Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002395.1 Hibiscus syriacus cultivar Beakdansim tig00004898_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: 81252
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13336 original size:17 final size:17
Alignment explanation
Indices: 13326--13372 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
13316 TATTTTTGTT
13326 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAAGTA
13343 TTTAATTTATTTAA-TA
1 TTTAATTTATTTAAGTA
* *
13359 TTTTATTTAATTAA
1 TTTAATTTATTTAA
13373 TTTTTTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTAATTTATTTAAGTA
Found at i:21337 original size:40 final size:40
Alignment explanation
Indices: 21286--21390 Score: 142
Period size: 40 Copynumber: 2.6 Consensus size: 40
21276 ACTTTGAACG
* **
21286 GGTACTAAAATGAAACAAAAACTAGAGTTTTAAACGG-TG
1 GGTACTAAAATGAAACAAAAACTAAAGTTTTAAACGGCAA
* *
21325 GTGTACCAAAATGAAACAAAAACTAAAGTTTTTAACGGCAA
1 G-GTACTAAAATGAAACAAAAACTAAAGTTTTAAACGGCAA
21366 GGTACTAAAA-GAAACAAAAACTAAA
1 GGTACTAAAATGAAACAAAAACTAAA
21391 CTTTATGTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 16 0.28
40 41 0.71
41 1 0.02
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.20
Consensus pattern (40 bp):
GGTACTAAAATGAAACAAAAACTAAAGTTTTAAACGGCAA
Found at i:24241 original size:170 final size:166
Alignment explanation
Indices: 23941--24272 Score: 378
Period size: 170 Copynumber: 2.0 Consensus size: 166
23931 ATCGAAGCGT
* * * * * *
23941 CTCGCCGCCATGATCAAAGCCCCCAAAATAATTCGTGGATAGTCGTTGACATTCGCCGAAATTGA
1 CTCGCCACCATGATCAAAGCACCCAAAATAATTCGTGGATAGCCATCGACATTCGCCGAAATCGA
* ** ** * * *
24006 GCCCTTGAAGTTTCACTGAAAACCCACCCCGATGCCTCGGATTTTGGACGACTCCGGCTGCCTCG
66 GCCCTTGAAGTTTCACTAAAAACCCACCCCGACACCTCAAATTTGGGACGACTACGGCCGCCTCG
*
24071 GACCTCCGTTCGCCTCACCGCAACCATAGTTAGCTTCTTC
131 G----CCGTTCGCATCACCGCAACCATAGTTAGCTTCTTC
** * * *
24111 CTCGCCACCATGATCAAAGCACCCAAAATAATTTTTGGATAGCCATCG-CTGTTCGTCGGAATCG
1 CTCGCCACCATGATCAAAGCACCCAAAATAATTCGTGGATAGCCATCGAC-ATTCGCCGAAATCG
* * * *
24175 ATCCCTTGAAGTTTCACTAAAAACCCACCCCGACACCTCAAATTTGGGATGATTATGGCCGCCTC
65 AGCCCTTGAAGTTTCACTAAAAACCCACCCCGACACCTCAAATTTGGGACGACTACGGCCGCCTC
* *
24240 GGCCGTTCGCATCACCGCCACCATATTTAGCTT
130 GGCCGTTCGCATCACCGCAACCATAGTTAGCTT
24273 TCTCGTCGCC
Statistics
Matches: 135, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
166 28 0.21
169 1 0.01
170 106 0.79
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (166 bp):
CTCGCCACCATGATCAAAGCACCCAAAATAATTCGTGGATAGCCATCGACATTCGCCGAAATCGA
GCCCTTGAAGTTTCACTAAAAACCCACCCCGACACCTCAAATTTGGGACGACTACGGCCGCCTCG
GCCGTTCGCATCACCGCAACCATAGTTAGCTTCTTC
Found at i:26186 original size:25 final size:27
Alignment explanation
Indices: 26154--26212 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
26144 CAAACAAGCA
26154 AAAC-ATCCAAAAT-ATATTCAAAA-C
1 AAACAATCCAAAATAATATTCAAAACC
26178 AAACAATCCAAAATAAATATTCAAAATCC
1 AAACAATCCAAAAT-AATATTCAAAA-CC
26207 AAACAA
1 AAACAA
26213 ACAAAGCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
27 10 0.33
29 7 0.23
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (27 bp):
AAACAATCCAAAATAATATTCAAAACC
Found at i:28209 original size:23 final size:22
Alignment explanation
Indices: 28183--28253 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
28173 TGCATAGTGT
28183 ATCGATGCACATTCAAGGCATGC
1 ATCGATGCACATTCAAGG-ATGC
* * *
28206 ATCGGTGCACCTTCATA-G-TGT
1 ATCGATGCACATTCA-AGGATGC
*
28227 ATCGATGCATATTCAAGGGATGC
1 ATCGATGCACATTCAA-GGATGC
28250 ATCG
1 ATCG
28254 GTACACTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 14 0.38
22 1 0.03
23 20 0.54
24 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGATGC
Found at i:28241 original size:21 final size:21
Alignment explanation
Indices: 28158--28241 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
28148 AAACCCGACG
* * *
28158 AGTGTATTGATACAC-TGCAT
1 AGTGTATCGATGCACATTCAT
28178 AGTGTATCGATGCACATTCA-
1 AGTGTATCGATGCACATTCAT
* * *
28198 AGGCATGCATCGGTGCACCTTCAT
1 A-G--TGTATCGATGCACATTCAT
*
28222 AGTGTATCGATGCATATTCA
1 AGTGTATCGATGCACATTCA
28242 AGGGATGCAT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
20 14 0.29
21 18 0.37
23 16 0.33
24 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTGTATCGATGCACATTCAT
Found at i:28241 original size:44 final size:44
Alignment explanation
Indices: 28175--28281 Score: 169
Period size: 44 Copynumber: 2.4 Consensus size: 44
28165 TGATACACTG
* *
28175 CATAGTGTATCGATGCACATTCAAGGCATGCATCGGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
* *
28219 CATAGTGTATCGATGCATATTCAAGGGATGCATCGGTACACTTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
*
28263 CATAGTGTATTGATGCATA
1 CATAGTGTATCGATGCATA
28282 GTGCACAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
Found at i:34770 original size:65 final size:64
Alignment explanation
Indices: 34667--34802 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 64
34657 ACACTAATTA
* * * * *
34667 CATTCGATGTTTCAAAAGAGTCAGGAGTGTATCGATGCATGGTTTGTGCATCGATACATAAAATG
1 CATTCGATGTTTCAAAAGAATCAGAAGTGTATCAATGCATAG-TTGTGCATCGATACACAAAATG
* *
34732 CATTCGATGTTTCAATAA-AATCAGAAGT-TCATCAATGCATAGTTGTGCATTGGTACACAAAAT
1 CATTCGATGTTTCAA-AAGAATCAGAAGTGT-ATCAATGCATAGTTGTGCATCGATACACAAAAT
34795 G
64 G
*
34796 TATTCGA
1 CATTCGA
34803 ATTAGGGTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
64 26 0.43
65 33 0.54
66 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (64 bp):
CATTCGATGTTTCAAAAGAATCAGAAGTGTATCAATGCATAGTTGTGCATCGATACACAAAATG
Found at i:35670 original size:293 final size:293
Alignment explanation
Indices: 35101--35686 Score: 1138
Period size: 293 Copynumber: 2.0 Consensus size: 293
35091 TAGAATAGTT
35101 TGTAATTGATGAAATCATCAATAACGCAGTGATAAAAAGGATTCATGTAATAAATTTTTCATATT
1 TGTAATTGATGAAATCATCAATAACGCAGTGATAAAAAGGATTCATGTAATAAATTTTTCATATT
*
35166 TTATATATTCACAAAAATTTATTTTTTAAAAGAGTTTATGTCGGACCAAAATATAAATAAAAGGA
66 TTATATATTCACAAAAATTTATTTTTTAAAAGAGTTTATGTCAGACCAAAATATAAATAAAAGGA
35231 AAAAATTCAAAACAATTTTGGATAAACCAAAAAATCCAACTGAATTTGATTTATATCCATCCTTA
131 AAAAATTCAAAACAATTTTGGATAAACCAAAAAATCCAACTGAATTTGATTTATATCCATCCTTA
35296 GTTTCATTGCCTAAAAAAATTAGAGGTAAGACTTTGATTAGATATCAATACAAATGAGAGACAAT
196 GTTTCATTGCCTAAAAAAATTAGAGGTAAGACTTTGATTAGATATCAATACAAATGAGAGACAAT
35361 GATCAAAAATAAAAAAAAGGTTGAAAGAGTTTA
261 GATCAAAAATAAAAAAAAGGTTGAAAGAGTTTA
*
35394 TGTAATTGATGAAATCATCAATAACGCAGTGATAAAAAGGATTCATGTAATAATTTTTTCATATT
1 TGTAATTGATGAAATCATCAATAACGCAGTGATAAAAAGGATTCATGTAATAAATTTTTCATATT
35459 TTATATATTCACAAAAATTTATTTTTTAAAAGAGTTTATGTCAGACCAAAATATAAATAAAAGGA
66 TTATATATTCACAAAAATTTATTTTTTAAAAGAGTTTATGTCAGACCAAAATATAAATAAAAGGA
35524 AAAAATTCAAAACAATTTTGGATAAACCAAAAAATCCAACTGAATTTGATTTATATCCATCCTTA
131 AAAAATTCAAAACAATTTTGGATAAACCAAAAAATCCAACTGAATTTGATTTATATCCATCCTTA
35589 GTTTCATTGCCT-AAAAAATTAGAGGTAAGACTTTGATTAGATATCAATACAAATGAGAGACAAT
196 GTTTCATTGCCTAAAAAAATTAGAGGTAAGACTTTGATTAGATATCAATACAAATGAGAGACAAT
35653 GATCAAAAATAAAAAAAAAGGTTGAAAGAGTTTA
261 GATCAAAAAT-AAAAAAAAGGTTGAAAGAGTTTA
35687 AAATTCAAAT
Statistics
Matches: 290, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
292 62 0.21
293 228 0.79
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (293 bp):
TGTAATTGATGAAATCATCAATAACGCAGTGATAAAAAGGATTCATGTAATAAATTTTTCATATT
TTATATATTCACAAAAATTTATTTTTTAAAAGAGTTTATGTCAGACCAAAATATAAATAAAAGGA
AAAAATTCAAAACAATTTTGGATAAACCAAAAAATCCAACTGAATTTGATTTATATCCATCCTTA
GTTTCATTGCCTAAAAAAATTAGAGGTAAGACTTTGATTAGATATCAATACAAATGAGAGACAAT
GATCAAAAATAAAAAAAAGGTTGAAAGAGTTTA
Found at i:36245 original size:23 final size:23
Alignment explanation
Indices: 36219--36288 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
36209 TGCATGTGTT
**
36219 ACACGTTTATCTCTACCTTTGTG
1 ACACGTTTATCTCTGTCTTTGTG
*
36242 ACACATTTATCTCTGTCTTTGTG
1 ACACGTTTATCTCTGTCTTTGTG
36265 ACACGTTTATCTCTGTCTTTGTG
1 ACACGTTTATCTCTGTCTTTGTG
36288 A
1 A
36289 AACTTTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (23 bp):
ACACGTTTATCTCTGTCTTTGTG
Found at i:37843 original size:21 final size:21
Alignment explanation
Indices: 37817--38013 Score: 121
Period size: 21 Copynumber: 9.5 Consensus size: 21
37807 GTTTCCAGAT
*
37817 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
37838 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
37859 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
37879 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
37900 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
37920 TCGCAATGCGATA-GTCCACTA
1 TCGCAATGCGA-ACTTCGACTA
* *
37941 TCGTAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
37961 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
37982 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
38003 TCGCATTGCGA
1 TCGCAATGCGA
38014 TTTACATATT
Statistics
Matches: 140, Mismatches: 20, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
20 47 0.34
21 93 0.66
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:37882 original size:41 final size:41
Alignment explanation
Indices: 37837--37993 Score: 262
Period size: 41 Copynumber: 3.8 Consensus size: 41
37827 AACTTCGACT
* *
37837 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
37878 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
* *
37919 ATCGCAATGCGATAGTCCACTATCGTAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
37960 ATCGCAATGCGATAGTCGACTATCGCAATGCGAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAA
37994 CTTGGACTAT
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 108 0.99
42 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:37883 original size:20 final size:20
Alignment explanation
Indices: 37858--37971 Score: 119
Period size: 20 Copynumber: 5.6 Consensus size: 20
37848 AACTTGGACT
37858 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
37878 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
37899 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
37919 ATCGCAATGCG-ATA-GTCCACT
1 ATCGCAATGCGAATATGT--A-A
*
37940 ATCGTAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
37960 ATCGCAATGCGA
1 ATCGCAATGCGA
37972 TAGTCGACTA
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.05
19 6 0.08
20 35 0.45
21 23 0.29
22 6 0.08
23 4 0.05
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:38033 original size:82 final size:81
Alignment explanation
Indices: 37817--38033 Score: 260
Period size: 82 Copynumber: 2.6 Consensus size: 81
37807 GTTTCCAGAT
* * *
37817 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGAC-TATCGCAATGCGAATATGTAAATC
1 TCGCAATGCGAACTTGGACTATCGCAATGCG-A-TT-TACATATCGCAATGCGAATATGTAAATC
37881 GCAATGCGATAGTCGACTA
63 GCAATGCGATAGTCGACTA
* * * * *
37900 TCGCAATGCGAA-TATGTA-AATCGCAATGCGATAGTCCACTATCGTAATGCGAATATGTAAATC
1 TCGCAATGCGAACT-TGGACTATCGCAATGCGAT-TTACA-TATCGCAATGCGAATATGTAAATC
37963 GCAATGCGATAGTCGACTA
63 GCAATGCGATAGTCGACTA
* *
37982 TCGCAATGCGAACTTGGACTATCGCATTGCGATTTACATATTCGCATTGCGA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGATTTACATA-TCGCAATGCGA
38034 TAGTCCAAAA
Statistics
Matches: 112, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
80 2 0.02
81 3 0.03
82 81 0.72
83 26 0.23
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (81 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGATTTACATATCGCAATGCGAATATGTAAATCGCA
ATGCGATAGTCGACTA
Found at i:38811 original size:21 final size:21
Alignment explanation
Indices: 38781--38957 Score: 159
Period size: 21 Copynumber: 8.5 Consensus size: 21
38771 AATATGTAAA
* *
38781 TCGCAATGCGATAATCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
38802 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
38822 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* *
38843 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
38863 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
38884 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
38905 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
38926 TCGCATTGCAATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
38947 TCGCGTTGCGA
1 TCGCATTGCGA
38958 ATCTGGAAAC
Statistics
Matches: 130, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.01
20 32 0.25
21 95 0.73
22 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:38846 original size:41 final size:41
Alignment explanation
Indices: 38801--38943 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
38791 ATAATCCAAG
38801 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
38842 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* * * *
38883 TTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCCA-A
1 TTCGCATTGCGATAGT-CGACTATCGCATTGCGAT-TTACATA
*
38924 GTTCGCATTGCAATAGTCGA
1 -TTCGCATTGCGATAGTCGA
38944 AGTTCGCGTT
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
41 72 0.77
42 21 0.23
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:38847 original size:62 final size:65
Alignment explanation
Indices: 38781--38943 Score: 180
Period size: 62 Copynumber: 2.6 Consensus size: 65
38771 AATATGTAAA
* * *
38781 TCGCAATGCGATAATCCAAGTTCGCATTGCGATAGTCGAC-TA-TCGCATTGCGAT-TTACATA-
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACATATTCGCATTGCGATAGTACA-AG
38842 T
65 T
* * * *
38843 TCGCATTGCGATAGT-CGACTATCGCATTGCGAT--T-TACATATTCGCATTGCGATAGTCCAAG
1 TCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCGACATATTCGCATTGCGATAGTACAAG
38904 T
65 T
*
38905 TCGCATTGCGATAGTCCAAGTTCGCATTGCAATAGTCGA
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
38944 AGTTCGCGTT
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
59 2 0.02
60 3 0.04
61 16 0.20
62 55 0.68
63 3 0.04
64 1 0.01
65 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (65 bp):
TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACATATTCGCATTGCGATAGTACAAGT
Found at i:38848 original size:20 final size:20
Alignment explanation
Indices: 38823--38895 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
38813 TAGTCGACTA
38823 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
38843 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
38864 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
38884 TCGCATTGCGAT
1 TCGCATTGCGAT
38896 AGTCCAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:46327 original size:29 final size:30
Alignment explanation
Indices: 46276--46332 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
46266 AACCAGAGGA
46276 AATATTTTTTTAATTTAATTATAATTTTGG
1 AATATTTTTTTAATTTAATTATAATTTTGG
*
46306 AATATTTTTTT-GTTTCAA-TATAATTTT
1 AATATTTTTTTAATTT-AATTATAATTTT
46333 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (30 bp):
AATATTTTTTTAATTTAATTATAATTTTGG
Found at i:48786 original size:2 final size:2
Alignment explanation
Indices: 48779--48805 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48769 GCTTCAAATT
48779 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 T
48806 GTGTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50699 original size:2 final size:2
Alignment explanation
Indices: 50692--50770 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
50682 GTCAGTCATA
50692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50771 ATAAAAAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50921 original size:23 final size:23
Alignment explanation
Indices: 50895--50956 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
50885 GACTAAAAAT
50895 TTAAAAATGTTAAAATATAATGA
1 TTAAAAATGTTAAAATATAATGA
50918 TTAAAAATGTTAAAATATAATGA
1 TTAAAAATGTTAAAATATAATGA
*
50941 TTAAAAATGTTTAAAT
1 TTAAAAATGTTAAAAT
50957 TTAGGGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (23 bp):
TTAAAAATGTTAAAATATAATGA
Found at i:51438 original size:18 final size:19
Alignment explanation
Indices: 51412--51449 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
51402 GGCCACCGAA
*
51412 TTGACTTTT-AACAATTGT
1 TTGAATTTTCAACAATTGT
51430 TTGAATTTTCAACAATTGT
1 TTGAATTTTCAACAATTGT
51449 T
1 T
51450 GGCTGGCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTGAATTTTCAACAATTGT
Found at i:51450 original size:52 final size:53
Alignment explanation
Indices: 51371--51478 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 53
51361 ACCCATCGAA
* * *
51371 AATTGCTTTAAATCTTCAACCATTGTTGGTTGGCCACCGAATTGACTTTTAAC
1 AATTGCTTTAAATCTTCAACAATTGTTGGCTGGCCACCGAATTAACTTTTAAC
* * *
51424 AATTG-TTTGAATTTTCAACAATTGTTGGCTGGCCACCGAATTAATTTTTAAC
1 AATTGCTTTAAATCTTCAACAATTGTTGGCTGGCCACCGAATTAACTTTTAAC
51476 AAT
1 AAT
51479 CTCCCACTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 44 0.90
53 5 0.10
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (53 bp):
AATTGCTTTAAATCTTCAACAATTGTTGGCTGGCCACCGAATTAACTTTTAAC
Found at i:64153 original size:96 final size:96
Alignment explanation
Indices: 64045--64228 Score: 307
Period size: 96 Copynumber: 1.9 Consensus size: 96
64035 CAACAAAAAG
*
64045 AAAAGTTAATCTAAATAATACATGAAAACA-GATAAATGCAACCAACAAATAGCTTCGTAAAACA
1 AAAAGTTAATCTAAATAATACAAGAAAACAGGATAAATGCAACCAACAAATAGCTTCG-AAAACA
*
64109 GCAACACAAGCCCTGAGACAAGGGGTAACAAA
65 GCAACACAAGCCCTAAGACAAGGGGTAACAAA
* * *
64141 AAAAGTTAATCTAAATAATACAAGAAAATAGGGTAAATGCAGCCAACAAATAGCTTCGAAAACAG
1 AAAAGTTAATCTAAATAATACAAGAAAACAGGATAAATGCAACCAACAAATAGCTTCGAAAACAG
64206 CAACACAAGCCCTAAGACAAGGG
66 CAACACAAGCCCTAAGACAAGGG
64229 TAAAGCGCAT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
96 57 0.70
97 25 0.30
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.15
Consensus pattern (96 bp):
AAAAGTTAATCTAAATAATACAAGAAAACAGGATAAATGCAACCAACAAATAGCTTCGAAAACAG
CAACACAAGCCCTAAGACAAGGGGTAACAAA
Found at i:71656 original size:17 final size:18
Alignment explanation
Indices: 71629--71669 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
71619 TTGAGATATT
71629 ACCCGCCCCGCATCCGCCC
1 ACCC-CCCCGCATCCGCCC
71648 -CCCCCCCGCATCCGCCC
1 ACCCCCCCGCATCCGCCC
71665 ACCCC
1 ACCCC
71670 ACATCCGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.10, C:0.73, G:0.12, T:0.05
Consensus pattern (18 bp):
ACCCCCCCGCATCCGCCC
Found at i:71669 original size:15 final size:15
Alignment explanation
Indices: 71634--71679 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
71624 ATATTACCCG
*
71634 CCCCGCATCCGCCCCCC
1 CCCCGCATCCG--CCCA
71651 CCCCGCATCCGCCCA
1 CCCCGCATCCGCCCA
*
71666 CCCCACATCCGCCC
1 CCCCGCATCCGCCC
71680 GCCCAGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 16 0.59
17 11 0.41
ACGTcount: A:0.11, C:0.72, G:0.11, T:0.07
Consensus pattern (15 bp):
CCCCGCATCCGCCCA
Found at i:72054 original size:14 final size:15
Alignment explanation
Indices: 72035--72077 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
72025 ATATTACCCG
72035 CCCCGCATCCGCCC-
1 CCCCGCATCCGCCCA
72049 CCCCGCATCCGCCCA
1 CCCCGCATCCGCCCA
*
72064 CCCCACATCCGCCC
1 CCCCGCATCCGCCC
72078 GCCCAGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.12, C:0.70, G:0.12, T:0.07
Consensus pattern (15 bp):
CCCCGCATCCGCCCA
Found at i:76036 original size:29 final size:31
Alignment explanation
Indices: 75990--76054 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
75980 TTTTTAATTT
* *
75990 TATTTAATTTATATTTTA-GT-AATTACCAG
1 TATTTAATATATATTTTAGGTAAAATACCAG
76019 TATTT-ATATATATATTTAGGTAAAATACCAG
1 TATTTAATATATAT-TTTAGGTAAAATACCAG
76050 -ATTTA
1 TATTTA
76055 GTCCTTAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
28 7 0.23
29 9 0.30
30 6 0.20
31 8 0.27
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (31 bp):
TATTTAATATATATTTTAGGTAAAATACCAG
Done.