Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012640.1 Kokia drynarioides strain JFW-HI SEQ_127650, 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: 77362
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4665 original size:21 final size:21
Alignment explanation
Indices: 4638--4691 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4628 GGAGTTTTTA
*
4638 GTATCGGTGGAAG-TATAACTT
1 GTATCGGTAGAAGTTAT-ACTT
*
4659 GTTTCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTTATACTT
4680 GTATCGGTAGAA
1 GTATCGGTAGAA
4692 CTATCACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGTTATACTT
Found at i:5819 original size:15 final size:15
Alignment explanation
Indices: 5799--5828 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5789 CCTTAGTTTT
5799 ATTTTCTCTATCCTC
1 ATTTTCTCTATCCTC
*
5814 ATTTTCTCTCTCCTC
1 ATTTTCTCTATCCTC
5829 CAACATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTCTCTATCCTC
Found at i:7767 original size:27 final size:26
Alignment explanation
Indices: 7720--7782 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
7710 AATTTTAATA
* *
7720 AAAAAATATAATATATTTAAAAATTAT
1 AAAAAAT-TAAAATATTTAAAAATCAT
7747 AAAAAATTAAAAT-TTTATAAAGATCAT
1 AAAAAATTAAAATATTTA-AAA-ATCAT
7774 AAAAAATTA
1 AAAAAATTA
7783 TAAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 8 0.25
27 20 0.62
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAAATTAAAATATTTAAAAATCAT
Found at i:8122 original size:28 final size:29
Alignment explanation
Indices: 8087--8189 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
8077 AAAAAATTTC
*
8087 TAATTTTTAATAAAATTTAAATATTTTTTA
1 TAATTTTTAATAAAATTT-AATAATTTTTA
* *
8117 T-ATTTTTATTAAAATTTAGTAATTTTTA
1 TAATTTTTAATAAAATTTAATAATTTTTA
* *** *
8145 TAATTTTTATTATTTTTTAATATATTTTTC
1 TAATTTTTAATAAAATTTAATA-ATTTTTA
*
8175 TAGTTTTTAATAAAA
1 TAATTTTTAATAAAA
8190 GTAGGAGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
28 10 0.17
29 31 0.53
30 17 0.29
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (29 bp):
TAATTTTTAATAAAATTTAATAATTTTTA
Found at i:8144 original size:10 final size:9
Alignment explanation
Indices: 8111--8165 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
8101 ATTTAAATAT
8111 TTTTTAT-A
1 TTTTTATAA
8119 TTTTTATTAA
1 TTTTTA-TAA
**
8129 AATTTAGTAA
1 TTTTTA-TAA
8139 TTTTTATAA
1 TTTTTATAA
*
8148 TTTTTATTA
1 TTTTTATAA
8157 TTTTT-TAA
1 TTTTTATAA
8165 T
1 T
8166 ATATTTTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 9 0.24
9 17 0.45
10 12 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:8618 original size:30 final size:28
Alignment explanation
Indices: 8584--8646 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
8574 ATTTATTCTC
* *
8584 GTAAAAGAAAAAGTAAATACATTTTTTTGG
1 GTAAAAAAAAAAGTAAAT--ATATTTTTGG
8614 GTAAAAAAAAAAGTAAATATATTTTTGG
1 GTAAAAAAAAAAGTAAATATATTTTTGG
8642 GTAAA
1 GTAAA
8647 CTATAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 14 0.45
30 17 0.55
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.32
Consensus pattern (28 bp):
GTAAAAAAAAAAGTAAATATATTTTTGG
Found at i:13946 original size:44 final size:44
Alignment explanation
Indices: 13877--13960 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
13867 TCGATGATGA
* *
13877 AATTAATATGTTTGCTCCAAGTTTATTTTAATACATCTAATTTG
1 AATTAATATATTTGCTCCAAATTTATTTTAATACATCTAATTTG
* * *
13921 AATTACTATATTTGTTCCAAATTTATTTTAGTACATCTAA
1 AATTAATATATTTGCTCCAAATTTATTTTAATACATCTAA
13961 ACCCTAAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (44 bp):
AATTAATATATTTGCTCCAAATTTATTTTAATACATCTAATTTG
Found at i:14051 original size:44 final size:45
Alignment explanation
Indices: 13979--14087 Score: 186
Period size: 44 Copynumber: 2.5 Consensus size: 45
13969 CCCTAAACAC
13979 ATTACTATGTTTGTTCCAA-TTTTGCTTTAATACATCTAATTTAA
1 ATTACTATGTTTGTTCCAAGTTTTGCTTTAATACATCTAATTTAA
* *
14023 ATTACTATGTTTGTTTCAAGTTTT-CTTTAATACATCTCATTTAA
1 ATTACTATGTTTGTTCCAAGTTTTGCTTTAATACATCTAATTTAA
14067 ATTACTATGTTTGTTCCAAGT
1 ATTACTATGTTTGTTCCAAGT
14088 CGGGATATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 57 0.93
45 4 0.07
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (45 bp):
ATTACTATGTTTGTTCCAAGTTTTGCTTTAATACATCTAATTTAA
Found at i:14058 original size:101 final size:101
Alignment explanation
Indices: 13878--14059 Score: 258
Period size: 101 Copynumber: 1.8 Consensus size: 101
13868 CGATGATGAA
* *
13878 ATTAATATGTTTGCTCCAAGTTTATTTTAATACATCTAATTTGAATTACTATATTTGTTCCAAAT
1 ATTAATATGTTTGCTCCAAGTTTACTTTAATACATCTAATTTAAATTACTATATTTGTTCCAAAT
*
13943 TTATTTTAGTACATCTAAACCCTAAACCCTAAACAC
66 TTATTTTAATACATCTAAACCCTAAACCCTAAACAC
* * * * * * *
13979 ATTACTATGTTTGTTCCAATTTTGCTTTAATACATCTAATTTAAATTACTATGTTTGTTTCAAGT
1 ATTAATATGTTTGCTCCAAGTTTACTTTAATACATCTAATTTAAATTACTATATTTGTTCCAAAT
14044 TT-TCTTTAATACATCT
66 TTAT-TTTAATACATCT
14060 CATTTAAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 69 0.99
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (101 bp):
ATTAATATGTTTGCTCCAAGTTTACTTTAATACATCTAATTTAAATTACTATATTTGTTCCAAAT
TTATTTTAATACATCTAAACCCTAAACCCTAAACAC
Found at i:14996 original size:9 final size:9
Alignment explanation
Indices: 14982--15066 Score: 93
Period size: 9 Copynumber: 9.4 Consensus size: 9
14972 TGAACTTTTT
*
14982 AAAATTGTA
1 AAAATTATA
14991 AAAATTATA
1 AAAATTATA
*
15000 AAAACTATAA
1 AAAATTAT-A
15010 AAAATTAT-
1 AAAATTATA
15018 -AAATTATA
1 AAAATTATA
15026 AAAATTATA
1 AAAATTATA
15035 ATAAATTATA
1 A-AAATTATA
* *
15045 TAAATTGTA
1 AAAATTATA
*
15054 AAAATTACA
1 AAAATTATA
15063 AAAA
1 AAAA
15067 ACTATTAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
7 7 0.11
9 41 0.64
10 16 0.25
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:15012 original size:10 final size:10
Alignment explanation
Indices: 14990--15084 Score: 71
Period size: 9 Copynumber: 10.2 Consensus size: 10
14980 TTAAAATTGT
14990 AAAAATTAT-
1 AAAAATTATA
*
14999 AAAAACTATA
1 AAAAATTATA
15009 AAAAATTAT-
1 AAAAATTATA
15018 --AAATTAT-
1 AAAAATTATA
15025 AAAAATTATA
1 AAAAATTATA
*
15035 ATAAATTAT-
1 AAAAATTATA
* *
15044 ATAAATTGT-
1 AAAAATTATA
*
15053 AAAAATTACA
1 AAAAATTATA
*
15063 AAAAACTATTA
1 AAAAATTA-TA
15074 AAAAATT-TA
1 AAAAATTATA
15083 AA
1 AA
15085 GATAGTAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
7 7 0.10
9 33 0.47
10 23 0.33
11 7 0.10
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:15013 original size:28 final size:27
Alignment explanation
Indices: 14982--15067 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 27
14972 TGAACTTTTT
* *
14982 AAAATTGTAAAAATTATAAAAACTATAA
1 AAAATT-TATAAATTATAAAAATTATAA
15010 AAAA-TTATAAATTATAAAAATTATAA
1 AAAATTTATAAATTATAAAAATTATAA
* * *
15036 TAAATTATATAAATTGTAAAAATTACAA
1 AAAATT-TATAAATTATAAAAATTATAA
15064 AAAA
1 AAAA
15068 CTATTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.44
27 2 0.04
28 26 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTTATAAATTATAAAAATTATAA
Found at i:15014 original size:19 final size:18
Alignment explanation
Indices: 14982--15066 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 18
14972 TGAACTTTTT
*
14982 AAAATTGTAAAAATTATA
1 AAAATTATAAAAATTATA
*
15000 AAAACTATAAAAAATTAT-
1 AAAATTAT-AAAAATTATA
15018 -AAATTATAAAAATTATA
1 AAAATTATAAAAATTATA
* *
15035 ATAAATTATATAAATTGTA
1 A-AAATTATAAAAATTATA
*
15054 AAAATTACAAAAA
1 AAAATTATAAAAA
15067 ACTATTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
16 9 0.16
17 6 0.11
18 16 0.29
19 25 0.45
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATTATAAAAATTATA
Found at i:18944 original size:25 final size:23
Alignment explanation
Indices: 18911--18957 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
18901 AGTTAGATCC
18911 AAATTAAATTCTAAAAAGATAATTA
1 AAATTAAATT-TAAAAA-ATAATTA
*
18936 AAATTAAATTTAAACAATAATT
1 AAATTAAATTTAAAAAATAATT
18958 CTCTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATTAAATTTAAAAAATAATTA
Found at i:22234 original size:109 final size:106
Alignment explanation
Indices: 22121--22415 Score: 407
Period size: 109 Copynumber: 2.7 Consensus size: 106
22111 TTTTTTTAAA
*
22121 AATCAATCCTTTATATTTATTTACGTATATATTAACTATTAATTTGTTTAGTTTATGTATTAAAT
1 AATCAATCCTTTATATTTATTTACTTATATATTAACTATTAATTTGTTTAGTTTATGTATTAAAT
22186 ATATATATATATATATATATCCTATCACCGTTTTGA-T-TTTT-TTT
66 ATATATATATATATAT-TA--C---CACCGTTTTGATTCTTTTATTT
*
22230 AATCAATCCTTTATATTTATTTACTTATATATTAACTATTAATTTGTTTATTTTATGTATTAAAT
1 AATCAATCCTTTATATTTATTTACTTATATATTAACTATTAATTTGTTTAGTTTATGTATTAAAT
*
22295 ATATATATATATATCTTACCACCGTTTTGATTCTTTTATTT
66 ATATATATATATATATTACCACCGTTTTGATTCTTTTATTT
** * * * *
22336 TTTCAATCCTTTTATACTTATGTACTTATATATTAACAATTAACTTGTTTAGTTTATGTATTAAA
1 AATCAATCC-TTTATATTTATTTACTTATATATTAACTATTAATTTGTTTAGTTTATGTATTAAA
* *
22401 TATGTAAATATATAT
65 TATATATATATATAT
22416 GATCGTTTCT
Statistics
Matches: 170, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
103 11 0.06
104 1 0.01
105 4 0.02
106 11 0.06
107 63 0.37
108 2 0.01
109 78 0.46
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (106 bp):
AATCAATCCTTTATATTTATTTACTTATATATTAACTATTAATTTGTTTAGTTTATGTATTAAAT
ATATATATATATATATTACCACCGTTTTGATTCTTTTATTT
Found at i:30755 original size:18 final size:19
Alignment explanation
Indices: 30721--30770 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
30711 AACAAAATAA
*
30721 TCAAAATAATTT-TTAAAAT
1 TCAAAAT-ATTTGTAAAAAT
30740 TCAAAATATTTGTAAAAAT
1 TCAAAATATTTGTAAAAAT
*
30759 TCTAATATATTT
1 TC-AAAATATTT
30771 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 15 0.56
20 8 0.30
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (19 bp):
TCAAAATATTTGTAAAAAT
Found at i:33690 original size:41 final size:42
Alignment explanation
Indices: 33627--33772 Score: 174
Period size: 41 Copynumber: 3.5 Consensus size: 42
33617 GCGTAATGAT
* * *
33627 TTAGGCCTTGAGCGTAGTAGGCTTTATGCTGGTGTAATT-TA
1 TTAGGCCTCGAGCCTAGCAGGCTTTATGCTGGTGTAATTGTA
33668 TTAGGCCTCGAGCCTAGCAGGCTTTATGCTGGTGT-ATTGTA
1 TTAGGCCTCGAGCCTAGCAGGCTTTATGCTGGTGTAATTGTA
** *
33709 TCGGGCCTCGAGCCTAGCAAGCTTTATGCTGGTGT-ATTGTA
1 TTAGGCCTCGAGCCTAGCAGGCTTTATGCTGGTGTAATTGTA
* * *
33750 -TCGAGCCTTGAGCCTAGGAGGCT
1 TTAG-GCCTCGAGCCTAGCAGGCT
33773 CCGTGCCAGT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 4 0.04
41 88 0.96
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (42 bp):
TTAGGCCTCGAGCCTAGCAGGCTTTATGCTGGTGTAATTGTA
Found at i:36846 original size:41 final size:41
Alignment explanation
Indices: 36801--36932 Score: 174
Period size: 41 Copynumber: 3.2 Consensus size: 41
36791 AACCTAGTAT
* * *
36801 GCTTTATGCTCGTGTACTATATTGGGCCTCGAGCTTAGCAA
1 GCTTTATGCTAGTGTACTGTATTGGGCCTCGAGCATAGCAA
* * * * *
36842 GCTTTATGCTAGTGTATTGTATTAGGCCTTGAGCCTAGCAG
1 GCTTTATGCTAGTGTACTGTATTGGGCCTCGAGCATAGCAA
* *
36883 GCTTTATGCTGGTGTACTGTATTGGGCCTCGAGCATATCAA
1 GCTTTATGCTAGTGTACTGTATTGGGCCTCGAGCATAGCAA
36924 GCTTTATGC
1 GCTTTATGC
36933 CGATGTATTG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (41 bp):
GCTTTATGCTAGTGTACTGTATTGGGCCTCGAGCATAGCAA
Found at i:36925 original size:82 final size:82
Alignment explanation
Indices: 36784--36968 Score: 239
Period size: 82 Copynumber: 2.3 Consensus size: 82
36774 TAATGATTCG
* * * *
36784 GGCCTTGAACCTAGTATGCTTTATGCTCGTGTACTATATTGGGCCTCGAGCTTAGCAAGCTTTAT
1 GGCCTTGAGCCTAGCAAGCTTTATGCTCGTGTACTATATTGGGCCTCGAGCATAGCAAGCTTTAT
*
36849 GCTAG-TGTATTGTATTA
66 GC-AGATGTATTGTATCA
* * * *
36866 GGCCTTGAGCCTAGCAGGCTTTATGCTGGTGTACTGTATTGGGCCTCGAGCATATCAAGCTTTAT
1 GGCCTTGAGCCTAGCAAGCTTTATGCTCGTGTACTATATTGGGCCTCGAGCATAGCAAGCTTTAT
* *
36931 GCCGATGTATTGTATCG
66 GCAGATGTATTGTATCA
36948 GGCCTT-ATGCCTAGCAAGCTT
1 GGCCTTGA-GCCTAGCAAGCTT
36969 CGTGTCGGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 2 0.02
82 88 0.98
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (82 bp):
GGCCTTGAGCCTAGCAAGCTTTATGCTCGTGTACTATATTGGGCCTCGAGCATAGCAAGCTTTAT
GCAGATGTATTGTATCA
Found at i:36945 original size:41 final size:41
Alignment explanation
Indices: 36801--36952 Score: 155
Period size: 41 Copynumber: 3.7 Consensus size: 41
36791 AACCTAGTAT
* *
36801 GCTTTATGCTCG-TGTACTATATTGGGCCTCGAGCTTAGCAA
1 GCTTTATGC-CGATGTACTGTATTGGGCCTCGAGCATAGCAA
* * * * * *
36842 GCTTTATG-CTAGTGTATTGTATTAGGCCTTGAGCCTAGCAG
1 GCTTTATGCCGA-TGTACTGTATTGGGCCTCGAGCATAGCAA
* * *
36883 GCTTTATGCTGGTGTACTGTATTGGGCCTCGAGCATATCAA
1 GCTTTATGCCGATGTACTGTATTGGGCCTCGAGCATAGCAA
* *
36924 GCTTTATGCCGATGTATTGTATCGGGCCT
1 GCTTTATGCCGATGTACTGTATTGGGCCT
36953 TATGCCTAGC
Statistics
Matches: 88, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
39 1 0.01
41 87 0.99
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (41 bp):
GCTTTATGCCGATGTACTGTATTGGGCCTCGAGCATAGCAA
Found at i:36966 original size:41 final size:40
Alignment explanation
Indices: 36783--36968 Score: 142
Period size: 41 Copynumber: 4.5 Consensus size: 40
36773 GTAATGATTC
* * * * *
36783 GGGCCTTGAACCTAGTATGCTTTATGCTCG-TGTACTATATT
1 GGGCCTT-AGCCTAGCAAGCTTTATGC-CGATGTATTGTATT
* * *
36824 GGGCCTCGAGCTTAGCAAGCTTTATG-CTAGTGTATTGTATT
1 GGGCCT-TAGCCTAGCAAGCTTTATGCCGA-TGTATTGTATT
* * * * *
36865 AGGCCTTGAGCCTAGCAGGCTTTATGCTGGTGTACTGTATT
1 GGGCCTT-AGCCTAGCAAGCTTTATGCCGATGTATTGTATT
* * * *
36906 GGGCCTCGAGCATATCAAGCTTTATGCCGATGTATTGTATC
1 GGGCCT-TAGCCTAGCAAGCTTTATGCCGATGTATTGTATT
36947 GGGCCTTATGCCTAGCAAGCTT
1 GGGCCTTA-GCCTAGCAAGCTT
36969 CGTGTCGGTG
Statistics
Matches: 110, Mismatches: 28, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 108 0.98
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.34
Consensus pattern (40 bp):
GGGCCTTAGCCTAGCAAGCTTTATGCCGATGTATTGTATT
Found at i:37826 original size:30 final size:30
Alignment explanation
Indices: 37790--37848 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
37780 ACAAATAGCC
* * * *
37790 TGCACACGGGGAACCCACATGGGCGTGTGG
1 TGCACACAGGCAACCCACACGGGCATGTGG
37820 TGCACACAGGCAACCCACACGGGCATGTG
1 TGCACACAGGCAACCCACACGGGCATGTG
37849 CCTTGAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.34, T:0.12
Consensus pattern (30 bp):
TGCACACAGGCAACCCACACGGGCATGTGG
Found at i:38553 original size:14 final size:14
Alignment explanation
Indices: 38534--38589 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
38524 AATCTAGAAT
38534 CCAAAACCTTAAAC
1 CCAAAACCTTAAAC
** *
38548 CCAAAAAATAAAAC
1 CCAAAACCTTAAAC
*
38562 CTAAAACC-TAAAC
1 CCAAAACCTTAAAC
*
38575 CCAAACCCTTAAAC
1 CCAAAACCTTAAAC
38589 C
1 C
38590 TTAAACTCGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.54, C:0.34, G:0.00, T:0.12
Consensus pattern (14 bp):
CCAAAACCTTAAAC
Found at i:38587 original size:21 final size:21
Alignment explanation
Indices: 38565--38604 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38555 ATAAAACCTA
38565 AAACC-TAAACCCAAACCCTT
1 AAACCTTAAACCCAAACCCTT
* *
38585 AAACCTTAAACTCGAACCCT
1 AAACCTTAAACCCAAACCCT
38605 AATCTCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.42, C:0.38, G:0.03, T:0.17
Consensus pattern (21 bp):
AAACCTTAAACCCAAACCCTT
Found at i:38635 original size:12 final size:12
Alignment explanation
Indices: 38613--38642 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
38603 CTAATCTCAT
38613 AACCATGAACCTA
1 AACC-TGAACCTA
38626 AACCTGAACCTA
1 AACCTGAACCTA
38638 AACCT
1 AACCT
38643 TGAATCTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (12 bp):
AACCTGAACCTA
Found at i:42356 original size:3 final size:3
Alignment explanation
Indices: 42348--42379 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42338 ACTATGTTTA
42348 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
42380 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:45798 original size:6 final size:6
Alignment explanation
Indices: 45787--45816 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
45777 TGAAAACAAT
45787 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
45817 TCTCTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:57488 original size:24 final size:24
Alignment explanation
Indices: 57461--57506 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
57451 TCAACCTTTT
*
57461 ACCTTTCATCTCCTTTGACCTTCC
1 ACCTTTCATCTCCTTTAACCTTCC
*
57485 ACCTTTCATCTTCTTTAACCTT
1 ACCTTTCATCTCCTTTAACCTT
57507 TTAACCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.37, G:0.02, T:0.46
Consensus pattern (24 bp):
ACCTTTCATCTCCTTTAACCTTCC
Done.