Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005678.1 Hibiscus syriacus cultivar Beakdansim tig00013277_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: 85963
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:21 original size:15 final size:15
Alignment explanation
Indices: 1--34 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
*
1 AAAAAGAAAAAATCA
1 AAAAAGAAAAAACCA
*
16 AAAAAGGAAAAACCA
1 AAAAAGAAAAAACCA
31 AAAA
1 AAAA
35 CCTTTAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAACCA
Found at i:5610 original size:18 final size:16
Alignment explanation
Indices: 5584--5635 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
5574 TAAATCATTT
5584 TTAAA-TTTAATTTTA
1 TTAAATTTTAATTTTA
5599 TTTAAAATTTTATATATTTA
1 -TT-AAATTTTA-AT-TTTA
5619 TTAAATTTTAAATTTTA
1 TTAAATTTT-AATTTTA
5636 ATACTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 7 0.23
18 13 0.42
19 5 0.16
20 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATTTTAATTTTA
Found at i:17494 original size:23 final size:23
Alignment explanation
Indices: 17468--17542 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
17458 ATGCATTGCT
17468 TGCTGTGCATGAGTCTGTTAAGC
1 TGCTGTGCATGAGTCTGTTAAGC
17491 TGCTGTGCATGAGTCTGTTAAGC
1 TGCTGTGCATGAGTCTGTTAAGC
* * *
17514 TGTTGTGCATGAGTTTGTTAGGC
1 TGCTGTGCATGAGTCTGTTAAGC
*
17537 AGCTGT
1 TGCTGT
17543 TAAGAGTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.16, C:0.15, G:0.32, T:0.37
Consensus pattern (23 bp):
TGCTGTGCATGAGTCTGTTAAGC
Found at i:18300 original size:15 final size:16
Alignment explanation
Indices: 18275--18308 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
18265 CCAATCTTTG
18275 CTCCTTAGTGTTCCCA
1 CTCCTTAGTGTTCCCA
18291 CTCC-TAGTGTTCCCA
1 CTCCTTAGTGTTCCCA
18306 CTC
1 CTC
18309 AATGGAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.12, C:0.41, G:0.12, T:0.35
Consensus pattern (16 bp):
CTCCTTAGTGTTCCCA
Found at i:20327 original size:7 final size:7
Alignment explanation
Indices: 20315--20350 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
20305 ATATTTACAT
20315 TTATTTA
1 TTATTTA
20322 TTATTT-
1 TTATTTA
20328 TTATTTA
1 TTATTTA
20335 TTATTTA
1 TTATTTA
*
20342 ATATTTA
1 TTATTTA
20349 TT
1 TT
20351 TAAATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:20332 original size:13 final size:13
Alignment explanation
Indices: 20314--20350 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20304 TATATTTACA
20314 TTTATTTATTATT
1 TTTATTTATTATT
20327 TTTATTTATTATT
1 TTTATTTATTATT
*
20340 TAATATTTATT
1 T-TTATTTATT
20351 TAAATCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTATTATT
Found at i:20542 original size:34 final size:34
Alignment explanation
Indices: 20477--20543 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
20467 GTTTGTTTTG
**
20477 TTCTAGAAAATATTTTCAATATTTTTATTTTTAT
1 TTCTAGAAAATATTTTCAATATCATTATTTTTAT
* *
20511 TTCTAGAAAATAGTTTTCATTCTCATT-TTTTTA
1 TTCTAGAAAATA-TTTTCAATATCATTATTTTTA
20544 AATTAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (34 bp):
TTCTAGAAAATATTTTCAATATCATTATTTTTAT
Found at i:21411 original size:28 final size:28
Alignment explanation
Indices: 21375--21429 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
21365 TTTTATTTCA
*
21375 AATAAAAGAGTCATACTTTTAATATCAT
1 AATAAAAGAGTCAGACTTTTAATATCAT
21403 AATAAAAGAGTCAGACTTTTAATATCA
1 AATAAAAGAGTCAGACTTTTAATATCA
21430 GAAAGGATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (28 bp):
AATAAAAGAGTCAGACTTTTAATATCAT
Found at i:22374 original size:12 final size:12
Alignment explanation
Indices: 22357--22381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22347 TTAGACTAAT
22357 AGTATCAGTACC
1 AGTATCAGTACC
22369 AGTATCAGTACC
1 AGTATCAGTACC
22381 A
1 A
22382 CATGAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
AGTATCAGTACC
Found at i:26747 original size:26 final size:28
Alignment explanation
Indices: 26707--26758 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
26697 ACACACACTT
26707 CTTTTATAAATCCATTT-AAAAAAAGCA
1 CTTTTATAAATCCATTTGAAAAAAAGCA
* *
26734 CTTTTA-ACATCCATTTGATAAAAAG
1 CTTTTATAAATCCATTTGAAAAAAAG
26759 TAAAACCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (28 bp):
CTTTTATAAATCCATTTGAAAAAAAGCA
Found at i:35754 original size:20 final size:20
Alignment explanation
Indices: 35718--35765 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
35708 TCAAAATCAT
* *
35718 TTTTCAAAATTTCATTTTGC
1 TTTTCAAAATTCCATTTTAC
35738 TTTTCAAAA-TCCAATTTTAC
1 TTTTCAAAATTCC-ATTTTAC
35758 TTTT-AAAA
1 TTTTCAAAA
35766 GAAAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAC
Found at i:37184 original size:20 final size:20
Alignment explanation
Indices: 37141--37192 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
37131 ATCAGTAATG
* * *
37141 TTCATATAGAATCAATATTG
1 TTCATATAGTATCAATACTA
*
37161 TTCATATAGTATCGATACTA
1 TTCATATAGTATCAATACTA
*
37181 TTCATTTAGTAT
1 TTCATATAGTAT
37193 TAGTACTACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
TTCATATAGTATCAATACTA
Found at i:39211 original size:27 final size:27
Alignment explanation
Indices: 39181--39241 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
39171 AGGATGTTTA
*
39181 GGTCATTGCAATA-CTCGAGGATATCTT
1 GGTCATT-CAAGAGCTCGAGGATATCTT
* * *
39208 GGTCATTTAAGAGCTCGAGGGTATTTT
1 GGTCATTCAAGAGCTCGAGGATATCTT
39235 GGTCATT
1 GGTCATT
39242 TTAGTACCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (27 bp):
GGTCATTCAAGAGCTCGAGGATATCTT
Found at i:43088 original size:2 final size:2
Alignment explanation
Indices: 43081--43115 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43071 ATTTTAGTAA
43081 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
43116 TATATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:43120 original size:2 final size:2
Alignment explanation
Indices: 43115--43142 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43105 ACACACACAC
43115 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
43143 TTAAATCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43885 original size:81 final size:81
Alignment explanation
Indices: 43772--44587 Score: 1097
Period size: 81 Copynumber: 10.1 Consensus size: 81
43762 AATCATTTAG
* * * *
43772 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
*
43837 ACAGCTAGGCATTTAA
66 ACAGCTAGGCAATTAA
* * * * * * *
43853 TCTTTAACTCAAAGGCAGTTAGCCTTTCATCTAACTTGTATAATTGACACATTTCTATCAAATGA
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
*
43918 ACAGCTAGACAATTAA
66 ACAGCTAGGCAATTAA
* * *
43934 TCTTTCACTCAAAGACATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
43999 ACATG-TAGGCAATTAA
66 ACA-GCTAGGCAATTAA
* * * *
44015 TCTTTTACTCAAAGGCATTTAACATTTCATATAAC-CGACATAATTGACACATTTCTGTCAAATG
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTG-CATAATTGACACCTTTCTGTCAAATG
*
44079 CACAGCTAGGAAATTAA
65 CACAGCTAGGCAATTAA
* * *
44096 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
44161 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
*
44177 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAAC-TGTCATAATTGACATCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTG-CATAATTGACACCTTTCTGTCAAATG
*
44241 CACAGCTAGACAATTAA
65 CACAGCTAGGCAATTAA
* * * * * *
44258 TCTTTTACTCAAATGTATTTAACCTTTCGTTTAACTGGCATAATTGACACCATTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
44323 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * *
44339 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGGCATAATTGACACCTTTCTATGAAATG
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTT-GCATAATTGACACCTTTCTGTCAAATG
*
44403 CATAGCTAGGCAATTAA
65 CACAGCTAGGCAATTAA
* * * *
44420 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TGTCATAATTGACACATTTCTGTAAAATA
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTG-CATAATTGACACCTTTCTGTCAAATG
*
44484 CACAG-TAAGACAATTAA
65 CACAGCT-AGGCAATTAA
* * * ** *
44501 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTAGCATAATTGACATATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
*
44566 ACATCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
44582 T-TTTTA
1 TCTTTTA
44588 TTTAAAACAG
Statistics
Matches: 653, Mismatches: 70, Indels: 25
0.87 0.09 0.03
Matches are distributed among these distances:
80 11 0.02
81 637 0.98
82 5 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:49586 original size:81 final size:81
Alignment explanation
Indices: 49476--50208 Score: 912
Period size: 81 Copynumber: 9.0 Consensus size: 81
49466 CATTTAGTTG
* * * * * * * **
49476 TTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGATATCTTTCTGCCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
*
49541 GCTAGGCATTTAATC-
66 GCTAGGCAATTAATCT
* * *
49556 TTTAGCTCAAAGGCATTTAGCCTTTCATCTAACTGTCATAATTGACACCTTTCTATCAAATGCAC
1 TTTA-CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCAC
** *
49621 AGCTACACAATTAATAT
65 AGCTAGGCAATTAATCT
* ** * * * * *
49638 TTTACTCAAAGGCATTTAATATTTCATCTAACTAGCATAATTGACAGCTTTTTGTCAAAGGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
*
49703 GGTAGGCAATTAATCT
66 GCTAGGCAATTAATCT
* * * * **
49719 TTTACTTAAAGGCATTTAACCTTTCATCTAACTGGCATATTTGACACCTTTCTGTCAAATATA-A
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
* *
49783 TACTAGGCAATTAATAT
66 -GCTAGGCAATTAATCT
* *
49800 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTATCAAATACACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
49865 GCTAGGCAATTAATCT
66 GCTAGGCAATTAATCT
* ** * *
49881 TTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGATGCCTTTATATCAAATGCAAA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
*
49946 ACTAGGCAATTAATCT
66 GCTAGGCAATTAATCT
* * *
49962 TTTACTCAAAGGTATTTAATCTTTCATCTAACTGGCATAATTGATACATTTCTATCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
* *
50027 ACTAGGCAATCAATCT
66 GCTAGGCAATTAATCT
* * *
50043 TTTACTCAAAGGTATTTAACCTTTAATCTAACTGGCATAATTGACACATTTCTATCAAACGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
* *
50108 GCTAGACAAGTAATCT
66 GCTAGGCAATTAATCT
* * * * * *
50124 TTTACTCAAAGGTTTTTAACTTTTAATCTATCTAGCATAATTGACACCTTTCTGTCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
*
50189 GCTAGGCAATTAATAT
66 GCTAGGCAATTAATCT
50205 TTTA
1 TTTA
50209 TTTAAAATAG
Statistics
Matches: 570, Mismatches: 79, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
80 5 0.01
81 560 0.98
82 5 0.01
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (81 bp):
TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
GCTAGGCAATTAATCT
Found at i:52825 original size:32 final size:32
Alignment explanation
Indices: 52767--52827 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
52757 GGTTTCATAC
* *
52767 CAGATCAATTAGATTTCGGGTCAGGTCAATAT
1 CAGATCAATTAGATTTCGAGTAAGGTCAATAT
*
52799 CAGATCAATT-GATTTTCGATTAAGGTCAA
1 CAGATCAATTAGA-TTTCGAGTAAGGTCAA
52828 CCTTTGGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (32 bp):
CAGATCAATTAGATTTCGAGTAAGGTCAATAT
Found at i:54747 original size:10 final size:10
Alignment explanation
Indices: 54732--54756 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54722 AATTTTCATT
54732 TTTTATTTCA
1 TTTTATTTCA
54742 TTTTATTTCA
1 TTTTATTTCA
54752 TTTTA
1 TTTTA
54757 GTTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATTTCA
Found at i:62108 original size:36 final size:37
Alignment explanation
Indices: 62051--62123 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
62041 CTTCATTACC
62051 ATGCTCTCATCTTGGACATGGGTGATTCTTGAAATGT
1 ATGCTCTCATCTTGGACATGGGTGATTCTTGAAATGT
* *
62088 ATGCTCTC-TCTTGGAGATGGGTTATTCTTGAAATGT
1 ATGCTCTCATCTTGGACATGGGTGATTCTTGAAATGT
62124 TTGGAGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (37 bp):
ATGCTCTCATCTTGGACATGGGTGATTCTTGAAATGT
Found at i:63205 original size:2 final size:2
Alignment explanation
Indices: 63200--63224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63190 AAAAATGAAT
63200 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 T
63225 CATGTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64452 original size:8 final size:9
Alignment explanation
Indices: 64434--64458 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
64424 TTCTGAAAAC
64434 AAAAATAAA
1 AAAAATAAA
64443 AAAAATAAA
1 AAAAATAAA
64452 AAAAATA
1 AAAAATA
64459 TATTTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:65057 original size:18 final size:18
Alignment explanation
Indices: 65034--65082 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
65024 TCCTCAAACA
65034 CATTATTATTATTGTTAT
1 CATTATTATTATTGTTAT
* *
65052 CATTATTTTTATTTTTAT
1 CATTATTATTATTGTTAT
*
65070 TATTATTATTATT
1 CATTATTATTATT
65083 CTCTTTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (18 bp):
CATTATTATTATTGTTAT
Found at i:65101 original size:3 final size:3
Alignment explanation
Indices: 65035--65082 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
65025 CCTCAAACAC
* * * *
65035 ATT ATT ATT ATT GTT ATC ATT ATT TTT ATT TTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65083 CTCTTTTCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:67513 original size:245 final size:245
Alignment explanation
Indices: 67083--67574 Score: 957
Period size: 245 Copynumber: 2.0 Consensus size: 245
67073 TTTCTTCAAG
67083 TTCATTATAAATGAACCACCCATACTCTATTATAAGAAATCATTAAGAATAAATATTCAATCTAA
1 TTCATTATAAATGAACCACCCATACTCTATTATAAGAAATCATTAAGAATAAATATTCAATCTAA
*
67148 TTAATCGGTGAATTCAATAAGTCATTCTCAGTAAAACCATCCAAATTCTTGGATTTGAATCCATT
66 TTAATCGGTGAATTCAATAAGTCATTCTCAGTAAAACCATCCAAACTCTTGGATTTGAATCCATT
67213 AAGAGTTTTCATAAAACTCAACCTTTCTAGCGGTAAGTTCATCTTGTCTTTCTCAATTACGACAA
131 AAGAGTTTTCATAAAACTCAACCTTTCTAGCGGTAAGTTCATCTTGTCTTTCTCAATTACGACAA
67278 TCCACTCAACTCTGGGTTATAAACTTATTAAGAATATATATTCAACCAAA
196 TCCACTCAACTCTGGGTTATAAACTTATTAAGAATATATATTCAACCAAA
67328 TTCATTATAAATGAACCACCCATACTCTATTATAAGAAATCATTAAGAATAAATATTCAATCTAA
1 TTCATTATAAATGAACCACCCATACTCTATTATAAGAAATCATTAAGAATAAATATTCAATCTAA
67393 TTAATCGGTGAATTCAATAAGTCATTCTCAGTAAAACCATCCAAACTCTTGGATTTGAATCCATT
66 TTAATCGGTGAATTCAATAAGTCATTCTCAGTAAAACCATCCAAACTCTTGGATTTGAATCCATT
* *
67458 AAGAGTTTTCATAAAACTCAACCTTTCTAGCGGTAAGTTCATCTTGTCTTTCTCAATTAGGACTA
131 AAGAGTTTTCATAAAACTCAACCTTTCTAGCGGTAAGTTCATCTTGTCTTTCTCAATTACGACAA
67523 TCCACTCAACTCTGGGTTATAAACTTATTAAGAATATATATTCAACCAAA
196 TCCACTCAACTCTGGGTTATAAACTTATTAAGAATATATATTCAACCAAA
67573 TT
1 TT
67575 TAGTAAATTC
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 244 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (245 bp):
TTCATTATAAATGAACCACCCATACTCTATTATAAGAAATCATTAAGAATAAATATTCAATCTAA
TTAATCGGTGAATTCAATAAGTCATTCTCAGTAAAACCATCCAAACTCTTGGATTTGAATCCATT
AAGAGTTTTCATAAAACTCAACCTTTCTAGCGGTAAGTTCATCTTGTCTTTCTCAATTACGACAA
TCCACTCAACTCTGGGTTATAAACTTATTAAGAATATATATTCAACCAAA
Found at i:79773 original size:43 final size:43
Alignment explanation
Indices: 79726--80076 Score: 424
Period size: 43 Copynumber: 8.2 Consensus size: 43
79716 TGTGAACAAA
* * *
79726 AAACGCCGCAATAGGTCAAGATCTATCGCGGCATTTTTGGA-AC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * *
79769 AAACGCCGCAAGAGGTCGATATCTATAGCGGCGTTTTCGGA-AC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
*
79812 AAACGCCGCAAAAGGTCGAGATCTATAGTGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * * *
79856 AAACGCCGCAAAAGGTCATATCGATAGCGGCATTTTTGGAGAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
*
79899 AAACGCCACAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * * * *
79941 AAAAGCCGTAAAAGGTCAGATCTATAACGGCATTTATAGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* **
79984 AAACGCCGTAAAAGGTCAGATCTATAGCTACGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * *
80026 AAACGCCGCAAAAAGTCAGATCTATAGCTGCGTTTTT-TATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
80068 AAACGCCGC
1 AAACGCCGC
80077 GAATTAAAAC
Statistics
Matches: 268, Mismatches: 37, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.00
42 82 0.31
43 166 0.62
44 19 0.07
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
Found at i:79975 original size:85 final size:85
Alignment explanation
Indices: 79726--80076 Score: 420
Period size: 85 Copynumber: 4.1 Consensus size: 85
79716 TGTGAACAAA
* * * * *
79726 AAACGCCGCAATAGGTCAAGATCTATCGCGGCATTTTTGGAACAAACGCCGCAAGAGGTCGATAT
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AGAT
* *
79791 CTATAGCGGCGTTTTCGGAAC
65 CTATAGCGGCATTTTTGGAAC
* * *
79812 AAACGCCGCAAAAGGTCGAGATCTATAGTGGCGTTTTTGGATACAAACGCCGCAAAAGGTCATAT
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAGAT
*
79877 CGATAGCGGCATTTTTGGAGAC
65 CTATAGCGGCATTTTTGGA-AC
* * *
79899 AAACGCCACAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAAGCCGTAAAAGGTCAGATC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATC
* * *
79963 TATAACGGCATTTATAGATAC
66 TATAGCGGCATTTTTGGA-AC
* ** *
79984 AAACGCCGTAAAAGGTC-AGATCTATAGCTACGTTTTTGGAACAAACGCCGCAAAAAGTCAGATC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATC
* * *
80048 TATAGCTGCGTTTTT-TATAC
66 TATAGCGGCATTTTTGGA-AC
80068 AAACGCCGC
1 AAACGCCGC
80077 GAATTAAAAC
Statistics
Matches: 231, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
84 12 0.05
85 105 0.45
86 78 0.34
87 36 0.16
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATC
TATAGCGGCATTTTTGGAAC
Found at i:83986 original size:42 final size:42
Alignment explanation
Indices: 83923--84063 Score: 192
Period size: 42 Copynumber: 3.4 Consensus size: 42
83913 TTAGTATCAC
* *
83923 ACGCCGCTAAATACTCATGCTTTAGCGGCGTTTTAAGAAAAA
1 ACGCCGCTAAATACTCATGCTTTAGCGGCGTTTTAAGCACAA
* * * *
83965 ACGCCGCTAAATACTCGTGCTTTAGCAGTGTGTTAAGCACAA
1 ACGCCGCTAAATACTCATGCTTTAGCGGCGTTTTAAGCACAA
* * * *
84007 ACGCCGCTAAAGACTCTTACTTTAGTGGCGTTTTAAGCACAA
1 ACGCCGCTAAATACTCATGCTTTAGCGGCGTTTTAAGCACAA
84049 ACGCCGCTAAATACT
1 ACGCCGCTAAATACT
84064 TATACTTTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
ACGCCGCTAAATACTCATGCTTTAGCGGCGTTTTAAGCACAA
Done.