Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008758.1 Hibiscus syriacus cultivar Beakdansim tig00111850_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: 120474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1377 original size:12 final size:11
Alignment explanation
Indices: 1346--1385 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1336 TAAATACATA
1346 ATATATTTAAT
1 ATATATTTAAT
*
1357 ATTTATTTAAT
1 ATATATTTAAT
1368 ATAATATTTAAT
1 AT-ATATTTAAT
1380 AT-TATT
1 ATATATT
1386 AGTTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 4 0.15
11 12 0.46
12 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:1433 original size:23 final size:23
Alignment explanation
Indices: 1394--1452 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1384 TTAGTTATAA
1394 ATTTTACAT--TATAATCGAAAC
1 ATTTTACATAATATAATCGAAAC
1415 ATTTTACATAATATAATCGAAAC
1 ATTTTACATAATATAATCGAAAC
1438 ATTTTACATAATATA
1 ATTTTACATAATATA
1453 TTATTAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.25
23 27 0.75
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (23 bp):
ATTTTACATAATATAATCGAAAC
Found at i:2546 original size:20 final size:19
Alignment explanation
Indices: 2518--2577 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 19
2508 TTTGTTAGTA
*
2518 TTTTATTAATTATGTATTAT
1 TTTTTTTAATTAT-TATTAT
2538 TTTTTTT-A--ATTATTAT
1 TTTTTTTAATTATTATTAT
*
2554 TTTATTTAATTATT-TTAT
1 TTTTTTTAATTATTATTAT
2572 TTTTTT
1 TTTTTT
2578 GCAGTTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 12 0.35
17 3 0.09
18 9 0.26
19 4 0.12
20 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTTTAATTATTATTAT
Found at i:2845 original size:15 final size:15
Alignment explanation
Indices: 2838--2866 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2828 AAAAATAATT
2838 AAATAAAATAATAAG
1 AAATAAAATAATAAG
2853 AAATAAAATAATAA
1 AAATAAAATAATAA
2867 AATAATTAAT
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:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAATAATAAG
Found at i:26286 original size:2 final size:2
Alignment explanation
Indices: 26279--26315 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
26269 TTTACAATAG
26279 AT AT AT AT AT AT AT AT AT A- AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26316 AAAAATTTAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:26768 original size:20 final size:22
Alignment explanation
Indices: 26743--26782 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
26733 AAAAATTATC
26743 TAAAACATT-AT-TTTTTTACT
1 TAAAACATTAATGTTTTTTACT
26763 TAAAACATTAATGTTTTTTA
1 TAAAACATTAATGTTTTTTA
26783 ATATTTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (22 bp):
TAAAACATTAATGTTTTTTACT
Found at i:27792 original size:21 final size:21
Alignment explanation
Indices: 27766--27821 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
27756 TAACTGTTAA
27766 GGTGCTGATGTAGTATTTCAT
1 GGTGCTGATGTAGTATTTCAT
27787 GGTGCTGATGTAGTATTTCAT
1 GGTGCTGATGTAGTATTTCAT
*
27808 AGTGCTGATGTAGT
1 GGTGCTGATGTAGT
27822 TGATGATGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (21 bp):
GGTGCTGATGTAGTATTTCAT
Found at i:27974 original size:24 final size:27
Alignment explanation
Indices: 27937--28001 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 27
27927 TATTTATAAT
* * *
27937 TTAAAATACAAAAAAATTTAAA-TAAA
1 TTAAATTACTAAAAAATATAAATTAAA
27963 TTAAA-TA-T-AAAAATATAAATTAAA
1 TTAAATTACTAAAAAATATAAATTAAA
27987 TTAAATTACTAAAAA
1 TTAAATTACTAAAAA
28002 CTAAAAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 10 0.30
24 9 0.27
25 4 0.12
26 6 0.18
27 4 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (27 bp):
TTAAATTACTAAAAAATATAAATTAAA
Found at i:28235 original size:24 final size:24
Alignment explanation
Indices: 28202--28249 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
28192 AAGTCAATTG
28202 ATATATATTTATAATAAATTTTATTT
1 ATATAT-TTTA-AATAAATTTTATTT
*
28228 ATATATTTTAAATATATTTTAT
1 ATATATTTTAAATAAATTTTAT
28250 GTTAGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATATTTTAAATAAATTTTATTT
Found at i:28237 original size:13 final size:12
Alignment explanation
Indices: 28202--28249 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
28192 AAGTCAATTG
28202 ATATATATTTATA
1 ATATAT-TTTATA
* *
28215 ATAAATTTTATTT
1 ATATATTTTA-TA
28228 ATATATTTTA-A
1 ATATATTTTATA
28239 ATATATTTTAT
1 ATATATTTTAT
28250 GTTAGATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 10 0.34
12 4 0.14
13 15 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTTTATA
Found at i:29397 original size:24 final size:24
Alignment explanation
Indices: 29356--29401 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
29346 TCAATATTTG
*
29356 AAATTTAATTTAATTATAACATAA
1 AAATTTAATTGAATTATAACATAA
29380 AAATTTAATTCGAA-TATAACAT
1 AAATTTAATT-GAATTATAACAT
29402 TAAATATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATTTAATTGAATTATAACATAA
Found at i:29415 original size:32 final size:31
Alignment explanation
Indices: 29379--29440 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
29369 TTATAACATA
* *
29379 AAAATTTAATTCGAATATAACATTAAATATCT
1 AAAATGTAATTCAAATATAAC-TTAAATATCT
* *
29411 AAAATGTATTTCAAATATAACTTTAATATC
1 AAAATGTAATTCAAATATAACTTAAATATC
29441 GATGAAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAATGTAATTCAAATATAACTTAAATATCT
Found at i:43822 original size:19 final size:19
Alignment explanation
Indices: 43798--43841 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
43788 TAGAGCACTA
43798 TAAAATCTAAAATTACTTC
1 TAAAATCTAAAATTACTTC
43817 TAAAATCTAAAATTACTTC
1 TAAAATCTAAAATTACTTC
43836 TAAAAT
1 TAAAAT
43842 ATGAACTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATCTAAAATTACTTC
Found at i:48160 original size:3 final size:3
Alignment explanation
Indices: 48152--48180 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48142 ACACAGTCAT
48152 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
48181 TGGCGGGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:49063 original size:116 final size:115
Alignment explanation
Indices: 48853--49074 Score: 297
Period size: 116 Copynumber: 1.9 Consensus size: 115
48843 ATATAGACAT
* *
48853 GAATAAAAAAGCTCATGTATATACATTTAAGTATCTATTACCACACCTCGCCTCACCGAGCATCC
1 GAATAAAAAAGCTCATGTATATACATATAAGTATCTATGACCACACCTCGCCTCACCGAGCATCC
* * *
48918 CAATAAGTAGGCTTGAAACAAGTTATCTAAATCAACACCAAAACACTCAC
66 CAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACACTCAC
* * *
48968 GAATACAAAAA-CTCAATGTATATACATATAAGTTTCTA-GAGCCACACCTCGCCTCGCCTG-GT
1 GAATA-AAAAAGCTC-ATGTATATACATATAAGTATCTATGA-CCACACCTCGCCTCACC-GAGC
* *
49030 GTCCCAACAAGTAGGCTCGAAACAAATTCTCTAAATCAACACCAA
62 ATCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAA
49075 GACTCTCAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
115 9 0.10
116 83 0.89
117 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.23
Consensus pattern (115 bp):
GAATAAAAAAGCTCATGTATATACATATAAGTATCTATGACCACACCTCGCCTCACCGAGCATCC
CAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACACTCAC
Found at i:54624 original size:46 final size:46
Alignment explanation
Indices: 54510--54645 Score: 229
Period size: 45 Copynumber: 3.0 Consensus size: 46
54500 CTAAGAAACA
*
54510 GGCAATTGTTATCCTTCTTTTATAAACCTTATTTTGAAATAAAAAT
1 GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
*
54556 -GCAATTTTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
1 GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
* *
54601 GGCAATTGTTATTCTTCTCATATAAACCTTATTTTGAAATAAAAA
1 GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAA
54646 AGAAGCCAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
45 43 0.51
46 41 0.49
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (46 bp):
GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
Found at i:59075 original size:48 final size:50
Alignment explanation
Indices: 59004--59101 Score: 164
Period size: 48 Copynumber: 2.0 Consensus size: 50
58994 TCATGACCAG
*
59004 TTGAAGTTGGACACAGTTAATGCTCCATAAT-AA-AAGAAAAGAGTGAAT
1 TTGAAGTTGGACACAGTTAATGCTCCATAATAAAGAAGAAAAGAGCGAAT
*
59052 TTGAAGTTGGACACTGTTAATGCTCCATAATAAAGAAGAAAAGAGCGAAT
1 TTGAAGTTGGACACAGTTAATGCTCCATAATAAAGAAGAAAAGAGCGAAT
59102 CAGCTAGCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 30 0.65
49 2 0.04
50 14 0.30
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.24
Consensus pattern (50 bp):
TTGAAGTTGGACACAGTTAATGCTCCATAATAAAGAAGAAAAGAGCGAAT
Found at i:61191 original size:21 final size:21
Alignment explanation
Indices: 61165--61204 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61155 ATATCAAACA
61165 ACCACCAAAATTGAATTCACG
1 ACCACCAAAATTGAATTCACG
* *
61186 ACCACCAGATTTGAATTCA
1 ACCACCAAAATTGAATTCA
61205 TCGTGTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (21 bp):
ACCACCAAAATTGAATTCACG
Found at i:69811 original size:36 final size:36
Alignment explanation
Indices: 69770--69838 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
69760 CTCGAGTTCG
69770 TATTCTAATAAAAAATAATATTCTTTTTTCGGATCA
1 TATTCTAATAAAAAATAATATTCTTTTTTCGGATCA
69806 TATTCTAATAAAAAATAATATTCTTTTTTCGGA
1 TATTCTAATAAAAAATAATATTCTTTTTTCGGA
69839 ATAAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (36 bp):
TATTCTAATAAAAAATAATATTCTTTTTTCGGATCA
Found at i:74927 original size:6 final size:6
Alignment explanation
Indices: 74916--74943 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
74906 AATGAAAATA
74916 TGCCAT TGCCAT TGCCAT TGCCAT TGCC
1 TGCCAT TGCCAT TGCCAT TGCCAT TGCC
74944 TTTGTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.18, T:0.32
Consensus pattern (6 bp):
TGCCAT
Found at i:75413 original size:57 final size:59
Alignment explanation
Indices: 75323--75435 Score: 176
Period size: 57 Copynumber: 1.9 Consensus size: 59
75313 GAGGGAGGAA
*
75323 AATATAAAAATGACAGAGAAAAGAAAGAATTGCTGGA-ACTTTTTAAAACATAACTGAAT
1 AATATAAAAATGACA-AGAAAAGAAAGAATTGCTGGATACTTTTTAAAACAGAACTGAAT
**
75382 AATATAAAAATGAC-AGAAAAGAAAGAATTGCTGGATTTTTTTTAAAACAGAACT
1 AATATAAAAATGACAAGAAAAGAAAGAATTGCTGGATACTTTTTAAAACAGAACT
75436 AAATCTCAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 21 0.42
58 15 0.30
59 14 0.28
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (59 bp):
AATATAAAAATGACAAGAAAAGAAAGAATTGCTGGATACTTTTTAAAACAGAACTGAAT
Found at i:86756 original size:36 final size:36
Alignment explanation
Indices: 86714--86786 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
86704 CATAATATTT
* *
86714 TTATTATATATTATAATTTAAAATATAAAGTAAAAA
1 TTATTATATAATATAATTTAAAATATAAAATAAAAA
*
86750 TTATTATATAATATAATTTATAATATAAAATAAAAA
1 TTATTATATAATATAATTTAAAATATAAAATAAAAA
86786 T
1 T
86787 AGAAGGTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
TTATTATATAATATAATTTAAAATATAAAATAAAAA
Found at i:93959 original size:14 final size:14
Alignment explanation
Indices: 93942--93973 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
93932 TTATTTTAAA
93942 AAAATTGAAATATT
1 AAAATTGAAATATT
93956 AAAATTGAAATATT
1 AAAATTGAAATATT
93970 AAAA
1 AAAA
93974 AATATAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (14 bp):
AAAATTGAAATATT
Found at i:99160 original size:24 final size:24
Alignment explanation
Indices: 99128--99183 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
99118 CTATTCTTTC
99128 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
99152 GCTTCAATTGAGCTTAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
99176 GCTTCAAT
1 GCTTCAAT
99184 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:99440 original size:11 final size:11
Alignment explanation
Indices: 99416--99471 Score: 52
Period size: 9 Copynumber: 5.5 Consensus size: 11
99406 ACGGTTCAAA
99416 CCGGTTTT--G
1 CCGGTTTTCAG
99425 CCGGTTTTCAG
1 CCGGTTTTCAG
*
99436 CCGG--TTCAC
1 CCGGTTTTCAG
99445 CTCGGTTTTC--
1 C-CGGTTTTCAG
99455 CCGGTTTTCAG
1 CCGGTTTTCAG
99466 CCGGTT
1 CCGGTT
99472 CTTCCGATTC
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 21 0.54
10 4 0.10
11 11 0.28
12 3 0.08
ACGTcount: A:0.05, C:0.30, G:0.27, T:0.38
Consensus pattern (11 bp):
CCGGTTTTCAG
Found at i:99443 original size:30 final size:30
Alignment explanation
Indices: 99407--99472 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
99397 AGTGAACCGA
*
99407 CGGTTCAAAC-CGGTTTTGCCGGTTTTCAGC
1 CGGTTC-AACTCGGTTTTCCCGGTTTTCAGC
*
99437 CGGTTCACCTCGGTTTTCCCGGTTTTCAGC
1 CGGTTCAACTCGGTTTTCCCGGTTTTCAGC
99467 CGGTTC
1 CGGTTC
99473 TTCCGATTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.09, C:0.30, G:0.26, T:0.35
Consensus pattern (30 bp):
CGGTTCAACTCGGTTTTCCCGGTTTTCAGC
Found at i:101474 original size:17 final size:17
Alignment explanation
Indices: 101452--101492 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
101442 CATAGCGGCG
* *
101452 CTAGCTCTCTCATACGC
1 CTAGCTCTCTCAGACCC
101469 CTAGCTCTCTCAGACCC
1 CTAGCTCTCTCAGACCC
101486 CTAGCTC
1 CTAGCTC
101493 GCTACTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.44, G:0.12, T:0.27
Consensus pattern (17 bp):
CTAGCTCTCTCAGACCC
Found at i:102779 original size:85 final size:85
Alignment explanation
Indices: 102636--102807 Score: 317
Period size: 85 Copynumber: 2.0 Consensus size: 85
102626 TGATGAATTT
*
102636 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAGATCATCGTATGAGTGCTCT
1 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
102701 ATCCTCATCCAATCGACTCA
66 ATCCTCATCCAATCGACTCA
*
102721 ATAAGAAGTTTTTCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
1 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
*
102786 GTCCTCATCCAATCGACTCA
66 ATCCTCATCCAATCGACTCA
102806 AT
1 AT
102808 TCGATTTATG
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (85 bp):
ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
ATCCTCATCCAATCGACTCA
Found at i:103627 original size:17 final size:18
Alignment explanation
Indices: 103592--103628 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
103582 TGAGTATTCC
103592 TTATAATTTGAGAGTATA
1 TTATAATTTGAGAGTATA
103610 TTATAATATT-AG-GTATA
1 TTATAAT-TTGAGAGTATA
103627 TT
1 TT
103629 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 9 0.50
19 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
TTATAATTTGAGAGTATA
Found at i:108385 original size:11 final size:11
Alignment explanation
Indices: 108369--108410 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
108359 TTTAATTGAA
108369 TTATTTATATT
1 TTATTTATATT
*
108380 TTATTTTTATT
1 TTATTTATATT
*
108391 TTATCTTAT-TA
1 TTAT-TTATATT
108402 TTATTTATA
1 TTATTTATA
108411 AATAGTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 19 0.73
12 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTATATT
Found at i:108405 original size:16 final size:17
Alignment explanation
Indices: 108368--108410 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
108358 TTTTAATTGA
*
108368 ATTATTTATATTTTATT
1 ATTATTTATATCTTATT
*
108385 TTTATTT-TATCTTATT
1 ATTATTTATATCTTATT
108401 ATTATTTATA
1 ATTATTTATA
108411 AATAGTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTATTTATATCTTATT
Found at i:108471 original size:15 final size:15
Alignment explanation
Indices: 108451--108479 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
108441 TTTATTATTA
108451 ATATTTAATGATTTT
1 ATATTTAATGATTTT
108466 ATATTTAATGATTT
1 ATATTTAATGATTT
108480 AGTAATGACA
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:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
ATATTTAATGATTTT
Found at i:108494 original size:16 final size:16
Alignment explanation
Indices: 108473--108503 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
108463 TTTATATTTA
108473 ATGATTTAGTAATGAC
1 ATGATTTAGTAATGAC
108489 ATGATTTAGTAATGA
1 ATGATTTAGTAATGA
108504 TTACTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (16 bp):
ATGATTTAGTAATGAC
Found at i:108516 original size:24 final size:23
Alignment explanation
Indices: 108471--108566 Score: 72
Period size: 24 Copynumber: 4.0 Consensus size: 23
108461 ATTTTATATT
*
108471 TAATGATTTAGTAATGACATGATTTA
1 TAATGA-TTAATAAT-A-ATGATTTA
*
108497 GTAATGATTACTAATAATGA--T-
1 -TAATGATTAATAATAATGATTTA
* *
108518 TAATTATTAATATTTAATGATTTAA
1 TAATGATTAATA-ATAATGATTT-A
*
108543 TAATGATTATTAATAATGATTTA
1 TAATGATTAATAATAATGATTTA
108566 T
1 T
108567 TATTAATATT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
20 10 0.18
21 6 0.11
22 1 0.02
23 3 0.05
24 13 0.23
25 11 0.19
26 7 0.12
27 6 0.11
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (23 bp):
TAATGATTAATAATAATGATTTA
Found at i:108537 original size:21 final size:21
Alignment explanation
Indices: 108511--108584 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
108501 TGATTACTAA
108511 TAATGATTAATTATTAATATT
1 TAATGATTAATTATTAATATT
* * *
108532 TAATGATTTAATAATGATTATT
1 TAATGA-TTAATTATTAATATT
*
108554 AATAATGATTTATTATTAATATT
1 --TAATGATTAATTATTAATATT
108577 TAATGATT
1 TAATGATT
108585 TGATACTAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 14 0.33
22 12 0.28
23 11 0.26
24 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TAATGATTAATTATTAATATT
Found at i:108541 original size:45 final size:45
Alignment explanation
Indices: 108489--108658 Score: 168
Period size: 45 Copynumber: 3.7 Consensus size: 45
108479 TAGTAATGAC
*
108489 ATGATTTAGTAATGATTACTAATAATGATTAATTATTAATATTTA
1 ATGATTTAATAATGATTACTAATAATGATTAATTATTAATATTTA
* *
108534 ATGATTTAATAATGATTATTAATAATGATTTATTATTAATATTTA
1 ATGATTTAATAATGATTACTAATAATGATTAATTATTAATATTTA
* * * *
108579 ATGATTTGATACTAATGATT--TAGTAATGATTAGTAATAATAAAATTATA
1 ATGATTT-A-A-TAATGATTACTAATAATGATTA--ATTATTAATATT-TA
*
108628 ATAATTACTAATAATGATT--TAATAATGATTA
1 ATGATT--TAATAATGATTACTAATAATGATTA
108659 CTAATAATTA
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
45 49 0.46
46 11 0.10
47 1 0.01
48 36 0.34
49 8 0.07
50 1 0.01
51 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (45 bp):
ATGATTTAATAATGATTACTAATAATGATTAATTATTAATATTTA
Found at i:108594 original size:21 final size:20
Alignment explanation
Indices: 108511--108600 Score: 63
Period size: 21 Copynumber: 4.1 Consensus size: 20
108501 TGATTACTAA
* *
108511 TAATGATTAATTATTAATATT
1 TAATGATTTA-TAATAATATT
*
108532 TAATGATTTAATAATGATTATT
1 TAATGATTT-ATAAT-AATATT
*
108554 AATAATGATTTATTATTAATATT
1 --TAATGATTTA-TAATAATATT
*
108577 TAATGATTTGATACTAATGATT
1 TAATGATTT-ATAATAAT-ATT
108599 TA
1 TA
108601 GTAATGATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
21 26 0.46
22 12 0.21
23 6 0.11
24 12 0.21
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (20 bp):
TAATGATTTATAATAATATT
Found at i:108606 original size:59 final size:60
Alignment explanation
Indices: 108440--108618 Score: 204
Period size: 59 Copynumber: 3.0 Consensus size: 60
108430 TTTACATTGA
* * *
108440 ATTTATTATTAATATTTAATGATTTTATATTTAATGATTTAGTAATGACATGATTTAGTAATG
1 ATTTATTATTAATATTTAATGATTTAATATTTAATGATTTAGTAATG--ATTA-TTAATAATG
* * * *
108503 A-TTACTAATAATGA-TTAATTA-TTAATATTTAATGATTTAATAATGATTATTAATAATG
1 ATTTATTATTAAT-ATTTAATGATTTAATATTTAATGATTTAGTAATGATTATTAATAATG
* * *
108561 ATTTATTATTAATATTTAATGATTTGATA-CTAATGATTTAGTAATGATTAGTAATAAT
1 ATTTATTATTAATATTTAATGATTTAATATTTAATGATTTAGTAATGATTATTAATAAT
108619 AAAATTATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
58 10 0.10
59 44 0.45
60 5 0.05
61 22 0.22
62 15 0.15
63 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (60 bp):
ATTTATTATTAATATTTAATGATTTAATATTTAATGATTTAGTAATGATTATTAATAATG
Found at i:108629 original size:24 final size:24
Alignment explanation
Indices: 108602--108682 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
108592 AATGATTTAG
*
108602 TAATGATTAGTAATAATAAAATT-A
1 TAATGATTACTAATAAT-AAATTAA
* * *
108626 TAATAATTACTAATAATGATTTAA
1 TAATGATTACTAATAATAAATTAA
* *
108650 TAATGATTACTAATAATTATTTAA
1 TAATGATTACTAATAATAAATTAA
108674 TAATGATTA
1 TAATGATTA
108683 AATATTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 3 0.06
24 47 0.94
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.42
Consensus pattern (24 bp):
TAATGATTACTAATAATAAATTAA
Found at i:108675 original size:45 final size:45
Alignment explanation
Indices: 108499--108686 Score: 136
Period size: 48 Copynumber: 4.0 Consensus size: 45
108489 ATGATTTAGT
* *
108499 AATGATTACTAATAATGA-TTAATTATTAATATTTAATGATTTAAT
1 AATGATTA-TAATAATGATTTAATAATTAATATATAATGATTTAAT
* *
108544 AATGATTATTAATAATGATTT-ATTATTAATATTTAATGATTTGATACT
1 AATGATTA-TAATAATGATTTAATAATTAATATATAATGATTT-A-A-T
* * *
108592 AATGATT-TAGTAATGATTAGTAATAA-TAAAATTATAATAATTACTAAT
1 AATGATTATAATAATGATT--TAATAATTAATA-TATAATGATT--TAAT
* *
108640 AATGATT-TAATAATGATTACTAATAATT-ATTTAATAATGATTAAAT
1 AATGATTATAATAATGATT--TAATAATTAATAT-ATAATGATTTAAT
108686 A
1 A
108687 TTTAAATAGA
Statistics
Matches: 119, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
45 38 0.32
46 17 0.14
47 2 0.02
48 47 0.39
49 13 0.11
50 1 0.01
51 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (45 bp):
AATGATTATAATAATGATTTAATAATTAATATATAATGATTTAAT
Found at i:108711 original size:20 final size:20
Alignment explanation
Indices: 108686--108727 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
108676 ATGATTAAAT
108686 ATTTAAATAGAATTTATTCA
1 ATTTAAATAGAATTTATTCA
*
108706 ATTTAAATCGAATTTATTCA
1 ATTTAAATAGAATTTATTCA
108726 AT
1 AT
108728 ATAACTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTAAATAGAATTTATTCA
Found at i:108758 original size:22 final size:23
Alignment explanation
Indices: 108713--108772 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
108703 TCAATTTAAA
* *
108713 TCGAATTTATTCA-ATATAACTAG
1 TCGAATTTATT-ATTTATAAATAG
108736 TCGAATTTA-TATTTATAAATAG
1 TCGAATTTATTATTTATAAATAG
108758 TCGAATTTATTATTT
1 TCGAATTTATTATTT
108773 TTACATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 18 0.55
23 14 0.42
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (23 bp):
TCGAATTTATTATTTATAAATAG
Found at i:112529 original size:75 final size:76
Alignment explanation
Indices: 112424--112634 Score: 259
Period size: 75 Copynumber: 2.8 Consensus size: 76
112414 GACCGTTGAA
*
112424 CAGGGGGGAATCGGTACC-CCT-TGGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTC
1 CAGGGGGGAATCGGTTCCTCCTAT---GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTC
**
112487 GGAACAAAAATGTT
63 GGAACAAAAACATT
* * * *
112501 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGTATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
* * *
112565 GCCAAACCATT
66 ACAAAAACATT
*
112576 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
112635 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
75 66 0.57
76 29 0.25
77 16 0.14
78 3 0.03
79 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
ACAAAAACATT
Done.