Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 188 of 292
Found at i:56071081 original size:81 final size:81
Alignment explanation
Indices: 56071037--56071236 Score: 280
Period size: 81 Copynumber: 2.5 Consensus size: 81
56071027 ATGGTATTTC
* *
56071037 AGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGT
1 AGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGT
* *
56071102 AATTCGAGGGTAAGAT
66 AATACAAGGGTAAGAT
* * *
56071118 GGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTAT
1 AGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGT
*
56071183 AA-ATCGAGGGTAA-A-
66 AATA-CAAGGGTAAGAT
56071197 AGGATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTAT
1 A-G-TAATTCTGTAAATCGAGGGTAAAATGGTAATTCTAT
56071237 CTTACAGGAG
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
80 2 0.02
81 107 0.98
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.32
Consensus pattern (81 bp):
AGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGT
AATACAAGGGTAAGAT
Found at i:56071096 original size:54 final size:54
Alignment explanation
Indices: 56071038--56071234 Score: 324
Period size: 54 Copynumber: 3.6 Consensus size: 54
56071028 TGGTATTTCA
*
56071038 GTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
* *
56071092 GTAATTCTGTAATTCGAGGGTAAGATGGTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
* * *
56071146 GTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAA-G
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
56071199 GATAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
1 G-TAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
56071235 ATCTTACAGG
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
53 2 0.02
54 130 0.98
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
Found at i:56071268 original size:81 final size:80
Alignment explanation
Indices: 56071038--56071275 Score: 273
Period size: 81 Copynumber: 2.9 Consensus size: 80
56071028 TGGTATTTCA
* * * * **
56071038 GTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAATTC-AGGGTAAAATAGTAATTCTACA
* *
56071103 ATTCGAGGGTAAGATG
65 AATCGAGGGTAAGAAG
* * *
56071119 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTAT-AATTCAGGGTAAAATAGTAATTCTACA
56071184 AATCGAGGGTAA-AAG
65 AATCGAGGGTAAGAAG
* *** *
56071199 GATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTAT-CTTACAGGAGTATTTTAGTAATTTTA
1 G-TAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAATT-CAGG-GTAAAATAGTAATTCTA
56071263 CAAATCGAGGGTA
63 CAAATCGAGGGTA
56071276 TTCTAGTAAT
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
79 2 0.01
80 6 0.04
81 127 0.92
82 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (80 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAATTCAGGGTAAAATAGTAATTCTACAA
ATCGAGGGTAAGAAG
Found at i:56076431 original size:21 final size:21
Alignment explanation
Indices: 56076403--56076443 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
56076393 CAAAACTTGT
56076403 ATAACTATCATCAAA-CATTC
1 ATAACTATCATCAAATCATTC
56076423 ATAACCTATCATCAAATCATT
1 ATAA-CTATCATCAAATCATT
56076444 AATATACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAACTATCATCAAATCATTC
Found at i:56079601 original size:45 final size:45
Alignment explanation
Indices: 56079545--56079631 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
56079535 CCAAAGCATG
*
56079545 TGTCACATATATCACGAACTCGGACCACAACTCAACGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAACGAGTTCGGA
* * * *
56079590 TGTCACGTATATCATGAACTCAGACTACAACTCAATGAGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAACGAGTTC
56079632 AGATTACATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.24
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAACGAGTTCGGA
Found at i:56081972 original size:48 final size:46
Alignment explanation
Indices: 56081921--56082056 Score: 254
Period size: 46 Copynumber: 3.0 Consensus size: 46
56081911 AGTTAAATAT
56081921 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56081967 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
56082013 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
56082057 AGATGTATAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:56082114 original size:47 final size:47
Alignment explanation
Indices: 56082060--56082170 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
56082050 ATGTATGAGA
* * *
56082060 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
56082107 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
56082154 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
56082171 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:56084840 original size:40 final size:40
Alignment explanation
Indices: 56084725--56084910 Score: 279
Period size: 39 Copynumber: 4.7 Consensus size: 40
56084715 AGGTCTCGAC
*
56084725 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
* *
56084764 GATATATCCGGGCTAAG-TCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
* *
56084803 GACGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
*
56084843 GATGTATCCGGACTAAGTTCCG-AGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
* *
56084882 GATGTATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTTCCGAAGAGCA
56084911 ATCATGCTGG
Statistics
Matches: 133, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
39 73 0.55
40 60 0.45
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
Found at i:56084860 original size:79 final size:79
Alignment explanation
Indices: 56084729--56084910 Score: 285
Period size: 79 Copynumber: 2.3 Consensus size: 79
56084719 CTCGACGATG
*
56084729 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAG-TCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCG-AGAGCAT
56084793 TCATGCTAGTGACGT
65 TCATGCTAGTGACGT
* * *
56084808 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAGAGCATT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCGAGAGCATT
* *
56084873 CGTGCTAGTGATGT
66 CATGCTAGTGACGT
*
56084887 ATCCGGGCTAGGTCCCGAAGAGCA
1 ATCCGGGCTAAGTCCCGAAGAGCA
56084911 ATCATGCTGG
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 89 0.96
80 4 0.04
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.24
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCGAGAGCATT
CATGCTAGTGACGT
Found at i:56085656 original size:40 final size:42
Alignment explanation
Indices: 56085570--56085674 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 42
56085560 TTCGAATGGT
* * *
56085570 ATCCGGGCTAAGTCCCGAAGGC--TTTTGTGCAAGTTACTAA
1 ATCCGGGCTAATTCCCGAAGGCAATTGTGTGCAAGTCACTAA
56085610 ATCCGGGCTAATTCCCGAAGGCAATTGTGTG-AA-TCACTATA
1 ATCCGGGCTAATTCCCGAAGGCAATTGTGTGCAAGTCACTA-A
*
56085651 A-CCGGGCT-ATGTCCCGAAGACAAT
1 ATCCGGGCTAAT-TCCCGAAGGCAAT
56085675 CGAGCGAGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
39 2 0.04
40 45 0.79
41 4 0.07
42 6 0.11
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (42 bp):
ATCCGGGCTAATTCCCGAAGGCAATTGTGTGCAAGTCACTAA
Found at i:56088429 original size:46 final size:46
Alignment explanation
Indices: 56088378--56088559 Score: 337
Period size: 46 Copynumber: 4.0 Consensus size: 46
56088368 AGTTAAATAT
56088378 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56088424 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
*
56088470 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
56088516 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
56088560 AGATGTATAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:56088617 original size:47 final size:47
Alignment explanation
Indices: 56088563--56088673 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
56088553 ATGTATGAGA
* * *
56088563 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
56088610 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
56088657 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
56088674 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:56091285 original size:40 final size:40
Alignment explanation
Indices: 56091230--56091493 Score: 429
Period size: 40 Copynumber: 6.6 Consensus size: 40
56091220 CTCGACGATG
*
56091230 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
*
56091270 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
56091310 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* **
56091350 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGACGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56091390 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56091430 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56091470 ATCCGGGCTAGGTCCCGAAGAGCA
1 ATCCGGGCTAAGTTCCGAAGAGCA
56091494 ATCATGCTGG
Statistics
Matches: 214, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 214 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
Found at i:56092221 original size:40 final size:40
Alignment explanation
Indices: 56092157--56092257 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 40
56092147 AATGGTATCT
* ** * *
56092157 GGGCTAAGTCCCGAAGGCTTTTGTGCGAGTTACTA-AATCC
1 GGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA-CC
*
56092197 GGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAACC
1 GGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACC
*
56092237 GGGCT-ATGTCCCGAAGACAAT
1 GGGCTAAT-TCCCGAAGGCAAT
56092258 CGAGTGAGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 48 0.92
41 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
GGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACC
Found at i:56092273 original size:40 final size:40
Alignment explanation
Indices: 56092195--56092291 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 40
56092185 GTTACTAAAT
* * *
56092195 CCGGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGTGAATCACTATAA
* * *
56092235 CCGGGCT-ATGTCCCGAAGACAATCGAGTGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGTGAATCACTATAA
* *
56092275 CC-GGTTAAATCCCGAAG
1 CCGGGCTAATTCCCGAAG
56092292 GTACGTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
39 13 0.28
40 34 0.72
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGTGAATCACTATAA
Found at i:56095012 original size:46 final size:46
Alignment explanation
Indices: 56094961--56095142 Score: 337
Period size: 46 Copynumber: 4.0 Consensus size: 46
56094951 AGTTAAATAT
56094961 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56095007 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
*
56095053 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
56095099 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
56095143 AGATGTATAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:56095200 original size:47 final size:47
Alignment explanation
Indices: 56095146--56095256 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
56095136 ATGTATGAGA
* * *
56095146 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
56095193 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
56095240 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
56095257 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:56099278 original size:6 final size:6
Alignment explanation
Indices: 56099255--56099370 Score: 85
Period size: 6 Copynumber: 18.8 Consensus size: 6
56099245 TATCAAAACT
* * * *
56099255 AGAATC AAAATG AGAATC AGAATC AGAATC AG-GTGAC AGAATT AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * *
56099304 AGAATC AGAATC AG-GTGAC AGAATT AGAATC AGAATC AGTATC AGGCAA-C
1 AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC A-G-AATC
*
56099354 AGAATC AAAATC AGAAT
1 AGAATC AGAATC AGAAT
56099371 GTGAATGCAA
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
5 4 0.05
6 69 0.81
7 9 0.11
8 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:56099305 original size:31 final size:31
Alignment explanation
Indices: 56099267--56099370 Score: 163
Period size: 31 Copynumber: 3.4 Consensus size: 31
56099257 AATCAAAATG
56099267 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTGACAGAATT
56099298 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTGACAGAATT
* ** *
56099329 AGAATCAGAATCAGTATCAGGCAACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATT
*
56099360 AAAATCAGAAT
1 AGAATCAGAAT
56099371 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.18
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATT
Found at i:56100204 original size:27 final size:27
Alignment explanation
Indices: 56100168--56100229 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
56100158 AATCCTACAA
*
56100168 GGGTGTTTTGGTAAATCTA-CAAACTAG
1 GGGTATTTTGGTAAATCTATCAAAC-AG
* *
56100195 GGGTATTTTGGTAATTCTATCATACAG
1 GGGTATTTTGGTAAATCTATCAAACAG
56100222 GGGTATTT
1 GGGTATTT
56100230 CAGTAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAAATCTATCAAACAG
Found at i:56100276 original size:27 final size:27
Alignment explanation
Indices: 56100242--56100441 Score: 233
Period size: 27 Copynumber: 7.4 Consensus size: 27
56100232 GTAATTTCAT
56100242 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
56100269 AA-CTGAGGGTAAAGCGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* *
56100296 ACTCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * **
56100323 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
56100350 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* *
56100377 AATCGAGGGTGAAACAGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* ****
56100404 AATCGGGGGTACTTTGGTAATTTTGCT-
1 AATCGAGGGTAAAACGGTAATTTTG-TA
56100431 AATCGAGGGTA
1 AATCGAGGGTA
56100442 TTTTGGTAAT
Statistics
Matches: 148, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 145 0.98
28 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:56101519 original size:16 final size:16
Alignment explanation
Indices: 56101495--56101562 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
56101485 TTAAATTTAT
*
56101495 TTATTATATAAATATC
1 TTATAATATAAATATC
*
56101511 TTATAATATAATTA-C
1 TTATAATATAAATATC
*
56101526 TTA-ATTAATAAATATC
1 TTATAAT-ATAAATATC
56101542 TTTTATAAATAGTAAATATC
1 --TTAT-AATA-TAAATATC
56101562 T
1 T
56101563 ATTAGTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.05
15 10 0.25
16 13 0.32
18 4 0.10
19 1 0.03
20 10 0.25
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (16 bp):
TTATAATATAAATATC
Found at i:56101653 original size:4 final size:4
Alignment explanation
Indices: 56101644--56101677 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
56101634 AACGTTTGTC
56101644 TTTA TTTA TTTA TTTTA TTTA TTTA CTTTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA
56101678 ATTAGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:56101662 original size:9 final size:8
Alignment explanation
Indices: 56101644--56101677 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
56101634 AACGTTTGTC
56101644 TTTATTTA
1 TTTATTTA
56101652 TTTATTTTA
1 TTTA-TTTA
56101661 TTTATTTA
1 TTTATTTA
56101669 CTTTATTTA
1 -TTTATTTA
56101678 ATTAGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATTTA
Found at i:56101662 original size:13 final size:13
Alignment explanation
Indices: 56101643--56101677 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
56101633 AAACGTTTGT
56101643 CTTTATTTATTTA
1 CTTTATTTATTTA
*
56101656 TTTTATTTATTTA
1 CTTTATTTATTTA
56101669 CTTTATTTA
1 CTTTATTTA
56101678 ATTAGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
CTTTATTTATTTA
Found at i:56103156 original size:24 final size:26
Alignment explanation
Indices: 56103110--56103161 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
56103100 TGACAAATCC
* * *
56103110 AAATAATTTTGAATTTTATAAGTTAT
1 AAATAATTTTGAATTTCAAAAGTAAT
56103136 AAAT-ATTTT-AATTTCAAAAGTAAT
1 AAATAATTTTGAATTTCAAAAGTAAT
56103160 AA
1 AA
56103162 TTCTGTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 5 0.22
26 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (26 bp):
AAATAATTTTGAATTTCAAAAGTAAT
Found at i:56103568 original size:8 final size:8
Alignment explanation
Indices: 56103555--56103582 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
56103545 AATAATATAT
56103555 TATTAAAA
1 TATTAAAA
56103563 TATTAAAA
1 TATTAAAA
56103571 TATTAAAA
1 TATTAAAA
56103579 TATT
1 TATT
56103583 TTATGTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATTAAAA
Found at i:56106480 original size:15 final size:16
Alignment explanation
Indices: 56106460--56106529 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 16
56106450 ACCCCTCCTA
56106460 TTATATTATATAAT-G
1 TTATATTATATAATAG
56106475 TTATATTATATCATATAG
1 TTATATTATAT-A-ATAG
*
56106493 TATATAATATATTAATAG
1 T-TATATTATA-TAATAG
56106511 -TATA-TATATAATAG
1 TTATATTATATAATAG
56106525 TTATA
1 TTATA
56106530 CATTATATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
14 6 0.12
15 19 0.40
16 5 0.10
17 2 0.04
18 6 0.12
19 9 0.19
20 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (16 bp):
TTATATTATATAATAG
Found at i:56106541 original size:7 final size:7
Alignment explanation
Indices: 56106461--56106541 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 7
56106451 CCCCTCCTAT
56106461 TATATTA
1 TATATTA
56106468 TATAATGT-
1 TAT-AT-TA
56106476 TATATTA
1 TATATTA
56106483 TATCATATA
1 TAT-AT-TA
*
56106492 GTATATAA
1 -TATATTA
56106500 TATATTA
1 TATATTA
*
56106507 -ATAGTA
1 TATATTA
56106513 TATA-TA
1 TATATTA
56106519 TAATAGTTA
1 T-ATA-TTA
*
56106528 TACATTA
1 TATATTA
56106535 TATATTA
1 TATATTA
56106542 CTTATTATTG
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
6 9 0.15
7 29 0.49
8 10 0.17
9 8 0.14
10 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (7 bp):
TATATTA
Found at i:56108766 original size:15 final size:17
Alignment explanation
Indices: 56108746--56108787 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
56108736 TTAGACCTCC
56108746 TACTATATTATAT-A-A
1 TACTATATTATATCATA
*
56108761 TACTATATCATATCATA
1 TACTATATTATATCATA
*
56108778 TAATATATTA
1 TACTATATTA
56108788 ATAGTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 1 0.05
17 9 0.41
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (17 bp):
TACTATATTATATCATA
Found at i:56111130 original size:37 final size:36
Alignment explanation
Indices: 56111080--56111166 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 36
56111070 TACGAAGTCT
56111080 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
*
56111116 GTACCCGGACATAATCTCTACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
56111153 TCACCCGGAACATA
1 T-ACCCGG-ACATA
56111167 TTTCCAAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 1 0.02
37 41 0.87
38 5 0.11
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:56111301 original size:49 final size:49
Alignment explanation
Indices: 56111243--56111397 Score: 292
Period size: 49 Copynumber: 3.2 Consensus size: 49
56111233 ATATATATAT
56111243 ACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATC
1 ACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATC
56111292 ACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATC
1 ACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATC
* *
56111341 ACATATGTATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATC
56111390 ACATATAT
1 ACATATAT
56111398 TATTATGTAC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 103 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (49 bp):
ACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATC
Found at i:56115506 original size:40 final size:40
Alignment explanation
Indices: 56115457--56115728 Score: 472
Period size: 40 Copynumber: 6.8 Consensus size: 40
56115447 CCAGCATGAT
* * *
56115457 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
56115497 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
56115537 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
56115577 TGCTCTTCGGAACTTAGTCCGGATGCGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
56115617 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
56115657 TGCTCTTCGGAACTTAGTCCGGATGCGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
56115697 TGCTCTTCGGAACTTAGTCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
56115729 CTCAATTCTC
Statistics
Matches: 220, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 220 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:56117588 original size:37 final size:36
Alignment explanation
Indices: 56117538--56117624 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
56117528 TACGAAGTCT
56117538 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
56117574 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
56117611 TCACCCGGAACATA
1 T-ACCCGG-ACATA
56117625 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:56117765 original size:49 final size:49
Alignment explanation
Indices: 56117693--56117845 Score: 279
Period size: 49 Copynumber: 3.1 Consensus size: 49
56117683 TTTACCACAT
*
56117693 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
56117742 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
56117791 ATATGTATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
56117840 ATATAT
1 ATATAT
56117846 TATTATGTAC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 99 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (49 bp):
ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:56126353 original size:11 final size:11
Alignment explanation
Indices: 56126337--56126364 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
56126327 TTATAATTGG
56126337 AAAATCTCATT
1 AAAATCTCATT
56126348 AAAATCTCATT
1 AAAATCTCATT
56126359 AAAATC
1 AAAATC
56126365 AGTCTTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATCTCATT
Found at i:56128660 original size:18 final size:17
Alignment explanation
Indices: 56128628--56128661 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56128618 AATACAGGTG
*
56128628 ATGGTGATGATGATGGT
1 ATGGTGATGAGGATGGT
56128645 ATGGTGTATGAGGATGG
1 ATGGTG-ATGAGGATGG
56128662 AGATATGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (17 bp):
ATGGTGATGAGGATGGT
Found at i:56129350 original size:3 final size:3
Alignment explanation
Indices: 56129342--56129367 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56129332 TCAATCTGTT
56129342 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
56129368 TATCATGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:56131734 original size:15 final size:15
Alignment explanation
Indices: 56131714--56131744 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56131704 GGACTTATTC
56131714 ATTAATGGTCAATTT
1 ATTAATGGTCAATTT
56131729 ATTAATGGTCAATTT
1 ATTAATGGTCAATTT
56131744 A
1 A
56131745 GGAATGCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ATTAATGGTCAATTT
Found at i:56131750 original size:15 final size:15
Alignment explanation
Indices: 56131717--56131750 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
56131707 CTTATTCATT
**
56131717 AATGGTCAATTTATT
1 AATGGTCAATTTAGG
56131732 AATGGTCAATTTAGG
1 AATGGTCAATTTAGG
56131747 AATG
1 AATG
56131751 CTTCTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (15 bp):
AATGGTCAATTTAGG
Found at i:56131977 original size:22 final size:22
Alignment explanation
Indices: 56131952--56132006 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
56131942 ACCTTTGAAA
56131952 CATATCACTTACATTAATAATT
1 CATATCACTTACATTAATAATT
* * *
56131974 CATATCACTTCCGTTTATAATT
1 CATATCACTTACATTAATAATT
56131996 CATATCACTTA
1 CATATCACTTA
56132007 TCACCTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.42
Consensus pattern (22 bp):
CATATCACTTACATTAATAATT
Found at i:56132521 original size:19 final size:19
Alignment explanation
Indices: 56132484--56132521 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56132474 GCCTAAACAT
*
56132484 ATTTTTACAAATTATAATA
1 ATTTTTACAAATTAAAATA
56132503 ATTTTT-CAAATTTAAAATA
1 ATTTTTACAAA-TTAAAATA
56132522 GGGGAACCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTTACAAATTAAAATA
Found at i:56139282 original size:36 final size:36
Alignment explanation
Indices: 56139233--56139305 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
56139223 AATTAAAGAT
*
56139233 TAAATCTTTTTATTTTTTTATTTAATATTGTTAGTA
1 TAAATCTTCTTATTTTTTTATTTAATATTGTTAGTA
*
56139269 TAAATCTTCTTATTTTTTTATTTACTATTGTTAGTA
1 TAAATCTTCTTATTTTTTTATTTAATATTGTTAGTA
56139305 T
1 T
56139306 TTTTTAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (36 bp):
TAAATCTTCTTATTTTTTTATTTAATATTGTTAGTA
Found at i:56139654 original size:19 final size:19
Alignment explanation
Indices: 56139605--56139655 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
56139595 TTAGGTTCAT
56139605 TAAATTTAAAT-TATATTAC
1 TAAATTTAAATAT-TATTAC
* *
56139624 TAAATTT--CTATTATTAG
1 TAAATTTAAATATTATTAC
56139641 TAAATTTAAATATTA
1 TAAATTTAAATATTA
56139656 GAATCTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.50
18 1 0.04
19 12 0.46
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATTTAAATATTATTAC
Found at i:56140289 original size:16 final size:16
Alignment explanation
Indices: 56140280--56140335 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
56140270 TGGAATAGGA
*
56140280 TTATAATGGAATAGAAA
1 TTATAATGGAATA-AAG
*
56140297 CTATAATGGAATAAAG
1 TTATAATGGAATAAAG
* *
56140313 TTGTAATGGAATAGAG
1 TTATAATGGAATAAAG
56140329 TTATAAT
1 TTATAAT
56140336 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (16 bp):
TTATAATGGAATAAAG
Found at i:56140449 original size:6 final size:6
Alignment explanation
Indices: 56140438--56140466 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56140428 TAGATAGACA
56140438 TTATTG TTATTG TTATTG TTATTG TTATT
1 TTATTG TTATTG TTATTG TTATTG TTATT
56140467 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTATTG
Found at i:56140525 original size:26 final size:26
Alignment explanation
Indices: 56140496--56140572 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 26
56140486 AATAAATAAT
56140496 TTAATCATATTTTAATATAATTATTA
1 TTAATCATATTTTAATATAATTATTA
* *
56140522 TTAAAT-ATAATTTAATAATATATAATTTA
1 TT-AATCATATTTTAAT-ATA-ATTA-TTA
*
56140551 ATAA-CAT-TTTTAATATAATTAT
1 TTAATCATATTTTAATATAATTAT
56140573 GTTTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
24 1 0.02
25 3 0.07
26 14 0.34
27 12 0.29
28 7 0.17
29 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAATCATATTTTAATATAATTATTA
Found at i:56140544 original size:15 final size:15
Alignment explanation
Indices: 56140526--56140554 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56140516 TTATTATTAA
56140526 ATATAATTTAATAAT
1 ATATAATTTAATAAT
56140541 ATATAATTTAATAA
1 ATATAATTTAATAA
56140555 CATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATTTAATAAT
Found at i:56145959 original size:46 final size:45
Alignment explanation
Indices: 56145906--56146162 Score: 225
Period size: 46 Copynumber: 5.6 Consensus size: 45
56145896 AGATTTGTGC
*
56145906 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCGTATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCGTA-GATGATA
* ** * **
56145952 GCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCGT-AGATGATA
* ** ** *
56146000 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCGTAG-ATGATA
* *
56146046 GCCAGTGTAAAACATGTCTGGGACATGCATCGGCC-TCAAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCGT--AGATGATA
* * * * *
56146092 ACCAGTGTCAGACATGTCTGAGACATGCGTCTGCTACG-AGATG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC--CGTAGATGATA
56146136 GCCAGTGTAAGACATGTCTGGGACATG
1 GCCAGTGTAAGACATGTCTGGGACATG
56146163 TGTCAGTACG
Statistics
Matches: 170, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
44 24 0.14
45 3 0.02
46 90 0.53
47 28 0.16
48 24 0.14
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCGTAGATGATA
Found at i:56146027 original size:94 final size:92
Alignment explanation
Indices: 56145909--56146079 Score: 252
Period size: 94 Copynumber: 1.8 Consensus size: 92
56145899 TTTGTGCGCC
** ** * * *
56145909 AGTGTAAGACATGTCTGGGACATGCATCGGCCGTATTATGATAGCCAGTGTAAGACCATGTCTGA
1 AGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAA-AACATGTCTGA
56145974 GACATGGCATCGGCATTGAGACGAGGGCT
65 GACAT-GCATCGGCATTGAGACGAGGGCT
*
56146003 AGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAAAACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAAAACATGTCTGAG
56146068 ACATGCATCGGC
66 ACATGCATCGGC
56146080 CTCAAGATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 8 0.12
93 14 0.20
94 47 0.68
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAAAACATGTCTGAG
ACATGCATCGGCATTGAGACGAGGGCT
Found at i:56152781 original size:22 final size:20
Alignment explanation
Indices: 56152753--56152793 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
56152743 ATTAATTTTA
56152753 ATTTTATGATATAAAAATAATT
1 ATTTTAT-AT-TAAAAATAATT
*
56152775 ATTTTATATTTAAAATAAT
1 ATTTTATATTAAAAATAAT
56152794 AAAATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTTATATTAAAAATAATT
Found at i:56153585 original size:111 final size:111
Alignment explanation
Indices: 56153391--56153612 Score: 336
Period size: 111 Copynumber: 2.0 Consensus size: 111
56153381 TAGAACATAT
* * * * * *
56153391 CAAATGCAAATGCAAAATCCTACCCCCATCCGCTACACACCATCTTTGATAATCTCTATATACCA
1 CAAATGCAAACGCAAAATCCTACCCCCATCCGCTACACACCATATCTAATAATCTCTACACACCA
* *
56153456 AATAGGGTATCAAATACCCATCCATCCCTACACATCGTATAGTGAC
66 AATAGGGTATCAAATACCCATCCATCCCTACACACCATATAGTGAC
* * * *
56153502 CAAATGCAAACGCAACATCCTACCCCCATCTGTTACACACCATATCTAATAATCTTTACACACCA
1 CAAATGCAAACGCAAAATCCTACCCCCATCCGCTACACACCATATCTAATAATCTCTACACACCA
56153567 AATAGGGTATCAAATACCCATCCATCCCTACACACCATATAGTGAC
66 AATAGGGTATCAAATACCCATCCATCCCTACACACCATATAGTGAC
56153613 TGTACGTCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.23
Consensus pattern (111 bp):
CAAATGCAAACGCAAAATCCTACCCCCATCCGCTACACACCATATCTAATAATCTCTACACACCA
AATAGGGTATCAAATACCCATCCATCCCTACACACCATATAGTGAC
Found at i:56156466 original size:44 final size:44
Alignment explanation
Indices: 56156411--56156605 Score: 202
Period size: 43 Copynumber: 4.5 Consensus size: 44
56156401 TCGCGGCGTT
* * * *
56156411 TTTTTAAAAAAAGCGCCGCTAAAAGTCCTGGTC-TTTAGCGGCGC
1 TTTTTGAAAAAA-CGCCGCTAAAAGACCAGGACTTTTAGCGGCGC
* * *
56156455 TTTTT-AGAAAAACGCCGC-AGAAGACCAGGATTTTTAGCAGCGC
1 TTTTTGA-AAAAACGCCGCTAAAAGACCAGGACTTTTAGCGGCGC
** * *
56156498 TTTTTGAAAAAGTGCCGCT-AAAGACCAAGACTTTTAGCGGCAC
1 TTTTTGAAAAAACGCCGCTAAAAGACCAGGACTTTTAGCGGCGC
* *
56156541 TTTTTGAAAAAACGTCGCT-AAAGACCAGGACTTTTAGCGGTGC
1 TTTTTGAAAAAACGCCGCTAAAAGACCAGGACTTTTAGCGGCGC
*
56156584 TTTTTTTAAAAAACGCCGCTAA
1 -TTTTTGAAAAAACGCCGCTAA
56156606 TTTGCCCAGT
Statistics
Matches: 124, Mismatches: 21, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
42 8 0.06
43 87 0.70
44 28 0.23
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TTTTTGAAAAAACGCCGCTAAAAGACCAGGACTTTTAGCGGCGC
Found at i:56156928 original size:21 final size:21
Alignment explanation
Indices: 56156899--56156943 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
56156889 TTCTATTCTA
* *
56156899 CTCCTCCTCCCTCGCTGCTGC
1 CTCCACCTCCCGCGCTGCTGC
56156920 CTCCACCTCCCGCGCTGCTGC
1 CTCCACCTCCCGCGCTGCTGC
56156941 CTC
1 CTC
56156944 TGCTCTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.58, G:0.16, T:0.24
Consensus pattern (21 bp):
CTCCACCTCCCGCGCTGCTGC
Found at i:56157501 original size:9 final size:9
Alignment explanation
Indices: 56157487--56157625 Score: 111
Period size: 9 Copynumber: 14.6 Consensus size: 9
56157477 ATGTATTAGT
56157487 TAAGTTATG
1 TAAGTTATG
56157496 TAAGTTGATATG
1 TAAG-T--TATG
56157508 TACA-TTATG
1 TA-AGTTATG
*
56157517 TGAGTTATG
1 TAAGTTATG
56157526 TAAGTTGTTATG
1 TAA---GTTATG
56157538 TAA-TTATG
1 TAAGTTATG
56157546 TAAGTTATG
1 TAAGTTATG
*
56157555 TGAGTTATG
1 TAAGTTATG
56157564 TAAGTTGTTATG
1 TAA---GTTATG
*
56157576 TAAATTATG
1 TAAGTTATG
*
56157585 TAAGTTATA
1 TAAGTTATG
*
56157594 TGAGTTATG
1 TAAGTTATG
56157603 TAAGTTATG
1 TAAGTTATG
* *
56157612 TAATTTATT
1 TAAGTTATG
56157621 TAAGT
1 TAAGT
56157626 AATGATCAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
8 9 0.09
9 69 0.66
10 1 0.01
11 1 0.01
12 24 0.23
13 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:56157523 original size:30 final size:29
Alignment explanation
Indices: 56157487--56157614 Score: 136
Period size: 30 Copynumber: 4.4 Consensus size: 29
56157477 ATGTATTAGT
56157487 TAAGTTATGTAAGTTGATATGTACATTATG
1 TAAGTTATGTAAGTTGATATGTA-ATTATG
* *
56157517 TGAGTTATGTAAGTTGTTATGTAATTATG
1 TAAGTTATGTAAGTTGATATGTAATTATG
* * **
56157546 TAAGTTATGTGAGTT-ATGTAAGTTGTTATG
1 TAAGTTATGTAAGTTGA--TATGTAATTATG
* *
56157576 TAAATTATGTAAGTT-ATATG-AGTTATG
1 TAAGTTATGTAAGTTGATATGTAATTATG
56157603 TAAGTTATGTAA
1 TAAGTTATGTAA
56157615 TTTATTTAAG
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
27 17 0.20
28 3 0.04
29 19 0.23
30 44 0.53
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (29 bp):
TAAGTTATGTAAGTTGATATGTAATTATG
Found at i:56157554 original size:38 final size:39
Alignment explanation
Indices: 56157504--56157608 Score: 178
Period size: 38 Copynumber: 2.7 Consensus size: 39
56157494 TGTAAGTTGA
56157504 TATGTACA-TTATGTGAGTTATGTAAGTTGTTATGT-AAT
1 TATGTA-AGTTATGTGAGTTATGTAAGTTGTTATGTAAAT
56157542 TATGTAAGTTATGTGAGTTATGTAAGTTGTTATGTAAAT
1 TATGTAAGTTATGTGAGTTATGTAAGTTGTTATGTAAAT
*
56157581 TATGTAAGTTATATGAGTTATGTAAGTT
1 TATGTAAGTTATGTGAGTTATGTAAGTT
56157609 ATGTAATTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
37 1 0.02
38 33 0.52
39 30 0.47
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (39 bp):
TATGTAAGTTATGTGAGTTATGTAAGTTGTTATGTAAAT
Found at i:56158228 original size:241 final size:241
Alignment explanation
Indices: 56157805--56158291 Score: 888
Period size: 241 Copynumber: 2.0 Consensus size: 241
56157795 TTAAGGTTAT
56157805 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCTAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCTAAGTCTTTTTGAATTTTTTAAGAT
* * *
56157870 TCATCATACGTGACGTTGTTACACCTAGGGAGGATCTATTATATCTTACAGCTCGATATAAGGTA
66 TCATCATACGTGACGTTGTTACACCTAGAGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
*
56157935 ACTCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
56158000 GGTCAGCTATTGTTGTAATTTTAAT-GAACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATAG-ACAAGCAAGCTACATGGTA
56158046 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTT-TCAAGTCTTTTTGAATTTTTTAAGA
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCT-AAGTCTTTTTGAATTTTTTAAGA
*
56158110 TTCATCATACGTGGCGTTGTTACACCTAGAGAGGATCCATTATATCTTACAGCTCGATATAAGGC
65 TTCATCATACGTGACGTTGTTACACCTAGAGAGGATCCATTATATCTTACAGCTCGATATAAGGC
56158175 AACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGA
130 AACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGA
*
56158240 AGGTCAGCTATTGTTGTAATTTTAATAGACAAGTAAGCTACATGGTA
195 AGGTCAGCTATTGTTGTAATTTTAATAGACAAGCAAGCTACATGGTA
56158287 ATAAA
1 ATAAA
56158292 ATTAATTCAT
Statistics
Matches: 238, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
240 1 0.00
241 236 0.99
242 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (241 bp):
ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCTAAGTCTTTTTGAATTTTTTAAGAT
TCATCATACGTGACGTTGTTACACCTAGAGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
GGTCAGCTATTGTTGTAATTTTAATAGACAAGCAAGCTACATGGTA
Found at i:56158816 original size:183 final size:183
Alignment explanation
Indices: 56158503--56158834 Score: 610
Period size: 183 Copynumber: 1.8 Consensus size: 183
56158493 CCTAGAACAT
* *
56158503 ATGTAAGATTATAAGATTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAATTTAAGCAAATATAAAAACTTTATCTAT
*
56158568 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGTAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
*
56158633 AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAAGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
*
56158686 ATGTAAGATTATAAGAGTGGCACCAAATATATTTCAATTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAATTTAAGCAAATATAAAAACTTTATCTAT
*
56158751 ATCCGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
56158816 AGCAAGAAGCAGTAACTGA
131 AGCAAGAAGCAGTAACTGA
56158835 TGCTGAATCT
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 143 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAATTTAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
AGCAAGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
Found at i:56160607 original size:22 final size:22
Alignment explanation
Indices: 56160579--56160622 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
56160569 GATTGAGTAA
56160579 ATGAGTTACCTTTTAAAGAGAC
1 ATGAGTTACCTTTTAAAGAGAC
56160601 ATGAGTTACCTTTTAAAGAGAC
1 ATGAGTTACCTTTTAAAGAGAC
56160623 TTCCTTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
ATGAGTTACCTTTTAAAGAGAC
Found at i:56161814 original size:22 final size:22
Alignment explanation
Indices: 56161786--56161828 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
56161776 CCTAGATCAA
*
56161786 GCAATAATCACGAAGCTAACAC
1 GCAATAATCACAAAGCTAACAC
56161808 GCAATAATCACAAAGCTAACA
1 GCAATAATCACAAAGCTAACA
56161829 AAACATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.14
Consensus pattern (22 bp):
GCAATAATCACAAAGCTAACAC
Found at i:56162416 original size:77 final size:77
Alignment explanation
Indices: 56162333--56162494 Score: 252
Period size: 77 Copynumber: 2.1 Consensus size: 77
56162323 ACAATTATGT
** * * * *
56162333 TTTTTTGCGGCGTTTTTTTAAAAAACACCGCTAATCCCCTAAATATTCATTAAAAACGATGTCGT
1 TTTTTTGCGGCGTTTTTAAAAAAAACACCGCTAATCCCCTAAATATCCATTAAAAACAATGCCAT
*
56162398 TTATTATTTTAA
66 TTACTATTTTAA
*
56162410 TTTTTTGCGGCGTTTTTAAAAAAAACGCCGCTAATCCCCTAAATATCCATTAAAAACAATGCCAT
1 TTTTTTGCGGCGTTTTTAAAAAAAACACCGCTAATCCCCTAAATATCCATTAAAAACAATGCCAT
56162475 TTACTATTTTAA
66 TTACTATTTTAA
56162487 TTTTTTGC
1 TTTTTTGC
56162495 TCCCTTAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (77 bp):
TTTTTTGCGGCGTTTTTAAAAAAAACACCGCTAATCCCCTAAATATCCATTAAAAACAATGCCAT
TTACTATTTTAA
Found at i:56163490 original size:77 final size:78
Alignment explanation
Indices: 56163387--56163543 Score: 253
Period size: 77 Copynumber: 2.0 Consensus size: 78
56163377 TTTTGAAAAA
* * *
56163387 AACGCCGGTACTCCCCTAAAAATCCAATAAAAACGACGTCGTTTTCGTTAAACTGCT-TTTTTTT
1 AACGCCGCTACTCCCCTAAAAATCCAATAAAAACGACGCCGTTTTCGTTAAACTGCTATGTTTTT
56163451 TGCGGCGTTTTTT
66 TGCGGCGTTTTTT
* * *
56163464 AACGCCGCTACTCTCCTAAATATCCAATTAAAACGACGCCGTTTTCGTTAAACTGCTATGTTTTT
1 AACGCCGCTACTCCCCTAAAAATCCAATAAAAACGACGCCGTTTTCGTTAAACTGCTATGTTTTT
56163529 TGCGGCGTTTTTT
66 TGCGGCGTTTTTT
56163542 AA
1 AA
56163544 ATAAACGCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 52 0.71
78 21 0.29
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (78 bp):
AACGCCGCTACTCCCCTAAAAATCCAATAAAAACGACGCCGTTTTCGTTAAACTGCTATGTTTTT
TGCGGCGTTTTTT
Found at i:56164270 original size:2 final size:2
Alignment explanation
Indices: 56164263--56164292 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56164253 TAAACCCTAA
56164263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56164293 TACAAGGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56164763 original size:41 final size:40
Alignment explanation
Indices: 56164706--56165044 Score: 437
Period size: 41 Copynumber: 8.3 Consensus size: 40
56164696 TTATATGACT
56164706 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GTC
* * * *
56164747 TTTAGTGGCGTTTTACCGAAAGTGCTGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GTC
* * * *
56164788 TTTAGCGGCGTTTTATCGAAAGCGCTGCTAATGCTATGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GTC
*
56164829 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GTC
**
56164870 TTTAGCGGCGTTTTACCGTAAGCGCCGCTAATGCTCTGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTC
* * *
56164910 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGTTCTATT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTC
* * *
56164950 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGTTCTATT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTC
* * *
56164990 TTTAGCGGCGTTTTTTACTAAAA-CGCCGCTATTGCTCTGTT
1 TTTAGCGGCG--TTTTACCAAAAGCGCCGCTAATGCTCTGTC
56165031 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
56165045 TGGTAAAACG
Statistics
Matches: 274, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
39 4 0.01
40 88 0.32
41 172 0.63
42 10 0.04
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTC
Found at i:56169905 original size:19 final size:19
Alignment explanation
Indices: 56169883--56169921 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
56169873 TGGGAGGAGT
*
56169883 AAGA-AGGAGGGGCAGTAAA
1 AAGAGAGGAGGAG-AGTAAA
56169902 AAGAGAGGAGGAGAGTAAA
1 AAGAGAGGAGGAGAGTAAA
56169921 A
1 A
56169922 TGAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.51, C:0.03, G:0.41, T:0.05
Consensus pattern (19 bp):
AAGAGAGGAGGAGAGTAAA
Found at i:56173026 original size:20 final size:20
Alignment explanation
Indices: 56173003--56173042 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56172993 CTTAATTAGG
56173003 GATTTAACAACTTGACTACT
1 GATTTAACAACTTGACTACT
56173023 GATTTAACAACTTGACTACT
1 GATTTAACAACTTGACTACT
56173043 CACTTACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
GATTTAACAACTTGACTACT
Found at i:56177169 original size:6 final size:6
Alignment explanation
Indices: 56177119--56177196 Score: 72
Period size: 6 Copynumber: 13.5 Consensus size: 6
56177109 AAAAGTCTAA
* * * * * *
56177119 AAAAAT AACAAT AAACAT AAAAAT AGAAAT AAAACT AATACT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
56177167 AAAAAT AAAAA- CAAAAT -AAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
56177197 TGGACTCAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 14 0.24
6 45 0.76
ACGTcount: A:0.76, C:0.06, G:0.01, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:56177942 original size:20 final size:20
Alignment explanation
Indices: 56177919--56177957 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56177909 TTTTACTGGA
*
56177919 CTTTTTTTTCTTTTATTCCC
1 CTTTTCTTTCTTTTATTCCC
* *
56177939 CTTTTCTTTGTTTTCTTCC
1 CTTTTCTTTCTTTTATTCC
56177958 TTTTGCTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.69
Consensus pattern (20 bp):
CTTTTCTTTCTTTTATTCCC
Found at i:56183919 original size:22 final size:21
Alignment explanation
Indices: 56183892--56183969 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 21
56183882 TGTGCCTCAG
56183892 TCACACGGCCGTATGCCCCTCT
1 TCACACGGCCGT-TGCCCCTCT
* **
56183914 TCACACGGGC-TTGTGCCTCAT
1 TCACACGGCCGTTGCCCCTC-T
* *
56183935 CCACACGGCTGTGTGCCCCTCT
1 TCACACGGCCGT-TGCCCCTCT
* *
56183957 TCATACGGGCGTT
1 TCACACGGCCGTT
56183970 TGACCCCCAA
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
20 6 0.15
21 10 0.24
22 19 0.46
23 6 0.15
ACGTcount: A:0.13, C:0.38, G:0.23, T:0.26
Consensus pattern (21 bp):
TCACACGGCCGTTGCCCCTCT
Found at i:56183920 original size:43 final size:43
Alignment explanation
Indices: 56183873--56183968 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 43
56183863 GCCCTAGTCA
*
56183873 ACACGAGCGTGTGCCTCAGT-CACACGGCCGTATGCCCCTCTTC
1 ACACGGGCGTGTGCCTCA-TCCACACGGCCGTATGCCCCTCTTC
* * *
56183916 ACACGGGCTTGTGCCTCATCCACACGGCTGTGTGCCCCTCTTC
1 ACACGGGCGTGTGCCTCATCCACACGGCCGTATGCCCCTCTTC
*
56183959 ATACGGGCGT
1 ACACGGGCGT
56183969 TTGACCCCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.23
Consensus pattern (43 bp):
ACACGGGCGTGTGCCTCATCCACACGGCCGTATGCCCCTCTTC
Found at i:56184206 original size:2 final size:2
Alignment explanation
Indices: 56184199--56184226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56184189 GGGTAATTGG
56184199 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
56184227 ACGCATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:56193543 original size:10 final size:11
Alignment explanation
Indices: 56193528--56193556 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
56193518 TTCAAAGGTG
56193528 TGAATTGAAT-
1 TGAATTGAATA
56193538 TGAATTGAATA
1 TGAATTGAATA
56193549 TGAATTGA
1 TGAATTGA
56193557 TGTTAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:56194159 original size:24 final size:24
Alignment explanation
Indices: 56194096--56194162 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
56194086 TTCTCGATTA
*
56194096 AATGGCTTTTCGGAGCTTCCCGAT
1 AATGGCTTTCCGGAGCTTCCCGAT
* * **
56194120 ATTGGCTCTCATGAGCTTCCC-ATT
1 AATGGCTTTCCGGAGCTTCCCGA-T
56194144 AATGGCTTTCCGGAGCTTC
1 AATGGCTTTCCGGAGCTTC
56194163 TTGTTACATG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.34
Consensus pattern (24 bp):
AATGGCTTTCCGGAGCTTCCCGAT
Found at i:56194714 original size:2 final size:2
Alignment explanation
Indices: 56194707--56194736 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56194697 CCCATTTCGG
56194707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56194737 ACTAATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56202071 original size:46 final size:46
Alignment explanation
Indices: 56202019--56202193 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
56202009 ATTTGGGCAT
* *
56202019 CCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * *
56202065 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGC
* * *
56202110 ATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
*
56202158 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56202194 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 62 0.57
47 26 0.24
48 5 0.05
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:56202173 original size:93 final size:93
Alignment explanation
Indices: 56202014--56202185 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
56202004 AGGATATTTG
*
56202014 GGCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
56202079 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * * *
56202107 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
56202172 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
56202186 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:56211384 original size:21 final size:21
Alignment explanation
Indices: 56211343--56211386 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
56211333 CCCCTTTATT
*
56211343 AACATAAAAATTTAAAATTTA
1 AACATAAAAATTGAAAATTTA
*
56211364 AACATAACAAA-TGAAACTTTA
1 AACATAA-AAATTGAAAATTTA
56211385 AA
1 AA
56211387 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.27
Consensus pattern (21 bp):
AACATAAAAATTGAAAATTTA
Found at i:56230406 original size:21 final size:21
Alignment explanation
Indices: 56230357--56230415 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
56230347 GTAATAAATC
*
56230357 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
56230377 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
56230399 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
56230416 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:56252207 original size:8 final size:8
Alignment explanation
Indices: 56252194--56252220 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
56252184 CACAAGTTGC
56252194 TAGAGGAT
1 TAGAGGAT
56252202 TAGAGGAT
1 TAGAGGAT
56252210 TAGAGGAT
1 TAGAGGAT
56252218 TAG
1 TAG
56252221 GTGTGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (8 bp):
TAGAGGAT
Found at i:56260988 original size:40 final size:40
Alignment explanation
Indices: 56260933--56261099 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
56260923 GAATGATACT
* *
56260933 CGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
* *
56260973 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATATC
* * ** *
56261013 CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
* * * *
56261053 CGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
56261093 C-GGCTAA
1 CGGGCTAA
56261100 ATTTCGAAGA
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 6 0.06
40 97 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
Found at i:56273841 original size:19 final size:20
Alignment explanation
Indices: 56273787--56273834 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
56273777 GATCTCGTAC
56273787 TTTGGCCCATTTTCTCTGTT
1 TTTGGCCCATTTTCTCTGTT
56273807 TTTGGCCCATTTTCTCTGTT
1 TTTGGCCCATTTTCTCTGTT
56273827 TTTGGCCC
1 TTTGGCCC
56273835 GTTTCTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.04, C:0.27, G:0.17, T:0.52
Consensus pattern (20 bp):
TTTGGCCCATTTTCTCTGTT
Found at i:56277244 original size:55 final size:55
Alignment explanation
Indices: 56277185--56277307 Score: 131
Period size: 55 Copynumber: 2.2 Consensus size: 55
56277175 GTTTAAGCTC
* * *
56277185 CACGCCCATGTTAATTTAACAAGTTCGACCACGGGTGTT-AGACACGGGCGTGTCG
1 CACGCCCATGTTAATTTAACAAGTTCAACCACGGGTCTTCA-ACACGGGCGTGTCA
* * * ** *
56277240 CACGCCCCTGCTAGTTTCTCAATTTCAACCACGGGTCTTCAACACGGGCGTGTCA
1 CACGCCCATGTTAATTTAACAAGTTCAACCACGGGTCTTCAACACGGGCGTGTCA
* *
56277295 CACACCCGTGTTA
1 CACGCCCATGTTA
56277308 TTTTGGTAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
55 54 0.98
56 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (55 bp):
CACGCCCATGTTAATTTAACAAGTTCAACCACGGGTCTTCAACACGGGCGTGTCA
Found at i:56279578 original size:46 final size:46
Alignment explanation
Indices: 56279528--56279700 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
56279518 TGGTTGAGCA
*
56279528 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
56279574 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
56279621 TCCGAACTCGTTGAGTTGAGTCAGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
56279667 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
56279701 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:56279684 original size:93 final size:93
Alignment explanation
Indices: 56279525--56279695 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
56279515 GGATGGTTGA
* * *
56279525 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
56279590 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
56279618 GCATCCGAACTCGTTGAGTTGAGTCAGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
56279683 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
56279696 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:56279961 original size:19 final size:20
Alignment explanation
Indices: 56279924--56279961 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
56279914 ATAAGGTGGT
56279924 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
56279944 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
56279962 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:56287092 original size:46 final size:46
Alignment explanation
Indices: 56287042--56287213 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
56287032 TGGTTGAGCA
*
56287042 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
56287088 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
56287135 TCCGAACTCGTTGAGTTGAGT-CGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
56287180 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
56287214 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 23 0.22
46 47 0.45
47 24 0.23
49 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:56287197 original size:92 final size:93
Alignment explanation
Indices: 56287039--56287208 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 93
56287029 GGATGGTTGA
* *
56287039 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
56287104 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
56287132 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
56287196 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
56287209 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 48 0.67
93 24 0.33
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:56287475 original size:19 final size:20
Alignment explanation
Indices: 56287438--56287475 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
56287428 ATAAGGTGGT
56287438 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
56287458 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
56287476 TGGTGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:56296546 original size:21 final size:21
Alignment explanation
Indices: 56296521--56296574 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
56296511 TATTAAATTA
56296521 ACACGGGCGTGGAGCTTGAAC
1 ACACGGGCGTGGAGCTTGAAC
56296542 ACACGGGCGTGGAGCTTGAAC
1 ACACGGGCGTGGAGCTTGAAC
56296563 ACACGGGCGTGG
1 ACACGGGCGTGG
56296575 GAGAAGCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.41, T:0.13
Consensus pattern (21 bp):
ACACGGGCGTGGAGCTTGAAC
Found at i:56296585 original size:23 final size:21
Alignment explanation
Indices: 56296521--56296585 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
56296511 TATTAAATTA
***
56296521 ACACGGGCGTGGAGCTTGAAC
1 ACACGGGCGTGGAGAGCGAAC
***
56296542 ACACGGGCGTGGAGCTTGAAC
1 ACACGGGCGTGGAGAGCGAAC
56296563 ACACGGGCGTGGGAGAAGCGAAC
1 ACACGGGCGT-GGAG-AGCGAAC
56296586 GAAGCTAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 31 0.79
22 4 0.10
23 4 0.10
ACGTcount: A:0.26, C:0.23, G:0.40, T:0.11
Consensus pattern (21 bp):
ACACGGGCGTGGAGAGCGAAC
Found at i:56304655 original size:45 final size:45
Alignment explanation
Indices: 56304590--56304755 Score: 171
Period size: 45 Copynumber: 3.6 Consensus size: 45
56304580 CGCCCCTAAG
*
56304590 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCATAAA
* *
56304636 TGAACTC-GACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCATAAA
* * * *
56304682 CGAACTCGGACTCAACTCAACGAGTTC-GACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCATAAA
56304727 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
56304756 ATGCTCAACC
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 6 0.06
43 2 0.02
44 1 0.01
45 46 0.46
46 16 0.16
47 21 0.21
48 2 0.02
49 3 0.03
50 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCATAAA
Found at i:56304748 original size:92 final size:92
Alignment explanation
Indices: 56304591--56304759 Score: 277
Period size: 92 Copynumber: 1.8 Consensus size: 92
56304581 GCCCCTAAGT
* *
56304591 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGACTCAACTCAAC
56304656 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* * *
56304683 GAACTCGGACTCAACTCAACGAGTTC-GACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTC-GACTCAACTCAA
56304747 CGAGTTCGGATGC
65 CGAGTTCGGATGC
56304760 TCAACCATCC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
91 21 0.30
92 50 0.70
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:56312283 original size:46 final size:46
Alignment explanation
Indices: 56312135--56312306 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
56312125 AACCCGCCCC
* * *
56312135 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
* * * *
56312181 TAAATGAACTC-GACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCATCCA
* * * *
56312228 TCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
56312273 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
56312307 TGCTCAATCA
Statistics
Matches: 102, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 22 0.22
46 43 0.42
47 23 0.23
48 2 0.02
49 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
Found at i:56314249 original size:68 final size:70
Alignment explanation
Indices: 56314177--56314374 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
56314167 ACACCCTGTA
* * * *
56314177 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
56314239 ATAAAT
65 ATAAAT
*
56314245 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
56314310 ATAAAT
65 ATAAAT
*
56314316 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
56314375 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:56314288 original size:41 final size:41
Alignment explanation
Indices: 56314243--56314360 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
56314233 TGAAAGATAA
56314243 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
56314284 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
56314314 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
56314355 ATGTAG
1 ATGTAG
56314361 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:56314300 original size:71 final size:71
Alignment explanation
Indices: 56314211--56314374 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
56314201 GAGATGTATC
56314211 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
56314276 AGGACA
66 AGGACA
56314282 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
56314347 AGGACA
66 AGGACA
56314353 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
56314375 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:56317576 original size:64 final size:63
Alignment explanation
Indices: 56317495--56317677 Score: 167
Period size: 67 Copynumber: 2.9 Consensus size: 63
56317485 AGACATTATG
* *
56317495 ATGTAGCTAGGTCGCATGGGTGACACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGACACTATGTGTACACCATGTAGACAAGAGAGCTAC-GAATAA
* * * * *
56317559 ATGTAGCTAGGTCGCATGCGTGGTTC-CAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAAT
1 ATGTAGCTAGGTCGCATGGGT-G-ACACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAAT
56317623 AA
62 AA
* ** * *
56317625 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGACACTATGTGTACACCATGTAG-ACAAGAGAGC
56317678 CGAACTATAT
Statistics
Matches: 96, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
61 1 0.01
62 19 0.20
63 1 0.01
64 23 0.24
65 17 0.18
66 8 0.08
67 27 0.28
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGACACTATGTGTACACCATGTAGACAAGAGAGCTACGAATAA
Found at i:56333598 original size:40 final size:40
Alignment explanation
Indices: 56333538--56333617 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
56333528 GGGAATGTAC
56333538 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
*
56333578 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
56333618 TTAACTCTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.36
Consensus pattern (40 bp):
AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
Found at i:56333627 original size:40 final size:40
Alignment explanation
Indices: 56333538--56333627 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
56333528 GGGAATGTAC
*
56333538 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
*
56333578 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
**
56333618 TTAACTCTTG
1 AGAACTCTTG
56333628 CTTCCATCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (40 bp):
AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
Found at i:56336305 original size:34 final size:34
Alignment explanation
Indices: 56336262--56336330 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
56336252 CGAAGATAAT
*
56336262 GCCAGTAGAACAGTCCATAGAGAGCTAATGGATG
1 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
56336296 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
1 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
56336330 G
1 G
56336331 TTCATCACCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.17
Consensus pattern (34 bp):
GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
Found at i:56342351 original size:17 final size:18
Alignment explanation
Indices: 56342310--56342352 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
56342300 TGTATTTACT
56342310 TATTATATAAGTAAATAG
1 TATTATATAAGTAAATAG
*
56342328 TAATATA-AAGTAAAATA-
1 TATTATATAAGT-AAATAG
56342345 TATTATAT
1 TATTATAT
56342353 TATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (18 bp):
TATTATATAAGTAAATAG
Found at i:56345329 original size:18 final size:18
Alignment explanation
Indices: 56345302--56345338 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56345292 ATTCGGGACT
*
56345302 AAATTGATAACATATAAA
1 AAATTCATAACATATAAA
*
56345320 AAATTCATAACTTATAAA
1 AAATTCATAACATATAAA
56345338 A
1 A
56345339 TTTTTAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATTCATAACATATAAA
Found at i:56346277 original size:232 final size:232
Alignment explanation
Indices: 56345972--56346431 Score: 848
Period size: 232 Copynumber: 2.0 Consensus size: 232
56345962 TAACATCTAT
*
56345972 ATATCAAGACTTCATTTGCATAATTTCATTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
1 ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
*
56346037 ACTTCAATTCAACCAAAATATAACATCAAAATAAGTCAAATCACATGGCTTAACATATACACAAA
66 ACTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACACAAA
56346102 AATAAGCCAAAGTCAAGATATCAAGTAGCATAACTATCATCCCTTAAACTAGCCTATACATGCCA
131 AATAAGCCAAAGTCAAGATATCAAGTAGCATAACTATCATCCCTTAAACTAGCCTATACATGCCA
*
56346167 TATTTACAAATTCACAAGTTTAAAAGTACCAATCGGA
196 TATTTACAAATTCACAAGTTCAAAAGTACCAATCGGA
56346204 ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
1 ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
* *
56346269 ATTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACATAAA
66 ACTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACACAAA
* * *
56346334 AATATGCTAAAGTCAAGATATCAAGTAGCATAACTATCATCCTTTAAACTAGCCTATACATGCCA
131 AATAAGCCAAAGTCAAGATATCAAGTAGCATAACTATCATCCCTTAAACTAGCCTATACATGCCA
56346399 TATTTACAAATTCACAAGTTCAAAAGTACCAAT
196 TATTTACAAATTCACAAGTTCAAAAGTACCAAT
56346432 TGAAATTTGG
Statistics
Matches: 220, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
232 220 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (232 bp):
ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
ACTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACACAAA
AATAAGCCAAAGTCAAGATATCAAGTAGCATAACTATCATCCCTTAAACTAGCCTATACATGCCA
TATTTACAAATTCACAAGTTCAAAAGTACCAATCGGA
Found at i:56346953 original size:46 final size:46
Alignment explanation
Indices: 56346898--56347045 Score: 151
Period size: 46 Copynumber: 3.2 Consensus size: 46
56346888 AGCTGATAAA
56346898 CAGTAAGCTCTATTGAGCTGAAAATGGTAAGCCCTATTGAGCTGAA-
1 CAGTAAGCTCTATTGAGCTG-AAATGGTAAGCCCTATTGAGCTGAAT
* * *
56346944 CAGTAAGCTCTATCGAGCT-AAATCGGTAAGCTCC-AATGAGTTGAAT
1 CAGTAAGCTCTATTGAGCTGAAAT-GGTAAGC-CCTATTGAGCTGAAT
* * * * * *
56346990 CGGTAAGCTCCAATGAGCTGAAATAGTAAGCTCT-TACGAGCTGAAT
1 CAGTAAGCTCTATTGAGCTGAAATGGTAAGCCCTAT-TGAGCTGAAT
56347036 CAGTAAGCTC
1 CAGTAAGCTC
56347046 ATACGAGCTA
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
44 4 0.05
45 17 0.20
46 58 0.70
47 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (46 bp):
CAGTAAGCTCTATTGAGCTGAAATGGTAAGCCCTATTGAGCTGAAT
Found at i:56346976 original size:23 final size:23
Alignment explanation
Indices: 56346894--56347055 Score: 97
Period size: 23 Copynumber: 7.1 Consensus size: 23
56346884 CCCGAGCTGA
*
56346894 TAAA-CAGTAAGCTCTATTGAGC
1 TAAATCAGTAAGCTCTATCGAGC
* * *
56346916 TGAAAAT-GGTAAGCCCTATTGAGC
1 T--AAATCAGTAAGCTCTATCGAGC
*
56346940 TGAA-CAGTAAGCTCTATCGAGC
1 TAAATCAGTAAGCTCTATCGAGC
* * *
56346962 TAAATCGGTAAGCTCCAAT-GAGT
1 TAAATCAGTAAGCT-CTATCGAGC
* * *
56346985 TGAATCGGTAAGCTCCAAT-GAGC
1 TAAATCAGTAAGCT-CTATCGAGC
56347008 TGAAAT-AGTAAGCTCT-TACGAGC
1 T-AAATCAGTAAGCTCTAT-CGAGC
*
56347031 TGAATCAGTAAGCTC-ATACGAGC
1 TAAATCAGTAAGCTCTAT-CGAGC
56347054 TA
1 TA
56347056 TGGTGAGTCC
Statistics
Matches: 112, Mismatches: 17, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.01
22 24 0.21
23 62 0.55
24 25 0.22
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (23 bp):
TAAATCAGTAAGCTCTATCGAGC
Found at i:56346976 original size:69 final size:69
Alignment explanation
Indices: 56346894--56347045 Score: 170
Period size: 69 Copynumber: 2.2 Consensus size: 69
56346884 CCCGAGCTGA
* * *
56346894 TAAA-CAGTAAGCTCTATTGAGCTGAAAAT-GGTAAGC-CCTATTGAGCTG-AACAGTAAGCTC-
1 TAAATCAGTAAGCTCCAATGAGCTG--AATCGGTAAGCTCC-AATGAGCTGAAACAGTAAGCTCT
56346954 TATCGAGC
63 TA-CGAGC
* * *
56346962 TAAATCGGTAAGCTCCAATGAGTTGAATCGGTAAGCTCCAATGAGCTGAAATAGTAAGCTCTTAC
1 TAAATCAGTAAGCTCCAATGAGCTGAATCGGTAAGCTCCAATGAGCTGAAACAGTAAGCTCTTAC
56347027 GAGC
66 GAGC
*
56347031 TGAATCAGTAAGCTC
1 TAAATCAGTAAGCTC
56347046 ATACGAGCTA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
67 3 0.04
68 19 0.27
69 47 0.66
70 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (69 bp):
TAAATCAGTAAGCTCCAATGAGCTGAATCGGTAAGCTCCAATGAGCTGAAACAGTAAGCTCTTAC
GAGC
Found at i:56349526 original size:13 final size:14
Alignment explanation
Indices: 56349510--56349551 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
56349500 TTTCAATTTT
56349510 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
56349523 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
56349538 ATTTTAAATAATAT
1 ATTTT-AATAATAT
56349552 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:56349536 original size:16 final size:16
Alignment explanation
Indices: 56349514--56349550 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
56349504 AATTTTATTT
56349514 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
56349531 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
56349546 TAATA
1 TAATA
56349551 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:56352573 original size:13 final size:15
Alignment explanation
Indices: 56352539--56352575 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
56352529 TAGTTATCAC
56352539 TTAATTAATATTAGAG
1 TTAATT-ATATTAGAG
56352555 TTAATTATATTA-A-
1 TTAATTATATTAGAG
56352568 TTAATTAT
1 TTAATTAT
56352576 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 6 0.29
16 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAATTATATTAGAG
Found at i:56353372 original size:36 final size:38
Alignment explanation
Indices: 56353332--56353415 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
56353322 TTGTAATTTT
* **
56353332 GTTGCTGGTAAATTGTTG-TTTATGT-TGGTATACATG
1 GTTGCTGGTAAATTGTTGCTTAACATATGGTATACATG
* * *
56353368 GTTGCTAGTATATTGTTGCTTAACATATGTTATACATG
1 GTTGCTGGTAAATTGTTGCTTAACATATGGTATACATG
56353406 GTTGCTGGTA
1 GTTGCTGGTA
56353416 TAAATGGCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 16 0.41
37 4 0.10
38 19 0.49
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.45
Consensus pattern (38 bp):
GTTGCTGGTAAATTGTTGCTTAACATATGGTATACATG
Found at i:56353728 original size:18 final size:18
Alignment explanation
Indices: 56353705--56353742 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56353695 TATTTCTCAA
*
56353705 TTCTCAATTCTCACACAT
1 TTCTCAATACTCACACAT
*
56353723 TTCTCAATAGTCACACAT
1 TTCTCAATACTCACACAT
56353741 TT
1 TT
56353743 TTTAGAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (18 bp):
TTCTCAATACTCACACAT
Found at i:56354199 original size:21 final size:22
Alignment explanation
Indices: 56354173--56354228 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
56354163 TTTTGTCTTA
56354173 GGGCAGCTTGTTGA-TGAGTTG
1 GGGCAGCTTGTTGACTGAGTTG
* * *
56354194 GGGCAG-TAGGTAACTGAGTTG
1 GGGCAGCTTGTTGACTGAGTTG
*
56354215 GGGCAGCCTGTTGA
1 GGGCAGCTTGTTGA
56354229 ATTGGTGTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.18, C:0.12, G:0.43, T:0.27
Consensus pattern (22 bp):
GGGCAGCTTGTTGACTGAGTTG
Found at i:56355035 original size:40 final size:40
Alignment explanation
Indices: 56354980--56355121 Score: 180
Period size: 40 Copynumber: 3.5 Consensus size: 40
56354970 AAAAAAATAC
56354980 TCACTGCATGCATATTAAAAAATAGACAACATACCAACAA
1 TCACTGCATGCATATTAAAAAATAGACAACATACCAACAA
* *
56355020 TCACTGCATGCATATTAAAATATAGGC-A-ATACCCAAACAA
1 TCACTGCATGCATATTAAAAAATAGACAACATA-CC-AACAA
* ** * *
56355060 TCACTGTATGCATATTAAAAAATAGTTAACACAACAACAA
1 TCACTGCATGCATATTAAAAAATAGACAACATACCAACAA
*
56355100 TCAGTGCATGCATATTAAAAAA
1 TCACTGCATGCATATTAAAAAA
56355122 CATTTACTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 78 0.89
41 2 0.02
42 2 0.02
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (40 bp):
TCACTGCATGCATATTAAAAAATAGACAACATACCAACAA
Found at i:56357323 original size:36 final size:35
Alignment explanation
Indices: 56357217--56357327 Score: 109
Period size: 36 Copynumber: 3.2 Consensus size: 35
56357207 CATTAATAAC
** *
56357217 AAAT-AAAATCAAAATCGAAA-TAACCCTAAATCG
1 AAATCAAAATCAAAATCGAAATTAAATCTAAATCT
* * * * *
56357250 AAATCCAAATCGAAATCAAAAATTAATTCTAATTCT
1 AAATCAAAATCAAAATC-GAAATTAAATCTAAATCT
*
56357286 AAATCAAAATCAAAATCGAAATTGAAATCAAAATCT
1 AAATCAAAATCAAAATCGAAATT-AAATCTAAATCT
56357322 AAATCA
1 AAATCA
56357328 GAATTGGTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
33 4 0.07
34 10 0.16
35 8 0.13
36 39 0.64
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (35 bp):
AAATCAAAATCAAAATCGAAATTAAATCTAAATCT
Found at i:56357360 original size:12 final size:12
Alignment explanation
Indices: 56357343--56357403 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
56357333 GGTGAGTGTT
*
56357343 TCAAAATTGTAA
1 TCAAAATTGAAA
*
56357355 TCAAAATCGAAA
1 TCAAAATTGAAA
**
56357367 TTGAAATTGAAA
1 TCAAAATTGAAA
**
56357379 TCAAAATCAAAA
1 TCAAAATTGAAA
*
56357391 TCAAAATTAAAA
1 TCAAAATTGAAA
56357403 T
1 T
56357404 TGAAACCGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (12 bp):
TCAAAATTGAAA
Found at i:56357397 original size:24 final size:24
Alignment explanation
Indices: 56357343--56357403 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
56357333 GGTGAGTGTT
* *
56357343 TCAAAATTGTAATCAAAATCGAAA
1 TCAAAATTGAAATCAAAATCAAAA
**
56357367 TTGAAATTGAAATCAAAATCAAAA
1 TCAAAATTGAAATCAAAATCAAAA
*
56357391 TCAAAATTAAAAT
1 TCAAAATTGAAAT
56357404 TGAAACCGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (24 bp):
TCAAAATTGAAATCAAAATCAAAA
Found at i:56358156 original size:27 final size:27
Alignment explanation
Indices: 56358126--56358177 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
56358116 TTAATAACTG
*
56358126 TAATTAAAAA-TATAATATTTAAAATTT
1 TAATTAAAAATTA-AATATATAAAATTT
*
56358153 TAATTAAATATTAAATATATAAAAT
1 TAATTAAAAATTAAATATATAAAAT
56358178 CACATGCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATTAAAAATTAAATATATAAAATTT
Found at i:56367428 original size:22 final size:20
Alignment explanation
Indices: 56367377--56367429 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
56367367 AAATTATATG
* *
56367377 AAAATTAAAATTAAAATATA
1 AAAATGAAAATTAAAAGATA
56367397 AAAGAGTGAAAATTAAAAGGATGA
1 AAA-A-TGAAAATTAAAA-GAT-A
56367421 AAAATGAAA
1 AAAATGAAA
56367430 GGGTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 16 0.59
23 3 0.11
24 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (20 bp):
AAAATGAAAATTAAAAGATA
Found at i:56369680 original size:26 final size:28
Alignment explanation
Indices: 56369649--56369703 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
56369639 TTACATTGTG
*
56369649 TATATTTTGAA-T-TTATATATATATAT
1 TATATTTTAAACTATTATATATATATAT
*
56369675 TATATTTTAAACTATTATATGTATATAT
1 TATATTTTAAACTATTATATATATATAT
56369703 T
1 T
56369704 GTCTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 1 0.04
28 14 0.56
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (28 bp):
TATATTTTAAACTATTATATATATATAT
Done.