Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003332.1 Hibiscus syriacus cultivar Beakdansim tig00007013_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: 82712
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1686 original size:75 final size:74
Alignment explanation
Indices: 1510--1711 Score: 290
Period size: 74 Copynumber: 2.7 Consensus size: 74
1500 TCTTAAATCC
*
1510 TAATTAAAACACTTAAAACTATTTAAAC--AAATACCTAAACAAAGATAAAATAT-AAAAATAAT
1 TAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAC-AAGATAAAATATAAAAAATAAT
*
1572 ATCCTAAAACT
64 AACCTAAAACT
1583 TAATTAAAATACTAAAACCTATTT-AACTAAAATACCTAAAACAAGATAAAATATAAAAAATAAT
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATACCT-AAACAAGATAAAATATAAAAAATAAT
1647 AACCT-AAACT
64 AACCTAAAACT
*
1657 TAATTAAAATACTAAAATCTATTTAAACTAAAATACATAAACAA-ATAAAATATAA
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAACAAGATAAAATATAA
1712 TATTTAAAAT
Statistics
Matches: 119, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
72 8 0.07
73 28 0.24
74 54 0.45
75 29 0.24
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.27
Consensus pattern (74 bp):
TAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAACAAGATAAAATATAAAAAATAATAA
CCTAAAACT
Found at i:6169 original size:19 final size:19
Alignment explanation
Indices: 6145--6184 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6135 GCATGAATAA
* *
6145 AAGACTGAAAACCGAAATT
1 AAGACTAAAAACCAAAATT
*
6164 AAGACTAAAAATCAAAATT
1 AAGACTAAAAACCAAAATT
6183 AA
1 AA
6185 AAAATATATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (19 bp):
AAGACTAAAAACCAAAATT
Found at i:6666 original size:29 final size:26
Alignment explanation
Indices: 6618--6675 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
6608 AATATCATTT
*
6618 TATATTTAATAATATATATATATTATA
1 TATATTTAATAAAATATATAT-TTATA
* *
6645 TATATATTAACTAAAATTTATATTTTTA
1 TATAT-TTAA-TAAAATATATATTTATA
6673 TAT
1 TAT
6676 TTGTTCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 11 0.42
29 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TATATTTAATAAAATATATATTTATA
Found at i:7875 original size:3 final size:3
Alignment explanation
Indices: 7867--7896 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7857 TTTTAAGGCG
7867 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7897 TTTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10740 original size:32 final size:32
Alignment explanation
Indices: 10676--10740 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
10666 CTAGAAATTT
* *
10676 AAAATAATTAAATAATTATTATGTATTTTAAA
1 AAAATAATTAAATAATTATTATATATTATAAA
* *
10708 AAAATTATTAAATGATT-TTATAATATTATAAA
1 AAAATAATTAAATAATTATTAT-ATATTATAAA
10740 A
1 A
10741 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
AAAATAATTAAATAATTATTATATATTATAAA
Found at i:10789 original size:19 final size:19
Alignment explanation
Indices: 10767--10803 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10757 TTAATTTCTA
* *
10767 AAACCATATTATTTATTTG
1 AAACAATATTAATTATTTG
10786 AAACAATATTAATTATTT
1 AAACAATATTAATTATTT
10804 ACTTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (19 bp):
AAACAATATTAATTATTTG
Found at i:10819 original size:23 final size:23
Alignment explanation
Indices: 10774--10819 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10764 CTAAAACCAT
*
10774 ATTATTTATTTGAAACAATATTA
1 ATTATTTATTTGAAACAACATTA
*
10797 ATTATTTACTTT-AAATAACATTA
1 ATTATTTA-TTTGAAACAACATTA
10820 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTATTTATTTGAAACAACATTA
Found at i:11434 original size:2 final size:2
Alignment explanation
Indices: 11427--11479 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
11417 GAATATTGTT
11427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11468 TA T- TA TA TA TA T
1 TA TA TA TA TA TA T
11480 TACGCATACA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11536 original size:19 final size:19
Alignment explanation
Indices: 11489--11527 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11479 TTACGCATAC
11489 ACAAAATTTTATGTTAGAG
1 ACAAAATTTTATGTTAGAG
11508 ACAAAATTTTATGTTAGAG
1 ACAAAATTTTATGTTAGAG
11527 A
1 A
11528 ATGAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (19 bp):
ACAAAATTTTATGTTAGAG
Found at i:12891 original size:43 final size:43
Alignment explanation
Indices: 12830--12912 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
12820 TAACTGTTAA
12830 CCATTTGATAGTGAATATTCAAATATCATTATAGATGGCGAGC
1 CCATTTGATAGTGAATATTCAAATATCATTATAGATGGCGAGC
12873 CCATTTGATAGTGAATATTCAAATATCATTATAGATGGCG
1 CCATTTGATAGTGAATATTCAAATATCATTATAGATGGCG
12913 TGCTCGAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (43 bp):
CCATTTGATAGTGAATATTCAAATATCATTATAGATGGCGAGC
Found at i:13001 original size:2 final size:2
Alignment explanation
Indices: 12994--13032 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12984 CTTAAATACC
*
12994 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13033 GTATGTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13068 original size:6 final size:6
Alignment explanation
Indices: 12996--13078 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
12986 TAAATACCTA
* * * * * * * *
12996 TATATA TATATA TATATA TATATG TATATA TATATA TGTATG TATGTA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * *
13044 TGTATG TACATG TACATG TGTATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
13079 TCATTTATGG
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:13538 original size:2 final size:2
Alignment explanation
Indices: 13531--13573 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
13521 CGGTTTTACC
13531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13572 TA
1 TA
13574 GTAATTACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13956 original size:2 final size:2
Alignment explanation
Indices: 13949--13985 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
13939 AAACGTTATG
13949 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13986 ATAGGATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13971 original size:15 final size:15
Alignment explanation
Indices: 13951--13985 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
13941 ACGTTATGAT
13951 ATATATATATATATA
1 ATATATATATATATA
*
13966 ATATATATATATATT
1 ATATATATATATATA
13981 ATATA
1 ATATA
13986 ATAGGATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:15600 original size:19 final size:21
Alignment explanation
Indices: 15563--15601 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
15553 TTTAAAACTT
*
15563 TTATTATTTTTAATTAGGTCC
1 TTATTATTTTTAATAAGGTCC
15584 TTATT-TTTTT-ATAAGGTC
1 TTATTATTTTTAATAAGGTC
15602 GAGTCGGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (21 bp):
TTATTATTTTTAATAAGGTCC
Found at i:19135 original size:30 final size:30
Alignment explanation
Indices: 19065--19153 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
19055 ATATTTATTA
*
19065 TATTTTAATAATATAATATAATAATAATAT
1 TATTTTAATAATATAATACAATAATAATAT
** * * *
19095 TATTACAATAATATACT-CAATATATATTCT
1 TATTTTAATAATATAATACAATA-ATAATAT
*
19125 TATTTTAATAAATATAATA-AATAGTAATA
1 TATTTTAAT-AATATAATACAATAATAATA
19154 AAAGTATATA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
29 4 0.09
30 29 0.66
31 11 0.25
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (30 bp):
TATTTTAATAATATAATACAATAATAATAT
Found at i:19488 original size:22 final size:20
Alignment explanation
Indices: 19436--19489 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
19426 ATTATTCTAG
*
19436 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
19456 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
19479 TATTTATTATA
1 TATTT-TTATA
19490 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:20645 original size:20 final size:20
Alignment explanation
Indices: 20622--20675 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
20612 AATTAATAAT
20622 ATATTATGTAAAATGTTTCG
1 ATATTATGTAAAATGTTTCG
20642 ATATTATGTAAAATGTTTCG
1 ATATTATGTAAAATGTTTCG
*
20662 ATTATAATGTAAAA
1 A-TATTATGTAAAA
20676 ATTAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.43
Consensus pattern (20 bp):
ATATTATGTAAAATGTTTCG
Found at i:20694 original size:13 final size:13
Alignment explanation
Indices: 20676--20721 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
20666 TAATGTAAAA
20676 ATTAAATAATAAT
1 ATTAAATAATAAT
*
20689 ATTAAAT-ATTAT
1 ATTAAATAATAAT
20701 ATTAAATAA-ATAT
1 ATTAAATAATA-AT
20714 ATTAAATA
1 ATTAAATA
20722 TATTTATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAATAATAAT
Found at i:23721 original size:8 final size:8
Alignment explanation
Indices: 23708--23748 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
23698 CTCATTTTCA
23708 GAGAATTT
1 GAGAATTT
23716 GAGAATTT
1 GAGAATTT
*
23724 -AGAGTTT
1 GAGAATTT
*
23731 GGGAATTT
1 GAGAATTT
23739 GAGAATTT
1 GAGAATTT
23747 GA
1 GA
23749 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:24263 original size:125 final size:126
Alignment explanation
Indices: 23816--24293 Score: 877
Period size: 126 Copynumber: 3.8 Consensus size: 126
23806 CTATAATCGG
23816 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
23881 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
23942 TTAACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
24007 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
24068 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
24133 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAGTACCTATTA-
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
24193 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
24258 TCATTGGCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
24294 ATAACTTAAA
Statistics
Matches: 340, Mismatches: 12, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
125 96 0.28
126 244 0.72
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:24742 original size:33 final size:34
Alignment explanation
Indices: 24681--24780 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
24671 AAATTTAATG
*
24681 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
24715 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
24748 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
24781 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:25386 original size:21 final size:21
Alignment explanation
Indices: 25298--25391 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
25288 TATGGTATAA
*
25298 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
25319 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
25340 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
25361 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
25382 AACCCTGCGG
1 AACCCTGCGG
25392 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:25421 original size:21 final size:21
Alignment explanation
Indices: 25395--25442 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
25385 CCTGCGGAGA
*
25395 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
25416 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
25437 GGGCAT
1 TGGCAT
25443 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:27208 original size:34 final size:32
Alignment explanation
Indices: 27163--27251 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
27153 TTAATAATTC
27163 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTATATAAATA-TA--TTAATA
* * *
27199 -ATAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTATATAAATATATTAATA
* *
27230 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
27252 AAATACTAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.14
32 16 0.36
33 2 0.05
34 18 0.41
35 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATTAATA
Found at i:27232 original size:14 final size:15
Alignment explanation
Indices: 27166--27238 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
27156 ATAATTCTAA
27166 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
27181 ATAAATATTATTTTAAT
1 ATAAATA--ATATTAAT
* *
27198 AATAAAATAATATTTAC
1 -AT-AAATAATATTAAT
27215 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
*
27229 ATAAAAAATA
1 ATAAATAATA
27239 ATAACTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 11 0.24
15 14 0.31
16 4 0.09
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:29664 original size:18 final size:19
Alignment explanation
Indices: 29641--29692 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
29631 TATTTAAACT
29641 TAAATAAAAAAATTAA-AA
1 TAAATAAAAAAATTAATAA
**
29659 TAAATATAAAATTTTAATAA
1 TAAATA-AAAAAATTAATAA
* *
29679 TATATAAAATAATT
1 TAAATAAAAAAATT
29693 TATATGATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 6 0.23
19 13 0.50
20 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAAAAAAATTAATAA
Found at i:29671 original size:17 final size:18
Alignment explanation
Indices: 29649--29739 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 18
29639 CTTAAATAAA
29649 AAAATTAAAATAA-ATAT
1 AAAATTAAAATAATATAT
**
29666 AAAATTTTAATAATATAT
1 AAAATTAAAATAATATAT
**
29684 AAAA-TAATTTATATGATAT
1 AAAATTAAAATA-AT-ATAT
*
29703 AAAATTAAATATCTATAATAT
1 AAAATTAAA-AT-AAT-ATAT
*
29724 AATATTAAAAATAATA
1 AAAATT-AAAATAATA
29740 ATATTTAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
17 14 0.25
18 10 0.18
19 9 0.16
20 5 0.09
21 14 0.25
22 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
AAAATTAAAATAATATAT
Found at i:29748 original size:27 final size:24
Alignment explanation
Indices: 29718--29768 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
29708 TAAATATCTA
29718 TAATATAATATTAAAAATAATAATATT
1 TAAT-TAAT-TTAAAAA-AATAATATT
* *
29745 TAATTTATTTAAAAAATTAATATT
1 TAATTAATTTAAAAAAATAATATT
29769 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 3 0.14
27 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATTAATTTAAAAAAATAATATT
Found at i:38239 original size:2 final size:2
Alignment explanation
Indices: 38232--38284 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
38222 ATCATATCTG
38232 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
38274 AT AT AT AT AT A
1 AT AT AT AT AT A
38285 AACAAATACG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38821 original size:3 final size:3
Alignment explanation
Indices: 38813--38856 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
38803 TCATTATTTA
*
38813 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TA- TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
38857 TTACAGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41461 original size:15 final size:15
Alignment explanation
Indices: 41443--41477 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41433 CGAGGGTATT
*
41443 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGAAC
41458 GTAGTCCTTCGGAAC
1 GTAGTCCTTCGGAAC
41473 GTAGT
1 GTAGT
41478 GGTCCTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGAAC
Found at i:43849 original size:2 final size:2
Alignment explanation
Indices: 43842--43899 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
43832 GTTGACTTGA
43842 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
43884 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
43900 TTCATAATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44724 original size:60 final size:60
Alignment explanation
Indices: 44609--44727 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
44599 TTGACCTGAG
* *
44609 CTTGAAAAACTTGAACTCGAAACATTCTCAAACTAAATTCGATTGAAACTCAAACTCGAA
1 CTTGAAAAACTTGAACTCGAAACATTCTCAAACTAAACTCGATTGAAACTAAAACTCGAA
* **
44669 CTTGAAAAAAC-TGAACTCGAAACATTCTCAAACTTAACTCGATTGAAGTTAAAACTCGA
1 CTTG-AAAAACTTGAACTCGAAACATTCTCAAACTAAACTCGATTGAAACTAAAACTCGA
44728 GTAACTCACA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 47 0.89
61 6 0.11
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (60 bp):
CTTGAAAAACTTGAACTCGAAACATTCTCAAACTAAACTCGATTGAAACTAAAACTCGAA
Found at i:46155 original size:18 final size:18
Alignment explanation
Indices: 46132--46173 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
46122 CTAAGTATAC
46132 GCTCCTCCAAAGGATCCT
1 GCTCCTCCAAAGGATCCT
46150 GCTCCTCCAAAGGATCCT
1 GCTCCTCCAAAGGATCCT
46168 GCTCCT
1 GCTCCT
46174 AACCTGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.24
Consensus pattern (18 bp):
GCTCCTCCAAAGGATCCT
Found at i:51991 original size:18 final size:17
Alignment explanation
Indices: 51954--51989 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
51944 AAGTTATTTT
51954 AATTTTAGATAGATTAA
1 AATTTTAGATAGATTAA
51971 AATTATTAGAT-GATTAA
1 AATT-TTAGATAGATTAA
51988 AA
1 AA
51990 ATAGACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
AATTTTAGATAGATTAA
Found at i:52377 original size:2 final size:2
Alignment explanation
Indices: 52370--52396 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52360 ATCTGAAGGC
52370 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
52397 GCGGATCTTG
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:54061 original size:2 final size:2
Alignment explanation
Indices: 54054--54079 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54044 TGATAAGAAT
54054 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
54080 ATAATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54692 original size:21 final size:21
Alignment explanation
Indices: 54667--54712 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
54657 ATCGCGTTAT
* *
54667 GATGGCACATCAACCATTTTA
1 GATGGCACAACAACCATTTCA
54688 GATGGCACAACAACCATTTCA
1 GATGGCACAACAACCATTTCA
54709 GATG
1 GATG
54713 CCATCGAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
GATGGCACAACAACCATTTCA
Found at i:64167 original size:14 final size:14
Alignment explanation
Indices: 64150--64176 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
64140 ATGTATTTTT
64150 AATATAATTTTAAC
1 AATATAATTTTAAC
64164 AATATAATTTTAA
1 AATATAATTTTAA
64177 AAAATCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAATTTTAAC
Found at i:64879 original size:29 final size:28
Alignment explanation
Indices: 64847--64910 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
64837 TTAGGATTTT
* * *
64847 AAATTAAGAGGTACGAATTTAAATTTATA
1 AAATTAAG-GATACAAATTTAAACTTATA
*
64876 AAATTTTAGGATACAAATTTAAACTTATA
1 AAA-TTAAGGATACAAATTTAAACTTATA
64905 AAATTA
1 AAATTA
64911 TAAGATGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.07
29 23 0.79
30 4 0.14
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (28 bp):
AAATTAAGGATACAAATTTAAACTTATA
Found at i:65380 original size:21 final size:21
Alignment explanation
Indices: 65355--65416 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
65345 CGGAATTGTT
65355 AAAAAATATTAATACTTTAAG
1 AAAAAATATTAATACTTTAAG
* *
65376 TAAAAATATTAATACTTTAGG
1 AAAAAATATTAATACTTTAAG
* *
65397 AAAAAATAATAATATTTTAA
1 AAAAAATATTAATACTTTAA
65417 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAAATATTAATACTTTAAG
Found at i:65681 original size:17 final size:18
Alignment explanation
Indices: 65648--65681 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65638 CCGCTACTAG
65648 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
65666 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
65682 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:67024 original size:57 final size:57
Alignment explanation
Indices: 66962--67077 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
66952 GCCAATTAAA
*
66962 ATTAATTAATAATAAGTTTACTTAATTAATCTAACATACAATTTAACAATTTATTTT
1 ATTAATTAATAACAAGTTTACTTAATTAATCTAACATACAATTTAACAATTTATTTT
* *
67019 ATTAATTAATAACAAGTTTAGTTAATTAATCTAACATATAATTTAACAATTTATTTT
1 ATTAATTAATAACAAGTTTACTTAATTAATCTAACATACAATTTAACAATTTATTTT
67076 AT
1 AT
67078 GTTTATATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (57 bp):
ATTAATTAATAACAAGTTTACTTAATTAATCTAACATACAATTTAACAATTTATTTT
Found at i:69958 original size:2 final size:2
Alignment explanation
Indices: 69951--70029 Score: 115
Period size: 2 Copynumber: 40.0 Consensus size: 2
69941 CTACTGCCTC
* *
69951 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
69993 CT CT CT CT CT CT CT CT CT AT CT CT CT CC CT C- CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
70030 ATTTCTTCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.01, C:0.53, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:71042 original size:12 final size:12
Alignment explanation
Indices: 71027--71071 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
71017 TGATGGAAGT
71027 GATGATGATTTC
1 GATGATGATTTC
71039 GATGATGAATTT-
1 GATGATG-ATTTC
* *
71051 GATGACGAGTTC
1 GATGATGATTTC
71063 GATGATGAT
1 GATGATGAT
71072 GAAGAAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 3 0.11
12 20 0.74
13 4 0.15
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (12 bp):
GATGATGATTTC
Found at i:71042 original size:24 final size:24
Alignment explanation
Indices: 71015--71096 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 24
71005 CTTGCCTGAG
71015 GATGATGGAAGTGATGATGATTTC
1 GATGATGGAAGTGATGATGATTTC
* * *
71039 GATGAT-GAATTTGATGACGAGTTC
1 GATGATGGAA-GTGATGATGATTTC
*
71063 GATGATGATGAAGAAGATGATGAGTTT-
1 GATGATG--GAAG-TGATGATGA-TTTC
71090 GATGATG
1 GATGATG
71097 AGGAACTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
23 3 0.07
24 23 0.51
27 17 0.38
28 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.33, T:0.32
Consensus pattern (24 bp):
GATGATGGAAGTGATGATGATTTC
Found at i:71093 original size:12 final size:12
Alignment explanation
Indices: 71026--71098 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
71016 ATGATGGAAG
71026 TGATGATGA-TT
1 TGATGATGAGTT
*
71037 TCGATGATGAATT
1 T-GATGATGAGTT
*
71050 TGATGACGAGTT
1 TGATGATGAGTT
*
71062 CGATGATGATGAAG-A
1 ---TGATGATG-AGTT
*
71077 AGATGATGAGTT
1 TGATGATGAGTT
71089 TGATGATGAG
1 TGATGATGAG
71099 GAACTTGGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.06
12 33 0.69
13 3 0.06
15 7 0.15
16 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (12 bp):
TGATGATGAGTT
Found at i:82611 original size:24 final size:24
Alignment explanation
Indices: 82584--82646 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
82574 CACCATAGCT
* *
82584 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTACCA
*
82608 CGTAGAATTTGCACCGAAGTACCA
1 CGTAGAAATTGCACCGAAGTACCA
82632 CGTAGAAA-TGCACCG
1 CGTAGAAATTGCACCG
82647 TAGTTCCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 7 0.20
24 28 0.80
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTACCA
Done.