Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001271.1 Hibiscus syriacus cultivar Beakdansim tig00002495_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: 78954
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6917 original size:20 final size:20
Alignment explanation
Indices: 6889--6927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6879 CAAGAAATTA
6889 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
6909 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
6928 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:9576 original size:23 final size:22
Alignment explanation
Indices: 9546--9624 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
9536 GCATGGCCTT
9546 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
9568 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
9590 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
9612 ATGTATCGATGCA
1 GTGCATCGATGCA
9625 GAAGCACAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:9602 original size:21 final size:21
Alignment explanation
Indices: 9550--9624 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 21
9540 GGCCTTGTGC
*
9550 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
9573 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
9594 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGG-TGT
9616 ATCGATGCA
1 ATCGATGCA
9625 GAAGCACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 18 0.41
22 13 0.30
23 13 0.30
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:15455 original size:45 final size:46
Alignment explanation
Indices: 15370--15457 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
15360 AAATAGCCTG
* * *
15370 AGTGCATCGATGCATGGTCTTGTGCATTGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
15416 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
15458 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:18043 original size:28 final size:28
Alignment explanation
Indices: 18008--18072 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
17998 TATTCACAAG
18008 TGGAGGAGAATATAGTAGCAGGGTCAGA
1 TGGAGGAGAATATAGTAGCAGGGTCAGA
18036 TGGAGGAGAATATAGTAGCAGGGTCAGA
1 TGGAGGAGAATATAGTAGCAGGGTCAGA
18064 TGGAGGAGA
1 TGGAGGAGA
18073 GAAATGTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.35, C:0.06, G:0.42, T:0.17
Consensus pattern (28 bp):
TGGAGGAGAATATAGTAGCAGGGTCAGA
Found at i:20935 original size:45 final size:45
Alignment explanation
Indices: 20870--21086 Score: 310
Period size: 45 Copynumber: 4.8 Consensus size: 45
20860 TTAGTAATTA
*
20870 TTCATTTA-GGACATCTTTTCATGCCTTTAATGCACCGTTATGCAT
1 TTCATTTATGG-CATCCTTTCATGCCTTTAATGCACCGTTATGCAT
* * *
20915 TTCATTTACGGTATCCTTTCATGCCTTTAATGCACTGTTATGCAT
1 TTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCAT
* * *
20960 TTTATTTATGGCATCCTTTCATGCCTTTAATGCAACATTATGCAT
1 TTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCAT
* * * *
21005 TTCATTTATTGCATCTTTTCATGCCTTTAATGCATCGTTATACAT
1 TTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCAT
*
21050 TTCATTTATGACATCCTTTCATGCCTTTAATGCACCG
1 TTCATTTATGGCATCCTTTCATGCCTTTAATGCACCG
21087 CTAGGCCTTT
Statistics
Matches: 152, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 150 0.99
46 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
TTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCAT
Found at i:21316 original size:55 final size:55
Alignment explanation
Indices: 21190--21408 Score: 253
Period size: 55 Copynumber: 4.0 Consensus size: 55
21180 TTCCACACGT
* * * * ** *
21190 AGTGCCAATACGGTAATTCACAAACTTATTAT-AATTTGCGT-GGGTTGCACACCC
1 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTT-CTTAGTTTTGCACACAC
* * ** *
21244 ACTACTAATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
1 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
* * * *
21299 AGTGCCCATACTGAAATTCATAAATTTATTATGAATTTCATAGTTTTGTACACAC
1 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
*
21354 AGTGCTCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACA
1 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACA
21409 TAATGCCATT
Statistics
Matches: 138, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
54 28 0.20
55 100 0.72
56 10 0.07
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (55 bp):
AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
Found at i:21800 original size:19 final size:19
Alignment explanation
Indices: 21778--21825 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
21768 CTCTATTGTG
*
21778 GTATCGATACTTCTTTACA
1 GTATCGATACTCCTTTACA
21797 GTATCGATACTCCTTTACA
1 GTATCGATACTCCTTTACA
21816 GTATCGATAC
1 GTATCGATAC
21826 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (19 bp):
GTATCGATACTCCTTTACA
Found at i:26334 original size:135 final size:135
Alignment explanation
Indices: 26092--26392 Score: 419
Period size: 135 Copynumber: 2.2 Consensus size: 135
26082 CATTATTTTC
* * * * *
26092 ATTTAGAGCATCATTTCATGCTTTTAA--CATACTGTTAAGTATTTCATTTATGGCATCCTTTCA
1 ATTTATAGCATCATTTCATGCCTTTAATGCAT-C-GTTATGCATTTCATTTATGGCACCCTTTCA
* *
26155 TGTATTTAATGCAACGTTATGCATTTAATTTATGACATCCTTTCATGCCTTCAATGCACCGTTAT
64 TGCATTTAATGCAACGTTATGCATTTAATTTATGACATCCTTTCATGCCTTCAATGCAACGTTAT
*
26220 GCATTTT
129 GCATTTA
*
26227 ATTTAT-GACATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGCACCCTTTCAT
1 ATTTATAG-CATCATTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGCACCCTTTCAT
* * * * * *
26291 GCCTTTAATGCATCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCAATGTTATG
65 GCATTTAATGCAACGTTATGCATTTAATTTATGACATCCTTTCATGCCTTCAATGCAACGTTATG
26356 CATTTA
130 CATTTA
26362 ATTTATAGCATCATTTCATGCCTTTAATGCA
1 ATTTATAGCATCATTTCATGCCTTTAATGCA
26393 ACATTAGGCC
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
134 1 0.01
135 140 0.96
136 2 0.01
137 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (135 bp):
ATTTATAGCATCATTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGCACCCTTTCATG
CATTTAATGCAACGTTATGCATTTAATTTATGACATCCTTTCATGCCTTCAATGCAACGTTATGC
ATTTA
Found at i:26389 original size:45 final size:45
Alignment explanation
Indices: 26088--26393 Score: 370
Period size: 45 Copynumber: 6.8 Consensus size: 45
26078 TATTCATTAT
* * * *
26088 TTTCATTTA-GAGCATCATTTCATGCTTTTAA--CATACTGTTAAGTA
1 TTTCATTTATG-GCATCCTTTCATGCCTTTAATGCA-A-TGTTATGCA
** *
26133 TTTCATTTATGGCATCCTTTCATGTATTTAATGCAACGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAATGTTATGCA
* * * **
26178 TTTAATTTATGACATCCTTTCATGCCTTCAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAATGTTATGCA
* *
26223 TTTTATTTATGACATCCTTTCATGCCTTTAATGC-ATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAAT-GTTATGCA
*
26268 TTTCATTTATGGCACCCTTTCATGCCTTTAATGC-ATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAAT-GTTATGCA
26313 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAATGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAATGTTATGCA
* * *
26358 TTTAATTTATAGCATCATTTCATGCCTTTAATGCAA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAA
26394 CATTAGGCCT
Statistics
Matches: 233, Mismatches: 23, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
45 227 0.97
46 4 0.02
47 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCAATGTTATGCA
Found at i:26627 original size:55 final size:55
Alignment explanation
Indices: 26567--26716 Score: 241
Period size: 53 Copynumber: 2.7 Consensus size: 55
26557 ACCAATACGA
26567 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCACATACTG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCACATACTG
* * *
26622 AAATTCATAAATTTATTATGAATTTCATAGTTTTG--CACACAGTGCTCATACTG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCACATACTG
*
26675 AAATTCATAAACTTAGTATGAATTTCTTAGTTTTTGCACACA
1 AAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACA
26717 TATTGCCATT
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
53 44 0.51
54 5 0.06
55 33 0.38
56 4 0.05
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (55 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCACATACTG
Found at i:45181 original size:12 final size:12
Alignment explanation
Indices: 45157--45190 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
45147 CCTTCTTCTT
*
45157 CTCCTCCTCCTC
1 CTCCTCTTCCTC
*
45169 CTCTTCTTCCTC
1 CTCCTCTTCCTC
45181 CTCCTCTTCC
1 CTCCTCTTCC
45191 CTCAGCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCCTCTTCCTC
Found at i:45181 original size:15 final size:15
Alignment explanation
Indices: 45161--45189 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45151 CTTCTTCTCC
45161 TCCTCCTCCTCTTCT
1 TCCTCCTCCTCTTCT
45176 TCCTCCTCCTCTTC
1 TCCTCCTCCTCTTC
45190 CCTCAGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (15 bp):
TCCTCCTCCTCTTCT
Found at i:45588 original size:240 final size:240
Alignment explanation
Indices: 45165--45646 Score: 928
Period size: 240 Copynumber: 2.0 Consensus size: 240
45155 TTCTCCTCCT
45165 CCTCCTCTTCTTCCTCCTCCTCTTCCCTCAGCTTTTTCTCTTCCGACTTTTCCATCTGATGCACA
1 CCTCCTCTTCTTCCTCCTCCTCTTCCCTCAGCTTTTTCTCTTCCGACTTTTCCATCTGATGCACA
*
45230 TCCAGCATTCAAGTTTCTAGTTGATTGATACAGATTAACAAAAGAATGAAAATGAGAAGAGAAAC
66 TCCAGCACTCAAGTTTCTAGTTGATTGATACAGATTAACAAAAGAATGAAAATGAGAAGAGAAAC
* *
45295 TCTAATTGCCAATGGCCAAAATAAAAATAAAAACCTGAAAATATGGTTGAGAAGAACACTCCAAT
131 TCTAATTGCCAATGACCAAAATAAAAATAAAAACCTGAAAATATGGTTGAGAAGAACACTACAAT
45360 GAAATTGATGATCGCCCAGAAAAAATCGATGGAAGTTCCCAGTCG
196 GAAATTGATGATCGCCCAGAAAAAATCGATGGAAGTTCCCAGTCG
45405 CCTCCTCTTCTTCCTCCTCCTCTTCCCTCAGCTTTTTCTCTTCCGACTTTTCCATCTGATGCACA
1 CCTCCTCTTCTTCCTCCTCCTCTTCCCTCAGCTTTTTCTCTTCCGACTTTTCCATCTGATGCACA
45470 TCCAGCACTCAAGTTTCTAGTTGATTGATACAGATTAACAAAAGAATGAAAATGAGAAGAGAAAC
66 TCCAGCACTCAAGTTTCTAGTTGATTGATACAGATTAACAAAAGAATGAAAATGAGAAGAGAAAC
45535 TCTAATTGCCAATGACCAAAATAAAAATAAAAACCTGAAAATATGGTTGAGAAGAACACTACAAT
131 TCTAATTGCCAATGACCAAAATAAAAATAAAAACCTGAAAATATGGTTGAGAAGAACACTACAAT
*
45600 GAAATTGATGATCGCCCAGAAAAAATCGATGGAAGTTTCCAGTCG
196 GAAATTGATGATCGCCCAGAAAAAATCGATGGAAGTTCCCAGTCG
45645 CC
1 CC
45647 ATATTGACCG
Statistics
Matches: 238, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
240 238 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (240 bp):
CCTCCTCTTCTTCCTCCTCCTCTTCCCTCAGCTTTTTCTCTTCCGACTTTTCCATCTGATGCACA
TCCAGCACTCAAGTTTCTAGTTGATTGATACAGATTAACAAAAGAATGAAAATGAGAAGAGAAAC
TCTAATTGCCAATGACCAAAATAAAAATAAAAACCTGAAAATATGGTTGAGAAGAACACTACAAT
GAAATTGATGATCGCCCAGAAAAAATCGATGGAAGTTCCCAGTCG
Found at i:45937 original size:20 final size:20
Alignment explanation
Indices: 45893--46267 Score: 336
Period size: 20 Copynumber: 18.5 Consensus size: 20
45883 AATGACCAAC
45893 AAAATCGCAACGCGATAT-C-
1 AAAATCGCAACGCGAT-TCCA
*
45912 AAAATCGCAACGCGATT-TA
1 AAAATCGCAACGCGATTCCA
* **
45931 GAAAATCGCAACGTTGA--AAA
1 -AAAATCGCAACG-CGATTCCA
*
45951 GAAAATCGCAACG-G--TCAAA
1 -AAAATCGCAACGCGATTC-CA
45970 AGAAAATCGCAACGCGATCTTCCA
1 A-AAA-TCGCAACGCGA--TTCCA
* *
45994 AGAATCGCAATGCGATTCCA
1 AAAATCGCAACGCGATTCCA
* * *
46014 AGAATCGCAATGCGATCTTCGA
1 AAAATCGCAACGCGA--TTCCA
* * *
46036 AGAATCGCAATGCGATTTTCGA
1 AAAATCGCAACGCGA--TTCCA
*
46058 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46078 ATAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46098 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46118 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46138 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46158 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46178 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
*
46198 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA
* *
46218 AGAATCGCAACGCGATT-GA
1 AAAATCGCAACGCGATTCCA
*
46237 GAAAATCGCAATGCGATTCCA
1 -AAAATCGCAACGCGATTCCA
*
46258 AGAATCGCAA
1 AAAATCGCAA
46268 AACGGCAAAA
Statistics
Matches: 321, Mismatches: 18, Indels: 33
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.01
19 22 0.07
20 237 0.74
21 4 0.01
22 49 0.15
23 2 0.01
24 2 0.01
25 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCCA
Found at i:46111 original size:40 final size:40
Alignment explanation
Indices: 45974--46267 Score: 437
Period size: 40 Copynumber: 7.2 Consensus size: 40
45964 GTCAAAAGAA
*
45974 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCCAAG
* * * *
46016 AATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTTTCGAAG
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGA--TTCCAAG
*
46060 AATCGCAACGCGATTCCAATAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
46100 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
46140 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
46180 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
* * *
46220 AATCGCAACGCGATT-GAGAAAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCAAG
46260 AATCGCAA
1 AATCGCAA
46268 AACGGCAAAA
Statistics
Matches: 237, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.00
40 168 0.71
42 50 0.21
44 18 0.08
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
Found at i:46144 original size:60 final size:60
Alignment explanation
Indices: 45974--46267 Score: 437
Period size: 60 Copynumber: 4.8 Consensus size: 60
45964 GTCAAAAGAA
* * *
45974 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCTTCGAAG
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGA--TTCCAAG
* * *
46038 AATCGCAATGCGATTTTCGAAGAATCGCAACGCGATTCCAATAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
46100 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
46160 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
* * *
46220 AATCGCAACGCGATT-GAGAAAATCGCAATGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCAAGAATCGCAA
46268 AACGGCAAAA
Statistics
Matches: 216, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
59 1 0.00
60 148 0.69
62 18 0.08
64 49 0.23
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (60 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
Found at i:46389 original size:6 final size:6
Alignment explanation
Indices: 46378--46428 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
46368 GACACGTATT
46378 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
46426 ACC
1 ACC
46429 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:47194 original size:6 final size:6
Alignment explanation
Indices: 47183--47285 Score: 188
Period size: 6 Copynumber: 17.2 Consensus size: 6
47173 TCTCGTCTCG
47183 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
**
47231 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTAAT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
47279 GGTCGT G
1 GGTCGT G
47286 ATAATGGTAA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.02, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:47429 original size:20 final size:20
Alignment explanation
Indices: 47404--47533 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
47394 TTTTGCCGTT
47404 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
47424 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCG
*
47444 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
47464 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
47484 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
47504 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
47526 TTGCGATT
1 TTGCGATT
47534 TTCTTTTGAC
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.03
20 70 0.78
21 4 0.04
22 13 0.14
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:47451 original size:40 final size:40
Alignment explanation
Indices: 47404--47511 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
47394 TTTTGCCGTT
47404 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
47444 TTGCGATTCCTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
47484 TTGCGATTCTTTGAATCGCATTGCGATT
1 TTGCGATTCTTGGAATCGCGTTGCGATT
47512 CTTGGAAGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
Found at i:47501 original size:60 final size:62
Alignment explanation
Indices: 47417--47537 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 62
47407 CGATTCTTGG
47417 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGG-A-ATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
* *
47477 AATCGCGTTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATT-TTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCT
47538 TTTGACCGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 35 0.62
61 3 0.05
62 18 0.32
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (62 bp):
AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
Found at i:47589 original size:20 final size:19
Alignment explanation
Indices: 47417--47595 Score: 121
Period size: 20 Copynumber: 8.9 Consensus size: 19
47407 CGATTCTTGG
47417 AATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATTTTCT
* *
47436 CAATCGCATTGCGA-TTCCT
1 -AATCGCGTTGCGATTTTCT
47455 GGAATCGCGTTGCGATTTTCT
1 --AATCGCGTTGCGATTTTCT
47476 CAATCGCGTTGCGATTCTT-T
1 -AATCGCGTTGCGATT-TTCT
* **
47496 GAATCGCATTGCGATTCTTGGA
1 -AATCGCGTTGCGATT-TT-CT
47518 AGATCGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATTTTCT
* *
47538 -TTTGACCGTTGCGATTTTCT
1 AATCG--CGTTGCGATTTTCT
** * *
47558 TTTCAACATTGCGATTTTCT
1 AATC-GCGTTGCGATTTTCT
47578 AAATCGCGTTGCGATTTT
1 -AATCGCGTTGCGATTTT
47596 TGTTTCGCAT
Statistics
Matches: 127, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 95 0.75
21 13 0.10
22 13 0.10
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (19 bp):
AATCGCGTTGCGATTTTCT
Found at i:51702 original size:22 final size:22
Alignment explanation
Indices: 51674--51730 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
51664 GATGGCCTTG
51674 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
51696 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
51718 TGCATCGATGCAC
1 TGCATCGATGCAC
51731 TGTTAGGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:57727 original size:20 final size:20
Alignment explanation
Indices: 57699--57737 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57689 CAAGAAATTA
57699 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
57719 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
57738 CACTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:59319 original size:28 final size:28
Alignment explanation
Indices: 59236--59320 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
59226 CGACACTATG
*
59236 TGTGCATCCATGGTATTCATAATGAGTT
1 TGTGCATCCATGGTATTCATAATTAGTT
* *
59264 TGTGAATGACCA---T-TTCA-ACACTA-TT
1 TGTGCAT--CCATGGTATTCATA-ATTAGTT
59289 TGTGCATCCATGGTATTCATAATTAGTT
1 TGTGCATCCATGGTATTCATAATTAGTT
59317 TGTG
1 TGTG
59321 AATTACTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 3 0.07
25 9 0.21
26 7 0.16
27 8 0.19
28 13 0.30
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (28 bp):
TGTGCATCCATGGTATTCATAATTAGTT
Found at i:59440 original size:53 final size:53
Alignment explanation
Indices: 59177--59439 Score: 393
Period size: 53 Copynumber: 5.0 Consensus size: 53
59167 TCGTATCAGT
* * *
59177 ACTATCTGTGCATCCATGGTATTCATAATTAGTTTGTAAATTACCATTTCGAC
1 ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGAC
* *
59230 ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATGACCATTTCAAC
1 ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGAC
* * * * *
59283 ACTATTTGTGCATCCATGGTATTCATAATTAGTTTGTGAATTACTATTTTGGC
1 ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGAC
* *
59336 ACTATGTGTGCATCTATGGTATTCATAATGAGTTTGTGAATTACCATTTCGTC
1 ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGAC
*
59389 ACTATGTGTGCA-CCTATGGTTTTCATAATGAGTTTGTGAATTACCATTTCG
1 ACTATGTGTGCATCC-ATGGTATTCATAATGAGTTTGTGAATTACCATTTCG
59440 TTACCTTAGT
Statistics
Matches: 189, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 1 0.01
53 188 0.99
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (53 bp):
ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGAC
Found at i:59754 original size:20 final size:20
Alignment explanation
Indices: 59725--59763 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59715 AGAGCTCATA
*
59725 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
59745 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
59764 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:67288 original size:20 final size:20
Alignment explanation
Indices: 67217--67281 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
67207 ATGCAATTAA
*
67217 TGCATCGATGCATCCTGTTG
1 TGCATCAATGCATCCTGTTG
*
67237 TGTATCAATGCATCCTGTTG
1 TGCATCAATGCATCCTGTTG
*
67257 TGCATCGATGCATCCTGTTG
1 TGCATCAATGCATCCTGTTG
67277 TGCAT
1 TGCAT
67282 TCATGCACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
TGCATCAATGCATCCTGTTG
Found at i:69248 original size:19 final size:19
Alignment explanation
Indices: 69213--69263 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
69203 TAAAGATAAT
69213 TTGATTTTG-AAAGCAAAA
1 TTGATTTTGAAAAGCAAAA
*
69231 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAAGCAAAA
69250 -TGAAATTTTGAAAA
1 TTG--ATTTTGAAAA
69264 ATGATTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.38
19 8 0.28
20 10 0.34
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAAGCAAAA
Found at i:70406 original size:21 final size:21
Alignment explanation
Indices: 70380--70423 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
70370 TTTCAAACAA
70380 TTGTTAACAATTGATATCATT
1 TTGTTAACAATTGATATCATT
* *
70401 TTGTTAACAATTGGTATCTTT
1 TTGTTAACAATTGATATCATT
70422 TT
1 TT
70424 CATTAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.52
Consensus pattern (21 bp):
TTGTTAACAATTGATATCATT
Found at i:70669 original size:21 final size:21
Alignment explanation
Indices: 70643--70700 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
70633 AGGGTGTCAA
70643 AGTGCATCCATGCACCCCAAC
1 AGTGCATCCATGCACCCCAAC
**
70664 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCAAC
*
70685 AGTGCATCGATGCACC
1 AGTGCATCCATGCACC
70701 ATGTAGTGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.40, G:0.19, T:0.17
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCAAC
Found at i:70710 original size:20 final size:20
Alignment explanation
Indices: 70643--70719 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
70633 AGGGTGTCAA
*
70643 AGTGCATCCATGCACCCCA-AC
1 AGTGCATCCATGCA--CCATGC
*
70664 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGC
* *
70685 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGC
70705 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
70720 TCCTTTTCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 21 0.43
21 28 0.57
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:71190 original size:34 final size:32
Alignment explanation
Indices: 71152--71221 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
71142 TTTTGTAATG
* *
71152 GGGAAAGGTTCTAGCTTATCCCGCGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
71186 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
71218 GGGA
1 GGGA
71222 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:71717 original size:17 final size:17
Alignment explanation
Indices: 71697--71739 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
71687 AATCGTATCG
71697 GGTCGATTATCGAGTCA
1 GGTCGATTATCGAGTCA
* * *
71714 GGTCAATTTTCGAGTTA
1 GGTCGATTATCGAGTCA
71731 GGT-GATTAT
1 GGTCGATTAT
71740 TGGATCGGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (17 bp):
GGTCGATTATCGAGTCA
Found at i:72509 original size:18 final size:19
Alignment explanation
Indices: 72472--72509 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
72462 CTCTTAACTT
* *
72472 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
72491 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
72509 T
1 T
72510 TATAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:72525 original size:17 final size:17
Alignment explanation
Indices: 72478--72528 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
72468 ACTTTCTATT
72478 ATTTTATTATAAATCTAATA
1 ATTTTATT-TAAAT-T-ATA
* *
72498 TTTTTA-ATAAATTATA
1 ATTTTATTTAAATTATA
72514 ATTTTATTTAAATTA
1 ATTTTATTTAAATTA
72529 ATTTATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 8 0.31
17 8 0.31
18 5 0.19
20 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATTTAAATTATA
Found at i:74923 original size:16 final size:17
Alignment explanation
Indices: 74887--74928 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
74877 AATATAAGCG
*
74887 TAAAATAAAATTTGATA
1 TAAAATAAAATTTAATA
74904 -AAAATAAAA-TTAATA
1 TAAAATAAAATTTAATA
74919 TAAAACTAAA
1 TAAAA-TAAA
74929 TCGTACTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAAATAAAATTTAATA
Done.