Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 58 of 352
Found at i:18390305 original size:39 final size:39
Alignment explanation
Indices: 18390262--18390343 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
18390252 GAAATCTAGT
*
18390262 TGAAGCACATAACTGCGAAACGGCAGCCCGAAGGCTAAC
1 TGAAGCACATAACTGCGAAACGGAAGCCCGAAGGCTAAC
* * *
18390301 TGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAAC
1 TGAAGCACATAACTGCGAAACGGAAGCCCGAAGGCTAAC
18390340 TGAA
1 TGAA
18390344 ACTCATCAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (39 bp):
TGAAGCACATAACTGCGAAACGGAAGCCCGAAGGCTAAC
Found at i:18390327 original size:21 final size:21
Alignment explanation
Indices: 18390263--18390327 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
18390253 AAATCTAGTT
* *
18390263 GAAGCACATAACTGCGAAACG
1 GAAGCACATAAGTGCTAAACG
* ** *
18390284 GCAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
18390302 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
18390323 GAAGC
1 GAAGC
18390328 CCGGAGGCTA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 6 0.19
21 12 0.39
ACGTcount: A:0.38, C:0.25, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:18391697 original size:37 final size:37
Alignment explanation
Indices: 18391647--18391725 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
18391637 TTATTACGAA
* * *
18391647 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
18391684 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
18391721 GTCTT
1 GTCTT
18391726 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:18391922 original size:47 final size:47
Alignment explanation
Indices: 18391844--18392019 Score: 271
Period size: 47 Copynumber: 3.7 Consensus size: 47
18391834 CCCTTCGGGA
* * * * *
18391844 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
18391891 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
18391938 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
18391985 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
18392020 ATATACACTT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 116 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:18391963 original size:38 final size:40
Alignment explanation
Indices: 18391920--18392129 Score: 115
Period size: 47 Copynumber: 5.2 Consensus size: 40
18391910 TTCACATTCA
*
18391920 TCACAT-C-GGCCATTAGGTCTTATCACATATATACACTT
1 TCACATACTGGCCATTAGGCCTTATCACATATATACACTT
18391958 TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTT
1 T--CA--CAT-AC--TGGCCATTAGGCCTTATCACATATATACACTT
* **
18392005 TCACATTCAT--CACATATATACACTT-TCAC--AT-T-CA---
1 TCACATAC-TGGC-CAT-TAGGC-CTTATCACATATATACACTT
*
18392039 TCACAT-C-GGCTATTAGGCCTTATCACATATATACACTT
1 TCACATACTGGCCATTAGGCCTTATCACATATATACACTT
18392077 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 T--CA--CAT-AC-T-GGCCATTAGGCCTTATCACATATATACACTT
18392124 TCACAT
1 TCACAT
18392130 TCATCACATC
Statistics
Matches: 132, Mismatches: 9, Indels: 57
0.67 0.05 0.29
Matches are distributed among these distances:
30 3 0.02
31 7 0.05
32 2 0.02
33 4 0.03
34 7 0.05
35 2 0.02
37 2 0.02
38 3 0.02
39 3 0.02
40 7 0.05
41 8 0.06
42 10 0.08
43 6 0.05
44 2 0.02
45 4 0.03
47 62 0.47
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (40 bp):
TCACATACTGGCCATTAGGCCTTATCACATATATACACTT
Found at i:18392019 original size:72 final size:72
Alignment explanation
Indices: 18391941--18392091 Score: 284
Period size: 72 Copynumber: 2.1 Consensus size: 72
18391931 ATTAGGTCTT
*
18391941 ATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
18392006 CACATTC
66 CACATTC
*
18392013 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
18392078 CACATTC
66 CACATTC
18392085 ATCACAT
1 ATCACAT
18392092 CGGCCATTAG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (72 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
CACATTC
Found at i:18392022 original size:25 final size:25
Alignment explanation
Indices: 18391941--18392044 Score: 124
Period size: 25 Copynumber: 4.3 Consensus size: 25
18391931 ATTAGGTCTT
18391941 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
*** *** *
18391966 ATCACAT-TGGCCA-TTAGGCCTT-
1 ATCACATATATACACTTTCACATTC
18391988 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
18392013 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
18392038 ATCACAT
1 ATCACAT
18392045 CGGCTATTAG
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
22 7 0.11
23 8 0.13
24 8 0.13
25 39 0.63
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:18392061 original size:119 final size:119
Alignment explanation
Indices: 18391895--18392138 Score: 461
Period size: 119 Copynumber: 2.1 Consensus size: 119
18391885 CTCGGCCCTG
*
18391895 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGTCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
18391960 ACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
*
18392014 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
18392079 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
18392133 TCACAT
1 TCACAT
18392139 CGGCCATTAG
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 122 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (119 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
Found at i:18392064 original size:47 final size:47
Alignment explanation
Indices: 18392013--18392185 Score: 294
Period size: 47 Copynumber: 3.7 Consensus size: 47
18392003 TTTCACATTC
*
18392013 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
18392060 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
18392107 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
* * *
18392154 ATCTCATATATGCA-TGTTCACATCCATCACAT
1 ATCACATATATACACT-TTCACATTCATCACAT
18392186 AGAATCCTAA
Statistics
Matches: 121, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.01
47 120 0.99
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:18392121 original size:166 final size:166
Alignment explanation
Indices: 18391847--18392186 Score: 538
Period size: 166 Copynumber: 2.0 Consensus size: 166
18391837 TTCGGGACTT
* * * * *
18391847 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACACTTT
1 ATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTT
* *
18391912 CACATTCATCACATCGGCCATTAGGTCTTATCACATATATACACTTTCACATTCATCACATTGGC
66 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
*
18391977 CATTAGGCCTTATCACATATATACACT-TTCACATTC
131 CATTAGGCCTTATCACATATATACA-TGTTCACATCC
* * * *
18392013 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTT
1 ATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTT
18392078 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
66 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
* *
18392143 CATTAGGCCTTATCTCATATATGCATGTTCACATCC
131 CATTAGGCCTTATCACATATATACATGTTCACATCC
18392179 ATCACATA
1 ATCACATA
18392187 GAATCCTAAA
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 1 0.01
166 158 0.99
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (166 bp):
ATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTT
CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
CATTAGGCCTTATCACATATATACATGTTCACATCC
Found at i:18397438 original size:15 final size:15
Alignment explanation
Indices: 18397420--18397462 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
18397410 GCTCTACTTT
*
18397420 TTATTGCTATTATCA
1 TTATTACTATTATCA
** *
18397435 TTATTTTTATTATTA
1 TTATTACTATTATCA
18397450 TTATTACTATTAT
1 TTATTACTATTAT
18397463 ATAATAGTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTACTATTATCA
Found at i:18397828 original size:3 final size:3
Alignment explanation
Indices: 18397820--18397864 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
18397810 CTATCAATAC
* *
18397820 TAT TAT TAT TA- TAT TGT TAT TAT TAC TAT TA- TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18397865 CTTTACCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18397849 original size:20 final size:19
Alignment explanation
Indices: 18397820--18397863 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
18397810 CTATCAATAC
* *
18397820 TATTATTATTATATTGTTAT
1 TATTACTATTATATTATT-T
18397840 TATTACTATTATATTATTT
1 TATTACTATTATATTATTT
18397859 TATTA
1 TATTA
18397864 TCTTTACCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTACTATTATATTATTT
Found at i:18399901 original size:51 final size:51
Alignment explanation
Indices: 18399825--18399924 Score: 200
Period size: 51 Copynumber: 2.0 Consensus size: 51
18399815 TTGTTTGGGA
18399825 TTTGTTTTAAAATATAATAAATTATCTCATACCCTAGGTAAAAAAAATTTT
1 TTTGTTTTAAAATATAATAAATTATCTCATACCCTAGGTAAAAAAAATTTT
18399876 TTTGTTTTAAAATATAATAAATTATCTCATACCCTAGGTAAAAAAAATT
1 TTTGTTTTAAAATATAATAAATTATCTCATACCCTAGGTAAAAAAAATT
18399925 ATGTAAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (51 bp):
TTTGTTTTAAAATATAATAAATTATCTCATACCCTAGGTAAAAAAAATTTT
Found at i:18403064 original size:25 final size:25
Alignment explanation
Indices: 18403030--18403079 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
18403020 TGTGGATGTG
18403030 TAAGAGAGGACACTCTCCATATTCT
1 TAAGAGAGGACACTCTCCATATTCT
18403055 TAAGAGAGGACACTCTCCATATTCT
1 TAAGAGAGGACACTCTCCATATTCT
18403080 CCGTGATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (25 bp):
TAAGAGAGGACACTCTCCATATTCT
Found at i:18405680 original size:5 final size:5
Alignment explanation
Indices: 18405670--18405724 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
18405660 ATAGAAGATA
* *
18405670 TTATT TTATT TTGTT TTATT AT-TT TTATT TT-TAT TTATTT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T TTA-TT TTATT TTATT
18405720 TTATT
1 TTATT
18405725 ATTTTAGGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.10
5 33 0.79
6 4 0.10
7 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:18405699 original size:6 final size:6
Alignment explanation
Indices: 18405673--18405721 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
18405663 GAAGATATTA
18405673 TTTTAT TTTGT-T TTATTAT TTTTAT TTTTA- -TTTAT TTTTA- TTTTAT
1 TTTTAT TTT-TAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
18405719 TTT
1 TTT
18405722 ATTATTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 23 0.62
7 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:18408311 original size:18 final size:18
Alignment explanation
Indices: 18408285--18408329 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
18408275 CCCGTACCTG
*
18408285 ACACAAGTCGCGGCCACA
1 ACACAAGTCGCGCCCACA
* *
18408303 ACACTAGTCGCGCCCACT
1 ACACAAGTCGCGCCCACA
*
18408321 ACGCAAGTC
1 ACACAAGTC
18408330 AAGATAAGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.40, G:0.20, T:0.11
Consensus pattern (18 bp):
ACACAAGTCGCGCCCACA
Found at i:18422270 original size:13 final size:14
Alignment explanation
Indices: 18422221--18422270 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
18422211 AAGAAATATG
18422221 AAGAAGAAGCAGG-
1 AAGAAGAAGCAGGA
* *
18422234 AAGAAGTAGCAGAAA
1 AAGAAGAAGCAG-GA
*
18422249 AACAAGAAG-AGGA
1 AAGAAGAAGCAGGA
18422262 AAGAAGAAG
1 AAGAAGAAG
18422271 GGAAACTGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 20 0.69
14 2 0.07
15 7 0.24
ACGTcount: A:0.60, C:0.06, G:0.32, T:0.02
Consensus pattern (14 bp):
AAGAAGAAGCAGGA
Found at i:18423864 original size:22 final size:22
Alignment explanation
Indices: 18423831--18423877 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
18423821 AATCATGGTA
*
18423831 TTACAATG-AAAATTTGGGATTT
1 TTACAATGAAAAATCT-GGATTT
18423853 TTACAA-GAAAAAATCTGGATTT
1 TTACAATG-AAAAATCTGGATTT
18423875 TTA
1 TTA
18423878 TGTAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.05
22 15 0.68
23 6 0.27
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (22 bp):
TTACAATGAAAAATCTGGATTT
Found at i:18423910 original size:13 final size:13
Alignment explanation
Indices: 18423892--18423927 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18423882 GAAAAATAAG
18423892 TTTTTCTTTGTTT
1 TTTTTCTTTGTTT
*
18423905 TTTTTCTTTCTTT
1 TTTTTCTTTGTTT
*
18423918 TTTTTTTTTG
1 TTTTTCTTTG
18423928 AGTTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTGTTT
Found at i:18423926 original size:17 final size:17
Alignment explanation
Indices: 18423894--18423925 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18423884 AAAATAAGTT
18423894 TTTCTTTGTTTTTTTTC
1 TTTCTTTGTTTTTTTTC
18423911 TTTCTTT-TTTTTTTT
1 TTTCTTTGTTTTTTTT
18423926 TGAGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTCTTTGTTTTTTTTC
Found at i:18430812 original size:24 final size:24
Alignment explanation
Indices: 18430770--18430831 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
18430760 TAAATTTTTT
*
18430770 TTAAAAATT-TAAAAGAAAA-ATA
1 TTAAAAATTATAAAAGAAAAGAGA
* *
18430792 TATAAAAATTATAATATAAAAGAGA
1 T-TAAAAATTATAAAAGAAAAGAGA
*
18430817 TTATAAATTATAAAA
1 TTAAAAATTATAAAA
18430832 ATAAATGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 8 0.25
24 20 0.62
25 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (24 bp):
TTAAAAATTATAAAAGAAAAGAGA
Found at i:18433283 original size:18 final size:17
Alignment explanation
Indices: 18433245--18433283 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
18433235 TGTTTGAAAA
18433245 TTTTAATTAATTAAATTT
1 TTTTAATTAA-TAAATTT
18433263 TTTTAATTAA-AAATTT
1 TTTTAATTAATAAATTT
18433279 ATTTT
1 -TTTT
18433284 CATCCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTAATAAATTT
Found at i:18435473 original size:18 final size:19
Alignment explanation
Indices: 18435450--18435494 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
18435440 CTGCAACAGT
18435450 AAAAAAAA-ACTGAAAAAG
1 AAAAAAAACACTGAAAAAG
*
18435468 AAAAAAAACACTGAAAACG
1 AAAAAAAACACTGAAAAAG
18435487 AAAAAAAA
1 AAAAAAAA
18435495 TAAAAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (19 bp):
AAAAAAAACACTGAAAAAG
Found at i:18435971 original size:147 final size:146
Alignment explanation
Indices: 18435639--18436074 Score: 635
Period size: 146 Copynumber: 3.0 Consensus size: 146
18435629 ATAAGTAAAA
* * * * * *
18435639 TATTTTCGTATATTATTTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* * *
18435704 TTTTTTATATTAATTTAATAAATAACCCTGATTTT-GACACTTTCTTCGTATTTTTTTCGTATCT
66 TTTTTTATATT-TTTTAATAAATAACCCTGATTTTAG-CACTTTATTCGTATTTTTTTTGTATCT
18435768 TATTTTTT-AAAATATAT
129 TATTTTTTAAAAATATAT
* *
18435785 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
18435850 TTTTTTATATTTTTTCAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTTGTATCTT
66 TTTTTTATATTTTTT-AATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTTGTATCTT
18435915 ATTTTTTAAAAATATAT
130 ATTTTTTAAAAATATAT
* *
18435932 TATTTTCATATTTTATTTCTTTATATTATTTTAGTACATAATATTTCAAATGTATTATTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* *
18435997 TTTTTTATATTTTTTTAATAAATAACCTTGA-TTTAGCACTTTATTTGTATTTTTATTTTCGTAT
66 TTTTTTATA-TTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA-TTTT-TTTT-GTAT
*
18436061 ATTATTTTATTAAA
127 CTTATTTT-TTAAA
18436075 TTAATATAAT
Statistics
Matches: 264, Mismatches: 18, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
145 3 0.01
146 137 0.52
147 98 0.37
148 10 0.04
149 11 0.04
150 5 0.02
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (146 bp):
TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
TTTTTTATATTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTTGTATCTTA
TTTTTTAAAAATATAT
Found at i:18440882 original size:13 final size:13
Alignment explanation
Indices: 18440864--18440888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18440854 AGCCTATACT
18440864 TTATTTTTTGTTA
1 TTATTTTTTGTTA
18440877 TTATTTTTTGTT
1 TTATTTTTTGTT
18440889 GTTTTGTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTATTTTTTGTTA
Found at i:18448565 original size:7 final size:7
Alignment explanation
Indices: 18448553--18448644 Score: 71
Period size: 7 Copynumber: 12.9 Consensus size: 7
18448543 AAAGTAATTT
18448553 AATAATA
1 AATAATA
18448560 AATAATA
1 AATAATA
18448567 AATAATA
1 AATAATA
18448574 AATAAT-
1 AATAATA
*
18448580 -TTAATCA
1 AATAAT-A
* **
18448587 TATTTTA
1 AATAATA
18448594 ATATAATA
1 A-ATAATA
* *
18448602 ATTATTA
1 AATAATA
*
18448609 AAGTAATTT
1 AA-TAA-TA
18448618 AATAATA
1 AATAATA
18448625 AATAATA
1 AATAATA
18448632 AATAATA
1 AATAATA
18448639 AATAAT
1 AATAAT
18448645 TTAATCATAT
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
5 4 0.06
7 47 0.71
8 12 0.18
9 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (7 bp):
AATAATA
Found at i:18448593 original size:65 final size:65
Alignment explanation
Indices: 18448523--18448731 Score: 333
Period size: 65 Copynumber: 3.3 Consensus size: 65
18448513 TTGTTATTAA
18448523 ATTTTAATATAATAATTATTAAAGTAATTTAATAATAAATAATAAATAATAAATAATTTAATCAT
1 ATTTTAATATAATAATTATTAAAGTAATTTAATAATAAATAATAAATAATAAATAATTTAATCAT
18448588 ATTTTAATATAATAATTATTAAAGTAATTTAATAATAAATAATAAATAATAAATAATTTAATCAT
1 ATTTTAATATAATAATTATTAAAGTAATTTAATAATAAATAATAAATAATAAATAATTTAATCAT
* * *
18448653 ATTTTAATATAATAATTATTAAATATAATTTGATAA-AAATAA-AAAT-AT--ATAATTTAATAA
1 ATTTTAATATAATAATTATTAAA-GTAATTTAATAATAAATAATAAATAATAAATAATTTAATCA
18448713 T
65 T
18448714 ATTTTAA-AT-ATAATTATT
1 ATTTTAATATAATAATTATT
18448732 TTTATATCAC
Statistics
Matches: 140, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
59 9 0.06
60 2 0.01
61 19 0.14
63 2 0.01
64 4 0.03
65 94 0.67
66 10 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (65 bp):
ATTTTAATATAATAATTATTAAAGTAATTTAATAATAAATAATAAATAATAAATAATTTAATCAT
Found at i:18448688 original size:24 final size:24
Alignment explanation
Indices: 18448661--18448728 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
18448651 ATATTTTAAT
*
18448661 ATAATAATTATTAAATATAATTTG
1 ATAATAATTATTAAATATAATTTA
* **
18448685 ATAA-AAATAAAAATATATAATTTA
1 ATAATAATTATTAA-ATATAATTTA
18448709 ATAAT-ATT-TTAAATATAATT
1 ATAATAATTATTAAATATAATT
18448729 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
22 8 0.23
23 8 0.23
24 19 0.54
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAATAATTATTAAATATAATTTA
Found at i:18450341 original size:2 final size:2
Alignment explanation
Indices: 18450330--18450360 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18450320 AAAACTAATC
18450330 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18450361 AAAGTACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18451454 original size:27 final size:27
Alignment explanation
Indices: 18451375--18451447 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
18451365 CCCAAATTAA
*
18451375 TACTTATGATTTTTTGTCCCTGATTGG
1 TACTTATGGTTTTTTGTCCCTGATTGG
*
18451402 TATTTATGGTTTTTTGTCCCTGATTGG
1 TACTTATGGTTTTTTGTCCCTGATTGG
18451429 TACTTATGGTTTTTTGTCC
1 TACTTATGGTTTTTTGTCC
18451448 TAGATTGACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.55
Consensus pattern (27 bp):
TACTTATGGTTTTTTGTCCCTGATTGG
Found at i:18451735 original size:16 final size:16
Alignment explanation
Indices: 18451714--18451747 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18451704 AATTTTCATT
18451714 ATTTTCTACCTCTTTC
1 ATTTTCTACCTCTTTC
*
18451730 ATTTTCTACCTTTTTC
1 ATTTTCTACCTCTTTC
18451746 AT
1 AT
18451748 CGGTTCATCC
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:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTCTACCTCTTTC
Found at i:18459498 original size:26 final size:24
Alignment explanation
Indices: 18459455--18459503 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
18459445 TATCATTTTT
* *
18459455 TATTTGTTTTTATGTTTTTAAATG
1 TATTTGTTTTTATATTTTAAAATG
18459479 TATTTGATTTATTATATTTTAAAAT
1 TATTTG-TTT-TTATATTTTAAAAT
18459504 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (24 bp):
TATTTGTTTTTATATTTTAAAATG
Found at i:18462058 original size:53 final size:53
Alignment explanation
Indices: 18461903--18462067 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
18461893 GACGAAAAAT
* **
18461903 ATGTGATAAGTGTG-C-CCGTTTAAGA-CATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
18461954 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
18462007 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
18462061 TATGTGA
1 -ATGTGA
18462068 ACCGTGTAAG
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
50 4 0.04
51 10 0.10
52 10 0.10
53 71 0.70
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:18469546 original size:53 final size:53
Alignment explanation
Indices: 18469390--18469555 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
18469380 GACGAAAAAT
* **
18469390 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
18469442 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
18469495 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
18469549 TATGTGA
1 -ATGTGA
18469556 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:18471208 original size:253 final size:253
Alignment explanation
Indices: 18470760--18471261 Score: 905
Period size: 253 Copynumber: 2.0 Consensus size: 253
18470750 CAAAACATAG
* *
18470760 TATACTTAGGCAACCAAAACACCCACATTTGTGACCAACACATGCCAATACAATTGCAACATCTA
1 TATACTTAGGCAACCAAAACACCCACAATTATGACCAACACATGCCAATACAATTGCAACATCTA
*
18470825 TCATACTCACAACATTTATTATGCCCTAAATCAATCATGCAAATTGCACATTCATTAAGCCTCAA
66 TCATACTCACAACATTTATTATACCCTAAATCAATCATGCAAATTGCACATTCATTAAGCCTCAA
*
18470890 TTTTCTACTTTCAAGACACCTAATTGTGCACAAATTTATCATCTCATCAATATATCACATTTCCA
131 TTTACTACTTTCAAGACACCTAATTGTGCACAAATTTATCATCTCATCAATATATCACATTTCCA
* * *
18470955 AACATTTCACATTCATGTTATGAATCACATTCTATCATTCACCAAGCATACCATATAA
196 AACAGTTCACATTCATGCTATGAATCACATTCCATCATTCACCAAGCATACCATATAA
18471013 TATACTTAGGCAACCAAAACACCCACAATTATGACCAACACATGCCAATACAATTGCAACATCTA
1 TATACTTAGGCAACCAAAACACCCACAATTATGACCAACACATGCCAATACAATTGCAACATCTA
* *
18471078 TCATACTCACAACATTTATTATACCCTAAATCAATCATGCAAATTTCACATTCATTAAGCCTCAG
66 TCATACTCACAACATTTATTATACCCTAAATCAATCATGCAAATTGCACATTCATTAAGCCTCAA
*
18471143 TTTACTACTTTTAAGACACCTAATTGTGCACAAATTTATCATCTCATCAATATATCACATTTCCA
131 TTTACTACTTTCAAGACACCTAATTGTGCACAAATTTATCATCTCATCAATATATCACATTTCCA
*
18471208 AACAGTTCATATTCATGCTATGAATCACATTCCATCATTCACCAAGCATACCAT
196 AACAGTTCACATTCATGCTATGAATCACATTCCATCATTCACCAAGCATACCAT
18471262 GACTATATCA
Statistics
Matches: 238, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
253 238 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.30
Consensus pattern (253 bp):
TATACTTAGGCAACCAAAACACCCACAATTATGACCAACACATGCCAATACAATTGCAACATCTA
TCATACTCACAACATTTATTATACCCTAAATCAATCATGCAAATTGCACATTCATTAAGCCTCAA
TTTACTACTTTCAAGACACCTAATTGTGCACAAATTTATCATCTCATCAATATATCACATTTCCA
AACAGTTCACATTCATGCTATGAATCACATTCCATCATTCACCAAGCATACCATATAA
Found at i:18473948 original size:20 final size:21
Alignment explanation
Indices: 18473927--18473966 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18473917 TATAGATGCC
18473927 TTGTTATAGGTATCGATACCTT
1 TTGTTATAGGTATCGATACC-T
*
18473949 TTGTTTTA-GTATCGATAC
1 TTGTTATAGGTATCGATAC
18473967 TTGCCCCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (21 bp):
TTGTTATAGGTATCGATACCT
Found at i:18482562 original size:18 final size:17
Alignment explanation
Indices: 18482534--18482581 Score: 78
Period size: 18 Copynumber: 2.8 Consensus size: 17
18482524 TACAATATCA
18482534 ATTAATAAAATATTATT
1 ATTAATAAAATATTATT
*
18482551 ACTTATTAAAATATTATT
1 A-TTAATAAAATATTATT
18482569 ATTAATAAAATAT
1 ATTAATAAAATAT
18482582 CATTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAATAAAATATTATT
Found at i:18486743 original size:14 final size:14
Alignment explanation
Indices: 18486724--18486754 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18486714 ACTAATGAAG
18486724 TCCATCTTATTCAC
1 TCCATCTTATTCAC
18486738 TCCATCTTATTCAC
1 TCCATCTTATTCAC
18486752 TCC
1 TCC
18486755 TACTTCCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (14 bp):
TCCATCTTATTCAC
Found at i:18488121 original size:47 final size:47
Alignment explanation
Indices: 18488064--18488240 Score: 220
Period size: 47 Copynumber: 3.8 Consensus size: 47
18488054 TGGTTGAACA
* *
18488064 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
18488111 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
*
18488158 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
*
18488204 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18488241 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 9, Indels: 17
0.81 0.06 0.12
Matches are distributed among these distances:
43 2 0.02
44 5 0.04
45 1 0.01
46 39 0.35
47 58 0.51
48 3 0.03
50 5 0.04
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:18488179 original size:94 final size:93
Alignment explanation
Indices: 18488062--18488232 Score: 297
Period size: 94 Copynumber: 1.8 Consensus size: 93
18488052 GATGGTTGAA
* * *
18488062 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGTGAAATGTCCGAACTCGTTGAGT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACGTCCGAACTCGTTGAGT
18488127 TGAGTCCGAGTTCGTGAGATGTAACTAGG
65 TGAGTCCGAGTTCGTGAGATGTAACTAGG
*
18488156 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
18488221 GAGTCCGAGTTC
66 GAGTCCGAGTTC
18488233 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 31 0.42
94 42 0.58
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAGG
Found at i:18492678 original size:8 final size:8
Alignment explanation
Indices: 18492665--18492697 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
18492655 AATTTAATAA
18492665 ATAATATT
1 ATAATATT
18492673 ATAATATT
1 ATAATATT
18492681 ATAATA-T
1 ATAATATT
18492688 ATAAATATT
1 AT-AATATT
18492697 A
1 A
18492698 GCCCACCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 3 0.13
8 18 0.78
9 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
ATAATATT
Found at i:18493043 original size:23 final size:23
Alignment explanation
Indices: 18492990--18493049 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
18492980 AATGTTCGGT
* * **
18492990 GTCCACCAGTCACATCGTCTGGC
1 GTCCACCAGTCACACCATCCAGC
* *
18493013 ATCTACCAGTCACACCATCCAGC
1 GTCCACCAGTCACACCATCCAGC
18493036 GTCCACCAAGTCAC
1 GTCCACC-AGTCAC
18493050 CATCTTAGTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.25, C:0.42, G:0.15, T:0.18
Consensus pattern (23 bp):
GTCCACCAGTCACACCATCCAGC
Found at i:18497023 original size:17 final size:18
Alignment explanation
Indices: 18496996--18497030 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
18496986 ATTATGTAGT
18496996 GATTCAATACTTTAATTC
1 GATTCAATACTTTAATTC
18497014 GATT-AATACTTTAATTC
1 GATTCAATACTTTAATTC
18497031 AGGTAATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (18 bp):
GATTCAATACTTTAATTC
Found at i:18498141 original size:20 final size:21
Alignment explanation
Indices: 18498102--18498142 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18498092 CTTGTCGACA
*
18498102 ATACTGGCAGCTTGTTTGCAT
1 ATACTGGCAGCTTATTTGCAT
*
18498123 ATACTGGCA-TTTATTTGCAT
1 ATACTGGCAGCTTATTTGCAT
18498143 TATTGTACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (21 bp):
ATACTGGCAGCTTATTTGCAT
Found at i:18499538 original size:129 final size:129
Alignment explanation
Indices: 18499308--18499558 Score: 416
Period size: 129 Copynumber: 1.9 Consensus size: 129
18499298 TTAATACTGT
18499308 AAATAAATTATATTATTTGGAGAGTATTATATTTTTTAAATAAAAATATAAAAATAATAAGATTT
1 AAATAAATTATATTATTTGGAGAGTATTATATTTTTTAAATAAAAATATAAAAATAATAAGATTT
* *
18499373 AAATTTAAAGCACTGTATTTTGATGATTTGTACTTTACCATTTCAACTAGATTCTTATTTTATA
66 AAATTTAAAACACTGTATTTTGAAGATTTGTACTTTACCATTTCAACTAGATTCTTATTTTATA
* *
18499437 AAATAAATTATATTATTTTGAGAGTGTTATA-TTTTTACACA-AAAAATATAAAAATAATAAGAT
1 AAATAAATTATATTATTTGGAGAGTATTATATTTTTTA-A-ATAAAAATATAAAAATAATAAGAT
* *
18499500 TTAAGTTTAAAACACTGTATTTTGAAGATTTGTACTTTACCATTTCAACTGGATTCTTA
64 TTAAATTTAAAACACTGTATTTTGAAGATTTGTACTTTACCATTTCAACTAGATTCTTA
18499559 CTTATTTTTA
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 6 0.05
129 107 0.94
130 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (129 bp):
AAATAAATTATATTATTTGGAGAGTATTATATTTTTTAAATAAAAATATAAAAATAATAAGATTT
AAATTTAAAACACTGTATTTTGAAGATTTGTACTTTACCATTTCAACTAGATTCTTATTTTATA
Found at i:18526195 original size:21 final size:20
Alignment explanation
Indices: 18526155--18526196 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
18526145 ATTATGAAAA
*
18526155 AATATAAAAAAAATTGAGGG
1 AATATAAAAAAAATTAAGGG
*
18526175 AATATAAAAAAATTATAAGGG
1 AATATAAAAAAAAT-TAAGGG
18526196 A
1 A
18526197 GTAACAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (20 bp):
AATATAAAAAAAATTAAGGG
Found at i:18530576 original size:18 final size:18
Alignment explanation
Indices: 18530538--18530583 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
18530528 TTTCTTTTAC
18530538 ATTATTATTTTTTAAACT
1 ATTATTATTTTTTAAACT
*
18530556 ATTATATATTTTTTATA-T
1 ATTAT-TATTTTTTAAACT
18530574 ATTATGTATT
1 ATTAT-TATT
18530584 CTAAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTATTATTTTTTAAACT
Found at i:18530590 original size:61 final size:60
Alignment explanation
Indices: 18530505--18530623 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 60
18530495 GTTTAAATTA
* *
18530505 TTTTATATGTTATTTACTTCAAATTTCTTTTACATTATTATTT-TTTAAACTATTATATATT
1 TTTTATATATTATGTACTTCAAATTTCTTTT-CA-TATTATTTATTTAAACTATTATATATT
* *
18530566 TTTTATATATTATGTA-TTCTAAATTTCTTTTTATATTATTTAGTTTAAACTTTTATAT
1 TTTTATATATTATGTACTTC-AAATTTCTTTTCATATTATTTA-TTTAAACTATTATAT
18530624 GTCATTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
59 8 0.16
60 4 0.08
61 39 0.76
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (60 bp):
TTTTATATATTATGTACTTCAAATTTCTTTTCATATTATTTATTTAAACTATTATATATT
Found at i:18534384 original size:19 final size:19
Alignment explanation
Indices: 18534360--18534407 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18534350 ACGCCTCTTT
*
18534360 TTACA-TTCATTCATTTGCA
1 TTACATTTCA-TCATATGCA
18534379 TTACATTTCATCATATGCA
1 TTACATTTCATCATATGCA
*
18534398 TTAAATTTCA
1 TTACATTTCA
18534408 CGAAAAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (19 bp):
TTACATTTCATCATATGCA
Found at i:18542576 original size:44 final size:44
Alignment explanation
Indices: 18542525--18542635 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
18542515 AATCACCATG
*
18542525 ACGAATCTTGTCTCCCTGAAGTTGTAGTGAAACAGATTGAAGTG
1 ACGAATCTTGTCTCCCTGAAGTTGTAGTGAAACAGATTGAAGTC
* * * *
18542569 GCGAATCTTGTCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGTC
1 ACGAATCTTGTCTCCCTGAAGTTGTAGTGAAACAGATTGAAGTC
* *
18542613 ACGAATCTTATCTCTCTGAAGTT
1 ACGAATCTTGTCTCCCTGAAGTT
18542636 ACAGTAGAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (44 bp):
ACGAATCTTGTCTCCCTGAAGTTGTAGTGAAACAGATTGAAGTC
Found at i:18542720 original size:45 final size:45
Alignment explanation
Indices: 18542670--18543290 Score: 210
Period size: 45 Copynumber: 13.7 Consensus size: 45
18542660 TATTACAGAG
*
18542670 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAACTCAATATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* * * ** *
18542715 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-TAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* ** ** * *
18542759 TCCTATAC-CTATGAAGTTGCAGTAG-GTTGGA-TCAAGTTACCATGGCGAA
1 TCTTAT-CTCCCTGAAGTTGCAGTAGAG-CAGACTCAA--T---ATAGCAAA
* * * * *
18542808 TCTCATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AGTCA-CAGAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATA-T-AGCA-AA
*
18542853 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* * * * * ** *
18542898 TCTTATCTCTCTAAAGTTGCAGTAGAGTAGATTAAAGCTA-TAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* * * ** * *
18542942 TCCTATAC-CTCTGGAGTTGCAGTAG-GTTGGA-TCAAGTTACCATGGCGAA
1 TCTTAT-CTCCCTGAAGTTGCAGTAGAG-CAGACTCAA--T---ATAGCAAA
* * * *
18542991 TCTCATCTCCCTGAAGTTACAGTGGAGCAGA-T---TAAAGTCATAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAG-CA-AA
* * * *
18543034 GTCTTATTTCCCT-AA-ATGTAGTGGAGCAGACTCAATATAGCAAA
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* * * ** *
18543078 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-TAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* * ** *
18543122 TCCTATAC-CTCTGAAGTTGCAGTAG-GTTGGA-TCAAGTTACCGTGGCAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTAGAG-CAGACTCAA--TA---TAGCAAA
* * * * * **
18543171 TCTTATCTCCCTAAAGTTACAGTGGAGCA-AATTAA-AGTCA-CAGG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATA-T-AGCAAA
* * * *
18543215 TCTTATCTCCCTGATGTTACAGTGGAGCAGACTCAATATAGGAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
* *
18543260 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
18543291 TTAAAGCTAT
Statistics
Matches: 416, Mismatches: 110, Indels: 100
0.66 0.18 0.16
Matches are distributed among these distances:
41 2 0.00
42 13 0.03
43 28 0.07
44 128 0.31
45 152 0.37
46 12 0.03
47 1 0.00
48 7 0.02
49 70 0.17
50 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAATATAGCAAA
Found at i:18542868 original size:183 final size:183
Alignment explanation
Indices: 18542664--18543371 Score: 1145
Period size: 183 Copynumber: 3.9 Consensus size: 183
18542654 GCTACATATT
* * *
18542664 ACAGAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAAACTCAATATAGCAAATCTTATCTCTCTGA
1 ACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTAA
*
18542729 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTATGAAGTTGCAGTAGGTTGGATCAA
66 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
*
18542794 GTTACCATGGCGAATCTCATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTC
131 GTTACCATGGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTC
18542847 ACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTAA
1 ACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTAA
* *
18542912 AGTTGCAGTAGAGTAGATTAAAGCTATAAATCCTATACCTCTGGAGTTGCAGTAGGTTGGATCAA
66 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
*
18542977 GTTACCATGGCGAATCTCATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTC
131 GTTACCATGGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTC
* * * * *
18543030 ATA-AGTCTTATTTCCCT-AA-ATGTAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTGA
1 ACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTAA
18543092 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
66 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
* * * *
18543157 GTTACCGTGGCAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAATTAAAGTC
131 GTTACCATGGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTC
* * *
18543210 ACAG-GTCTTATCTCCCTGATGTTACAGTGGAGCAGACTCAATATAGGAAATCTTATCTCTCTAA
1 ACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTAA
* **
18543274 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTTTGAAGTTGCAGTAGGTCAGATCAA
66 AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
* * *
18543339 ATCTATCATGGCGAATCTTATCTCCCTAAAGTT
131 GT-TACCATGGCGAATCTCATCTCCCTAAAGTT
18543372 TTAGTGGACT
Statistics
Matches: 488, Mismatches: 33, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
180 165 0.34
181 3 0.01
182 114 0.23
183 206 0.42
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (183 bp):
ACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATATAGCAAATCTTATCTCTCTAA
AGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
GTTACCATGGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTC
Found at i:18543365 original size:363 final size:363
Alignment explanation
Indices: 18542694--18543371 Score: 1169
Period size: 363 Copynumber: 1.9 Consensus size: 363
18542684 AGTTGCAGTA
18542694 GAGCAAACTCAATATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAA
1 GAGCAAACTCAATATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAA
* *
18542759 TCCTATACCTATGAAGTTGCAGTAGGTTGGATCAAGTTACCATGGCGAATCTCATCTCCCTGAAG
66 TCCTATACCTATGAAGTTGCAGTAGGTTGGATCAAGTTACCATGGCAAATCTCATCTCCCTAAAG
* *
18542824 TTACAGTGGAGCAGATTAAAGTCACAGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAA
131 TTACAGTGGAGCAAATTAAAGTCACAGAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTCAA
*
18542889 TATAGCAAATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATTAAAGCTATAAATCCTATACCTCT
196 TATAGCAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCT
* ** * *
18542954 GGAGTTGCAGTAGGTTGGATCAAGTTACCATGGCGAATCTCATCTCCCTGAAGTTACAGTGGAGC
261 GAAGTTGCAGTAGGTCAGATCAAATTACCATGGCGAATCTCATCTCCCTAAAGTTACAGTGGAGC
18543019 AGATTAAAGTCATAAGTCTTATTTCCCTAAATGTAGTG
326 AGATTAAAGTCATAAGTCTTATTTCCCTAAATGTAGTG
*
18543057 GAGCAGACTCAATATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAA
1 GAGCAAACTCAATATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAA
* * *
18543122 TCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAAGTTACCGTGGCAAATCTTATCTCCCTAAAG
66 TCCTATACCTATGAAGTTGCAGTAGGTTGGATCAAGTTACCATGGCAAATCTCATCTCCCTAAAG
*
18543187 TTACAGTGGAGCAAATTAAAGTCACAG-GTCTTATCTCCCTGATGTTACAGTGGAGCAGACTCAA
131 TTACAGTGGAGCAAATTAAAGTCACAGAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTCAA
* *
18543251 TATAGGAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTTT
196 TATAGCAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCT
* *
18543316 GAAGTTGCAGTAGGTCAGATCAAATCTATCATGGCGAATCTTATCTCCCTAAAGTT
261 GAAGTTGCAGTAGGTCAGATCAAAT-TACCATGGCGAATCTCATCTCCCTAAAGTT
18543372 TTAGTGGACT
Statistics
Matches: 295, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
362 118 0.40
363 177 0.60
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (363 bp):
GAGCAAACTCAATATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAA
TCCTATACCTATGAAGTTGCAGTAGGTTGGATCAAGTTACCATGGCAAATCTCATCTCCCTAAAG
TTACAGTGGAGCAAATTAAAGTCACAGAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTCAA
TATAGCAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCCTATACCTCT
GAAGTTGCAGTAGGTCAGATCAAATTACCATGGCGAATCTCATCTCCCTAAAGTTACAGTGGAGC
AGATTAAAGTCATAAGTCTTATTTCCCTAAATGTAGTG
Found at i:18545141 original size:62 final size:61
Alignment explanation
Indices: 18545019--18545141 Score: 160
Period size: 61 Copynumber: 2.0 Consensus size: 61
18545009 TCGGTTTAAA
* *
18545019 TTTTTTTATATGTTATTTACTTCAAATTTCTTTTACATTATTATTTTTTAAACTATTATAT
1 TTTTTTTATATATTATGTACTTCAAATTTCTTTTACATTATTATTTTTTAAACTATTATAT
** *
18545080 TTTTTTTATATATTATGTA-TTCTAAATTTCTTTTTTA-TATTATTTAGTTTAAACTTTTATAT
1 TTTTTTTATATATTATGTACTTC-AAATTTCTTTTACATTATTATTT--TTTAAACTATTATAT
18545142 GTCATTTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 11 0.20
61 29 0.54
62 14 0.26
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (61 bp):
TTTTTTTATATATTATGTACTTCAAATTTCTTTTACATTATTATTTTTTAAACTATTATAT
Found at i:18547611 original size:15 final size:15
Alignment explanation
Indices: 18547572--18547608 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
18547562 GCCACGAAAC
*
18547572 TGAAAAA-TAAGTAT
1 TGAAAAATTAAATAT
18547586 TGAAAAATTAAATAT
1 TGAAAAATTAAATAT
18547601 T-AAAAATT
1 TGAAAAATT
18547609 TAATTACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (15 bp):
TGAAAAATTAAATAT
Found at i:18555434 original size:4 final size:4
Alignment explanation
Indices: 18555425--18555472 Score: 64
Period size: 4 Copynumber: 12.2 Consensus size: 4
18555415 AACTTGAGCC
*
18555425 TTTA TTTA TTTA TTTA TTT- TTT- TTCA TTTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
18555472 T
1 T
18555473 GTACAAGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 5 0.12
4 32 0.80
5 3 0.08
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:18558055 original size:49 final size:49
Alignment explanation
Indices: 18557987--18558102 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 49
18557977 TTTTCTTTTC
* * * * *
18557987 TTTTCTTTTTTTCACTTTTCCTTGT-GGCTAT-TTAGGCC-TTCTTGTCCAT
1 TTTTCTTTTTTT-TCTTTTTCTTGTGGGCT-TGTTAGGCCATTC-GGCCCAA
*
18558036 TTTTCTTTTTTTTCTTTTTCTTTTGGGCTTGTTAGGCCATTCGGCCCAA
1 TTTTCTTTTTTTTCTTTTTCTTGTGGGCTTGTTAGGCCATTCGGCCCAA
*
18558085 TTTTCTTTCTTTTCTTTT
1 TTTTCTTTTTTTTCTTTT
18558103 CTTTTTCCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
48 10 0.18
49 44 0.77
50 3 0.05
ACGTcount: A:0.07, C:0.21, G:0.12, T:0.60
Consensus pattern (49 bp):
TTTTCTTTTTTTTCTTTTTCTTGTGGGCTTGTTAGGCCATTCGGCCCAA
Found at i:18560137 original size:20 final size:20
Alignment explanation
Indices: 18560112--18560152 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
18560102 TAATTGCTTT
*
18560112 GGGCAACATTCAAAGTCTTA
1 GGGCAACATCCAAAGTCTTA
18560132 GGGCAACATCCAAAGTCTTA
1 GGGCAACATCCAAAGTCTTA
18560152 G
1 G
18560153 ACGCATAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
GGGCAACATCCAAAGTCTTA
Found at i:18562026 original size:9 final size:9
Alignment explanation
Indices: 18562012--18562036 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18562002 TTTGCATCAT
18562012 TTTCTCTTA
1 TTTCTCTTA
18562021 TTTCTCTTA
1 TTTCTCTTA
18562030 TTTCTCT
1 TTTCTCT
18562037 ACAGTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTCTCTTA
Found at i:18572766 original size:18 final size:20
Alignment explanation
Indices: 18572739--18572787 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
18572729 TGAAATATAA
* *
18572739 TAAAATAATAAAATATCTCAT
1 TAAAATAAT-ATATATCTAAT
18572760 TAAAATAATATATATCTAAT
1 TAAAATAATATATATCTAAT
18572780 T-AAATAAT
1 TAAAATAAT
18572788 CATAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 7 0.27
20 10 0.38
21 9 0.35
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATAATATATATCTAAT
Found at i:18572776 original size:20 final size:21
Alignment explanation
Indices: 18572718--18572798 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
18572708 TAATTAATAA
*
18572718 TAAAATAATAATGAA-ATATAA-
1 TAAAATAATAA--AATATCTAAT
*
18572739 TAAAATAATAAAATATCTCAT
1 TAAAATAATAAAATATCTAAT
*
18572760 TAAAATAAT-ATATATCTAAT
1 TAAAATAATAAAATATCTAAT
*
18572780 TAAATAATCATAAAATATC
1 T-AA-AATAATAAAATATC
18572799 ATCAACATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 2 0.04
20 14 0.29
21 22 0.45
22 5 0.10
23 6 0.12
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.33
Consensus pattern (21 bp):
TAAAATAATAAAATATCTAAT
Found at i:18574219 original size:55 final size:53
Alignment explanation
Indices: 18574078--18574219 Score: 140
Period size: 55 Copynumber: 2.6 Consensus size: 53
18574068 GTGCAAGCCC
* * *
18574078 CACGCCCGTGTTCTTTTAACAGGTTCGACCACGGGTGTTAGACACGGGCATGTCG
1 CACGCCCGTGTTGTTTT--CAGGTTCGACCACGGGTCTTACACACGGGCATGTCG
* * * * * *
18574133 CACGCCCGTGCTAGTTTCTCAGTTTCAACCACGGGTCTTCCATACGGGCGTGTCG
1 CACGCCCGTG-TTGTTT-TCAGGTTCGACCACGGGTCTTACACACGGGCATGTCG
*
18574188 CACGCCCGTGTTGTTTTGGCAGGCTCGACCAC
1 CACGCCCGTGTTGTTTT--CAGGTTCGACCAC
18574220 AGCCATATCG
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
53 1 0.01
54 5 0.07
55 59 0.84
56 4 0.06
57 1 0.01
ACGTcount: A:0.15, C:0.31, G:0.27, T:0.26
Consensus pattern (53 bp):
CACGCCCGTGTTGTTTTCAGGTTCGACCACGGGTCTTACACACGGGCATGTCG
Found at i:18581196 original size:15 final size:15
Alignment explanation
Indices: 18581176--18581210 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18581166 TATTTATATG
*
18581176 CTTTTTCTTTTCTTT
1 CTTTTTATTTTCTTT
*
18581191 CTTTTTATTTTTTTT
1 CTTTTTATTTTCTTT
18581206 CTTTT
1 CTTTT
18581211 CGAATCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTATTTTCTTT
Found at i:18581925 original size:21 final size:21
Alignment explanation
Indices: 18581901--18581947 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18581891 TAAATTTATT
*
18581901 TATTAAATTTCTTATTATTAC
1 TATTAAATTTATTATTATTAC
** *
18581922 TATTATTTTTATTTTTATTAC
1 TATTAAATTTATTATTATTAC
18581943 TATTA
1 TATTA
18581948 TTACACTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTAAATTTATTATTATTAC
Found at i:18582129 original size:14 final size:14
Alignment explanation
Indices: 18582110--18582167 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
18582100 CTATATTATG
18582110 TATATATTTTATAT
1 TATATATTTTATAT
18582124 TATATATTATTATTAT
1 TATATATT-TTA-TAT
*
18582140 TATTATTATATTTTTAT
1 TA-TA-TAT-TTTATAT
18582157 GTATATATTTT
1 -TATATATTTT
18582168 TAATATCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 8 0.22
15 6 0.16
16 8 0.22
17 7 0.19
18 7 0.19
19 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TATATATTTTATAT
Found at i:18582129 original size:25 final size:23
Alignment explanation
Indices: 18582105--18582173 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 23
18582095 TAATACTATA
*
18582105 TTATGTATATATT-TTATATTATATA
1 TTAT-TATATATTATTATA-TAT-TT
18582130 TTATTAT-TATTATTATTATATTT
1 TTATTATATATTATTA-TATATTT
*
18582153 TTATGTATATATTTTTA-ATAT
1 TTAT-TATATATTATTATATAT
18582174 CACATTATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 13 0.34
24 12 0.32
25 13 0.34
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (23 bp):
TTATTATATATTATTATATATTT
Found at i:18582136 original size:3 final size:3
Alignment explanation
Indices: 18582103--18582148 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
18582093 TTTAATACTA
18582103 TAT TAT GTAT ATAT T-T TA- TAT TAT ATAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
18582149 ATTTTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.11
3 25 0.66
4 9 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:18582161 original size:12 final size:12
Alignment explanation
Indices: 18582105--18582198 Score: 63
Period size: 12 Copynumber: 7.8 Consensus size: 12
18582095 TAATACTATA
18582105 TTATGTATATATT
1 TTAT-TATATATT
*
18582118 TTA-TATTATATA
1 TTATTA-TATATT
18582130 TTATTAT-TATT
1 TTATTATATATT
18582141 ATTATTATAT-TT
1 -TTATTATATATT
18582153 TTATGTATATATT
1 TTAT-TATATATT
* **
18582166 TT-TAATATCACA
1 TTATTATAT-ATT
18582178 TTATTCATATATT
1 TTATT-ATATATT
18582191 TT-TTATAT
1 TTATTATAT
18582199 TATCCCATGT
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
11 17 0.27
12 29 0.45
13 14 0.22
14 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATATATT
Found at i:18582168 original size:14 final size:14
Alignment explanation
Indices: 18582105--18582169 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 14
18582095 TAATACTATA
18582105 TTATGTATATATTT
1 TTATGTATATATTT
18582119 TATAT-TATATATTATT
1 T-TATGTATATA-T-TT
*
18582135 ATTATTATTATTATATTT
1 -TTA-T-GTA-TATATTT
18582153 TTATGTATATATTT
1 TTATGTATATATTT
18582167 TTA
1 TTA
18582170 ATATCACATT
Statistics
Matches: 42, Mismatches: 1, Indels: 16
0.71 0.02 0.27
Matches are distributed among these distances:
14 17 0.40
15 6 0.14
16 5 0.12
17 5 0.12
18 2 0.05
19 3 0.07
20 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTATGTATATATTT
Found at i:18582181 original size:25 final size:23
Alignment explanation
Indices: 18582080--18582198 Score: 98
Period size: 25 Copynumber: 5.0 Consensus size: 23
18582070 AATGTGTATG
*
18582080 TATTA-TATATAATTTTAATACTA
1 TATTATTATATATTTTTAATA-TA
*
18582103 TATTATGTATATATTTTATATTATA
1 TATTAT-TATATATTTT-TAATATA
* *
18582128 TATTATTAT-TATTATTATTATA
1 TATTATTATATATTTTTAATATA
*
18582150 TTTTTATGTATATATTTTTAATATCA
1 -TATTAT-TATATATTTTTAATAT-A
* *
18582176 CATTATTCATATATTTTTTATAT
1 TATTATT-ATATATTTTTAATAT
18582199 TATCCCATGT
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
22 7 0.09
23 15 0.19
24 7 0.09
25 45 0.57
26 5 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTATTATATATTTTTAATATA
Found at i:18582181 original size:48 final size:48
Alignment explanation
Indices: 18582105--18582244 Score: 126
Period size: 50 Copynumber: 2.9 Consensus size: 48
18582095 TAATACTATA
* *
18582105 TTATGTATATATTTTATATTATATATTATT-AT-TATTATTATTATATTT
1 TTATGTATATATTTTATAATATACATTATTCATATATT-TT-TTATATTT
18582153 TTATGTATATATTTT-TAATATCACATTATTCATATATTTTTTATATTAT
1 TTATGTATATATTTTATAATAT-ACATTATTCATATATTTTTTATATT-T
** * * * *
18582202 CCCATGTAAATACTTT-CAATACTACATTATGCATATATTTTTT
1 -TTATGTATATATTTTATAATA-TACATTATTCATATATTTTTT
18582245 GTCTATATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
47 5 0.06
48 29 0.37
49 5 0.06
50 38 0.49
51 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (48 bp):
TTATGTATATATTTTATAATATACATTATTCATATATTTTTTATATTT
Found at i:18582534 original size:26 final size:26
Alignment explanation
Indices: 18582504--18582555 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
18582494 ATTATGTATA
*
18582504 TATTTTTAATACTACGTATATATTTT
1 TATTTCTAATACTACGTATATATTTT
* *
18582530 TATTTCTATTATTACGTATATATTTT
1 TATTTCTAATACTACGTATATATTTT
18582556 AATACATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.60
Consensus pattern (26 bp):
TATTTCTAATACTACGTATATATTTT
Found at i:18582565 original size:26 final size:26
Alignment explanation
Indices: 18582516--18582576 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
18582506 TTTTTAATAC
* *
18582516 TACGTATATATTTTTATTTCTATTAT
1 TACGTATATATTTTTAATACTATTAT
18582542 TACGTATATA-TTTTAATAC-A-TAT
1 TACGTATATATTTTTAATACTATTAT
*
18582565 T-TGTATATATTT
1 TACGTATATATTT
18582577 ATATATCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 7 0.23
23 6 0.19
24 1 0.03
25 7 0.23
26 10 0.32
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (26 bp):
TACGTATATATTTTTAATACTATTAT
Found at i:18582764 original size:15 final size:15
Alignment explanation
Indices: 18582744--18582775 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18582734 TTATTATCTC
18582744 TTTATACTATTATTA
1 TTTATACTATTATTA
*
18582759 TTTATATTATTATTA
1 TTTATACTATTATTA
18582774 TT
1 TT
18582776 ATCGTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATACTATTATTA
Found at i:18585427 original size:63 final size:63
Alignment explanation
Indices: 18585306--18585438 Score: 149
Period size: 63 Copynumber: 2.1 Consensus size: 63
18585296 CAATCATTAT
* ** * * ** **
18585306 TTTATTTTACACAAGCACCACTGCACGTGCAACCATTCCTTACACCGACGTATTCATCACCAA
1 TTTATTTCACACAAGCACCACAACACGCGCAACCATTCCCTACACCGACACAGCCATCACCAA
* * * *
18585369 TTTATTTCACACAAGCATCACAACACGCGCAATCATTCCCTGCACCGACACAGCCATCACCGA
1 TTTATTTCACACAAGCACCACAACACGCGCAACCATTCCCTACACCGACACAGCCATCACCAA
18585432 TTTATTT
1 TTTATTT
18585439 TTTACAAACA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (63 bp):
TTTATTTCACACAAGCACCACAACACGCGCAACCATTCCCTACACCGACACAGCCATCACCAA
Found at i:18586628 original size:20 final size:22
Alignment explanation
Indices: 18586595--18586686 Score: 65
Period size: 21 Copynumber: 4.4 Consensus size: 22
18586585 CCCCTTGTAG
18586595 AAAAGAAGATAAGCAGTA-AAA
1 AAAAGAAGATAAGCAGTAGAAA
*
18586616 AAAATAAGA-AAGCAGTAGAAA
1 AAAAGAAGATAAGCAGTAGAAA
*
18586637 AGAAGACA-ATAAG-A--AGAAA
1 AAAAGA-AGATAAGCAGTAGAAA
* *
18586656 GAAAGAAAGA-AATG-AGAAGAAA
1 AAAAG-AAGATAA-GCAGTAGAAA
18586678 AAAAGAAGA
1 AAAAGAAGA
18586687 AGAAGAAGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
19 11 0.19
20 12 0.21
21 21 0.37
22 13 0.23
ACGTcount: A:0.68, C:0.03, G:0.22, T:0.07
Consensus pattern (22 bp):
AAAAGAAGATAAGCAGTAGAAA
Found at i:18586673 original size:22 final size:23
Alignment explanation
Indices: 18586634--18586684 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
18586624 AAAGCAGTAG
18586634 AAAAG-AAGACAATAAGAAGAAA
1 AAAAGAAAGACAATAAGAAGAAA
* *
18586656 GAAAGAAAGA-AATGAGAAGAAA
1 AAAAGAAAGACAATAAGAAGAAA
18586678 AAAAGAA
1 AAAAGAA
18586685 GAAGAAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGACAATAAGAAGAAA
Found at i:18592877 original size:43 final size:42
Alignment explanation
Indices: 18592835--18592917 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
18592825 TGAGACACTA
* *
18592835 TATGTGTCATAATATTACTTTGGA-TAATTCCGATGAGGCAC
1 TATGTGTCATAATATTACTTCGGATTAAATCCGATGAGGCAC
* * * *
18592876 TATGTGTCGTATTATTGCTTCGGATTAAATCCGATAAGGCAC
1 TATGTGTCATAATATTACTTCGGATTAAATCCGATGAGGCAC
18592918 AAGGTGTCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (42 bp):
TATGTGTCATAATATTACTTCGGATTAAATCCGATGAGGCAC
Found at i:18592916 original size:42 final size:41
Alignment explanation
Indices: 18592835--18592928 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 41
18592825 TGAGACACTA
* * * *
18592835 TATGTGTCATAATATTACTTTGGATAATTCCGATGAGGCAC
1 TATGTGTCGTAATATTACTTCGGATAAATCCGATAAGGCAC
* *
18592876 TATGTGTCGTATTATTGCTTCGGATTAAATCCGATAAGGCAC
1 TATGTGTCGTAATATTACTTCGGA-TAAATCCGATAAGGCAC
* *
18592918 AAGGTGTCGTA
1 TATGTGTCGTA
18592929 CTAGTGTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (41 bp):
TATGTGTCGTAATATTACTTCGGATAAATCCGATAAGGCAC
Found at i:18596831 original size:55 final size:55
Alignment explanation
Indices: 18596748--18596860 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
18596738 ATAATGTTCC
* * *
18596748 ACTTGTTTGGGATGATTAATGCTAAGAAATTTTTGAGAAATTGAAGCAAATGTTG
1 ACTTGTTTGGGATAATCAATGCTAAGAAAATTTTGAGAAATTGAAGCAAATGTTG
18596803 ACTTGTTTGGGATAATCAATGGCT-AGAAAATTTTGAGAAATTGAAGCAAATGTTG
1 ACTTGTTTGGGATAATCAAT-GCTAAGAAAATTTTGAGAAATTGAAGCAAATGTTG
18596858 ACT
1 ACT
18596861 AAGGCACTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 51 0.94
56 3 0.06
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (55 bp):
ACTTGTTTGGGATAATCAATGCTAAGAAAATTTTGAGAAATTGAAGCAAATGTTG
Found at i:18598292 original size:27 final size:27
Alignment explanation
Indices: 18598209--18598292 Score: 127
Period size: 27 Copynumber: 3.1 Consensus size: 27
18598199 CCAAAACAGA
18598209 CAGATCAGATAATTGTGGCATAGCCAC
1 CAGATCAGATAATTGTGGCATAGCCAC
*
18598236 CAAGA-CAGAT-ATATGTGGCAGAGCCAC
1 C-AGATCAGATAAT-TGTGGCATAGCCAC
18598263 CAGATCAGATAATTGTGGCATAGCCAC
1 CAGATCAGATAATTGTGGCATAGCCAC
18598290 CAG
1 CAG
18598293 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
26 5 0.10
27 41 0.80
28 5 0.10
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATCAGATAATTGTGGCATAGCCAC
Found at i:18604584 original size:42 final size:41
Alignment explanation
Indices: 18604494--18604589 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
18604484 GACCTCAAGT
* * *
18604494 CGATGAGGCACTATATGTGTCGTAATATTACTTCGATAATTG
1 CGATGAGGCAC-ATATCTGTCGTAATATTACTTCGATAAATC
* * *
18604536 CTATGAGGCAC-TATCTGTCGTATTATTGCTTCAGATTAAATC
1 CGATGAGGCACATATCTGTCGTAATATTACTTC-GA-TAAATC
18604578 CGATGAGGCACA
1 CGATGAGGCACA
18604590 AGGTGCCGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 18 0.41
41 2 0.05
42 24 0.55
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (41 bp):
CGATGAGGCACATATCTGTCGTAATATTACTTCGATAAATC
Found at i:18613258 original size:24 final size:24
Alignment explanation
Indices: 18613213--18613258 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
18613203 ATGTGGAGGG
** *
18613213 AATCAAGGGGAGGATTGGGGAGAA
1 AATCAAGAAGAGGATTAGGGAGAA
*
18613237 AATCAAGAAGAGGATTATGGAG
1 AATCAAGAAGAGGATTAGGGAG
18613259 TGATTTTAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.04, G:0.39, T:0.15
Consensus pattern (24 bp):
AATCAAGAAGAGGATTAGGGAGAA
Found at i:18614631 original size:27 final size:27
Alignment explanation
Indices: 18614601--18614654 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
18614591 ATGACCAAAA
*
18614601 TACCCCTATAGGGTAAAGTGACT-ATTT
1 TACCCCTAGAGGGTAAA-TGACTGATTT
*
18614628 TACCCCTCGAGGGTAAATGACTGATTT
1 TACCCCTAGAGGGTAAATGACTGATTT
18614655 GTGGTATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (27 bp):
TACCCCTAGAGGGTAAATGACTGATTT
Found at i:18616447 original size:22 final size:21
Alignment explanation
Indices: 18616413--18616465 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
18616403 CATTAATATT
*
18616413 ATATAATAAATAATACGATAA
1 ATATAATAAATAATAAGATAA
* *
18616434 ATATAGTACAATAATAATATAA
1 ATATAATA-AATAATAAGATAA
*
18616456 ATACAATAAA
1 ATATAATAAA
18616466 AAATCTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (21 bp):
ATATAATAAATAATAAGATAA
Found at i:18621852 original size:18 final size:17
Alignment explanation
Indices: 18621822--18621855 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18621812 TTGGCCTCCC
18621822 TTTTTTTCATTTATAAG
1 TTTTTTTCATTTATAAG
*
18621839 TTTTTCTTCCTTTATAA
1 TTTTT-TTCATTTATAA
18621856 ACATCCTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTTTCATTTATAAG
Found at i:18623450 original size:20 final size:20
Alignment explanation
Indices: 18623425--18623469 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
18623415 ATTTAATGCC
18623425 TTAATG-CCTTTCCTCTACAT
1 TTAATGTCCTTTCCT-TACAT
* *
18623445 TTAATGTCTTTTCCTTGCAT
1 TTAATGTCCTTTCCTTACAT
18623465 TTAAT
1 TTAAT
18623470 TCATAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (20 bp):
TTAATGTCCTTTCCTTACAT
Found at i:18640258 original size:12 final size:13
Alignment explanation
Indices: 18640240--18640291 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 13
18640230 AAAAAATATG
18640240 ATATTTAATAATA
1 ATATTTAATAATA
18640253 AT-TTTAA-AATA
1 ATATTTAATAATA
*
18640264 GTATTTAATATATA
1 ATATTTAATA-ATA
*
18640278 ATATATAATAATA
1 ATATTTAATAATA
18640291 A
1 A
18640292 AAATTATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 5 0.15
12 10 0.30
13 7 0.21
14 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:18640287 original size:24 final size:24
Alignment explanation
Indices: 18640232--18640290 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 24
18640222 TACTTATAAA
*
18640232 AAAATATGATATTTAATAATAATTTT
1 AAAATA-G-TATTTAATAATAATTAT
18640258 AAAATAGTATTTAATATATAATATAT
1 AAAATAGTATTTAATA-ATAAT-TAT
18640284 AATAATA
1 AA-AATA
18640291 AAAATTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.31
25 6 0.21
26 10 0.34
27 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (24 bp):
AAAATAGTATTTAATAATAATTAT
Found at i:18641774 original size:26 final size:28
Alignment explanation
Indices: 18641744--18641819 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
18641734 ATTATTTGTT
18641744 TTATTTTAATTTTACTTTTA-TATAA-TA
1 TTATTTTAATTTTA-TTTTATTATAAGTA
* **
18641771 -TATTATAAAATTATTTTATTATAAGTA
1 TTATTTTAATTTTATTTTATTATAAGTA
* *
18641798 TTATTTTAATTATATATTATTA
1 TTATTTTAATTTTATTTTATTA
18641820 CTACTTATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
25 5 0.13
26 15 0.39
27 2 0.05
28 16 0.42
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TTATTTTAATTTTATTTTATTATAAGTA
Found at i:18641818 original size:16 final size:17
Alignment explanation
Indices: 18641771--18641811 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
18641761 TTATATAATA
*
18641771 TATTATAA-AATTATTT
1 TATTATAAGTATTATTT
18641787 TATTATAAGTATTATTT
1 TATTATAAGTATTATTT
18641804 TAATTATA
1 T-ATTATA
18641812 TATTATTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTATAAGTATTATTT
Found at i:18642001 original size:24 final size:22
Alignment explanation
Indices: 18641945--18642016 Score: 55
Period size: 23 Copynumber: 3.4 Consensus size: 22
18641935 ATATTATATC
*
18641945 TATTATTTTTCTTATATGTTTA
1 TATTATTTTTCTTATATATTTA
*
18641967 TATTACATTTTCTTATATAATCTT-
1 TATTA-TTTTTCTTATAT-AT-TTA
*
18641991 TATTA-TGTT-TTAT-T-TTTA
1 TATTATTTTTCTTATATATTTA
18642009 TATTATTT
1 TATTATTT
18642017 ATTGCTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
17 2 0.05
18 6 0.15
19 1 0.02
20 1 0.02
21 4 0.10
22 8 0.20
23 11 0.27
24 6 0.15
25 2 0.05
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (22 bp):
TATTATTTTTCTTATATATTTA
Found at i:18642454 original size:18 final size:18
Alignment explanation
Indices: 18642431--18642485 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
18642421 ACATTTATTC
18642431 TATTTGTATATCATGCAT
1 TATTTGTATATCATGCAT
*
18642449 TATTTG-AT-T-ATG-TT
1 TATTTGTATATCATGCAT
*
18642463 TATTTTTATATCATGCAT
1 TATTTGTATATCATGCAT
*
18642481 CATTT
1 TATTT
18642486 AAATATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 6 0.21
15 5 0.17
16 2 0.07
17 5 0.17
18 11 0.38
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.56
Consensus pattern (18 bp):
TATTTGTATATCATGCAT
Found at i:18642573 original size:16 final size:17
Alignment explanation
Indices: 18642552--18642587 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
18642542 GCATTTTTTT
*
18642552 TTCTTTATAT-GTATTA
1 TTCTTTATATCGTAGTA
18642568 TTCTTTATATCGTAGTA
1 TTCTTTATATCGTAGTA
18642585 TTC
1 TTC
18642588 ATTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (17 bp):
TTCTTTATATCGTAGTA
Found at i:18643551 original size:21 final size:20
Alignment explanation
Indices: 18643527--18643673 Score: 76
Period size: 21 Copynumber: 7.2 Consensus size: 20
18643517 TAATATAGAG
*
18643527 AAAAAAATATATAATAGTAT
1 AAAAAAATATATAATAATAT
*
18643547 AAAAAAATGACATAATAATAT
1 AAAAAAAT-ATATAATAATAT
18643568 AAAATAAATATAATATATAATAT
1 AAAA-AAATAT-ATA-ATAATAT
* * *
18643591 --GAAAGTATAT-AT-GTA-
1 AAAAAAATATATAATAATAT
* *
18643606 AAAATAACATATAAT-ATAT
1 AAAAAAATATATAATAATAT
*
18643625 ATAAATAATATGAATAATAA-AT
1 A-AAAAAATAT--ATAATAATAT
18643647 AAAAAAATA-ATTATATAATAT
1 AAAAAAATATA-TA-ATAATAT
18643668 ATAAAA
1 A-AAAA
18643674 TAAAAATAAG
Statistics
Matches: 98, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
16 2 0.02
17 8 0.08
18 5 0.05
19 5 0.05
20 25 0.26
21 26 0.27
22 19 0.19
23 8 0.08
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAAAAATATATAATAATAT
Found at i:18643644 original size:32 final size:34
Alignment explanation
Indices: 18643560--18643647 Score: 87
Period size: 38 Copynumber: 2.6 Consensus size: 34
18643550 AAAATGACAT
18643560 AATAATAT-AAAATAAATATAATATATAATATGA
1 AATAATATGAAAATAAATATAATATATAATATGA
18643593 AAGTATATATGTAAAAATAACATAT-A-ATAT-ATAT-A
1 AA-TA-ATATG--AAAATAA-ATATAATATATAATATGA
18643628 AATAATATGAATAATAAATA
1 AATAATATGAA-AATAAATA
18643648 AAAAAATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
31 5 0.10
32 5 0.10
33 7 0.15
34 4 0.08
35 7 0.15
36 4 0.08
37 4 0.08
38 8 0.17
39 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (34 bp):
AATAATATGAAAATAAATATAATATATAATATGA
Found at i:18645804 original size:205 final size:206
Alignment explanation
Indices: 18645339--18646097 Score: 1125
Period size: 205 Copynumber: 3.7 Consensus size: 206
18645329 AAATCTGCTT
* * *
18645339 CTTTGGTTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTTGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
18645404 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATG-TCAAATCATCT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGAATGCT-AAATCATCT
* ** * *
18645468 TGGATCTTACTTCAGTGA-AATTATTTGAAGGTGAGATCTGCTATGTATCTGCTCCCGGTTGAAG
130 TGGATCTTGCTTCAGT-ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTGAAG
18645532 TGGAGATGCCAGA
194 TGGAGATGCCAGA
* *
18645545 CTTTGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTTGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
18645610 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCTAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGAATGCTAAATCATCTT
* * *
18645675 AGATC-TGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATATATCTGCTCCCCATTGAAGTG
131 GGATCTTGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTGAAGTG
*
18645739 GAGATGCCAAA
196 GAGATGCCAGA
* * *
18645750 ATTTGATTTGCTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACCC
1 CTTTGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
18645815 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTAGTAAGCACAAGGATGCT-AATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGAATGCTAAATCATCTT
* * *
18645879 GG-TTTTGCTTCAGTATAAACATCTGAAGGTGAGATCT-CTTATGTATCTACTCCCCGTTGAACT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGTGAGATCTGC-TATGTATCTGCTCCCCGTTGAAGT
18645942 GGAGATGCCAGA
195 GGAGATGCCAGA
* * * * * *
18645954 CTTCGATTTGCTCTTTGACAATACAGAAATGCCAAATCATCTTAGATTTGCTTTAACGTAAACAT
1 CTTTGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * * *
18646019 GTGAAAGCCAAATCAGCTATGTCTTTGGTTTGTTCCTTGTAAGCACAAGAATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGAATGCTAAATCATCTT
18646084 GGATCTTGCTTCAG
131 GGATCTTGCTTCAG
18646098 CCAGATCTGC
Statistics
Matches: 502, Mismatches: 45, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
203 2 0.00
204 179 0.36
205 184 0.37
206 136 0.27
207 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (206 bp):
CTTTGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGAATGCTAAATCATCTT
GGATCTTGCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTGAAGTG
GAGATGCCAGA
Found at i:18647949 original size:22 final size:22
Alignment explanation
Indices: 18647924--18647973 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
18647914 GGAGAAGTCA
18647924 TAACATGTAAAAGTGAAGATGG
1 TAACATGTAAAAGTGAAGATGG
*
18647946 TAACATGTAAAGGTGAAGATGG
1 TAACATGTAAAAGTGAAGATGG
18647968 T-ACATG
1 TAACATG
18647974 AATTTTGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.24
Consensus pattern (22 bp):
TAACATGTAAAAGTGAAGATGG
Found at i:18657948 original size:12 final size:13
Alignment explanation
Indices: 18657930--18657978 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
18657920 AAAAAATATG
18657930 ATATTTAATAATA
1 ATATTTAATAATA
18657943 AT-TTTAA-AATA
1 ATATTTAATAATA
*
18657954 GTATTTAATATATA
1 ATATTTAATA-ATA
*
18657968 ATATATAATAA
1 ATATTTAATAA
18657979 AAAAATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 5 0.17
12 10 0.33
13 4 0.13
14 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:18657977 original size:24 final size:24
Alignment explanation
Indices: 18657922--18657975 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
18657912 ATACTTATAA
*
18657922 AAAATATGATATTTAATAATAATTTT
1 AAAATA-G-TATTTAATAATAATTAT
18657948 AAAATAGTATTTAATATATAATATAT
1 AAAATAGTATTTAATA-ATAAT-TAT
18657974 AA
1 AA
18657976 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 6 0.24
26 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATAGTATTTAATAATAATTAT
Found at i:18658165 original size:17 final size:17
Alignment explanation
Indices: 18658145--18658206 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
18658135 TCATAATAAT
18658145 ATAGATAAAAAAATATA
1 ATAGATAAAAAAATATA
*
18658162 ATAGTATAAAAAATGACATA
1 ATAG-ATAAAAAA--ATATA
* *
18658182 ATAAATAAAATAATATA
1 ATAGATAAAAAAATATA
*
18658199 ATATATAA
1 ATAGATAA
18658207 TATGAAAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 15 0.41
18 8 0.22
19 7 0.19
20 7 0.19
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
ATAGATAAAAAAATATA
Found at i:18658204 original size:7 final size:7
Alignment explanation
Indices: 18658194--18658298 Score: 70
Period size: 7 Copynumber: 14.1 Consensus size: 7
18658184 AAATAAAATA
18658194 ATATAAT
1 ATATAAT
18658201 ATATAAT
1 ATATAAT
18658208 ATGA-AAGT
1 AT-ATAA-T
*
18658216 ATATATGT
1 ATATA-AT
*
18658224 AAAATAAT
1 -ATATAAT
18658232 ATATAAT
1 ATATAAT
18658239 ATAT-AT
1 ATATAAT
*
18658245 AAATAAT
1 ATATAAT
18658252 ATGAATAAT
1 AT--ATAAT
*
18658261 AAATAAT
1 ATATAAT
*
18658268 AAAATAATT
1 -ATATAA-T
18658277 ATATAAT
1 ATATAAT
18658284 ATATAAT
1 ATATAAT
*
18658291 ATAAAAT
1 ATATAAT
18658298 A
1 A
18658299 AGATTAAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.06
7 45 0.57
8 18 0.23
9 11 0.14
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (7 bp):
ATATAAT
Found at i:18658227 original size:36 final size:33
Alignment explanation
Indices: 18658187--18658269 Score: 93
Period size: 36 Copynumber: 2.5 Consensus size: 33
18658177 ACATAATAAA
18658187 TAAAATAATATAAT-ATATAATATGAAAGTATATATG
1 TAAAATAATATAATAATAT-ATAT-AAA-TA-ATATG
18658223 TAAAATAATAT-ATAATATATATAAATAATATG
1 TAAAATAATATAATAATATATATAAATAATATG
18658255 -AATAATAA-ATAATAA
1 TAA-AATAATATAATAA
18658270 AATAATTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
31 4 0.09
32 14 0.32
33 2 0.05
34 3 0.07
35 6 0.14
36 15 0.34
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (33 bp):
TAAAATAATATAATAATATATATAAATAATATG
Found at i:18658307 original size:36 final size:38
Alignment explanation
Indices: 18658184--18658307 Score: 110
Period size: 44 Copynumber: 3.1 Consensus size: 38
18658174 ATGACATAAT
* * *
18658184 AAATAAAATAATATAATATATAATATGAAAGTATATATGTA
1 AAATAATAT-ATATAATATATAATATGAAA--ATAAATATA
18658225 AAATAATATATAATATATATAAATAATATGAATAATAAATAATA
1 AAATAATATAT-ATA-ATAT--ATAATATGAA-AATAAAT-ATA
18658269 AAATAAT-TATATAATATATAATAT-AAAATAAGAT-TA
1 AAATAATATATATAATATATAATATGAAAATAA-ATATA
18658305 AAA
1 AAA
18658308 ATAAAACAGA
Statistics
Matches: 73, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
36 5 0.07
37 5 0.07
38 4 0.05
39 7 0.10
40 2 0.03
41 15 0.21
42 7 0.10
43 8 0.11
44 19 0.26
45 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (38 bp):
AAATAATATATATAATATATAATATGAAAATAAATATA
Found at i:18672959 original size:47 final size:47
Alignment explanation
Indices: 18672893--18673084 Score: 224
Period size: 47 Copynumber: 4.1 Consensus size: 47
18672883 CATGACAACA
* *
18672893 TGTGATATGTGATTCCCGTATAAGACCATAGCTGGGCTATGGCATCGG
1 TGTGATATGTGCTT-CCGTATAAGACCATAGCTGGGATATGGCATCGG
* ** *
18672941 TATGATATGTGCTTCCGTATAAGACCATATTTAGGATATGGCATCGG
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG
** * * *
18672988 TGTGATATGTGCTTCTATGTAAGACCATATCTGGGATATGGCATCAG
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG
* * * * *
18673035 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCTTCGG
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG
18673081 TGTG
1 TGTG
18673085 TGATATATGA
Statistics
Matches: 123, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
46 31 0.25
47 80 0.65
48 12 0.10
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (47 bp):
TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG
Found at i:18673100 original size:93 final size:94
Alignment explanation
Indices: 18672913--18673112 Score: 217
Period size: 94 Copynumber: 2.1 Consensus size: 94
18672903 GATTCCCGTA
* * * **
18672913 TAAGACCATAGCTGGGCTATGGCATCGGTATGATATGTGCTTCCGTATAAGACCATATTTAGGAT
1 TAAGACCATAGCTGGGATATGGCATCAGTATGATATGTGCATCCGTATAAGACCATAGCTAGGAT
* *
18672978 ATGGCATCGGTGTGATATGTGCTTCTATG
66 ATGGCATCGGTGTGATATATGCATCTATG
* * * * * *
18673007 TAAGACCATATCTGGGATATGGCATCAGTGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGCT
1 TAAGACCATAGCTGGGATATGGCATCAGTATGATATGTGCATCCGTATAAGACCATAGCTAGGAT
*
18673071 ATGGCTTCGGTGTGTGATATATG-AT-TATG
66 ATGGCATC-G-GTGTGATATATGCATCTATG
18673100 TGCAAGACCATAG
1 T--AAGACCATAG
18673113 TTATACTATG
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
93 30 0.34
94 37 0.43
95 20 0.23
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (94 bp):
TAAGACCATAGCTGGGATATGGCATCAGTATGATATGTGCATCCGTATAAGACCATAGCTAGGAT
ATGGCATCGGTGTGATATATGCATCTATG
Found at i:18677895 original size:32 final size:32
Alignment explanation
Indices: 18677853--18677917 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
18677843 AATGCTTACC
*
18677853 ATGCCTATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
18677885 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
18677917 A
1 A
18677918 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:18678875 original size:8 final size:8
Alignment explanation
Indices: 18678862--18678893 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
18678852 ACTTAAGTAT
18678862 ATAATATA
1 ATAATATA
18678870 ATAATATA
1 ATAATATA
*
18678878 TTAATATA
1 ATAATATA
18678886 ATAATATA
1 ATAATATA
18678894 TTATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATA
Found at i:18678886 original size:13 final size:13
Alignment explanation
Indices: 18678860--18678902 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
18678850 ATACTTAAGT
18678860 ATATAATATAATAA
1 ATATAATATAAT-A
18678874 TATATTAATATAATA
1 -ATA-TAATATAATA
*
18678889 ATATATTATAATA
1 ATATAATATAATA
18678902 A
1 A
18678903 AACATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 10 0.38
14 3 0.12
15 4 0.15
16 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:18678902 original size:16 final size:16
Alignment explanation
Indices: 18678859--18678896 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
18678849 AATACTTAAG
18678859 TATA-TAATATAATAA
1 TATATTAATATAATAA
18678874 TATATTAATATAATAA
1 TATATTAATATAATAA
18678890 TATATTA
1 TATATTA
18678897 TAATAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATTAATATAATAA
Found at i:18678946 original size:24 final size:24
Alignment explanation
Indices: 18678902--18678947 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
18678892 TATTATAATA
*
18678902 AAACATAAAAAAAATAAAAGAAAT
1 AAACATAAAAAAAAGAAAAGAAAT
*
18678926 AAAC-TAAACAAAAGAATAAGAA
1 AAACATAAAAAAAAGAA-AAGAA
18678948 CAGAGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.11
Consensus pattern (24 bp):
AAACATAAAAAAAAGAAAAGAAAT
Found at i:18680163 original size:34 final size:34
Alignment explanation
Indices: 18680120--18680187 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
18680110 ATTAAGAAAG
18680120 AACTTTGAATATAAGTTGTGCTATTAGATTTGAA
1 AACTTTGAATATAAGTTGTGCTATTAGATTTGAA
18680154 AACTTTGAATATAAGTTGTGCTATTAGATTTGAA
1 AACTTTGAATATAAGTTGTGCTATTAGATTTGAA
18680188 TATAATAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (34 bp):
AACTTTGAATATAAGTTGTGCTATTAGATTTGAA
Found at i:18687089 original size:20 final size:20
Alignment explanation
Indices: 18687066--18687105 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18687056 TAAACAAGAA
18687066 GTAATTTTAAACTAAACTTT
1 GTAATTTTAAACTAAACTTT
18687086 GTAATTTTAAACTAAACTTT
1 GTAATTTTAAACTAAACTTT
18687106 CTTGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
GTAATTTTAAACTAAACTTT
Found at i:18688970 original size:21 final size:22
Alignment explanation
Indices: 18688944--18688985 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18688934 CACTATTTTT
18688944 ATTAAAAA-TTAATTTTAATCC
1 ATTAAAAATTTAATTTTAATCC
18688965 ATTAAAAATTTAATTTTAATC
1 ATTAAAAATTTAATTTTAATC
18688986 TCATATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAAAATTTAATTTTAATCC
Found at i:18698446 original size:46 final size:46
Alignment explanation
Indices: 18698376--18698696 Score: 448
Period size: 46 Copynumber: 7.0 Consensus size: 46
18698366 TTCGACATGA
* * * * * *
18698376 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* * ** *** *
18698422 TTCCATGGTATCATTCAACCATGGTCTTATTCATTTCCCCGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT-CATATCAGGT
* *
18698469 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
18698515 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
18698561 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
18698607 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
18698653 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
18698697 AGAGCACACT
Statistics
Matches: 254, Mismatches: 18, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
45 3 0.01
46 209 0.82
47 42 0.17
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:18700852 original size:11 final size:11
Alignment explanation
Indices: 18700836--18700887 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
18700826 TATACTAAAT
18700836 AAATAATAATA
1 AAATAATAATA
*
18700847 AAATAAT-ATT
1 AAATAATAATA
* *
18700857 AAATATCTCATA
1 AAATA-ATAATA
*
18700869 AAATATTAATA
1 AAATAATAATA
18700880 AAATAATA
1 AAATAATA
18700888 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:18710130 original size:20 final size:20
Alignment explanation
Indices: 18710105--18710146 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
18710095 GAAAGAACAA
18710105 ACTAAAGAGAAAATATCAAT
1 ACTAAAGAGAAAATATCAAT
18710125 ACTAAAGAGAAAATATCAAT
1 ACTAAAGAGAAAATATCAAT
18710145 AC
1 AC
18710147 AATGAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19
Consensus pattern (20 bp):
ACTAAAGAGAAAATATCAAT
Found at i:18711667 original size:69 final size:69
Alignment explanation
Indices: 18711512--18711705 Score: 209
Period size: 67 Copynumber: 2.9 Consensus size: 69
18711502 AAGTGATAAT
* * * * **
18711512 TTCTTCACTATTTTCCTTAAAAAAAGTTAATTTTAATCCCATATTGACTAAAGAATACTCTTATA
1 TTCTTCACTATTTTCATT-AAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTCGGATA
18711577 ACTCA
65 ACTCA
* * * *
18711582 --CTTCACTATTTTCATTAAAAAATTTATTTTTAATTCCACACTGATTAGAGAATACT-GGATAA
1 TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTCGGATAA
18711644 CTCA
66 CTCA
* * * *
18711648 CTTCTTCACTATTTTCATTAAAAAA--TAATTTTAATCCCTCATTGGCTAGAGAATACTC
1 -TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTC
18711706 CCAGGCTCCA
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
66 8 0.08
67 59 0.57
68 15 0.14
69 22 0.21
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (69 bp):
TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTCGGATAA
CTCA
Done.