**
2075037 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
2075062 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
2075087 TG
1 TG
2075089 TTAAGCCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:2077653 original size:61 final size:62
Alignment explanation
Indices: 2077577--2077714 Score: 206
Period size: 63 Copynumber: 2.2 Consensus size: 62
2077567 CCATTTTTGT
* *
2077577 CAGACAATAACCAATAC-AAAATAATTTAATATAAACACAATCATTTCTGTCATGCACATAG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATAG
* * * *
2077638 CAGACAATAATCAATACAAAAAATAATTTAGTACAAGCACAACCATTTCTGTCATGCACATGG
1 CAGACAATAACCAATAC-AAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATAG
2077701 CAGACAATAACCAA
1 CAGACAATAACCAA
2077715 ACATTTTAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 16 0.24
63 52 0.76
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (62 bp):
CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATAG
Found at i:2078080 original size:6 final size:6
Alignment explanation
Indices: 2078029--2078062 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2078019 CCCTAAATTG
2078029 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
2078063 TAGCATCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:2078092 original size:18 final size:18
Alignment explanation
Indices: 2078023--2078084 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
2078013 AAATAACCCT
2078023 AAATTGAAATCAAAATCA
1 AAATTGAAATCAAAATCA
**
2078041 AAATCAAAATCAAAATCA
1 AAATTGAAATCAAAATCA
* *
2078059 AAATT-AGCATCGAAATCA
1 AAATTGA-AATCAAAATCA
2078077 AAATTGAA
1 AAATTGAA
2078085 GTCGAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATTGAAATCAAAATCA
Found at i:2078109 original size:16 final size:16
Alignment explanation
Indices: 2078088--2078118 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2078078 AATTGAAGTC
*
2078088 GAAATAATCCTAAATT
1 GAAATAACCCTAAATT
2078104 GAAATAACCCTAAAT
1 GAAATAACCCTAAAT
2078119 CCAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (16 bp):
GAAATAACCCTAAATT
Found at i:2084136 original size:44 final size:44
Alignment explanation
Indices: 2084086--2084173 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2084076 TCATCAATAA
2084086 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
1 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
2084130 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
1 AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
2084174 GGCCCCCACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (44 bp):
AAGTTAGCATATAATTAACTTCACCTCTCGAAGGCACTTTGGAT
Found at i:2089322 original size:22 final size:23
Alignment explanation
Indices: 2089280--2089324 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2089270 ATTGATTTGG
* *
2089280 ATTTTATATTTTTTTATAATTTT
1 ATTTTATATTTCTTTAAAATTTT
2089303 ATTTTAT-TTTCTTTAAAATTTT
1 ATTTTATATTTCTTTAAAATTTT
2089325 TAATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTTATATTTCTTTAAAATTTT
Found at i:2089540 original size:18 final size:18
Alignment explanation
Indices: 2089500--2089541 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2089490 ATTAAAATTT
2089500 AATTAATTAATTTTATAA
1 AATTAATTAATTTTATAA
*
2089518 TATTAATTAATTTTA-AA
1 AATTAATTAATTTTATAA
2089535 CAATTAA
1 -AATTAA
2089542 CATCAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAATTTTATAA
Found at i:2092205 original size:38 final size:38
Alignment explanation
Indices: 2092157--2092280 Score: 167
Period size: 38 Copynumber: 3.2 Consensus size: 38
2092147 GGCACGAAGG
* * * *
2092157 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
2092195 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
2092233 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
2092272 GCCCGGATA
1 -CCCGGATA
2092281 CACATCAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 64 0.83
39 5 0.06
40 8 0.10
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:2098093 original size:48 final size:48
Alignment explanation
Indices: 2098033--2098145 Score: 122
Period size: 48 Copynumber: 2.3 Consensus size: 48
2098023 GTCCAACTAT
* * * *
2098033 GGTCTTATACTAGCTCTGCTCT-GCCCGTGCTGATGCCTATTCCC-GATA
1 GGTCTTACACTAGCACT-CACTGGCCCGTGCCGATGCCTA-TCCCAGATA
* *
2098081 GGTCTTACACTAGCACTCACTGGGCTGTGCCGATGCCTATCCCAGATA
1 GGTCTTACACTAGCACTCACTGGCCCGTGCCGATGCCTATCCCAGATA
*
2098129 GGTCTTACGCTTAGCAC
1 GGTCTTACAC-TAGCAC
2098146 AAGTCGAGCT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
47 7 0.13
48 42 0.76
49 6 0.11
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (48 bp):
GGTCTTACACTAGCACTCACTGGCCCGTGCCGATGCCTATCCCAGATA
Found at i:2099818 original size:43 final size:43
Alignment explanation
Indices: 2099770--2099881 Score: 224
Period size: 43 Copynumber: 2.6 Consensus size: 43
2099760 CCGGCATTAC
2099770 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
2099813 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
2099856 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
2099882 TAATACCAGC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.29, C:0.34, G:0.27, T:0.10
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:2099922 original size:38 final size:38
Alignment explanation
Indices: 2099874--2099997 Score: 167
Period size: 38 Copynumber: 3.2 Consensus size: 38
2099864 GGCACGAAGG
* * * *
2099874 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
2099912 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
2099950 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
2099989 GCCCGGATA
1 -CCCGGATA
2099998 CACATCAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 64 0.83
39 5 0.06
40 8 0.10
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:2105284 original size:33 final size:33
Alignment explanation
Indices: 2105242--2105307 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2105232 ATGGATATTG
2105242 AGTTAAATTACAAAATCATTTTGATTTTTTATC
1 AGTTAAATTACAAAATCATTTTGATTTTTTATC
*
2105275 AGTTAAATTACATAATCATTTTGATTTTTTATC
1 AGTTAAATTACAAAATCATTTTGATTTTTTATC
2105308 TCATTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (33 bp):
AGTTAAATTACAAAATCATTTTGATTTTTTATC
Found at i:2105829 original size:22 final size:22
Alignment explanation
Indices: 2105801--2105856 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2105791 GACTATTAAA
2105801 ATCGTAAAAATACATTTTTATC
1 ATCGTAAAAATACATTTTTATC
2105823 ATCGTAAAAATACATTTTTATC
1 ATCGTAAAAATACATTTTTATC
*
2105845 ATCATAAAAATA
1 ATCGTAAAAATA
2105857 TACAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (22 bp):
ATCGTAAAAATACATTTTTATC
Found at i:2107239 original size:19 final size:18
Alignment explanation
Indices: 2107217--2107257 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2107207 GATTTTATAT
* *
2107217 TTTTTAAATATTTTTTTTA
1 TTTTT-AATAATTTATTTA
2107236 TTTTTAATAATTTATTTA
1 TTTTTAATAATTTATTTA
2107254 TTTT
1 TTTT
2107258 GAACAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTAATAATTTATTTA
Found at i:2108402 original size:16 final size:16
Alignment explanation
Indices: 2108383--2108461 Score: 90
Period size: 16 Copynumber: 4.9 Consensus size: 16
2108373 TCATATTTTA
2108383 ATATAATAATTATTAT
1 ATATAATAATTATTAT
2108399 ATATAATAATTATTAT
1 ATATAATAATTATTAT
*
2108415 ATATAATAATATATAAT
1 ATATAATAAT-TATTAT
* *
2108432 TTAATAA-AATTCTTA-
1 AT-ATAATAATTATTAT
*
2108447 ATATAATTATTATTA
1 ATATAATAATTATTA
2108462 AAATATGAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.08
15 7 0.13
16 29 0.55
17 9 0.17
18 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAATTATTAT
Found at i:2108402 original size:24 final size:23
Alignment explanation
Indices: 2108358--2108402 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2108348 TAATAATAAA
2108358 TAATAAATAATTTTATCATATTT
1 TAATAAATAATTTTATCATATTT
2108381 TAATATAATAATTATTAT-ATAT
1 TAATA-AATAATT-TTATCATAT
2108403 AATAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAAATAATTTTATCATATTT
Found at i:2108413 original size:19 final size:19
Alignment explanation
Indices: 2108381--2108432 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2108371 TATCATATTT
2108381 TAAT-ATAATAATTAT-TA
1 TAATAATAATAATTATATA
*
2108398 TATATAATAATTATTATATA
1 TA-ATAATAATAATTATATA
2108418 TAATAATATATAATT
1 TAATAATA-ATAATT
2108433 TAATAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 16 0.55
20 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATAATAATAATTATATA
Found at i:2108488 original size:64 final size:62
Alignment explanation
Indices: 2108316--2108495 Score: 190
Period size: 64 Copynumber: 2.9 Consensus size: 62
2108306 TATTGTTATT
** * *
2108316 AAATTTTAATAGGATTATTATT-AAATATAATTTAATAATAAATAAT-A-A-ATAATTTTATC
1 AAATTTTAATATAATTATTATTAAAATATAA-TTAATAATAAATAATAATATATAATTTAATA
* * * * *
2108375 ATATTTTAATATAATAATTATTATATATAATAATT-ATTATATATAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTA-AAAT-ATAATTAATAATAAATAATAATATATAATTTAATA
*
2108438 AAATTCTTAATATAATTATTATTAAAATATGAATTAATAAAAAATAATAATATATAAT
1 AAATT-TTAATATAATTATTATTAAAATAT-AATTAATAATAAATAATAATATATAAT
2108496 ATTAGAAAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
59 18 0.19
60 10 0.10
61 6 0.06
62 7 0.07
63 20 0.21
64 36 0.37
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (62 bp):
AAATTTTAATATAATTATTATTAAAATATAATTAATAATAAATAATAATATATAATTTAATA
Found at i:2120579 original size:28 final size:27
Alignment explanation
Indices: 2120531--2120609 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
2120521 ATTTATTCTT
* *
2120531 TTTAAACG-GTTTTGTATATTATTTAG
1 TTTAAACGTTTTTTATATATTATTTAG
* * *
2120557 TTTAGACTTCTTTTTATATATTATTTAT
1 TTTAAACGT-TTTTTATATATTATTTAG
*
2120585 TTTAAACGTTTTTCATATATTATTT
1 TTTAAACGTTTTTTATATATTATTT
2120610 TAAGTTGTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 6 0.14
27 15 0.35
28 22 0.51
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (27 bp):
TTTAAACGTTTTTTATATATTATTTAG
Found at i:2120653 original size:26 final size:26
Alignment explanation
Indices: 2120530--2120730 Score: 130
Period size: 26 Copynumber: 7.9 Consensus size: 26
2120520 CATTTATTCT
** *
2120530 TTTTAAACGGTTTTGTATATTATTTA
1 TTTTAAATTGTTTTATATATTATTTA
* * *
2120556 GTTTAGACTTCTTTTTATATATTATTTA
1 TTTTA-AATT-GTTTTATATATTATTTA
*
2120584 TTTTAAA-CGTTTT-TCATA-TA-TTA
1 TTTTAAATTGTTTTAT-ATATTATTTA
* * * *
2120607 TTTTAAGTTGTCTTATGTATTATTTG
1 TTTTAAATTGTTTTATATATTATTTA
* *
2120633 TTTTAAATTGCTTTGTATATTATTCT-
1 TTTTAAATTGTTTTATATATTATT-TA
* *
2120659 TCTT-AATTGTTTTACATATTATTTA
1 TTTTAAATTGTTTTATATATTATTTA
* *
2120684 TCTTAAATTG-TTT-TATACTATTTA
1 TTTTAAATTGTTTTATATATTATTTA
* * *
2120708 CTTCAAACTGTTTTATATATTAT
1 TTTTAAATTGTTTTATATATTAT
2120731 GTTGTTTTGC
Statistics
Matches: 132, Mismatches: 31, Indels: 24
0.71 0.17 0.13
Matches are distributed among these distances:
23 9 0.07
24 25 0.19
25 36 0.27
26 40 0.30
27 3 0.02
28 19 0.14
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (26 bp):
TTTTAAATTGTTTTATATATTATTTA
Found at i:2120719 original size:24 final size:23
Alignment explanation
Indices: 2120678--2120728 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2120668 TTTTACATAT
*
2120678 TATTTATCTTAAATTGTTTTATA
1 TATTTATCTTAAACTGTTTTATA
2120701 CTATTTA-CTTCAAACTGTTTTATA
1 -TATTTATCTT-AAACTGTTTTATA
2120725 TATT
1 TATT
2120729 ATGTTGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTTATCTTAAACTGTTTTATA
Done.