Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007044.1 Hibiscus syriacus cultivar Beakdansim tig00018262_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: 77038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5185 original size:3 final size:3
Alignment explanation
Indices: 5177--5205 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5167 ACACAGTCAT
5177 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
5206 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:6088 original size:116 final size:115
Alignment explanation
Indices: 5875--6113 Score: 320
Period size: 116 Copynumber: 2.1 Consensus size: 115
5865 TATATATAGA
* **
5875 CATGAATAAAAAAGCTCATGTATATACATTTAAGTATCTATTGCCACACCTCGCCTCACCGAGCA
1 CATGAATAAAAAAGCTCATGTATATACATATAAGTATCTAGAGCCACACCTCGCCTCACCGAGCA
* * *
5940 TCCCAATAAGTAGGCTTGAAACAAGTTATCTAAATCAACACCAAAACTCT
66 TCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACTCT
* *
5990 CATGAATACAAAAA-CTCAATGTATATACATATAAGTTTCTAGAGCCACACCTCGCCTCGCCTG-
1 CATGAATA-AAAAAGCTC-ATGTATATACATATAAGTATCTAGAGCCACACCTCGCCTCACC-GA
** * *
6053 GTGTCCCAACAAGTAGGCTCGAAACAAATTCTCTAAATCAACACCAAGACTCT
63 GCATCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACTCT
6106 CAATGAAT
1 C-ATGAAT
6114 TCAGTTTCAC
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
115 11 0.10
116 90 0.83
117 7 0.06
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (115 bp):
CATGAATAAAAAAGCTCATGTATATACATATAAGTATCTAGAGCCACACCTCGCCTCACCGAGCA
TCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACTCT
Found at i:8839 original size:19 final size:19
Alignment explanation
Indices: 8811--8852 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
8801 TGAATGATTA
* *
8811 AATACGTAGTATACCCTTC
1 AATACATAGTATAACCTTC
*
8830 AATACATAGTTTAACCTTC
1 AATACATAGTATAACCTTC
8849 AATA
1 AATA
8853 ATACATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (19 bp):
AATACATAGTATAACCTTC
Found at i:8861 original size:19 final size:19
Alignment explanation
Indices: 8825--8863 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
8815 CGTAGTATAC
*
8825 CCTTCAATACATAGTTTAA
1 CCTTCAATACATAATTTAA
8844 CCTTCAATA-ATACATTTAA
1 CCTTCAATACATA-ATTTAA
8863 C
1 C
8864 TCTTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (19 bp):
CCTTCAATACATAATTTAA
Found at i:11658 original size:46 final size:46
Alignment explanation
Indices: 11544--11679 Score: 229
Period size: 45 Copynumber: 3.0 Consensus size: 46
11534 CTAAGAAACA
*
11544 GGCAATTGTTATCCTTCTTTTATAAACCTTATTTTGAAATAAAAAT
1 GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
*
11590 -GCAATTTTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
1 GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAAT
* *
11635 GGCAATTGTTATTCTTCTCATATAAACCTTATTTTGAAATAAAAA
1 GGCAATTGTTATCCTTCTTATATAAACCTTATTTTGAAATAAAAA
11680 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:16110 original size:51 final size:51
Alignment explanation
Indices: 16034--16135 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
16024 TCATGACCAG
*
16034 TTGAAGTTGGACACAGTTAATGCTCCATAATAAAAGAAGAAAAGAGTGAAT
1 TTGAAGTTGGACACAGTTAATGCTCCATAATAAAAGAAGAAAAGAGCGAAT
*
16085 TTGAAGTTGGACACTGTTAATGCTCCATAATAAAAGAAGAAAAGAGCGAAT
1 TTGAAGTTGGACACAGTTAATGCTCCATAATAAAAGAAGAAAAGAGCGAAT
16136 CAGCTAGCAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (51 bp):
TTGAAGTTGGACACAGTTAATGCTCCATAATAAAAGAAGAAAAGAGCGAAT
Found at i:18225 original size:21 final size:21
Alignment explanation
Indices: 18199--18238 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18189 GTATCAAACA
18199 ACCACCAAAATTGAATTCACG
1 ACCACCAAAATTGAATTCACG
* *
18220 ACCACCAGATTTGAATTCA
1 ACCACCAAAATTGAATTCA
18239 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:20407 original size:130 final size:130
Alignment explanation
Indices: 20174--20435 Score: 524
Period size: 130 Copynumber: 2.0 Consensus size: 130
20164 TCCAACCAAA
20174 ACTGATAGATTTATAAAAGTATAGTAAATTTAGATTGATTTCTTACTCGAACTGAATGGCAGCGA
1 ACTGATAGATTTATAAAAGTATAGTAAATTTAGATTGATTTCTTACTCGAACTGAATGGCAGCGA
20239 GGAAGGATCGACGTTACGACGTGTACGTTGATGATAATTCTGGTATTCTTATCTGTTGTGCACAC
66 GGAAGGATCGACGTTACGACGTGTACGTTGATGATAATTCTGGTATTCTTATCTGTTGTGCACAC
20304 ACTGATAGATTTATAAAAGTATAGTAAATTTAGATTGATTTCTTACTCGAACTGAATGGCAGCGA
1 ACTGATAGATTTATAAAAGTATAGTAAATTTAGATTGATTTCTTACTCGAACTGAATGGCAGCGA
20369 GGAAGGATCGACGTTACGACGTGTACGTTGATGATAATTCTGGTATTCTTATCTGTTGTGCACAC
66 GGAAGGATCGACGTTACGACGTGTACGTTGATGATAATTCTGGTATTCTTATCTGTTGTGCACAC
20434 AC
1 AC
20436 CGATTGTTGT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 132 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (130 bp):
ACTGATAGATTTATAAAAGTATAGTAAATTTAGATTGATTTCTTACTCGAACTGAATGGCAGCGA
GGAAGGATCGACGTTACGACGTGTACGTTGATGATAATTCTGGTATTCTTATCTGTTGTGCACAC
Found at i:26971 original size:36 final size:36
Alignment explanation
Indices: 26930--26998 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
26920 CTCGAGTTCG
26930 TATTCTAATAAAAAATAATATTCTTTTTTCGGATCA
1 TATTCTAATAAAAAATAATATTCTTTTTTCGGATCA
26966 TATTCTAATAAAAAATAATATTCTTTTTTCGGA
1 TATTCTAATAAAAAATAATATTCTTTTTTCGGA
26999 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:32564 original size:57 final size:59
Alignment explanation
Indices: 32474--32586 Score: 185
Period size: 57 Copynumber: 1.9 Consensus size: 59
32464 GAGGGAGGAA
*
32474 AATATAAAAATGACAGAGAAAAGAAAGAATTGCTGGAA-CTTTTTAAAACATAACTGAAT
1 AATATAAAAATGACA-AGAAAAGAAAGAATTGCTGGAATCTTTTTAAAACAGAACTGAAT
*
32533 AATATAAAAATGAC-AGAAAAGAAAGAATTGCTGGAATTTTTTTAAAACAGAACT
1 AATATAAAAATGACAAGAAAAGAAAGAATTGCTGGAATCTTTTTAAAACAGAACT
32587 AAATCTCAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
57 22 0.43
58 15 0.29
59 14 0.27
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (59 bp):
AATATAAAAATGACAAGAAAAGAAAGAATTGCTGGAATCTTTTTAAAACAGAACTGAAT
Found at i:42654 original size:2 final size:2
Alignment explanation
Indices: 42643--42674 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
42633 GTAATCATAC
42643 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42675 ATCTTATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43899 original size:40 final size:41
Alignment explanation
Indices: 43848--43924 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 41
43838 GATATAACAC
43848 AAATTTTGTTTTAAGGTTTATATGG-TTTTTTATCTTACAA
1 AAATTTTGTTTTAAGGTTTATATGGTTTTTTTATCTTACAA
43888 AAATTTTGTTTTAAGGTTTATATGGTTTTTTTATCTT
1 AAATTTTGTTTTAAGGTTTATATGGTTTTTTTATCTT
43925 TCGATTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 25 0.69
41 11 0.31
ACGTcount: A:0.25, C:0.04, G:0.13, T:0.58
Consensus pattern (41 bp):
AAATTTTGTTTTAAGGTTTATATGGTTTTTTTATCTTACAA
Found at i:49090 original size:16 final size:17
Alignment explanation
Indices: 49057--49090 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
49047 CCTTCTATTT
*
49057 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
49074 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
49090 T
1 T
49091 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:49937 original size:15 final size:16
Alignment explanation
Indices: 49917--49957 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
49907 GTTTACTTCA
*
49917 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
49932 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
49948 GAATGATTCA
1 GAATGATTCA
49958 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:55974 original size:14 final size:14
Alignment explanation
Indices: 55955--55986 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
55945 ATTATTTTAA
55955 AAAATTGAAATATT
1 AAAATTGAAATATT
55969 AAAATTGAAATATT
1 AAAATTGAAATATT
55983 AAAA
1 AAAA
55987 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:58291 original size:2 final size:2
Alignment explanation
Indices: 58284--58313 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58274 TCTTTATTAC
58284 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
58314 TATTCATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62426 original size:17 final size:17
Alignment explanation
Indices: 62404--62444 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
62394 CATAGCGGCG
*
62404 CTAGCTCTCTCATACGC
1 CTAGCTCTCTCAGACGC
62421 CTAGCTCTCTCAGACGC
1 CTAGCTCTCTCAGACGC
62438 CTAGCTC
1 CTAGCTC
62445 GCTACTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.15, T:0.27
Consensus pattern (17 bp):
CTAGCTCTCTCAGACGC
Found at i:63738 original size:85 final size:85
Alignment explanation
Indices: 63595--63766 Score: 326
Period size: 85 Copynumber: 2.0 Consensus size: 85
63585 TGATGAATTT
*
63595 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAGATCATCGTATGAGTGCTCT
1 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
63660 ATCCTCATCCAATCGACTCA
66 ATCCTCATCCAATCGACTCA
63680 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
1 ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
*
63745 GTCCTCATCCAATCGACTCA
66 ATCCTCATCCAATCGACTCA
63765 AT
1 AT
63767 TCGATTTATG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (85 bp):
ATAAGAAGTTTTCCCTTATATTCTTTGTTGACTGCTGAGTGAAAAAATCATCGTATGAGTGCTCT
ATCCTCATCCAATCGACTCA
Found at i:64586 original size:17 final size:18
Alignment explanation
Indices: 64551--64587 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
64541 TGAGTATTCC
64551 TTATAATTTGAGAGTATA
1 TTATAATTTGAGAGTATA
64569 TTATAATATT-AG-GTATA
1 TTATAAT-TTGAGAGTATA
64586 TT
1 TT
64588 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:69353 original size:11 final size:11
Alignment explanation
Indices: 69337--69378 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
69327 TTTAATTGAA
69337 TTATTTATATT
1 TTATTTATATT
*
69348 TTATTTTTATT
1 TTATTTATATT
*
69359 TTATCTTAT-TA
1 TTAT-TTATATT
69370 TTATTTATA
1 TTATTTATA
69379 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:69373 original size:16 final size:17
Alignment explanation
Indices: 69336--69378 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
69326 TTTTAATTGA
*
69336 ATTATTTATATTTTATT
1 ATTATTTATATCTTATT
*
69353 TTTATTT-TATCTTATT
1 ATTATTTATATCTTATT
69369 ATTATTTATA
1 ATTATTTATA
69379 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:69439 original size:15 final size:15
Alignment explanation
Indices: 69419--69447 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
69409 TTTATTATTA
69419 ATATTTAATGATTTT
1 ATATTTAATGATTTT
69434 ATATTTAATGATTT
1 ATATTTAATGATTT
69448 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:69462 original size:16 final size:16
Alignment explanation
Indices: 69441--69471 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
69431 TTTATATTTA
69441 ATGATTTAGTAATGAC
1 ATGATTTAGTAATGAC
69457 ATGATTTAGTAATGA
1 ATGATTTAGTAATGA
69472 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:69515 original size:45 final size:45
Alignment explanation
Indices: 69457--69551 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
69447 TAGTAATGAC
* *
69457 ATGATTTAGTAATGATTACTAATAATGATTAATTATTAATATTTA
1 ATGATATAATAATGATTACTAATAATGATTAATTATTAATATTTA
* *
69502 ATGATATAATAATGATTATTAATAATGATTTATTATTAATATTTA
1 ATGATATAATAATGATTACTAATAATGATTAATTATTAATATTTA
69547 ATGAT
1 ATGAT
69552 TTGATACTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.47
Consensus pattern (45 bp):
ATGATATAATAATGATTACTAATAATGATTAATTATTAATATTTA
Found at i:69547 original size:24 final size:25
Alignment explanation
Indices: 69511--69649 Score: 71
Period size: 24 Copynumber: 5.8 Consensus size: 25
69501 AATGATATAA
69511 TAATGATTATTAATAATGATTTATTAT
1 TAATGA-T-TTAATAATGATTTATTAT
*
69538 TAAT-A-TT--TAATGATTTGA-TAC
1 TAATGATTTAATAATGATTT-ATTAT
* * *
69559 TAATGATTTAGTAATGA-TTAGTAA
1 TAATGATTTAATAATGATTTATTAT
* * * * *
69583 TAATAAAATT-ATAAT-AATTACTAA
1 TAAT-GATTTAATAATGATTTATTAT
* *
69607 TAATGATTTAATAATGA-TTACTAA
1 TAATGATTTAATAATGATTTATTAT
*
69631 TAATTATTTAATAATGATT
1 TAATGATTTAATAATGATT
69650 AAATATTTAA
Statistics
Matches: 92, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
21 15 0.16
22 2 0.02
23 9 0.10
24 50 0.54
25 11 0.12
26 1 0.01
27 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (25 bp):
TAATGATTTAATAATGATTTATTAT
Found at i:69553 original size:21 final size:21
Alignment explanation
Indices: 69479--69552 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
69469 TGATTACTAA
69479 TAATGATTAATTATTAATATT
1 TAATGATTAATTATTAATATT
* * *
69500 TAATGATATAATAATGATTATT
1 TAATGAT-TAATTATTAATATT
*
69522 AATAATGATTTATTATTAATATT
1 --TAATGATTAATTATTAATATT
69545 TAATGATT
1 TAATGATT
69553 TGATACTAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 15 0.35
22 11 0.26
23 10 0.23
24 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TAATGATTAATTATTAATATT
Found at i:69562 original size:21 final size:22
Alignment explanation
Indices: 69479--69568 Score: 60
Period size: 21 Copynumber: 4.1 Consensus size: 22
69469 TGATTACTAA
* *
69479 TAATGATTAATTATTAAT-ATT
1 TAATGATTTATTACTAATGATT
* * * * *
69500 TAATGATATAATAATGATTATT
1 TAATGATTTATTACTAATGATT
*
69522 AATAATGATTTATTATTAAT-ATT
1 --TAATGATTTATTACTAATGATT
69545 TAATGATTTGA-TACTAATGATT
1 TAATGATTT-ATTACTAATGATT
69567 TA
1 TA
69569 GTAATGATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
21 28 0.52
22 9 0.17
23 3 0.06
24 14 0.26
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (22 bp):
TAATGATTTATTACTAATGATT
Found at i:69574 original size:59 final size:60
Alignment explanation
Indices: 69408--69586 Score: 195
Period size: 59 Copynumber: 3.0 Consensus size: 60
69398 TTTACATTGA
* * *
69408 ATTTATTATTAATATTTAATGATTTTATATTTAATGATTTAGTAATGACATGATTTAGTAATG
1 ATTTATTATTAATATTTAATGATTTAATATTTAATGATTTAGTAATG--ATTA-TTAATAATG
* * * * *
69471 A-TTACTAATAATGA-TTAATTA-TTAATATTTAATGATATAATAATGATTATTAATAATG
1 ATTTATTATTAAT-ATTTAATGATTTAATATTTAATGATTTAGTAATGATTATTAATAATG
* * *
69529 ATTTATTATTAATATTTAATGATTTGATA-CTAATGATTTAGTAATGATTAGTAATAAT
1 ATTTATTATTAATATTTAATGATTTAATATTTAATGATTTAGTAATGATTATTAATAAT
69587 AAAATTATAA
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
58 10 0.10
59 43 0.45
60 5 0.05
61 21 0.22
62 15 0.16
63 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (60 bp):
ATTTATTATTAATATTTAATGATTTAATATTTAATGATTTAGTAATGATTATTAATAATG
Found at i:69654 original size:11 final size:11
Alignment explanation
Indices: 69605--69654 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
69595 AATAATTACT
*
69605 AATAATGATTT
1 AATAATGATTA
69616 AATAATGATTA
1 AATAATGATTA
* *
69627 CTAATAATTATTT
1 --AATAATGATTA
69640 AATAATGATTA
1 AATAATGATTA
69651 AATA
1 AATA
69655 TTTAAATAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 23 0.72
13 9 0.28
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (11 bp):
AATAATGATTA
Found at i:69679 original size:20 final size:20
Alignment explanation
Indices: 69654--69695 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
69644 ATGATTAAAT
69654 ATTTAAATAGAATTTATTCA
1 ATTTAAATAGAATTTATTCA
*
69674 ATTTAAATCGAATTTATTCA
1 ATTTAAATAGAATTTATTCA
69694 AT
1 AT
69696 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:69726 original size:22 final size:23
Alignment explanation
Indices: 69681--69740 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
69671 TCAATTTAAA
* *
69681 TCGAATTTATTCA-ATATAACTAG
1 TCGAATTTATT-ATTTATAAATAG
69704 TCGAATTTA-TATTTATAAATAG
1 TCGAATTTATTATTTATAAATAG
69726 TCGAATTTATTATTT
1 TCGAATTTATTATTT
69741 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:73466 original size:75 final size:75
Alignment explanation
Indices: 73386--73571 Score: 241
Period size: 75 Copynumber: 2.5 Consensus size: 75
73376 ACCCCTTGGG
** *
73386 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTAGGGGGGAATCG
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAACATTCA-GGGGGAATCG
73451 GTTCCTCCTAT
65 GTTCCTCCTAT
* * * * * *
73462 -GGGGGAATCGGTTCCCTCCGAGTATTCTGGAAATCTCGGAGCCAAACCATTCAGGGGGAATCGG
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAACATTCAGGGGGAATCGG
73526 TTCCTCCTAT
66 TTCCTCCTAT
*
73536 GGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 -GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
73572 TTTGGCTTTG
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
74 21 0.22
75 44 0.47
76 29 0.31
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.25
Consensus pattern (75 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAACATTCAGGGGGAATCGG
TTCCTCCTAT
Found at i:76172 original size:21 final size:21
Alignment explanation
Indices: 76146--76185 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
76136 CAGAACCCCA
*
76146 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
76167 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
76186 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Done.