Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009437.1 Hibiscus syriacus cultivar Beakdansim tig00113495_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 392309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:258506 original size:6 final size:6
Alignment explanation
Indices: 258489--258549 Score: 113
Period size: 6 Copynumber: 10.0 Consensus size: 6
258479 CTTGCCTACC
258489 ATTACAA ATTACA ATTACA ATTACA ATTACA ATTACA ATTACA ATTACA
1 ATTAC-A ATTACA ATTACA ATTACA ATTACA ATTACA ATTACA ATTACA
258538 ATTACA ATTACA
1 ATTACA ATTACA
258550 TATTCATAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 49 0.91
7 5 0.09
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTACA
Found at i:260819 original size:4 final size:4
Alignment explanation
Indices: 260810--260856 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
260800 TCAAAAGCTA
260810 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCT
260857 ATCTATCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.00, C:0.26, G:0.23, T:0.51
Consensus pattern (4 bp):
TCTG
Found at i:260861 original size:4 final size:4
Alignment explanation
Indices: 260854--263992 Score: 5996
Period size: 4 Copynumber: 791.0 Consensus size: 4
260844 TGTCTGTCTG
260854 TCTA TCTA TCTA TCTA TCTA TC-A GTCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA -TCTA TCTA TCTA TCTA TCTA TCTA
260902 TCTA TCTA TC-A GTCTA TC-A GTCTA TC-A GTCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA -TCTA TCTA -TCTA TCTA -TCTA TCTA TCTA TCTA TCTA
260950 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
260998 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261046 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261094 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261142 TCTA TCTA TCTA T-TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261189 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261237 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261285 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261333 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261381 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261429 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261477 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261525 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261573 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261621 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261667 TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261713 TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261759 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261807 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261855 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261903 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261951 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
261999 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262047 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262095 TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262141 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262189 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262237 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262285 TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262331 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262379 --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262425 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262473 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262521 TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262567 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
262615 TATA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262663 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262711 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262759 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262807 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
262855 TCTA TCTA TCTA TCTA TCTA TATA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262903 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262951 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
262999 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263047 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263095 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263143 TCTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263189 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263235 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263283 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263331 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263379 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263427 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263475 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263523 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263571 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263619 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263667 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263715 TCTA TCTA TCTA TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263761 TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263807 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
263855 TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA TATA TCTA -CTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263900 TCCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 T-CTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263949 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
263993 ATGGTGTGGA
Statistics
Matches: 3094, Mismatches: 6, Indels: 70
0.98 0.00 0.02
Matches are distributed among these distances:
2 24 0.01
3 10 0.00
4 3052 0.99
5 8 0.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:265576 original size:16 final size:17
Alignment explanation
Indices: 265555--265611 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 17
265545 CAAGAGCTCC
*
265555 AGGGGTGGCACTT-TTG
1 AGGGGTGACACTTGTTG
*
265571 AGGGGTGACACTTGTATA
1 AGGGGTGACACTTGT-TG
* *
265589 AGGGGTGTCACTTGTGG
1 AGGGGTGACACTTGTTG
265606 AGGGGT
1 AGGGGT
265612 TGCTTGGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
18 15 0.44
ACGTcount: A:0.18, C:0.11, G:0.44, T:0.28
Consensus pattern (17 bp):
AGGGGTGACACTTGTTG
Found at i:265956 original size:28 final size:27
Alignment explanation
Indices: 265924--265999 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
265914 AAATATTAGT
265924 AATTTATTATAAAATATATAAATT-TAA
1 AATTTATTATAAAATATAT-AATTATAA
** * *
265951 CAATTTAAAATATAATAAATAATTATAA
1 -AATTTATTATAAAATATATAATTATAA
265979 ATATATTATTATAAAATATAT
1 A-AT-TTATTATAAAATATAT
266000 TATTTTAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
27 5 0.14
28 20 0.54
29 12 0.32
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTTATTATAAAATATATAATTATAA
Found at i:265989 original size:14 final size:15
Alignment explanation
Indices: 265972--266003 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
265962 ATAATAAATA
265972 ATTAT-AAATATATT
1 ATTATAAAATATATT
265986 ATTATAAAATATATT
1 ATTATAAAATATATT
266001 ATT
1 ATT
266004 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:267969 original size:16 final size:16
Alignment explanation
Indices: 267948--267979 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
267938 AATAAATAAG
267948 CGAACATAAACGAACA
1 CGAACATAAACGAACA
267964 CGAACATAAACGAACA
1 CGAACATAAACGAACA
267980 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:268059 original size:10 final size:10
Alignment explanation
Indices: 268044--268118 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
268034 CATTTAATAA
268044 ATAAACGAAC
1 ATAAACGAAC
268054 ATAAACGAAC
1 ATAAACGAAC
*
268064 ----ACAAAC
1 ATAAACGAAC
268070 ATAAACGAAC
1 ATAAACGAAC
** *
268080 ACGAAC-ATAA
1 ATAAACGA-AC
268090 ATGAACACGAAC
1 AT-AA-ACGAAC
268102 ATAAACGAAC
1 ATAAACGAAC
268112 ATAAACG
1 ATAAACG
268119 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:268072 original size:16 final size:16
Alignment explanation
Indices: 268051--268117 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
268041 TAAATAAACG
268051 AACATAAACGAACACA
1 AACATAAACGAACACA
*
268067 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
268083 AACATAAATGAACACG
1 AACATAAACGAACACA
*
268099 AACATAAACGAACATA
1 AACATAAACGAACACA
268115 AAC
1 AAC
268118 GTTGGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:268084 original size:32 final size:32
Alignment explanation
Indices: 268048--268112 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
268038 TAATAAATAA
268048 ACGAACATAAACGAACACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
* *
268080 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
268112 A
1 A
268113 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAC
Found at i:269688 original size:24 final size:24
Alignment explanation
Indices: 269627--269688 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
269617 TATTAGGTTA
*
269627 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
269651 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
269675 AACATAACCGAACG
1 AACATAACTGAACG
269689 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:275130 original size:27 final size:27
Alignment explanation
Indices: 275092--275147 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
275082 TGGTTTTGGC
275092 ATCCTTTCATGCCGATAATGCACCCAT
1 ATCCTTTCATGCCGATAATGCACCCAT
275119 ATCCTTTCATGCCGATAATGCACCCAT
1 ATCCTTTCATGCCGATAATGCACCCAT
275146 AT
1 AT
275148 ACATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (27 bp):
ATCCTTTCATGCCGATAATGCACCCAT
Found at i:278385 original size:68 final size:68
Alignment explanation
Indices: 278185--278390 Score: 268
Period size: 68 Copynumber: 3.0 Consensus size: 68
278175 AAAGATTAAT
* * *
278185 GGCCTAGCTGTGCATTTGATAGAAATGGTGTCAATTATGCCAGTTAGATGAAACGCTAAGCGCCT
1 GGCCTAGCTGTGCATTTGACAGAAAT-GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
278250 TTGA
65 TTGA
* * * * * * *
278254 GGCCTAGCTCTACATGTGACAGAAAGGTGTCAATTATGCCATTTACATGAAAGACTAAGTGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
278319 TGA
66 TGA
* * * * *
278322 GGCCTAGCTGTGCATTTGACAAAAATGTGTCAATTATACTAGTTAGATGAAAGGTTAAATGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
278387 TGA
66 TGA
278390 G
1 G
278391 CAAAAGACTA
Statistics
Matches: 115, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
68 94 0.82
69 21 0.18
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (68 bp):
GGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:278492 original size:45 final size:45
Alignment explanation
Indices: 278423--278594 Score: 220
Period size: 45 Copynumber: 3.8 Consensus size: 45
278413 TGCATAACAT
278423 TGTATAAAA-GACATGAAAGGATGCCATAAATAAAATGTATAATAG
1 TGTATAAAAGGA-ATGAAAGGATGCCATAAATAAAATGTATAATAG
* * ** *
278468 TGTATAAAATGAATGAAAGAATGCCATAAAGGAAATGTATAAGAG
1 TGTATAAAAGGAATGAAAGGATGCCATAAATAAAATGTATAATAG
* * * *
278513 TGCATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAA
1 TGTATAAAAGGAATGAAAGGATGCCATAAATAAAATGTATAATAG
* * *
278558 TGTATAAAAGGCATGAAATGATGCCACAAATAAAATG
1 TGTATAAAAGGAATGAAAGGATGCCATAAATAAAATG
278595 CATATGGGTG
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
45 109 0.98
46 2 0.02
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.23
Consensus pattern (45 bp):
TGTATAAAAGGAATGAAAGGATGCCATAAATAAAATGTATAATAG
Found at i:278504 original size:22 final size:22
Alignment explanation
Indices: 278479--278549 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
278469 GTATAAAATG
278479 AATGAAAGAATGCCATAAAGGA
1 AATGAAAGAATGCCATAAAGGA
*
278501 AATGTATAAGAGTG-CATAAAAGG-
1 AATG-A-AAGAATGCCAT-AAAGGA
* * *
278524 CATGAAAGGATGCCATAAATGA
1 AATGAAAGAATGCCATAAAGGA
278546 AATG
1 AATG
278550 TATAATAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 9 0.24
22 11 0.29
23 7 0.18
24 11 0.29
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.18
Consensus pattern (22 bp):
AATGAAAGAATGCCATAAAGGA
Found at i:278522 original size:24 final size:24
Alignment explanation
Indices: 278455--278523 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
278445 GCCATAAATA
* * *
278455 AAATGTATAATAGTGTATAAAATG
1 AAATGTATAAGAGTGCATAAAAGG
*
278479 -AATG-A-AAGAATGCCAT-AAAGG
1 AAATGTATAAGAGTG-CATAAAAGG
278500 AAATGTATAAGAGTGCATAAAAGG
1 AAATGTATAAGAGTGCATAAAAGG
278524 CATGAAAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
21 9 0.26
22 7 0.20
23 8 0.23
24 11 0.31
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.23
Consensus pattern (24 bp):
AAATGTATAAGAGTGCATAAAAGG
Found at i:278549 original size:90 final size:89
Alignment explanation
Indices: 278426--278728 Score: 322
Period size: 90 Copynumber: 3.4 Consensus size: 89
278416 ATAACATTGT
* * * *
278426 ATAAAAGACATGAAAGGATGCCATAAATAAAATGTATAATAGTGTATAAAATGAATGAAAGAATG
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAG-ATG
* *
278491 CCATAAAGGAAATGTATAAGAGTGC
65 CCATAAATGAAATGTATATGAGTGC
*
278516 ATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAATGTATAAAAGGCATGAAATGATG
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAA-GATG
* * * *
278581 CCACAAATAAAATGCATATGGGTGC
65 CCATAAATGAAATGTATATGAGTGC
* ** * * * * ** *
278606 ATTATTGGCAAGAAAGGATGCCATAAATGAAATGCAT-ATAGGTGCATTATCGGCACGAAAGGAT
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATA-GTGTATAAAAGGCATGAAA-GAT
*
278670 GTCATAAATGAAATGTATATGAGTGC
64 GCCATAAATGAAATGTATATGAGTGC
* ** *
278696 ATTATTGGCACGAAA-GATGCCATAAATGAAATG
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAATG
278729 CATATGGGTG
Statistics
Matches: 182, Mismatches: 29, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
89 21 0.12
90 160 0.88
91 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (89 bp):
ATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGATGC
CATAAATGAAATGTATATGAGTGC
Found at i:278626 original size:45 final size:45
Alignment explanation
Indices: 278480--278880 Score: 412
Period size: 45 Copynumber: 8.9 Consensus size: 45
278470 TATAAAATGA
* * * * * * **
278480 ATGAAAGAATGCCATAAAGGAAATGTATAAGAGTGCATAAAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
* ** * * **
278525 ATGAAAGGATGCCATAAATGAAATGTATAAT-AATGTATAAAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCAT-ATGGGTGCATTATCGGC
* * * *
278570 ATGAAATGATGCCACAAATAAAATGCATATGGGTGCATTATTGGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
* *
278615 AAGAAAGGATGCCATAAATGAAATGCATATAGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
* * * * *
278660 ACGAAAGGATGTCATAAATGAAATGTATATGAGTGCATTATTGGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
*
278705 ACGAAA-GATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
* * * * * *
278749 ATGAAAGGATGTCATAATTAAAATGCATAAGGGTGTATTATCAGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
* * *
278794 ATGAAAGGATGCCATAATTGAAATGCACATGGGTGCATTATTGGC
1 ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
* *
278839 ATGAAAGAATGCCATTAATGAACATGCATAAT-GGTGCATTAT
1 ATGAAAGGATGCCATAAATGAA-ATGCAT-ATGGGTGCATTAT
278881 ATGTATGAAG
Statistics
Matches: 302, Mismatches: 49, Indels: 9
0.84 0.14 0.03
Matches are distributed among these distances:
44 41 0.14
45 243 0.80
46 16 0.05
47 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (45 bp):
ATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCGGC
Found at i:284712 original size:45 final size:45
Alignment explanation
Indices: 284654--284862 Score: 278
Period size: 45 Copynumber: 4.6 Consensus size: 45
284644 TTTTATGTTG
* * * *
284654 ATAATGCATCCATATGCATT-TCCACTATGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTAT-TATTTTGACATCCTTTCATGCCA
* * * *
284699 ATAATGCACCCATATGCATTATTGTTTTGGCATCCTTTCATGTCG
1 ATAATGCACCCATATGCATTATTATTTTGACATCCTTTCATGCCA
* * *
284744 ATAATGCACCCATATGCATTATTATTTTGGCATCCATTCATGCCG
1 ATAATGCACCCATATGCATTATTATTTTGACATCCTTTCATGCCA
*
284789 ATAATGCACCCATATGCATTATTATTTT-AGCATCATTTCATGCCA
1 ATAATGCACCCATATGCATTATTATTTTGA-CATCCTTTCATGCCA
284834 ATAATGCACCCATATGCATTATTATTTTG
1 ATAATGCACCCATATGCATTATTATTTTG
284863 TTCATTCGTT
Statistics
Matches: 146, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
45 145 0.99
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTATTATTTTGACATCCTTTCATGCCA
Found at i:284778 original size:90 final size:90
Alignment explanation
Indices: 284592--284862 Score: 312
Period size: 90 Copynumber: 3.0 Consensus size: 90
284582 TTCATTAATA
*** * * * * * *
284592 ACATCCATTCATGTTTATAATGCACCAATATACATT-TTCAATTATAGCATACTTTTATGTTGAT
1 ACATCCATTCATGCCAATAATGCACCCATATGCATTATT--ATTTTAGCATCCTTTCATGTCGAT
* * * *
284656 AATGCATCCATATGCATT-TCCACTATG
64 AATGCACCCATATGCATTAT-TATTTTG
* * *
284683 ACATCCTTTCATGCCAATAATGCACCCATATGCATTATTGTTTTGGCATCCTTTCATGTCGATAA
1 ACATCCATTCATGCCAATAATGCACCCATATGCATTATTATTTTAGCATCCTTTCATGTCGATAA
284748 TGCACCCATATGCATTATTATTTTG
66 TGCACCCATATGCATTATTATTTTG
* * * * *
284773 GCATCCATTCATGCCGATAATGCACCCATATGCATTATTATTTTAGCATCATTTCATGCCAATAA
1 ACATCCATTCATGCCAATAATGCACCCATATGCATTATTATTTTAGCATCCTTTCATGTCGATAA
284838 TGCACCCATATGCATTATTATTTTG
66 TGCACCCATATGCATTATTATTTTG
284863 TTCATTCGTT
Statistics
Matches: 154, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
90 121 0.79
91 31 0.20
92 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (90 bp):
ACATCCATTCATGCCAATAATGCACCCATATGCATTATTATTTTAGCATCCTTTCATGTCGATAA
TGCACCCATATGCATTATTATTTTG
Found at i:292142 original size:20 final size:21
Alignment explanation
Indices: 292119--292234 Score: 62
Period size: 19 Copynumber: 5.5 Consensus size: 21
292109 AAATATAAAT
*
292119 ATAAATATTATTAT-ATTTTA
1 ATAAATATTATTATAATTATA
*
292139 ATAAA-AATATTATAATTATA
1 ATAAATATTATTATAATTATA
*
292159 TTAAATATTTATTA-AA--ATA
1 ATAAATA-TTATTATAATTATA
* *
292178 AAAAATATATATTATTAAGTATA
1 ATAAATAT-TATTA-TAATTATA
* * * *
292201 TTAATTACTTATTAAAATAATA
1 ATAAATA-TTATTATAATTATA
*
292223 ATATTATATTAT
1 ATA-AATATTAT
292235 ATTTTAAAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 18
0.68 0.14 0.17
Matches are distributed among these distances:
18 1 0.01
19 20 0.28
20 14 0.20
21 5 0.07
22 16 0.23
23 14 0.20
24 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
ATAAATATTATTATAATTATA
Found at i:292213 original size:42 final size:42
Alignment explanation
Indices: 292145--292234 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
292135 TTTAATAAAA
* *
292145 ATATTA-TAATTATATTAAATATTTATTAAAATAAAAA-ATAT
1 ATATTATTAAGTATATTAAATACTTATTAAAATAAAAATAT-T
* *
292186 ATATTATTAAGTATATTAATTACTTATTAAAATAATAATATT
1 ATATTATTAAGTATATTAAATACTTATTAAAATAAAAATATT
292228 ATATTAT
1 ATATTAT
292235 ATTTTAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 6 0.14
42 35 0.81
43 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
ATATTATTAAGTATATTAAATACTTATTAAAATAAAAATATT
Found at i:292377 original size:27 final size:28
Alignment explanation
Indices: 292326--292387 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
292316 TAATTTATTA
292326 TATATTATTAAAATAAAAATATTAT-AT
1 TATATTATTAAAATAAAAATATTATAAT
*
292353 TATATTA-TAAAA-AATATAATTTTATAAT
1 TATATTATTAAAATAA-A-AATATTATAAT
292381 TAATATT
1 T-ATATT
292388 TTGTTGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
27 14 0.47
28 3 0.10
29 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATATTATTAAAATAAAAATATTATAAT
Found at i:292412 original size:27 final size:26
Alignment explanation
Indices: 292383--292439 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 26
292373 TTTATAATTA
*
292383 ATATTTTGTTGAAATTATACTAAAATAAT
1 ATATTATGTT-AAA-TATA-TAAAATAAT
292412 ATATTAATGTTAAATATATAAAATAAT
1 ATATT-ATGTTAAATATATAAAATAAT
292439 A
1 A
292440 ATGTTTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 4 0.15
29 8 0.31
30 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (26 bp):
ATATTATGTTAAATATATAAAATAAT
Found at i:293261 original size:38 final size:38
Alignment explanation
Indices: 293218--293295 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 38
293208 TATAGCAAGC
*
293218 AAAAAAAG-ATATA-ATAATAATAATAATAGA-AAATAAAAT
1 AAAAAACGTATATATAT-ATAATAA-AA-AGATAAA-AAAAT
293257 AAAAAACGTATATATATATAATAAAAAGATAAAAAAAT
1 AAAAAACGTATATATATATAATAAAAAGATAAAAAAAT
293295 A
1 A
293296 TGTAAGTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
38 9 0.26
39 12 0.34
40 12 0.34
41 2 0.06
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (38 bp):
AAAAAACGTATATATATATAATAAAAAGATAAAAAAAT
Found at i:293468 original size:2 final size:2
Alignment explanation
Indices: 293461--293504 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
293451 TGAAAGAATA
293461 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293502 AT A
1 AT A
293505 AATGATAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:296553 original size:24 final size:24
Alignment explanation
Indices: 296522--296581 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
296512 TTTCTATCGA
296522 GAAG-AATCGATTTCTCATACCTT
1 GAAGCAATCGATTTCTCATACCTT
296545 GAAGCAATCGATTTCTCATACCTT
1 GAAGCAATCGATTTCTCATACCTT
296569 GAAGCAATCGATT
1 GAAGCAATCGATT
296582 CTTACTCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (24 bp):
GAAGCAATCGATTTCTCATACCTT
Found at i:302866 original size:21 final size:21
Alignment explanation
Indices: 302840--302880 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
302830 GTTTATTTTA
302840 AAACTTTATTTCAATTATCGT
1 AAACTTTATTTCAATTATCGT
*
302861 AAACTTTGTTTCAATTATCG
1 AAACTTTATTTCAATTATCG
302881 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (21 bp):
AAACTTTATTTCAATTATCGT
Found at i:302928 original size:33 final size:33
Alignment explanation
Indices: 302875--302973 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
302865 TTTGTTTCAA
302875 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
302907 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
302940 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
302973 T
1 T
302974 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:304126 original size:15 final size:15
Alignment explanation
Indices: 304075--304130 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
304065 TTTAATAATA
*
304075 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
* *
304090 TTATAACAG-TTTTT
1 TTAAAACCGATTTTT
*
304104 TAAAAAAACCGATTTTT
1 T--TAAAACCGATTTTT
304121 TTAAAACCGA
1 TTAAAACCGA
304131 AACCGATTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 6 0.19
15 14 0.45
16 5 0.16
17 6 0.19
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:304242 original size:19 final size:21
Alignment explanation
Indices: 304218--304257 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
304208 TTCTATAGAA
304218 AAAAACCGAT-CGG-TCGGAT
1 AAAAACCGATCCGGATCGGAT
304237 AAAAACCGATCCGGATCGGAT
1 AAAAACCGATCCGGATCGGAT
304258 TGAAATCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (21 bp):
AAAAACCGATCCGGATCGGAT
Found at i:305310 original size:19 final size:19
Alignment explanation
Indices: 305286--305322 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
305276 AACAGTACCA
305286 AAATATATCACCAAATCAG
1 AAATATATCACCAAATCAG
305305 AAATATATCACCAAATCA
1 AAATATATCACCAAATCA
305323 AAAAACCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.22
Consensus pattern (19 bp):
AAATATATCACCAAATCAG
Found at i:306167 original size:14 final size:14
Alignment explanation
Indices: 306148--306178 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
306138 TGGCTGTTCG
306148 TTTAGGTATTTATA
1 TTTAGGTATTTATA
306162 TTTAGGTATTTATA
1 TTTAGGTATTTATA
306176 TTT
1 TTT
306179 TTGACTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (14 bp):
TTTAGGTATTTATA
Found at i:306492 original size:28 final size:28
Alignment explanation
Indices: 306421--306519 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
306411 ACGTATGCAT
* *
306421 ATATTATATTGATATACACATTTTGTAC
1 ATATTATATTTATATACATATTTTGTAC
306449 ATATTATATTTATATACATATTTTGTAC
1 ATATTATATTTATATACATATTTTGTAC
*
306477 ATATTATAATTT-TATATATATTTTGCTAC
1 ATATTAT-ATTTATATACATATTTTG-TAC
* *
306506 TTATT-TATATATAT
1 ATATTATATTTATAT
306520 TTTCATGTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 3 0.05
28 49 0.78
29 11 0.17
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (28 bp):
ATATTATATTTATATACATATTTTGTAC
Found at i:306768 original size:3 final size:3
Alignment explanation
Indices: 306760--306849 Score: 88
Period size: 3 Copynumber: 32.3 Consensus size: 3
306750 TTATTTATAC
* *
306760 TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT TAC T-T TAT T-T TAC T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
306803 TAT T-T ATAC TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
306846 TAT T
1 TAT T
306850 CTATGTTCAT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
2 13 0.18
3 59 0.82
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:306806 original size:52 final size:53
Alignment explanation
Indices: 306733--306849 Score: 202
Period size: 52 Copynumber: 2.2 Consensus size: 53
306723 TTTCTAATAT
306733 TTTTACTTTATTTTACTTTATTTATACTATTATTATTATTATTATT-TTATT-
1 TTTTACTTTATTTTACTTTATTTATACTATTATTATTATTATTATTATTATTA
306784 TTATTACTTTATTTTACTTTATTTATACTATTATTATTATTATTATTATTATTA
1 TT-TTACTTTATTTTACTTTATTTATACTATTATTATTATTATTATTATTATTA
*
306838 TTTTATTTTATT
1 TTTTACTTTATT
306850 CTATGTTCAT
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
51 2 0.03
52 44 0.71
53 14 0.23
54 2 0.03
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (53 bp):
TTTTACTTTATTTTACTTTATTTATACTATTATTATTATTATTATTATTATTA
Found at i:306841 original size:61 final size:61
Alignment explanation
Indices: 306733--306849 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 61
306723 TTTCTAATAT
306733 TTTTACTTTATTTTACTTTATTTATACTATTATTATTATTATTATTTTATTTTATTACTTTA
1 TTTTACTTTATTTTACTTTATTTATA-TATTATTATTATTATTATTTTATTTTATTACTTTA
306795 TTTTACTTTATTTATACTATTA-TTAT-TATTATTATTATTATTATTTTATTTTATT
1 TTTTACTTTATTT-TACT-TTATTTATATATTATTATTATTATTATTTTATTTTATT
306850 CTATGTTCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
61 29 0.55
62 13 0.25
63 8 0.15
64 3 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (61 bp):
TTTTACTTTATTTTACTTTATTTATATATTATTATTATTATTATTTTATTTTATTACTTTA
Found at i:309519 original size:15 final size:16
Alignment explanation
Indices: 309499--309531 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
309489 GCTGAATTTG
309499 ATTATA-AAGAAGTCA
1 ATTATAGAAGAAGTCA
309514 ATTATAGGAAGAAGTCA
1 ATTATA-GAAGAAGTCA
309531 A
1 A
309532 AGATGTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
ATTATAGAAGAAGTCA
Found at i:313756 original size:14 final size:14
Alignment explanation
Indices: 313734--313771 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
313724 ACCCAATTAA
313734 ATTTGTGTTCGTTC
1 ATTTGTGTTCGTTC
*
313748 ATTTATGTTCGTTC
1 ATTTGTGTTCGTTC
*
313762 GTTTGTGTTC
1 ATTTGTGTTC
313772 ATTTACGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.58
Consensus pattern (14 bp):
ATTTGTGTTCGTTC
Found at i:327525 original size:39 final size:39
Alignment explanation
Indices: 327478--327555 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
327468 TTGTGTAGTG
* *
327478 TTGCATTTGTTAATTTCGATATATTATTTTACTTTGTTA
1 TTGCATTTGTTAAGTTCGATATATTATGTTACTTTGTTA
327517 TTGCATTTGTTAAGTTCGATATATTATGTTACTTTGTTA
1 TTGCATTTGTTAAGTTCGATATATTATGTTACTTTGTTA
327556 ATTATGATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (39 bp):
TTGCATTTGTTAAGTTCGATATATTATGTTACTTTGTTA
Found at i:332424 original size:22 final size:25
Alignment explanation
Indices: 332394--332443 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
332384 GTTAATTTTT
* *
332394 TTATTTATAT-TTAATAAAAGAAAA
1 TTATATATATATTAAAAAAAGAAAA
332418 TTATATATATATTAAAAAAAGAAAA
1 TTATATATATATTAAAAAAAGAAAA
332443 T
1 T
332444 ATAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TTATATATATATTAAAAAAAGAAAA
Found at i:332454 original size:24 final size:25
Alignment explanation
Indices: 332399--332457 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
332389 TTTTTTTATT
* *
332399 TATATTTAATAAAAGAAAATTATATA
1 TATA-TTAAAAAAAGAAAATTATAAA
332425 TATATTAAAAAAAGAAAA-TATAAA
1 TATATTAAAAAAAGAAAATTATAAA
332449 -ATTATTAAA
1 TA-TATTAAA
332458 TATTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.03
24 12 0.40
25 13 0.43
26 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
TATATTAAAAAAAGAAAATTATAAA
Found at i:336185 original size:21 final size:21
Alignment explanation
Indices: 336171--336218 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
336161 GATACTGATG
336171 TGTCATTATAAGATAATGTCA
1 TGTCATTATAAGATAATGTCA
336192 TGTCATTATAAGATAATGTCA
1 TGTCATTATAAGATAATGTCA
336213 TGTCAT
1 TGTCAT
336219 CATTGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTCATTATAAGATAATGTCA
Found at i:337364 original size:85 final size:85
Alignment explanation
Indices: 337270--337426 Score: 260
Period size: 85 Copynumber: 1.8 Consensus size: 85
337260 GACGCGCAAC
*
337270 TGTGCGTCATAAATTTATGACGCACATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCAT
1 TGTGCGTCATAAATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCAT
337335 AAATGAAGATGACACATATT
66 AAATGAAGATGACACATATT
* * * * *
337355 TGTGTGTCATAAATTTATGACACGCATTTATGACTTACGTTGCGTGTCATTGAAGCCCCCGTCAT
1 TGTGCGTCATAAATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCAT
337420 AAATGAA
66 AAATGAA
337427 AATCTCGTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (85 bp):
TGTGCGTCATAAATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCAT
AAATGAAGATGACACATATT
Found at i:343357 original size:60 final size:60
Alignment explanation
Indices: 343286--343828 Score: 716
Period size: 60 Copynumber: 9.1 Consensus size: 60
343276 AATGCTTTAA
* * *
343286 AATGTAAGTTAGATAAAAAGTTAAATGCCTAACGGTGCATTTTGGAAGAAAGGTGCCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * * *
343346 AATGTAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAACGTTCCATT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * * *
343406 AATGCAAGTTAAATGAAAAGTTAAACGCCTAACGGTGTATTTTGGCAGAAAGATGCCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
*
343466 AATGCAAGTTAGATGAAAAGTTAAGTGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * * * *
343526 AATGTAAGTTAGATGAAAAGTTAAATGCATAGCGGTGCATTTTGGTAGAAAGGTGTCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * ** * * *
343586 AAAGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCCTTTTGATAGAAATGTGTCATT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
*
343646 AATGCAAGTTAGATGAAAAGTTAAATGCCT----GTGCATTTTGGTAGAAAGGTGCCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * * *
343702 AATGAAAGTTAGATGAAAAGTTAAATGCCTAATGGTGCATTTTGGCAGAAAGGAGTCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * * * * *
343762 AATGCAAGTTAGATGAAAATTTAAATACATAACGGTGCATAATCGGCATGAAAGGATGCCACA
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCAT-TTTGGCA-GAAAGG-TGCCACT
343825 AATG
1 AATG
343829 AAAAATACAT
Statistics
Matches: 424, Mismatches: 52, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
56 50 0.12
60 355 0.84
61 5 0.01
62 6 0.01
63 8 0.02
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (60 bp):
AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
Found at i:350165 original size:24 final size:22
Alignment explanation
Indices: 350133--350239 Score: 62
Period size: 21 Copynumber: 5.0 Consensus size: 22
350123 GCACAAGAGC
*
350133 TAAAAAAATATAATATAAGAAAAA
1 TAAAAAAATAGAA-A-AAGAAAAA
*
350157 TAAAGAAATAGAAAAAGAAAAA
1 TAAAAAAATAGAAAAAGAAAAA
* * *
350179 GAATAAAA-AGAGAAAGAATAAA
1 TAAAAAAATAGAAAAAGAA-AAA
* * *
350201 -AAGAAAA-CGAAGAAG--AAA
1 TAAAAAAATAGAAAAAGAAAAA
* *
350219 CAAAATAATAGAAAAAGAAAA
1 TAAAAAAATAGAAAAAGAAAA
350240 GAAAAGAGAA
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
18 3 0.05
19 5 0.08
20 6 0.09
21 20 0.31
22 18 0.28
23 1 0.02
24 11 0.17
ACGTcount: A:0.75, C:0.02, G:0.13, T:0.10
Consensus pattern (22 bp):
TAAAAAAATAGAAAAAGAAAAA
Found at i:350175 original size:6 final size:6
Alignment explanation
Indices: 350158--350258 Score: 73
Period size: 6 Copynumber: 16.5 Consensus size: 6
350148 TAAGAAAAAT
* * * *
350158 AAAGAA ATAGAA AAAGAA AAAGAA TAA-AA AGAGAA AGAATAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* * *
350206 AACGAA GAAGAA ACAA-AA TAATAGAA AAAG-A AAAGAA AAGAGAA AGAGAA
1 AAAGAA AAAGAA A-AAGAA -AA-AGAA AAAGAA AAAGAA AA-AGAA AAAGAA
350256 AAA
1 AAA
350259 AATGATGAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
5 8 0.11
6 48 0.66
7 15 0.21
8 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:350186 original size:15 final size:15
Alignment explanation
Indices: 350168--350207 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
350158 AAAGAAATAG
350168 AAAAAGAAAAAGAAT
1 AAAAAGAAAAAGAAT
*
350183 AAAAAGAGAAAGAAT
1 AAAAAGAAAAAGAAT
350198 AAAAAGAAAA
1 AAAAAGAAAA
350208 CGAAGAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAGAAAAAGAAT
Found at i:350207 original size:21 final size:20
Alignment explanation
Indices: 350153--350260 Score: 71
Period size: 21 Copynumber: 5.3 Consensus size: 20
350143 TAATATAAGA
*
350153 AAAATAAAGAAATAGAAAAAG
1 AAAA-AAAGAAAAAGAAAAAG
* *
350174 AAAAAGAATAAAAAGAGAAAG
1 AAAAA-AAGAAAAAGAAAAAG
* *
350195 AATAAAAAGAAAACGAAGAAG
1 AA-AAAAAGAAAAAGAAAAAG
* *
350216 AAACAAAA-TAATAGAAAAAG
1 AAA-AAAAGAAAAAGAAAAAG
*
350236 ---AAAAGAAAAGAGAAAGAG
1 AAAAAAAGAAAA-AGAAAAAG
350254 AAAAAAA
1 AAAAAAA
350261 TGATGAGAGA
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
16 4 0.06
17 2 0.03
18 7 0.11
20 10 0.15
21 39 0.60
22 3 0.05
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (20 bp):
AAAAAAAGAAAAAGAAAAAG
Found at i:350234 original size:11 final size:11
Alignment explanation
Indices: 350149--350258 Score: 62
Period size: 13 Copynumber: 9.2 Consensus size: 11
350139 AATATAATAT
*
350149 AAGAAAA-ATA
1 AAGAAAAGAAA
350159 AAGAAATAGAAA
1 AAGAAA-AGAAA
350171 AAGAAAAAGAATA
1 AAG-AAAAGAA-A
*
350184 AA-AAGAGAAA
1 AAGAAAAGAAA
*
350194 GAATAAAAAGAAA
1 -AA-GAAAAGAAA
*
350207 ACGAAGAAGAAA
1 AAGAA-AAGAAA
*
350219 CAAAATAATAGAAA
1 -AAGA-AA-AGAAA
350233 AAGAAAAGAAA
1 AAGAAAAGAAA
350244 AGAGAAAGAGAAA
1 A-AGAAA-AGAAA
350257 AA
1 AA
350259 AATGATGAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
10 7 0.09
11 17 0.22
12 24 0.30
13 25 0.32
14 6 0.08
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.05
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:353814 original size:40 final size:40
Alignment explanation
Indices: 353759--353919 Score: 243
Period size: 40 Copynumber: 4.0 Consensus size: 40
353749 TGCAGGTTTA
353759 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
353799 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
353839 TAACACACTTCAGTGTATATGGTGAGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * **
353879 T-ATACACTTTGGTGTATATGGTGGGTATAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
353918 TA
1 TA
353920 GCACTACGGT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 32 0.30
40 76 0.70
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:353918 original size:79 final size:80
Alignment explanation
Indices: 353763--353919 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 80
353753 GGTTTATAAT
* *
353763 ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGGTAC
1 ACACTTCAGTGTATATGGTGAGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGGTAC
*
353828 GACCTTATGTGTAAC
66 AACCTTATGTGTAAC
* *
353843 ACACTTCAGTGTATATGGTGAGCACGACCTTATGTGT-ATACACTTTGGTGTATATGGTGGGTAT
1 ACACTTCAGTGTATATGGTGAGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGGTAC
353907 AACCTTATGTGTA
66 AACCTTATGTGTA
353920 GCACTACGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 37 0.51
80 35 0.49
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (80 bp):
ACACTTCAGTGTATATGGTGAGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGGTAC
AACCTTATGTGTAAC
Found at i:354150 original size:90 final size:89
Alignment explanation
Indices: 354024--354343 Score: 448
Period size: 90 Copynumber: 3.6 Consensus size: 89
354014 GTAAGCATGC
*
354024 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
* *
354087 GTGATAAATGGTAAGTCTATGGGTA
66 G-GATAAATGGTAAGTATATAGGTA
* *
354112 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
*
354177 GGA-ATAATGGCAAGTATATAGGTA
66 GGATA-AATGGTAAGTATATAGGTA
* *
354201 AAATAAGCTTATGAGCTTATGAGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
354266 TGGAATTAAATGGTAAGTATATTGGTA
65 TGG-A-TAAATGGTAAGTATATAGGTA
* * * *
354293 AAATAAGCTTACGATCTTATGGGATTAAAGGGTAAGTATAATGGTAAAATA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTAAAATA
354344 CTGGATATGC
Statistics
Matches: 208, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
88 21 0.10
89 41 0.20
90 81 0.39
91 1 0.00
92 62 0.30
93 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (89 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
GGATAAATGGTAAGTATATAGGTA
Found at i:354249 original size:46 final size:45
Alignment explanation
Indices: 354024--354343 Score: 450
Period size: 46 Copynumber: 7.1 Consensus size: 45
354014 GTAAGCATGC
* *
354024 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* *
354067 AAATAAGCTTACGAGCTTATGTGA-TAAATGGTAAGTCTATGGGTA
1 AAATAAGCTTACGAGCTTATG-GATTAAATGGTAAGTATATTGGTA
** *
354112 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* * *
354157 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATAGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
*
354201 AAATAAGCTTATGAGCTTATGAGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GATTAAATGGTAAGTATATTGGTA
354247 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGG-ATTAAATGGTAAGTATATTGGTA
* * *
354293 AAATAAGCTTACGATCTTATGGGATTAAAGGGTAAGTATAATGGTA
1 AAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGTA
354339 AAATA
1 AAATA
354344 CTGGATATGC
Statistics
Matches: 250, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
43 20 0.08
44 39 0.16
45 84 0.34
46 105 0.42
47 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
Found at i:354803 original size:21 final size:21
Alignment explanation
Indices: 354763--354820 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
354753 ATGCTACAGG
*
354763 GGTACTGATACCCT-GCTACA
1 GGTACCGATACCCTCGCTACA
354783 GGTACCGATACCCTCGCTACA
1 GGTACCGATACCCTCGCTACA
354804 GGTACCGATACCCTCGC
1 GGTACCGATACCCTCGC
354821 AGTTCACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 13 0.36
21 23 0.64
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTACCGATACCCTCGCTACA
Found at i:356675 original size:60 final size:60
Alignment explanation
Indices: 356582--357038 Score: 639
Period size: 60 Copynumber: 7.7 Consensus size: 60
356572 ACTGCTCTAA
* * *
356582 AATGCAAGTTAGACGAAAAGTTAAATGCCTAACGGTGCATTTTGGAAGAAATGTGCCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * *
356642 AATGCAAGTTAGATGAAAAGTTAAATGTCTAACGGTTCATTTTGGCATAAAGGTGCCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * *
356702 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGATGCATTTTGGTAGAAAGGTGTCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * * * ** * *
356762 AATGCAAGTGAGATGAAAAATTAAATGCATACCATTGCATTTTGGTAGAAAGGTGTCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
** * * *
356822 AATGCAAGTTAGATGAAAAGTTAAATGTATAATGGTGCATTTTGGCAGAAAGGTGTCATT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* * *
356882 AATGGAAGTTAGATGAAAAGTTAAATCCCTAACGGTGCATTTTGGCAGAAAGGTGCCAGT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* *
356942 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGTA-TTTGGCAGAAAGGTACCACT
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
* *
357001 AATGCAAGTTAGATG-AAAGTTAAATGCATAATGGTGCA
1 AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCA
357039 CAATCACATG
Statistics
Matches: 355, Mismatches: 42, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
58 20 0.06
59 33 0.09
60 302 0.85
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (60 bp):
AATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACT
Found at i:365310 original size:3 final size:3
Alignment explanation
Indices: 365302--365385 Score: 98
Period size: 3 Copynumber: 28.0 Consensus size: 3
365292 TTTGTGTGTA
*
365302 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
** * * *
365351 AAT -AT TGT AAT AAT AAT ACT AAA AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
365386 GGGCAGGTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:365671 original size:36 final size:37
Alignment explanation
Indices: 365578--365675 Score: 130
Period size: 36 Copynumber: 2.7 Consensus size: 37
365568 CATATATAGA
* * *
365578 TTTTGAAAACATATAATACATAG-TTAAAAAAATGAT
1 TTTTGAAAACATATAATATATAGTTTAAAAAAATCAG
365614 TTTTGAAAACATATAATATATAGTTTAAAAAAA-CAG
1 TTTTGAAAACATATAATATATAGTTTAAAAAAATCAG
*
365650 TTTTGAAGACATAT-ATAATATAGTTT
1 TTTTGAAAACATATAAT-ATATAGTTT
365676 TTGAAAACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 2 0.04
36 45 0.80
37 9 0.16
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (37 bp):
TTTTGAAAACATATAATATATAGTTTAAAAAAATCAG
Found at i:365744 original size:39 final size:40
Alignment explanation
Indices: 365660--365757 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 40
365650 TTTTGAAGAC
* * *
365660 ATATATA-ATATAGTTTTTGAAAACATATTATTTTGAAAA
1 ATATATATATATAGTTTTTTAAAACACATTATTTTAAAAA
365699 AT-TATATATATAGTTTTTTAAAA-ACA-T-TTTTAAACATA
1 ATATATATATATAGTTTTTTAAAACACATTATTTTAAA-A-A
*
365737 ATATATATTATAAAGTTTTTT
1 ATATATA-TATATAGTTTTTT
365758 TAAATATACA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
36 6 0.12
37 2 0.04
38 9 0.18
39 21 0.42
40 12 0.24
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (40 bp):
ATATATATATATAGTTTTTTAAAACACATTATTTTAAAAA
Found at i:365782 original size:10 final size:10
Alignment explanation
Indices: 365767--365795 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
365757 TTAAATATAC
365767 ATATATTATT
1 ATATATTATT
365777 ATATATTATT
1 ATATATTATT
365787 AT-TATTATT
1 ATATATTATT
365796 TTACTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATATTATT
Found at i:365837 original size:19 final size:19
Alignment explanation
Indices: 365791--365840 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
365781 ATTATTATTA
*
365791 TTAT-TTTACTTTCCTTTT
1 TTATCTTTATTTTCCTTTT
* *
365809 TTCTCATTTATTTTCTTTTT
1 TTATC-TTTATTTTCCTTTT
365829 TTATCTTTATTT
1 TTATCTTTATTT
365841 AAGGTCGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 7 0.27
20 16 0.62
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATCTTTATTTTCCTTTT
Found at i:367023 original size:15 final size:14
Alignment explanation
Indices: 367003--367061 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 14
366993 ACCCTTGACT
367003 TTTAATTCTTTTCAA
1 TTTAATTCTTTT-AA
* *
367018 TTTAATCCTTTTAG
1 TTTAATTCTTTTAA
367032 TTTAA-T-TTTTAA
1 TTTAATTCTTTTAA
*
367044 TTTTTATTCTTTT-A
1 -TTTAATTCTTTTAA
367058 TTTA
1 TTTA
367062 TTTAATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
12 5 0.14
13 7 0.20
14 8 0.23
15 15 0.43
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAATTCTTTTAA
Found at i:376184 original size:3 final size:3
Alignment explanation
Indices: 376135--376164 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
376125 TTTGTATGTA
376135 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
376165 TTATTTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:377901 original size:24 final size:24
Alignment explanation
Indices: 377855--377903 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
377845 AGTTTAATTT
*
377855 TTTTTATTTCTTTTAATTATTTAA
1 TTTTTATTTATTTTAATTATTTAA
*
377879 TTTTTATTTAATTTT-ATTGTTTAA
1 TTTTTATTT-ATTTTAATTATTTAA
377903 T
1 T
377904 AGTTGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTTATTTATTTTAATTATTTAA
Found at i:390939 original size:22 final size:22
Alignment explanation
Indices: 390903--390948 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
390893 AAATTTTGGC
*
390903 TTTTTTTGGCTCTTTTTTTGTTT
1 TTTTTTTGGCTCTTTTATT-TTT
*
390926 TTTTTTTTGC-CTTTTATTTTT
1 TTTTTTTGGCTCTTTTATTTTT
390947 TT
1 TT
390949 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 9 0.43
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (22 bp):
TTTTTTTGGCTCTTTTATTTTT
Done.