Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008877.1 Hibiscus syriacus cultivar Beakdansim tig00112116_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: 70397
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:6360 original size:80 final size:80
Alignment explanation
Indices: 6261--6535 Score: 194
Period size: 80 Copynumber: 3.3 Consensus size: 80
6251 ACAACATTGG
*
6261 ATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
1 ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
6326 TTTCATTCAGAGCCA
66 TTTCATTCAGAGCCA
* * ** *
6341 ATTTCAACTTCAC-GACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCAC-GACGAA
1 ATTTCAACTTCACAG-CGAAGGATA-T---C-C---A-ATTCA-AAGCTCAACTCCACAG-CGAA
* * *
6404 --GGATAT--C-GTGCTCA--CA-AACAACA
54 GGGGCT-TCCCAGT-TTCATTCAGAGC--CA
*
6427 TTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
1 ----ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
6492 CCAGTTTCATTCAGAGCCA
62 CCAGTTTCATTCAGAGCCA
6511 ATTTCAACTTCAC-GACGAAGGATAT
1 ATTTCAACTTCACAG-CGAAGGATAT
6536 TGGACTCAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 62
0.64 0.08 0.27
Matches are distributed among these distances:
79 2 0.01
80 57 0.39
81 7 0.05
82 4 0.03
83 4 0.03
84 7 0.05
85 6 0.04
86 7 0.05
87 4 0.03
88 4 0.03
89 7 0.05
90 35 0.24
91 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (80 bp):
ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
TTTCATTCAGAGCCA
Found at i:6768 original size:170 final size:170
Alignment explanation
Indices: 6164--6753 Score: 1126
Period size: 170 Copynumber: 3.5 Consensus size: 170
6154 GGTTCTAGCT
* *
6164 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
6229 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
6294 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
6334 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
6399 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
6464 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
*
6504 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
6569 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
*
6634 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAATTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
* *
6674 AGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGATTTTAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
6739 ACGAAGGATATCGTG
66 ACGAAGGATATCGTG
6754 TCCACCAGCA
Statistics
Matches: 413, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 413 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (170 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
Found at i:7404 original size:19 final size:19
Alignment explanation
Indices: 7375--7418 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
7365 TGGCCACCAA
7375 GCCTCCACTAGTCCTTGTCT
1 GCCT-CACTAGTCCTTGTCT
7395 GCCTCACTAGTCCTTGTCT
1 GCCTCACTAGTCCTTGTCT
*
7414 CCCTC
1 GCCTC
7419 CACTCACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.09, C:0.43, G:0.14, T:0.34
Consensus pattern (19 bp):
GCCTCACTAGTCCTTGTCT
Found at i:7682 original size:23 final size:23
Alignment explanation
Indices: 7656--7707 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
7646 TCTGTTTTGA
*
7656 ATTTTTAATAG-TTTTTATTATTT
1 ATTTTCAATAGTTTTTTATTA-TT
7679 ATTTTCAATAGTTTTTTATTATT
1 ATTTTCAATAGTTTTTTATTATT
7702 ATTTTC
1 ATTTTC
7708 GAAATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
ATTTTCAATAGTTTTTTATTATT
Found at i:11493 original size:24 final size:24
Alignment explanation
Indices: 11463--11519 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
11453 TGTAACTTTT
11463 AAAAGATACTAAGACATGCAGGAA
1 AAAAGATACTAAGACATGCAGGAA
11487 AAAAGATACTAAGACATGCAGGAA
1 AAAAGATACTAAGACATGCAGGAA
11511 AAAAGATAC
1 AAAAGATAC
11520 AAGTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (24 bp):
AAAAGATACTAAGACATGCAGGAA
Found at i:15279 original size:3 final size:3
Alignment explanation
Indices: 15273--15332 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
15263 CACCCACGTG
* *
15273 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTC CTT CTT CTA CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
15321 CTC CTT CTT CTT
1 CTT CTT CTT CTT
15333 AAATACCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:15390 original size:43 final size:44
Alignment explanation
Indices: 15325--15408 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
15315 CTTCTTCTCC
15325 TTCTTCTTAAATACCAAATCTCAAAT-CCCATTATCACGTCTTA
1 TTCTTCTTAAATACCAAATCTCAAATCCCCATTATCACGTCTTA
* * *
15368 TTCTTCTTGAATACCAAGTCTCAAGTCCCCATTATCACGTC
1 TTCTTCTTAAATACCAAATCTCAAATCCCCATTATCACGTC
15409 CACTGTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 23 0.62
44 14 0.38
ACGTcount: A:0.29, C:0.30, G:0.06, T:0.36
Consensus pattern (44 bp):
TTCTTCTTAAATACCAAATCTCAAATCCCCATTATCACGTCTTA
Found at i:23762 original size:3 final size:3
Alignment explanation
Indices: 23754--23778 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23744 TGTCTATGCA
23754 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
23779 TTATATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:25130 original size:60 final size:60
Alignment explanation
Indices: 25006--25123 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
24996 AATAGTTAAT
* * * * * *
25006 GGATAAAATTATAAAGTTTAAAAGTTTAAGTATTAATTTAGAATGAGAGTCATAATTTGA
1 GGATAAAATTATAAAGTTTAAAAGTTTAAGGATCAATATAAAATAAGAATCATAATTTGA
* *
25066 GGATAAAATTGA-AATGTTTAAAAGTTTAAGGATCAATATAAAATAAGAATTATAATTT
1 GGATAAAATT-ATAAAGTTTAAAAGTTTAAGGATCAATATAAAATAAGAATCATAATTT
25124 AGGGATATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (60 bp):
GGATAAAATTATAAAGTTTAAAAGTTTAAGGATCAATATAAAATAAGAATCATAATTTGA
Found at i:25712 original size:16 final size:17
Alignment explanation
Indices: 25688--25720 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25678 CAAGGTGTCA
25688 CATTGACTTTT-CAAAG
1 CATTGACTTTTACAAAG
*
25704 CATTTACTTTTACAAAG
1 CATTGACTTTTACAAAG
25721 TGACTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (17 bp):
CATTGACTTTTACAAAG
Found at i:26447 original size:22 final size:22
Alignment explanation
Indices: 26381--26447 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
26371 GGTATGTGAA
*
26381 ATATGTCCCGAAGGACCTATGC
1 ATATGTCCCGAAGGACCTATGT
* * *
26403 ATGTGTCCCGAAAGACCTGTGT
1 ATATGTCCCGAAGGACCTATGT
26425 ATATGTCCCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
26447 A
1 A
26448 ACCCTCAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATGT
Found at i:28790 original size:42 final size:42
Alignment explanation
Indices: 28731--28816 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
28721 GATTTTGAAA
*
28731 TCAAGTTTTGAAATTACTCACCCTTACTTTAACACTAATACT
1 TCAAGTTTTGAAATTACTCACCCTTACTTTAACACTAACACT
*
28773 TCAAGTTTTGAAATTACTCCCCCTTACTTTAACACTAACACT
1 TCAAGTTTTGAAATTACTCACCCTTACTTTAACACTAACACT
28815 TC
1 TC
28817 TCCCATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (42 bp):
TCAAGTTTTGAAATTACTCACCCTTACTTTAACACTAACACT
Found at i:37725 original size:44 final size:44
Alignment explanation
Indices: 37666--37930 Score: 395
Period size: 44 Copynumber: 6.0 Consensus size: 44
37656 ATATCATGAG
* *
37666 TGGCACTTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
37710 TGGCACATTTCTGCCAATAATACACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
37754 TGGAACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
37798 TGGCACATTTCTGCCAATAATGCATCGTTATTCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
37842 TGACACCTTTCTGTCAATAATGAATCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* **
37886 TGGCACATTTCTACCAATAATGCACCGTTACACATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
37930 T
1 T
37931 TTCGGTAACA
Statistics
Matches: 198, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 198 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:38841 original size:20 final size:20
Alignment explanation
Indices: 38816--38856 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38806 CCGAATCTAA
*
38816 TGAATCTACTTATACACTAT
1 TGAATCTACTTATACAATAT
*
38836 TGAATCTATTTATACAATAT
1 TGAATCTACTTATACAATAT
38856 T
1 T
38857 ATTAACTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
TGAATCTACTTATACAATAT
Found at i:40773 original size:16 final size:18
Alignment explanation
Indices: 40752--40788 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40742 AGAGATTTAA
40752 AAGAGAG-AAC-AGTAAC
1 AAGAGAGTAACAAGTAAC
*
40768 AAGAGAGTATCAAGTAAC
1 AAGAGAGTAACAAGTAAC
40786 AAG
1 AAG
40789 CAGTAACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.54, C:0.11, G:0.24, T:0.11
Consensus pattern (18 bp):
AAGAGAGTAACAAGTAAC
Found at i:48530 original size:23 final size:24
Alignment explanation
Indices: 48502--48557 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
48492 TACTAATAAT
* *
48502 TAATATTTTATTAAATAT-TAAAA
1 TAATATTATAATAAATATATAAAA
* *
48525 TAATATAATAATAAATATATAACA
1 TAATATTATAATAAATATATAAAA
48549 TAATATTAT
1 TAATATTAT
48558 TTTGAGGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATATTATAATAAATATATAAAA
Found at i:49267 original size:30 final size:30
Alignment explanation
Indices: 49228--49298 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
49218 AAATTTGATA
*
49228 ATTAAATTTT-ATTTTTTTCTTATTTTATTT
1 ATTAAATTTTAATTTTTTT-TTAATTTATTT
* *
49258 ATTATATTTTAATTTTTTTTTAATTTAATAT
1 ATTAAATTTTAATTTTTTTTTAATTT-ATTT
*
49289 ATTTAATTTT
1 ATTAAATTTT
49299 TTTTCACCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (30 bp):
ATTAAATTTTAATTTTTTTTTAATTTATTT
Found at i:49278 original size:25 final size:25
Alignment explanation
Indices: 49250--49302 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
49240 TTTTTTCTTA
*
49250 TTTT-ATTTATTATATTTTAATTTTT
1 TTTTAATTTAATATA-TTTAATTTTT
49275 TTTTAATTTAATATATTTAATTTTT
1 TTTTAATTTAATATATTTAATTTTT
49300 TTT
1 TTT
49303 CACCCAACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTAATTTAATATATTTAATTTTT
Found at i:49298 original size:31 final size:31
Alignment explanation
Indices: 49219--49302 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
49209 ATAAATTATA
* *
49219 AATTTGATA-ATTAAATTTTATTTTTTTCTT
1 AATTTAATATATTTAATTTTATTTTTTTCTT
* *
49249 -ATTTTATTTA-TTATATTTTAATTTTTTT-TT
1 AATTTAATATATTTA-ATTTT-ATTTTTTTCTT
49279 AATTTAATATATTTAATTTT-TTTT
1 AATTTAATATATTTAATTTTATTTT
49303 CACCCAACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
29 12 0.27
30 8 0.18
31 21 0.48
32 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (31 bp):
AATTTAATATATTTAATTTTATTTTTTTCTT
Found at i:58246 original size:2 final size:2
Alignment explanation
Indices: 58239--58299 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
58229 ACATCTACAA
58239 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
58281 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
58300 GTTTGGATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61185 original size:244 final size:242
Alignment explanation
Indices: 60756--61240 Score: 925
Period size: 244 Copynumber: 2.0 Consensus size: 242
60746 ATATCAATAT
60756 CGGTGCTTCATATATGAAGTATTAAAAACCATTAAGTGGCTGCTATAGAATTCCTATTTCTTCCA
1 CGGTGCTTCATATATGAAGTATTAAAAACCATTAAGTGGCTGCTATAGAATTCCTATTTCTTCCA
*
60821 CCAGCTAGCCAAAAAAATTCATGCATGAATAAGCCAACCATGGATGTTATGACAACAATTTGGAA
66 CCAGCTAGCCAAAAAAATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGGAA
60886 AATTTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTA
131 AATTTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTA
60951 TGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAAC
196 TGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAAC
60998 CGGTGCTTCATATATGAAGTATTAAAAAACCATTAAGTGGCTGCTATAGAATTCCTATTTCTTCC
1 CGGTGCTTCATATATGAAGTATT-AAAAACCATTAAGTGGCTGCTATAGAATTCCTATTTCTTCC
61063 ACCAGCTAGCCAAAAACAATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGG
65 ACCAGCTAGCCAAAAA-AATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGG
* *
61128 AAAATTTAGAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGGAAGGACGGCACCGC
129 AAAATTTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGC
61193 TATGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAA
194 TATGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAA
61241 TTTCAAACCC
Statistics
Matches: 238, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
242 23 0.10
243 57 0.24
244 158 0.66
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (242 bp):
CGGTGCTTCATATATGAAGTATTAAAAACCATTAAGTGGCTGCTATAGAATTCCTATTTCTTCCA
CCAGCTAGCCAAAAAAATTCATGCATGAATAAGCCAACCATAGATGTTATGACAACAATTTGGAA
AATTTACAGGTCTGAGCCTTACAGTGTCAATGAGATTTCTAGGTGTGGAAAGGACGGCACCGCTA
TGGTAGTAATCTATCCCCAAACCACCTCCAATGTTCAAATAATCAAC
Found at i:65092 original size:2 final size:2
Alignment explanation
Indices: 65085--65111 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65075 AACCTAATTA
65085 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 A
65112 CTTCTACATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66074 original size:31 final size:31
Alignment explanation
Indices: 66028--66103 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
66018 AATGACAGAT
* * * *
66028 TATTTTATTATTATTTTTATATGATGTGATA
1 TATTATATTAATATTTTAATATGATATGATA
*
66059 TATTATATTAATATTTTAATATGATATGTTA
1 TATTATATTAATATTTTAATATGATATGATA
66090 TATTATATT-ATATT
1 TATTATATTAATATT
66104 AATAGTGCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (31 bp):
TATTATATTAATATTTTAATATGATATGATA
Done.