Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 42
Found at i:5288504 original size:3 final size:3
Alignment explanation
Indices: 5288496--5288547 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5288486 ATAGGTTATT
5288496 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5288544 TAA T
1 TAA T
5288548 TGTGAGCCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5291141 original size:19 final size:19
Alignment explanation
Indices: 5291117--5291168 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
5291107 CATACCTGTA
5291117 TATATACATATAAATGAAT
1 TATATACATATAAATGAAT
5291136 TATATACATAT-AATGAAT
1 TATATACATATAAATGAAT
5291154 TATGTATACATATAA
1 TA--TATACATATAA
5291169 CGTTTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.30
19 11 0.37
20 9 0.30
21 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (19 bp):
TATATACATATAAATGAAT
Found at i:5295897 original size:21 final size:21
Alignment explanation
Indices: 5295871--5295910 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5295861 GGTATGACAA
5295871 TGAACCGGCTGAAAACCGGGG
1 TGAACCGGCTGAAAACCGGGG
5295892 TGAACCGGCTGAAAACCGG
1 TGAACCGGCTGAAAACCGG
5295911 CAAAACCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.35, T:0.10
Consensus pattern (21 bp):
TGAACCGGCTGAAAACCGGGG
Found at i:5299144 original size:16 final size:16
Alignment explanation
Indices: 5299123--5299156 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5299113 TTACTATTCA
*
5299123 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
5299139 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
5299155 CG
1 CG
5299157 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:5305221 original size:9 final size:8
Alignment explanation
Indices: 5305203--5305246 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
5305193 TTTTTCATTA
5305203 ATAATTTT
1 ATAATTTT
5305211 ATAAGTTTT
1 ATAA-TTTT
*
5305220 ATAAATTT
1 ATAATTTT
*
5305228 ATCA-TTT
1 ATAATTTT
5305235 ATAATTTT
1 ATAATTTT
5305243 ATAA
1 ATAA
5305247 ATTCAATTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 6 0.19
8 17 0.55
9 8 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (8 bp):
ATAATTTT
Found at i:5308189 original size:20 final size:20
Alignment explanation
Indices: 5308164--5308208 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
5308154 TTGGTGAATC
5308164 GAGCTCCATCAACTGCAATA
1 GAGCTCCATCAACTGCAATA
5308184 GAGCTCCATCAACTGCAATA
1 GAGCTCCATCAACTGCAATA
5308204 GAGCT
1 GAGCT
5308209 AAAGACACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (20 bp):
GAGCTCCATCAACTGCAATA
Found at i:5310270 original size:18 final size:17
Alignment explanation
Indices: 5310227--5310272 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
5310217 ATGGAATTGA
*
5310227 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTCACAG
* *
5310244 ATTCTAATTCCTTCACAT
1 ATTCCAATTCC-TCACAG
5310262 ATTCCAATTCC
1 ATTCCAATTCC
5310273 CTCATAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTCCAATTCCTCACAG
Found at i:5316170 original size:21 final size:20
Alignment explanation
Indices: 5316146--5316188 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
5316136 AACAAGTAAT
5316146 ATTGATAGTATAAAAAACA-AA
1 ATTGAT-GT-TAAAAAACATAA
*
5316167 ATTGATGTTAAGAAACATAA
1 ATTGATGTTAAAAAACATAA
5316187 AT
1 AT
5316189 AGACTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTGATGTTAAAAAACATAA
Found at i:5317763 original size:83 final size:81
Alignment explanation
Indices: 5317658--5318075 Score: 322
Period size: 83 Copynumber: 5.1 Consensus size: 81
5317648 GTACGTGATT
** * * *
5317658 TTGCGGCGTTTTA-ATTTAAAACGCCAATATTGCACATGTTTATAGCGGCATTTTTACAAAAACG
1 TTGCGGCGTTTTATACAT-AAACGCCAATAATGCACATGTTT-TAGCGGCGTTTTCACAAAAACG
*
5317722 CCACTATATATCTGGGATA
64 CCACTATATAT-TCGGATA
* * *
5317741 TTGCGGCGTTTTATACATAAACGCCACTAAAGTACATGTTTTTAGCGGCGTTTTCACAAAAAACG
1 TTGCGGCGTTTTATACATAAACGCCAATAATGCACATG-TTTTAGCGGCGTTTTCAC-AAAAACG
**
5317806 CTGCTATATATTCGGATA
64 CCACTATATATTCGGATA
* * * * * * *
5317824 TTGCGGCATTTTTTACATAAATGCCACTAAAGTACGCAT-TTTTAGCGGCGTTTGCACAAAAACG
1 TTGCGGCGTTTTATACATAAACGCCAAT-AA-TGCACATGTTTTAGCGGCGTTTTCACAAAAACG
* *
5317888 CCATTATATATTTGGATA
64 CCACTATATATTCGGATA
* * * * * * * * ** * * **** *
5317906 TCGCGGCG-TTTGTCCAAAAACACCACTAAAGTATGTAATTTTAGCGGCATTTTTGTGAAAACGT
1 TTGCGGCGTTTTATACATAAACGCCAATAATGCACAT-GTTTTAGCGGCGTTTTCACAAAAACGC
*
5317970 CGCTATATATTCGGATA
65 CACTATATATTCGGATA
* * * * *
5317987 TTGCGGCATTTTTTACATAAATGCCACTAAAGTACACAT-TTTTAGCGGCGTTTTCACAAAAACG
1 TTGCGGCGTTTTATACATAAACGCCAAT-AA-TGCACATGTTTTAGCGGCGTTTTCACAAAAACG
*
5318051 CCACTATATATTTGGATA
64 CCACTATATATTCGGATA
5318069 TTGCGGC
1 TTGCGGC
5318076 CTACATATAA
Statistics
Matches: 259, Mismatches: 66, Indels: 21
0.75 0.19 0.06
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 53 0.20
82 83 0.32
83 92 0.36
84 25 0.10
85 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (81 bp):
TTGCGGCGTTTTATACATAAACGCCAATAATGCACATGTTTTAGCGGCGTTTTCACAAAAACGCC
ACTATATATTCGGATA
Found at i:5317947 original size:82 final size:83
Alignment explanation
Indices: 5317700--5318075 Score: 406
Period size: 82 Copynumber: 4.6 Consensus size: 83
5317690 CACATGTTTA
* * *
5317700 TAGCGGCATTTTTACAAAAACGCCACTATATATCTGGGATATTGCGGC-GTTTTATACATAAACG
1 TAGCGGCGTTTTCACAAAAACGCCACTATATAT-TCGGATATTGCGGCAGTTTT-TACATAAACG
* *
5317764 CCACTAAAGTACAT-GTTTT
64 CCACTAAAGTACGTAATTTT
** * *
5317783 TAGCGGCGTTTTCACAAAAAACGCTGCTATATATTCGGATATTGCGGCATTTTTTACATAAATGC
1 TAGCGGCGTTTTCAC-AAAAACGCCACTATATATTCGGATATTGCGGCAGTTTTTACATAAACGC
*
5317848 CACTAAAGTACG-CATTTT
65 CACTAAAGTACGTAATTTT
* * * * * * * *
5317866 TAGCGGCGTTTGCACAAAAACGCCATTATATATTTGGATATCGCGGC-GTTTGTCCAAAAACACC
1 TAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCAGTTTTTACATAAACGCC
*
5317930 ACTAAAGTATGTAA-TTT
66 ACTAAAGTACGTAATTTT
* **** * * * *
5317947 TAGCGGCATTTTTGTGAAAACGTCGCTATATATTCGGATATTGCGGCATTTTTTACATAAATGCC
1 TAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCAGTTTTTACATAAACGCC
5318012 ACTAAAGTAC--ACATTTT
66 ACTAAAGTACGTA-ATTTT
*
5318029 TAGCGGCGTTTTCACAAAAACGCCACTATATATTTGGATATTGCGGC
1 TAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGC
5318076 CTACATATAA
Statistics
Matches: 237, Mismatches: 49, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
80 1 0.00
81 61 0.26
82 90 0.38
83 65 0.27
84 20 0.08
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (83 bp):
TAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCAGTTTTTACATAAACGCC
ACTAAAGTACGTAATTTT
Found at i:5317996 original size:163 final size:164
Alignment explanation
Indices: 5317690--5318075 Score: 528
Period size: 163 Copynumber: 2.3 Consensus size: 164
5317680 GCCAATATTG
* ** *
5317690 CACATGTTTATAGCGGCATTTTTACAAAAACGCCACTATATATCTGGGATATTGCGGCGTTTTAT
1 CACAT-TTT-TAGCGGCGTTTGCACAAAAACGCCACTATATAT-TTGGATATTGCGGCGTTTTAT
* * *
5317755 ACATAAACGCCACTAAAGTACATGTTTTTAGCGGCGTTTTCACAAAAAACGCTGCTATATATTCG
63 ACAAAAACACCACTAAAGTA-ATGTTTTTAGCGGCATTTTCACAAAAAACGCTGCTATATATTCG
5317820 GATATTGCGGCATTTTTTACATAAATGCCACTAAAGTA
127 GATATTGCGGCATTTTTTACATAAATGCCACTAAAGTA
* * * * *
5317858 CGCATTTTTAGCGGCGTTTGCACAAAAACGCCATTATATATTTGGATATCGCGGCG-TTTGTCCA
1 CACATTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATTGCGGCGTTTTATACA
****
5317922 AAAACACCACTAAAGT-ATGTAATTTTAGCGGCATTTT-TGTGAAAACG-TCGCTATATATTCGG
66 AAAACACCACTAAAGTAATGT--TTTTAGCGGCATTTTCACAAAAAACGCT-GCTATATATTCGG
5317984 ATATTGCGGCATTTTTTACATAAATGCCACTAAAGTA
128 ATATTGCGGCATTTTTTACATAAATGCCACTAAAGTA
*
5318021 CACATTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTTGGATATTGCGGC
1 CACATTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATTGCGGC
5318076 CTACATATAA
Statistics
Matches: 195, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
162 5 0.03
163 107 0.55
164 34 0.17
165 13 0.07
166 29 0.15
167 3 0.02
168 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (164 bp):
CACATTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATTGCGGCGTTTTATACA
AAAACACCACTAAAGTAATGTTTTTAGCGGCATTTTCACAAAAAACGCTGCTATATATTCGGATA
TTGCGGCATTTTTTACATAAATGCCACTAAAGTA
Found at i:5321570 original size:2 final size:2
Alignment explanation
Indices: 5321563--5321587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5321553 ACTTGGTGAA
5321563 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5321588 CCTAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5326997 original size:16 final size:15
Alignment explanation
Indices: 5326971--5327000 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5326961 TGTTGTGTCC
5326971 GGTCATCCCGGGATA
1 GGTCATCCCGGGATA
5326986 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
5327001 TTCAGGCCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.27, G:0.37, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATA
Found at i:5327223 original size:9 final size:10
Alignment explanation
Indices: 5327197--5327237 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
5327187 TGCAAAAAGC
5327197 ATAAATAATA
1 ATAAATAATA
*
5327207 AGAAATAA-A
1 ATAAATAATA
5327216 ATAAATAAT-
1 ATAAATAATA
5327225 AT-AATAATA
1 ATAAATAATA
5327234 ATAA
1 ATAA
5327238 TACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 6 0.23
9 12 0.46
10 8 0.31
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
ATAAATAATA
Found at i:5327271 original size:24 final size:23
Alignment explanation
Indices: 5327244--5327290 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5327234 ATAATACTAT
*
5327244 ATATATATATAAATATTTTCAAAA
1 ATATATA-ATAAATAATTTCAAAA
* *
5327268 ATATGTAATATATAATTTCAAAA
1 ATATATAATAAATAATTTCAAAA
5327291 TGTTTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATATAATAAATAATTTCAAAA
Found at i:5327467 original size:36 final size:35
Alignment explanation
Indices: 5327275--5327603 Score: 321
Period size: 35 Copynumber: 9.0 Consensus size: 35
5327265 AAAATATGTA
* *
5327275 ATATATAATTTCAAAATGTTTTTAAAAACTATAT-T
1 ATATATATTTTCAAAATG-TTTTAAAATCTATATAT
* *
5327310 ATACATATTTTCAAAATCGTTTTAAAAACTATATAAT
1 ATATATATTTTCAAAAT-GTTTTAAAATCTATAT-AT
*
5327347 ATATATTTTTTTCAAAATGTTTTAAAATCTATATAT
1 ATATA-TATTTTCAAAATGTTTTAAAATCTATATAT
*
5327383 -TATATATTTTTCAAAATGTTTTAAAAACTATATAAT
1 ATATATA-TTTTCAAAATGTTTTAAAATCTATAT-AT
* *
5327419 ATATAAATGTTTTCAGAAATGTTTTCAAATCTATATAT
1 ATAT--ATATTTTCA-AAATGTTTTAAAATCTATATAT
*
5327457 ATATA-AGTTTTCAAAATGATTTTAAAAACTATATAT
1 ATATATA-TTTTCAAAATG-TTTTAAAATCTATATAT
5327493 -TATATATTTTTCTAAAATGTTTTAAAAAT-TATATACT
1 ATATATA-TTTTC-AAAATGTTTT-AAAATCTATATA-T
*
5327530 ATATATATAGCTTTCAAAAATATTTTAAAAT-TATATATT
1 ATATATAT---TTTC-AAAATGTTTTAAAATCTATATA-T
*
5327569 ATATACATTTTCAAAATGTTTTAAAAAT-TATATAT
1 ATATATATTTTCAAAATGTTTT-AAAATCTATATAT
5327604 CACATGTTTT
Statistics
Matches: 253, Mismatches: 20, Indels: 42
0.80 0.06 0.13
Matches are distributed among these distances:
34 1 0.00
35 78 0.31
36 58 0.23
37 35 0.14
38 29 0.11
39 39 0.15
40 13 0.05
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
ATATATATTTTCAAAATGTTTTAAAATCTATATAT
Found at i:5327526 original size:111 final size:109
Alignment explanation
Indices: 5327283--5327603 Score: 388
Period size: 111 Copynumber: 2.9 Consensus size: 109
5327273 TAATATATAA
* *
5327283 TTTCAAAATGTTTTTAAAAAC--TAT-AT-TATACATA-TTTTCAAAATCGTTTTAAAAACTATA
1 TTTCAAAATG-TTTTAAAAACTATATAATATATAAATAGTTTTCAAAAT-GTTTTAAAATCTATA
** *
5327343 TAATATATATTTTTTTCAAAATGTTTTAAAATCTATATATTATATATT
64 T-ATATATA-CATTTTCAAAATGTTTTAAAAACTATATATTATATATT
*
5327391 TTTCAAAATGTTTTAAAAACTATATAATATATAAAT-GTTTTCAGAAATGTTTTCAAATCTATAT
1 TTTCAAAATGTTTTAAAAACTATATAATATATAAATAGTTTTCA-AAATGTTTTAAAATCTATAT
5327455 ATATATA-AGTTTTCAAAATGATTTTAAAAACTATATATTATATATT
65 ATATATACA-TTTTCAAAATG-TTTTAAAAACTATATATTATATATT
* * * * *
5327501 TTTCTAAAATGTTTTAAAAATTATATACTATATATATAGCTTTCAAAAATATTTTAAAAT-TATA
1 TTTC-AAAATGTTTTAAAAACTATATAATATATAAATAGTTTTC-AAAATGTTTTAAAATCTATA
*
5327565 TATTATATACATTTTCAAAATGTTTTAAAAATTATATAT
64 TA-TATATACATTTTCAAAATGTTTTAAAAACTATATAT
5327604 CACATGTTTT
Statistics
Matches: 188, Mismatches: 12, Indels: 23
0.84 0.05 0.10
Matches are distributed among these distances:
107 10 0.05
108 10 0.05
109 14 0.07
110 37 0.20
111 77 0.41
112 38 0.20
113 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (109 bp):
TTTCAAAATGTTTTAAAAACTATATAATATATAAATAGTTTTCAAAATGTTTTAAAATCTATATA
TATATACATTTTCAAAATGTTTTAAAAACTATATATTATATATT
Found at i:5327733 original size:2 final size:2
Alignment explanation
Indices: 5327728--5327760 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5327718 TAAGTCTTTG
5327728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5327761 GTATGTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5330312 original size:256 final size:255
Alignment explanation
Indices: 5329862--5330404 Score: 808
Period size: 256 Copynumber: 2.1 Consensus size: 255
5329852 TTTTATTATT
*
5329862 TCGGGTCGGGTTTCTAATTCATATATTCGAGTCAGGTTGGGTGAAATTTTATTTTGTTCGGGTCG
1 TCGGGTCGGGTTTCTAATTCATATATTCGAGTCAGGTTGGGTGAAACTTTATTTTGTTCGGGTCG
* *
5329927 GGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCA
66 GGTTTTTTAAGTGTGATATTCGGGTC--G-AGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCA
*
5329992 AAAATATATATAATTTTATCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA-
128 AAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAAT
*
5330056 TTTTTTTCAATTAAATCACTATTTTTATTGAAT-AAAT-TCTTTTTTTATTATTTCGGGTCGGG
193 TTTTTTTCAATTAAATCAATATTTTTATTGAATAAAATAT-TTTTTTTATTATTTCGGGTCGGG
* * * *
5330118 TCGGGCCGGATTTCTAATTCATATATTCGGGTCGGGTTGGGTGAAACTTTATTTTGTTCGGGTCG
1 TCGGGTCGGGTTTCTAATTCATATATTCGAGTCAGGTTGGGTGAAACTTTATTTTGTTCGGGTCG
*
5330183 GGTTTTTTAAGTGTGTTATTCGGGTC-AG-GTTCGGGTTTAGGGTGAAAAAACCGGACCCGACCC
66 GGTTTTTTAAGTGTGATATTCGGGTCGAGAGTTCGGGTTTAGGGTG-AAAAA---GACCCGACCC
*
5330246 GAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTTTATATATA
127 -AAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA
* * * *
5330311 ATTTTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATATTTTTTTTATTATTTCGTGTTG
191 A-TTTTTTTTCAATTAAATCAATATTTTTATTGAAT-AAAATATTTTTTTTATTATTTCGGGTCG
*
5330376 TG
254 GG
5330378 TCGGGTCGGGTTTCTAATTCATATATT
1 TCGGGTCGGGTTTCTAATTCATATATT
5330405 GAATAAAAAA
Statistics
Matches: 259, Mismatches: 18, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
251 16 0.06
252 6 0.02
255 9 0.03
256 148 0.57
258 30 0.12
260 49 0.19
261 1 0.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (255 bp):
TCGGGTCGGGTTTCTAATTCATATATTCGAGTCAGGTTGGGTGAAACTTTATTTTGTTCGGGTCG
GGTTTTTTAAGTGTGATATTCGGGTCGAGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCAAAA
ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTT
TTTTCAATTAAATCAATATTTTTATTGAATAAAATATTTTTTTTATTATTTCGGGTCGGG
Found at i:5344803 original size:59 final size:59
Alignment explanation
Indices: 5344711--5344824 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
5344701 GAGGTTCATT
*
5344711 TTTCATACGAATCGGGAGCTGCACTGGATGAACATTCGAAATGATTA-AATGAATTTGAG
1 TTTCATACGAATCAGGAGCTGCACTGGATGAACATTCGAAATGATTAGAA-GAATTTGAG
* *
5344770 TTTCATACGAATCAGGAGGTGCACTGGATGAACATTCGTAATGATTAGAAGAATT
1 TTTCATACGAATCAGGAGCTGCACTGGATGAACATTCGAAATGATTAGAAGAATT
5344825 CGAGGTCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 49 0.96
60 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (59 bp):
TTTCATACGAATCAGGAGCTGCACTGGATGAACATTCGAAATGATTAGAAGAATTTGAG
Found at i:5352619 original size:3 final size:3
Alignment explanation
Indices: 5352611--5352654 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5352601 TTAAAAGTAA
5352611 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5352655 ATATATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5352664 original size:8 final size:7
Alignment explanation
Indices: 5352610--5352666 Score: 63
Period size: 6 Copynumber: 8.9 Consensus size: 7
5352600 ATTAAAAGTA
5352610 AAATAAT
1 AAATAAT
5352617 -AATAAT
1 AAATAAT
5352623 -AATAAT
1 AAATAAT
5352629 -AATAAT
1 AAATAAT
5352635 -AATAAT
1 AAATAAT
5352641 -AATAAT
1 AAATAAT
5352647 -AATAAT
1 AAATAAT
5352653 AAATATAT
1 AAATA-AT
5352661 AAATAA
1 AAATAA
5352667 AACATAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 36 0.75
7 5 0.10
8 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAATAAT
Found at i:5354470 original size:17 final size:16
Alignment explanation
Indices: 5354429--5354470 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5354419 AATATTGAGA
5354429 ATTTA-AATATTTTAT
1 ATTTATAATATTTTAT
*
5354444 ATTTTTTAATATTTTACT
1 A-TTTATAATATTTTA-T
5354462 ATTTATAAT
1 ATTTATAAT
5354471 TTTATGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 16 0.73
18 2 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATAATATTTTAT
Found at i:5354520 original size:16 final size:17
Alignment explanation
Indices: 5354485--5354521 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5354475 TGGAATGAAA
5354485 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
5354502 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
5354518 AAAA
1 AAAA
5354522 TGATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:5354559 original size:16 final size:17
Alignment explanation
Indices: 5354540--5354571 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5354530 TACTACCATA
5354540 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
5354556 ATATTATATTTTATAT
1 ATATTATATTTTATAT
5354572 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:5356461 original size:2 final size:2
Alignment explanation
Indices: 5356454--5356486 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5356444 ACAAATTTTA
5356454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5356487 GTTTTAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5356596 original size:20 final size:21
Alignment explanation
Indices: 5356563--5356610 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
5356553 TAGCTTTTGT
*
5356563 AATTTTTTCAATTG-TATTTTTA
1 AATTTTTT-AATTGATA-ATTTA
5356585 AATTTTTT-ATTGATAATTTA
1 AATTTTTTAATTGATAATTTA
5356605 AATTTT
1 AATTTT
5356611 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 14 0.58
21 2 0.08
22 8 0.33
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
AATTTTTTAATTGATAATTTA
Found at i:5359758 original size:24 final size:24
Alignment explanation
Indices: 5359729--5359777 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5359719 TTTATCCTTT
5359729 TTCTCATTTTAGTTATTGACAATG
1 TTCTCATTTTAGTTATTGACAATG
*
5359753 TTCTCATTTTAGTTATTGATAATG
1 TTCTCATTTTAGTTATTGACAATG
5359777 T
1 T
5359778 AGGTAACGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.53
Consensus pattern (24 bp):
TTCTCATTTTAGTTATTGACAATG
Found at i:5384752 original size:18 final size:19
Alignment explanation
Indices: 5384717--5384761 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
5384707 TATGATTTCA
*
5384717 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
5384736 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
5384754 ATAATAAA
1 AAAATAAA
5384762 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:5392286 original size:21 final size:21
Alignment explanation
Indices: 5392247--5392301 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
5392237 ATCAAATTAA
5392247 ATATT-AAAATAAAATTGAG-
1 ATATTAAAAATAAAATTGAGT
*
5392266 ATATTAAAAATATATATTGAGT
1 ATATTAAAAATA-AAATTGAGT
*
5392288 ATTTTAAAAGATAA
1 ATATTAAAA-ATAA
5392302 TGAAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.17
20 6 0.20
21 7 0.23
22 9 0.30
23 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATTAAAAATAAAATTGAGT
Found at i:5392863 original size:2 final size:2
Alignment explanation
Indices: 5392856--5392885 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5392846 TTCATCAATA
5392856 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
5392886 TCATATTCAA
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:5393549 original size:3 final size:3
Alignment explanation
Indices: 5393541--5393580 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
5393531 GTAATTGGAT
*
5393541 ATA ATA ATA ATA ATA ATA ATA GTA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
5393581 TGACCTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5405807 original size:38 final size:38
Alignment explanation
Indices: 5405755--5405850 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
5405745 GTATAAACTA
* * *
5405755 TGTCCCGAAGGACCTATCATCCCAAAGGATGTCATCTG
1 TGTCCCGAAAGACCTATCATCCCAAAGGATGTAATATG
* * *
5405793 TGTCCCGAATGACCTATCATCTCGAAGGATGTAATATG
1 TGTCCCGAAAGACCTATCATCCCAAAGGATGTAATATG
5405831 TGTCCCGAAAGACCTATCAT
1 TGTCCCGAAAGACCTATCAT
5405851 ATGTCTCGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAAGACCTATCATCCCAAAGGATGTAATATG
Found at i:5411669 original size:13 final size:13
Alignment explanation
Indices: 5411651--5411680 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5411641 CTTAGTTGCG
5411651 AAAATTAAAATTT
1 AAAATTAAAATTT
*
5411664 AAAATTGAAATTT
1 AAAATTAAAATTT
5411677 AAAA
1 AAAA
5411681 ATTCGGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:5411843 original size:5 final size:5
Alignment explanation
Indices: 5411829--5411870 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
5411819 TATACCAAAG
* *
5411829 AAATA AAATA CAATA AAATTA AAATT AAATA AAA-A AAATA AA
1 AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAATA AA
5411871 GAAGTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:5413068 original size:21 final size:20
Alignment explanation
Indices: 5413039--5413083 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
5413029 ACACAAAATT
5413039 AATAAAACAAATAAAAATAAA
1 AATAAAACAAATAAAAA-AAA
* *
5413060 AATAGAACAAATAATAAAAA
1 AATAAAACAAATAAAAAAAA
5413080 AATA
1 AATA
5413084 TAATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (20 bp):
AATAAAACAAATAAAAAAAA
Found at i:5413088 original size:25 final size:23
Alignment explanation
Indices: 5413019--5413088 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 23
5413009 TGGATCTGAA
* *
5413019 AAAACAAAATACACAAAAT-TAAT
1 AAAAC-AAATAAAAAAAATATAAT
*
5413042 AAAACAAATAAAAATAA-A-AAT
1 AAAACAAATAAAAAAAATATAAT
*
5413063 AGAACAAATAATAAAAAAATATAAT
1 AAAACAAAT-A-AAAAAAATATAAT
5413088 A
1 A
5413089 TATATATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 11 0.30
22 10 0.27
23 11 0.30
24 1 0.03
25 4 0.11
ACGTcount: A:0.74, C:0.07, G:0.01, T:0.17
Consensus pattern (23 bp):
AAAACAAATAAAAAAAATATAAT
Found at i:5413264 original size:36 final size:36
Alignment explanation
Indices: 5413165--5413344 Score: 168
Period size: 36 Copynumber: 4.9 Consensus size: 36
5413155 ACTTTGAAAA
* *
5413165 ATATGTAT-TATATGTTCCAAAATATTTTAAAAA-T-T
1 ATAT-TATATATAT-TTTCAAAATGTTTTAAAAACTAT
* * *
5413200 ATATAATATATTTTTTAAAAATGTTTTAAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTAAAAACTAT
* * *
5413236 ATGTTATATTTATTTTCAAAATGTTTTAAAAATTAT
1 ATATTATATATATTTTCAAAATGTTTTAAAAACTAT
* *
5413272 ATAATATATAAATATTTTCAAACATGTTTTCAAAACTAT
1 AT-AT-TATATATATTTTCAAA-ATGTTTTAAAAACTAT
* *
5413311 ATATTATATATATATTTAAAAATGGTTTCAAAAA
1 ATATTATATATAT-TTTCAAAAT-GTTTTAAAAA
5413345 TCATATAATA
Statistics
Matches: 117, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
34 18 0.15
35 9 0.08
36 33 0.28
37 11 0.09
38 30 0.26
39 16 0.14
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATTATATATATTTTCAAAATGTTTTAAAAACTAT
Found at i:5413280 original size:77 final size:77
Alignment explanation
Indices: 5413199--5413354 Score: 208
Period size: 75 Copynumber: 2.0 Consensus size: 77
5413189 TTTTAAAAAT
* * * *
5413199 TATATAATATATTTTTTAAAAATGTTTTAAAAACTATATGTTATATTTAT-TTTCAAAAT-GTTT
1 TATATAA-ATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATATATATTTAAAAATGGTTT
* *
5413262 TAAAAATTATATAA
64 CAAAAATCATATAA
* *
5413276 TATATAAATATTTTCAAACATGTTTTCAAAACTATATATTATATATATATTTAAAAATGGTTTCA
1 TATATAAATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATATTTAAAAATGGTTTCA
5413341 AAAATCATATAA
66 AAAATCATATAA
5413353 TA
1 TA
5413355 CTTATTTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
75 33 0.48
76 11 0.16
77 25 0.36
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (77 bp):
TATATAAATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATATTTAAAAATGGTTTCA
AAAATCATATAA
Found at i:5413437 original size:2 final size:2
Alignment explanation
Indices: 5413419--5413473 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
5413409 TTTCAAAGAT
** * *
5413419 TA TA T- TA TA TA CG TA TA TA CA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5413460 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
5413474 AAGCAAACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5414149 original size:84 final size:83
Alignment explanation
Indices: 5413965--5415432 Score: 1410
Period size: 84 Copynumber: 17.8 Consensus size: 83
5413955 AACAGTAGTG
* * * * **
5413965 AATGATGTGTCATGGAGCTGA-TCGTAGTCGAACTCGAATGTC-TTTGTAACAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGT-GTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
* * * *
5414028 CGCCTTGAGTTATACTGTA
65 CGACTTAAGTTATGCTGCA
* * * *
5414047 AATGATGTGTCGTT-GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGACAACCCTTC
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTC
* * *
5414111 TAGACTTAAGTTGTGTTGCA
64 TCGACTTAAGTTATGCTGCA
* * * *
5414131 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
* *
5414196 CGACTTAAGTTGTGTTGCA
65 CGACTTAAGTTATGCTGCA
* * * *
5414215 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
5414280 CGACTTAAGTTATGCTGCA
65 CGACTTAAGTTATGCTGCA
*** ** *
5414299 AATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
*
5414361 CGACTTAAGCTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * * * * *
5414380 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGT-CACATAACCCTCCTA
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCTC
* * *
5414444 GCCTTGAGTTATGCTGTA
66 GACTTAAGTTATGCTGCA
* ** *
5414462 AATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
**
5414524 CGACTTAAACTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * * *
5414543 AATGATGTGCCTTGGAGCTGAGCGCAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTTT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
5414608 CGACTTAAGTTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * ** * *
5414627 AATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTAT
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
*
5414689 CGACTTAAGCTATGCTGCA
65 CGACTTAAGTTATGCTGCA
** * * **
5414708 AATGATGTGCCTTTTATGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTC
1 AATGATGTGCCTTGGA-GCTGAGTGTAATCGAACTCGAAGGTCTTTT-GTTGCAGATAACCCTTC
* * * *
5414773 TAGCCTTGAGTTATGCTGTA
64 TCGACTTAAGTTATGCTGCA
* * * ** *
5414793 AATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
* * *
5414855 CGAGTTAAGCTATGCTGCG
65 CGACTTAAGTTATGCTGCA
* * *
5414874 AATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTC
1 AATGATGTGCC-TTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTC
* * *
5414938 TAGACTTAAGTTGTGTTGCA
64 TCGACTTAAGTTATGCTGCA
* * * *
5414958 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
5415023 CGACTTAAGTTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * *
5415042 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-GGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
*
5415103 CGACTTAAGCTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * ** *
5415122 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTCCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTT-GTTGCAGATAACCCTTCT
* * * *
5415187 AGCCTTGAGTTATGCTGTA
65 CGACTTAAGTTATGCTGCA
* * ** *
5415206 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC---T-TTGCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
* *
5415267 CGACTTAAGCTATGCTGTA
65 CGACTTAAGTTATGCTGCA
* * * *
5415286 AATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACATATAACTCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG-CAGATAACCCTTCT
* * ** *
5415351 AGCCTTGGGTTATGCTGTA
65 CGACTTAAGTTATGCTGCA
* * *
5415370 AATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-TTTG--GCAGATAGCCCTTC
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAA-GGTCTTTTGTTGCAGATAACCCTTC
5415431 TC
64 TC
5415433 ACCTTGAGCT
Statistics
Matches: 1141, Mismatches: 203, Indels: 85
0.80 0.14 0.06
Matches are distributed among these distances:
79 50 0.04
80 160 0.14
81 196 0.17
82 78 0.07
83 46 0.04
84 424 0.37
85 183 0.16
86 4 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCTC
GACTTAAGTTATGCTGCA
Found at i:5414623 original size:328 final size:328
Alignment explanation
Indices: 5413992--5415431 Score: 1510
Period size: 328 Copynumber: 4.4 Consensus size: 328
5413982 CTGATCGTAG
* * * * * * * *
5413992 TCGAACTCGAATGTCTTTGTAACAGATAACCCTTCTCGCCTTGAGTTATACTGTAAATGATGTGT
1 TCGAACTCGAAGGTCTTTG--GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* * * * * *
5414057 CGTT-GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAG
64 CCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGT--CACATAACCCTTCTAGACTTAAG
* * * * *
5414121 TTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
127 TTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTC-TT--TTGGCAGA
* * * * *
5414186 TAACCCTTCTCGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCG
189 TAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCA
* * *
5414251 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAA
254 AAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTCGAA
5414316 GCTGAGTGTAA
318 GCTGAGTGTAA
** *
5414327 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CC
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCC
* * * *
5414391 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACATAACCCTCCTAGCCTTGAGTTAT
66 TTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACATAACCCTTCTAGACTTAAGTTAT
* * ** *
5414456 GCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGCAGATAGCCC
131 GCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCC
* *
5414520 TTCTCGACTTAAACTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGCAGTCGAACTCAAAGGTC
195 TTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
*
5414585 TTTTGTTGGCAGATAACCCTTTTCGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAG
260 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTCGAAGCTGAG
5414650 TGTAA
324 TGTAA
** * *
5414655 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATGTG-CC
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCC
** * *
5414719 TTTTATGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGT
66 TTGGA-GCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCAC--ATAACCCTTCTAGACTTAAGT
* * * * ** *
5414784 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC-TTTGGCAGATAG
128 TATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAA
* *
5414848 CCCTTCTCGAGTTAAGCTATGCTGCGAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAA
192 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAA
* * * * *
5414912 GGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCT
256 GGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTCGAAGCT
* *
5414977 GAGCGTAG
321 GAGTGTAA
*
5414985 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * ** * * *
5415050 GCCCTCGAAGCTGAGTGTAATCGAACTC-GGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAG
62 GCCCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACATAACCCTTCTAGACTTAAG
* * * *
5415112 CTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGA
127 TTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG---CAGA
* * * * * * * * * *
5415177 TAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
189 TAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTC
*** * * * * *
5415242 GGGGGTC---T-TT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTTG-
253 AAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TCGA
5415301 AGCTGAGTGTAA
317 AGCTGAGTGTAA
* * * * ** * *
5415313 TCGAACTCGAAGGTCTTTTGGTGACATATAACTCTTCTAGCCTTGGGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * * * *
5415378 GCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TTTGG-CAGATAGCCCTTCT
62 GCCCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACATAACCCTTCT
5415432 CACCTTGAGC
Statistics
Matches: 964, Mismatches: 119, Indels: 50
0.85 0.11 0.04
Matches are distributed among these distances:
325 2 0.00
326 1 0.00
327 3 0.00
328 351 0.36
329 102 0.11
330 29 0.03
331 225 0.23
332 73 0.08
333 97 0.10
334 61 0.06
335 20 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (328 bp):
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCC
TTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACATAACCCTTCTAGACTTAAGTTAT
GCTGCAAATGATGTGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCT
TCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTCGAAGCTGAGTG
TAA
Found at i:5415390 original size:743 final size:742
Alignment explanation
Indices: 5413981--5415453 Score: 2337
Period size: 743 Copynumber: 2.0 Consensus size: 742
5413971 GTGTCATGGA
* * * * *
5413981 GCTGATCGTAGTCGAACTCGAATGTCTTTGTAACAGATAACCCTTCTCGCCTTGAGTTATACTGT
1 GCTGAGCGTAATCGAACTCAAAGGTCTTTGTAACAGATAACCCTTCTAGCCTTGAGTTATACTGT
* * * * *
5414046 AAATGATGTGTCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGACAACCCTTC
66 AAATGATGTGCCCTCGAGCTGAGTGTAATCAAACTCAAAGGTCTTTTG-T-GCAGACAACCCTTC
* * * *
5414111 TAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
129 TAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
*
5414176 GGTTGGCAGATAACCCTTCTCGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTA
194 GGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTA
5414241 GTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
259 GTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
5414306 TGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
324 TGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
5414371 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACATAA
389 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACATAA
*
5414436 CCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGG
454 CCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
5414501 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
519 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * * * *
5414566 GCAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTTTCGACTTAAGTTATGCTGCAAATG
584 GCAATCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
**
5414631 ATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTATCGA-CTT
649 ATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTATC-ACCTT
*
5414695 AAGCTATGCTGCAAATGATGTGCCTTTTAT
713 AAGCTAAGCTGCAAATGATGTGCCTTTTAT
* *
5414725 GCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCT
1 GCTGAGCGTAATCGAACTCAAAGGTC-TTT-GTAACAGATAACCCTTCTAGCCTTGAGTTATACT
*** * *
5414790 GTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC-TTTG-GCAGATAGCCCTT
64 GTAAATGATGTGCCCTCG-AGCTGAGTGTAATCAAACTCAAAGGTCTTTTGTGCAGACAACCCTT
* * * *
5414853 CTCGAGTTAAGCTATGCTGCGAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCT
128 CTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
*
5414917 TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCG
192 TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCG
5414982 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
257 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
5415047 TGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
322 TGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
5415111 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
387 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCAC--
5415176 ATAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
450 ATAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * *
5415241 CGGGGGTCTTT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCT
515 CGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCTTGGAGCT
* * * * * * ** *
5415305 GAGTGTAATCGAACTCGAAGGTCTTTTGGTGACATATAACTCTTCTAGCCTTGGGTTATGCTGTA
580 GAGCGCAATCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCA
* * * *
5415370 AATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCAC
645 AATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTATCAC
*
5415435 CTTGAGCTAAGCTGCAAAT
710 CTTAAGCTAAGCTGCAAAT
5415454 AGTTTGTTTA
Statistics
Matches: 668, Mismatches: 54, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
742 97 0.15
743 397 0.59
744 99 0.15
745 3 0.00
746 50 0.07
747 22 0.03
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (742 bp):
GCTGAGCGTAATCGAACTCAAAGGTCTTTGTAACAGATAACCCTTCTAGCCTTGAGTTATACTGT
AAATGATGTGCCCTCGAGCTGAGTGTAATCAAACTCAAAGGTCTTTTGTGCAGACAACCCTTCTA
GACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
TTGGCAGATAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
CCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACATAACC
CTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGG
TCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGC
AATCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
ATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTATCACCTTAAG
CTAAGCTGCAAATGATGTGCCTTTTAT
Found at i:5418869 original size:18 final size:17
Alignment explanation
Indices: 5418846--5418888 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
5418836 AGTTAATGTG
5418846 AATGCAAAG-AAATAACAA
1 AATGCAAAGAAAAT-A-AA
5418864 AATGCAAAGAAAATAAA
1 AATGCAAAGAAAATAAA
5418881 AATGCAAA
1 AATGCAAA
5418889 TGTCTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (17 bp):
AATGCAAAGAAAATAAA
Found at i:5418884 original size:17 final size:18
Alignment explanation
Indices: 5418846--5418888 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5418836 AGTTAATGTG
5418846 AATGCAAAGAAATAACAA
1 AATGCAAAGAAATAACAA
5418864 AATGCAAAGAAA-ATA-AA
1 AATGCAAAGAAATA-ACAA
5418881 AATGCAAA
1 AATGCAAA
5418889 TGTCTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (18 bp):
AATGCAAAGAAATAACAA
Found at i:5419079 original size:125 final size:124
Alignment explanation
Indices: 5418880--5419130 Score: 484
Period size: 125 Copynumber: 2.0 Consensus size: 124
5418870 AAGAAAATAA
5418880 AAATGCAAATGTCTAAATGTCTAAATATATGATGCATGAAATGATCGAGGCATTAATCCAAAAAT
1 AAATGCAAATGTCTAAATGTCTAAATATATGATGCATGAAATGATCGAGGCATTAATCCAAAAAT
*
5418945 GTATCTGTTATTAAAAATAATCCTTATTGGGGACAAAAGTGTTTTATCTTTTAAGAGAC
66 GTATATGTTATTAAAAATAATCCTTATTGGGGACAAAAGTGTTTTATCTTTTAAGAGAC
5419004 AAATGCAAAATGTCTAAATGTCTAAATATATGATGCATGAAATGATCGAGGCATTAATCCAAAAA
1 AAATGC-AAATGTCTAAATGTCTAAATATATGATGCATGAAATGATCGAGGCATTAATCCAAAAA
5419069 TGTATATGTTATTAAAAATAATCCTTATTGGGGACAAAAGTGTTTTATCTTTTAAGAGAC
65 TGTATATGTTATTAAAAATAATCCTTATTGGGGACAAAAGTGTTTTATCTTTTAAGAGAC
5419129 AA
1 AA
5419131 GAATATTCTG
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 6 0.05
125 119 0.95
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (124 bp):
AAATGCAAATGTCTAAATGTCTAAATATATGATGCATGAAATGATCGAGGCATTAATCCAAAAAT
GTATATGTTATTAAAAATAATCCTTATTGGGGACAAAAGTGTTTTATCTTTTAAGAGAC
Found at i:5420693 original size:13 final size:13
Alignment explanation
Indices: 5420675--5420704 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5420665 GTTAGTTGCG
5420675 AAAATTAAAATTT
1 AAAATTAAAATTT
5420688 AAAATTAAAATTT
1 AAAATTAAAATTT
5420701 AAAA
1 AAAA
5420705 ATTCGGTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:5420883 original size:19 final size:19
Alignment explanation
Indices: 5420852--5420895 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5420842 TATGTATACC
*
5420852 AAAT-AAATAAAATACAAA
1 AAATAAAATAAAATAAAAA
* *
5420870 AATTAAAATTAAATAAAAA
1 AAATAAAATAAAATAAAAA
5420889 AAATAAA
1 AAATAAA
5420896 GAAGTATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAA
Found at i:5422220 original size:68 final size:68
Alignment explanation
Indices: 5422136--5422293 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 68
5422126 TCAGAAACCT
* *
5422136 TTTTCAAACTATATAATATATACTTTCAAAAAAACTTGAAAAA-ATATG-TATTATATATTTCCA
1 TTTTAAAATTATATAATATATA-TTTCAAAAAAACTTGAAAAACATATGTTA-TATATATTTCCA
5422199 AAATA
64 AAATA
* *** * * *
5422204 TTTTAAAATTATATAATATAT-TTTTAAAAATGTTTTAAAAACTATATGTTATATTTATTTTCAA
1 TTTTAAAATTATATAATATATATTTCAAAAAAACTTGAAAAAC-ATATGTTATATATATTTCCAA
*
5422268 AATG
65 AATA
*
5422272 TTTAAAAATTATATAATATATA
1 TTTTAAAATTATATAATATATA
5422294 AATATTTTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
66 15 0.20
68 58 0.77
69 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (68 bp):
TTTTAAAATTATATAATATATATTTCAAAAAAACTTGAAAAACATATGTTATATATATTTCCAAA
ATA
Found at i:5422300 original size:37 final size:38
Alignment explanation
Indices: 5422213--5422366 Score: 124
Period size: 37 Copynumber: 4.1 Consensus size: 38
5422203 ATTTTAAAAT
* * *
5422213 TATATAATATATTTTTAAAAATGTTTTAAAAACTATAT-G
1 TATATAA-ATA-TTTTCAAAATGATTTAAAAACTATATAA
** *
5422252 T-TATATTTATTTTCAAAATG-TTTAAAAATTATATAA
1 TATATAAATATTTTCAAAATGATTTAAAAACTATATAA
* * *
5422288 TATATAAATATTTTCAAACAT-TTTTTAAAACTATATAT
1 TATATAAATATTTTCAAA-ATGATTTAAAAACTATATAA
*
5422326 TATATATATA-TTT-AAAATGATTTCAAAAA-TCATATAA
1 TATATAAATATTTTCAAAATGATTT-AAAAACT-ATATAA
5422363 TATA
1 TATA
5422367 CTTATTTTCG
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
35 15 0.16
36 18 0.19
37 32 0.34
38 28 0.30
39 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (38 bp):
TATATAAATATTTTCAAAATGATTTAAAAACTATATAA
Found at i:5422330 original size:38 final size:37
Alignment explanation
Indices: 5422211--5422338 Score: 134
Period size: 38 Copynumber: 3.4 Consensus size: 37
5422201 ATATTTTAAA
*
5422211 ATTATATAATATATTTTTAAAAATGTTTTAAAAACTATAT
1 ATTATATAA-ATA-TTTTCAAAAT-TTTTAAAAACTATAT
* * * *
5422251 GTTATAT--TTATTTTCAAAATGTTTAAAAATTATAT
1 ATTATATAAATATTTTCAAAATTTTTAAAAACTATAT
* *
5422286 AATATATAAATATTTTCAAACATTTTTTAAAACTATAT
1 ATTATATAAATATTTTCAAA-ATTTTTAAAAACTATAT
*
5422324 ATTATATATATATTT
1 ATTATATAAATATTT
5422339 AAAATGATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
35 18 0.25
36 9 0.12
37 12 0.17
38 27 0.38
40 6 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (37 bp):
ATTATATAAATATTTTCAAAATTTTTAAAAACTATAT
Found at i:5422343 original size:73 final size:77
Alignment explanation
Indices: 5422213--5422366 Score: 210
Period size: 73 Copynumber: 2.1 Consensus size: 77
5422203 ATTTTAAAAT
* * *
5422213 TATATAATATATTTTTAAAAATGTTTTAAAAACTATATGTTATATTTATTTTCAAAATG-TTT-A
1 TATATAATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGATTTCA
*
5422276 AAAATTATATAA
66 AAAATCATATAA
* *
5422288 TATATAA-ATATTTTCAAACAT-TTTTTAAAACTATATATTATATATATATTT-AAAATGATTTC
1 TATATAATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATAT-TTTCAAAATGATTTC
5422350 AAAAATCATATAA
65 AAAAATCATATAA
5422363 TATA
1 TATA
5422367 CTTATTTTCG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
73 29 0.41
74 18 0.26
75 23 0.33
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (77 bp):
TATATAATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGATTTCA
AAAATCATATAA
Found at i:5422373 original size:73 final size:72
Alignment explanation
Indices: 5422187--5422380 Score: 195
Period size: 73 Copynumber: 2.7 Consensus size: 72
5422177 AAATATGTAT
* * * *
5422187 TATATATTTCCAAAATATTTTAAAAT--TAT-ATA-ATATATTTTTAAAAATGTTTTAAAAACTA
1 TATATATTTTCAAAATGTTTAAAAATCATATAATATATATATTTTCAAAAATGTTTTAAAAACTA
*
5422248 TATGTTA
66 TATATTA
* * * *
5422255 TATTTATTTTCAAAATGTTTAAAAATTATATAATATATAAATATTTTCAAACAT-TTTTTAAAAC
1 TATATATTTTCAAAATGTTTAAAAATCATATAATATAT--ATATTTTCAAAAATGTTTTAAAAAC
5422319 TATATATTA
64 TATATATTA
*
5422328 TATATATATTT-AAAATGATTTCAAAAATCATATAATATACT-TATTTTCGAAAA
1 TATATAT-TTTCAAAATG-TTT-AAAAATCATATAATATA-TATATTTTCAAAAA
5422381 CTGATTTATG
Statistics
Matches: 104, Mismatches: 12, Indels: 15
0.79 0.09 0.11
Matches are distributed among these distances:
68 22 0.21
70 3 0.03
71 3 0.03
72 2 0.02
73 39 0.38
74 18 0.17
75 16 0.15
76 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (72 bp):
TATATATTTTCAAAATGTTTAAAAATCATATAATATATATATTTTCAAAAATGTTTTAAAAACTA
TATATTA
Found at i:5422434 original size:2 final size:2
Alignment explanation
Indices: 5422427--5422495 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
5422417 ACATTTTCAA
5422427 AT AT AT AT AT AT 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 AT AT AT AT AT AT
5422469 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5422496 AAGCAAACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5423167 original size:38 final size:40
Alignment explanation
Indices: 5423078--5423223 Score: 167
Period size: 38 Copynumber: 3.7 Consensus size: 40
5423068 TAACTTGTAA
* * *
5423078 TTAATATAATTATAATAATTTAAAATAT-CATTTAAGTTTT
1 TTAATATTA-TATAATAATTTAAAATCTACATTTAAATTTT
* *
5423118 TTAAAATTATATAATAATTT-AAATCTACATTTAATTTTT
1 TTAATATTATATAATAATTTAAAATCTACATTTAAATTTT
* *
5423157 TTAATA-TATATAATAATTTAAAATCT-CAATGAAATTTT
1 TTAATATTATATAATAATTTAAAATCTACATTTAAATTTT
5423195 TTAA-ATTATATAATAATTTGAAATATCTA
1 TTAATATTATATAATAATTT-AAA-ATCTA
5423224 GAGTACTAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
37 1 0.01
38 44 0.48
39 36 0.39
40 11 0.12
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (40 bp):
TTAATATTATATAATAATTTAAAATCTACATTTAAATTTT
Found at i:5423345 original size:35 final size:35
Alignment explanation
Indices: 5423274--5423349 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
5423264 GGGACATTAA
*
5423274 AAAGCTAAGGTCCAACATTTAATAATAATAATAAT
1 AAAGCTAAGGTCCAACATTTAATAAAAATAATAAT
*
5423309 AAAGCTAAGGTCCAACATTGTATTAGAAAATAAATAAT
1 AAAGCTAAGGTCCAACATT-TAATA-AAAAT-AATAAT
5423347 AAA
1 AAA
5423350 TAATATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 19 0.53
36 4 0.11
37 4 0.11
38 9 0.25
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (35 bp):
AAAGCTAAGGTCCAACATTTAATAAAAATAATAAT
Found at i:5428274 original size:26 final size:27
Alignment explanation
Indices: 5428238--5428290 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
5428228 TTCTCAGTTC
*
5428238 ATCATATTGAAAAATAAA-CAGAGAAT
1 ATCATAATGAAAAATAAAGCAGAGAAT
5428264 ATCATAATGAAAAATAAAGCAGAGAAT
1 ATCATAATGAAAAATAAAGCAGAGAAT
5428291 GTCGTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (27 bp):
ATCATAATGAAAAATAAAGCAGAGAAT
Found at i:5428335 original size:18 final size:18
Alignment explanation
Indices: 5428314--5428350 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5428304 ATCACCCTTC
5428314 ATTTTATTCTCCGATCAA
1 ATTTTATTCTCCGATCAA
5428332 ATTTTATTCTCCGATCAA
1 ATTTTATTCTCCGATCAA
5428350 A
1 A
5428351 ATCAATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (18 bp):
ATTTTATTCTCCGATCAA
Found at i:5430092 original size:36 final size:35
Alignment explanation
Indices: 5430040--5430235 Score: 252
Period size: 36 Copynumber: 5.5 Consensus size: 35
5430030 ACGAAAGAAT
5430040 GCATCGCACTTCCGATTCAAGTCGAACGGAAGGAA
1 GCATCGCACTTCCGATTCAAGTCGAACGGAAGGAA
5430075 GCATCGACACTTCCGATTCAAGTCGAACGG-AGGAAA
1 GCATCG-CACTTCCGATTCAAGTCGAACGGAAGG-AA
* * *
5430111 GCGTCGGCACTCCCGATTCAAGTCGAAC-GAGGGAA
1 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAA
* *
5430146 GCATCGGCACTTTCGATTCAAGTCGAACGGAATGAA
1 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAA
* *
5430182 GCATCAGCACTTCCGATTCAAGTTGAACGGAAGGAT
1 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAA
* *
5430218 GTATCGCACTTTCGATTC
1 GCATCGCACTTCCGATTC
5430236 GAGTGTTCAT
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
35 49 0.35
36 91 0.65
37 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (35 bp):
GCATCGCACTTCCGATTCAAGTCGAACGGAAGGAA
Found at i:5430163 original size:71 final size:72
Alignment explanation
Indices: 5430040--5430235 Score: 265
Period size: 71 Copynumber: 2.8 Consensus size: 72
5430030 ACGAAAGAAT
* *
5430040 GCATC-GCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
1 GCATCAGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTCGAACG
5430104 G-AGGAAA
66 GAAGG-AA
* * * *
5430111 GCGTCGGCACTCCCGATTCAAGTCGAAC-GAGGGAAGCATCGGCACTTTCGATTCAAGTCGAACG
1 GCATCAGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTCGAACG
*
5430175 GAATGAA
66 GAAGGAA
* * *
5430182 GCATCAGCACTTCCGATTCAAGTTGAACGGAAGGATGTATC-GCACTTTCGATTC
1 GCATCAGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTTCGATTC
5430236 GAGTGTTCAT
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 77 0.71
72 32 0.29
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (72 bp):
GCATCAGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTCGAACG
GAAGGAA
Found at i:5431035 original size:25 final size:26
Alignment explanation
Indices: 5430994--5431055 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
5430984 GGGAAAAACA
* *
5430994 AATTAAAGAGGCTAGGAAAGTCTTAG
1 AATTAAAGAAGCTAGGAAAGTCCTAG
5431020 AATTAAA-AAGCTAGGAAAGTCCTAG
1 AATTAAAGAAGCTAGGAAAGTCCTAG
5431045 AATTAAAGAAG
1 AATTAAAGAAG
5431056 AGCCTTGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (26 bp):
AATTAAAGAAGCTAGGAAAGTCCTAG
Found at i:5433543 original size:20 final size:20
Alignment explanation
Indices: 5433507--5433544 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5433497 TCAACTTGGA
*
5433507 CTGAGTCAAACCGAACCGCC
1 CTGAGTCAAACCCAACCGCC
5433527 CTGAGTC-AACTCCAACCG
1 CTGAGTCAAAC-CCAACCG
5433545 GTCTGACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.29, C:0.39, G:0.18, T:0.13
Consensus pattern (20 bp):
CTGAGTCAAACCCAACCGCC
Found at i:5433630 original size:16 final size:17
Alignment explanation
Indices: 5433591--5433648 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
5433581 GACCCAGATC
* *
5433591 GTTAACTTTGATC-AGA
1 GTTAACTTTGACCAAAA
* *
5433607 GTTGACTTTGACCAACA
1 GTTAACTTTGACCAAAA
*
5433624 -TTAACTTTTACCAAAA
1 GTTAACTTTGACCAAAA
5433640 GTTAACTTT
1 GTTAACTTT
5433649 TTCGAAAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 24 0.71
17 10 0.29
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (17 bp):
GTTAACTTTGACCAAAA
Found at i:5435682 original size:32 final size:32
Alignment explanation
Indices: 5435643--5435740 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
5435633 CCTGGGTATA
*
5435643 CTCTTAGGCCCCAAGGTACT-TCTTTGAGTAGG
1 CTCTTAGGCCCCAAGGTACTCTCTTGGA-TAGG
* **
5435675 CTTTTAGG-TTCAAGGTACTCTCTTGGATAGG
1 CTCTTAGGCCCCAAGGTACTCTCTTGGATAGG
* * * *
5435706 CTCTAAGGCCCCAAGGTACTCCCTTAGATTGG
1 CTCTTAGGCCCCAAGGTACTCTCTTGGATAGG
5435738 CTC
1 CTC
5435741 CTATGCTCAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 19 0.36
32 34 0.64
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (32 bp):
CTCTTAGGCCCCAAGGTACTCTCTTGGATAGG
Found at i:5436425 original size:14 final size:14
Alignment explanation
Indices: 5436406--5436438 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5436396 ACTTATCAAA
5436406 TTCACATTCA-TAAG
1 TTCACATT-ATTAAG
5436420 TTCACATTATTAAG
1 TTCACATTATTAAG
5436434 TTCAC
1 TTCAC
5436439 TAGCCCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCACATTATTAAG
Found at i:5436540 original size:23 final size:23
Alignment explanation
Indices: 5436514--5436582 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
5436504 CACCACAACT
*
5436514 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
5436537 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
5436560 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
5436583 TATAATAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:5436832 original size:30 final size:30
Alignment explanation
Indices: 5436798--5436859 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
5436788 TTGTATCATG
* *
5436798 TAGACATATTATTTTCATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTATCACA
5436828 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTATCACA
5436858 TA
1 TA
5436860 ACTCATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTATCACA
Found at i:5443341 original size:14 final size:14
Alignment explanation
Indices: 5443322--5443354 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5443312 ATTTATCAAA
5443322 TTCACATTCA-TAAG
1 TTCACATT-ATTAAG
5443336 TTCACATTATTAAG
1 TTCACATTATTAAG
5443350 TTCAC
1 TTCAC
5443355 TAGCCCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCACATTATTAAG
Found at i:5443461 original size:23 final size:23
Alignment explanation
Indices: 5443435--5443499 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
5443425 CAGCTCGTAT
5443435 AATTGCACCGAAGTGCCATGTAA
1 AATTGCACCGAAGTGCCATGTAA
* ** *
5443458 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCATGTAA
*
5443481 AATTGCACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
5443500 ATAATAATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAA
Found at i:5443747 original size:30 final size:30
Alignment explanation
Indices: 5443706--5443774 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
5443696 ACATAATTTG
* * *
5443706 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
5443736 TATCACATAGACATATCATTTCCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
5443766 TATCACATA
1 TATCACATA
5443775 ACTCATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACCTT
Found at i:5444173 original size:24 final size:22
Alignment explanation
Indices: 5444115--5444175 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 22
5444105 CTAAATAAAG
5444115 GTATGCATCGATGCACTCTACA
1 GTATGCATCGATGCACTCTACA
5444137 GTAT--ATCGATGCACTCTACA
1 GTATGCATCGATGCACTCTACA
*
5444157 GTGTGTGCATCGATGCACT
1 --GTATGCATCGATGCACT
5444176 AACTGTGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 16 0.47
22 7 0.21
24 11 0.32
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (22 bp):
GTATGCATCGATGCACTCTACA
Found at i:5444311 original size:63 final size:63
Alignment explanation
Indices: 5444231--5444366 Score: 218
Period size: 63 Copynumber: 2.2 Consensus size: 63
5444221 GGAGGTACAC
* * * *
5444231 CGATGCACTCCTTATGCATCGATGCACTGAGGGCATTCGATGTTCATTTAATTGAAAATGCAT
1 CGATGCACTCCTTATGCATCGATGCACTAACGACATTCGATGTTCAATTAATTGAAAATGCAT
**
5444294 CGATGCACTCCTTATGCATCGATGCACTAACGACATTCGATGTTCAATTAATTGAGGATGCAT
1 CGATGCACTCCTTATGCATCGATGCACTAACGACATTCGATGTTCAATTAATTGAAAATGCAT
5444357 CGATGCACTC
1 CGATGCACTC
5444367 TACTTAGAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (63 bp):
CGATGCACTCCTTATGCATCGATGCACTAACGACATTCGATGTTCAATTAATTGAAAATGCAT
Found at i:5460641 original size:31 final size:31
Alignment explanation
Indices: 5460605--5460663 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5460595 AACTTAAAAG
* *
5460605 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
5460636 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
5460664 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:5460714 original size:22 final size:22
Alignment explanation
Indices: 5460688--5460730 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5460678 TAATAAATTA
5460688 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
5460710 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
5460731 CTAATAAGTT
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:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:5460785 original size:80 final size:80
Alignment explanation
Indices: 5460693--5460843 Score: 257
Period size: 80 Copynumber: 1.9 Consensus size: 80
5460683 AATTATTTAA
* * * *
5460693 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAGTTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAACCAAT
*
5460758 CTATACAACTACAAT
66 ATATACAACTACAAT
5460773 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAACCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAACCAAT
5460838 ATATAC
66 ATATAC
5460844 TAATAAATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAACCAAT
ATATACAACTACAAT
Found at i:5460829 original size:32 final size:32
Alignment explanation
Indices: 5460790--5461120 Score: 308
Period size: 32 Copynumber: 10.4 Consensus size: 32
5460780 CAATCCATAT
*
5460790 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* **
5460822 TTTAAAATAAACCAATATATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5460854 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5460886 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
5460918 TTTAAAATAAATTAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
5460950 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TA
* * * ** * * *
5460987 TATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 TTTA-AAATAAATCAATCCATACT-AATAAAT---TA
5461023 TTTTAAAATAAATCAAT-CATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
5461055 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5461077 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5461109 TTTAAAATAAAT
1 TTTAAAATAAAT
5461121 TATTAAAATA
Statistics
Matches: 246, Mismatches: 33, Indels: 40
0.77 0.10 0.13
Matches are distributed among these distances:
22 16 0.07
23 2 0.01
24 1 0.00
26 3 0.01
28 3 0.01
30 1 0.00
31 18 0.07
32 149 0.61
34 8 0.03
35 7 0.03
36 18 0.07
37 13 0.05
38 7 0.03
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:5460863 original size:64 final size:64
Alignment explanation
Indices: 5460790--5461120 Score: 350
Period size: 64 Copynumber: 5.7 Consensus size: 64
5460780 CAATCCATAT
* * * *
5460790 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAACCAATATATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACAAATAAATTA
* *
5460854 TTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACAAATAAATTA
* *
5460918 TTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACAAATAAATTA
5460972 TTTAAAATAAATCAAT--ATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACAAATAAATTA
5461024 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACAAATAAATTA
*
5461077 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
5461121 TATTAAAATA
Statistics
Matches: 255, Mismatches: 10, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
52 52 0.20
53 52 0.20
54 42 0.16
55 1 0.00
56 1 0.00
58 2 0.01
60 1 0.00
63 1 0.00
64 103 0.40
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (64 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACAAATAAATTA
Found at i:5460906 original size:96 final size:95
Alignment explanation
Indices: 5460790--5461120 Score: 368
Period size: 96 Copynumber: 3.8 Consensus size: 95
5460780 CAATCCATAT
*
5460790 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAACCAATATATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAATAAATTAT
5460855 TTAAAATAAATCAATCGATACTAATAAATTA
66 TTAAAATAAATCAATC-ATACTAATAAATTA
*
5460886 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATTAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATAT-ATACTAATAAATTA
5460950 TTTAAAATAAATCAATC---C--AT--A-T-
65 TTTAAAATAAATCAATCATACTAATAAATTA
* *
5460972 TTTAAAATAAATCAAT--ATACTAATAAATTATTTAAAATAAATC---A-AT-C-CAT--A-T-T
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAATAAATTAT
5461025 TTAAAATAAATCAATCATACTAATAAATTA
66 TTAAAATAAATCAATCATACTAATAAATTA
5461055 TTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATAT-ATACTAATAAATTA
5461109 TTTAAAATAAAT
65 TTTAAAATAAAT
5461121 TATTAAAATA
Statistics
Matches: 206, Mismatches: 6, Indels: 57
0.77 0.02 0.21
Matches are distributed among these distances:
74 17 0.08
75 14 0.07
76 2 0.01
77 2 0.01
78 2 0.01
79 7 0.03
80 3 0.01
81 4 0.02
82 1 0.00
83 17 0.08
84 26 0.13
85 12 0.06
86 16 0.08
87 1 0.00
88 1 0.00
90 2 0.01
92 1 0.00
95 1 0.00
96 77 0.37
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (95 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAATAAATTAT
TTAAAATAAATCAATCATACTAATAAATTA
Found at i:5461051 original size:22 final size:22
Alignment explanation
Indices: 5461004--5461051 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5460994 ATAAATTATT
**
5461004 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
5461026 TAAAATAAATCAAT-CATACTAA
1 TAAAATAAATCAATCCATA-TAA
5461048 TAAA
1 TAAA
5461052 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5461054 original size:105 final size:108
Alignment explanation
Indices: 5460918--5461120 Score: 376
Period size: 105 Copynumber: 1.9 Consensus size: 108
5460908 AAATAAATTA
*
5460918 TTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
5460983 TCAA-T-ATACTAATAAATTATTTAAAATAAATCAATCCATAT
66 TCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
5461024 TTTAAAATAAATCAA-TCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
5461088 TCAATTCATACTAATAAATTATTTAAAATAAAT
66 TCAATTCATACTAATAAATTATTTAAAATAAAT
5461121 TATTAAAATA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
105 53 0.56
106 15 0.16
107 26 0.28
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (108 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:5461081 original size:22 final size:22
Alignment explanation
Indices: 5461055--5461097 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5461045 TAATAAATTA
5461055 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
5461077 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
5461098 CTAATAAATT
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:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:5461106 original size:22 final size:22
Alignment explanation
Indices: 5461057--5461105 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5461047 ATAAATTATT
**
5461057 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
5461079 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
5461102 TAAA
1 TAAA
5461106 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5461128 original size:13 final size:13
Alignment explanation
Indices: 5461100--5461234 Score: 71
Period size: 13 Copynumber: 9.8 Consensus size: 13
5461090 AATTCATACT
5461100 AATAAATTATTTAA
1 AATAAATTA-TTAA
5461114 AATAAATTATTAA
1 AATAAATTATTAA
* *
5461127 AATAAATCAATCTATTT
1 AATAAAT-TAT-TA--A
*
5461144 TATAATATTTATTTAA
1 AATAA-A-TTA-TTAA
*
5461160 AATAAA-T-TTAT
1 AATAAATTATTAA
5461171 AAT-AATTATTTAA
1 AATAAATTA-TTAA
**
5461184 AAT-AATTATTTT
1 AATAAATTATTAA
**
5461196 AATAAATTATTTT
1 AATAAATTATTAA
5461209 AATAAATTATTTTAA
1 AATAAATTA--TTAA
5461224 AATAAATTATT
1 AATAAATTATT
5461235 TTATTTTATA
Statistics
Matches: 96, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
10 2 0.02
11 7 0.07
12 5 0.05
13 43 0.45
14 11 0.11
15 14 0.15
16 4 0.04
17 4 0.04
18 4 0.04
19 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
AATAAATTATTAA
Found at i:5461129 original size:45 final size:46
Alignment explanation
Indices: 5461078--5461167 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 46
5461068 AATCCATATT
5461078 TTAAAATAAATCAAT-TCATACTAATAA-A-TTATTTAAAATAAATTA
1 TTAAAATAAATCAATCT-AT-CTAATAATATTTATTTAAAATAAATTA
* *
5461123 TTAAAATAAATCAATCTATTTTATAATATTTATTTAAAATAAATT
1 TTAAAATAAATCAATCTATCTAATAATATTTATTTAAAATAAATT
5461168 TATAATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 5 0.12
45 18 0.45
46 17 0.43
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (46 bp):
TTAAAATAAATCAATCTATCTAATAATATTTATTTAAAATAAATTA
Found at i:5461143 original size:32 final size:33
Alignment explanation
Indices: 5460790--5461166 Score: 237
Period size: 32 Copynumber: 11.4 Consensus size: 33
5460780 CAATCCATAT
*
5460790 TTTAAAATAAATCAATCCA-TACAAATAAATTA
1 TTTAAAATAAATCAATCTATTACAAATAAATTA
* * *
5460822 TTTAAAATAAACCAATATA-TACTAATAAATTA
1 TTTAAAATAAATCAATCTATTACAAATAAATTA
* *
5460854 TTTAAAATAAATCAATCGA-TACTAATAAATTA
1 TTTAAAATAAATCAATCTATTACAAATAAATTA
*
5460886 TTTAAAATAAATCAATCCA-TACAAATAAATTA
1 TTTAAAATAAATCAATCTATTACAAATAAATTA
* *
5460918 TTTAAAATAAATTAAT-TCA-TACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATTACAAATAAATTA
*
5460950 TTTAAAATAAATCAATCCATATTTTA-AAATAAATCAA
1 TTTAAAATAAATCAAT-C-TA--TTACAAATAAAT-TA
* * * * ** * *
5460987 TATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 TTTA-AAATAAATCAATCTATTACAAATAAAT---TA
*
5461023 TTTTAAAATAAATCAATC-A-TACTAATAAATTA
1 -TTTAAAATAAATCAATCTATTACAAATAAATTA
*
5461055 TTTAAAATAAATCAATCCATATTTTA-AAATAAATCAA
1 TTTAAAATAAATCAAT-C-TA--TTACAAATAAAT-TA
* * * *
5461092 TTCATACT-AATAAAT-TATTTA-AAATAAATTA
1 TTTAAAATAAATCAATCTA-TTACAAATAAATTA
** *
5461123 -TTAAAATAAATCAATCTATTTTATAAT-ATTTA
1 TTTAAAATAAATCAATCTATTACA-AATAAATTA
5461155 TTTAAAATAAAT
1 TTTAAAATAAAT
5461167 TTATAATAAT
Statistics
Matches: 274, Mismatches: 45, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
30 4 0.01
31 25 0.09
32 152 0.55
33 17 0.06
34 9 0.03
35 10 0.04
36 29 0.11
37 21 0.08
38 7 0.03
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (33 bp):
TTTAAAATAAATCAATCTATTACAAATAAATTA
Found at i:5461173 original size:24 final size:24
Alignment explanation
Indices: 5461142--5461216 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
5461132 ATCAATCTAT
*
5461142 TTTATAATATTTATTTAAAATAAA
1 TTTATAATAATTATTTAAAATAAA
5461166 TTTATAATAATTATTTAAAATAATTA
1 TTTATAATAATTATTTAAAATAA--A
*
5461192 TTT-TAATAAATTATTT-TAATAAA
1 TTTATAAT-AATTATTTAAAATAAA
5461215 TT
1 TT
5461217 ATTTTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
23 3 0.07
24 22 0.48
25 9 0.20
26 12 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTATAATAATTATTTAAAATAAA
Found at i:5461200 original size:28 final size:28
Alignment explanation
Indices: 5461100--5461306 Score: 94
Period size: 32 Copynumber: 7.2 Consensus size: 28
5461090 AATTCATACT
*
5461100 AATAAATTA-TTTAAAATAAATTA-TTAA
1 AATAAATTATTTTATAAT-AATTATTTAA
*
5461127 AATAAATCAATCTATTTTATAATATTTATTTAA
1 AAT--A--AAT-TATTTTATAATAATTATTTAA
5461160 AAT-AA--A-TTTATAATAATTATTTAA
1 AATAAATTATTTTATAATAATTATTTAA
*
5461184 AAT-AATTA-TTT-TAATAAATTATTT-T
1 AATAAATTATTTTATAAT-AATTATTTAA
* *
5461209 AATAAATTATTTTAAAATAAATTATTTTATTT
1 AATAAATTATTTTATAAT-AATTA-TTTA--A
* * * * *
5461241 TATAATTTATTTTATTAAATATAATAATATAT
1 AATAAATTATTTTA-T--A-ATAATTATTTAA
* *
5461273 AATAAATTA-TTTAAAAAAATTATTTAA
1 AATAAATTATTTTATAATAATTATTTAA
5461300 AATAAAT
1 AATAAAT
5461307 AACCTTTTAA
Statistics
Matches: 142, Mismatches: 17, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
24 22 0.15
25 8 0.06
26 17 0.12
27 21 0.15
28 12 0.08
29 4 0.03
31 7 0.05
32 27 0.19
33 14 0.10
34 3 0.02
35 5 0.04
36 2 0.01
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
AATAAATTATTTTATAATAATTATTTAA
Found at i:5461292 original size:13 final size:14
Alignment explanation
Indices: 5461273--5461306 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
5461263 AATAATATAT
5461273 AATAAATTATTTAA
1 AATAAATTATTTAA
5461287 AA-AAATTATTTAA
1 AATAAATTATTTAA
5461300 AATAAAT
1 AATAAAT
5461307 AACCTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:5461318 original size:103 final size:95
Alignment explanation
Indices: 5461115--5461328 Score: 236
Period size: 103 Copynumber: 2.2 Consensus size: 95
5461105 ATTATTTAAA
*
5461115 ATAAATTA-TTAAAATAAATCAATCTATTTTATAATATTTATTTAAAATAAATTTATAATAATTA
1 ATAAATTATTTAAAATAAATCAATCTATTTTATAATATTTATTTAAAATAAATATATAATAATTA
* * * *
5461179 TTTAAAATAATTATTTTAATAAATTATTTT
66 TTTAAAAAAATTATTTAAATAAATAACTTT
* * *
5461209 AATAAATTATTTTAAAATAAATTATTTTATTTTATAATTTATTT-TATTAAATATAATAATATAT
1 -ATAAATTA-TTTAAAATAAATCAATCTATTTTATAA--TATTTAT-TTAAA-AT-A-AATATAT
5461273 AATAAATTATTTAAAAAAATTATTTAAAATAAATAACCTTT
58 AAT-AATTATTTAAAAAAATTATTT-AAATAAATAA-CTTT
5461314 -TAAATTATTTAAAAT
1 ATAAATTATTTAAAAT
5461329 TATTTTAATA
Statistics
Matches: 100, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
95 8 0.08
97 23 0.23
98 1 0.01
99 10 0.10
100 2 0.02
101 1 0.01
102 17 0.17
103 27 0.27
104 8 0.08
105 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (95 bp):
ATAAATTATTTAAAATAAATCAATCTATTTTATAATATTTATTTAAAATAAATATATAATAATTA
TTTAAAAAAATTATTTAAATAAATAACTTT
Found at i:5466202 original size:23 final size:22
Alignment explanation
Indices: 5466176--5466220 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5466166 GATTTCAAAT
*
5466176 TTCAACATCTACAACTTTTTTTC
1 TTCAACA-CTACAACCTTTTTTC
* *
5466199 TTCAATACTACGACCTTTTTTC
1 TTCAACACTACAACCTTTTTTC
5466221 AATAAGGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47
Consensus pattern (22 bp):
TTCAACACTACAACCTTTTTTC
Found at i:5472583 original size:23 final size:23
Alignment explanation
Indices: 5472551--5472595 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5472541 ATTAAAAGAC
5472551 AAAAAAATGTCATCAAA-ATAAAT
1 AAAAAAATGTCAT-AAAGATAAAT
*
5472574 AAAAATATGTCATAAAGATAAA
1 AAAAAAATGTCATAAAGATAAA
5472596 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (23 bp):
AAAAAAATGTCATAAAGATAAAT
Found at i:5472644 original size:34 final size:32
Alignment explanation
Indices: 5472585--5472648 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 32
5472575 AAAATATGTC
5472585 ATAAAGATAAAATTATTAAAAATTAAAAAAAA
1 ATAAAGATAAAATTATTAAAAATTAAAAAAAA
5472617 ATAAA-ATAAAATGTCATATAAAAATTAAAAAA
1 ATAAAGATAAAAT-T-AT-TAAAAATTAAAAAA
5472649 TACTAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 7 0.24
32 6 0.21
33 2 0.07
34 14 0.48
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (32 bp):
ATAAAGATAAAATTATTAAAAATTAAAAAAAA
Found at i:5481947 original size:2 final size:2
Alignment explanation
Indices: 5481912--5481936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5481902 GAGGAGCACC
5481912 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5481937 CCAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5482416 original size:15 final size:15
Alignment explanation
Indices: 5482387--5482423 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
5482377 AAATTAATTA
*
5482387 ATTTAGTTAATATATT
1 ATTTA-TTAAAATATT
5482403 ATTTATTAAAATATT
1 ATTTATTAAAATATT
5482418 ATTTAT
1 ATTTAT
5482424 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
ATTTATTAAAATATT
Found at i:5483034 original size:16 final size:17
Alignment explanation
Indices: 5483010--5483042 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5483000 TAATATTATT
*
5483010 TTTACTAATA-ATTTAA
1 TTTAATAATATATTTAA
5483026 TTTAATAATATATTTAA
1 TTTAATAATATATTTAA
5483043 AATTAGATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATAATATATTTAA
Found at i:5483971 original size:11 final size:10
Alignment explanation
Indices: 5483925--5484015 Score: 62
Period size: 11 Copynumber: 8.9 Consensus size: 10
5483915 AATAACTTTG
5483925 AAATATTATA
1 AAATATTATA
*
5483935 AAATTATCAATA
1 AAA-TAT-TATA
5483947 AAATATTATA
1 AAATATTATA
*
5483957 AAATAATTATT
1 AAAT-ATTATA
*
5483968 AAAT-TCATCA
1 AAATATTAT-A
*
5483978 AATTATTATA
1 AAATATTATA
*
5483988 AAATAATTATT
1 AAAT-ATTATA
*
5483999 AAAT-TTATC
1 AAATATTATA
5484008 AAAT-TTAT
1 AAATATTAT
5484016 TATGATTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
9 15 0.23
10 17 0.26
11 27 0.42
12 6 0.09
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATATTATA
Found at i:5483988 original size:31 final size:32
Alignment explanation
Indices: 5483950--5484018 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
5483940 ATCAATAAAA
5483950 TATTATAAAATAATTATTAAATTCATCAAA-T
1 TATTATAAAATAATTATTAAATTCATCAAATT
*
5483981 TATTATAAAATAATTATTAAATTTATCAAATT
1 TATTATAAAATAATTATTAAATTCATCAAATT
5484013 TATTAT
1 TATTAT
5484019 GATTTATAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (32 bp):
TATTATAAAATAATTATTAAATTCATCAAATT
Found at i:5490964 original size:31 final size:32
Alignment explanation
Indices: 5490912--5490973 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
5490902 CAATATCAAA
5490912 AAAAGATTAAACTAATAAAATT-TTTAAATAT
1 AAAAGATTAAACTAATAAAATTATTTAAATAT
* * *
5490943 AAAAGATTAAATTTATTAAATTAATTTAAAT
1 AAAAGATTAAACTAATAAAATT-ATTTAAAT
5490974 TAGGACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
33 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (32 bp):
AAAAGATTAAACTAATAAAATTATTTAAATAT
Found at i:5491363 original size:43 final size:42
Alignment explanation
Indices: 5491267--5491364 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 42
5491257 CAACTGAAGC
* * * *
5491267 CTCTAATTTTTCGAATCTCATTTTTTACTTTTATAATTGAGG
1 CTCTAATTTTTCGAATATCACTTTCTACCTTTATAATTGAGG
*
5491309 CACTTAAATTTTCTC-AATATCACTTTCTACCTTTATAATTGAGG
1 CTC-T-AATTTT-TCGAATATCACTTTCTACCTTTATAATTGAGG
5491353 TCTCTAATTTTT
1 -CTCTAATTTTT
5491365 TTAATTTCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.07
43 7 0.15
44 32 0.70
45 4 0.09
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (42 bp):
CTCTAATTTTTCGAATATCACTTTCTACCTTTATAATTGAGG
Found at i:5501431 original size:58 final size:58
Alignment explanation
Indices: 5501348--5501457 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 58
5501338 GGTCGGGTTT
* *
5501348 GGGTTTTATATCAAAAAGTCGGGTCGGGTGAAGTCAC-CTCTAAATTCGGGTCAAGTTC
1 GGGTTTTATATCAAAAAGTCAGGTCGGGTGAAGTCACTCT-TAAACTCGGGTCAAGTTC
*
5501406 GGGTTTTATATCAAAAAGTTAGGTCGGGTGAAGTCACTCTTAAACTCGGGTC
1 GGGTTTTATATCAAAAAGTCAGGTCGGGTGAAGTCACTCTTAAACTCGGGTC
5501458 GGATCGAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 46 0.96
59 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (58 bp):
GGGTTTTATATCAAAAAGTCAGGTCGGGTGAAGTCACTCTTAAACTCGGGTCAAGTTC
Found at i:5508382 original size:35 final size:37
Alignment explanation
Indices: 5508333--5508401 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
5508323 CAAATTCAAG
*
5508333 ATTTAATATTTATCTTTT-TA-TTT-TTAGGATTTAA
1 ATTTAATAATTATCTTTTGTATTTTCTTAGGATTTAA
5508367 ATTTAAATAATTATCTTTTGTATTTTCTTAGGATT
1 ATTT-AATAATTATCTTTTGTATTTTCTTAGGATT
5508402 ATCTTTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 4 0.13
35 13 0.43
36 2 0.07
37 3 0.10
38 8 0.27
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.59
Consensus pattern (37 bp):
ATTTAATAATTATCTTTTGTATTTTCTTAGGATTTAA
Found at i:5512355 original size:29 final size:29
Alignment explanation
Indices: 5512291--5512356 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
5512281 AGTCTAGAAA
*
5512291 AGGGGTATTTTATATGTAAGCAAATGTAG
1 AGGGGTCTTTTATATGTAAGCAAATGTAG
5512320 AGGGGTCTTTTATATGTAAGCAAATGTAG
1 AGGGGTCTTTTATATGTAAGCAAATGTAG
5512349 AGGGGTCT
1 AGGGGTCT
5512357 AGAAGGTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (29 bp):
AGGGGTCTTTTATATGTAAGCAAATGTAG
Found at i:5513376 original size:12 final size:12
Alignment explanation
Indices: 5513359--5513399 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5513349 CACCGATAAT
*
5513359 AATAAAAAACAA
1 AATAAAAACCAA
5513371 AAT--AAACCGAA
1 AATAAAAACC-AA
5513382 AATAAAAACCAA
1 AATAAAAACCAA
5513394 AATAAA
1 AATAAA
5513400 TCCCATTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 4 0.16
11 5 0.20
12 11 0.44
13 5 0.20
ACGTcount: A:0.76, C:0.12, G:0.02, T:0.10
Consensus pattern (12 bp):
AATAAAAACCAA
Found at i:5515001 original size:36 final size:37
Alignment explanation
Indices: 5514928--5515002 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 37
5514918 TCTGTTGATC
* * **
5514928 GAAAACGTTAGGCTTGTGACTAATCCCTTTCTGGTCA
1 GAAAACGTTAGACTTGTGACTAATCCCTGTCCAGTCA
*
5514965 GAAAA-GTTAGACTTGTGACTAGTCCCTGTCCAGTCA
1 GAAAACGTTAGACTTGTGACTAATCCCTGTCCAGTCA
5515001 GA
1 GA
5515003 TTTAAACACA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (37 bp):
GAAAACGTTAGACTTGTGACTAATCCCTGTCCAGTCA
Found at i:5515729 original size:59 final size:59
Alignment explanation
Indices: 5515657--5515776 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
5515647 ACGAGCCGAA
5515657 TCTTTCAATTGAAACAAATTTATGACATCCTAGAGAAAGGGGAGGAAGAAAGGATTATT
1 TCTTTCAATTGAAACAAATTTATGACATCCTAGAGAAAGGGGAGGAAGAAAGGATTATT
* * *
5515716 TCTTTCAGTTGAAACAAATTTATGACATCCTAGAGATAGGGGAGGATGAAAGGATTATT
1 TCTTTCAATTGAAACAAATTTATGACATCCTAGAGAAAGGGGAGGAAGAAAGGATTATT
5515775 TC
1 TC
5515777 AATTAAAGCG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (59 bp):
TCTTTCAATTGAAACAAATTTATGACATCCTAGAGAAAGGGGAGGAAGAAAGGATTATT
Found at i:5517899 original size:14 final size:14
Alignment explanation
Indices: 5517880--5517910 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5517870 TCGATAATAT
*
5517880 GTTCGTTTATGTTC
1 GTTCGTCTATGTTC
5517894 GTTCGTCTATGTTC
1 GTTCGTCTATGTTC
5517908 GTT
1 GTT
5517911 TATATGCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGTCTATGTTC
Found at i:5518108 original size:10 final size:10
Alignment explanation
Indices: 5518086--5518129 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
5518076 AGAAAAAAAA
*
5518086 TTATTTTCAT
1 TTATGTTCAT
*
5518096 TTATGTTCGT
1 TTATGTTCAT
*
5518106 TTAAGTTCAT
1 TTATGTTCAT
5518116 TTATGTTCAT
1 TTATGTTCAT
5518126 TTAT
1 TTAT
5518130 TGTGTTCGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (10 bp):
TTATGTTCAT
Found at i:5537825 original size:17 final size:17
Alignment explanation
Indices: 5537803--5537835 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5537793 TAATGACATG
*
5537803 AAAAGTGGTAAAAAAAA
1 AAAAGTGATAAAAAAAA
5537820 AAAAGTGATAAAAAAA
1 AAAAGTGATAAAAAAA
5537836 TGAGAATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
AAAAGTGATAAAAAAAA
Found at i:5547649 original size:22 final size:22
Alignment explanation
Indices: 5547607--5547651 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5547597 CATTCTAGAT
* *
5547607 TAATTAAAAAATATACTTAATA
1 TAATAAAAAAATATACCTAATA
5547629 TAATAAAAAAAT-TACACTAATA
1 TAATAAAAAAATATAC-CTAATA
5547651 T
1 T
5547652 TCATTGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAAAAAAATATACCTAATA
Found at i:5549467 original size:15 final size:16
Alignment explanation
Indices: 5549425--5549468 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
5549415 TCCGATTGCC
5549425 GTCACTAAACTAGAGG
1 GTCACTAAACTAGAGG
*
5549441 GTACAGTAAACTAGA-G
1 GT-CACTAAACTAGAGG
5549457 GTCACTAAACTA
1 GTCACTAAACTA
5549469 TGTCAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 11 0.44
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (16 bp):
GTCACTAAACTAGAGG
Found at i:5550432 original size:55 final size:57
Alignment explanation
Indices: 5550342--5550454 Score: 149
Period size: 55 Copynumber: 2.0 Consensus size: 57
5550332 TTATTTGTTT
* * * *
5550342 ATAATTTTCTTAATCACCTTACAAATATAATTGTCTAGACTC-A-ACCTCTAAGAAA
1 ATAACTTTCTTAATCACCTTACAAACATAACTGTCTAAACTCAAGACCTCTAAGAAA
* * *
5550397 ATAACTTTCTTGATCACCTTACAAACGTAACTGTCTAAACTCAAGACCTCTGAGAAA
1 ATAACTTTCTTAATCACCTTACAAACATAACTGTCTAAACTCAAGACCTCTAAGAAA
5550454 A
1 A
5550455 GTAATATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
55 36 0.73
56 1 0.02
57 12 0.24
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (57 bp):
ATAACTTTCTTAATCACCTTACAAACATAACTGTCTAAACTCAAGACCTCTAAGAAA
Found at i:5558126 original size:13 final size:12
Alignment explanation
Indices: 5558102--5558133 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
5558092 AGATAAAATT
5558102 AAAAAATTAAAA
1 AAAAAATTAAAA
5558114 AAAAAATTAAAA
1 AAAAAATTAAAA
5558126 AAACAAAT
1 AAA-AAAT
5558134 ATAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATTAAAA
Found at i:5558564 original size:37 final size:36
Alignment explanation
Indices: 5558489--5558565 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
5558479 TTTTTATATT
*
5558489 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
5558525 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
5558562 TTTA
1 TTTA
5558566 TAATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:5558585 original size:18 final size:18
Alignment explanation
Indices: 5558541--5558588 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5558531 TTTTTAAAGA
*
5558541 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
5558560 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
5558577 AAATATATAATA
1 AAATATATAATA
5558589 AGGATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:5558821 original size:16 final size:16
Alignment explanation
Indices: 5558787--5558826 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5558777 TTTACTTCAT
*
5558787 AATGATT-AAACGCTG
1 AATGATTCAAACGATG
*
5558802 AATGATTCAAATGATG
1 AATGATTCAAACGATG
5558818 AATGATTCA
1 AATGATTCA
5558827 GATGCTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (16 bp):
AATGATTCAAACGATG
Found at i:5560189 original size:29 final size:29
Alignment explanation
Indices: 5560147--5560207 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
5560137 TTTGTGCCGA
5560147 AAGTATTGATTAATTAAGCTTATTAAGGT
1 AAGTATTGATTAATTAAGCTTATTAAGGT
5560176 AAGTATTGATTAATTAAGCTTATTAAGGT
1 AAGTATTGATTAATTAAGCTTATTAAGGT
5560205 AAG
1 AAG
5560208 GATCGCTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (29 bp):
AAGTATTGATTAATTAAGCTTATTAAGGT
Found at i:5568637 original size:13 final size:13
Alignment explanation
Indices: 5568619--5568645 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5568609 GGAAACCGTC
5568619 GTGTTTAACGGTT
1 GTGTTTAACGGTT
5568632 GTGTTTAACGGTT
1 GTGTTTAACGGTT
5568645 G
1 G
5568646 AAAACGTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.44
Consensus pattern (13 bp):
GTGTTTAACGGTT
Found at i:5578121 original size:20 final size:20
Alignment explanation
Indices: 5578096--5578186 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
5578086 TAAATTAAAT
*
5578096 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
5578116 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
5578136 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
5578148 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
5578168 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
5578187 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:5578211 original size:53 final size:52
Alignment explanation
Indices: 5578095--5578244 Score: 275
Period size: 53 Copynumber: 2.9 Consensus size: 52
5578085 CTAAATTAAA
*
5578095 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
5578147 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
5578200 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
5578245 GTTGCTAATT
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 10 0.10
52 35 0.36
53 51 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:5578226 original size:20 final size:20
Alignment explanation
Indices: 5578201--5578240 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5578191 TCTATTAGTT
*
5578201 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
5578221 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
5578241 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Done.