Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:1932225 original size:26 final size:26
Alignment explanation
Indices: 1932191--1932244 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
1932181 TATTATTTTC
1932191 TTTTAAAAG-TTTATAAGTTCATCTCT
1 TTTTAAAAGTTTTATAAGTTCATC-CT
*
1932217 TTTTTAAAGTTTTATAAGTTCATCCT
1 TTTTAAAAGTTTTATAAGTTCATCCT
1932243 TT
1 TT
1932245 AACATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTTAAAAGTTTTATAAGTTCATCCT
Found at i:1941005 original size:221 final size:221
Alignment explanation
Indices: 1940622--1941280 Score: 1192
Period size: 221 Copynumber: 3.0 Consensus size: 221
1940612 AACCTAAAGT
1940622 CTTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGG
1 CTTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGG
* * *
1940687 ACATCGATAAGATTGACGAGACACCAAAGGAGAATGAGAAGAAGAAAAACATTGTAGTTGCTCTC
66 ACCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTC
*
1940752 AAATCCATAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGC
131 AAATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGC
1940817 CAAACGGTTCAGAAAAATGATGAGAC
196 CAAACGGTTCAGAAAAATGATGAGAC
* * * * *
1940843 CTTAACTCTTGAAGAGCTAATCGATTTCCTCCTCTCTCATGAAATGATGATTAAAGATGAGGTGG
1 CTTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGG
*
1940908 GCCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTC
66 ACCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTC
*
1940973 AAATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTTC
131 AAATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGC
1941038 CAAACGGTTCAGAAAAATGATGAGAC
196 CAAACGGTTCAGAAAAATGATGAGAC
1941064 CTTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGG
1 CTTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGG
*
1941129 ACCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTT
66 ACCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTC
*
1941194 AAATCCACAAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGACATTGTTTG
131 AAATCCAC-AAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTG
1941259 CCAAACGGTTCAGAAAAATGAT
195 CCAAACGGTTCAGAAAAATGAT
1941281 CTTACTGAGG
Statistics
Matches: 417, Mismatches: 20, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
221 341 0.82
222 76 0.18
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (221 bp):
CTTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGG
ACCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTC
AAATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGC
CAAACGGTTCAGAAAAATGATGAGAC
Found at i:1942202 original size:24 final size:24
Alignment explanation
Indices: 1942170--1942216 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1942160 GGATGCTCAA
1942170 GACACATGACCGGAGACAAAAGTC
1 GACACATGACCGGAGACAAAAGTC
1942194 GACACATGACCGGAGACAAAAGT
1 GACACATGACCGGAGACAAAAGT
1942217 GATTCATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.23, G:0.26, T:0.09
Consensus pattern (24 bp):
GACACATGACCGGAGACAAAAGTC
Found at i:1945539 original size:21 final size:21
Alignment explanation
Indices: 1945503--1945590 Score: 95
Period size: 21 Copynumber: 4.0 Consensus size: 21
1945493 TTAGTACAGA
* *
1945503 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCC-TGAAG
* *
1945525 GGGAACCAATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC--TGAAG
*
1945548 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATTCCCCCTGAAG
*
1945569 GGGAACCGATACCCCCTGAAG
1 GGGAACCGATTCCCCCTGAAG
1945590 G
1 G
1945591 TTCTGGTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
21 23 0.41
22 13 0.23
23 20 0.36
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:1945548 original size:23 final size:22
Alignment explanation
Indices: 1945503--1945585 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
1945493 TTAGTACAGA
* * *
1945503 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTTAAG
*
1945525 GGGAACCAATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCCTTT-AAG
*
1945548 GGGAACCGATTCCCCCTGT-AG
1 GGGAACCGATTCCCCCTTTAAG
*
1945569 GGGAACCGATACCCCCT
1 GGGAACCGATTCCCCCT
1945586 GAAGGTTCTG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.34
22 15 0.28
23 20 0.38
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTTAAG
Found at i:1951229 original size:3 final size:3
Alignment explanation
Indices: 1951221--1951273 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
1951211 CGAGACTATA
1951221 TAT TAT TAT TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
1951266 TAT TAT TA
1 TAT TAT TA
1951274 CAAATCCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1953882 original size:33 final size:33
Alignment explanation
Indices: 1953816--1953883 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1953806 GGCTTCCCTT
* * *
1953816 GGATTCCCTCGCATAGCTCGCTTGGTTGCCCTC
1 GGATGCCCTCGCATAGCTCGCTTGGATGACCTC
1953849 GGATGCCCTCGCATAGCTCG-TTCGGATGACCTC
1 GGATGCCCTCGCATAGCTCGCTT-GGATGACCTC
1953882 GG
1 GG
1953884 TCGGATGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.26
Consensus pattern (33 bp):
GGATGCCCTCGCATAGCTCGCTTGGATGACCTC
Found at i:1965716 original size:15 final size:15
Alignment explanation
Indices: 1965698--1965728 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1965688 AAATTCTAAA
1965698 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1965713 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1965728 T
1 T
1965729 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1973513 original size:2 final size:2
Alignment explanation
Indices: 1973506--1973536 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1973496 GCTGTATATT
1973506 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1973537 GGTAGGGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1978772 original size:64 final size:64
Alignment explanation
Indices: 1978692--1978912 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
1978682 TTGAAGGTGT
** ** * * *
1978692 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATACAATTAGTG
1978755 C
64 C
*
1978756 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATACAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATACAATTAGTGC
* * *
1978820 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAA-ACAAACATCGAATACATTTTA-T
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAAGA-AAACATCGAATACA-ATTAGT
1978882 GC
63 GC
* ** *
1978884 ACCGATGCATCTGTAATGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
1978913 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.01
64 123 0.91
65 10 0.07
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATACAATTAGTGC
Found at i:1979376 original size:14 final size:14
Alignment explanation
Indices: 1979357--1979389 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1979347 ATGGGATAAC
1979357 ATGATAAGATGACA
1 ATGATAAGATGACA
1979371 ATGATAAGATGACA
1 ATGATAAGATGACA
1979385 ATGAT
1 ATGAT
1979390 TTACATGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (14 bp):
ATGATAAGATGACA
Found at i:1979846 original size:103 final size:103
Alignment explanation
Indices: 1979666--1979879 Score: 392
Period size: 103 Copynumber: 2.1 Consensus size: 103
1979656 AGGGTCTATG
1979666 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
* *
1979731 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
1979769 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
* *
1979834 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
1979872 TGGTCCTT
1 TGGTCCTT
1979880 ATGAACATTA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
Found at i:1979940 original size:47 final size:47
Alignment explanation
Indices: 1979886--1980005 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
1979876 CCTTATGAAC
* *
1979886 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCTGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTACA
1979933 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTACA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTACA
* *
1979980 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
1980006 ATATGAGTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
46 20 0.29
47 49 0.71
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTACA
Found at i:1980006 original size:23 final size:23
Alignment explanation
Indices: 1979886--1980010 Score: 117
Period size: 23 Copynumber: 5.3 Consensus size: 23
1979876 CCTTATGAAC
*
1979886 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
1979910 ATTCTACGCGGCACT-CTGGTGCA
1 ATTATATGTGGCACTAC-GGTGCA
*
1979933 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
1979957 ATTCTACGCGGCACTCCGGTACA
1 ATTATATGTGGCACTACGGTGCA
*
1979980 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
1980003 ATTATATG
1 ATTATATG
1980011 AGTTGTGGTG
Statistics
Matches: 79, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.01
23 57 0.72
24 20 0.25
25 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1988518 original size:19 final size:19
Alignment explanation
Indices: 1988476--1988518 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1988466 TAACATAATG
*
1988476 TTTA-AAAGTATCGATACC
1 TTTATAAAGTATCGAAACC
* *
1988494 TATATAAAGTATCGAAACT
1 TTTATAAAGTATCGAAACC
1988513 TTTATA
1 TTTATA
1988519 GTAGTACAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (19 bp):
TTTATAAAGTATCGAAACC
Found at i:1990000 original size:2 final size:2
Alignment explanation
Indices: 1989993--1990056 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
1989983 CCTTAAATTG
* *
1989993 AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT CT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1990034 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1990057 AAAGATTCGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1991116 original size:32 final size:32
Alignment explanation
Indices: 1991073--1991137 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1991063 GAGTAAAGTT
* *
1991073 TAATGATTCATGGTGTAATTTACCCTTTTTCC
1 TAATGACTCATGGTGTAATTTACACTTTTTCC
1991105 TAATGACTCATGGTGTAATTTACACTTTTTCC
1 TAATGACTCATGGTGTAATTTACACTTTTTCC
1991137 T
1 T
1991138 TCTCTTCTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (32 bp):
TAATGACTCATGGTGTAATTTACACTTTTTCC
Found at i:1991703 original size:15 final size:14
Alignment explanation
Indices: 1991657--1991703 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1991647 TAATTTACCT
1991657 TAAAAATAGTTAAAA
1 TAAAAATA-TTAAAA
* *
1991672 TTAAAATA-AAAAA
1 TAAAAATATTAAAA
1991685 TAAAAATATTAATAA
1 TAAAAATATTAA-AA
1991700 TAAA
1 TAAA
1991704 CAGGGGTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 13 0.50
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
TAAAAATATTAAAA
Found at i:1992543 original size:58 final size:58
Alignment explanation
Indices: 1992454--1992585 Score: 230
Period size: 58 Copynumber: 2.2 Consensus size: 58
1992444 AATGAGAACA
1992454 AGTCGAGCAACAAAATTTTTAACAAGCATGATTCGAGCAAAATTTAAACGAATTTAACG
1 AGTCGAG-AACAAAATTTTTAACAAGCATGATTCGAGCAAAATTTAAACGAATTTAACG
1992513 AGTCGAG-ACAAAATTTTTTAACAAGCATGATTCGAGCAAAATTTAAACGAATTTAACG
1 AGTCGAGAACAAAA-TTTTTAACAAGCATGATTCGAGCAAAATTTAAACGAATTTAACG
1992571 AGTCGAGCAACAAAA
1 AGTCGAG-AACAAAA
1992586 AATTTTGACG
Statistics
Matches: 70, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
57 6 0.09
58 51 0.73
59 7 0.10
60 6 0.09
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (58 bp):
AGTCGAGAACAAAATTTTTAACAAGCATGATTCGAGCAAAATTTAAACGAATTTAACG
Found at i:1992547 original size:29 final size:27
Alignment explanation
Indices: 1992464--1992556 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 27
1992454 AGTCGAGCAA
1992464 CAAAATTTTTAACAAGCATGATTCGAG
1 CAAAATTTTTAACAAGCATGATTCGAG
* ** * *
1992491 CAAAA-TTTAAACGAATTTAACGAGTCGAG
1 CAAAATTTTTAAC-AA--GCATGATTCGAG
1992520 ACAAAATTTTTTAACAAGCATGATTCGAG
1 -CAAAA-TTTTTAACAAGCATGATTCGAG
1992549 CAAAATTT
1 CAAAATTT
1992557 AAACGAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 6 0.12
27 10 0.20
28 5 0.10
29 16 0.32
30 5 0.10
31 2 0.04
32 6 0.12
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (27 bp):
CAAAATTTTTAACAAGCATGATTCGAG
Found at i:1996414 original size:45 final size:48
Alignment explanation
Indices: 1996347--1996444 Score: 157
Period size: 45 Copynumber: 2.1 Consensus size: 48
1996337 TTATTTTCGT
1996347 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTA-GATTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
1996394 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
1996440 TTTTT
1 TTTTT
1996445 GTGAATAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
45 26 0.54
46 13 0.27
47 9 0.19
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:2005873 original size:6 final size:7
Alignment explanation
Indices: 2005855--2006020 Score: 55
Period size: 7 Copynumber: 22.9 Consensus size: 7
2005845 AAATAAAAGA
2005855 GAAAAAT
1 GAAAAAT
2005862 GAAAAAT
1 GAAAAAT
2005869 GAAAAAAAT
1 G--AAAAAT
2005878 GAAAAAAAT
1 G--AAAAAT
*
2005887 -AATAAT
1 GAAAAAT
2005893 -AAAAAT
1 GAAAAAT
2005899 GATAAGAA-
1 GA-AA-AAT
2005907 GAAAAA-
1 GAAAAAT
*
2005913 GAAGAAAA
1 GAA-AAAT
2005921 GAAAAAT
1 GAAAAAT
*
2005928 GAGAAAAAA
1 --GAAAAAT
2005937 GAAAAAT
1 GAAAAAT
2005944 GATGGAAAAT
1 GA---AAAAT
*
2005954 G-AAAAG
1 GAAAAAT
*
2005960 GAAAAAAA
1 G-AAAAAT
2005968 GAAAAAT
1 GAAAAAT
*
2005975 GGAAAAT
1 GAAAAAT
2005982 GGAAAAAAAT
1 -G--AAAAAT
*
2005992 GAAAGA-
1 GAAAAAT
2005998 GAAAAA-
1 GAAAAAT
2006004 -AAAAA-
1 GAAAAAT
2006009 G-AAAAT
1 GAAAAAT
2006015 GAAAAA
1 GAAAAA
2006021 AAAAAATAGA
Statistics
Matches: 127, Mismatches: 12, Indels: 40
0.71 0.07 0.22
Matches are distributed among these distances:
5 9 0.07
6 26 0.20
7 44 0.35
8 13 0.10
9 24 0.19
10 11 0.09
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (7 bp):
GAAAAAT
Found at i:2005877 original size:16 final size:15
Alignment explanation
Indices: 2005856--2006026 Score: 92
Period size: 15 Copynumber: 11.7 Consensus size: 15
2005846 AATAAAAGAG
*
2005856 AAAAATGAAAAATGA
1 AAAAAAGAAAAATGA
2005871 AAAAAATGAAAAA--A
1 AAAAAA-GAAAAATGA
* *
2005885 ATAATAATAAAAATGA
1 A-AAAAAGAAAAATGA
* *
2005901 TAAGAAGAAAAA-GA
1 AAAAAAGAAAAATGA
*
2005915 AGAAAAGAAAAATGA
1 AAAAAAGAAAAATGA
2005930 GAAAAAAGAAAAATGA
1 -AAAAAAGAAAAATGA
* * *
2005946 TGGAAAATG-AAAAGGA
1 --AAAAAAGAAAAATGA
*
2005962 AAAAAAGAAAAATGG
1 AAAAAAGAAAAATGA
**
2005977 AAAATGGAAAAA--A
1 AAAAAAGAAAAATGA
** *
2005990 ATGAAAGAGAAA--A
1 AAAAAAGAAAAATGA
2006003 AAAAAAG-AAAATGA
1 AAAAAAGAAAAATGA
2006017 AAAAAA-AAAA
1 AAAAAAGAAAA
2006027 TAGAGGGTTC
Statistics
Matches: 117, Mismatches: 28, Indels: 23
0.70 0.17 0.14
Matches are distributed among these distances:
12 3 0.03
13 13 0.11
14 33 0.28
15 35 0.30
16 27 0.23
17 6 0.05
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (15 bp):
AAAAAAGAAAAATGA
Found at i:2005899 original size:30 final size:29
Alignment explanation
Indices: 2005849--2005973 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 29
2005839 AAGAATAAAT
*
2005849 AAAAGAGAA-AAATGAAAAATGAAAAAAATG
1 AAAA-AGAAGAAAAGAAAAATGAAAAAAA-G
* * * *
2005879 AAAAA-AATAATAATAAAAATGATAAGAAG
1 AAAAAGAAGAA-AAGAAAAATGAAAAAAAG
2005908 AAAAAGAAGAAAAGAAAAATGAGAAAAAAG
1 AAAAAGAAGAAAAGAAAAATGA-AAAAAAG
* *
2005938 AAAAATGATGGAAAATG-AAAAGGAAAAAAAG
1 AAAAA-GA-AGAAAA-GAAAAATGAAAAAAAG
2005969 AAAAA
1 AAAAA
2005974 TGGAAAATGG
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
28 2 0.03
29 19 0.24
30 31 0.40
31 14 0.18
32 11 0.14
33 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (29 bp):
AAAAAGAAGAAAAGAAAAATGAAAAAAAG
Found at i:2005991 original size:38 final size:36
Alignment explanation
Indices: 2005849--2006022 Score: 146
Period size: 38 Copynumber: 4.8 Consensus size: 36
2005839 AAGAATAAAT
*
2005849 AAAAGAGAAAAATGAAAAATGAAAAAAATGAAAA-A
1 AAAAAAGAAAAATGAAAAATGAAAAAAATGAAAAGA
*
2005884 AATAATAATAAAAATGATAAGAA-GAAAAAGAA-GAAAAGA
1 AA-AA-AAGAAAAATGA-AA-AATGAAAAA-AATGAAAAGA
* * **
2005923 AAAATGAGAAAAAAGAAAAATGATGGAAAATGAAAAGGA
1 AAAA-AAGAAAAATGAAAAATGA-AAAAAATGAAAA-GA
*
2005962 AAAAAAGAAAAATGGAAAATGGAAAAAAATG-AAAGA
1 AAAAAAGAAAAATGAAAAAT-GAAAAAAATGAAAAGA
*
2005998 GAAAAA-AAAAA-G-AAAATGAAAAAAA
1 AAAAAAGAAAAATGAAAAATGAAAAAAA
2006023 AAAATAGAGG
Statistics
Matches: 115, Mismatches: 13, Indels: 25
0.75 0.08 0.16
Matches are distributed among these distances:
32 8 0.07
33 5 0.04
34 1 0.01
35 7 0.06
36 11 0.10
37 18 0.16
38 50 0.43
39 15 0.13
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (36 bp):
AAAAAAGAAAAATGAAAAATGAAAAAAATGAAAAGA
Found at i:2006003 original size:23 final size:22
Alignment explanation
Indices: 2005849--2006003 Score: 72
Period size: 23 Copynumber: 6.9 Consensus size: 22
2005839 AAGAATAAAT
* *
2005849 AAAAGAGAAAAATGAAAAATGA
1 AAAAAAGAAAAATGAAAAAGGA
* *
2005871 AAAAAATGAAAAA--AATAA-TA
1 AAAAAA-GAAAAATGAAAAAGGA
2005891 ATAAAAATGATAAGAA-GAAAAA-GA
1 A-AAAAA-GA-AA-AATGAAAAAGGA
* *
2005915 AGAAAAGAAAAATGAGAAAAAAGA
1 AAAAAAGAAAAAT--GAAAAAGGA
* *
2005939 AAAATGATGGAAAATG-AAAAGGA
1 AAAA--AAGAAAAATGAAAAAGGA
*
2005962 AAAAAAGAAAAATGGAAAATGGA
1 AAAAAAGAAAAAT-GAAAAAGGA
*
2005985 AAAAAATGAAAGA-GAAAAA
1 AAAAAA-GAAAAATGAAAAA
2006004 AAAAAGAAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
20 4 0.04
21 21 0.20
22 15 0.14
23 40 0.38
24 17 0.16
26 7 0.07
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (22 bp):
AAAAAAGAAAAATGAAAAAGGA
Found at i:2006023 original size:17 final size:17
Alignment explanation
Indices: 2005984--2006025 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2005974 TGGAAAATGG
*
2005984 AAAAAAATGAAAGAGAA
1 AAAAAAAAGAAAGAGAA
2006001 AAAAAAAAGAAA-ATGAA
1 AAAAAAAAGAAAGA-GAA
2006018 AAAAAAAA
1 AAAAAAAA
2006026 ATAGAGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGAAAGAGAA
Found at i:2006026 original size:38 final size:38
Alignment explanation
Indices: 2005949--2006026 Score: 88
Period size: 39 Copynumber: 2.1 Consensus size: 38
2005939 AAAATGATGG
* * **
2005949 AAAATGAAAAGGAAAAAAAGAAAAATGGAAAATGGAAA
1 AAAATGAAAAGAAAAAAAAAAAAAATGGAAAATAAAAA
2005987 AAAATGAAAGAGAAAAAAAAAAGAAAAT-GAAAA-AAAAA
1 AAAATGAAA-AGAAAAAAAAAA-AAAATGGAAAATAAAAA
2006025 AA
1 AA
2006027 TAGAGGGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
38 14 0.41
39 15 0.44
40 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (38 bp):
AAAATGAAAAGAAAAAAAAAAAAAATGGAAAATAAAAA
Found at i:2007339 original size:32 final size:34
Alignment explanation
Indices: 2007298--2007363 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 34
2007288 TTCAATCTTA
2007298 AGCCTTCACGAAGAG-TATGAAGCAAA-TCATTT
1 AGCCTTCACGAAGAGTTATGAAGCAAACTCATTT
*
2007330 AGCCTTCACGAAGAGTTGTGAAGCAAACTCATTT
1 AGCCTTCACGAAGAGTTATGAAGCAAACTCATTT
2007364 TATGAAGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 15 0.48
33 10 0.32
34 6 0.19
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (34 bp):
AGCCTTCACGAAGAGTTATGAAGCAAACTCATTT
Found at i:2007537 original size:55 final size:55
Alignment explanation
Indices: 2007372--2007823 Score: 468
Period size: 55 Copynumber: 8.6 Consensus size: 55
2007362 TTTATGAAGA
* * *
2007372 TCGAG-TCTATA--CTCTGAAGGAATAGGGA-TGGACA-GTTCGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
**
2007422 TCGAGTTCTATA--CTCTGAAGGAAT--AGAGCGGAC-CGTTTCATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
* *
2007472 TCGAGTTCTATACTCTCTGAAGGAAAAGAAAGCGGACACGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
* *
2007527 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGC
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGT-TGAAGATTGT
* * *
2007582 TCGAGTTCTATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTAAAGA---T
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
* * * * * *
2007634 T-GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGGCATGTTTATTGAAGATTTT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
* *
2007688 TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGAC-CGTTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
* * *
2007742 TCAAG-TCTTATACTCT-TGAATGAATAGAGA---GACAC-ATT-TTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
* *
2007791 TCGAG-TCTTATACT-TCCTGAACGAATAGGGAGC
1 TCGAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
2007824 AGGCTTGTCA
Statistics
Matches: 343, Mismatches: 39, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
48 1 0.00
49 26 0.08
50 51 0.15
51 60 0.17
52 12 0.03
53 15 0.04
54 37 0.11
55 140 0.41
56 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGT
Found at i:2007693 original size:161 final size:160
Alignment explanation
Indices: 2007372--2007768 Score: 458
Period size: 161 Copynumber: 2.5 Consensus size: 160
2007362 TTTATGAAGA
* * * **
2007372 TCGAG-TCTAT-A-CTCTGAAGGAATAGGGA-TGGACAGTTCGTTGAAGATTGTTCGAGTTCTAT
1 TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACCGTTTATTGAAGATTGTTCGAGTTCTAT
* * * *
2007433 A--CTCTGAAGGAATA-GAGCGGACCGTTTCATGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
66 ACTCTCTGAAGGAATAGGAACGGACCGTTTCATAAAGA-T-TTCGAGTCCTATACTCTCTGAAAG
*
2007495 AAAAGAAAGCGGACACGTTTGTTGAAGATTGT
129 AAAAGAAAGCGGACACGTTTATTGAAGATTGT
* *
2007527 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGCTCGAGTTCT
1 TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGA-CCGTTTAT-TGAAGATTGTTCGAGTTCT
**
2007591 ATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTAAAGA-TT-GAGTCCTATACTCTCTGAA
64 ATACTCTCTGAAGGAATA-GGAACGGAC-CGTTTCATAAAGATTTCGAGTCCTATACTCTCTGAA
* * * * *
2007654 AGAATAGAGAGCGGGCATGTTTATTGAAGATTTT
127 AGAAAAGAAAGCGGACACGTTTATTGAAGATTGT
*
2007688 TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACCGTTTATTGAAGATTGTTCAAG-TCTTA
1 TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACCGTTTATTGAAGATTGTTCGAGTTC-TA
*
2007752 TACTCT-TGAATGAATAG
65 TACTCTCTGAAGGAATAG
2007769 AGAGACACAT
Statistics
Matches: 207, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
155 5 0.02
156 5 0.02
158 17 0.08
159 15 0.07
160 52 0.25
161 81 0.39
162 15 0.07
164 7 0.03
165 10 0.05
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (160 bp):
TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACCGTTTATTGAAGATTGTTCGAGTTCTAT
ACTCTCTGAAGGAATAGGAACGGACCGTTTCATAAAGATTTCGAGTCCTATACTCTCTGAAAGAA
AAGAAAGCGGACACGTTTATTGAAGATTGT
Found at i:2007698 original size:106 final size:106
Alignment explanation
Indices: 2007372--2007821 Score: 402
Period size: 106 Copynumber: 4.3 Consensus size: 106
2007362 TTTATGAAGA
* * *
2007372 TCGAG-TCTATA--CTCTGAAGGAATAGGG-ATGGACA-GTTCGTTGAAGATTGTTCGAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTGAAGA---TT-GAGTCCTA
* *
2007432 TA--CTCTGAAGGAAT--AGAGCGGAC-CGTTTCATGAAGATTGT
62 TACTCTCTGAAAGAATAGAGAGCGGACACGTTTTATGAAGATTGT
* * *
2007472 TCGAGTTCTATACTCTCTGAAGGAA-AAGAAAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAA-CGGACACGTTTGTTGAAGA---TT-GAGTCCT
* * *
2007536 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGC
61 ATACTCTCTGAAAGAATAGAGAGCGGACACGTTTTATGAAGATTGT
*
2007582 TCGAGTTCTATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTAAAGATTGAGTCCTATACT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTGAAGATTGAGTCCTATACT
* * *
2007647 CTCTGAAAGAATAGAGAGCGGGCATG-TTTATTGAAGATTTT
66 CTCTGAAAGAATAGAGAGCGGACACGTTTTA-TGAAGATTGT
* * * * *
2007688 TCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGAC-CGTTTATTGAAGATTGTTCAAGTCTTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTGAAGATTG----AGTCCTA
* *
2007752 TACTCT-TGAATGAATAGAGA---GACAC-ATTT-TGAAGATTGT
62 TACTCTCTGAAAGAATAGAGAGCGGACACGTTTTATGAAGATTGT
*
2007791 TCGAG-TCTTATACT-TCCTGAACGAATAGGGA
1 TCGAGTTC-TATACTCT-CTGAAGGAATAGGGA
2007822 GCAGGCTTGT
Statistics
Matches: 301, Mismatches: 29, Indels: 37
0.82 0.08 0.10
Matches are distributed among these distances:
100 5 0.02
101 6 0.02
102 5 0.02
103 44 0.15
104 5 0.02
105 51 0.17
106 75 0.25
107 14 0.05
108 13 0.04
109 21 0.07
110 58 0.19
111 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (106 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGGGAACGGACACGTTTGTTGAAGATTGAGTCCTATACT
CTCTGAAAGAATAGAGAGCGGACACGTTTTATGAAGATTGT
Found at i:2017267 original size:36 final size:36
Alignment explanation
Indices: 2017220--2017441 Score: 327
Period size: 36 Copynumber: 6.2 Consensus size: 36
2017210 GTCGAACGAT
*
2017220 TCGAACGGAAGGAGGCATCGGTACTTCCGATTCAAG
1 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
2017256 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
1 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
* *
2017292 TCGAACGGAAGGAGGCATTGACACTTCCGATTCAAG
1 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
* *
2017328 TCGAACGGAAGAAGGCATCGTCACTTCCGATTCAAG
1 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
* *
2017364 TCGAACGAAAGGAGGCATCGGCACTTCCGATTCAAA
1 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
* * * ** *
2017400 TCAAACGGAAGAAAGCATCAACACTTCCGATTCAAA
1 TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
2017436 TCGAAC
1 TCGAAC
2017442 AGAAAGATGT
Statistics
Matches: 169, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 169 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (36 bp):
TCGAACGGAAGGAGGCATCGGCACTTCCGATTCAAG
Found at i:2020028 original size:24 final size:25
Alignment explanation
Indices: 2020001--2020047 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2019991 TAAAATCCCC
* *
2020001 ACGA-TTTTTTAAGCGGGGACGGTT
1 ACGAGTTTTTTAAACAGGGACGGTT
2020025 ACGAGTTTTTTAAACAGGGACGG
1 ACGAGTTTTTTAAACAGGGACGG
2020048 GGGACCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.30
Consensus pattern (25 bp):
ACGAGTTTTTTAAACAGGGACGGTT
Found at i:2025373 original size:3 final size:3
Alignment explanation
Indices: 2025367--2025544 Score: 241
Period size: 3 Copynumber: 58.7 Consensus size: 3
2025357 TTTATCCATT
* * *
2025367 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * **
2025415 TTA TTA TCA TTA CTA TTA TTA TTA GTA TTA TTA TTA TTA TTA GCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2025463 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
2025509 TTA -TA TATA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TT
2025545 TAAATAATTA
Statistics
Matches: 154, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.01
3 143 0.93
4 9 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2026898 original size:20 final size:21
Alignment explanation
Indices: 2026852--2026898 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2026842 CCACTTTTAA
2026852 ATATATTGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
2026873 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
2026892 ATATATT
1 ATATATT
2026899 TAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:2038216 original size:6 final size:6
Alignment explanation
Indices: 2038205--2038284 Score: 87
Period size: 6 Copynumber: 13.3 Consensus size: 6
2038195 ATTATGCTTG
2038205 AAGAAA AAG-AA AAGAAA AA-AGAA AAGAAA AAGAAGA GAA-AGAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGA-AA AAGAAA AAGAA-A -AAGA-AA AAGAAA
*
2038254 AA-AAA AGGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
2038285 AGGGGTCAAG
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
5 10 0.16
6 46 0.72
7 5 0.08
8 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:2038219 original size:5 final size:5
Alignment explanation
Indices: 2038209--2038283 Score: 62
Period size: 5 Copynumber: 13.8 Consensus size: 5
2038199 TGCTTGAAGA
* *
2038209 AAAAG AAAAG AAAAAAG AAAAG AAAA- AGAAG AGAAAG AAAAG AAAAA
1 AAAAG AAAAG --AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG
2038256 AAAAGG AAAAAG AAAAAG AAAAAG AAAA
1 AAAA-G -AAAAG -AAAAG -AAAAG AAAA
2038284 AAGGGGTCAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
4 3 0.05
5 31 0.52
6 17 0.28
7 9 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2038221 original size:11 final size:11
Alignment explanation
Indices: 2038205--2038283 Score: 101
Period size: 11 Copynumber: 7.2 Consensus size: 11
2038195 ATTATGCTTG
2038205 AAGAAAAAGAA
1 AAGAAAAAGAA
2038216 AAGAAAAAAGAA
1 AAG-AAAAAGAA
2038228 AAGAAAAAG--
1 AAGAAAAAGAA
*
2038237 AAGAGAAAGAA
1 AAGAAAAAGAA
2038248 AAGAAAAA-AA
1 AAGAAAAAGAA
2038258 AAGGAAAAAGAAA
1 AA-GAAAAAG-AA
2038271 AAGAAAAAGAA
1 AAGAAAAAGAA
2038282 AA
1 AA
2038284 AAGGGGTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
9 8 0.13
10 4 0.07
11 26 0.43
12 18 0.30
13 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:2038631 original size:16 final size:16
Alignment explanation
Indices: 2038612--2038654 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
2038602 ATTTCAAGTG
*
2038612 CAATTTATTTGAGATT
1 CAATTTATTTGAAATT
2038628 CAATTTATTTTTGAAATT
1 CAATTTA--TTTGAAATT
2038646 CAATTTATT
1 CAATTTATT
2038655 CTTTTCTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
18 15 0.62
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
CAATTTATTTGAAATT
Found at i:2038646 original size:18 final size:18
Alignment explanation
Indices: 2038619--2038654 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2038609 GTGCAATTTA
*
2038619 TTTGAGATTCAATTTATT
1 TTTGAAATTCAATTTATT
2038637 TTTGAAATTCAATTTATT
1 TTTGAAATTCAATTTATT
2038655 CTTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTGAAATTCAATTTATT
Found at i:2039386 original size:52 final size:52
Alignment explanation
Indices: 2039308--2039411 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
2039298 GAATTTATCA
*
2039308 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATGGTTGAACAGAAC
* * *
2039360 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATGGTTGAACAGAAC
2039412 TAATCAGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATGGTTGAACAGAAC
Found at i:2039505 original size:52 final size:51
Alignment explanation
Indices: 2039443--2039598 Score: 267
Period size: 52 Copynumber: 3.0 Consensus size: 51
2039433 GAATTTATCA
2039443 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGA-CAGAAC
*
2039495 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAAC
*
2039547 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGACAGAAC
2039599 TAATCAGTGA
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
52 95 0.96
53 4 0.04
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.38
Consensus pattern (51 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAAC
Found at i:2039520 original size:135 final size:135
Alignment explanation
Indices: 2039278--2039546 Score: 468
Period size: 135 Copynumber: 2.0 Consensus size: 135
2039268 ATCTTAGTCC
*
2039278 AATCATTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
1 AATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
* *
2039343 ATATGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACA
66 ATATGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAACA
2039408 GAACT
131 GAACT
*
2039413 AATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
* *
2039478 ATCTGGTT-GATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGAC
66 ATATGGTTGGA-CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAAC
2039542 AGAAC
130 AGAAC
2039547 ATAGCATCTT
Statistics
Matches: 127, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
134 2 0.02
135 125 0.98
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (135 bp):
AATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
ATATGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAACA
GAACT
Found at i:2039623 original size:187 final size:187
Alignment explanation
Indices: 2039308--2039733 Score: 791
Period size: 187 Copynumber: 2.3 Consensus size: 187
2039298 GAATTTATCA
*
2039308 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
2039373 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACTAATCAGTGAATTTAGAAGATGAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACTAATCAGTGAATTTAGAAGATGAATT
*
2039438 TATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
131 TATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGA-CAGAAC
2039495 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
2039560 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACTAATCAGTGAATTTAGAAGATGAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACTAATCAGTGAATTTAGAAGATGAATT
2039625 TATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
131 TATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
* **
2039682 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
2039734 CAATCAGTGA
Statistics
Matches: 233, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
187 231 0.99
188 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (187 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACTAATCAGTGAATTTAGAAGATGAATT
TATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
Found at i:2039634 original size:135 final size:135
Alignment explanation
Indices: 2039495--2039854 Score: 652
Period size: 135 Copynumber: 2.7 Consensus size: 135
2039485 TGATCAGAAC
2039495 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
*
2039560 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACTAATCAGTGAATTTAGAAGATGAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATTTAGAAGATGAATT
*
2039625 TATCA
131 TACCA
2039630 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
2039695 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATTTAGAAGATGAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATTTAGAAGATGAATT
*
2039760 TGCCA
131 TACCA
* * *
2039765 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-ATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
2039828 GAAGTGTTCTTTGAGTTATCTGATCTG
66 GAAGTGTTCTTTGAGTTATCTGATCTG
2039855 ATTAGACAGA
Statistics
Matches: 219, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
133 40 0.18
134 1 0.00
135 178 0.81
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (135 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATTTAGAAGATGAATT
TACCA
Found at i:2039692 original size:52 final size:52
Alignment explanation
Indices: 2039630--2039733 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
2039620 GAATTTATCA
*
2039630 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAACAGAAC
* *
2039682 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAACAGAAC
2039734 CAATCAGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAACAGAAC
Found at i:2039839 original size:50 final size:50
Alignment explanation
Indices: 2039764--2039904 Score: 282
Period size: 50 Copynumber: 2.8 Consensus size: 50
2039754 TGAATTTGCC
2039764 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
2039814 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
2039864 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
2039905 GTTTGGTAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:2040590 original size:113 final size:113
Alignment explanation
Indices: 2040419--2041044 Score: 1159
Period size: 113 Copynumber: 5.5 Consensus size: 113
2040409 TGCAAGGTAG
2040419 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
2040484 TTCAACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
63 TTCAACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
2040535 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
2040600 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
2040648 AGTTCATAAT--GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
2040711 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
2040759 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
2040824 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
2040872 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
2040937 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
2040985 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAACT
2041045 CATCAAGAGT
Statistics
Matches: 504, Mismatches: 3, Indels: 9
0.98 0.01 0.02
Matches are distributed among these distances:
111 111 0.22
112 2 0.00
113 372 0.74
114 1 0.00
116 18 0.04
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
Found at i:2040685 original size:224 final size:225
Alignment explanation
Indices: 2040419--2041044 Score: 1148
Period size: 224 Copynumber: 2.8 Consensus size: 225
2040409 TGCAAGGTAG
2040419 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAAT-AGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
2040484 TTCAACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGA
62 TTCAACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGA
*
2040549 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGA
127 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGA
2040614 ATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
192 ATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
2040648 AGTTCATAAT-GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
2040712 ACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
*
2040777 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
131 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATCC
2040842 ATCATTTGGTGGATCATCTTTTCCAGAGAA
196 ATCATTTGGTGGATCATCTTTTCCAGAGAA
*
2040872 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
2040937 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
65 AACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
2041002 ACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGAGAAGAACT
130 ACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAACT
2041045 CATCAAGAGT
Statistics
Matches: 389, Mismatches: 5, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
224 215 0.55
225 3 0.01
226 155 0.40
227 6 0.02
229 10 0.03
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (225 bp):
AGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATCC
ATCATTTGGTGGATCATCTTTTCCAGAGAA
Found at i:2041298 original size:3 final size:3
Alignment explanation
Indices: 2041292--2041466 Score: 242
Period size: 3 Copynumber: 57.7 Consensus size: 3
2041282 TTTATCCATT
* * *
2041292 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * **
2041340 TTA TTA TCA TTA CTA TTA TTA TTA GTA TTA TTA TTA TTA TTA GCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2041388 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
2041434 ATA TTA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
2041467 TAATAAATAA
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
3 145 0.97
4 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2042834 original size:20 final size:21
Alignment explanation
Indices: 2042788--2042834 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2042778 CCACTTTTAA
2042788 ATATATTGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
2042809 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
2042828 ATATATT
1 ATATATT
2042835 TAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:2044875 original size:9 final size:9
Alignment explanation
Indices: 2044854--2044930 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
2044844 AAATTAAATG
2044854 AATATAATA
1 AATATAATA
2044863 AATA-AATA
1 AATATAATA
*
2044871 TA-ATAAT-
1 AATATAATA
2044878 AATAATAAT-
1 AAT-ATAATA
*
2044887 AATATTATTA
1 AATA-TAATA
2044897 AATATAATA
1 AATATAATA
*
2044906 AATA-ATTAA
1 AATATAAT-A
2044915 AATATAATA
1 AATATAATA
2044924 ATATATA
1 A-ATATA
2044931 TAGTAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
7 2 0.04
8 11 0.20
9 30 0.56
10 11 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATAATA
Found at i:2045256 original size:21 final size:20
Alignment explanation
Indices: 2045224--2045262 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2045214 GCTAATAGAG
*
2045224 CCATTCACTCCCATTCATCA
1 CCATACACTCCCATTCATCA
*
2045244 CCATACACATCCCTTTCAT
1 CCATACAC-TCCCATTCAT
2045263 ATATTCAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.31
Consensus pattern (20 bp):
CCATACACTCCCATTCATCA
Found at i:2049209 original size:32 final size:32
Alignment explanation
Indices: 2049168--2049237 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
2049158 GACGTCAACA
2049168 GAAAATCTATTCCTATTACCTTCGTAATTGTT
1 GAAAATCTATTCCTATTACCTTCGTAATTGTT
2049200 GAAAATCTATTCCTATTACCTTCGTAATTGTT
1 GAAAATCTATTCCTATTACCTTCGTAATTGTT
2049232 GAAAAT
1 GAAAAT
2049238 GAATATATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (32 bp):
GAAAATCTATTCCTATTACCTTCGTAATTGTT
Found at i:2054261 original size:23 final size:23
Alignment explanation
Indices: 2054231--2054304 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
2054221 GACCTGCTCT
*
2054231 TCTTCTTCTTCAACCCAATCCCA
1 TCTTCTTCCTCAACCCAATCCCA
*
2054254 TCTTCTTCCTCAACCCAA-CCTCT
1 TCTTCTTCCTCAACCCAATCC-CA
* **
2054277 TATTCTTCCTCAACCCAATTGCA
1 TCTTCTTCCTCAACCCAATCCCA
2054300 TCTTC
1 TCTTC
2054305 GGGTAAACAG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.20, C:0.42, G:0.01, T:0.36
Consensus pattern (23 bp):
TCTTCTTCCTCAACCCAATCCCA
Found at i:2055231 original size:23 final size:23
Alignment explanation
Indices: 2055205--2055281 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
2055195 AAGAGAAAGA
* *
2055205 AAGAAGAAGATGGGTTGAGGAAG
1 AAGAAGAGGTTGGGTTGAGGAAG
* *
2055228 AAGATGGGGTTGGGTTGAGGAAG
1 AAGAAGAGGTTGGGTTGAGGAAG
* * *
2055251 AAGATGGGGTTGGGTTGAAGAAG
1 AAGAAGAGGTTGGGTTGAGGAAG
2055274 AAGAAGAG
1 AAGAAGAG
2055282 CGGGTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.17
Consensus pattern (23 bp):
AAGAAGAGGTTGGGTTGAGGAAG
Found at i:2055287 original size:26 final size:23
Alignment explanation
Indices: 2055215--2055277 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
2055205 AAGAAGAAGA
2055215 TGGGTTGAGGAAGAAGATGGGGT
1 TGGGTTGAGGAAGAAGATGGGGT
2055238 TGGGTTGAGGAAGAAGATGGGGT
1 TGGGTTGAGGAAGAAGATGGGGT
*
2055261 TGGGTTGAAGAAGAAGA
1 TGGGTTGAGGAAGAAGA
2055278 AGAGCGGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.49, T:0.21
Consensus pattern (23 bp):
TGGGTTGAGGAAGAAGATGGGGT
Found at i:2056364 original size:23 final size:23
Alignment explanation
Indices: 2056338--2056393 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
2056328 TTTTATGTTG
*
2056338 AATCATTCAACATTGTTTTGCTA
1 AATCAGTCAACATTGTTTTGCTA
*
2056361 AATCAGTCATCATTGTTTTGCTA
1 AATCAGTCAACATTGTTTTGCTA
2056384 AATCAGTCAA
1 AATCAGTCAA
2056394 TACCAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (23 bp):
AATCAGTCAACATTGTTTTGCTA
Found at i:2060619 original size:19 final size:19
Alignment explanation
Indices: 2060595--2060641 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2060585 GAAGGCGAAT
2060595 GATACCATGTTATGATTTA
1 GATACCATGTTATGATTTA
2060614 GATACCATGTTATGATTTA
1 GATACCATGTTATGATTTA
*
2060633 GAAACCATG
1 GATACCATG
2060642 ACTGAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (19 bp):
GATACCATGTTATGATTTA
Found at i:2062822 original size:23 final size:24
Alignment explanation
Indices: 2062796--2062840 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2062786 ATATAGATGC
*
2062796 ATGTATA-CATTTTGTTATATGGA
1 ATGTATATCATTTTATTATATGGA
* *
2062819 ATGTTTATGATTTTATTATATG
1 ATGTATATCATTTTATTATATG
2062841 TTTTATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (24 bp):
ATGTATATCATTTTATTATATGGA
Found at i:2063218 original size:22 final size:21
Alignment explanation
Indices: 2063176--2063219 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2063166 TATAGCAGTA
*
2063176 CTGTAGCAGGGTATCGATTCC
1 CTGTAGCAGGGAATCGATTCC
*
2063197 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCA-GGGAATCGATTCC
2063219 C
1 C
2063220 CTATGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGATTCC
Found at i:2064308 original size:28 final size:31
Alignment explanation
Indices: 2064254--2064322 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 31
2064244 TTAATTATTT
*
2064254 TATATATTTTATTATGTTTTTGAAAATATGA
1 TATATGTTTTATTATGTTTTTGAAAATATGA
2064285 TATATGTTTTA-TA-GTTTTTG-AAATATGA
1 TATATGTTTTATTATGTTTTTGAAAATATGA
*
2064313 CATATGTTTT
1 TATATGTTTT
2064323 TGAAAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 17 0.47
29 7 0.19
30 2 0.06
31 10 0.28
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (31 bp):
TATATGTTTTATTATGTTTTTGAAAATATGA
Found at i:2064345 original size:15 final size:16
Alignment explanation
Indices: 2064314--2064348 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2064304 GAAATATGAC
*
2064314 ATATGTTTTTGAAAAT
1 ATATGTTTCTGAAAAT
2064330 ATATGTTTCT-AAAAT
1 ATATGTTTCTGAAAAT
2064345 ATAT
1 ATAT
2064349 ATATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATATGTTTCTGAAAAT
Found at i:2066166 original size:14 final size:16
Alignment explanation
Indices: 2066139--2066171 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2066129 TTATATGTTA
2066139 TATATATTTATCATTT
1 TATATATTTATCATTT
2066155 TATATA-TT-TCATTT
1 TATATATTTATCATTT
2066169 TAT
1 TAT
2066172 CTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATATTTATCATTT
Found at i:2066264 original size:15 final size:14
Alignment explanation
Indices: 2066092--2066264 Score: 74
Period size: 15 Copynumber: 11.7 Consensus size: 14
2066082 TTCTTTTTCA
2066092 TATATCATTATTA-TT
1 TATAT-ATT-TTATTT
2066107 TATATATTTT-TTAT
1 TATATATTTTATT-T
*
2066121 TACTATAATTATATGTT
1 TA-TAT-ATTTTAT-TT
2066138 ATATATATTTATCATTT
1 -TATATATTT-T-ATTT
*
2066155 TATATATTTCA-TT
1 TATATATTTTATTT
*
2066168 T-TATCTTTTATTT
1 TATATATTTTATTT
*
2066181 T-TTTATCTTCTATTT
1 TATATAT-TT-TATTT
2066196 T-TA-ATTTTATTT
1 TATATATTTTATTT
*
2066208 T-TGTATTGTTATTGT
1 TATATATT-TTATT-T
*
2066223 TATTATCTTCTTTATTT
1 TA-TAT-AT-TTTATTT
*
2066240 TATGTATTTTATTT
1 TATATATTTTATTT
2066254 ATATATATTTT
1 -TATATATTTT
2066265 TATATTTGTT
Statistics
Matches: 124, Mismatches: 14, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
12 14 0.11
13 17 0.14
14 23 0.19
15 27 0.22
16 18 0.15
17 13 0.10
18 11 0.09
19 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.66
Consensus pattern (14 bp):
TATATATTTTATTT
Found at i:2071617 original size:29 final size:29
Alignment explanation
Indices: 2071570--2071679 Score: 152
Period size: 29 Copynumber: 3.8 Consensus size: 29
2071560 TTTCATATGT
*
2071570 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTTATTTCTCTTGTGA
*
2071598 TCATGTAGTTCATGTTATTTCTCTTGTGA
1 TCATGTAGCTCATGTTATTTCTCTTGTGA
2071627 TCATGTAGCTCAT-TTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTT-ATTTCTCTTGTGA
* *
2071656 TCATGTAACTCATGTCATGTTCTC
1 TCATGTAGCTCATGTTAT-TTCTC
2071680 ACATCACATA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
28 9 0.12
29 58 0.79
30 6 0.08
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (29 bp):
TCATGTAGCTCATGTTATTTCTCTTGTGA
Found at i:2071669 original size:58 final size:58
Alignment explanation
Indices: 2071570--2071679 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
2071560 TTTCATATGT
** *
2071570 TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGTTCATGTTAT-TTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGATCATGTAACTCATGTCATGTTCTCTTGTGA
*
2071627 TCATGTAGCTCATTTCATTTCTCTTGTGATCATGTAACTCATGTCATGTTCTC
1 TCATGTA-CTCATGTCATTTCTCTTGTGATCATGTAACTCATGTCATGTTCTC
2071680 ACATCACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
57 7 0.15
58 35 0.74
59 5 0.11
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (58 bp):
TCATGTACTCATGTCATTTCTCTTGTGATCATGTAACTCATGTCATGTTCTCTTGTGA
Found at i:2078559 original size:29 final size:29
Alignment explanation
Indices: 2078512--2078621 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
2078502 TTTCGTATGT
*
2078512 TCATGTA-CTCATGTCATTTTTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
2078540 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2078569 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2078598 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
2078622 ATATCACATA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 65 0.84
30 5 0.06
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:2079093 original size:46 final size:45
Alignment explanation
Indices: 2079024--2079130 Score: 128
Period size: 46 Copynumber: 2.4 Consensus size: 45
2079014 TGCACTACTT
* * * *
2079024 GTGCATCGGTGCA-TAAAATGCATTCGATGTTTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATCTTTTTATT-TTAAAAGA
*
2079069 GATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATCTTTTTATTTTAAAAGA
2079115 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
2079131 CCAGTGCATC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
45 18 0.33
46 35 0.65
47 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATCTTTTTATTTTAAAAGA
Found at i:2088300 original size:2 final size:2
Alignment explanation
Indices: 2088295--2088329 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2088285 TTATTCTTAT
2088295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2088330 TATTATCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2088360 original size:17 final size:18
Alignment explanation
Indices: 2088340--2088377 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2088330 TATTATCTTC
*
2088340 ATTTGGTT-ATTTTTTAT
1 ATTTGGTTAATTTTCTAT
*
2088357 ATTTGTTTAATTTTCTAT
1 ATTTGGTTAATTTTCTAT
2088375 ATT
1 ATT
2088378 CTATCGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (18 bp):
ATTTGGTTAATTTTCTAT
Found at i:2088451 original size:17 final size:16
Alignment explanation
Indices: 2088384--2088495 Score: 76
Period size: 16 Copynumber: 6.9 Consensus size: 16
2088374 TATTCTATCG
2088384 TTATTATTTATATATA
1 TTATTATTTATATATA
* *
2088400 -TATATATATATATACTT
1 TTAT-TATTTATATA-TA
*
2088417 TTAATTTTTTTCATATATCA
1 TT-A-TTATTT-ATATAT-A
2088437 TTATTATTTATATAT-
1 TTATTATTTATATATA
2088452 TT-TTA-TTACTATA-A
1 TTATTATTTA-TATATA
2088466 TTA-TATGTTATATATA
1 TTATTAT-TTATATATA
2088482 TTATTATTT-TATAT
1 TTATTATTTATATAT
2088496 TTCATTTTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 29
0.68 0.05 0.26
Matches are distributed among these distances:
13 3 0.04
14 11 0.14
15 14 0.18
16 18 0.24
17 10 0.13
18 6 0.08
19 6 0.08
20 8 0.11
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (16 bp):
TTATTATTTATATATA
Found at i:2088547 original size:20 final size:19
Alignment explanation
Indices: 2088488--2088567 Score: 58
Period size: 20 Copynumber: 4.2 Consensus size: 19
2088478 TATATTATTA
* *
2088488 TTTTATATTTCAT-TTTAT
1 TTTTATTTTTTATCTTTAT
2088506 CTTTTATTTTTTATCTTCTAT
1 -TTTTATTTTTTATCTT-TAT
2088527 TTTTATTTTTGTAT-TGTTAT
1 TTTTATTTTT-TATCT-TTAT
* * *
2088547 TGTTATTATCT-TCTTTAT
1 TTTTATTTTTTATCTTTAT
2088565 TTT
1 TTT
2088568 ATGTATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
18 7 0.14
19 13 0.26
20 23 0.46
21 7 0.14
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTTATTTTTTATCTTTAT
Found at i:2088597 original size:33 final size:32
Alignment explanation
Indices: 2088526--2088603 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
2088516 TTATCTTCTA
2088526 TTTTTATTTTTGTATTGTTATTGTTATTATCT
1 TTTTTATTTTTGTATTGTTATTGTTATTATCT
* *
2088558 TCTTTATTTTATGTATT-TTATT-TATATATATTT
1 TTTTTATTTT-TGTATTGTTATTGT-TAT-TATCT
*
2088591 TTTTTATATTTGT
1 TTTTTATTTTTGT
2088604 TTTTGTGCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.03
32 20 0.51
33 18 0.46
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (32 bp):
TTTTTATTTTTGTATTGTTATTGTTATTATCT
Found at i:2088598 original size:13 final size:14
Alignment explanation
Indices: 2088430--2088599 Score: 73
Period size: 14 Copynumber: 11.4 Consensus size: 14
2088420 ATTTTTTTCA
2088430 TATATCATTATTA-TT
1 TATAT-ATT-TTATTT
*
2088445 TATATATTTT-TAT
1 TATATATTTTATTT
*
2088458 TACTATAATTATATGTT
1 TA-TAT-ATTTTAT-TT
2088475 ATATATATTATTATTT
1 -TATATATT-TTATTT
2088491 TATATTTCATTTTATCTT
1 TATA--T-ATTTTAT-TT
* *
2088509 T-TATTTTTTATCT
1 TATATATTTTATTT
*
2088522 TCTAT-TTTTATTT
1 TATATATTTTATTT
*
2088535 T-TGTATTGTTATTGT
1 TATATATT-TTATT-T
*
2088550 TATTATCTTCTTTATTT
1 TA-TAT-AT-TTTATTT
*
2088567 TATGTATTTTATTT
1 TATATATTTTATTT
2088581 ATATATATTTT-TTT
1 -TATATATTTTATTT
2088595 TATAT
1 TATAT
2088600 TTGTTTTTGT
Statistics
Matches: 122, Mismatches: 13, Indels: 42
0.69 0.07 0.24
Matches are distributed among these distances:
12 2 0.02
13 22 0.18
14 30 0.25
15 26 0.21
16 8 0.07
17 19 0.16
18 14 0.11
19 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (14 bp):
TATATATTTTATTT
Found at i:2090089 original size:21 final size:21
Alignment explanation
Indices: 2090063--2090112 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2090053 GGTCACGGTC
2090063 TCGAGACCCCCAAGTTTGATA
1 TCGAGACCCCCAAGTTTGATA
*
2090084 TCGAGACCCCCAGGTTTGATA
1 TCGAGACCCCCAAGTTTGATA
2090105 TCGAGACC
1 TCGAGACC
2090113 AAAATTTCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGAGACCCCCAAGTTTGATA
Found at i:2098984 original size:10 final size:10
Alignment explanation
Indices: 2098943--2098986 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
2098933 TTCTCAGTCG
2098943 AAGAAATGAA
1 AAGAAATGAA
*
2098953 ATGAAATGAA
1 AAGAAATGAA
*
2098963 ATGAAATGAA
1 AAGAAATGAA
*
2098973 AAGAAAAGAA
1 AAGAAATGAA
2098983 AAGA
1 AAGA
2098987 GAACTAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (10 bp):
AAGAAATGAA
Found at i:2098986 original size:5 final size:5
Alignment explanation
Indices: 2098945--2098983 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2098935 CTCAGTCGAA
* *
2098945 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAA GAAAA GAAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAA
2098984 AGAGAACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (5 bp):
GAAAT
Found at i:2104287 original size:14 final size:14
Alignment explanation
Indices: 2104258--2104327 Score: 94
Period size: 14 Copynumber: 5.1 Consensus size: 14
2104248 CGATAGTGAA
2104258 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
2104274 CGTTCATTTATGTT
1 CGTTCATTTATGTT
2104288 CGTTCATTTA---T
1 CGTTCATTTATGTT
2104299 -GTTCATTTATGTT
1 CGTTCATTTATGTT
2104312 CGTTCATTTATGTT
1 CGTTCATTTATGTT
2104326 CG
1 CG
2104328 AACAGAGGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.18
11 1 0.02
13 1 0.02
14 31 0.62
15 3 0.06
16 5 0.10
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:2104303 original size:24 final size:24
Alignment explanation
Indices: 2104275--2104326 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2104265 TTATATGTTC
2104275 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCGTTCATTTAT
2104299 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCGTTCATTTAT
2104323 GTTC
1 GTTC
2104327 GAACAGAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTCATTTAT
Found at i:2104821 original size:22 final size:22
Alignment explanation
Indices: 2104795--2104837 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2104785 TAATTATTAC
*
2104795 TATTATTATCATT-ATATTAATA
1 TATTATTA-AATTAATATTAATA
2104817 TATTATTAAATTAATATTAAT
1 TATTATTAAATTAATATTAAT
2104838 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATTAAATTAATATTAATA
Found at i:2105140 original size:18 final size:18
Alignment explanation
Indices: 2105114--2105155 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2105104 TGAAAAGAAA
2105114 AAATATCACATCATACAT
1 AAATATCACATCATACAT
*
2105132 AAATGTCACATCATACAT
1 AAATATCACATCATACAT
2105150 AAATAT
1 AAATAT
2105156 TAATAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATATCACATCATACAT
Found at i:2108648 original size:26 final size:26
Alignment explanation
Indices: 2108592--2108643 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2108582 GTCTGTCTGA
*
2108592 TTATTAGTTAAATTGTTGTGTTTGAG
1 TTATTAGTTAAAATGTTGTGTTTGAG
*
2108618 TTATTGGTTAAAATG-T-TGTTTGAG
1 TTATTAGTTAAAATGTTGTGTTTGAG
2108642 TT
1 TT
2108644 TTATTAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (26 bp):
TTATTAGTTAAAATGTTGTGTTTGAG
Found at i:2108662 original size:29 final size:29
Alignment explanation
Indices: 2108630--2108692 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
2108620 ATTGGTTAAA
2108630 ATGTTGTTTGAGTTTTATTAGTATTTTCT
1 ATGTTGTTTGAGTTTTATTAGTATTTTCT
2108659 ATGTTGTTTGAGTTTTATTAGTATTTTCT
1 ATGTTGTTTGAGTTTTATTAGTATTTTCT
2108688 ATGTT
1 ATGTT
2108693 TTTATGTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.62
Consensus pattern (29 bp):
ATGTTGTTTGAGTTTTATTAGTATTTTCT
Found at i:2108838 original size:18 final size:19
Alignment explanation
Indices: 2108797--2108841 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2108787 TGAATTTAAA
2108797 AAAAAATCAGACAAATTAC
1 AAAAAATCAGACAAATTAC
2108816 AAAAAATCAGACAAATTAC
1 AAAAAATCAGACAAATTAC
2108835 AAAAAAT
1 AAAAAAT
2108842 AGTATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.67, C:0.13, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAAAATCAGACAAATTAC
Found at i:2108857 original size:113 final size:104
Alignment explanation
Indices: 2108721--2109019 Score: 386
Period size: 102 Copynumber: 2.8 Consensus size: 104
2108711 TTTATGTTTT
2108721 AAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTAA
1 AAAAAA-TAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTAA
*
2108786 TTGAATTTAAAAAAAAATCAGACAAATTACAAAAAATCAGACAAATTAC
65 TTGAATTTAAAAAAAAATCAGAAAAATTAC----AA--A-A-AAA-TAC
* * *
2108835 AAAAAATAGTATTTTTATTTATCTAATTGCAATGTATTTTTATCTATCTTGCAATTTAATCTATT
1 AAAAAATAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTAAT
2108900 TGAATTT--AAAAAAATCAGAAAAATTACAAAAAAATAC
66 TGAATTTAAAAAAAAATCAGAAAAATTACAAAAAAATAC
* * * * * *
2108937 AAAAAATAATATGTTTATTTAACTAATTTCAATGTGTTTTTATCTATCTTACAATTTAATTTACT
1 AAAAAATAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTAAT
2109002 TGAATTTTTAAAAAAAAA
66 TGAA--TTTAAAAAAAAA
2109020 AGAAATTGTA
Statistics
Matches: 169, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
102 64 0.38
103 3 0.02
104 4 0.02
105 1 0.01
106 7 0.04
107 2 0.01
111 19 0.11
113 63 0.37
114 6 0.04
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (104 bp):
AAAAAATAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTAAT
TGAATTTAAAAAAAAATCAGAAAAATTACAAAAAAATAC
Found at i:2108907 original size:15 final size:17
Alignment explanation
Indices: 2108876--2108908 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2108866 ATGTATTTTT
2108876 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
2108893 ATCTAT-TTG-AATTTA
1 ATCTATCTTGCAATTTA
2108908 A
1 A
2108909 AAAAATCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:2109145 original size:18 final size:19
Alignment explanation
Indices: 2109122--2109172 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2109112 GGGAATACTA
*
2109122 TCTCCAAAGTGGAG-ATAT
1 TCTCCACAGTGGAGAATAT
2109140 TCTCCACAGTGGAGAATAT
1 TCTCCACAGTGGAGAATAT
2109159 TCTCCACAGTGGAG
1 TCTCCACAGTGGAG
2109173 CAGTATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (19 bp):
TCTCCACAGTGGAGAATAT
Found at i:2109684 original size:13 final size:13
Alignment explanation
Indices: 2109653--2109677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2109643 CTTAAATAAA
2109653 AAATATTTATTTT
1 AAATATTTATTTT
2109666 AAATATTTATTT
1 AAATATTTATTT
2109678 GTGATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATATTTATTTT
Found at i:2115535 original size:15 final size:15
Alignment explanation
Indices: 2115515--2115544 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2115505 CTATTATGAA
2115515 AAAATTGAGAAAAAT
1 AAAATTGAGAAAAAT
2115530 AAAATTGAGAAAAAT
1 AAAATTGAGAAAAAT
2115545 TATTACTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (15 bp):
AAAATTGAGAAAAAT
Found at i:2122743 original size:21 final size:21
Alignment explanation
Indices: 2122719--2122766 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2122709 CATTTTGCAT
2122719 TGCGATAGTTGGAGATCGCGG
1 TGCGATAGTTGGAGATCGCGG
*
2122740 TGCGATAGTTGGAGATCGCGT
1 TGCGATAGTTGGAGATCGCGG
2122761 TGCGAT
1 TGCGAT
2122767 TTTCCATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.40, T:0.27
Consensus pattern (21 bp):
TGCGATAGTTGGAGATCGCGG
Found at i:2122785 original size:41 final size:41
Alignment explanation
Indices: 2122734--2122917 Score: 316
Period size: 41 Copynumber: 4.5 Consensus size: 41
2122724 TAGTTGGAGA
* * *
2122734 TCGCGGTGCGATAGTTGGAGATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
2122775 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
*
2122816 TCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
2122857 TCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
*
2122897 TCGCGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
2122918 AAAGATTTGT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
40 38 0.28
41 98 0.72
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:2122801 original size:21 final size:21
Alignment explanation
Indices: 2122718--2122912 Score: 139
Period size: 20 Copynumber: 9.5 Consensus size: 21
2122708 GCATTTTGCA
* *
2122718 TTGCGATAGTTGGAGATCGCG
1 TTGCGATAGTTGCAAATCGCG
* * *
2122739 GTGCGATAGTTGGAGATCGCG
1 TTGCGATAGTTGCAAATCGCG
* * **
2122760 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGCAAATCGCG
*
2122780 TTGCGATAGTTGAAAATCGCG
1 TTGCGATAGTTGCAAATCGCG
* * **
2122801 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGCAAATCGCG
* *
2122821 TTGCGATAGTTGAAAATCACG
1 TTGCGATAGTTGCAAATCGCG
* * **
2122842 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGCAAATCGCG
2122862 TTGCGATAGTTG-AAATCGCG
1 TTGCGATAGTTGCAAATCGCG
* * **
2122882 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGCAAATCGCG
2122902 TTGCGATAGTT
1 TTGCGATAGTT
2122913 AAAAAAAAGA
Statistics
Matches: 131, Mismatches: 38, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
19 2 0.02
20 70 0.53
21 59 0.45
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTTGCAAATCGCG
Found at i:2123033 original size:39 final size:40
Alignment explanation
Indices: 2122979--2123062 Score: 161
Period size: 39 Copynumber: 2.1 Consensus size: 40
2122969 GTTGAAACAC
2122979 TATTGGGAACAAGTGTTGGTAATGCTCAAAT-CCACATAG
1 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
2123018 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
1 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
2123058 TATTG
1 TATTG
2123063 AAAACACTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 31 0.70
40 13 0.30
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
Found at i:2123186 original size:6 final size:6
Alignment explanation
Indices: 2123173--2123237 Score: 114
Period size: 6 Copynumber: 11.0 Consensus size: 6
2123163 CTCGTTCTCG
*
2123173 GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2123220 GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT
2123238 ACGTGTCTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
5 5 0.09
6 53 0.91
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2123354 original size:19 final size:19
Alignment explanation
Indices: 2123326--2123383 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2123316 AACGAATTTG
2123326 GAAAATCGCAATGACAACT
1 GAAAATCGCAATGACAACT
* * **
2123345 GAATATCGCAACGA-ATTT
1 GAAAATCGCAATGACAACT
2123363 GGAAAATCGCAATGACAACT
1 -GAAAATCGCAATGACAACT
2123383 G
1 G
2123384 TAGAAAATCG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
18 2 0.07
19 25 0.86
20 2 0.07
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
GAAAATCGCAATGACAACT
Found at i:2123358 original size:38 final size:38
Alignment explanation
Indices: 2123310--2123383 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
2123300 TTTTTTTAAC
2123310 TATCACAACGAATTTGGAAAATCGCAATGACAACTGAA
1 TATCACAACGAATTTGGAAAATCGCAATGACAACTGAA
*
2123348 TATCGCAACGAATTTGGAAAATCGCAATGACAACTG
1 TATCACAACGAATTTGGAAAATCGCAATGACAACTG
2123384 TAGAAAATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (38 bp):
TATCACAACGAATTTGGAAAATCGCAATGACAACTGAA
Found at i:2126532 original size:20 final size:20
Alignment explanation
Indices: 2126509--2126546 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2126499 CAATTAAAAT
2126509 TATAAATCT-TAAATTCTATA
1 TATAAA-CTATAAATTCTATA
2126529 TATAAACTATAAATTCTA
1 TATAAACTATAAATTCTA
2126547 AACTCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAACTATAAATTCTATA
Found at i:2127044 original size:25 final size:27
Alignment explanation
Indices: 2127015--2127068 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
2127005 ATGTTATGGT
*
2127015 AATTTAAAAA-AATTAT-TTTTTAAAA
1 AATTTAAAAATAATTATATTTATAAAA
*
2127040 AATTTAAAAATTATTATATTTATAAAA
1 AATTTAAAAATAATTATATTTATAAAA
2127067 AA
1 AA
2127069 AAATCCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 5 0.20
27 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTTAAAAATAATTATATTTATAAAA
Found at i:2130249 original size:17 final size:17
Alignment explanation
Indices: 2130229--2130267 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2130219 GATTTTCAAA
2130229 AAAATATATA-AAAATTT
1 AAAATATA-AGAAAATTT
*
2130246 AAAATATAAGATAATTT
1 AAAATATAAGAAAATTT
2130263 AAAAT
1 AAAAT
2130268 TTCAGAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATATAAGAAAATTT
Found at i:2133010 original size:101 final size:102
Alignment explanation
Indices: 2132834--2133093 Score: 319
Period size: 102 Copynumber: 2.5 Consensus size: 102
2132824 ATGTGCCAAC
* * * *
2132834 AATATCGATACTA-ATCCTTGGGTATCGATACTCAAGC-TGAGTATTAATACAAAAATAACTTCA
1 AATATCAATACTATACCCTT-GGTATCGATACTC--CCTTGAGTATCAATACAAAAATAACTTCA
2132897 ATGTTTTGAAAAAAAACTCAGTATCGATACAC-TATGGGG
63 ATGTTTTGAAAAAAAACTCAGTATCGATACACATATGGGG
* * *
2132936 AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAGTACAAAAATAGCTTCGATG
1 AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAATACAAAAATAACTTCAATG
* * *
2133001 TTTTGAAAAATACCTCAGTATCGATACCCATATGGGG
66 TTTTGAAAAAAAACTCAGTATCGATACACATATGGGG
* * * * * *
2133038 AGTATCAATACTCTACCCTTGGTTTCAATACTCCATTGAGTATCCATACCAAAAAT
1 AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAATA-CAAAAAT
2133094 GGCTACTAGA
Statistics
Matches: 137, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
100 1 0.01
101 51 0.37
102 73 0.53
103 12 0.09
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (102 bp):
AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAATACAAAAATAACTTCAATG
TTTTGAAAAAAAACTCAGTATCGATACACATATGGGG
Found at i:2133861 original size:20 final size:22
Alignment explanation
Indices: 2133827--2133866 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
2133817 CTCTCAACCA
*
2133827 CTTTAGGTATTGATA-TCAAGC
1 CTTTAGGTATGGATACTCAAGC
2133848 CTTT-GGTATGGATACTCAA
1 CTTTAGGTATGGATACTCAA
2133867 TCTTCGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (22 bp):
CTTTAGGTATGGATACTCAAGC
Found at i:2133938 original size:18 final size:20
Alignment explanation
Indices: 2133890--2133940 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2133880 TCAGTCCTCC
*
2133890 GGTATGGAGACCAGTCTTTT
1 GGTATGGAGACCAGTCTCTT
* *
2133910 GGTATGAAGACTAGTC-CTT
1 GGTATGGAGACCAGTCTCTT
2133929 -GTATGGAGACCA
1 GGTATGGAGACCA
2133941 ATTTTTTAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 10 0.38
19 2 0.08
20 14 0.54
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (20 bp):
GGTATGGAGACCAGTCTCTT
Found at i:2136294 original size:157 final size:157
Alignment explanation
Indices: 2135994--2136303 Score: 570
Period size: 157 Copynumber: 2.0 Consensus size: 157
2135984 AAATCGTCCC
2135994 CAAATCATCCATATTTTTTCTTAATGGTACAATTAAACTCTAGCTCATGTATTCTCTCTAAGCTT
1 CAAATCATCCATATTTTTTCTTAATGGTACAATTAAACTCTAGCTCATGTATTCTCTCTAAGCTT
2136059 AAAACTCCATTTTATCTATTCTACAAGGCTAATTCTTACCGATTAAACTCAATTTCGAACCAATA
66 AAAACTCCATTTTATC-ATTCTACAAGGCTAATTCTTACCGATTAAACTCAATTTCGAACCAATA
2136124 GACCCTCATGCTATAATAAATATATTAA
130 GACCCTCATGCTATAATAAATATATTAA
2136152 CAAATCATCCATA-TTTTTCTTAATGGTACAATTAAACTCTAGCTCATGTATTCTCTCTAAGCTT
1 CAAATCATCCATATTTTTTCTTAATGGTACAATTAAACTCTAGCTCATGTATTCTCTCTAAGCTT
*
2136216 AAAACTCCATTTTATC-TTCTACAAGGCTAATTTCTTACCCGATTAAACTCAATTTCGAGCCAAT
66 AAAACTCCATTTTATCATTCTACAAGGCTAA-TTCTTA-CCGATTAAACTCAATTTCGAACCAAT
2136280 AGACCCTCATGCTATAATAAATAT
129 AGACCCTCATGCTATAATAAATAT
2136304 TAAATAAATA
Statistics
Matches: 149, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
155 14 0.09
156 6 0.04
157 116 0.78
158 13 0.09
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.36
Consensus pattern (157 bp):
CAAATCATCCATATTTTTTCTTAATGGTACAATTAAACTCTAGCTCATGTATTCTCTCTAAGCTT
AAAACTCCATTTTATCATTCTACAAGGCTAATTCTTACCGATTAAACTCAATTTCGAACCAATAG
ACCCTCATGCTATAATAAATATATTAA
Found at i:2141887 original size:20 final size:20
Alignment explanation
Indices: 2141864--2141912 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2141854 TTGGGTAGGA
* *
2141864 TATCGATACTGATCAGA-GAG
1 TATCGATACTG-TAAGACCAG
*
2141884 TATCAATACTGTAAGACCAG
1 TATCGATACTGTAAGACCAG
2141904 TATCGATAC
1 TATCGATAC
2141913 CAAGGTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (20 bp):
TATCGATACTGTAAGACCAG
Found at i:2143253 original size:16 final size:16
Alignment explanation
Indices: 2143211--2143254 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2143201 TTTTAAGGTC
*
2143211 TTTTCACTTAAGTTAT
1 TTTTCACTTAAGATAT
***
2143227 TTTTTGTTTAAGATAT
1 TTTTCACTTAAGATAT
2143243 TTTTCACTTAAG
1 TTTTCACTTAAG
2143255 TTAATGATTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (16 bp):
TTTTCACTTAAGATAT
Found at i:2145670 original size:20 final size:20
Alignment explanation
Indices: 2145645--2145687 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2145635 TAAGGGTGTT
2145645 CAAACGGTTAATTCGATCAC
1 CAAACGGTTAATTCGATCAC
* *
2145665 CAAACGGTTAATTTGGTCAC
1 CAAACGGTTAATTCGATCAC
2145685 CAA
1 CAA
2145688 CTGAAGCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (20 bp):
CAAACGGTTAATTCGATCAC
Found at i:2151692 original size:24 final size:25
Alignment explanation
Indices: 2151660--2151714 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2151650 ATTTTTACAA
* * *
2151660 TTTAGATTAT-AAAAAAATAGTTGT
1 TTTAAATTATAAAAAAAATAGTCGC
2151684 TTTAAATTATAAAAAAAATAGTCGC
1 TTTAAATTATAAAAAAAATAGTCGC
2151709 TTTAAA
1 TTTAAA
2151715 GCTAGAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (25 bp):
TTTAAATTATAAAAAAAATAGTCGC
Found at i:2151876 original size:41 final size:41
Alignment explanation
Indices: 2151831--2151917 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
2151821 TAGTTCATAT
2151831 AAAATTATATGTTCTATCAGGGTTGAATAAA-TGTCATTCCC
1 AAAATTATATGTTCTATCAGGGTTGAA-AAATTGTCATTCCC
2151872 AAAATTATATGTTCTATCAGGGTTGAAAAATTGTCATTCCC
1 AAAATTATATGTTCTATCAGGGTTGAAAAATTGTCATTCCC
2151913 AAAAT
1 AAAAT
2151918 GTAAAACATG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 3 0.07
41 42 0.93
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (41 bp):
AAAATTATATGTTCTATCAGGGTTGAAAAATTGTCATTCCC
Found at i:2155592 original size:20 final size:20
Alignment explanation
Indices: 2155531--2155652 Score: 138
Period size: 20 Copynumber: 6.1 Consensus size: 20
2155521 GATTTTCCAG
* ** *
2155531 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2155551 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2155571 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2155591 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2155611 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2155631 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2155651 AA
1 AA
2155653 GCGCCATTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 83 0.97
21 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2156062 original size:33 final size:33
Alignment explanation
Indices: 2156023--2156093 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2156013 TTCACTTAGA
2156023 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2156056 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2156089 TTTCA
1 TTTCA
2156094 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2156379 original size:19 final size:19
Alignment explanation
Indices: 2156184--2156373 Score: 290
Period size: 19 Copynumber: 9.8 Consensus size: 19
2156174 CGCAACGAGA
*
2156184 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
** *
2156203 GAAAATGACTATCTGCAACGA
1 G-AAATGAAAATC-GCAACGC
2156224 GAAAAATGAAAATCGCAACGC
1 G--AAATGAAAATCGCAACGC
2156245 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2156264 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2156283 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2156302 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2156321 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2156340 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
2156359 GAAACAAAAATCGCA
1 GAAATGAAAATCGCA
2156374 TTGCGATTTT
Statistics
Matches: 160, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
19 127 0.79
20 9 0.06
21 14 0.09
22 10 0.06
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2156410 original size:14 final size:14
Alignment explanation
Indices: 2156391--2156447 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2156381 TTTCATTTCA
2156391 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2156405 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2156424 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2156438 CGTTGCGATT
1 CGTTGCGATT
2156448 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2156416 original size:33 final size:33
Alignment explanation
Indices: 2156374--2156497 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
2156364 AAAAATCGCA
2156374 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
2156407 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
2156440 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
2156481 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
2156498 ACCAAAAGAC
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:2156458 original size:21 final size:21
Alignment explanation
Indices: 2156432--2156496 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2156422 CGCGTTGCGA
2156432 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2156453 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2156473 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2156494 TTC
1 TTC
2156497 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2158487 original size:19 final size:19
Alignment explanation
Indices: 2158463--2158520 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
2158453 GCAACGACAG
2158463 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
2158482 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
2158496 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
2158515 AATCGC
1 AATCGC
2158521 GTTGCGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.50
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:2158490 original size:33 final size:33
Alignment explanation
Indices: 2158399--2158520 Score: 174
Period size: 33 Copynumber: 3.7 Consensus size: 33
2158389 TAGTTTACTT
* * *
2158399 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
2158433 TCGCAACGCGAAA-TGAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
2158465 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
2158498 TCGCAACGCGAAACCAAAATCGC
1 TCGCAACGCGAAACCAAAATCGC
2158521 GTTGCGATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.37
33 39 0.48
34 12 0.15
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:2158498 original size:14 final size:14
Alignment explanation
Indices: 2158415--2158505 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
2158405 CACGAAACTT
*
2158415 AAAATCGCAACGAG
1 AAAATCGCAACGAC
* *
2158429 AGAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2158445 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
2158461 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
2158480 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2158494 AAAATCGCAACG
1 AAAATCGCAACG
2158506 CGAAACCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 9 0.15
19 10 0.16
ACGTcount: A:0.46, C:0.26, G:0.20, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2158539 original size:19 final size:19
Alignment explanation
Indices: 2158517--2158688 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
2158507 GAAACCAAAA
2158517 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2158536 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2158550 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2158569 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2158585 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2158602 TCGCGTTGCGA-TTTGGTT
1 TCGCGTTGCGATTTTCATT
**
2158620 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2158639 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2158658 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2158678 TCGTGTTGCGA
1 TCGCGTTGCGA
2158689 AAGTAAACTA
Statistics
Matches: 125, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 8 0.06
18 16 0.13
19 64 0.51
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.