Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008126.1 Hibiscus syriacus cultivar Beakdansim tig00110681_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: 59641
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:390 original size:20 final size:20
Alignment explanation
Indices: 365--402 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
355 CTATATGAGT
365 TTGTTTTATTTATCTTTTGA
1 TTGTTTTATTTATCTTTTGA
*
385 TTGTTTTATTTATGTTTT
1 TTGTTTTATTTATCTTTT
403 AAGTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTGA
Found at i:1492 original size:25 final size:25
Alignment explanation
Indices: 1454--1504 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1444 AATCCCCGTA
* *
1454 GTTTTTTAAGCGGGGACGGGTATGG
1 GTTTTTTAAACGGGGACGGGGATGG
1479 GTTTTTTAAACGGGGACGGGGATGG
1 GTTTTTTAAACGGGGACGGGGATGG
1504 G
1 G
1505 GGGACCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.08, G:0.45, T:0.29
Consensus pattern (25 bp):
GTTTTTTAAACGGGGACGGGGATGG
Found at i:8493 original size:21 final size:20
Alignment explanation
Indices: 8464--8503 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
8454 ATGAAACGGA
8464 TGAATAGTATCGATACTGAT
1 TGAATAGTATCGATACTGAT
8484 TGAAGTAGTATCGATACTGA
1 TGAA-TAGTATCGATACTGA
8504 AGTGGGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TGAATAGTATCGATACTGAT
Found at i:23625 original size:16 final size:16
Alignment explanation
Indices: 23604--23638 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
23594 CAAAGCATCT
23604 GCCACAACATTAGTAC
1 GCCACAACATTAGTAC
23620 GCCACAACATTAGTAC
1 GCCACAACATTAGTAC
23636 GCC
1 GCC
23639 CTTTTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (16 bp):
GCCACAACATTAGTAC
Found at i:36747 original size:2 final size:2
Alignment explanation
Indices: 36740--36775 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36730 AATCAATCTA
36740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36776 GCCATCCACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43020 original size:3 final size:3
Alignment explanation
Indices: 43012--43082 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
43002 ATTTTAAAAT
* *
43012 TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
43060 ATA TATA TTA TTTA TTA ATA TTA
1 TTA T-TA TTA -TTA TTA TTA TTA
43083 CAAAACCCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:48518 original size:15 final size:15
Alignment explanation
Indices: 48498--48529 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
48488 ATCAATACCT
48498 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
48513 TTTTGCATACATTCA
1 TTTTGCATACATGCA
48528 TT
1 TT
48530 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:55884 original size:6 final size:6
Alignment explanation
Indices: 55875--55928 Score: 78
Period size: 6 Copynumber: 9.3 Consensus size: 6
55865 GAAGAAAGAG
55875 AAGAAA AAGAAA GAAGAAA AAGAAA AA-AAA AAGAAA AAG-AA AAG-AA
1 AAGAAA AAGAAA -AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
55921 AAGAAA AA
1 AAGAAA AA
55929 AGGGGGTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.33
6 24 0.53
7 6 0.13
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:55889 original size:22 final size:22
Alignment explanation
Indices: 55864--55926 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
55854 ATGCTTGAAG
55864 AGAAGAAAGAGAAGAAAAAGAA
1 AGAAGAAAGAGAAGAAAAAGAA
*
55886 AGAAGAAAAAGAA-AAAAA-AA
1 AGAAGAAAGAGAAGAAAAAGAA
*
55906 AGAA-AAAGAAAAG-AAAAGAA
1 AGAAGAAAGAGAAGAAAAAGAA
55926 A
1 A
55927 AAAGGGGGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.28
20 9 0.25
21 5 0.14
22 12 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AGAAGAAAGAGAAGAAAAAGAA
Found at i:55891 original size:13 final size:12
Alignment explanation
Indices: 55875--55928 Score: 78
Period size: 11 Copynumber: 4.7 Consensus size: 12
55865 GAAGAAAGAG
55875 AAGAAAAAGAAA
1 AAGAAAAAGAAA
55887 GAAGAAAAAGAAA
1 -AAGAAAAAGAAA
55900 AA-AAAAAGAAA
1 AAGAAAAAGAAA
55911 AAG-AAAAG-AA
1 AAGAAAAAGAAA
55921 AAGAAAAA
1 AAGAAAAA
55929 AGGGGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.13
11 20 0.51
12 2 0.05
13 12 0.31
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:55910 original size:17 final size:17
Alignment explanation
Indices: 55875--55928 Score: 74
Period size: 16 Copynumber: 3.1 Consensus size: 17
55865 GAAGAAAGAG
55875 AAGAAAAAGAAAGAAGAAA
1 AAGAAAAA-AAA-AAGAAA
55894 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
*
55911 AAG-AAAAGAAAAGAAA
1 AAGAAAAAAAAAAGAAA
55927 AA
1 AA
55929 AGGGGGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 14 0.41
17 9 0.26
18 3 0.09
19 8 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:57308 original size:83 final size:83
Alignment explanation
Indices: 57158--57797 Score: 1016
Period size: 83 Copynumber: 7.6 Consensus size: 83
57148 AACAAATGCC
*
57158 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
57223 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* * *
57241 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
57306 ATT-AATTTTGAAGAGGA
66 ATTGAATTTGGAAGAGGA
57323 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
57388 ATTGAATTCGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* * *
57406 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
57471 ATT-AATTTTGAAGAGGA
66 ATTGAATTTGGAAGAGGA
*
57488 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
57553 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
57571 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
57636 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
57654 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCA-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA--AA--ATC
*
57718 AGAACCAGTTATTGAATTTGGAAGAGGA
62 ---A--A-TCATTGAATTTGGAAGAGGA
* * * * *
57746 ATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTCTCTGATTTGGTTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
57798 TATATAAAAC
Statistics
Matches: 518, Mismatches: 27, Indels: 15
0.93 0.05 0.03
Matches are distributed among these distances:
82 154 0.30
83 292 0.56
85 2 0.00
86 1 0.00
87 1 0.00
89 1 0.00
91 1 0.00
92 66 0.13
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAGGA
Found at i:57430 original size:165 final size:165
Alignment explanation
Indices: 57158--57797 Score: 1057
Period size: 165 Copynumber: 3.8 Consensus size: 165
57148 AACAAATGCC
*
57158 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
57223 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
57288 GGTTTGGTAGAACCAGTCATTAATTTTGAAGAGGA
131 GGTTTGGTAGAACCAGTCATTAATTTTGAAGAGGA
57323 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
57388 ATTGAATTCGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
57453 GGTTTGGTAGAACCAGTCATTAATTTTGAAGAGGA
131 GGTTTGGTAGAACCAGTCATTAATTTTGAAGAGGA
*
57488 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
57553 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* * * *
57618 GGTTTGGTAAAATCAATCATTGAATTTGGAAGAGGA
131 GGTTTGGTAGAACCAGTCATT-AATTTTGAAGAGGA
57654 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCA-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA--AA--ATC
* * * *
57718 AGAACCAGTTATTGAATTTGGAAGAGGAATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGT
62 ---A--A-TCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
* *
57783 TCTCTGATTTGGTTT
121 TATCTGATCTGGTTT
57798 TATATAAAAC
Statistics
Matches: 449, Mismatches: 15, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
165 309 0.69
166 68 0.15
168 2 0.00
169 1 0.00
170 1 0.00
172 1 0.00
174 1 0.00
175 66 0.15
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (165 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGTAGAACCAGTCATTAATTTTGAAGAGGA
Found at i:57596 original size:248 final size:248
Alignment explanation
Indices: 57158--57797 Score: 1030
Period size: 248 Copynumber: 2.5 Consensus size: 248
57148 AACAAATGCC
* * * *
57158 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
57223 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* * * *
57288 GGTTTGGTAGAACCAGTCATTAATTTTGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTC
131 GGTTTGGAAAAACCAATCATTAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTC
57353 TTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATTCGGAAGAGGA
196 TTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATTCGGAAGAGGA
57406 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
*
57471 ATT-AATTTTGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
*
57535 GGTTTGGAAAAATCAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTT
131 GGTTTGGAAAAACCAATCATT-AATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTT
*
57600 CTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATTTGGAAGAGGA
195 CTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATTCGGAAGAGGA
57654 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-------A
* * * *
57719 GAACCAGTTATTGAATTTGGAAGAGGAATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTT
57 GAACCAGTCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* *
57784 CTCTGATTTGGTTT
122 ATCTGATCTGGTTT
57798 TATATAAAAC
Statistics
Matches: 363, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
247 77 0.21
248 213 0.59
250 1 0.00
257 12 0.03
258 60 0.17
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (248 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGAAAAACCAATCATTAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTC
TTTGAGTTATCTGATCTGGTTTGGTAAAATCAATCATTGAATTCGGAAGAGGA
Found at i:57813 original size:92 final size:92
Alignment explanation
Indices: 57636--57813 Score: 268
Period size: 92 Copynumber: 1.9 Consensus size: 92
57626 AAAATCAATC
* * *
57636 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGGAAGAGGAATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
* *
57701 GGTTTGGTATGAACCACAGAACCAGTT
66 GGTTTGATATAAACCACAGAACCAGTT
* *
57728 ATTGAATTTGGAAGAGGAATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTCTCTGATTT
1 ATTGAATTTGGAAGAGGAATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
*
57793 GGTTTTATATAAAACC-CAGAA
66 GGTTTGATAT-AAACCACAGAA
57814 ACAATCATTG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 73 0.95
93 4 0.05
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (92 bp):
ATTGAATTTGGAAGAGGAATATGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGATATAAACCACAGAACCAGTT
Found at i:58901 original size:115 final size:110
Alignment explanation
Indices: 58515--58944 Score: 461
Period size: 111 Copynumber: 4.0 Consensus size: 110
58505 TTAGCAAAGA
58515 TTCAAATCCATCA-TTGATGGATCAGA-TTTCCAGAGAGTTCATAATGAGAAGAA--C--TCTGA
1 TTCAAAT-CATCACTTGATGGATCA-ACTTTCCAGAGAGTTCATAATGAGAAGAACTCATTCTGA
58574 AGAAGGAAGAAGAAGTTCATAATGAG-AGAATTTGTTTAACCTTTTG
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTG
* * * *
58620 TTGAATTCATCA-TTGATGGATTAAAATTTCCAGAGAGTTCATAATGAGAAGAACTCATTGCTTG
1 TTCAAATCATCACTTGATGGA-TCAACTTTCCAGAGAGTTCATAATGAGAAGAACTCATT-C-TG
* * *
58684 AAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTG
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTG
* * * *
58731 CTCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCA-TCT
1 TTCAAAT-CATCACTTGATGGATCAAC-TTTCCAG--AGAGTTCATAATGAGAAGAACTCATTCT
*
58795 GAAGAAGGAAGAA-AAGTTCATAATGAGAAG-ACTTGTTTAACCTTTTG
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTG
*
58842 TTCAAATCATCACTTGATGGATCAACTTTCCAGAGAAAGTTCGTAAT---AAG-A---ATT-TGA
1 TTCAAATCATCACTTGATGGATCAACTTTCCAGAG--AGTTCATAATGAGAAGAACTCATTCTGA
* ** *
58899 AG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTG
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTG
58945 CATAATTCTA
Statistics
Matches: 280, Mismatches: 25, Indels: 42
0.81 0.07 0.12
Matches are distributed among these distances:
101 8 0.03
102 22 0.08
103 16 0.06
104 14 0.05
105 35 0.12
106 3 0.01
107 2 0.01
109 17 0.06
110 29 0.10
111 61 0.22
112 34 0.12
113 16 0.06
114 1 0.00
115 22 0.08
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (110 bp):
TTCAAATCATCACTTGATGGATCAACTTTCCAGAGAGTTCATAATGAGAAGAACTCATTCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTG
Found at i:58942 original size:213 final size:211
Alignment explanation
Indices: 58516--58942 Score: 539
Period size: 222 Copynumber: 2.0 Consensus size: 211
58506 TAGCAAAGAT
58516 TCAAATCCATCATTGATGGATCAGATTTCCAGAGAGTTCATAATGAGAAGAACTCTGAAGAAGGA
1 TCAAATCCATCATTGATGGATCAGATTTCCAGAGAGTTCATAATGAGAAGAACTCTGAAGAAGGA
* * *
58581 AGAAGAAGTTCATAATGAGAGAATTTGTTTAACCTTTTGTTGAATTCATCATTGATGGATTAAAA
66 AGAAGAAGTTCATAATGAGAGAACTTGTTTAACCTTTTGTTCAAATCATCATTGATGGATTAAAA
*
58646 TTTCCAGAGAGTTCATAATGAGAAGAACTCATTGCTTGAAGGAGGAAGAAGAAATTCATAATGAG
131 TTTCCAGAGAGTTCATAAT--GAAGAA--CATT-CTTGAAGGAGGAAGAAGAAATTCACAATGAG
*
58711 AAGAATTTGTTCAACCTTTGC
191 AAGAACTTGTTCAACCTTTGC
* *
58732 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCA-TTGATGGATCAG-ATTTCCAG--AGAGTTCATAATGAGAAGAA--C-TCTGA
58797 AGAAGGAAGAA-AAGTTCATAATGAGA-AGACTTGTTTAACCTTTTGTTCAAATCATCACTTGAT
59 AGAAGGAAGAAGAAGTTCATAATGAGAGA-ACTTGTTTAACCTTTTGTTCAAATCATCA-TTGAT
* * * *
58860 GGA-TCAACTTTCCAGAGAAAGTTCGTAAT-AAG-A-A-T-TTGAA-GAGGAAGAAGAAGTTCAC
122 GGATTAAAATTTCCAGAG--AGTTCATAATGAAGAACATTCTTGAAGGAGGAAGAAGAAATTCAC
*
58918 AATGAGAAGAGCTTGTTCAACCTTT
185 AATGAGAAGAACTTGTTCAACCTTT
58943 TGCATAATTC
Statistics
Matches: 188, Mismatches: 12, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
213 39 0.21
214 5 0.03
216 13 0.07
217 13 0.07
218 7 0.04
220 20 0.11
221 4 0.02
222 54 0.29
223 24 0.13
224 9 0.05
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (211 bp):
TCAAATCCATCATTGATGGATCAGATTTCCAGAGAGTTCATAATGAGAAGAACTCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAGAACTTGTTTAACCTTTTGTTCAAATCATCATTGATGGATTAAAA
TTTCCAGAGAGTTCATAATGAAGAACATTCTTGAAGGAGGAAGAAGAAATTCACAATGAGAAGAA
CTTGTTCAACCTTTGC
Found at i:59290 original size:3 final size:3
Alignment explanation
Indices: 59282--59351 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
59272 ATTTTAAAAT
* * *
59282 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
59330 ATA TATA TTA TTA TTA ATA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
59352 CAAAACCCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Done.