Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 56 of 279
Found at i:18737050 original size:17 final size:17
Alignment explanation
Indices: 18737010--18737051 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
18737000 TGATATACAG
* *
18737010 TTGTATCTTTTGAATAG
1 TTGTATCTTTTGAACAA
*
18737027 TTATATCTTTTGAACAA
1 TTGTATCTTTTGAACAA
18737044 TTGTATCT
1 TTGTATCT
18737052 CTTGGTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (17 bp):
TTGTATCTTTTGAACAA
Found at i:18740472 original size:3 final size:3
Alignment explanation
Indices: 18740466--18740501 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18740456 ACACTACTAT
18740466 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18740502 TAGAAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18743105 original size:39 final size:39
Alignment explanation
Indices: 18743023--18743218 Score: 214
Period size: 39 Copynumber: 4.9 Consensus size: 39
18743013 GCTGGCTATA
* * *
18743023 TGCTGGAATTATATCAGGGCTTAAAGATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGACTT-AAGGT-CCGCAGGCTTCG
*
18743064 TGCTGGAATTGTATCCGGACTTAAGGTCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTTCG
* * *
18743103 TGCTGGAATTGTATCCGGACTTAAGATCTGCAGGCTTCG
1 TGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTTCG
* *
18743142 TGCTGGTACTATATCCGGACTTAAGG-CCTGCAGGCTTCG
1 TGCTGGAATTATATCCGGACTTAAGGTCC-GCAGGCTTCG
* * * * * *
18743181 TACTGGTACTATATCCGGGCTTAAAGTCCCGTAGGCTT
1 TGCTGGAATTATATCCGGACTTAAGGT-CCGCAGGCTT
18743219 TGTGTTGGTG
Statistics
Matches: 137, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 104 0.76
40 11 0.08
41 21 0.15
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (39 bp):
TGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTTCG
Found at i:18743146 original size:78 final size:79
Alignment explanation
Indices: 18743023--18743218 Score: 245
Period size: 78 Copynumber: 2.5 Consensus size: 79
18743013 GCTGGCTATA
* * *
18743023 TGCTGGAATTATATCAGGGCTTAAAGATCCCGCAGGCTTCGTGCTGGAATTGTATCCGGACTTAA
1 TGCTGGAATTATATCCGGGCTT-AAGATCCCGCAGGCTTCGTGCTGGAACTATATCCGGACTTAA
18743088 GGTCC-GCAGGCTTCG
65 GG-CCTGCAGGCTTCG
* * * *
18743103 TGCTGGAATTGTATCCGGACTTAAGAT-CTGCAGGCTTCGTGCTGGTACTATATCCGGACTTAAG
1 TGCTGGAATTATATCCGGGCTTAAGATCCCGCAGGCTTCGTGCTGGAACTATATCCGGACTTAAG
18743167 GCCTGCAGGCTTCG
66 GCCTGCAGGCTTCG
* * * *
18743181 TACTGGTACTATATCCGGGCTTAA-AGTCCCGTAGGCTT
1 TGCTGGAATTATATCCGGGCTTAAGA-TCCCGCAGGCTT
18743219 TGTGTTGGTG
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
77 3 0.03
78 64 0.65
79 13 0.13
80 19 0.19
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (79 bp):
TGCTGGAATTATATCCGGGCTTAAGATCCCGCAGGCTTCGTGCTGGAACTATATCCGGACTTAAG
GCCTGCAGGCTTCG
Found at i:18745882 original size:46 final size:45
Alignment explanation
Indices: 18745824--18746090 Score: 155
Period size: 47 Copynumber: 5.7 Consensus size: 45
18745814 ATTCGTGTGT
* *
18745824 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACACTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GATGA
* * * **
18745870 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GACATTGAGACAA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA--CAGATGA
* * * * * *
18745918 GGGCTAGTGTAAGAC-TGTTTGGGACATGCAACGGCCTCAAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AGATG-A
** * *
18745964 -AAACAGTGTAAGATATGTCTGGGACATGCATCGGCTACTAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AGATGA
* * * * ***
18746009 TAGTCAGTGTAAGACCATGTCTGAGACATGGCATCGACTTGAGAT-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAGATGA
* *
18746055 TGAGCCAGTATAAGACCATGTCTAGGACATGGCATC
1 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
18746091 AGCACCTTAC
Statistics
Matches: 170, Mismatches: 39, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
45 18 0.11
46 61 0.36
47 63 0.37
48 27 0.16
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (45 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATGA
Found at i:18747244 original size:21 final size:21
Alignment explanation
Indices: 18747218--18747257 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18747208 TTGAATTGGA
*
18747218 CACACGGGGGTGTGCCCCTTT
1 CACACGGGCGTGTGCCCCTTT
18747239 CACACGGGCGTGTGCCCCT
1 CACACGGGCGTGTGCCCCT
18747258 ATGTCAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.38, G:0.33, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTGTGCCCCTTT
Found at i:18755447 original size:31 final size:31
Alignment explanation
Indices: 18755404--18755466 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
18755394 AAAGTACAAC
18755404 AAAACATTAATTACAATAAAGAGTAAAAAGG
1 AAAACATTAATTACAATAAAGAGTAAAAAGG
* * * *
18755435 AAAATATTAATTATAGTAAAGATTAAAAAGG
1 AAAACATTAATTACAATAAAGAGTAAAAAGG
18755466 A
1 A
18755467 TGGTTTAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.24
Consensus pattern (31 bp):
AAAACATTAATTACAATAAAGAGTAAAAAGG
Found at i:18755638 original size:36 final size:36
Alignment explanation
Indices: 18755588--18755661 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
18755578 CATTAACTTT
18755588 AACTTTCAGCATTTTTATATTGAAAAAAATCAAATC
1 AACTTTCAGCATTTTTATATTGAAAAAAATCAAATC
* *
18755624 AACTTTCAGTATTTTTATATTGAAAAAATTCAAATC
1 AACTTTCAGCATTTTTATATTGAAAAAAATCAAATC
18755660 AA
1 AA
18755662 AACATATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (36 bp):
AACTTTCAGCATTTTTATATTGAAAAAAATCAAATC
Found at i:18756566 original size:51 final size:51
Alignment explanation
Indices: 18756511--18756646 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 51
18756501 TGGAAACATT
*
18756511 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATATGAAATGTA
1 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATAAGAAATGTA
* * ** * * *
18756562 ATCTTATAAGATATTATTTTATAAGATTACATATCTTAGATAAGATATGTA
1 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATAAGAAATGTA
* *
18756613 ATCTTAGAAGATATGATTTTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATTTTATAATCTTAGAGAT
18756647 TTGATTGTAG
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (51 bp):
ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATAAGAAATGTA
Found at i:18761768 original size:51 final size:51
Alignment explanation
Indices: 18761713--18761848 Score: 191
Period size: 51 Copynumber: 2.7 Consensus size: 51
18761703 TGGAAACATT
*
18761713 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATATGATATGTA
1 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
* * ** * *
18761764 ATCTTATAAGATATTATTTTATAAGATTACATATCTTAGATAAGATATGTA
1 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
* *
18761815 ATCTTAGAAGATATGATTTTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATTTTATAATCTTAGAGAT
18761849 TTGATTGTAG
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (51 bp):
ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
Found at i:18761818 original size:19 final size:19
Alignment explanation
Indices: 18761745--18761822 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 19
18761735 AATCTTAGAG
*
18761745 ATCTTAGATATGATATGTA
1 ATCTTAGATAAGATATGTA
18761764 ATCTT--ATAAGATAT-T-
1 ATCTTAGATAAGATATGTA
* **
18761779 AT-TT-TATAAGAT-TACA
1 ATCTTAGATAAGATATGTA
18761795 TATCTTAGATAAGATATGTA
1 -ATCTTAGATAAGATATGTA
18761815 ATCTTAGA
1 ATCTTAGA
18761823 AGATATGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
14 3 0.06
15 9 0.19
16 1 0.02
17 10 0.21
18 2 0.04
19 20 0.43
20 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (19 bp):
ATCTTAGATAAGATATGTA
Found at i:18769866 original size:11 final size:11
Alignment explanation
Indices: 18769850--18769993 Score: 56
Period size: 11 Copynumber: 14.5 Consensus size: 11
18769840 AAAATTAATT
18769850 AAAATATTATA
1 AAAATATTATA
*
18769861 AAAATA-TATTG
1 AAAATATTA-TA
*
18769872 AAAATTTTATA
1 AAAATATTATA
*
18769883 AAATTA-T-TA
1 AAAATATTATA
* *
18769892 GATAT-TTATA
1 AAAATATTATA
18769902 AAAA-A-TATA
1 AAAATATTATA
18769911 AAAATATT-T-
1 AAAATATTATA
*
18769920 -AAATTTTATTA
1 AAAATATTA-TA
18769931 AAAAT-TTA-A
1 AAAATATTATA
18769940 AAAATA-T-T-
1 AAAATATTATA
18769948 AAAA-ATT-TA
1 AAAATATTATA
18769957 AAAATA-TATA
1 AAAATATTATA
*
18769967 GAAAT-TTATTA
1 AAAATATTA-TA
18769978 AAAACTA-TATA
1 AAAA-TATTATA
18769989 AAAAT
1 AAAAT
18769994 CGTTACAAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 43
0.64 0.08 0.28
Matches are distributed among these distances:
7 1 0.01
8 12 0.12
9 25 0.25
10 20 0.20
11 32 0.32
12 9 0.09
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAATATTATA
Found at i:18769885 original size:21 final size:20
Alignment explanation
Indices: 18769838--18769965 Score: 90
Period size: 19 Copynumber: 6.5 Consensus size: 20
18769828 ATTTTAATCA
*
18769838 ATAAAAT-TAATTAAAATATT
1 ATAAAATAT-ATTAAAATTTT
18769858 ATAAAAATATATTGAAAATTTT
1 AT-AAAATATATT-AAAATTTT
*
18769880 ATAAAAT-TATT-AGATATTT
1 ATAAAATATATTAAAAT-TTT
* * *
18769899 ATAAAAAATATAAAAATATT
1 ATAAAATATATTAAAATTTT
* * *
18769919 -TAAATTTTATTAAAAATTT
1 ATAAAATATATTAAAATTTT
*
18769938 A-AAAA-ATATTAAAAATTT
1 ATAAAATATATTAAAATTTT
18769956 A-AAAATATAT
1 ATAAAATATAT
18769966 AGAAATTTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 17
0.74 0.12 0.15
Matches are distributed among these distances:
18 20 0.23
19 29 0.34
20 11 0.13
21 16 0.19
22 10 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAAATATATTAAAATTTT
Found at i:18769914 original size:29 final size:29
Alignment explanation
Indices: 18769882--18769979 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 29
18769872 AAAATTTTAT
*
18769882 AAAATTATTAGATATTTATAAAAAATATA
1 AAAATTATTAAATATTTATAAAAAATATA
* *
18769911 AAAA-TATTTAAAT-TTTATTAAAAATTTA
1 AAAATTA-TTAAATATTTATAAAAAATATA
* * *
18769939 AAAAATATTAAAAATTTA-AAAATATATA
1 AAAATTATTAAATATTTATAAAAAATATA
*
18769967 GAAATTTATTAAA
1 -AAAATTATTAAA
18769980 AACTATATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
28 31 0.55
29 25 0.45
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAATTATTAAATATTTATAAAAAATATA
Found at i:18769939 original size:18 final size:18
Alignment explanation
Indices: 18769847--18769993 Score: 89
Period size: 18 Copynumber: 7.5 Consensus size: 18
18769837 AATAAAATTA
18769847 ATTAAAATATTATAAAAATAT
1 ATTAAAA-ATT-TAAAAA-AT
* *
18769868 ATTGAAAATTTTATAAAATT
1 ATT-AAAAATTTA-AAAAAT
* *
18769888 ATTAGATATTTATAAAAAAT
1 ATTA-AAAATT-TAAAAAAT
* ***
18769908 ATAAAAATATTTAAATTTT
1 ATTAAAA-ATTTAAAAAAT
18769927 ATTAAAAATTTAAAAAAT
1 ATTAAAAATTTAAAAAAT
18769945 ATTAAAAATTT-AAAAAT
1 ATTAAAAATTTAAAAAAT
*
18769962 ATATAGAAATTTATTAAAAACT
1 AT-TAAAAATTTA--AAAAA-T
18769984 ATATAAAAAT
1 AT-TAAAAAT
18769994 CGTTACAAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
17 8 0.08
18 27 0.27
19 14 0.14
20 21 0.21
21 16 0.16
22 14 0.14
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTAAAAATTTAAAAAAT
Found at i:18770038 original size:22 final size:23
Alignment explanation
Indices: 18770006--18770048 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
18769996 TTACAAAATA
18770006 TAAAAGATATAGAAAAATTATTT
1 TAAAAGATATAGAAAAATTATTT
18770029 TAAAA-ATATAGAAAAATTAT
1 TAAAAGATATAGAAAAATTAT
18770049 AAAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
TAAAAGATATAGAAAAATTATTT
Found at i:18770055 original size:22 final size:22
Alignment explanation
Indices: 18770007--18770055 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18769997 TACAAAATAT
* **
18770007 AAAAGATATAGAAAAATTATTT
1 AAAAAATATAGAAAAATTATAA
*
18770029 TAAAAATATAGAAAAATTATAA
1 AAAAAATATAGAAAAATTATAA
18770051 AAAAA
1 AAAAA
18770056 TAACTTTAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (22 bp):
AAAAAATATAGAAAAATTATAA
Found at i:18770814 original size:24 final size:24
Alignment explanation
Indices: 18770766--18770814 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
18770756 AATTTTTTAA
**
18770766 TTTTATTTAATATTAATATGAATT
1 TTTTATTTAATATTAATAAAAATT
18770790 TTTTATTTAATATT-ATAAAATATT
1 TTTTATTTAATATTAATAAAA-ATT
18770814 T
1 T
18770815 ATGTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTATTTAATATTAATAAAAATT
Found at i:18775058 original size:11 final size:11
Alignment explanation
Indices: 18775042--18775094 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
18775032 TAAGTTCTTG
18775042 AAAAAATTTCA
1 AAAAAATTTCA
*
18775053 AAAAAA-TTGA
1 AAAAAATTTCA
**
18775063 AAAAAATTAGA
1 AAAAAATTTCA
18775074 AAAAAA-TTCAA
1 AAAAAATTTC-A
18775085 AAAAAATTTC
1 AAAAAATTTC
18775095 GAAACAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 10 0.29
11 22 0.63
12 3 0.09
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.23
Consensus pattern (11 bp):
AAAAAATTTCA
Found at i:18775089 original size:10 final size:10
Alignment explanation
Indices: 18775042--18775089 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
18775032 TAAGTTCTTG
*
18775042 AAAAAATTTC
1 AAAAAAATTC
*
18775052 AAAAAAATTG
1 AAAAAAATTC
*
18775062 AAAAAAATTAG
1 AAAAAAATT-C
18775073 AAAAAAATTC
1 AAAAAAATTC
18775083 AAAAAAA
1 AAAAAAA
18775090 ATTTCGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 24 0.71
11 10 0.29
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:18776350 original size:18 final size:20
Alignment explanation
Indices: 18776329--18776374 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
18776319 GCATGTGACC
18776329 AAGAAAAGA-AAATTGAA-A
1 AAGAAAAGAGAAATTGAAGA
*
18776347 AAG-AGAGAGAAATTGAAGA
1 AAGAAAAGAGAAATTGAAGA
18776366 AAGAAAAGA
1 AAGAAAAGA
18776375 TAGTGAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 4 0.17
20 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (20 bp):
AAGAAAAGAGAAATTGAAGA
Found at i:18776506 original size:15 final size:15
Alignment explanation
Indices: 18776486--18776530 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
18776476 AAATGAGTTA
*
18776486 GAAAAAGAAACGAGT
1 GAAAAAGAAACAAGT
*
18776501 GAAAAAGATACAAGT
1 GAAAAAGAAACAAGT
*
18776516 GAACAAGAAA-AAGT
1 GAAAAAGAAACAAGT
18776530 G
1 G
18776531 TAACACCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.60, C:0.07, G:0.24, T:0.09
Consensus pattern (15 bp):
GAAAAAGAAACAAGT
Found at i:18777695 original size:27 final size:27
Alignment explanation
Indices: 18777664--18777740 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
18777654 GTGCAAAACA
18777664 ATCATTTTAC-CTTACAAGGGTATGTCG
1 ATCATTTTACAC-TACAAGGGTATGTCG
* *
18777691 GTCATTTTACACTACAAGGGTATTTCG
1 ATCATTTTACACTACAAGGGTATGTCG
* *
18777718 ATAATTTTACACTATAAGGGTAT
1 ATCATTTTACACTACAAGGGTAT
18777741 TTTAATAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (27 bp):
ATCATTTTACACTACAAGGGTATGTCG
Found at i:18777741 original size:27 final size:27
Alignment explanation
Indices: 18777707--18778210 Score: 594
Period size: 27 Copynumber: 18.7 Consensus size: 27
18777697 TTACACTACA
* *
18777707 AGGGTATTTCGATAATTTTACACTAT-A
1 AGGGTATTTCGATAATTTTACA-AATCG
** *
18777734 AGGGTATTTTAATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18777761 AGGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
**
18777788 AGGGTATTTTAATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
18777815 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
18777842 AGGGTGTTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
18777869 AGGGTGTTTC-AGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
*
18777896 AGGGTGTTTC-AGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * * * *
18777923 AGAGTGTTCCGATAATTTCACAAAT-T
1 AGGGTATTTCGATAATTTTACAAATCG
18777949 AGGGGTATTTCGATAATTTTACAAATCG
1 A-GGGTATTTCGATAATTTTACAAATCG
* *
18777977 AGGCTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18778004 AGGGTGTTTTGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * * *
18778031 AGGGTGTTTCGGTAATTTCACAAGTCA
1 AGGGTATTTCGATAATTTTACAAATCG
18778058 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18778085 AGGATATTTC-AGTAATTTCAC-AATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
*
18778111 AGGGTATTTC-AGTAATTTTACAAAT-T
1 AGGGTATTTCGA-TAATTTTACAAATCG
18778137 AGGGGTATTTCGATAATTTTACAAATCG
1 A-GGGTATTTCGATAATTTTACAAATCG
*
18778165 AGGGTATTTCGATAATTTTACAAA-CA
1 AGGGTATTTCGATAATTTTACAAATCG
*
18778191 AGGGGCATTTCGATAATTTT
1 A-GGGTATTTCGATAATTTT
18778211 TCTTTATTAT
Statistics
Matches: 417, Mismatches: 49, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
26 32 0.08
27 381 0.91
28 4 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:18781120 original size:27 final size:27
Alignment explanation
Indices: 18781090--18781151 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
18781080 TATGTCGGTC
* *
18781090 ATTTTACACTATAAGGGAATTTTGATA
1 ATTTTACACTACAAGGGAATTTCGATA
*
18781117 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGAATTTCGATA
18781144 ATTTTACA
1 ATTTTACA
18781152 AATTGAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGAATTTCGATA
Found at i:18781160 original size:27 final size:27
Alignment explanation
Indices: 18781103--18781576 Score: 414
Period size: 27 Copynumber: 17.7 Consensus size: 27
18781093 TTACACTATA
* * * *
18781103 AGGGAATTTTGATAATTTTAC-ACTACA
1 AGGGTATTTCGATAATTTTACAAAT-CG
*
18781130 AGGGTATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18781157 AGGGTGTTTCCG-TAATTTTACAAATTG
1 AGGGTATTT-CGATAATTTTACAAATCG
18781184 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * **
18781211 AGAGT-TTTCGATAATTTTAAAAATTA
1 AGGGTATTTCGATAATTTTACAAATCG
*
18781237 AGGGTGTTTC-AGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * *
18781264 AGGGTGTTTC-AGTAATTTTATAAATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * *
18781291 AGGATGTTTC-AGTAATTTCACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
18781318 GGGGTATTTC-AGTAATTTTACAAATCA
1 AGGGTATTTCGA-TAATTTTACAAATCG
18781345 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
18781372 AGGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * * *
18781399 AGGGTGTGTCGTTAATTTCATAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
18781426 GGGGTATTTTGATAATTTTTCAAATCA
1 AGGGTATTTCGATAATTTTACAAATCG
** * *
18781453 AGGGTATTTAAATAATTTCAC-AGTCG
1 AGGGTATTTCGATAATTTTACAAATCG
**
18781479 AGGGTATTTCGATAATTTTACAAATTA
1 AGGGTATTTCGATAATTTTACAAATCG
*
18781506 AAGGTATTTC-AGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
18781533 A-GATATTTCGGTAATTTTACAAA-CTG
1 AGGGTATTTCGATAATTTTACAAATC-G
*
18781559 GGGGTATTTCCG-TAATTT
1 AGGGTATTT-CGATAATTT
18781577 CTCTTTATTA
Statistics
Matches: 371, Mismatches: 64, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.00
26 67 0.18
27 296 0.80
28 7 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:18784453 original size:27 final size:27
Alignment explanation
Indices: 18784406--18784497 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
18784396 GGGCAAAAAA
* * *
18784406 ATCATTTTACCCTATAGGGGTATGTCG
1 ATCATTTTACACTACAAGGGTATGTCG
* * *
18784433 GTCATTTTACACTACAAGGGTATTTTG
1 ATCATTTTACACTACAAGGGTATGTCG
* * *
18784460 ATAATTTTACACTACAAGGGTATTTTG
1 ATCATTTTACACTACAAGGGTATGTCG
*
18784487 ATAATTTTACA
1 ATCATTTTACA
18784498 AATCGAGGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (27 bp):
ATCATTTTACACTACAAGGGTATGTCG
Found at i:18784506 original size:27 final size:27
Alignment explanation
Indices: 18784447--18784538 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
18784437 TTTTACACTA
*
18784447 CAAGGGTATTTTGATAATTTTAC-ACT
1 CAAGGGTATTTTGATAATTTTACAAAT
18784473 ACAAGGGTATTTTGATAATTTTACAAAT
1 -CAAGGGTATTTTGATAATTTTACAAAT
* * * * *
18784501 CGAGGGTGTTTCGGTAATTTTAAAAAT
1 CAAGGGTATTTTGATAATTTTACAAAT
18784528 CAAGGGTATTT
1 CAAGGGTATTT
18784539 GTAACACCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 54 0.96
28 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGATAATTTTACAAAT
Found at i:18786148 original size:29 final size:29
Alignment explanation
Indices: 18786114--18786187 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
18786104 TAATCAACCG
*
18786114 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
18786143 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
18786172 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
18786188 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:18787916 original size:27 final size:27
Alignment explanation
Indices: 18787876--18788320 Score: 390
Period size: 27 Copynumber: 16.6 Consensus size: 27
18787866 GGCTATCACA
*
18787876 GTATTTCGGTAATTTTACAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
18787903 GCATTTCGATAATTTTACAAATTGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
18787930 GTGTTTCAATAATTTTACAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* * *
18787957 GTGTTTTGGTAATTTTACAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* ** *
18787984 GTGTTTC-AGTAATTTTACAAATTTAGT
1 GTATTTCGA-TAATTTTACAAATCGAGG
*
18788011 GTGTTTCGATAATTTTACAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
18788038 GTGTTTC-AGTAATTTCACAAATCG-GAG
1 GTATTTCGA-TAATTTTACAAATCGAG-G
* *
18788065 GTATTTCGGTAATTTTACAAATCGAAG
1 GTATTTCGATAATTTTACAAATCGAGG
*
18788092 GTATTTCGATAATTTTATAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* * * *
18788119 GTGTTT-TAGTAATTTTACAAATTGATG
1 GTATTTCGA-TAATTTTACAAATCGAGG
*
18788146 GTGTTTC-AGT-ATTTTCACAAATCG-GG
1 GTATTTCGA-TAATTTT-ACAAATCGAGG
* * * *
18788172 GGATTTTGGTAATTTTACAAATCAAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* * *
18788199 GTATTTC-AGTAATTTCAC-AGTTGAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
* *
18788225 GTATTTTGGTAATTTTACAAATC-AGGG
1 GTATTTCGATAATTTTACAAATCGA-GG
* *
18788252 GTATTTCGATAATTTTACTAA-CTGGGG
1 GTATTTCGATAATTTTACAAATC-GAGG
* * *
18788279 GTGTTTCGGTAATTTTACAAATCGGGG
1 GTATTTCGATAATTTTACAAATCGAGG
*
18788306 GTATTTCGGTAATTT
1 GTATTTCGATAATTT
18788321 CTCTTTATTA
Statistics
Matches: 341, Mismatches: 58, Indels: 38
0.78 0.13 0.09
Matches are distributed among these distances:
26 42 0.12
27 297 0.87
28 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (27 bp):
GTATTTCGATAATTTTACAAATCGAGG
Found at i:18787970 original size:54 final size:54
Alignment explanation
Indices: 18787879--18788320 Score: 452
Period size: 54 Copynumber: 8.2 Consensus size: 54
18787869 TATCACAGTA
* ** * *
18787879 TTTCGGTAATTTTACAAATCGAGGGCATTTCGATAATTTTACAAATTGAGGGTG
1 TTTCAGTAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTG
* *
18787933 TTTCAATAATTTTACAAATCGAGGGTGTTTTGGTAATTTTACAAATCGAGGGTG
1 TTTCAGTAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTG
** * *
18787987 TTTCAGTAATTTTACAAATTTAGTGTGTTTCGATAATTTTACAAATCGAGGGTG
1 TTTCAGTAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTG
* * * *
18788041 TTTCAGTAATTTCACAAATCG-GAGGTATTTCGGTAATTTTACAAATCGAAGGTA
1 TTTCAGTAATTTTACAAATCGAG-GGTGTTTCGGTAATTTTACAAATCGAGGGTG
* ** * *
18788095 TTTC-GATAATTTTATAAATCGAGGGTGTTTTAGTAATTTTACAAATTGATGGTG
1 TTTCAG-TAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTG
* * *
18788149 TTTCAGT-ATTTTCACAAATCG-GGG-GATTTTGGTAATTTTACAAATCAAGGGTA
1 TTTCAGTAATTTT-ACAAATCGAGGGTG-TTTCGGTAATTTTACAAATCGAGGGTG
* * * * * *
18788202 TTTCAGTAATTTCAC-AGTTGAGGGTATTTTGGTAATTTTACAAATC-AGGGGTA
1 TTTCAGTAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGA-GGGTG
* * * *
18788255 TTTC-GATAATTTTACTAA-CTGGGGGTGTTTCGGTAATTTTACAAATCGGGGGTA
1 TTTCAG-TAATTTTACAAATC-GAGGGTGTTTCGGTAATTTTACAAATCGAGGGTG
*
18788309 TTTCGGTAATTT
1 TTTCAGTAATTT
18788321 CTCTTTATTA
Statistics
Matches: 327, Mismatches: 46, Indels: 30
0.81 0.11 0.07
Matches are distributed among these distances:
52 6 0.02
53 81 0.25
54 237 0.72
55 3 0.01
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (54 bp):
TTTCAGTAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTG
Found at i:18788023 original size:81 final size:81
Alignment explanation
Indices: 18787879--18788320 Score: 457
Period size: 81 Copynumber: 5.5 Consensus size: 81
18787869 TATCACAGTA
* * * * *
18787879 TTTCGGTAATTTTACAAATCGAGGGCATTTCGATAATTTTACAAATTGAGGGTGTTTCAATAATT
1 TTTCAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTTAGGGTGTTTCGATAATT
18787944 TTACAAATCGAGGGTG
66 TTACAAATCGAGGGTG
** * * *
18787960 TTTTGGTAATTTTACAAATCGAGGGTGTTTCAGTAATTTTACAAATTTAGTGTGTTTCGATAATT
1 TTTCAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTTAGGGTGTTTCGATAATT
18788025 TTACAAATCGAGGGTG
66 TTACAAATCGAGGGTG
* ** * *
18788041 TTTCAGTAATTTCACAAATCG-GAGGTATTTCGGTAATTTTACAAATCGAAGGTATTTCGATAAT
1 TTTCAGTAATTTTACAAATCGAG-GGTATTTCGGTAATTTTACAAATTTAGGGTGTTTCGATAAT
*
18788105 TTTATAAATCGAGGGTG
65 TTTACAAATCGAGGGTG
* * * * * * * * *
18788122 TTTTAGTAATTTTACAAATTGATGGTGTTTCAGT-ATTTTCACAAA--TCGGGGGATTTTGGTAA
1 TTTCAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTT-ACAAATTTAGGGTG-TTTCGATAA
* *
18788184 TTTTACAAATCAAGGGTA
64 TTTTACAAATCGAGGGTG
* * * * * *
18788202 TTTCAGTAATTTCAC-AGTTGAGGGTATTTTGGTAATTTTACAAA-TCAGGGGTATTTCGATAAT
1 TTTCAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTTA-GGGTGTTTCGATAAT
* *
18788265 TTTACTAA-CTGGGGGTG
65 TTTACAAATC-GAGGGTG
* *
18788282 TTTCGGTAATTTTACAAATCGGGGGTATTTCGGTAATTT
1 TTTCAGTAATTTTACAAATCGAGGGTATTTCGGTAATTT
18788321 CTCTTTATTA
Statistics
Matches: 294, Mismatches: 58, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
79 21 0.07
80 78 0.27
81 195 0.66
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (81 bp):
TTTCAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTTAGGGTGTTTCGATAATT
TTACAAATCGAGGGTG
Found at i:18788734 original size:28 final size:28
Alignment explanation
Indices: 18788649--18788726 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
18788639 GCCCAATCTC
* *
18788649 ATTCACATGGCCCATCAGGCCCCATCAT
1 ATTCATATGGCCCATCAAGCCCCATCAT
*
18788677 ATTCATATGGCCAATCAAGCCCCATCAT
1 ATTCATATGGCCCATCAAGCCCCATCAT
*
18788705 ATTCATATGGCCCATCACGCCC
1 ATTCATATGGCCCATCAAGCCC
18788727 TATAATATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (28 bp):
ATTCATATGGCCCATCAAGCCCCATCAT
Found at i:18790073 original size:46 final size:46
Alignment explanation
Indices: 18790023--18790198 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
18790013 TGGTTGAGCA
*
18790023 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
18790069 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
18790116 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
18790162 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18790199 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 62 0.58
47 28 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:18790179 original size:93 final size:93
Alignment explanation
Indices: 18790020--18790191 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
18790010 GGATGGTTGA
* * *
18790020 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
18790085 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
18790113 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
18790178 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
18790192 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:18802419 original size:59 final size:59
Alignment explanation
Indices: 18802327--18802445 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
18802317 CTTTGCTCTT
*
18802327 GAGCTTAATTAGACAAATAAATTGATTTAATCATTTGAGCATC-AAAATGAGGAACACAA
1 GAGCTTAATTAAACAAATAAATTGATTTAATCATTTGAGCATCGAAAA-GAGGAACACAA
18802386 GAGCTTAATTAAACAAATAAATTGATTTAATCATTTGAGCATCGAAAAGAGGAACACAA
1 GAGCTTAATTAAACAAATAAATTGATTTAATCATTTGAGCATCGAAAAGAGGAACACAA
18802445 G
1 G
18802446 GCACTTAGCC
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 54 0.93
60 4 0.07
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (59 bp):
GAGCTTAATTAAACAAATAAATTGATTTAATCATTTGAGCATCGAAAAGAGGAACACAA
Found at i:18810277 original size:39 final size:40
Alignment explanation
Indices: 18810112--18810283 Score: 249
Period size: 40 Copynumber: 4.3 Consensus size: 40
18810102 GCTCCTCGTT
* *
18810112 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
18810152 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
18810192 CCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
18810232 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
18810271 CAAATGCCTTCGG
1 CAAATGCCTTCGG
18810284 ATCTTAGTCC
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.27
40 88 0.72
41 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:18810320 original size:79 final size:79
Alignment explanation
Indices: 18810112--18810333 Score: 232
Period size: 79 Copynumber: 2.8 Consensus size: 79
18810102 GCTCCTCGTT
* * ** * *
18810112 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
* *
18810177 ATTTAGTAACTCGCA
65 AATTAGTAACTCACA
* * * * *
18810192 CCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
*
18810256 AATTAGTATCTCACA
65 AATTAGTAACTCACA
** * *
18810271 CAAATGCCTTC-GGATCTTAGTCCGAATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGAATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCC
18810334 AGACATCATT
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
78 3 0.03
79 57 0.48
80 56 0.47
81 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCACA
Found at i:18810320 original size:119 final size:120
Alignment explanation
Indices: 18810114--18810329 Score: 269
Period size: 119 Copynumber: 1.8 Consensus size: 120
18810104 TCCTCGTTCA
* * *
18810114 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGAAT
* * *
18810179 TTAGTAACTCGCACCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACCAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
18810234 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACACAAATGCCTTC-GGATCTTAGTCCGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGA
* *
18810296 ATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTA
64 ATATAGTAAC-TAGCACCAAAGCCTTCGGGACTTA
18810330 GCCCAGACAT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
118 4 0.05
119 61 0.75
120 16 0.20
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGAAT
ATAGTAACTAGCACCAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:18814798 original size:5 final size:6
Alignment explanation
Indices: 18814783--18814807 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18814773 GTTGAGTTTA
18814783 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
18814808 TTTTGCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:18833152 original size:46 final size:46
Alignment explanation
Indices: 18833088--18833901 Score: 1469
Period size: 46 Copynumber: 17.7 Consensus size: 46
18833078 CCGCCCCTAA
* * * *
18833088 GTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAG
*
18833134 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-
1 GTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCAT-AG
*
18833182 -CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833227 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833273 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833319 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833365 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833411 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833457 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833503 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833549 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833595 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833641 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833687 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833733 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833779 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833825 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
18833871 GTGAACTCGGACTCAACTCAACGAGTTCGGA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGA
18833902 TGCTCAACCA
Statistics
Matches: 750, Mismatches: 6, Indels: 24
0.96 0.01 0.03
Matches are distributed among these distances:
42 2 0.00
43 4 0.01
44 3 0.00
45 3 0.00
46 700 0.93
47 29 0.04
48 1 0.00
49 3 0.00
50 3 0.00
51 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
Found at i:18834356 original size:30 final size:30
Alignment explanation
Indices: 18834322--18834381 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
18834312 ATTTAATACG
18834322 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
18834352 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
18834382 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:18836262 original size:45 final size:45
Alignment explanation
Indices: 18836187--18836323 Score: 220
Period size: 45 Copynumber: 3.0 Consensus size: 45
18836177 AAATGGGAGC
* *
18836187 ACATGGCCATGTCCCAGCCTATGTCCGACCCCGTGTAACTCTCTG
1 ACATGGCCATGTCCCAGCCTGTGTCTGACCCCGTGTAACTCTCTG
* * *
18836232 ACATGGCCATGTCCCAGCCCGTGTCTGACCCTGTGTAACTTTCTG
1 ACATGGCCATGTCCCAGCCTGTGTCTGACCCCGTGTAACTCTCTG
*
18836277 ACATGGCCATGTCCCAGCCTGTGTCTGATCCCGTGTAACTCTCTG
1 ACATGGCCATGTCCCAGCCTGTGTCTGACCCCGTGTAACTCTCTG
18836322 AC
1 AC
18836324 TTAGGTTACA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (45 bp):
ACATGGCCATGTCCCAGCCTGTGTCTGACCCCGTGTAACTCTCTG
Found at i:18838161 original size:21 final size:20
Alignment explanation
Indices: 18838135--18838173 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18838125 AAACTTGTAT
*
18838135 ATCTATCAATAAGCATTCATA
1 ATCTATCAAGAAGC-TTCATA
18838156 ATCTATCAAGAAGCTTCA
1 ATCTATCAAGAAGCTTCA
18838174 AAGTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (20 bp):
ATCTATCAAGAAGCTTCATA
Found at i:18845356 original size:42 final size:42
Alignment explanation
Indices: 18845243--18845404 Score: 152
Period size: 42 Copynumber: 3.8 Consensus size: 42
18845233 TACGATACCA
* *
18845243 ATGCCATATCCCAGATATGGTCTTACATGTAA-TCTCATA-TCG
1 ATGCCATATCCCAGACATGGTCTTACACG-AAGTCTCATACT-G
* * * *
18845285 ATTCTAATAGCCTAG-CTATGGTCTTACACGAAGTCTCATA-TCG
1 ATGC-CATATCCCAGAC-ATGGTCTTACACGAAGTCTCATACT-G
** *
18845328 ATGCCATATCTTAGACATGGTTTTACACGAAGTCTCATACTG
1 ATGCCATATCCCAGACATGGTCTTACACGAAGTCTCATACTG
* *
18845370 ATGCCATATCCCAGATATGGTCTTACACGTAGTCT
1 ATGCCATATCCCAGACATGGTCTTACACGAAGTCT
18845405 TAGTAACCCT
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 65 0.66
43 34 0.34
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAGTCTCATACTG
Found at i:18845890 original size:22 final size:22
Alignment explanation
Indices: 18845865--18845906 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18845855 CTACATTTTT
*
18845865 CATTTAATCACACTTTTACACA
1 CATTTAATAACACTTTTACACA
* *
18845887 CATTTTATAACATTTTTACA
1 CATTTAATAACACTTTTACA
18845907 AATTGGTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (22 bp):
CATTTAATAACACTTTTACACA
Found at i:18847320 original size:11 final size:12
Alignment explanation
Indices: 18847297--18847326 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
18847287 AATCAAATGG
18847297 CCAAAATCATTA
1 CCAAAATCATTA
18847309 CCAAAA-CATTA
1 CCAAAATCATTA
18847320 CCAAAAT
1 CCAAAAT
18847327 GACTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (12 bp):
CCAAAATCATTA
Found at i:18848507 original size:21 final size:20
Alignment explanation
Indices: 18848483--18848521 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18848473 AAACCTATAT
18848483 ATCTATCAACAAACATTCATA
1 ATCTATCAACAAA-ATTCATA
*
18848504 ATCTATCAAGAAAATTCA
1 ATCTATCAACAAAATTCA
18848522 AATTGCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.28
Consensus pattern (20 bp):
ATCTATCAACAAAATTCATA
Found at i:18850656 original size:40 final size:40
Alignment explanation
Indices: 18850612--18850692 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
18850602 TTGAATTAAG
* *
18850612 AAAAATATTACGAGGGTGAGAAAT-AGTGCATTTATGGCAT
1 AAAAATAATACAAGGGTGAGAAATGA-TGCATTTATGGCAT
*
18850652 AAAAATAATGCAAGGGTGAGAAATGATGCATTTATGGCAT
1 AAAAATAATACAAGGGTGAGAAATGATGCATTTATGGCAT
18850692 A
1 A
18850693 TTTGGTGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (40 bp):
AAAAATAATACAAGGGTGAGAAATGATGCATTTATGGCAT
Found at i:18852780 original size:39 final size:39
Alignment explanation
Indices: 18852737--18852825 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
18852727 TAATTTATTT
18852737 TAGGAGTAGTTCTCTAAATTATAGGAAGTAGAGGGTGAA
1 TAGGAGTAGTTCTCTAAATTATAGGAAGTAGAGGGTGAA
* * *
18852776 TAGGAATAGTTTTCTATATTATAGGAAGTAGAGGGTGAA
1 TAGGAGTAGTTCTCTAAATTATAGGAAGTAGAGGGTGAA
*
18852815 TAAGAGTAGTT
1 TAGGAGTAGTT
18852826 TTACTATTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.31
Consensus pattern (39 bp):
TAGGAGTAGTTCTCTAAATTATAGGAAGTAGAGGGTGAA
Found at i:18864585 original size:42 final size:39
Alignment explanation
Indices: 18864527--18864635 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 39
18864517 CTAGAGTTCA
18864527 ACATTAGCGGCG-TTTCTAAACAAACGCCACTATAGATCGG
1 ACATTAGCGGCGTTTTCTAAA-AAACGCCACTATAGATC-G
* *
18864567 ACATTAGCGGCGTTTTTCT-AAAAGCGCCGCTATAGATCG
1 ACATTAGCGGCG-TTTTCTAAAAAACGCCACTATAGATCG
*
18864606 AGCATTAGCGGCGCTTTTATAAAAAACGCC
1 A-CATTAGCGGCG-TTTTCTAAAAAACGCC
18864636 GCAAATGCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
39 2 0.03
40 43 0.72
41 10 0.17
42 5 0.08
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (39 bp):
ACATTAGCGGCGTTTTCTAAAAAACGCCACTATAGATCG
Found at i:18865379 original size:29 final size:28
Alignment explanation
Indices: 18865321--18865399 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
18865311 TAAAGTTCAG
* *
18865321 GGATTAGTGGG-TAAAGGTTAAGGGTTAT
1 GGATTA-TGGGTTTAAGGTTAAGGGTCAT
18865349 GGATTATGGGTTTAAGGATTAAGGGTCAT
1 GGATTATGGGTTTAAGG-TTAAGGGTCAT
*
18865378 GGGTTATGGGTTTAATGGTTAA
1 GGATTATGGGTTTAA-GGTTAA
18865400 AGGGATAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.09
28 11 0.24
29 28 0.62
30 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.37, T:0.35
Consensus pattern (28 bp):
GGATTATGGGTTTAAGGTTAAGGGTCAT
Found at i:18865459 original size:42 final size:41
Alignment explanation
Indices: 18865389--18865470 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
18865379 GGTTATGGGT
* **
18865389 TTAATGGTTAAAGGGATAGGGGTTAGGGGTTAATGGGTTTAA
1 TTAATGGTTAAAGGGACAGGGGAAAGGGGTTAAT-GGTTTAA
* * *
18865431 TTAATGGTTAAGGGGACATGGGAAAGGGGTTTATGGTTTA
1 TTAATGGTTAAAGGGACAGGGGAAAGGGGTTAATGGTTTA
18865471 TGAGCTAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 6 0.18
42 28 0.82
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.33
Consensus pattern (41 bp):
TTAATGGTTAAAGGGACAGGGGAAAGGGGTTAATGGTTTAA
Found at i:18865525 original size:14 final size:15
Alignment explanation
Indices: 18865508--18865540 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18865498 TTTGGTTTAT
18865508 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
18865522 GGTTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
18865537 GGTT
1 GGTT
18865541 AGGGTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.39
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:18865525 original size:21 final size:21
Alignment explanation
Indices: 18865501--18865556 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
18865491 TAGAGATTTT
*
18865501 GGTTTATGGTTTAAGGGTTGG
1 GGTTTATGGTTTAAGGGTTAG
* *
18865522 GGTTTAAGGTTTAGGGGTTAG
1 GGTTTATGGTTTAAGGGTTAG
18865543 GGTTTCATGGTTTA
1 GGTTT-ATGGTTTA
18865557 GGTATTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.16, C:0.02, G:0.39, T:0.43
Consensus pattern (21 bp):
GGTTTATGGTTTAAGGGTTAG
Found at i:18867379 original size:20 final size:20
Alignment explanation
Indices: 18867356--18867394 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
18867346 TAAACATGGT
18867356 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
18867376 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
18867395 TGTATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:18867523 original size:24 final size:24
Alignment explanation
Indices: 18867444--18867588 Score: 179
Period size: 25 Copynumber: 6.0 Consensus size: 24
18867434 GGAGGAAGTG
*
18867444 TAAAAGGGCTTATCCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
18867468 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
* *
18867493 GATAAAGGGCTTATGCCCAAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
18867518 TAAAAGGGCTTATG-CCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
18867541 TAAAAGGGCTT-TGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
18867564 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
18867589 ATGATAAAGT
Statistics
Matches: 108, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
22 2 0.02
23 34 0.31
24 19 0.18
25 53 0.49
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:18875391 original size:11 final size:11
Alignment explanation
Indices: 18875356--18875410 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
18875346 ATGGTATGTG
18875356 TGATATGCACA
1 TGATATGCACA
* *
18875367 TGACATG--TA
1 TGATATGCACA
18875376 TGATATGCACA
1 TGATATGCACA
*
18875387 TGATATG--TA
1 TGATATGCACA
18875396 TGATATGCACA
1 TGATATGCACA
18875407 TGAT
1 TGAT
18875411 GTATTCATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (11 bp):
TGATATGCACA
Found at i:18875410 original size:20 final size:20
Alignment explanation
Indices: 18875344--18875410 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
18875334 ATTTTGATAA
* *
18875344 ACATGGTATGTGTGATATGC
1 ACATGATATGTATGATATGC
*
18875364 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
18875384 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
18875404 ACATGAT
1 ACATGAT
18875411 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:18875525 original size:23 final size:24
Alignment explanation
Indices: 18875459--18875564 Score: 162
Period size: 23 Copynumber: 4.4 Consensus size: 24
18875449 GGAGGAAGTG
18875459 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
18875483 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
18875508 TAAAAGGGCTTATG-CCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
18875531 TAAAAAGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
18875554 TAAAAGAGGCT
1 TAAAAG-GGCT
18875565 AGGTCTCCAG
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
22 2 0.03
23 33 0.44
24 17 0.23
25 23 0.31
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:18875575 original size:48 final size:48
Alignment explanation
Indices: 18875459--18875578 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 48
18875449 GGAGGAAGTG
* *
18875459 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTA-GGCCCAGTTATGATAAAAGGCTTATGCCCCAGTTAT
* *
18875508 TAAAAGGGCTTATGCCCAGTTATTA-AAAAGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTAGGCCCAGTTATGATAAAAGGCTTATGCCCCAGTTAT
18875554 TAAAAGAGGC-TAGGTCTCCAGTTAT
1 TAAAAG-GGCTTAGG-C-CCAGTTAT
18875579 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
46 21 0.33
47 12 0.19
48 18 0.29
49 12 0.19
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (48 bp):
TAAAAGGGCTTAGGCCCAGTTATGATAAAAGGCTTATGCCCCAGTTAT
Found at i:18875807 original size:31 final size:31
Alignment explanation
Indices: 18875772--18875835 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
18875762 CGTTTACAGT
18875772 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* ** *
18875803 AAAGGCTTTGGCCCAGTGTTATGAAATGTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
18875834 AA
1 AA
18875836 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:18876656 original size:26 final size:27
Alignment explanation
Indices: 18876583--18876657 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
18876573 AATAATTTAA
*
18876583 AATTTTAAAGATTTCAAA-TTTAGAAT
1 AATTTTCAAGATTTCAAATTTTAGAAT
*
18876609 AAATTTCAAGATTTCAAATTTTA-AAT
1 AATTTTCAAGATTTCAAATTTTAGAAT
*
18876635 AATTTTCAATATTTCAAATTTTA
1 AATTTTCAAGATTTCAAATTTTA
18876658 TCTAATTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 40 0.91
27 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (27 bp):
AATTTTCAAGATTTCAAATTTTAGAAT
Found at i:18876803 original size:18 final size:17
Alignment explanation
Indices: 18876772--18876806 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
18876762 TAGTTGATTG
*
18876772 TTTTTTAATTTATATTA
1 TTTTTAAATTTATATTA
18876789 TTTTTAAATTATATATTA
1 TTTTTAAATT-TATATTA
18876807 AATAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTAAATTTATATTA
Found at i:18877347 original size:13 final size:13
Alignment explanation
Indices: 18877315--18877346 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
18877305 CTTAAGTGTT
18877315 TTTCCCCTAAAAC
1 TTTCCCCTAAAAC
18877328 TTTCCCCTAAAA-
1 TTTCCCCTAAAAC
18877340 TTTCCCC
1 TTTCCCC
18877347 CCTAACCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.25, C:0.41, G:0.00, T:0.34
Consensus pattern (13 bp):
TTTCCCCTAAAAC
Found at i:18880329 original size:10 final size:10
Alignment explanation
Indices: 18880314--18880341 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
18880304 TTCAATCAAG
18880314 GTATGAATAA
1 GTATGAATAA
18880324 GTATGAATAA
1 GTATGAATAA
18880334 GTATGAAT
1 GTATGAAT
18880342 TAATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.32
Consensus pattern (10 bp):
GTATGAATAA
Found at i:18881286 original size:9 final size:9
Alignment explanation
Indices: 18881263--18881390 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
18881253 ATTGATCATT
*
18881263 ACTTAAATA
1 ACTTACATA
*
18881272 AATTACATA
1 ACTTACATA
18881281 ACTTACATA
1 ACTTACATA
* *
18881290 ACTCATATA
1 ACTTACATA
18881299 ACTTACATA
1 ACTTACATA
*
18881308 ATTTACATAACA
1 ACTTACAT---A
18881320 ACTTACATA
1 ACTTACATA
*
18881329 ACTCACATA
1 ACTTACATA
18881338 ACTTACATA
1 ACTTACATA
*
18881347 ATTTACATA
1 ACTTACATA
*
18881356 ACTCACATA
1 ACTTACATA
*
18881365 ACGTACATAACA
1 ACTTACAT---A
18881377 ACTTACATA
1 ACTTACATA
18881386 ACTTA
1 ACTTA
18881391 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 80 0.83
12 16 0.17
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:18881332 original size:39 final size:39
Alignment explanation
Indices: 18881280--18881357 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
18881270 TAAATTACAT
*
18881280 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
18881319 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
18881358 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:18881357 original size:57 final size:57
Alignment explanation
Indices: 18881276--18881388 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
18881266 TAAATAAATT
* * **
18881276 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
18881333 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
18881389 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:18884501 original size:40 final size:40
Alignment explanation
Indices: 18884433--18884609 Score: 198
Period size: 40 Copynumber: 4.5 Consensus size: 40
18884423 ACCCAAGTAT
**
18884433 CTTCGGGAT-TTAG-CCGGATATAAAAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
18884472 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
18884512 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * * * *
18884552 CTTCGAGACATAGCCCAGATTTAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
18884592 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
18884610 TTATCATCCG
Statistics
Matches: 114, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 98 0.86
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:18884566 original size:80 final size:79
Alignment explanation
Indices: 18884433--18884609 Score: 221
Period size: 80 Copynumber: 2.2 Consensus size: 79
18884423 ACCCAAGTAT
* * * * *
18884433 CTTCGGGAT-TTAGCCGGATATAAAAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGC
1 CTTCGGG-TCTTAGCCGGATATAAAAACTAGCACAAATGCCTTCGAGACATAGCCCAGATATAGC
18884497 AACTCGCACAAATGC
65 AACTCGCACAAATGC
** * *
18884512 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGAGACATAGCCCAGATTTAGC
1 CTTCGGGTCTTAG-CCGGATATAAAAACTAGCACAAATGCCTTCGAGACATAGCCCAGATATAGC
*
18884577 AACTCGCACGAATGC
65 AACTCGCACAAATGC
*
18884592 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAG-CCGG
18884610 TTATCATCCG
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 1 0.01
79 11 0.13
80 72 0.86
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGGATATAAAAACTAGCACAAATGCCTTCGAGACATAGCCCAGATATAGCA
ACTCGCACAAATGC
Found at i:18912422 original size:34 final size:34
Alignment explanation
Indices: 18912384--18912449 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
18912374 GTAAAAGTCC
* *
18912384 AGTATCAGTTTGGGCCTTAGCCAATTACAGTATT
1 AGTATCAGTGTGAGCCTTAGCCAATTACAGTATT
* *
18912418 AGTATCAGTGTGAGCCTTAGCCCATTTCAGTA
1 AGTATCAGTGTGAGCCTTAGCCAATTACAGTA
18912450 ACAGTAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (34 bp):
AGTATCAGTGTGAGCCTTAGCCAATTACAGTATT
Found at i:18912518 original size:22 final size:22
Alignment explanation
Indices: 18912477--18912518 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
18912467 ATCAGAAATC
*
18912477 CTACCCGTCCATCCTCTACACT
1 CTACCCGTCCAGCCTCTACACT
18912499 CTACTCCGTCCAGCCT-TACA
1 CTAC-CCGTCCAGCCTCTACA
18912519 TTCCATGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.19, C:0.48, G:0.07, T:0.26
Consensus pattern (22 bp):
CTACCCGTCCAGCCTCTACACT
Found at i:18922164 original size:41 final size:41
Alignment explanation
Indices: 18922107--18922188 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
18922097 TACCACTAAA
* * *
18922107 TGTAACACCTCAAACCC-GACCTAGACGTTATGGCTGAATCT
1 TGTAACACCCCAAACCCAG-CCCAGACGTTATGGCCGAATCT
18922148 TGTAACACCCCAAACCCAGCCCAGACGTTATGGCCGAATCT
1 TGTAACACCCCAAACCCAGCCCAGACGTTATGGCCGAATCT
18922189 GATGTGTCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (41 bp):
TGTAACACCCCAAACCCAGCCCAGACGTTATGGCCGAATCT
Found at i:18923236 original size:11 final size:11
Alignment explanation
Indices: 18923222--18923275 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
18923212 ATATATCATA
18923222 GCATATCATGT
1 GCATATCATGT
*
18923233 GCATATCAT-A
1 GCATATCATGT
*
18923243 ACATATCATGT
1 GCATATCATGT
*
18923254 GCATATCACGT
1 GCATATCATGT
18923265 -CATATCATGT
1 GCATATCATGT
18923275 G
1 G
18923276 TATCAGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (11 bp):
GCATATCATGT
Found at i:18923238 original size:21 final size:21
Alignment explanation
Indices: 18923214--18923275 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
18923204 TATAGTGAAT
18923214 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
18923235 ATATCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
18923256 ATATCA-CGTCATATCATGTG
1 ATATCATAG-CATATCATGTG
18923276 TATCAGTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:18931130 original size:11 final size:11
Alignment explanation
Indices: 18931116--18931169 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
18931106 ATATATCATA
18931116 GCATATCATGT
1 GCATATCATGT
*
18931127 GCATATCAT-A
1 GCATATCATGT
*
18931137 ACATATCATGT
1 GCATATCATGT
*
18931148 GCATATCACGT
1 GCATATCATGT
18931159 -CATATCATGT
1 GCATATCATGT
18931169 G
1 G
18931170 TATCAGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (11 bp):
GCATATCATGT
Found at i:18931132 original size:21 final size:21
Alignment explanation
Indices: 18931108--18931169 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
18931098 TATAGTGAAT
18931108 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
18931129 ATATCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
18931150 ATATCA-CGTCATATCATGTG
1 ATATCATAG-CATATCATGTG
18931170 TATCAGTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:18935557 original size:23 final size:23
Alignment explanation
Indices: 18935514--18935557 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
18935504 CCAATTCAAT
*
18935514 ATATTTTCAAGATAAATTCATGC
1 ATATTTTCAAGATAAAGTCATGC
*
18935537 ATATTTAT-AAGATAACGTCAT
1 ATATTT-TCAAGATAAAGTCAT
18935558 CACATACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATTTTCAAGATAAAGTCATGC
Found at i:18941860 original size:54 final size:54
Alignment explanation
Indices: 18941738--18941915 Score: 155
Period size: 54 Copynumber: 3.3 Consensus size: 54
18941728 TATCCTACAA
* * * *** *
18941738 GGGTGTTTTGGTAAATCTACAAATCAAGGGTATTTCTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCTGTAATTTCACAAACCAG
**
18941792 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC-GATAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCTG-TAATTTCACAAACCAG
* * * * * *
18941846 TGGTATTTTGGTAATTTTACTAA-CTAGGGGTGTTT-TGGTAATTTGACAAACTAG
1 GGGTATTTTGGTAATTTTACAAATC-AAGGGTATTTCT-GTAATTTCACAAACCAG
* *
18941900 GGGTACTGTGGTAATT
1 GGGTATTTTGGTAATT
18941916 CTATCCTACA
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
53 1 0.01
54 98 0.98
55 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCTGTAATTTCACAAACCAG
Found at i:18941897 original size:27 final size:27
Alignment explanation
Indices: 18941738--18941915 Score: 139
Period size: 27 Copynumber: 6.6 Consensus size: 27
18941728 TATCCTACAA
* * * *
18941738 GGGTGTTTTGGTAAATCTACAAA-TCAA
1 GGGTATTTTGGTAATTTTACAAACT-AG
**
18941765 GGGTATTTCT-GTAATTTTGTAAA-TCAG
1 GGGTATTT-TGGTAATTTTACAAACT-AG
*
18941792 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * *
18941818 AGGGTATTTCGATAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
18941846 TGGTATTTTGGTAATTTTACTAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
18941873 GGGTGTTTTGGTAATTTGACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
18941900 GGGTACTGTGGTAATT
1 GGGTATTTTGGTAATT
18941916 CTATCCTACA
Statistics
Matches: 120, Mismatches: 27, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
26 2 0.02
27 116 0.97
28 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:18941980 original size:27 final size:27
Alignment explanation
Indices: 18941951--18942117 Score: 210
Period size: 27 Copynumber: 6.2 Consensus size: 27
18941941 TTTAACAATT
*
18941951 GAGGGTAAAACGATAATTTTGTAAA-C
1 GAGGGTAAAACGGTAATTTTGTAAATC
*
18941977 TGAGGGTAAAATGGTAATTTTGTAAATC
1 -GAGGGTAAAACGGTAATTTTGTAAATC
*
18942005 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
* * * *
18942032 GAAGGTAAAATGGTAATTCTATAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
18942059 GAGGGTAAAACGGTAATTTTGTAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
* * * **
18942086 GAGGGTGAAATGGTAATTCTACAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC
18942113 GAGGG
1 GAGGG
18942118 CATTTCAGTA
Statistics
Matches: 123, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
27 122 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAACGGTAATTTTGTAAATC
Found at i:18942137 original size:54 final size:54
Alignment explanation
Indices: 18941951--18942117 Score: 255
Period size: 54 Copynumber: 3.1 Consensus size: 54
18941941 TTTAACAATT
* * *
18941951 GAGGGTAAAACGATAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTATAAATC
* *
18942005 GAGGGTAAAACGGTAATTCTGTAAATCGAAGGTAAAATGGTAATTCTATAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATC
* *
18942059 GAGGGTAAAACGGTAATTTTGTAAATCGAGGGTGAAATGGTAATTCTACAAATC
1 GAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATC
18942113 GAGGG
1 GAGGG
18942118 CATTTCAGTA
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 102 0.99
55 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (54 bp):
GAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATC
Found at i:18944433 original size:31 final size:31
Alignment explanation
Indices: 18944390--18944499 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
18944380 TTTAACAGTT
*
18944390 ACTGTGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
18944421 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
18944452 ACTGGGCTGAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
18944483 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
18944500 ACTGTAAACG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:18944573 original size:42 final size:42
Alignment explanation
Indices: 18944523--18944614 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
18944513 TGGCCCATAG
* ** *
18944523 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
* *
18944565 GCTCATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
18944607 GCCCATTT
1 GCCCATTT
18944615 GGGGAGACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:18944831 original size:26 final size:26
Alignment explanation
Indices: 18944747--18944882 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
18944737 CTGGAGGCCT
18944747 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
18944771 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
18944796 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
18944822 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
18944848 AGCCCTTTTCAATAAACAAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
18944874 AGCCCTTTT
1 AGCCCTTTT
18944883 ACACTTCCTC
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 33 0.33
26 56 0.57
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:18944873 original size:52 final size:51
Alignment explanation
Indices: 18944765--18944882 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
18944755 TTAATAACTG
**
18944765 GGGCA-AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTG
1 GGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACAA
18944815 GGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACAA
1 GGGCATAAGCCCTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATAAACAA
18944867 GGGCATAAGCCCTTTT
1 GGGCATAAGCCCTTTT
18944883 ACACTTCCTC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 5 0.08
51 25 0.39
52 34 0.53
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (51 bp):
GGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACAA
Found at i:18944961 original size:20 final size:20
Alignment explanation
Indices: 18944932--18944982 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
18944922 TTATGAATAC
*
18944932 ATCATATGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
18944952 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
18944972 ACCATGTGCAT
1 ATCATGTGCAT
18944983 ATCACATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:18945062 original size:25 final size:25
Alignment explanation
Indices: 18945034--18945081 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18945024 ATAATTAAAC
* * *
18945034 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
18945059 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
18945082 CATACTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:18945869 original size:54 final size:54
Alignment explanation
Indices: 18945803--18946013 Score: 142
Period size: 54 Copynumber: 3.9 Consensus size: 54
18945793 CATCCTACAA
* * *** *
18945803 GGGTGTTTTGGTAAATCTACAAATCAAGGGTATTTCTATAATTTTGTAAATCAG
1 GGGTATTTTGGTAAATCTACAAATCAAGGGTATTTCGATAATTTCACAAACCAG
* * ** *
18945857 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAAATCTACAAATCAAGGGTATTTCGATAATTTCACAAACCAG
* * * * * * * *
18945911 TGGTATTTTGGTAATTTTACTAACTAAAGGTGT-TTT-GGTAATTTTACAAACTAG
1 GGGTATTTTGGTAAATCTAC-AAATCAAGG-GTATTTCGATAATTTCACAAACCAG
* * ** *
18945965 GGGTATTGTGGTAATTCTATCCTA-CAGGGGTATTTC-AGTAATTTCACAA
1 GGGTATTTTGGTAAATCTA-CAAATCAAGGGTATTTCGA-TAATTTCACAA
18946014 TTGAAGGTAA
Statistics
Matches: 124, Mismatches: 27, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
52 2 0.02
53 6 0.05
54 104 0.84
55 10 0.08
56 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAAATCTACAAATCAAGGGTATTTCGATAATTTCACAAACCAG
Found at i:18945871 original size:27 final size:27
Alignment explanation
Indices: 18945803--18945980 Score: 139
Period size: 27 Copynumber: 6.6 Consensus size: 27
18945793 CATCCTACAA
* * * *
18945803 GGGTGTTTTGGTAAATCTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAG
* **
18945830 GGGTATTTCT-ATAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAATCAG
*
18945857 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * *
18945883 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAATCAG
* * *
18945911 TGGTATTTTGGTAATTTTACTAA-CTAA
1 GGGTATTTTGGTAATTTTACAAATC-AG
* *
18945938 AGGTGTTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
*
18945965 GGGTATTGTGGTAATT
1 GGGTATTTTGGTAATT
18945981 CTATCCTACA
Statistics
Matches: 119, Mismatches: 27, Indels: 10
0.76 0.17 0.06
Matches are distributed among these distances:
26 3 0.03
27 114 0.96
28 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:18946058 original size:27 final size:27
Alignment explanation
Indices: 18946019--18946160 Score: 185
Period size: 27 Copynumber: 5.3 Consensus size: 27
18946009 CACAATTGAA
* *
18946019 GGTAAAACGGTAATTTTGTAGATCAAG
1 GGTAAAACGGTAATTTTGTAAATCGAG
** *
18946046 GGTAAAATAGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTTTGTAAATCGAG
* *
18946073 GGTAAAATGGTAATTTTATAAATCGAG
1 GGTAAAACGGTAATTTTGTAAATCGAG
18946100 GGTAAAACGGTAATTTTGTAAATCGAG
1 GGTAAAACGGTAATTTTGTAAATCGAG
* * * *
18946127 GGTGAAACGGTAATTCTATAAATCGAT
1 GGTAAAACGGTAATTTTGTAAATCGAG
18946154 GGTAAAA
1 GGTAAAA
18946161 TGATAATTCT
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
GGTAAAACGGTAATTTTGTAAATCGAG
Found at i:18946129 original size:81 final size:81
Alignment explanation
Indices: 18946019--18946182 Score: 229
Period size: 81 Copynumber: 2.0 Consensus size: 81
18946009 CACAATTGAA
* * * *
18946019 GGTAAAACGGTAATTTTGTAGATCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATGGT
1 GGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGAT
* * *
18946084 AATTTTATAAATCGAG
66 AATTCTACAAATCAAG
* * * *
18946100 GGTAAAACGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTATAAATCGATGGTAAAATGAT
1 GGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGAT
18946165 AATTCTACAAATCAAG
66 AATTCTACAAATCAAG
18946181 GG
1 GG
18946183 CATTTCAGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (81 bp):
GGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGAT
AATTCTACAAATCAAG
Found at i:18946167 original size:27 final size:27
Alignment explanation
Indices: 18946019--18946182 Score: 175
Period size: 27 Copynumber: 6.1 Consensus size: 27
18946009 CACAATTGAA
* * * * *
18946019 GGTAAAACGGTAATTTTGTAGATCAAG
1 GGTAAAATGGTAATTCTATAAATCGAG
* *
18946046 GGTAAAATAGTAATTCTGTAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
*
18946073 GGTAAAATGGTAATTTTATAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
* * *
18946100 GGTAAAACGGTAATTTTGTAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
* * *
18946127 GGTGAAACGGTAATTCTATAAATCGAT
1 GGTAAAATGGTAATTCTATAAATCGAG
* * *
18946154 GGTAAAATGATAATTCTACAAATCAAG
1 GGTAAAATGGTAATTCTATAAATCGAG
18946181 GG
1 GG
18946183 CATTTCAGTA
Statistics
Matches: 117, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 117 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
GGTAAAATGGTAATTCTATAAATCGAG
Found at i:18946194 original size:81 final size:81
Alignment explanation
Indices: 18946022--18946202 Score: 200
Period size: 81 Copynumber: 2.2 Consensus size: 81
18946012 AATTGAAGGT
* * * * *
18946022 AAAACGGTAATTTTGTAGATCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATGGTAAT
1 AAAACAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGATAAT
* * * *
18946087 TTTATAAATCGAGGGT
66 TCTACAAATCAAGGGC
* * * * *
18946103 AAAACGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTATAAATCGATGGTAAAATGATAAT
1 AAAACAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGATAAT
18946168 TCTACAAATCAAGGGC
66 TCTACAAATCAAGGGC
*** *
18946184 ATTTCAGTAATTTGGTAAA
1 AAAACAGTAATTTTGTAAA
18946203 CTAAAGTATT
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (81 bp):
AAAACAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGATAAT
TCTACAAATCAAGGGC
Found at i:18951576 original size:31 final size:31
Alignment explanation
Indices: 18951535--18951635 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 31
18951525 AAAAATAAAA
*
18951535 AAATTGCATTTTGACCCCTAAACTTTTCTTT
1 AAATTACATTTTGACCCCTAAACTTTTCTTT
* * *
18951566 AAATTTCATTTAGACCCCTAAAC-TTTCCTT
1 AAATTACATTTTGACCCCTAAACTTTTCTTT
* **
18951596 AAATTACATTTT-AACCCTAAA-TTTTCTAA
1 AAATTACATTTTGACCCCTAAACTTTTCTTT
18951625 AAATTACATTT
1 AAATTACATTT
18951636 AGCCCCAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
29 23 0.38
30 16 0.27
31 21 0.35
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.43
Consensus pattern (31 bp):
AAATTACATTTTGACCCCTAAACTTTTCTTT
Found at i:18951600 original size:30 final size:31
Alignment explanation
Indices: 18951535--18951641 Score: 109
Period size: 31 Copynumber: 3.6 Consensus size: 31
18951525 AAAAATAAAA
* * *
18951535 AAATTGCATTTTGACCCCTAAACTTTTCTTT
1 AAATTACATTTAGACCCCTAAACTTTTCCTT
*
18951566 AAATTTCATTTAGACCCCTAAAC-TTTCCTT
1 AAATTACATTTAGACCCCTAAACTTTTCCTT
*
18951596 AAATTACATTTTA-A-CCCTAAA-TTTT-CTAA
1 AAATTACA-TTTAGACCCCTAAACTTTTCCT-T
18951625 AAATTACATTTAG-CCCC
1 AAATTACATTTAGACCCC
18951642 AGAAGTTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
28 6 0.09
29 21 0.32
30 14 0.21
31 25 0.38
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (31 bp):
AAATTACATTTAGACCCCTAAACTTTTCCTT
Found at i:18951865 original size:15 final size:15
Alignment explanation
Indices: 18951847--18951943 Score: 112
Period size: 15 Copynumber: 6.7 Consensus size: 15
18951837 GAGAAAAAAG
*
18951847 AGCAAAAAAAAATCC
1 AGCAAAAAAAATTCC
18951862 AGCAAAAAAAATTCC
1 AGCAAAAAAAATTCC
*
18951877 AGCAAAAAAATTTCC
1 AGCAAAAAAAATTCC
*
18951892 AGCAAAAAAAA---A
1 AGCAAAAAAAATTCC
* *
18951904 ACCAATAAAAATTCC
1 AGCAAAAAAAATTCC
18951919 AG-AAAAAAAATTCC
1 AGCAAAAAAAATTCC
*
18951933 AACAAAAAAAA
1 AGCAAAAAAAA
18951944 ACCAAAAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.13
14 12 0.18
15 47 0.69
ACGTcount: A:0.66, C:0.18, G:0.05, T:0.11
Consensus pattern (15 bp):
AGCAAAAAAAATTCC
Found at i:18951900 original size:42 final size:41
Alignment explanation
Indices: 18951864--18951953 Score: 137
Period size: 40 Copynumber: 2.2 Consensus size: 41
18951854 AAAAATCCAG
* *
18951864 CAAAAAAAATTCCAGCAAAAAAATTTCCAGCAAAAAAAAAAC
1 CAAAAAAAATTCCAG-AAAAAAAATTCCAACAAAAAAAAAAC
*
18951906 CAATAAAAATTCCAGAAAAAAAATTCCAAC-AAAAAAAAAC
1 CAAAAAAAATTCCAGAAAAAAAATTCCAACAAAAAAAAAAC
18951946 CAAAAAAA
1 CAAAAAAA
18951954 GGAACATTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 17 0.39
41 13 0.30
42 14 0.32
ACGTcount: A:0.68, C:0.18, G:0.03, T:0.11
Consensus pattern (41 bp):
CAAAAAAAATTCCAGAAAAAAAATTCCAACAAAAAAAAAAC
Found at i:18952491 original size:57 final size:56
Alignment explanation
Indices: 18952423--18952538 Score: 196
Period size: 57 Copynumber: 2.1 Consensus size: 56
18952413 TGGGCTGAGA
*
18952423 TTGGTTTATGTTGGGCTAAAGTAATTTGGATTTTGTATATTTTATGTAGATTTTAAT
1 TTGGTTAATGTTGGGCTAAAGTAATTTGGATTTTGTATATTTTATGTAGATTTT-AT
* *
18952480 TTGGTTAATGTTGGGTTGAAGTAATTTGGATTTTGTATATTTTATGTAGATTTTAT
1 TTGGTTAATGTTGGGCTAAAGTAATTTGGATTTTGTATATTTTATGTAGATTTTAT
18952536 TTG
1 TTG
18952539 TAATTGGTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 5 0.09
57 51 0.91
ACGTcount: A:0.23, C:0.01, G:0.22, T:0.53
Consensus pattern (56 bp):
TTGGTTAATGTTGGGCTAAAGTAATTTGGATTTTGTATATTTTATGTAGATTTTAT
Found at i:18952573 original size:15 final size:16
Alignment explanation
Indices: 18952540--18952573 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18952530 TTTTATTTGT
18952540 AATTGGTCTAAACAAA
1 AATTGGTCTAAACAAA
*
18952556 AATTGGTCTTAA-AAA
1 AATTGGTCTAAACAAA
18952571 AAT
1 AAT
18952574 AAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (16 bp):
AATTGGTCTAAACAAA
Found at i:18952824 original size:17 final size:17
Alignment explanation
Indices: 18952794--18952826 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18952784 CTATATTATA
18952794 TACATATATATATTTTG
1 TACATATATATATTTTG
18952811 TACATATCAT-TATTTT
1 TACATAT-ATATATTTT
18952827 ATATTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (17 bp):
TACATATATATATTTTG
Found at i:18955947 original size:39 final size:39
Alignment explanation
Indices: 18955893--18955978 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
18955883 TTTATTTTAG
* * * **
18955893 GAGTAATTTTTTATATTATAGGAAGTAGGGGGTGAATAA
1 GAGTAGTTTTCTATATTATAGGAAGTAGAGGGAAAATAA
*
18955932 GAGTAGTTTTCTATATTATAGGAAGTAGAGGGAAAATAG
1 GAGTAGTTTTCTATATTATAGGAAGTAGAGGGAAAATAA
18955971 GAGTAGTT
1 GAGTAGTT
18955979 ATACCATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.36, C:0.01, G:0.29, T:0.34
Consensus pattern (39 bp):
GAGTAGTTTTCTATATTATAGGAAGTAGAGGGAAAATAA
Found at i:18959483 original size:45 final size:45
Alignment explanation
Indices: 18959434--18959523 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
18959424 CATTTAATGG
*
18959434 CCATCATCATCATTACCTACTATTAACATAAAGAAAAATGGATTA
1 CCATCATCATCATTACCCACTATTAACATAAAGAAAAATGGATTA
*
18959479 CCATCATCATCATTACCCACTATTAACATAAATAAAAATGGATTA
1 CCATCATCATCATTACCCACTATTAACATAAAGAAAAATGGATTA
18959524 ATAACCATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (45 bp):
CCATCATCATCATTACCCACTATTAACATAAAGAAAAATGGATTA
Found at i:18960892 original size:15 final size:16
Alignment explanation
Indices: 18960860--18960892 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18960850 TTTTATTTAT
18960860 TTTCTTCACCTACTCC
1 TTTCTTCACCTACTCC
*
18960876 TTTCTTCCCCT-CTCC
1 TTTCTTCACCTACTCC
18960891 TT
1 TT
18960893 AGCCGAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.45, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCTTCACCTACTCC
Found at i:18968168 original size:14 final size:15
Alignment explanation
Indices: 18968149--18968179 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18968139 GAAGTCATTT
18968149 ATTTTG-AAAACAAA
1 ATTTTGAAAAACAAA
18968163 ATTTTGAAAAACAAA
1 ATTTTGAAAAACAAA
18968178 AT
1 AT
18968180 CAACTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (15 bp):
ATTTTGAAAAACAAA
Found at i:18970972 original size:293 final size:293
Alignment explanation
Indices: 18970445--18971024 Score: 1054
Period size: 293 Copynumber: 2.0 Consensus size: 293
18970435 GGCCCGATCA
*
18970445 CGCAAAAAGAGATGTGTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAA
1 CGCAAAAAGAGATGAGTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAA
*
18970510 CTCAGTAAGTCATAAGCTATGCACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATG
66 CTCAGTAAGTCATAAGCAATGCACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATG
* *
18970575 GAACGAGGCTAATTACTCCATCCATTCCGAACCATACCATAGTTCCTCCAACCTATCGATTCAAT
131 GAACGAGACTAATTACTCCATCCATACCGAACCATACCATAGTTCCTCCAACCTATCGATTCAAT
18970640 TTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAGGACATTGAGGCATTTTCATAA
196 TTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAGGACATTGAGGCATTTTCATAA
18970705 ATCAATTTATTTTCGTTACAATCAAACTGACCC
261 ATCAATTTATTTTCGTTACAATCAAACTGACCC
* * * *
18970738 CGCAAAAATAGATGAGTCCAAGCAACCTATAATGGGTGACAAGGAAACACCGAGTGAGTTTATAA
1 CGCAAAAAGAGATGAGTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAA
*
18970803 CTCAGTAAGTCATAAGCAATGCACTACCATCCATCAATAACATTATCACAAGAGGAAACAAAATG
66 CTCAGTAAGTCATAAGCAATGCACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATG
*
18970868 GAACGAGAC-AATTTACTCCATCCATACCGAACCATACCATAGTTCCTCCAACCTATCGATTCAG
131 GAACGAGACTAA-TTACTCCATCCATACCGAACCATACCATAGTTCCTCCAACCTATCGATTCAA
18970932 TTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAGGACATTGAGGCATTTTCATA
195 TTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAGGACATTGAGGCATTTTCATA
18970997 AATCAATTTATTTTCGTTACAATCAAAC
260 AATCAATTTATTTTCGTTACAATCAAAC
18971025 GACTAAACGG
Statistics
Matches: 276, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
292 2 0.01
293 274 0.99
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (293 bp):
CGCAAAAAGAGATGAGTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAA
CTCAGTAAGTCATAAGCAATGCACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATG
GAACGAGACTAATTACTCCATCCATACCGAACCATACCATAGTTCCTCCAACCTATCGATTCAAT
TTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAGGACATTGAGGCATTTTCATAA
ATCAATTTATTTTCGTTACAATCAAACTGACCC
Found at i:18971272 original size:27 final size:27
Alignment explanation
Indices: 18971242--18971364 Score: 147
Period size: 27 Copynumber: 4.5 Consensus size: 27
18971232 ATATTGAGTC
* *
18971242 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
18971269 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
18971296 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
18971324 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
18971351 CGCACACTTAGTGC
1 CGCACACTTAGTGC
18971365 ATCATATTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 61 0.73
28 23 0.27
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:18971334 original size:55 final size:54
Alignment explanation
Indices: 18971242--18971364 Score: 156
Period size: 55 Copynumber: 2.3 Consensus size: 54
18971232 ATATTGAGTC
* * * *
18971242 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* * ** *
18971296 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCCACATAATCAAAT
18971351 CGCACACTTAGTGC
1 CGCACACTTAGTGC
18971365 ATCATATTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
54 20 0.34
55 39 0.66
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:18971379 original size:27 final size:26
Alignment explanation
Indices: 18971242--18971384 Score: 124
Period size: 27 Copynumber: 5.3 Consensus size: 26
18971232 ATATTGAGTC
* *
18971242 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCT-CATAATCAACT
* *
18971269 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCT-CATAATCAACT
*
18971296 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCT-CATAATC-AACT
* ** *
18971324 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTG-CTCATAATCAACT
* **
18971351 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGC-TCATAATCAACT
18971378 CGCACAC
1 CGCACAC
18971385 ATATACATGA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.01
27 75 0.76
28 22 0.22
29 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (26 bp):
CGCACACTTAGTGCTCATAATCAACT
Found at i:18974182 original size:101 final size:100
Alignment explanation
Indices: 18974003--18974295 Score: 363
Period size: 101 Copynumber: 2.9 Consensus size: 100
18973993 ATTGTGAGAA
* *** * * *
18974003 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG--TTAGATCACATGTGTAGTA
*
18974068 CTAAGTGCA-GCTACTACGTGTACCAGATTGTTAGGT
64 CTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGT
* * * *
18974104 CGCATGTGTAGTACTAAGTTCAGGCTACTATGTGTACCCGATAGCTTCGATCACATGTGTAGTAC
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTAGATCACATGTGTAGTAC
* **
18974169 TAAATGCAGGCTACTACGTGTATTAGATGGTTAGGT
65 TAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGT
* * **
18974205 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTTGCATGTGTAGTACT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGATCACATGTGTAGTACT
* *
18974270 AAGTGCAGGCTACTATGCGTACCAGA
66 AAGTGCAGGCTACTACGTGTACCAGA
18974296 GAACTTCGGT
Statistics
Matches: 162, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
100 62 0.38
101 100 0.62
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (100 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGATCACATGTGTAGTACT
AAGTGCAGGCTACTACGTGTACCAGATGGTTAGGT
Found at i:18974227 original size:50 final size:50
Alignment explanation
Indices: 18974003--18974295 Score: 345
Period size: 50 Copynumber: 5.8 Consensus size: 50
18973993 ATTGTGAGAA
* *** * *
18974003 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACAGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA-TG-GTTAGGT
* * *
18974055 CACGTGTGTAGTACTAAGTGCA-GCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
* * * * * *
18974104 CGCATGTGTAGTACTAAGTTCAGGCTACTATGTGTACCCGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-GGTTAGGT
* * **
18974155 CACATGTGTAGTACTAAATGCAGGCTACTACGTGTATTAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
*
18974205 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
** *
18974255 TGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
18974296 GAACTTCGGT
Statistics
Matches: 203, Mismatches: 36, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
49 25 0.12
50 105 0.52
51 53 0.26
52 20 0.10
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
Found at i:18974279 original size:151 final size:152
Alignment explanation
Indices: 18974003--18974292 Score: 451
Period size: 151 Copynumber: 1.9 Consensus size: 152
18973993 ATTGTGAGAA
** * * *
18974003 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTGTAGTA
1 CACATGTGTAGTACTAAATGCAGGCTACTACGTGTTTAAGACAGTGTTAGGTCACATGTGTAGTA
*
18974068 CTAAGTGCAGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTTCAGGCTACT
66 CTAAGTGCAGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACT
*
18974133 ATGTGTACCCGATAGCTTCGAT
131 ATGCGTACCCGATAGCTTCGAT
*
18974155 CACATGTGTAGTACTAAATGCAGGCTACTACGTGTATT-AGA-TG-GTTAGGTCACATGTGTAGT
1 CACATGTGTAGTACTAAATGCAGGCTACTACGTGT-TTAAGACAGTGTTAGGTCACATGTGTAGT
* *
18974217 ACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTTGCATGTGTAGTACTAAGTGCAGGCTA
65 ACTAAGTGCA-GCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTA
18974282 CTATGCGTACC
129 CTATGCGTACC
18974293 AGAGAACTTC
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
150 27 0.21
151 62 0.49
152 35 0.28
153 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (152 bp):
CACATGTGTAGTACTAAATGCAGGCTACTACGTGTTTAAGACAGTGTTAGGTCACATGTGTAGTA
CTAAGTGCAGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACT
ATGCGTACCCGATAGCTTCGAT
Found at i:18974330 original size:151 final size:150
Alignment explanation
Indices: 18974049--18974330 Score: 393
Period size: 151 Copynumber: 1.9 Consensus size: 150
18974039 TAAGACAGTT
*
18974049 TTAGGTCACGTGTGTAGTACTAAGTGCAGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTA
* * * * * * * * *
18974114 GTACTAAGTTCAGGCTACTATGTGTACCCGATAGCTTCGATCACATGTGTAGTACTAAATGCAGG
66 GTACTAAGTGCAGGCTACTATGCGTACCAGAGAACTTCGATCACAAGGGTAGTAATAAATACAGG
18974179 CTACTACGTGTATTAGATGG
131 CTACTACGTGTATTAGATGG
* *
18974199 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTTGCATGTGT
1 TTAGGTCACATGTGTAGTACTAAGTGCA-GCTACTACGTGTACCAGATTGTTAGGTCGCATGTGT
* * * * **
18974264 AGTACTAAGTGCAGGCTACTATGCGTACCAGAGAACTTCGGTTATAAGGGTGGTAATATGTACAG
65 AGTACTAAGTGCAGGCTACTATGCGTACCAGAGAACTTCGATCACAAGGGTAGTAATAAATACAG
18974329 GC
130 GC
18974331 CACCAGGTAT
Statistics
Matches: 113, Mismatches: 18, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
150 27 0.24
151 86 0.76
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (150 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTA
GTACTAAGTGCAGGCTACTATGCGTACCAGAGAACTTCGATCACAAGGGTAGTAATAAATACAGG
CTACTACGTGTATTAGATGG
Found at i:18978610 original size:46 final size:45
Alignment explanation
Indices: 18978505--18978720 Score: 179
Period size: 46 Copynumber: 4.7 Consensus size: 45
18978495 GCATATCTGT
* * * *
18978505 GTCGATGCCATGTCCCATACATGGTCTTACACTGAC-AC-TTTCGTA-
1 GTCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCATCTCG-AG
* *
18978550 GTCAATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GTCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGAG
* * * *
18978596 GTCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCAAT
1 GTCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTCGAG
* * * *
18978642 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAGT-GTG
1 GTCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-CTCGAG
* *
18978690 GCCAATGCATGTCCCAGACATGTCTTACACT
1 GTCGATGCATGTCCCAGACATGTCTTACACT
18978721 AGCTCACAAT
Statistics
Matches: 141, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
43 12 0.09
44 13 0.09
45 8 0.06
46 57 0.40
47 29 0.21
48 21 0.15
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (45 bp):
GTCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCGAG
Found at i:18978716 original size:140 final size:140
Alignment explanation
Indices: 18978458--18978720 Score: 345
Period size: 140 Copynumber: 1.9 Consensus size: 140
18978448 TGCAGGTGCT
* ** * *
18978458 GATGCTATGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTGTGTCGATGCCATGTCCCAT
1 GATGCTATGTCCCAGACATGGTCTTACACAAGCACTA-CATATCAATGCCGATGCCATGTCCCAG
*
18978523 ACATGGTCTTACACTGACACTTTCGTAGTCAATGCATGTCCCAGACATGTCTTACACTGGCTTAC
65 ACATGGTCTTACACTGACACTTTCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGCTTAC
18978588 GTCTCGAGGTC
130 GTCTCGAGGTC
* *
18978599 GATGC-ATGTCCCAGACAT-GTCTTACACTAGCACT-CATCTCAATGCCGATGCCATGTCCCAGA
1 GATGCTATGTCCCAGACATGGTCTTACACAAGCACTACATATCAATGCCGATGCCATGTCCCAGA
* * * *
18978661 CATGGTCTTACATTGGCTCTCATAGT-GTGGCCAATGCATGTCCCAGACATGTCTTACACT
66 CATGGTCTTACACTGACACT--T--TCGTAGCCAATGCATGTCCCAGACATGTCTTACACT
18978721 AGCTCACAAT
Statistics
Matches: 106, Mismatches: 12, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
137 40 0.38
139 15 0.14
140 45 0.42
141 6 0.06
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (140 bp):
GATGCTATGTCCCAGACATGGTCTTACACAAGCACTACATATCAATGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGACACTTTCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGCTTACG
TCTCGAGGTC
Found at i:18980728 original size:49 final size:49
Alignment explanation
Indices: 18980656--18980753 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
18980646 TTTCCCAACT
*
18980656 GCCTTGAAACTTAAGAATACAACACTGCAACATTTTTTCTAAAATCTGA
1 GCCTTGAAACTTAAGAATACAACACTGCAACATTTTTTCTAAAACCTGA
* *
18980705 GCCTTGAAACTTAAGCATACAACACTGCAACCTTTTTTCTAAAACCTGA
1 GCCTTGAAACTTAAGAATACAACACTGCAACATTTTTTCTAAAACCTGA
18980754 ATCTCTCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (49 bp):
GCCTTGAAACTTAAGAATACAACACTGCAACATTTTTTCTAAAACCTGA
Found at i:18982981 original size:21 final size:21
Alignment explanation
Indices: 18982957--18982998 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
18982947 TTACTCCAAG
18982957 AAAGCCGATTGATCCATCTCA
1 AAAGCCGATTGATCCATCTCA
18982978 AAAGCCGATTGATCCATCTCA
1 AAAGCCGATTGATCCATCTCA
18982999 GAAGTCGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGCCGATTGATCCATCTCA
Found at i:18983147 original size:41 final size:41
Alignment explanation
Indices: 18983102--18983179 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
18983092 GAGATGTTTT
18983102 CTTATTTAGTTATGAACTAAATCCCCTAAATACCTAAGGGG
1 CTTATTTAGTTATGAACTAAATCCCCTAAATACCTAAGGGG
18983143 CTTATTTAGTTATGAACTAAATCCCCTAAATACCTAA
1 CTTATTTAGTTATGAACTAAATCCCCTAAATACCTAA
18983180 AGGGAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (41 bp):
CTTATTTAGTTATGAACTAAATCCCCTAAATACCTAAGGGG
Found at i:19011709 original size:28 final size:28
Alignment explanation
Indices: 19011675--19011739 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
19011665 TCAGTGTACG
* *
19011675 AAATATTGAGAATGGCACTTAATGTGCG
1 AAATATTGAGAATGACACTTAATGTGCA
* *
19011703 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAATGTGCA
19011731 AAATATTGA
1 AAATATTGA
19011740 ATGATTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAATGTGCA
Done.