Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 9 of 279
Found at i:2744071 original size:7 final size:7
Alignment explanation
Indices: 2744061--2744128 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
2744051 CTTAAATACA
2744061 AAATCCT
1 AAATCCT
2744068 AAATCCT
1 AAATCCT
*
2744075 AAATCAT
1 AAATCCT
*
2744082 AAATCAT
1 AAATCCT
*
2744089 AAAACTCT
1 AAATC-CT
2744097 AAA-CCTT
1 AAATCC-T
2744104 AAA-CCTT
1 AAATCC-T
*
2744111 AAACCCT
1 AAATCCT
2744118 AAATCCT
1 AAATCCT
2744125 AAAT
1 AAAT
2744129 AATAAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
6 1 0.02
7 47 0.87
8 6 0.11
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATCCT
Found at i:2744085 original size:21 final size:21
Alignment explanation
Indices: 2744053--2744142 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 21
2744043 CTTAAGCACT
*
2744053 TAAATACA-AAATCCTAAATCC
1 TAAAT-CATAAATCCTAAAACC
*
2744074 TAAATCATAAATCATAAAACTC
1 TAAATCATAAATCCTAAAAC-C
* * *
2744096 TAAACCTTAAA-CCTTAAACCC
1 TAAATCATAAATCC-TAAAACC
* **
2744117 TAAATCCTAAATAATAAAACAC
1 TAAATCATAAATCCTAAAAC-C
2744139 TAAA
1 TAAA
2744143 CTATAGACAC
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.04
21 31 0.58
22 20 0.38
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAATCATAAATCCTAAAACC
Found at i:2748753 original size:23 final size:23
Alignment explanation
Indices: 2748723--2748916 Score: 189
Period size: 23 Copynumber: 8.5 Consensus size: 23
2748713 TGGTTGCTGC
*
2748723 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
*
2748746 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
* *
2748769 TGTTTAAATATTGCAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
** * *
2748792 TGTTTAGTTGCTGAAAATTG-AG
1 TGTTTAAATGTTGTAAATTGAAG
* * *
2748814 ATGTTTTATTGTTGT-AATTGAGG
1 -TGTTTAAATGTTGTAAATTGAAG
* *
2748837 TGTATAAATGTTGTTAATTG-AG
1 TGTTTAAATGTTGTAAATTGAAG
* *
2748859 ATG-CTAAAGTGTTGTAAATTGAAA
1 -TGTTTAAA-TGTTGTAAATTGAAG
2748883 TGTTTAAATGTTGTAAATTGAAG
1 TGTTTAAATGTTGTAAATTGAAG
*
2748906 TGCTTAAATGT
1 TGTTTAAATGT
2748917 AGCACCCCAA
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
22 23 0.16
23 113 0.80
24 5 0.04
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (23 bp):
TGTTTAAATGTTGTAAATTGAAG
Found at i:2751599 original size:26 final size:26
Alignment explanation
Indices: 2751568--2751675 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2751558 TGAAATTCCC
*
2751568 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2751594 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2751620 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2751646 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2751672 ATCA
1 ATCA
2751676 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2752033 original size:23 final size:23
Alignment explanation
Indices: 2752007--2752723 Score: 407
Period size: 23 Copynumber: 31.3 Consensus size: 23
2751997 CATTAAATGT
*
2752007 TGTAAATTGAAGTGTTTAAGTAC
1 TGTAAATTGAAGTGTTTAAGTGC
2752030 TGTAAATTGAAGTGTTT-AGTTGC
1 TGTAAATTGAAGTGTTTAAG-TGC
* * *
2752053 TGGAAATTG-AGATGTTTTA-TCGT
1 TGTAAATTGAAG-TGTTTAAGT-GC
* * * *
2752076 TGT-AATTGAGGTGTATAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
* * *
2752098 TGTTAATTG-AGATGTTAAAGTAC
1 TGTAAATTGAAG-TGTTTAAGTGC
* * *
2752121 AGCAAATTGAAGTGTTTAAATGC
1 TGTAAATTGAAGTGTTTAAGTGC
*
2752144 TGTAAATTGAAGTGTTAAAGTGC
1 TGTAAATTGAAGTGTTTAAGTGC
* * *
2752167 TGCAAATTGGAA-TGTTAAAATGC
1 TGTAAATT-GAAGTGTTTAAGTGC
* *
2752190 TGCAAATTGAAGTG-TTAAATGC
1 TGTAAATTGAAGTGTTTAAGTGC
* *
2752212 TGTAAATTGAAGTGTTTAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
* * * *
2752235 TATAAATTGAAGTGCTTAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
*
2752258 TGTAAATTGAAGTGTTTTAAGTAC
1 TGTAAATTGAAGTG-TTTAAGTGC
** *
2752282 TACAAATTGAAGGGTTT-AGTTG-
1 TGTAAATTGAAGTGTTTAAG-TGC
* * *
2752304 TTTGGAATTG-AGATGTTTTA-TCGC
1 TGT-AAATTGAAG-TGTTTAAGT-GC
* * * *
2752328 TGT-AATTGAGGTGTATAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
* *
2752350 TGTTAATTG-AGATGTTAAAGTGC
1 TGTAAATTGAAG-TGTTTAAGTGC
** * * *
2752373 TACAAATTAAAGTGTTTAAATCC
1 TGTAAATTGAAGTGTTTAAGTGC
*
2752396 TGTAAATTGAAGTGTTAAAGTGC
1 TGTAAATTGAAGTGTTTAAGTGC
** *
2752419 TACAAATTGAAGTGTTTGAA-TGT
1 TGTAAATTGAAGTGTTT-AAGTGC
* *
2752442 TGTAAATTGAAGTGTTTAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
* * * *
2752465 TATAAATTGAAGTGCTTAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
*
2752488 TGTAAATTGAAGTGTTTAAGTAC
1 TGTAAATTGAAGTGTTTAAGTGC
** *
2752511 TACAAATTGAAGTGTTT-AGTTGA
1 TGTAAATTGAAGTGTTTAAG-TGC
* *
2752534 TGGAAATTG-AGATGTTTTA-TCGC
1 TGTAAATTGAAG-TGTTTAAGT-GC
* * * *
2752557 TGT-AATTGAGGAGTTTAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
* *
2752579 TGTTAATTG-AGATGTTAAAGTGC
1 TGTAAATTGAAG-TGTTTAAGTGC
* * *
2752602 TGCAAATTGAAGTGTTAAAGTGT
1 TGTAAATTGAAGTGTTTAAGTGC
*
2752625 TGCAAATTGAAGTG-TTAATGTGC
1 TGTAAATTGAAGTGTTTAA-GTGC
* * * *
2752648 TGCAAATTGGAGTGTTTAAATGT
1 TGTAAATTGAAGTGTTTAAGTGC
* * *
2752671 TGTAAATTAAAGTTTTTAAGTAC
1 TGTAAATTGAAGTGTTTAAGTGC
* *
2752694 TGCAAATTGAATTGTTT-AGTTGC
1 TGTAAATTGAAGTGTTTAAG-TGC
2752717 TG-AAATT
1 TGTAAATT
2752724 TAGTTTATGT
Statistics
Matches: 540, Mismatches: 116, Indels: 77
0.74 0.16 0.11
Matches are distributed among these distances:
22 97 0.18
23 407 0.75
24 36 0.07
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (23 bp):
TGTAAATTGAAGTGTTTAAGTGC
Found at i:2752085 original size:22 final size:22
Alignment explanation
Indices: 2752057--2752116 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2752047 AGTTGCTGGA
**
2752057 AATTGAGATGTTTTATCGTTG-T
1 AATTGAGATGTTAAAT-GTTGTT
*
2752079 AATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGT-TAAATGTTGTT
2752102 AATTGAGATGTTAAA
1 AATTGAGATGTTAAA
2752117 GTACAGCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (22 bp):
AATTGAGATGTTAAATGTTGTT
Found at i:2752210 original size:114 final size:114
Alignment explanation
Indices: 2752010--2752689 Score: 298
Period size: 114 Copynumber: 5.9 Consensus size: 114
2752000 TAAATGTTGT
* * * * **
2752010 AAATTGAAGTGTTTAAGTACTGTAAATTGAAGTGTTTAGTTGCTGGAAATTGAGATGTTTTATCG
1 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAGTTGCTGCAAATTGAGATGTTAAATCG
* * * * *
2752075 TTGTAATTGAGGTGTATAAATGTTGTTAATTG-AGATG-TTAAA-GTACAGC
66 CTGAAATTGAAGTGTATAAATGCTGTAAATTGAAG-TGTTTAAATGT-CA-C
2752124 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAG-TGCTGCAAATTG-GAATGTTAAAA
1 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTT-AAGTTGCTGCAAATTGAG-ATGTT-AAA
* *
2752187 T-GCTGCAAATTGAAGTGT-TAAATGCTGTAAATTGAAGTGTTTAAATGTTAT
63 TCGCTG-AAATTGAAGTGTATAAATGCTGTAAATTGAAGTGTTTAAATGTCAC
* * * * * * *
2752238 AAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTTTAAG-TACTACAAATTGA-AGGGTTTAG
1 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTG--TTAAGTTGCTGCAAATTGAGA-TGTTAAA
* * * ** * * ***
2752301 TTGTTTGGAATTG-AGATGT-TTTATCGCTGT-AATTGAGGTGTATAAATGTTGT
63 TCG-CTGAAATTGAAG-TGTATAAAT-GCTGTAAATTGAAGTGTTTAAATGTCAC
* ** * * * *
2752353 TAATTG-AGATG-TTAAAGTGCTACAAATTAAAGTGTTTAA-ATCCTGTAAATTGA-AGTGTTAA
1 AAATTGAAG-TGTTTAAA-TGCTGTAAATTGAAGTG-TTAAGTTGCTGCAAATTGAGA-TGTTAA
* * * * * *
2752414 AGT-GCTACAAATTGAAGTGTTTGAATGTTGTAAATTGAAGTGTTTAAATGTTAT
62 A-TCGCT-GAAATTGAAGTGTATAAATGCTGTAAATTGAAGTGTTTAAATGTCAC
* * * * * *
2752468 AAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTTAAG-TACTACAAATTGA-AGTGTTTAGT
1 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAGTTGCTGCAAATTGAGA-TGTTAAAT
* * ** * * ***
2752531 TGATGGAAATTG-AGATGT-TTTATCGCTGT-AATTGAGGAGTTTAAATGTTGT
64 CGCT-GAAATTGAAG-TGTATAAAT-GCTGTAAATTGAAGTGTTTAAATGTCAC
* * *
2752582 TAATTG-AGATG-TTAAAGTGCTGCAAATTGAAGTGTTAAAG-TGTTGCAAATTGA-AGTGTT-A
1 AAATTGAAG-TGTTTAAA-TGCTGTAAATTGAAGTGTT-AAGTTGCTGCAAATTGAGA-TGTTAA
* * * * * *
2752642 ATGTGCTGCAAATTGGAGTGTTTAAATGTTGTAAATTAAAGTTTTTAA
62 AT-CGCTG-AAATTGAAGTGTATAAATGCTGTAAATTGAAGTGTTTAA
2752690 GTACTGCAAA
Statistics
Matches: 448, Mismatches: 81, Indels: 73
0.74 0.13 0.12
Matches are distributed among these distances:
113 14 0.03
114 229 0.51
115 187 0.42
116 18 0.04
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (114 bp):
AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAGTTGCTGCAAATTGAGATGTTAAATCG
CTGAAATTGAAGTGTATAAATGCTGTAAATTGAAGTGTTTAAATGTCAC
Found at i:2752473 original size:138 final size:137
Alignment explanation
Indices: 2752010--2752711 Score: 476
Period size: 137 Copynumber: 5.1 Consensus size: 137
2752000 TAAATGTTGT
** * **
2752010 AAATTGAAGTGTTTAA-GTACTGTAAATTGAAGTGTTTAGTTGCTGGAAATTG-AGATGTTTTAT
1 AAATTGAAGTGTTTAATGT--TGTAAATTGAAGTGTTTAAATGCTGTAAATTGAAG-TGTTAAAT
* * *** * * *
2752073 CGTTGT-AATTGAGGTGTATAAA-TGTTGTTAATTG-AGATG-TTAAAGTACAGCAAATTGAAGT
63 -GTTGTAAATTGAAGTGT-TAAAGTGCTACAAATTGAAG-TGTTTAAA-TCCTGTAAATTGAAGT
**
2752134 GTTTAAA-TGCTGT
124 GTTTAAAGTGCTAC
* * * * *
2752147 AAATTGAAGTGTTAAAGTGCTGCAAATTGGAA-TGTTAAAATGCTGCAAATTGAAGTGTTAAATG
1 AAATTGAAGTGTTTAA-TGTTGTAAATT-GAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAATG
* * * * **
2752211 CTGTAAATTGAAGTGTTTAAA-TGTTATAAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTT
64 TTGTAAATTGAAGTG-TTAAAGTGCTACAAATTGAAGTGTTTAAATCCTGTAAATTGAAGTGTTT
* *
2752275 TAAGTACTAC
128 AAAGTGCTAC
* * * * *
2752285 AAATTGAAGGGTTTAGTTGTT-TGGAATTG-AGATGTTT-TATCGCTGT-AATTGAGGTGTATAA
1 AAATTGAAGTGTTTA-ATGTTGT-AAATTGAAG-TGTTTAAAT-GCTGTAAATTGAAGTGT-TAA
* *
2752346 ATGTTGTTAATTG-AGATGTTAAAGTGCTACAAATTAAAGTGTTTAAATCCTGTAAATTGAAGTG
61 ATGTTGTAAATTGAAG-TGTTAAAGTGCTACAAATTGAAGTGTTTAAATCCTGTAAATTGAAGTG
2752410 -TTAAAGTGCTAC
125 TTTAAAGTGCTAC
* *
2752422 AAATTGAAGTGTTTGAATGTTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATG
1 AAATTGAAGTGTTT-AATGTTGTAAATTGAAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAATG
* * ** ** *
2752487 TTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTTGATGGAAATTG-AGATGTTT
64 TTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATCCTGTAAATTGAAG-TGTTT
* *
2752551 -TA-TCGCT-G
128 AAAGT-GCTAC
* * * * *
2752559 TAATTGAGGAGTTTAAATGTTGTTAATTG-AGATG-TTAAAGTGCTGCAAATTGAAGTGTTAAAG
1 AAATTGAAGTGTTT-AATGTTGTAAATTGAAG-TGTTTAAA-TGCTGTAAATTGAAGTGTTAAA-
* * * * ** *
2752622 TGTTGCAAATTGAAGTGTTAATGTGCTGCAAATTGGAGTGTTTAAATGTTGTAAATTAAAGT-TT
62 TGTTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATCCTGTAAATTGAAGTGTT
* * *
2752686 TTAAGTACTGC
127 TAAAGTGCTAC
*
2752697 AAATTGAATTGTTTA
1 AAATTGAAGTGTTTA
2752712 GTTGCTGAAA
Statistics
Matches: 446, Mismatches: 85, Indels: 68
0.74 0.14 0.11
Matches are distributed among these distances:
136 20 0.04
137 242 0.54
138 178 0.40
139 6 0.01
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (137 bp):
AAATTGAAGTGTTTAATGTTGTAAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAATGTT
GTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATCCTGTAAATTGAAGTGTTTAAA
GTGCTAC
Found at i:2752543 original size:252 final size:251
Alignment explanation
Indices: 2752010--2752528 Score: 765
Period size: 252 Copynumber: 2.1 Consensus size: 251
2752000 TAAATGTTGT
* *
2752010 AAATTGAAGTGTTTAAGTACTGTAAATTGAAGTGTTTAGTTGCTGGAAATTGAGATGTTTTATCG
1 AAATTGAAGTGTTTAAGTACTGCAAATTGAAGGGTTTAGTTGCTGGAAATTGAGATGTTTTATCG
* *
2752075 TTGTAATTGAGGTGTATAAATGTTGTTAATTGAGATGTTAAAGTACAGCAAATTGAAGTGTTTAA
66 CTGTAATTGAGGTGTATAAATGTTGTTAATTGAGATGTTAAAGTACAGCAAATTAAAGTGTTTAA
* *
2752140 ATGCTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGGAATGTTAAAATGCTGCAAATTGAAGTGT
131 ATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTGGAATGTTAAAATGCTGCAAATTGAAGTGT
* * ** **
2752205 TAAATGCTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGT
196 TAAATGCTATAAATTGAAGTGCTTAAATGTTATAAATTGAAGTGCTTAAATACTAC
* *
2752261 AAATTGAAGTGTTTTAAGTACTACAAATTGAAGGGTTTAGTTGTTTGG-AATTGAGATGTTTTAT
1 AAATTGAAGTG-TTTAAGTACTGCAAATTGAAGGGTTTAGTTG-CTGGAAATTGAGATGTTTTAT
*
2752325 CGCTGTAATTGAGGTGTATAAATGTTGTTAATTGAGATGTTAAAGTGCTA-CAAATTAAAGTGTT
64 CGCTGTAATTGAGGTGTATAAATGTTGTTAATTGAGATGTTAAAGTAC-AGCAAATTAAAGTGTT
** * *
2752389 TAAATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATT-GAAGTGTTTGAATGTTGTAAATTGAA
128 TAAATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTGGAA-TGTTAAAATGCTGCAAATTGAA
* * * *
2752453 GTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTTAAGTACTAC
192 GTG-TTAAATGCTATAAATTGAAGTGCTTAAATGTTATAAATTGAAGTGCTTAAATACTAC
2752514 AAATTGAAGTGTTTA
1 AAATTGAAGTGTTTA
2752529 GTTGATGGAA
Statistics
Matches: 240, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
251 14 0.06
252 164 0.68
253 62 0.26
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (251 bp):
AAATTGAAGTGTTTAAGTACTGCAAATTGAAGGGTTTAGTTGCTGGAAATTGAGATGTTTTATCG
CTGTAATTGAGGTGTATAAATGTTGTTAATTGAGATGTTAAAGTACAGCAAATTAAAGTGTTTAA
ATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTGGAATGTTAAAATGCTGCAAATTGAAGTGT
TAAATGCTATAAATTGAAGTGCTTAAATGTTATAAATTGAAGTGCTTAAATACTAC
Found at i:2752616 original size:183 final size:181
Alignment explanation
Indices: 2752386--2752723 Score: 466
Period size: 183 Copynumber: 1.9 Consensus size: 181
2752376 AAATTAAAGT
* *
2752386 GTTTAAATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTGAA-TGTTGTAAATT
1 GTTTAAATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTG-TTAAAGTGTTGCAAATT
* *
2752450 GAAGTGTTTAAATGT-TATAAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTTAAGTACTAC
65 GAAGTG-TT-AATGTCTACAAATTGAAGTGCTTAAATGTTGTAAATTAAAGTGTTTAAGTACTAC
2752514 AAATTGAAGTGTTTAGTTGATGGAAATTGAGATGTTTTATCGCTGTAATTGAGGA
128 AAATTGAAGTGTTTAGTTGAT-GAAATTGAGATGTTTTATCGCTGTAATTGAGGA
** * *
2752569 GTTTAAATGTTGTTAATTG-AGATGTTAAAGTGCTGCAAATTGAAGTGTTAAAGTGTTGCAAATT
1 GTTTAAATCCTGTAAATTGAAG-TGTTAAAGTGCTACAAATTGAAGTGTTAAAGTGTTGCAAATT
* * * * *
2752633 GAAGTGTTAATGTGCTGCAAATTGGAGTGTTTAAATGTTGTAAATTAAAGTTTTTAAGTACTGCA
65 GAAGTGTTAATGT-CTACAAATTGAAGTGCTTAAATGTTGTAAATTAAAGTGTTTAAGTACTACA
* *
2752698 AATTGAATTGTTTAGTTGCTGAAATT
129 AATTGAAGTGTTTAGTTGATGAAATT
2752724 TAGTTTATGT
Statistics
Matches: 136, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
181 5 0.04
182 14 0.10
183 117 0.86
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.39
Consensus pattern (181 bp):
GTTTAAATCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTAAAGTGTTGCAAATTG
AAGTGTTAATGTCTACAAATTGAAGTGCTTAAATGTTGTAAATTAAAGTGTTTAAGTACTACAAA
TTGAAGTGTTTAGTTGATGAAATTGAGATGTTTTATCGCTGTAATTGAGGA
Found at i:2752704 original size:229 final size:230
Alignment explanation
Indices: 2752136--2752689 Score: 877
Period size: 229 Copynumber: 2.4 Consensus size: 230
2752126 ATTGAAGTGT
* *
2752136 TTAAA-TGCTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGGAA-TGTTAAAATGCTGCAAATTG
1 TTAAAGTGCTGCAAATTGAAGTGTTAAAGTGCTGCAAATT-GAAGTGTTAAAGTGCTGCAAATTG
*
2752199 AAGTG-TTAAATGCTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGTAA
65 AAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGTAA
*
2752263 ATTGAAGTGTTTTAAGTACTACAAATTGAAGGGTTTAGTTGTTTGGAATTGAGATGTTTTATCGC
130 ATTGAAGTGTTTTAAGTACTACAAATTGAAGGGTTTAGTTGTATGGAATTGAGATGTTTTATCGC
*
2752328 TGTAATTGAGGTGTATAAATGTTGTTAATTGAGATG
195 TGTAATTGAGGAGTATAAATGTTGTTAATTGAGATG
* * * * *
2752364 TTAAAGTGCTACAAATTAAAGTGTTTAAA-TCCTGTAAATTGAAGTGTTAAAGTGCTACAAATTG
1 TTAAAGTGCTGCAAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTAAAGTGCTGCAAATTG
*
2752428 AAGTGTTTGAATGTTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGTAA
65 AAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGTAA
*
2752493 ATTGAAGTG-TTTAAGTACTACAAATTGAAGTGTTTAGTTG-ATGGAAATTGAGATGTTTTATCG
130 ATTGAAGTGTTTTAAGTACTACAAATTGAAGGGTTTAGTTGTATGG-AATTGAGATGTTTTATCG
*
2752556 CTGTAATTGAGGAGTTTAAATGTTGTTAATTGAGATG
194 CTGTAATTGAGGAGTATAAATGTTGTTAATTGAGATG
* * *
2752593 TTAAAGTGCTGCAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTAATGTGCTGCAAATTGG
1 TTAAAGTGCTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGA
* *
2752658 AGTGTTTAAATGTTGTAAATTAAAGTTTTTAA
66 AGTGTTTAAATGTTGTAAATTGAAGTGTTTAA
2752690 GTACTGCAAA
Statistics
Matches: 296, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
228 16 0.05
229 209 0.71
230 71 0.24
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (230 bp):
TTAAAGTGCTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGA
AGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTATAAATTGAAGTGCTTAAATGTTGTAAA
TTGAAGTGTTTTAAGTACTACAAATTGAAGGGTTTAGTTGTATGGAATTGAGATGTTTTATCGCT
GTAATTGAGGAGTATAAATGTTGTTAATTGAGATG
Found at i:2753480 original size:43 final size:43
Alignment explanation
Indices: 2753395--2753544 Score: 212
Period size: 43 Copynumber: 3.5 Consensus size: 43
2753385 AGGTTCTTTA
* * *
2753395 GTCATGTTTTTTAGCGGCGTTT-TTGGGAAAGTGCCGCTAAAG
1 GTCATGTTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAG
*
2753437 GTCATGTTCTTTAGCGGCGTTTGTGGGGAAAGCGCTGCTAAAG
1 GTCATGTTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAG
* * *
2753480 GTCATGTTCTTTAGCGACGTTTGTGGGGAAAGCGCCACTAAAA
1 GTCATGTTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAG
* *
2753523 GTCATGTTCTATAGAGGCGTTT
1 GTCATGTTCTTTAGCGGCGTTT
2753545 TTTCACATAA
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 21 0.22
43 75 0.78
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.33
Consensus pattern (43 bp):
GTCATGTTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAG
Found at i:2758883 original size:17 final size:18
Alignment explanation
Indices: 2758863--2758896 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2758853 AAGTGAATTG
2758863 AAATTGCA-AAATTAAAT
1 AAATTGCAGAAATTAAAT
2758880 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
2758897 ATGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:2759645 original size:20 final size:20
Alignment explanation
Indices: 2759622--2759661 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2759612 TGAAATTGTA
2759622 AAAGATAAAT-ACAAATAAAT
1 AAAGATAAATGA-AAATAAAT
2759642 AAAGATAAATGAAAATAAAT
1 AAAGATAAATGAAAATAAAT
2759662 CCTAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAGATAAATGAAAATAAAT
Found at i:2763753 original size:74 final size:74
Alignment explanation
Indices: 2763632--2763779 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
2763622 AATATTTTTA
2763632 TAAATATTTATGGAGTGTTAGTAAGTTACTATTAAAGTTTCATTAAGAAATTTTAAGGTTTCGGT
1 TAAATATTTATGGAGTGTTAGTAAGTTACTATTAAAGTTTCATTAAGAAATTTTAAGGTTTCGGT
2763697 AGTCAATTG
66 AGTCAATTG
* *
2763706 TAAATATTTATGGAGTGTTAGTAAGTTAGTATTAAAGTTTCGTTAAGAAATTTTAAGGTTTCGGT
1 TAAATATTTATGGAGTGTTAGTAAGTTACTATTAAAGTTTCATTAAGAAATTTTAAGGTTTCGGT
2763771 AGTCAATTG
66 AGTCAATTG
2763780 GGTAAAAAGG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (74 bp):
TAAATATTTATGGAGTGTTAGTAAGTTACTATTAAAGTTTCATTAAGAAATTTTAAGGTTTCGGT
AGTCAATTG
Found at i:2764975 original size:53 final size:51
Alignment explanation
Indices: 2764829--2764984 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 51
2764819 GACGGAAAAG
* * * * *
2764829 ATGTGATATATGCTTCTGTATAAGACCATAGCTGGGCTATGGAATTGGTACA
1 ATGTGATAT-TGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
*
2764881 ATGTGAT-TCGAGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATATTGA-TT-CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
2764933 ATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCTGTAT
1 ATGTGAT-AT-TGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT
2764985 GTTATGTGAT
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
50 1 0.01
51 3 0.03
52 47 0.53
53 33 0.37
54 3 0.03
55 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (51 bp):
ATGTGATATTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:2769002 original size:24 final size:23
Alignment explanation
Indices: 2768975--2769112 Score: 82
Period size: 26 Copynumber: 5.6 Consensus size: 23
2768965 TTATCATTTC
2768975 AGCTCTTTCGAGCT-ATAATCAGTA
1 AGCTCTTT-GAGCTGATAA-CAGTA
*
2768999 AGCTCCTCTTGAGCTGATGGACAGTA
1 AGCT-CT-TTGAGCTGAT-AACAGTA
*
2769025 AGCTCTATTAAGCTGA-AACAGTA
1 AGCTCT-TTGAGCTGATAACAGTA
** * *
2769048 AGCTCTGACGAGCTAAAAACAGTA
1 AGCTCT-TTGAGCTGATAACAGTA
* *
2769072 AGCTCTTAGGAGCTGATATATCGGTA
1 AGCTCTT-TGAGCTGATA-A-CAGTA
*
2769098 AGCTCATATGAGCTG
1 AGCTC-TTTGAGCTG
2769113 TGGTGAGTCC
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
23 17 0.19
24 24 0.27
25 18 0.20
26 28 0.31
27 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (23 bp):
AGCTCTTTGAGCTGATAACAGTA
Found at i:2776128 original size:23 final size:23
Alignment explanation
Indices: 2776102--2776149 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2776092 AACATATATA
2776102 ATAAATAAATTTAAAATGA-TTAT
1 ATAAATAAATTTAAAAT-ATTTAT
*
2776125 AT-AATTAATTTAAAATATTTAT
1 ATAAATAAATTTAAAATATTTAT
2776147 ATA
1 ATA
2776150 TATTATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.05
22 19 0.86
23 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAATAAATTTAAAATATTTAT
Found at i:2776137 original size:22 final size:23
Alignment explanation
Indices: 2776109--2776154 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
2776099 ATAATAAATA
2776109 AATTTAAAATGA-TTATATA-ATT
1 AATTTAAAAT-ATTTATATATATT
2776131 AATTTAAAATATTTATATATATT
1 AATTTAAAATATTTATATATATT
2776154 A
1 A
2776155 TGATACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTTAAAATATTTATATATATT
Found at i:2776633 original size:19 final size:19
Alignment explanation
Indices: 2776611--2776672 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2776601 TATAATTACC
2776611 ATTTACTACTAAAATTAAT
1 ATTTACTACTAAAATTAAT
* * **
2776630 ATTT-CTCTCTCATAATTACC
1 ATTTACT-ACT-AAAATTAAT
*
2776650 ATTTACTATTAAAATTAAT
1 ATTTACTACTAAAATTAAT
2776669 ATTT
1 ATTT
2776673 CTCTCTCACA
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 2 0.06
19 16 0.52
20 11 0.35
21 2 0.06
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTACTACTAAAATTAAT
Found at i:2776645 original size:39 final size:39
Alignment explanation
Indices: 2776602--2776680 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
2776592 TTAGTAGGAT
2776602 ATAATTACCATTTACTACTAAAATTAATATTTCTCTCTC
1 ATAATTACCATTTACTACTAAAATTAATATTTCTCTCTC
*
2776641 ATAATTACCATTTACTATTAAAATTAATATTTCTCTCTC
1 ATAATTACCATTTACTACTAAAATTAATATTTCTCTCTC
2776680 A
1 A
2776681 CAAAATTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (39 bp):
ATAATTACCATTTACTACTAAAATTAATATTTCTCTCTC
Found at i:2779473 original size:47 final size:44
Alignment explanation
Indices: 2779400--2779757 Score: 245
Period size: 47 Copynumber: 7.7 Consensus size: 44
2779390 TGATTTGTGC
* * *
2779400 GCCAGTGTAAGACATGTCTGGAACATGCTTCGGCCACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GA-GAGA
* *
2779446 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-GTCATAGAGATGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAGAGA-GA
* * *
2779492 GTGCCAGAGTAAAACATGTCTGGGACATGCATCGGCCTCTACAGAGATA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGG-C-C-ACAGAGAGA
* * * * * *
2779541 GCTAGTGTAAGATATGTCTGGGACACGCATCGGCTA-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGAG-AGA
* * * *
2779585 GCTAGAGTAAGACATGTCTGGGACATGCATCGGCCTTAATAGAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC---ACAGAGAGA
* * * * *
2779632 GCCAGTGTAAGACGTGTCTGGGACATGCATTGGCTA-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGAG-AGA
* * * *
2779676 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATGCATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC---CACAGA-GAGA
* *
2779724 GCCAGTGTAAGTCCATGTCTGAGACATGGCATCG
1 GCCAGTGTAAG-ACATGTCTGGGACAT-GCATCG
2779758 ACAATTTATC
Statistics
Matches: 244, Mismatches: 46, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
43 8 0.03
44 63 0.26
45 2 0.01
46 21 0.09
47 92 0.38
48 31 0.13
49 16 0.07
50 11 0.05
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (44 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGAGAGA
Found at i:2779604 original size:44 final size:45
Alignment explanation
Indices: 2779449--2779706 Score: 247
Period size: 47 Copynumber: 5.6 Consensus size: 45
2779439 TATGAGAGCC
* * *
2779449 AGTGTAAGACCATGTCTGGGACATGGCATCGTC-ATAGAGATGAGTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTATAGAG-T-TGTGCT
* * * * *
2779497 AGAGTAAAACATGTCTGGGACATGCATCGGCCTCTACAGAGAT-AGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGG---CTATAGAGTTGTGCT
* *
2779544 AGTGTAAGATATGTCTGGGACACGCATCGGCTA-AGAGTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTATAGAGTTGTGCT
* * * *
2779588 AGAGTAAGACATGTCTGGGACATGCATCGGCCTTAATAGAGAT-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-C-T-ATAGAGTTGTGCT
* *
2779635 AGTGTAAGACGTGTCTGGGACATGCATTGGCTA-AGAGTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTATAGAGTTGTGCT
2779679 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
2779707 AGCATGCATA
Statistics
Matches: 172, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
43 10 0.06
44 62 0.36
45 2 0.01
46 8 0.05
47 72 0.42
48 12 0.07
49 1 0.01
50 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTATAGAGTTGTGCT
Found at i:2779612 original size:91 final size:91
Alignment explanation
Indices: 2779406--2779706 Score: 351
Period size: 91 Copynumber: 3.3 Consensus size: 91
2779396 GTGCGCCAGT
* * * *
2779406 GTAAGACATGTCTGGAACATGCTTCGG-C-C-ACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 GTAAGACATGTCTGGGACATGCATCGGCCTCTACA-GA-GATAGCCAGTGTAAGA-CATGTCTGG
* * * *
2779468 GACATGGCATCGTC-ATAGAGATGAGTGCCAGA
63 GACA-CGCATCGGCTA-AGAG-T-TGTGCTAGA
* * *
2779500 GTAAAACATGTCTGGGACATGCATCGGCCTCTACAGAGATAGCTAGTGTAAGATATGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCTCTACAGAGATAGCCAGTGTAAGACATGTCTGGGAC
2779565 ACGCATCGGCTAAGAGTTGTGCTAGA
66 ACGCATCGGCTAAGAGTTGTGCTAGA
* *
2779591 GTAAGACATGTCTGGGACATGCATCGGCCT-TAATAGAGATAGCCAGTGTAAGACGTGTCTGGGA
1 GTAAGACATGTCTGGGACATGCATCGGCCTCT-ACAGAGATAGCCAGTGTAAGACATGTCTGGGA
* * *
2779655 CATGCATTGGCTAAGAGTTGTGCTAGT
65 CACGCATCGGCTAAGAGTTGTGCTAGA
2779682 GTAAGACATGTCTGGGACATGCATC
1 GTAAGACATGTCTGGGACATGCATC
2779707 AGCATGCATA
Statistics
Matches: 183, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
90 1 0.01
91 113 0.62
92 1 0.01
93 11 0.06
94 37 0.20
95 15 0.08
96 2 0.01
97 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (91 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCTACAGAGATAGCCAGTGTAAGACATGTCTGGGAC
ACGCATCGGCTAAGAGTTGTGCTAGA
Found at i:2780982 original size:19 final size:19
Alignment explanation
Indices: 2780958--2780995 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2780948 GAGTTTAAGT
2780958 CAGGTAGCACCATGAACCC
1 CAGGTAGCACCATGAACCC
2780977 CAGGTAGCACCATGAACCC
1 CAGGTAGCACCATGAACCC
2780996 TATCCTAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CAGGTAGCACCATGAACCC
Found at i:2785765 original size:19 final size:19
Alignment explanation
Indices: 2785741--2785778 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2785731 GAGTTTAAGT
2785741 CAGGTAGCACCATGAACCC
1 CAGGTAGCACCATGAACCC
2785760 CAGGTAGCACCATGAACCC
1 CAGGTAGCACCATGAACCC
2785779 TATCCTAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CAGGTAGCACCATGAACCC
Found at i:2791987 original size:47 final size:47
Alignment explanation
Indices: 2791836--2792102 Score: 192
Period size: 47 Copynumber: 5.7 Consensus size: 47
2791826 TAATTTGTGC
* * *
2791836 GCCAGTGTAAGACATGTCTGGGACATGCTTCGG-C-C-ACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GA-GATA
* * * * *
2791882 GCCAGTGAAAGACCATGTCTGGGACATGGCATCGGCATAGAGATA-AGT-
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGACAGAGA-TA
* * *
2791930 GGCAGAGTAAGACATGTTTGGGACATGCATCGGCCTCGACAGAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATA
* * * *
2791977 GCCAGTGTAAGACGTGTCTGGGACACGCATCGG-CT--A-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGAT-A
* * * * * *
2792021 GCTAGAGTAATACATGTCTAGGACATGCATTGACCTCGACAGAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATA
* * * *
2792068 GCCAGTGTAAGACGTGTCTTGGACACGCATTGGCC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC
2792103 AAGAGTTGTG
Statistics
Matches: 170, Mismatches: 38, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
43 5 0.03
44 26 0.15
45 2 0.01
46 27 0.16
47 85 0.50
48 21 0.12
50 2 0.01
51 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATA
Found at i:2792058 original size:91 final size:90
Alignment explanation
Indices: 2791881--2792142 Score: 319
Period size: 91 Copynumber: 2.8 Consensus size: 90
2791871 ACATTATGAG
* * * *
2791881 AGCCAGTGAAAGACCATGTCTGGGACATGGCATCGGCATAGAGATAAGTGGC-AGAGTAAGACAT
1 AGCCAGTGTAAGA-CGTGTCTGGGACA-CGCATCGGCA-AGAG-T-TGT-GCTAGAGTAAGACAT
* * *
2791945 GTTTGGGACATGCATCGGCCTCGACAGAGAT
60 GTCTAGGACATGCATCGACCTCGACAGAGAT
*
2791976 AGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGAGTAATACATGTCTA
1 AGCCAGTGTAAGACGTGTCTGGGACACGCATCGGC-AAGAGTTGTGCTAGAGTAAGACATGTCTA
*
2792041 GGACATGCATTGACCTCGACAGAGAT
65 GGACATGCATCGACCTCGACAGAGAT
* * * *
2792067 AGCCAGTGTAAGACGTGTCTTGGACACGCATTGGCCAAGAGTTGTGCTAGTGAAAGACATGTCTA
1 AGCCAGTGTAAGACGTGTCTGGGACACGCATCGG-CAAGAGTTGTGCTAGAGTAAGACATGTCTA
*
2792132 GGATATGCATC
65 GGACATGCATC
2792143 AGCACGCATA
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
90 2 0.01
91 107 0.72
92 2 0.01
93 12 0.08
94 13 0.09
95 12 0.08
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (90 bp):
AGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCAAGAGTTGTGCTAGAGTAAGACATGTCTAG
GACATGCATCGACCTCGACAGAGAT
Found at i:2794753 original size:43 final size:43
Alignment explanation
Indices: 2794692--2794780 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
2794682 ATTAAAATGG
*
2794692 TAAAACGAGTCAACTATTCCCAAACCTTGTTCTTTCCACGATC
1 TAAAACGAGTCAACTATTCCCAAACCTTGTTCTTTCCACAATC
2794735 TAAAACGAGTCAACTATTCCCAAACCTTGTTCTTTCCACAATC
1 TAAAACGAGTCAACTATTCCCAAACCTTGTTCTTTCCACAATC
2794778 TAA
1 TAA
2794781 GTCCGTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.30
Consensus pattern (43 bp):
TAAAACGAGTCAACTATTCCCAAACCTTGTTCTTTCCACAATC
Found at i:2797093 original size:29 final size:29
Alignment explanation
Indices: 2797041--2797099 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2797031 CAAGTAGACT
* *
2797041 TTTATCACTTAAGGTCTCTTTTCTCTCTA
1 TTTATCACTTAAAGTCTCTGTTCTCTCTA
*
2797070 TTTATCACTTAAAGTTTCTGTTCTCTCTA
1 TTTATCACTTAAAGTCTCTGTTCTCTCTA
2797099 T
1 T
2797100 CTTTTTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.22, G:0.07, T:0.53
Consensus pattern (29 bp):
TTTATCACTTAAAGTCTCTGTTCTCTCTA
Found at i:2800777 original size:63 final size:63
Alignment explanation
Indices: 2800698--2800824 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
2800688 CTAATATGCA
2800698 AGAAGGGGATAGAATAATTATTTCCAGGATTCTTAGAGTGCAAAGTTCTAATAACCCGAAACG
1 AGAAGGGGATAGAATAATTATTTCCAGGATTCTTAGAGTGCAAAGTTCTAATAACCCGAAACG
2800761 AGAAGGGGATAGAATAATTATTTCCAGGATTCTTAGAGTGCAAAGTTCTAATAACCCGAAACG
1 AGAAGGGGATAGAATAATTATTTCCAGGATTCTTAGAGTGCAAAGTTCTAATAACCCGAAACG
2800824 A
1 A
2800825 TATCTTGGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (63 bp):
AGAAGGGGATAGAATAATTATTTCCAGGATTCTTAGAGTGCAAAGTTCTAATAACCCGAAACG
Found at i:2803623 original size:14 final size:13
Alignment explanation
Indices: 2803604--2803634 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2803594 TAAGATTAGA
2803604 TATTTATTTTATAT
1 TATTTATTTTAT-T
2803618 TATTTATTTTATT
1 TATTTATTTTATT
2803631 TATT
1 TATT
2803635 AGATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:2805453 original size:42 final size:43
Alignment explanation
Indices: 2805395--2805497 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
2805385 ATCGATTTGA
*
2805395 GATTTACGTGTAAGACCATGTCTAGGACA-TCGCCATC-ATATTT
1 GATTT-CGTGTAAGACCATGTCTAGGACAGT-GCAATCGATATTT
* * * *
2805438 GATTTCGTGTAAGACCCTGTTTGGGACAGTGGAATCGATATTT
1 GATTTCGTGTAAGACCATGTCTAGGACAGTGCAATCGATATTT
* *
2805481 GATTACATGTAAGACCA
1 GATTTCGTGTAAGACCA
2805498 CGTTTGGAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 24 0.48
43 26 0.52
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTAGGACAGTGCAATCGATATTT
Found at i:2806062 original size:10 final size:11
Alignment explanation
Indices: 2806043--2806086 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
2806033 AGCCATGTGA
2806043 TATGGCTTGAT
1 TATGGCTTGAT
2806054 TATGG-TTGATCT
1 TATGGCTTGA--T
2806066 TATGGCTTGAT
1 TATGGCTTGAT
2806077 TATGG-TTGAT
1 TATGGCTTGAT
2806087 CTTATGTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.30
11 11 0.37
12 6 0.20
13 4 0.13
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (11 bp):
TATGGCTTGAT
Found at i:2806070 original size:12 final size:12
Alignment explanation
Indices: 2806053--2806098 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
2806043 TATGGCTTGA
2806053 TTATGGTTGATC
1 TTATGGTTGATC
2806065 TTATGGCTTGA--
1 TTATGG-TTGATC
2806076 TTATGGTTGATC
1 TTATGGTTGATC
2806088 TTATGTGTTGA
1 TTATG-GTTGA
2806099 GGAAACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.13
11 6 0.20
12 11 0.37
13 9 0.30
ACGTcount: A:0.17, C:0.07, G:0.26, T:0.50
Consensus pattern (12 bp):
TTATGGTTGATC
Found at i:2806098 original size:23 final size:23
Alignment explanation
Indices: 2806043--2806092 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2806033 AGCCATGTGA
2806043 TATGGCTTGATTATGGTTGATCT
1 TATGGCTTGATTATGGTTGATCT
2806066 TATGGCTTGATTATGGTTGATCT
1 TATGGCTTGATTATGGTTGATCT
2806089 TATG
1 TATG
2806093 TGTTGAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.48
Consensus pattern (23 bp):
TATGGCTTGATTATGGTTGATCT
Found at i:2815379 original size:46 final size:46
Alignment explanation
Indices: 2815236--2815443 Score: 203
Period size: 46 Copynumber: 4.5 Consensus size: 46
2815226 TTTGTGTGCT
* *
2815236 AGTGTAAGACAT-TCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCC
* * *
2815281 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCC
* * * *
2815329 AGTGTAAGACATATTTGCGACATGCATCGGCCTCGAGATGTA-TGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCC
* * *
2815375 AGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGA-G-GTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGCC
*
2815419 AGTGTAAGACCATATCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
2815444 GCATTAACAC
Statistics
Matches: 137, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
44 12 0.09
45 26 0.19
46 51 0.37
47 22 0.16
48 25 0.18
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCC
Found at i:2815395 original size:93 final size:92
Alignment explanation
Indices: 2815233--2815402 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 92
2815223 TTATTTGTGT
* *
2815233 GCTAGTGTAAGACATTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCT
1 GCTAGTGTAAGACATTCTGCGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCT
2815298 GGGACATGGCATCGGCATTGAGATGAGA
66 GGGACAT-GCATCGGCATTGAGATGAGA
* * *
2815326 GCTAGTGTAAGACATATTTGCGACATGCATCGGCCTCGA-GATGTA-TGCCAGTGTAAGA-CATG
1 GCTAGTGTAAGACAT-TCTGCGACATGCATCGGCCAC-ATGATG-AGAGCCAGTGTAAGACCATG
2815388 TCTGGGACATGCATC
63 TCTGGGACATGCATC
2815403 AGCTACGAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
92 5 0.07
93 29 0.42
94 33 0.48
95 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (92 bp):
GCTAGTGTAAGACATTCTGCGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCT
GGGACATGCATCGGCATTGAGATGAGA
Found at i:2817676 original size:63 final size:63
Alignment explanation
Indices: 2817572--2817693 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
2817562 TTCGGGTACG
* *
2817572 ATCTGATTACTCGCTTGATAAGTTAAGTGAATTATATATTTTTTATATTGTGAGATTGCTACA
1 ATCTGATTACTCGCTTGATAAATTAAGTGAATTATACATTTTTTATATTGTGAGATTGCTACA
2817635 ATCTGATTACTCGCTTGATAAATTAAGTGAATTATACATTTTTTATATTGTGAGATTGC
1 ATCTGATTACTCGCTTGATAAATTAAGTGAATTATACATTTTTTATATTGTGAGATTGC
2817694 ACAGAGTGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (63 bp):
ATCTGATTACTCGCTTGATAAATTAAGTGAATTATACATTTTTTATATTGTGAGATTGCTACA
Found at i:2819919 original size:39 final size:39
Alignment explanation
Indices: 2819755--2819937 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
2819745 TTGAATGCTG
* * * * * * *
2819755 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
2819795 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
2819835 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
2819875 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
2819914 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
2819938 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:2819957 original size:79 final size:80
Alignment explanation
Indices: 2819791--2819972 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
2819781 GCTAAGTGAA
* * * *
2819791 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
2819855 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
2819871 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
2819935 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
2819950 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
2819973 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:2827824 original size:39 final size:40
Alignment explanation
Indices: 2827729--2827951 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
2827719 TTGAATGATG
*
2827729 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
2827767 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
2827808 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
2827847 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
2827886 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
2827925 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
2827952 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:2827915 original size:79 final size:81
Alignment explanation
Indices: 2827729--2827951 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
2827719 TTGAATGATG
* * *
2827729 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
2827791 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
2827808 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
2827869 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
2827886 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
2827950 TG
66 TG
2827952 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:2827973 original size:79 final size:79
Alignment explanation
Indices: 2827729--2827984 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
2827719 TTGAATGATG
* * * *
2827729 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
2827790 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
2827808 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
2827872 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
2827886 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
2827949 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
2827966 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
2827985 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:2830252 original size:41 final size:44
Alignment explanation
Indices: 2830184--2830291 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
2830174 ATGGATTTGA
*
2830184 GATTTACGTGTAA-ACCATGTCTGGGACATTGCCATC-ATA-TTT
1 GATTT-CGTGTAAGACCATGTCTGGGACAGTGCCATCGATATTTT
* *
2830226 GATTTCGTGTAAGACCCTGTCT-GGACAGTGGCATCGATATTTTT
1 GATTTCGTGTAAGACCATGTCTGGGACAGTGCCATCGATA-TTTT
* * *
2830270 GATTACATGTAAGACCACGTCT
1 GATTTCGTGTAAGACCATGTCT
2830292 AGGATGTTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 18 0.33
42 16 0.29
44 21 0.38
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (44 bp):
GATTTCGTGTAAGACCATGTCTGGGACAGTGCCATCGATATTTT
Found at i:2836242 original size:30 final size:29
Alignment explanation
Indices: 2836206--2836280 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
2836196 ATTATTAGGG
2836206 TTTATCAGACACTATTTAC-TGTTGATTATA
1 TTTATCAGACACTATTTACTTG-TG-TTATA
*
2836236 TTTATCAGGTACA-TTTTTACTTGTGTTATA
1 TTTATCA-G-ACACTATTTACTTGTGTTATA
*
2836266 TTTATCAGGCACTAT
1 TTTATCAGACACTAT
2836281 GTGCCGATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.05
29 3 0.08
30 19 0.50
31 9 0.24
32 5 0.13
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTATCAGACACTATTTACTTGTGTTATA
Found at i:2839206 original size:30 final size:30
Alignment explanation
Indices: 2839139--2839330 Score: 160
Period size: 30 Copynumber: 6.4 Consensus size: 30
2839129 TCATTGGCTG
*
2839139 ATGAAAAGGGATAGCTTCGGCTATCAAAATA
1 ATGAAAAGGGATAGCTTCGGCTATC-AAATT
2839170 ATGAAAAGGGATAGTCTT-GGCTATCAAATT
1 ATGAAAAGGGATAG-CTTCGGCTATCAAATT
* * ** * *
2839200 ATGAAAAGGGAT-GGTGACAACCATCCACA--
1 ATGAAAAGGGATAGCT-TCGGCTAT-CAAATT
* * * * * * **
2839229 ATGAAAAGGTAT-GGTGACGACCATCGAACA
1 ATGAAAAGGGATAGCT-TCGGCTATCAAATT
2839259 ATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
*
2839289 TTGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
2839319 ATGAAAAGGGAT
1 ATGAAAAGGGAT
2839331 GGTGATGACC
Statistics
Matches: 133, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.02
29 23 0.17
30 78 0.59
31 26 0.20
32 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAATT
Found at i:2839242 original size:29 final size:30
Alignment explanation
Indices: 2839200--2839270 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
2839190 CTATCAAATT
*
2839200 ATGAAAAGGGATGGTGACAACCATC-CACA
1 ATGAAAAGGGATGGTGACAACCATCGAACA
* *
2839229 ATGAAAAGGTATGGTGACGACCATCGAACA
1 ATGAAAAGGGATGGTGACAACCATCGAACA
2839259 ATGAAAAGGGAT
1 ATGAAAAGGGAT
2839271 AGCTTCGGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGACAACCATCGAACA
Found at i:2839345 original size:30 final size:30
Alignment explanation
Indices: 2839165--2839389 Score: 120
Period size: 30 Copynumber: 7.6 Consensus size: 30
2839155 TCGGCTATCA
* ** * *
2839165 AAATAATGAAAAGGGATAGTCTTGGCTATC
1 AAATAATGAAAAGGGATGGTGATGACCATC
* **
2839195 AAATTATGAAAAGGGATGGTGACAACCATC
1 AAATAATGAAAAGGGATGGTGATGACCATC
* * * *
2839225 -CACAATGAAAAGGTATGGTGACGACCATC
1 AAATAATGAAAAGGGATGGTGATGACCATC
* * * * *
2839254 GAACAATGAAAAGGGATAGCT--TCGGCTATC
1 AAATAATGAAAAGGGAT-GGTGAT-GACCATC
** * * *
2839284 AAATTTTGAAAAGGGATAGCT--TCGGCTATC
1 AAATAATGAAAAGGGAT-GGTGAT-GACCATC
*
2839314 AAATTATGAAAAGGGATGGTGATGACCATC
1 AAATAATGAAAAGGGATGGTGATGACCATC
* * **
2839344 -AACAATGAAATGTAATGGTGATGACCATC
1 AAATAATGAAAAGGGATGGTGATGACCATC
*
2839373 AAATAATGAGAAGGGAT
1 AAATAATGAAAAGGGAT
2839390 AGCTTTGACT
Statistics
Matches: 152, Mismatches: 37, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
29 50 0.33
30 99 0.65
31 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (30 bp):
AAATAATGAAAAGGGATGGTGATGACCATC
Found at i:2839348 original size:89 final size:89
Alignment explanation
Indices: 2839169--2839353 Score: 225
Period size: 89 Copynumber: 2.1 Consensus size: 89
2839159 CTATCAAAAT
* *
2839169 AATGAAAAGGGATAGTCTTGGCTATCAAATTATGAAAAGGGATGGTGACAACCATCCACAATGAA
1 AATGAAAAGGGATAGTCTTGGCTATCAAATTATGAAAAGGGATGCTGACAACCATCCAAAATGAA
*
2839234 AAGGTATGGTGACGACCATCGAAC
66 AAGGGATGGTGACGACCATCGAAC
* * ** *
2839258 AATGAAAAGGGATAG-CTTCGGCTATCAAATTTTGAAAAGGGATAGCT-TCGGCTAT-CAAATTA
1 AATGAAAAGGGATAGTCTT-GGCTATCAAATTATGAAAAGGGAT-GCTGACAACCATCCAAA--A
*
2839320 TGAAAAGGGATGGTGATGACCATC-AAC
62 TGAAAAGGGATGGTGACGACCATCGAAC
2839347 AATGAAA
1 AATGAAA
2839354 TGTAATGGTG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 6 0.07
89 52 0.63
90 25 0.30
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (89 bp):
AATGAAAAGGGATAGTCTTGGCTATCAAATTATGAAAAGGGATGCTGACAACCATCCAAAATGAA
AAGGGATGGTGACGACCATCGAAC
Found at i:2839351 original size:119 final size:118
Alignment explanation
Indices: 2839139--2839459 Score: 385
Period size: 119 Copynumber: 2.7 Consensus size: 118
2839129 TCATTGGCTG
*
2839139 ATGAAAAGGGATAGCTTCGGCTATCAAAATAATGAAAAGGGATAGTCTTGGCTATCAAATTATGA
1 ATGAAAAGGGATAGCTTCGGCTATC-AAATTATGAAAAGGGATAG-CTTGGCTATCAAATTATGA
* *
2839204 AAAGGGATGGTGACAACCATCCACAATGAAAAGGT-ATGGTGACGACCATCGAACA
64 AAAGGGATGGTGACAACCATCAACAATG-AAAGGTAATGGTGACGACCATCAAACA
*
2839259 ATGAAAAGGGATAGCTTCGGCTATCAAATTTTGAAAAGGGATAGCTTCGGCTATCAAATTATGAA
1 ATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATAGCTT-GGCTATCAAATTATGAA
** * * *
2839324 AAGGGATGGTGATGACCATCAACAATGAAATGTAATGGTGATGACCATCAAATA
65 AAGGGATGGTGACAACCATCAACAATGAAAGGTAATGGTGACGACCATCAAACA
* * * * ** * * ****
2839378 ATGAGAAGGGATAGCTTTGACTATCGAGCTGTGAAAAGGGATAACTTTGGCTATCCGGCTATGAA
1 ATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATAGC-TTGGCTATCAAATTATGAA
*
2839443 AAGGGTTGG-GACAACCA
65 AAGGGATGGTGACAACCA
2839460 ACGTGATTTT
Statistics
Matches: 174, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
118 14 0.08
119 133 0.76
120 27 0.16
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (118 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATAGCTTGGCTATCAAATTATGAAA
AGGGATGGTGACAACCATCAACAATGAAAGGTAATGGTGACGACCATCAAACA
Found at i:2839419 original size:30 final size:30
Alignment explanation
Indices: 2839378--2839447 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
2839368 CCATCAAATA
* *
2839378 ATGAGAAGGGATAGCTTTGACTAT-CGAGCT
1 ATGAAAAGGGATAACTTTGACTATCCG-GCT
* *
2839408 GTGAAAAGGGATAACTTTGGCTATCCGGCT
1 ATGAAAAGGGATAACTTTGACTATCCGGCT
2839438 ATGAAAAGGG
1 ATGAAAAGGG
2839448 TTGGGACAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAACTTTGACTATCCGGCT
Found at i:2851177 original size:17 final size:17
Alignment explanation
Indices: 2851151--2851313 Score: 98
Period size: 17 Copynumber: 9.6 Consensus size: 17
2851141 ACCTATGACA
*
2851151 ATATACGAGCTGTGTTT
1 ATATGCGAGCTGTGTTT
* * *
2851168 ATATGTGAGCCGTGTGT
1 ATATGCGAGCTGTGTTT
* * * *
2851185 ATAAGCAAGTTTTGTTT
1 ATATGCGAGCTGTGTTT
* * * *
2851202 AGATGTGAGCTATATTT
1 ATATGCGAGCTGTGTTT
*
2851219 ATATGCG-GGTG-GTTTT
1 ATATGCGAGCTGTG-TTT
* * * *
2851235 ATTACGCGAGGTATATTT
1 A-TATGCGAGCTGTGTTT
2851253 ATATGCGAG-TGGTGTTT
1 ATATGCGAGCT-GTGTTT
*
2851270 ATATGCAAGCTGTGTTT
1 ATATGCGAGCTGTGTTT
* *
2851287 ATATGCGAGATTTGTTT
1 ATATGCGAGCTGTGTTT
2851304 ATATGCGAGC
1 ATATGCGAGC
2851314 ACTATATATA
Statistics
Matches: 106, Mismatches: 34, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
16 7 0.07
17 91 0.86
18 8 0.08
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.40
Consensus pattern (17 bp):
ATATGCGAGCTGTGTTT
Found at i:2851401 original size:17 final size:17
Alignment explanation
Indices: 2851335--2851403 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
2851325 GCGAGTTTTT
*
2851335 TTTATATACTAGTTGTG
1 TTTATATACAAGTTGTG
*
2851352 TTTATA-A-AAGATCTATG
1 TTTATATACAAG-T-TGTG
**
2851369 TTTATATGTGAA-TTGTG
1 TTTATAT-ACAAGTTGTG
2851386 TTTATATACAAGTTGTG
1 TTTATATACAAGTTGTG
2851403 T
1 T
2851404 CAATGTGTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.05
16 4 0.10
17 31 0.77
18 1 0.03
20 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.49
Consensus pattern (17 bp):
TTTATATACAAGTTGTG
Found at i:2853289 original size:43 final size:43
Alignment explanation
Indices: 2853125--2853289 Score: 129
Period size: 43 Copynumber: 3.8 Consensus size: 43
2853115 ACATTAGATT
* * * *
2853125 ATCGAGATGTGATTACATGTAAGACCATGTCTGGTACATTGGT
1 ATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGC
* *
2853168 ATTGCAT-TGTGA-ATACGTGTAAGACCATGTCTGGGACATTGGC
1 ATCG-ATATGTGATA-ACATGTAAGACCATGTCTGGGACATTGGC
* * ** * * * * * *
2853211 ATCGTTAT-TCAATTTCGTGTAAGATCTTTTTTGGGACAATGGC
1 ATCGATATGT-GATAACATGTAAGACCATGTCTGGGACATTGGC
*
2853254 ATCGATATGTGATAACATGTAAGACCATATCTGGGA
1 ATCGATATGTGATAACATGTAAGACCATGTCTGGGA
2853290 TATGCCTTTG
Statistics
Matches: 91, Mismatches: 25, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
42 2 0.02
43 87 0.96
44 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
ATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGC
Found at i:2856672 original size:15 final size:15
Alignment explanation
Indices: 2856652--2856681 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2856642 AAGGTTATTT
2856652 TGCTTTGTATGGTCA
1 TGCTTTGTATGGTCA
2856667 TGCTTTGTATGGTCA
1 TGCTTTGTATGGTCA
2856682 CTGGTGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (15 bp):
TGCTTTGTATGGTCA
Found at i:2857636 original size:23 final size:23
Alignment explanation
Indices: 2857587--2857636 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2857577 TTTCACCCTT
* *
2857587 AAAACCCTAAACCTAATTCCTAA
1 AAAAACCTAAACCTAATCCCTAA
*
2857610 AAAAACCTAACCCTAA-CCCTAA
1 AAAAACCTAAACCTAATCCCTAA
*
2857632 CAAAA
1 AAAAA
2857637 TTTTAAAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAAACCTAAACCTAATCCCTAA
Found at i:2858140 original size:27 final size:27
Alignment explanation
Indices: 2858092--2858147 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2858082 GCCAATATCG
*
2858092 TAGGTGGCACCAGTAGTGCCCATGTCA
1 TAGGTGGCACCAGTAGTACCCATGTCA
* *
2858119 TAGGTGGCACTAGTGGTACCCATGTCA
1 TAGGTGGCACCAGTAGTACCCATGTCA
2858146 TA
1 TA
2858148 AGCTGTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (27 bp):
TAGGTGGCACCAGTAGTACCCATGTCA
Found at i:2862724 original size:16 final size:16
Alignment explanation
Indices: 2862703--2862733 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2862693 ATACTGTGCT
2862703 TATGTTTCAATTATAG
1 TATGTTTCAATTATAG
2862719 TATGTTTCAATTATA
1 TATGTTTCAATTATA
2862734 AAGGGTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (16 bp):
TATGTTTCAATTATAG
Found at i:2872160 original size:26 final size:26
Alignment explanation
Indices: 2872124--2872198 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
2872114 TTTCTCACCC
2872124 CAATTTTACCCCTAGTAAAATTTTGA
1 CAATTTTACCCCTAGTAAAATTTTGA
* *
2872150 CAATCTTACCCTTTA-TAAAATTTTGA
1 CAATTTTACCC-CTAGTAAAATTTTGA
**
2872176 TGATTTTACCCCTAGTAAAATTT
1 CAATTTTACCCCTAGTAAAATTT
2872199 CGAGAAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 37 0.90
27 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (26 bp):
CAATTTTACCCCTAGTAAAATTTTGA
Found at i:2874851 original size:121 final size:121
Alignment explanation
Indices: 2874649--2874883 Score: 398
Period size: 121 Copynumber: 1.9 Consensus size: 121
2874639 TTACGATCCA
* * *
2874649 ACCACGTAATACCGCTTAATATTAGTTAAACATTAGACGACCAATGAGCCACATTTGCTTCCATT
1 ACCACGTAATACCGCTTAATATCAGTTAAACATTAGACAACCAATAAGCCACATTTGCTTCCATT
* *
2874714 TTTCTGTGTGTGCAAAAATCATTTGAGGATAATAATACAAAGTATATTACGATATG
66 TTGCTGTGTGTGCAAAAATCATTTGAGGACAATAATACAAAGTATATTACGATATG
* *
2874770 ACCATGTAATACCGCTTAGTATCAGTTAAACATTAGACAACCAATAAGCCACATTTGCTTCCATT
1 ACCACGTAATACCGCTTAATATCAGTTAAACATTAGACAACCAATAAGCCACATTTGCTTCCATT
*
2874835 TTGCTTTGTGTGCAAAAATCATTTGAGGACAATAATACAAAGTATATTA
66 TTGCTGTGTGTGCAAAAATCATTTGAGGACAATAATACAAAGTATATTA
2874884 GTTGTAATCA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 106 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (121 bp):
ACCACGTAATACCGCTTAATATCAGTTAAACATTAGACAACCAATAAGCCACATTTGCTTCCATT
TTGCTGTGTGTGCAAAAATCATTTGAGGACAATAATACAAAGTATATTACGATATG
Found at i:2880562 original size:21 final size:21
Alignment explanation
Indices: 2880532--2880580 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2880522 AACAACAGTG
*
2880532 GCGGTAAGATT-AGTTACTGTA
1 GCGGTAAGATTGA-ATACTGTA
*
2880553 GCGGTGAGATTGAATACTGTA
1 GCGGTAAGATTGAATACTGTA
2880574 GCGGTAA
1 GCGGTAA
2880581 AATTAGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (21 bp):
GCGGTAAGATTGAATACTGTA
Found at i:2882514 original size:22 final size:19
Alignment explanation
Indices: 2882502--2882546 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
2882492 AACGGCAGCT
2882502 AAGAAGAAGAGAAAGGAAG
1 AAGAAGAAGAGAAAGGAAG
*
2882521 AAGAAGAAGAGAAAAG-AG
1 AAGAAGAAGAGAAAGGAAG
2882539 AAG-AGAAG
1 AAGAAGAAG
2882547 GGGGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 15 0.60
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
AAGAAGAAGAGAAAGGAAG
Found at i:2888224 original size:23 final size:22
Alignment explanation
Indices: 2888198--2888241 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2888188 TTCTTTTATT
*
2888198 TTAATTACAAAAATTCATATTTG
1 TTAAATACAAAAATT-ATATTTG
* *
2888221 TTAAATATAAATATTATATTT
1 TTAAATACAAAAATTATATTT
2888242 TGATAGCTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATACAAAAATTATATTTG
Found at i:2889923 original size:31 final size:31
Alignment explanation
Indices: 2889857--2889929 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
2889847 TTATTTGAAC
* * *
2889857 AATTATAGTCTCTATACTTTTCAACTTGGTC
1 AATTTTAGTCCCTATACTTTTCAACTTGGTA
* *
2889888 AATTTTAGTCCCTATACTTTTCAAATT-TTGA
1 AATTTTAGTCCCTATACTTTTCAACTTGGT-A
2889919 AATTTTAGTCC
1 AATTTTAGTCC
2889930 TAACCTAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (31 bp):
AATTTTAGTCCCTATACTTTTCAACTTGGTA
Found at i:2893118 original size:13 final size:13
Alignment explanation
Indices: 2893100--2893137 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
2893090 ATATAACTCC
2893100 AAAAATATTTAAT
1 AAAAATATTTAAT
2893113 AAAAATATTTTAAT
1 AAAAATA-TTTAAT
2893127 AAAAATATTTA
1 AAAAATATTTA
2893138 CAAATTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAATATTTAAT
Found at i:2893408 original size:24 final size:24
Alignment explanation
Indices: 2893381--2893426 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2893371 AAACAACAAA
*
2893381 ACTTAACTTTATGAATTTAACAGC
1 ACTTAACTTTATGAACTTAACAGC
2893405 ACTTAACTTTATGAACTTAACA
1 ACTTAACTTTATGAACTTAACA
2893427 ATTATCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (24 bp):
ACTTAACTTTATGAACTTAACAGC
Found at i:2894045 original size:61 final size:60
Alignment explanation
Indices: 2893975--2894100 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 60
2893965 TCTTAAATAT
* * ** * * * * *
2893975 TAAAAATTCAACAAATTTAGCCCTC-AATGTTTATAAAATTTGTCATTTTAGTTCTAATTC
1 TAAAAATTCAAAAAATTT-GCCCCCTAACATTTACAAAATTTGTCAATCTAGTCCTAACTC
2894035 TAAAAGATTCAAAAAATTTGCCCCCTAACATTTACAAAATTTGTCAATCTAGTCCTAACTC
1 TAAAA-ATTCAAAAAATTTGCCCCCTAACATTTACAAAATTTGTCAATCTAGTCCTAACTC
2894096 TAAAA
1 TAAAA
2894101 CTTAATATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
60 10 0.18
61 45 0.82
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (60 bp):
TAAAAATTCAAAAAATTTGCCCCCTAACATTTACAAAATTTGTCAATCTAGTCCTAACTC
Found at i:2896079 original size:24 final size:24
Alignment explanation
Indices: 2896034--2896093 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
2896024 ATTTTTCGTA
2896034 AATTT-ATAATTTATAATTTTTAAG
1 AATTTAATAATTTATAATTTTT-AG
2896058 AATTTAATATATTTAT-A-TTTTAG
1 AATTTAATA-ATTTATAATTTTTAG
*
2896081 ATTTTAA-AATTTA
1 AATTTAATAATTTA
2896094 GGCTAACGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 5 0.15
22 1 0.03
23 8 0.24
24 9 0.27
25 4 0.12
26 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (24 bp):
AATTTAATAATTTATAATTTTTAG
Found at i:2899455 original size:4 final size:4
Alignment explanation
Indices: 2899433--2899471 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
2899423 ACGAAAATAG
* *
2899433 AGAA GGAA AGAA GGAA AGAA AGAAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AG
2899472 GGAAATTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2899461 original size:17 final size:17
Alignment explanation
Indices: 2899439--2899471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2899429 ATAGAGAAGG
*
2899439 AAAGAAGGAAAGAAAGA
1 AAAGAAAGAAAGAAAGA
2899456 AAAGAAAGAAAGAAAG
1 AAAGAAAGAAAGAAAG
2899472 GGAAATTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAGA
Found at i:2902620 original size:28 final size:28
Alignment explanation
Indices: 2902561--2902621 Score: 115
Period size: 27 Copynumber: 2.2 Consensus size: 28
2902551 AAGTAACTAT
2902561 GCAAGTAACCGTTCGGGGGGCACTTGTC
1 GCAAGTAACCGTTCGGGGGGCACTTGTC
2902589 -CAAGTAACCGTTCGGGGGGCACTTGTC
1 GCAAGTAACCGTTCGGGGGGCACTTGTC
2902616 GCAAGT
1 GCAAGT
2902622 GGCCCAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (28 bp):
GCAAGTAACCGTTCGGGGGGCACTTGTC
Found at i:2904895 original size:22 final size:22
Alignment explanation
Indices: 2904861--2904908 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2904851 AAATAACCAG
2904861 AAAA-TTTCCAAATTTCTTTTT
1 AAAATTTTCCAAATTTCTTTTT
*
2904882 AAAATTTTCGAAATTTCTTTTT
1 AAAATTTTCCAAATTTCTTTTT
2904904 AAAAT
1 AAAAT
2904909 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATTTTCCAAATTTCTTTTT
Found at i:2917939 original size:38 final size:40
Alignment explanation
Indices: 2917865--2917944 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
2917855 CGAAGCCTTG
*
2917865 ATATGTGGGTGAGAAGTCATTAAAAAAAAAACCTATGGTC
1 ATATGCGGGTGAGAAGTCATTAAAAAAAAAACCTATGGTC
2917905 ATATGCGGGTGAGAAGTCATT-AAAAAAAAA-CTATGGTC
1 ATATGCGGGTGAGAAGTCATTAAAAAAAAAACCTATGGTC
2917943 AT
1 AT
2917945 TTAAAATTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 10 0.26
39 9 0.23
40 20 0.51
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (40 bp):
ATATGCGGGTGAGAAGTCATTAAAAAAAAAACCTATGGTC
Found at i:2924668 original size:17 final size:17
Alignment explanation
Indices: 2924648--2924682 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2924638 TATGTATGAC
2924648 TTTGAAATTGAATGTGA
1 TTTGAAATTGAATGTGA
* *
2924665 TTTGATATTGAATTTGA
1 TTTGAAATTGAATGTGA
2924682 T
1 T
2924683 ACTGTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (17 bp):
TTTGAAATTGAATGTGA
Found at i:2925063 original size:17 final size:18
Alignment explanation
Indices: 2925030--2925063 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2925020 ATATATATAT
*
2925030 ATAACCCAATTAGCCCAA
1 ATAACCCAATTACCCCAA
2925048 ATAACCC-ATTACCCCA
1 ATAACCCAATTACCCCA
2925064 GGCTCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.18
Consensus pattern (18 bp):
ATAACCCAATTACCCCAA
Found at i:2928316 original size:43 final size:42
Alignment explanation
Indices: 2928187--2928361 Score: 161
Period size: 42 Copynumber: 4.1 Consensus size: 42
2928177 TATAGGTTTA
* * *
2928187 TACTTCGGTATATCCGATGATGCACTTATGTACTAGTATATT
1 TACTTCGGTTTATCCGATGATGCACTTATGTGCTAGTATAAT
* * * * * * *
2928229 TTCTTCGGCTTATCTGATAATGCACTTACGTGCTAGTTTGAT
1 TACTTCGGTTTATCCGATGATGCACTTATGTGCTAGTATAAT
* *
2928271 TACTTCGGTTTATTCGATGATGCACTATGTGTGCTAGTATAAT
1 TACTTCGGTTTATCCGATGATGCACT-TATGTGCTAGTATAAT
* * * * * * *
2928314 TACTTTGATTCATCCAATGATGCACCTTGTGTGCCAGTTTAAT
1 TACTTCGGTTTATCCGATGATGCA-CTTATGTGCTAGTATAAT
2928357 TACTT
1 TACTT
2928362 TGGCTTGCCC
Statistics
Matches: 105, Mismatches: 26, Indels: 3
0.78 0.19 0.02
Matches are distributed among these distances:
42 53 0.50
43 50 0.48
44 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (42 bp):
TACTTCGGTTTATCCGATGATGCACTTATGTGCTAGTATAAT
Found at i:2928377 original size:43 final size:42
Alignment explanation
Indices: 2928285--2928389 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 42
2928275 TCGGTTTATT
*
2928285 CGATGATGCACTATGTGTGCTAGTATAATTACTTTGATTCATC
1 CGATGATGCACTATGTGTGCCAGTATAATTACTTTGATTCA-C
* * *
2928328 CAATGATGCACCT-TGTGTGCCAGTTTAATTACTTTGGCTTGC-C
1 CGATGATGCA-CTATGTGTGCCAGTATAATTACTTT-GATT-CAC
* *
2928371 CGATGATGTACTATTTGTG
1 CGATGATGCACTATGTGTG
2928390 TCAAGTATCA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
42 2 0.04
43 43 0.84
44 5 0.10
45 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (42 bp):
CGATGATGCACTATGTGTGCCAGTATAATTACTTTGATTCAC
Found at i:2931468 original size:46 final size:47
Alignment explanation
Indices: 2931364--2931538 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 47
2931354 GGATATTGTG
* * *
2931364 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCAACATTGAGATGA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTTGAGATGA
* * *
2931411 GAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGACCTCGAGATGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTTGAGATG-A
* * *
2931458 AGCCAATGTAAGA-CATGTCTGGGACAT-ACATCG-GCTATGAGATG-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCT-TGAGATGA
2931502 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
2931539 ATCCTACCCC
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
44 12 0.11
45 16 0.15
46 54 0.50
47 15 0.14
48 12 0.11
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTTGAGATGA
Found at i:2932546 original size:13 final size:13
Alignment explanation
Indices: 2932528--2932562 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
2932518 CCGTGTGAAA
2932528 GACACGAGCTACG
1 GACACGAGCTACG
2932541 GACACGAGCTACG
1 GACACGAGCTACG
2932554 GACACGAGC
1 GACACGAGC
2932563 ATGTGCCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.31, T:0.06
Consensus pattern (13 bp):
GACACGAGCTACG
Found at i:2934332 original size:29 final size:28
Alignment explanation
Indices: 2934259--2934341 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
2934249 TGGTGCAAAT
2934259 AATGATAAGCACTGAAGTGCAAA--ATA
1 AATGATAAGCACTGAAGTGCAAATTATA
* * *
2934285 ATATCAATAAGCACCGAAGTGCAAATTTTA
1 A-AT-GATAAGCACTGAAGTGCAAATTATA
2934315 CAATGATAAGCACTGAAGTGCGAAATT
1 -AATGATAAGCACTGAAGTGC-AAATT
2934342 GTAATACCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 18 0.39
29 15 0.33
30 9 0.20
31 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (28 bp):
AATGATAAGCACTGAAGTGCAAATTATA
Found at i:2937176 original size:19 final size:19
Alignment explanation
Indices: 2937139--2937177 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2937129 ATCATCCATT
2937139 TTCATTTTGTATATGCATA
1 TTCATTTTGTATATGCATA
*
2937158 TTCATCTTTTTATAT-CATA
1 TTCAT-TTTGTATATGCATA
2937177 T
1 T
2937178 GAACATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (19 bp):
TTCATTTTGTATATGCATA
Found at i:2939977 original size:28 final size:28
Alignment explanation
Indices: 2939946--2940042 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 28
2939936 ACATGGTGCA
*
2939946 AATAACGATAAGCACTGAAGTGCAAAAT
1 AATAACGATAAGCACCGAAGTGCAAAAT
* * * *
2939974 AATATCTATAAGCACCGAATTGCAAATTT
1 AATAACGATAAGCACCGAAGTGCAAA-AT
* *
2940003 TACAACGATAAGCACCGAAGTGCAAAAT
1 AATAACGATAAGCACCGAAGTGCAAAAT
2940031 AAT-ACGATAAGC
1 AATAACGATAAGC
2940043 GCGCTAATTT
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
27 9 0.16
28 24 0.44
29 22 0.40
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (28 bp):
AATAACGATAAGCACCGAAGTGCAAAAT
Found at i:2953108 original size:21 final size:22
Alignment explanation
Indices: 2953084--2953133 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
2953074 CCAATTCAAG
*
2953084 ATCATGTGCCGGGTAATT-TTT
1 ATCATGTGCCAGGTAATTCTTT
*
2953105 ATCATGTGTCAGGTAATTCTTT
1 ATCATGTGCCAGGTAATTCTTT
2953127 -TCATGTG
1 ATCATGTG
2953134 GCTTTAGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (22 bp):
ATCATGTGCCAGGTAATTCTTT
Found at i:2955921 original size:19 final size:20
Alignment explanation
Indices: 2955897--2955946 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2955887 GTAATAGTAA
*
2955897 ATACATGTGTA-AAAATAAT
1 ATACATATGTATAAAATAAT
*
2955916 ATACATATGTATAAATTAAT
1 ATACATATGTATAAAATAAT
*
2955936 A-AAATATGTAT
1 ATACATATGTAT
2955947 TACCTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (20 bp):
ATACATATGTATAAAATAAT
Found at i:2956098 original size:22 final size:22
Alignment explanation
Indices: 2956031--2956101 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
2956021 ACAAATAAAT
*
2956031 AGAAAAAGA-AACAGAGATAGAA
1 AGAAAAAGAGAA-AGAGAAAGAA
** * *
2956053 ACTAAAACAGAAAGGGAAAGAA
1 AGAAAAAGAGAAAGAGAAAGAA
2956075 AGAAAAAGAGAAAGAGAAAGAA
1 AGAAAAAGAGAAAGAGAAAGAA
2956097 AGAAA
1 AGAAA
2956102 GGAGAAATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 37 0.95
23 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.24, T:0.03
Consensus pattern (22 bp):
AGAAAAAGAGAAAGAGAAAGAA
Found at i:2956794 original size:7 final size:7
Alignment explanation
Indices: 2956782--2956822 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
2956772 ATTTGTGATT
2956782 AATGTGA
1 AATGTGA
2956789 AATGTGA
1 AATGTGA
2956796 AATGTGA
1 AATGTGA
*
2956803 AATGTTA
1 AATGTGA
2956810 AATGTGA
1 AATGTGA
2956817 AATGTG
1 AATGTG
2956823 GATATTGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (7 bp):
AATGTGA
Found at i:2970237 original size:24 final size:24
Alignment explanation
Indices: 2970188--2970237 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2970178 GAGAAGTAAT
* *
2970188 TAAAATATATTTTTATATTTAAAA
1 TAAAATATATTATTATATATAAAA
2970212 TAAAATATATTATTAT-TATAATAA
1 TAAAATATATTATTATATATAA-AA
2970236 TA
1 TA
2970238 TTTTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATATATTATTATATATAAAA
Found at i:2973143 original size:23 final size:25
Alignment explanation
Indices: 2973098--2973143 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2973088 ATTAAACAAG
**
2973098 AATTAAAAAAATGAATGTGAAATAA
1 AATTAAAAAAATGAATGAAAAATAA
2973123 AATT-AAAAAATG-ATGAAAAAT
1 AATTAAAAAAATGAATGAAAAAT
2973144 TTAATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 8 0.42
25 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (25 bp):
AATTAAAAAAATGAATGAAAAATAA
Found at i:2974574 original size:45 final size:44
Alignment explanation
Indices: 2974510--2974807 Score: 212
Period size: 45 Copynumber: 6.7 Consensus size: 44
2974500 TCCGCTGCAA
* * *
2974510 CTGCTCCACTGCAACTTCAGGGAGATACGGTTGTGTATTTTTAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTGTGTAATTTCAT
* * * **
2974554 CCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTG-ACTTAGAT
1 -CTGCTCCACTGCAACTTCAGGGAGATAAGG-TTGTGTAATTTCAT
* * * *
2974599 CTGCTCCACTGCAACTTTAGGGAGATAAGATCTG-CTAACTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGT-TGTGTAATTTCA-T
* * *
2974644 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAG-GTTGTGTAATTTCAT
* * * ** *
2974689 CCTGCTCTACTACAACTTCAGAGAGATAAGGATTGTG-GCTTTGAT
1 -CTGCTCCACTGCAACTTCAGGGAGATAAGG-TTGTGTAATTTCAT
* * * * *
2974734 TTGCTCCACTGCAACCTCAGGGAGACAAGATCTG-CT-ATCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGT-TGTGTAAT-TTC-AT
*
2974779 CTGTTCCACTGCAAC-TCTAGGGAGATAAG
1 CTGCTCCACTGCAACTTC-AGGGAGATAAG
2974808 ACTTGTTTCT
Statistics
Matches: 198, Mismatches: 42, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
43 3 0.02
44 60 0.30
45 93 0.47
46 42 0.21
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGGTTGTGTAATTTCAT
Found at i:2974739 original size:135 final size:135
Alignment explanation
Indices: 2974510--2974812 Score: 439
Period size: 135 Copynumber: 2.3 Consensus size: 135
2974500 TCCGCTGCAA
* * * * * * *
2974510 CTGCTCCACTGCAACTTCAGGGAGATACG-GTTGTGTATTTTTATCCTGCTCTACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCATCCTGCTCTACTACAACTTCA
* * *
2974574 GAGAGATAAGGATTGTGACTTAGATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTAACT
66 GAGAGATAAGGATTGTGACTTAGATCTGCTCCACTGCAACCTCAGGGAGACAAGATCTGCTAACT
*
2974639 TCAGT
131 TCAAT
2974644 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCATCCTGCTCTACTACAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCATCCTGCTCTACTACAACTTCA
* * * *
2974709 GAGAGATAAGGATTGTGGCTTTGATTTGCTCCACTGCAACCTCAGGGAGACAAGATCTGCTATCT
66 GAGAGATAAGGATTGTGACTTAGATCTGCTCCACTGCAACCTCAGGGAGACAAGATCTGCTAACT
2974774 TCAAT
131 TCAAT
*
2974779 CTGTTCCACTGCAAC-TCTAGGGAGATAAGACTTG
1 CTGCTCCACTGCAACTTC-AGGGAGATAAGACTTG
2974813 TTTCTTCAAC
Statistics
Matches: 151, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
134 30 0.20
135 121 0.80
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (135 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCATCCTGCTCTACTACAACTTCA
GAGAGATAAGGATTGTGACTTAGATCTGCTCCACTGCAACCTCAGGGAGACAAGATCTGCTAACT
TCAAT
Found at i:2974897 original size:135 final size:135
Alignment explanation
Indices: 2974510--2974850 Score: 420
Period size: 135 Copynumber: 2.5 Consensus size: 135
2974500 TCCGCTGCAA
* * * * * * * **
2974510 CTGCTCCACTGCAACTTCAGGGAGATACG-GTTGTGTATTTTTATCCTGCTCTACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCAACCCACTCTACTGCAACTTCA
* *
2974574 GAGAGATAAGGATTGTGACTTAGATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTAACT
66 GAGAGATAAGGATTGTGACTTTGATCTGCTCCACTGCAACTTTAGGGAGACAAGATCTGCTAACT
*
2974639 TCAGT
131 TCAAT
* ** *
2974644 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCATCCTGCTCTACTACAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCAACCCACTCTACTGCAACTTCA
* * * * *
2974709 GAGAGATAAGGATTGTGGCTTTGATTTGCTCCACTGCAACCTCAGGGAGACAAGATCTGCTATCT
66 GAGAGATAAGGATTGTGACTTTGATCTGCTCCACTGCAACTTTAGGGAGACAAGATCTGCTAACT
2974774 TCAAT
131 TCAAT
* * **
2974779 CTGTTCCACTGCAAC-TCTAGGGAGATAAGACTT-GTTTCT-TCAACCCACTCTACTGCAACTTC
1 CTGCTCCACTGCAACTTC-AGGGAGATAAGACTTGGGTAATGTCAACCCACTCTACTGCAACTTC
2974841 AGAGAGATAA
65 AGAGAGATAA
2974851 AGTTTGCATA
Statistics
Matches: 182, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
133 29 0.16
134 33 0.18
135 120 0.66
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (135 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATGTCAACCCACTCTACTGCAACTTCA
GAGAGATAAGGATTGTGACTTTGATCTGCTCCACTGCAACTTTAGGGAGACAAGATCTGCTAACT
TCAAT
Found at i:2980331 original size:52 final size:52
Alignment explanation
Indices: 2980266--2980370 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 52
2980256 AACTTTAATT
* *
2980266 CTTCCCTGGAGATGTCTTCCA-AGCCCCTTTT-CTGGTAAAGCTCCTTTCCCTA
1 CTTCCCTGAAGATGTC-TCCACA-ACCCTTTTCCTGGTAAAGCTCCTTTCCCTA
* * *
2980318 CTTCCCTGAAGATGTCTCCACAATCTTTTTCCTGGTAAGGCTCCTTTCCCTA
1 CTTCCCTGAAGATGTCTCCACAACCCTTTTCCTGGTAAAGCTCCTTTCCCTA
2980370 C
1 C
2980371 CATCAACTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 9 0.20
52 37 0.80
ACGTcount: A:0.16, C:0.34, G:0.14, T:0.35
Consensus pattern (52 bp):
CTTCCCTGAAGATGTCTCCACAACCCTTTTCCTGGTAAAGCTCCTTTCCCTA
Found at i:2983204 original size:35 final size:35
Alignment explanation
Indices: 2983165--2983233 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
2983155 CCTTTTCCCT
2983165 TATCCATTCTTCTTATCAACAACTGGGACAACTAA
1 TATCCATTCTTCTTATCAACAACTGGGACAACTAA
*
2983200 TATCCATTCTTCTTATCAGCAACTGGGACAACTA
1 TATCCATTCTTCTTATCAACAACTGGGACAACTA
2983234 GCTCATCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (35 bp):
TATCCATTCTTCTTATCAACAACTGGGACAACTAA
Found at i:2988042 original size:12 final size:12
Alignment explanation
Indices: 2988027--2988061 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2988017 ATAATATACA
2988027 AAAAAAAATTAT
1 AAAAAAAATTAT
2988039 AAAAAAAATTAT
1 AAAAAAAATTAT
* *
2988051 ACAAAATATTA
1 AAAAAAAATTA
2988062 AAATGATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:2992388 original size:12 final size:13
Alignment explanation
Indices: 2992370--2992399 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2992360 GATTAATTTT
2992370 CTAAAAATAAAAA
1 CTAAAAATAAAAA
2992383 -TAAAAATAAAAA
1 CTAAAAATAAAAA
2992395 CTAAA
1 CTAAA
2992400 TTCTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
CTAAAAATAAAAA
Found at i:2996066 original size:47 final size:47
Alignment explanation
Indices: 2995997--2996090 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
2995987 ATTGATTTTA
2995997 GGACCTAATTGTGAAAAAGTTGTGAATTAAGGTTTAGTGTTAAAATT
1 GGACCTAATTGTGAAAAAGTTGTGAATTAAGGTTTAGTGTTAAAATT
*
2996044 GGACCTAATTGTGAAAAAGTTGTGAATTAAGGTTTAGTGTTATAATT
1 GGACCTAATTGTGAAAAAGTTGTGAATTAAGGTTTAGTGTTAAAATT
2996091 CTGATTTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (47 bp):
GGACCTAATTGTGAAAAAGTTGTGAATTAAGGTTTAGTGTTAAAATT
Found at i:2998383 original size:43 final size:42
Alignment explanation
Indices: 2998292--2998412 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 42
2998282 AACTTATGAT
* * * ** *
2998292 TTACGTGTAAGACTACGTCT-GGACGTTGGCATCGTATTTAA
1 TTACATGTAAGACCATGTCTGGGACAATGGCATTGTATTTAA
* * * *
2998333 TTTCATGTAAGACCTTGTTTGGGACAATGGCATTGATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAATGGCATTG-TATTTAA
**
2998376 TTACATGTAAGACCATGTCTGGGACGTTGGCATTGTA
1 TTACATGTAAGACCATGTCTGGGACAATGGCATTGTA
2998413 CGAGCTTTCT
Statistics
Matches: 63, Mismatches: 15, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
41 14 0.22
42 13 0.21
43 36 0.57
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACAATGGCATTGTATTTAA
Found at i:2999168 original size:10 final size:10
Alignment explanation
Indices: 2999128--2999170 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
2999118 TATTGAAACA
*
2999128 TATGCTTTGG
1 TATGATTTGG
2999138 TATGATTTTGG
1 TATGA-TTTGG
*
2999149 TTTAGATTTGG
1 TAT-GATTTGG
2999160 TATGATTTGG
1 TATGATTTGG
2999170 T
1 T
2999171 TGGTGAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.43
11 14 0.50
12 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.28, T:0.53
Consensus pattern (10 bp):
TATGATTTGG
Found at i:3002241 original size:26 final size:26
Alignment explanation
Indices: 3002212--3002284 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
3002202 TCTCATCTCC
*
3002212 ATTTTACCCCTAGTAAAATTTTGACG
1 ATTTTACCCCTAGTAAAATTTTAACG
*
3002238 ATTTTACCCCTGGTAAAATTTTAACG
1 ATTTTACCCCTAGTAAAATTTTAACG
*
3002264 ATTTTGCCCCTAGTAAAATTT
1 ATTTTACCCCTAGTAAAATTT
3002285 CAAGAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTAACG
Found at i:3011615 original size:23 final size:23
Alignment explanation
Indices: 3011589--3011703 Score: 117
Period size: 23 Copynumber: 4.9 Consensus size: 23
3011579 ACAGCTCGTA
*
3011589 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTGTTTCAGCTCAAT
* *
3011612 AGAGCTTACCGATTCAGCTCGAA-
1 AGAGCTTACTGTTTCAGCTC-AAT
3011635 AGAGCTTACTG-TTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
* *
3011657 AGAGCTTACCGTTTTCAGTTCAAT
1 AGAGCTTACTG-TTTCAGCTCAAT
* *
3011681 GGACCTTACTGTTTATCAGCTCA
1 AGAGCTTACTG-TT-TCAGCTCA
3011704 GGAGGAGCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.03
22 18 0.23
23 28 0.36
24 22 0.29
25 7 0.09
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:3011674 original size:46 final size:46
Alignment explanation
Indices: 3011580--3011667 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
3011570 AGACTCACCA
* *
3011580 CAGCTCGTAAGAGCTTACTGTTTCAGCTCATTAGAGCTTACCGATT
1 CAGCTCGAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCGATT
3011626 CAGCTCGAAAGAGCTTACTG-TTCAGCTCAATAGAGCTTACCG
1 CAGCTCGAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCG
3011668 TTTTCAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (46 bp):
CAGCTCGAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCGATT
Found at i:3011689 original size:46 final size:45
Alignment explanation
Indices: 3011580--3011693 Score: 131
Period size: 46 Copynumber: 2.5 Consensus size: 45
3011570 AGACTCACCA
* * *
3011580 CAGCTCGTAAGAGCTTACTGTTTCAGCTCATTAGAGCTTACCGATT
1 CAGCTCGAAAGACCTTACTG-TTCAGCTCAATAGAGCTTACCGATT
* *
3011626 CAGCTCGAAAGAGCTTACTGTTCAGCTCAATAGAGCTTACCGTTTT
1 CAGCTCGAAAGACCTTACTGTTCAGCTCAATAGAGCTTACCG-ATT
* *
3011672 CAGTTC-AATGGACCTTACTGTT
1 CAGCTCGAA-AGACCTTACTGTT
3011694 TATCAGCTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
45 23 0.38
46 37 0.62
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
CAGCTCGAAAGACCTTACTGTTCAGCTCAATAGAGCTTACCGATT
Found at i:3012905 original size:10 final size:10
Alignment explanation
Indices: 3012878--3012917 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
3012868 TTAAATTCTA
3012878 AAAGATAAAT
1 AAAGATAAAT
3012888 ACAA-ATAAAT
1 A-AAGATAAAT
*
3012898 AAAGATAATT
1 AAAGATAAAT
3012908 AAAGATAAAT
1 AAAGATAAAT
3012918 GGAAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:3013584 original size:18 final size:18
Alignment explanation
Indices: 3013550--3013583 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3013540 ATACATCTAT
*
3013550 TTTTTTTCTATTTTTTTC
1 TTTTTTCCTATTTTTTTC
3013568 TTTTTTCCT-TTTTTTT
1 TTTTTTCCTATTTTTTT
3013584 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTCCTATTTTTTTC
Found at i:3013786 original size:99 final size:99
Alignment explanation
Indices: 3013602--3013890 Score: 404
Period size: 99 Copynumber: 2.9 Consensus size: 99
3013592 TTTAATTAAT
* * * *
3013602 TAATTTATCTAT-TTTTGCTTAAGAATAAATTGAACCTTTTGACGTGAAGAGAGATGACAGCCAA
1 TAATTTAT-TATATTTTTCTTAAGAATATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAA
*
3013666 GCATCC-CACCACGGTTACTCAGCCCAAGATACTCC
65 GCA-CCTCACCACGATTACTCAGCCCAAGATACTCC
*
3013701 TAATTTATTATATTTTTCTTAAGAATATGTCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAG
1 TAATTTATTATATTTTTCTTAAGAATATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAG
* *
3013766 CACCTCACTC-CGATTGCTCAGCCCAATATACTCC
66 CACCTCAC-CACGATTACTCAGCCCAAGATACTCC
* * *
3013800 TAATTTATTATATTTTTCTTAAGAATATATCAAACCTTTTGACGCAAAGAGAGATGATAGCCAAG
1 TAATTTATTATATTTTTCTTAAGAATATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAG
* * *
3013865 CACCTTACCTCGGTTACTCAGCCCAA
66 CACCTCACCACGATTACTCAGCCCAA
3013891 CACATTCTTA
Statistics
Matches: 171, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
98 6 0.04
99 164 0.96
100 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (99 bp):
TAATTTATTATATTTTTCTTAAGAATATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAG
CACCTCACCACGATTACTCAGCCCAAGATACTCC
Found at i:3014910 original size:25 final size:24
Alignment explanation
Indices: 3014882--3014930 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3014872 ATATCCAAAC
*
3014882 AAAATAAAATAATAAATAATAAAAT
1 AAAATAAAATAAAAAATAA-AAAAT
* *
3014907 AAAATAGAGTAAAAAATAAAAAAT
1 AAAATAAAATAAAAAATAAAAAAT
3014931 TTACGTTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAATAAAATAAAAAATAAAAAAT
Found at i:3015359 original size:89 final size:89
Alignment explanation
Indices: 3015256--3015441 Score: 354
Period size: 89 Copynumber: 2.1 Consensus size: 89
3015246 GTATCCATAG
*
3015256 GAGCCAATAATTCATTAATAGATTCAAAATCATTAAACATCATTTTAGATTTATCTCCATAAGAT
1 GAGCCAATAATTCATTAATAGATTCAAAATCATCAAACATCATTTTAGATTTATCTCCATAAGAT
3015321 GACTTAAAAGTTTCTTCTACTAAT
66 GACTTAAAAGTTTCTTCTACTAAT
3015345 GAGCCAATAATTCATTAATAGATTCAAAATCATCAAACATCATTTTAGATTTATCTCCATAAGAT
1 GAGCCAATAATTCATTAATAGATTCAAAATCATCAAACATCATTTTAGATTTATCTCCATAAGAT
3015410 GACTTAAAAGTTTCTTCTACTAAT
66 GACTTAAAAGTTTCTTCTACTAAT
*
3015434 GAGTCAAT
1 GAGCCAAT
3015442 TATGTCGACA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 95 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (89 bp):
GAGCCAATAATTCATTAATAGATTCAAAATCATCAAACATCATTTTAGATTTATCTCCATAAGAT
GACTTAAAAGTTTCTTCTACTAAT
Found at i:3025575 original size:42 final size:42
Alignment explanation
Indices: 3025516--3025633 Score: 146
Period size: 43 Copynumber: 2.8 Consensus size: 42
3025506 AGGGTTAGTT
3025516 GAGATTACATGTAAGACCATATCTGGGATATGGAATCGATAC
1 GAGATTACATGTAAGACCATATCTGGGATATGGAATCGATAC
* * * * *
3025558 GAGATTTCATGTAAGACCATAGCTGGGCTATTGGTATCGATAT
1 GAGATTACATGTAAGACCATATCTGGGATA-TGGAATCGATAC
* ** *
3025601 AAGATCCCATGTAAGACCATATCTAGGATATGG
1 GAGATTACATGTAAGACCATATCTGGGATATGG
3025634 CATTGGTATG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 30 0.47
43 34 0.53
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (42 bp):
GAGATTACATGTAAGACCATATCTGGGATATGGAATCGATAC
Found at i:3035894 original size:6 final size:6
Alignment explanation
Indices: 3035883--3035929 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
3035873 GAAAATGGAT
3035883 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
3035930 TTGGAAACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (6 bp):
CATTTC
Found at i:3058506 original size:28 final size:28
Alignment explanation
Indices: 3058466--3058524 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
3058456 CAACAATAAA
3058466 TCTGAAAGAGGAAATATGTGTTGTTCTT
1 TCTGAAAGAGGAAATATGTGTTGTTCTT
3058494 TCTGAAAGAGGAAATATGTGTTGTTCTT
1 TCTGAAAGAGGAAATATGTGTTGTTCTT
3058522 TCT
1 TCT
3058525 TGGCATTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (28 bp):
TCTGAAAGAGGAAATATGTGTTGTTCTT
Found at i:3059935 original size:56 final size:55
Alignment explanation
Indices: 3059875--3059979 Score: 138
Period size: 56 Copynumber: 1.9 Consensus size: 55
3059865 TCCTCTTAAT
** * *
3059875 TGTTGAAATGTTGCTTCTTTTGAATATATTTTTTTATATATTTAAATCGATTGTCA
1 TGTTGAAATACTGCTTCTTTTGAATAGA-TTATTTATATATTTAAATCGATTGTCA
* * *
3059931 TGTTGGAATACTGCTTCTTTTGAATCGATTATTTATATGTTTAAATCGA
1 TGTTGAAATACTGCTTCTTTTGAATAGATTATTTATATATTTAAATCGA
3059980 CTGTTACATG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 19 0.45
56 23 0.55
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (55 bp):
TGTTGAAATACTGCTTCTTTTGAATAGATTATTTATATATTTAAATCGATTGTCA
Found at i:3060328 original size:41 final size:41
Alignment explanation
Indices: 3060231--3060362 Score: 113
Period size: 41 Copynumber: 3.2 Consensus size: 41
3060221 AACCTTGTAG
* *
3060231 GCTTCGTGCTAGTGTAACGATTTTGGCCTTGAGCCTAGCAA
1 GCTTCGTGCTAGTGTAACGATTTAGGCCTTGAGCCTAGTAA
* * * * ** * *
3060272 ACCTCATACCGGTGTAACGATTTAAGCCTTGAGCCTAGTAC
1 GCTTCGTGCTAGTGTAACGATTTAGGCCTTGAGCCTAGTAA
* * * * *
3060313 GCTTCGTGCTTGTGT-ATGAAATCAGGCCTTGAGCCTAGTAG
1 GCTTCGTGCTAGTGTAACG-ATTTAGGCCTTGAGCCTAGTAA
3060354 GCTTCGTGC
1 GCTTCGTGC
3060363 CAATTTAGTG
Statistics
Matches: 69, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
40 2 0.03
41 67 0.97
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.30
Consensus pattern (41 bp):
GCTTCGTGCTAGTGTAACGATTTAGGCCTTGAGCCTAGTAA
Found at i:3064956 original size:131 final size:131
Alignment explanation
Indices: 3064722--3065280 Score: 650
Period size: 131 Copynumber: 4.3 Consensus size: 131
3064712 TTACTTTATC
*
3064722 TATCATGAATAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
** * * * * *
3064787 AAGATTGCAGCTGATATCGTTAAGGTTCGTTGATTTAAGATCACAACTTAAGTTCATTCAATTTA
66 AAGATCACAGCTAATATCATTAAGGTTCGTTAATTTAAGATCACAACCTAAGTTTATTCAATTTA
3064852 A
131 A
* * *
3064853 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCACTACTTCAAACAACTCATTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
*** * * **
3064918 AAGATTGTAGCTAATATCATTAAGGTTCGTTAATTTAAGACCACAACCTAAGTTAATTTGATTTA
66 AAGATCACAGCTAATATCATTAAGGTTCGTTAATTTAAGATCACAACCTAAGTTTATTCAATTTA
3064983 A
131 A
* * * *
3064984 TATCATGAACAATCTTATTTAAGTTAGCTAATTTAATATTGCTACTCCAAACAACTCGCTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
* * ** ** *** * * **
3065049 AAGATCACAACTAATTTTTGTTAAGGTTCACTAATTTAAGATTGTAGCTTAAGTTTATTTGATTT
66 AAGATCACAGCTAA-TATCATTAAGGTTCGTTAATTTAAGATCACAACCTAAGTTTATTCAATTT
3065114 AA
130 AA
* * * * * * ** *
3065116 TATTATCAACAATCATATTTGAGTTAGCTAATTTACTATCGCTACTCCAAATAGTTCGCTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
* * * * *
3065181 AAGATCATAGTTGACATCATTAAGGTTCGTTGATTTAAGATCACAACCTAAGTTTATTCAATTTA
66 AAGATCACAGCTAATATCATTAAGGTTCGTTAATTTAAGATCACAACCTAAGTTTATTCAATTTA
3065246 A
131 A
* *
3065247 TATCATGAACAATCTCATTTGTGTTAGCTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTT
3065281 TCCAAACAAT
Statistics
Matches: 358, Mismatches: 69, Indels: 2
0.83 0.16 0.00
Matches are distributed among these distances:
131 252 0.70
132 106 0.30
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (131 bp):
TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
AAGATCACAGCTAATATCATTAAGGTTCGTTAATTTAAGATCACAACCTAAGTTTATTCAATTTA
A
Found at i:3065202 original size:263 final size:262
Alignment explanation
Indices: 3064722--3065280 Score: 704
Period size: 263 Copynumber: 2.1 Consensus size: 262
3064712 TTACTTTATC
*
3064722 TATCATGAATAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
** * * ** *
3064787 AAGATTGCAGCTGATATCGTTAAGGTTCGTTGATTTAAGATCACAACTTAAGTTCATTCAATTTA
66 AAGATCACAACTAATATCGTTAAGGTTCACTAATTTAAGATCACAACTTAAGTTCATTCAATTTA
* * * * *
3064852 ATATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCACTACTTCAAACAACTCATTGATT
131 ATATCATCAACAATCATATTTGAGTTAGCTAATTTAATATCACTACTCCAAACAACTCACTGATT
** * **
3064917 TAAGATTGTAGCTAATATCATTAAGGTTCGTTAATTTAAGACCACAACCTAAGTTAATTTGATTT
196 TAAGATCATAGCTAACATCATTAAGGTTCGTTAATTTAAGACCACAACCTAAGTTAATTCAATTT
3064982 AA
261 AA
* * * *
3064984 TATCATGAACAATCTTATTTAAGTTAGCTAATTTAATATTGCTACTCCAAACAACTCGCTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
* * *** * * **
3065049 AAGATCACAACTAATTTTTGTTAAGGTTCACTAATTTAAGATTGTAGCTTAAGTTTATTTGATTT
66 AAGATCACAACTAA-TATCGTTAAGGTTCACTAATTTAAGATCACAACTTAAGTTCATTCAATTT
* * * * ** *
3065114 AATATTATCAACAATCATATTTGAGTTAGCTAATTTACTATCGCTACTCCAAATAGTTCGCTGAT
130 AATATCATCAACAATCATATTTGAGTTAGCTAATTTAATATCACTACTCCAAACAACTCACTGAT
* * * * *
3065179 TTAAGATCATAGTTGACATCATTAAGGTTCGTTGATTTAAGATCACAACCTAAGTTTATTCAATT
195 TTAAGATCATAGCTAACATCATTAAGGTTCGTTAATTTAAGACCACAACCTAAGTTAATTCAATT
3065244 TAA
260 TAA
* *
3065247 TATCATGAACAATCTCATTTGTGTTAGCTGATTT
1 TATCATGAACAATCTTATTTGAGTTAGCTGATTT
3065281 TCCAAACAAT
Statistics
Matches: 249, Mismatches: 47, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
262 70 0.28
263 179 0.72
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (262 bp):
TATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCCAAACAACTCACTGATTT
AAGATCACAACTAATATCGTTAAGGTTCACTAATTTAAGATCACAACTTAAGTTCATTCAATTTA
ATATCATCAACAATCATATTTGAGTTAGCTAATTTAATATCACTACTCCAAACAACTCACTGATT
TAAGATCATAGCTAACATCATTAAGGTTCGTTAATTTAAGACCACAACCTAAGTTAATTCAATTT
AA
Found at i:3069118 original size:25 final size:25
Alignment explanation
Indices: 3069089--3069138 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3069079 CTTAATTGTG
3069089 AAAAAGTTTAGAATTAGGGTTTGGT
1 AAAAAGTTTAGAATTAGGGTTTGGT
3069114 AAAAAGTTTAGAATTAGGGTTTGGT
1 AAAAAGTTTAGAATTAGGGTTTGGT
3069139 GCTAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (25 bp):
AAAAAGTTTAGAATTAGGGTTTGGT
Found at i:3071640 original size:14 final size:14
Alignment explanation
Indices: 3071621--3071648 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3071611 CAAAATACGA
3071621 CTCATTTCTTCCTC
1 CTCATTTCTTCCTC
3071635 CTCATTTCTTCCTC
1 CTCATTTCTTCCTC
3071649 GTTAGTGATG
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:0.07, C:0.43, G:0.00, T:0.50
Consensus pattern (14 bp):
CTCATTTCTTCCTC
Found at i:3080527 original size:12 final size:12
Alignment explanation
Indices: 3080510--3080534 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3080500 TGTGAAAAAT
3080510 AAAATAAAATAA
1 AAAATAAAATAA
3080522 AAAATAAAATAA
1 AAAATAAAATAA
3080534 A
1 A
3080535 GAAACACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:3081397 original size:42 final size:42
Alignment explanation
Indices: 3081333--3081421 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
3081323 TCCTAATTGG
* *
3081333 GAAAATAATTCCATTGTTCTAATAAACTACTAAAATATAAAA
1 GAAAATAATTCCATTGTCCTAATAAACTACTAAAAGATAAAA
*
3081375 GAAAATAGTTTCC-TTGTCCTAATAAACTACTAAAAGATAAAA
1 GAAAATA-ATTCCATTGTCCTAATAAACTACTAAAAGATAAAA
*
3081417 TAAAA
1 GAAAA
3081422 ATATTCCTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (42 bp):
GAAAATAATTCCATTGTCCTAATAAACTACTAAAAGATAAAA
Found at i:3084313 original size:56 final size:56
Alignment explanation
Indices: 3084227--3084335 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
3084217 GATGTTTAGT
*
3084227 CAATTCACAAAATTCACAATGATATGAAAAAGGACTTTTATTTTTAAATAGATAGC
1 CAATTCACAAAATTCACAATGATATGAAAAAGGACTTTTATTTTTAAAAAGATAGC
3084283 CAATTCACAAAATTCACAATGATATGAAAAAGGACTTTTATTTTTAAAAAGAT
1 CAATTCACAAAATTCACAATGATATGAAAAAGGACTTTTATTTTTAAAAAGAT
3084336 TAGGTAACAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (56 bp):
CAATTCACAAAATTCACAATGATATGAAAAAGGACTTTTATTTTTAAAAAGATAGC
Done.