Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010684.1 Kokia drynarioides strain JFW-HI SEQ_125630, 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: 53575
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:124 original size:2 final size:2
Alignment explanation
Indices: 117--147 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
107 TTATTAACTA
117 AT AT 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 A
148 AAATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:195 original size:27 final size:28
Alignment explanation
Indices: 147--201 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
137 ATATATATAT
* *
147 AAAATAAATAAAAGAATAAAGAA-AGAA
1 AAAATAAACAAAAGAAGAAAGAACAGAA
*
174 AAAATAAACAAAAGAAGGAAGAACAGAA
1 AAAATAAACAAAAGAAGAAAGAACAGAA
202 GCTCAAACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.75, C:0.04, G:0.15, T:0.07
Consensus pattern (28 bp):
AAAATAAACAAAAGAAGAAAGAACAGAA
Found at i:643 original size:17 final size:18
Alignment explanation
Indices: 621--656 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
611 TAAATAAGTT
621 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
638 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
656 A
1 A
657 TCGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:6867 original size:17 final size:18
Alignment explanation
Indices: 6845--6878 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6835 CATTTAAAAC
*
6845 GAATAT-TTTTTGCTGAG
1 GAATATATTGTTGCTGAG
6862 GAATATATTGTTGCTGA
1 GAATATATTGTTGCTGA
6879 TGGTGCCATA
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:0.06, G:0.24, T:0.44
Consensus pattern (18 bp):
GAATATATTGTTGCTGAG
Found at i:10903 original size:20 final size:21
Alignment explanation
Indices: 10858--10903 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
10848 AAAGATATAA
10858 ATATGTTTATAATAAAATCACT
1 ATAT-TTTATAATAAAATCACT
10880 -TATTTTATAA-AAAAT-ACAT
1 ATATTTTATAATAAAATCAC-T
10899 ATATT
1 ATATT
10904 GTTTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 11 0.50
21 3 0.14
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATTTTATAATAAAATCACT
Found at i:11254 original size:17 final size:17
Alignment explanation
Indices: 11232--11281 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
11222 AAACTTATAA
11232 AAATATTTTTAAAAATT
1 AAATATTTTTAAAAATT
**
11249 AAATATCATT-AAAATT
1 AAATATTTTTAAAAATT
11265 -AATAATTTTTAAAAATT
1 AAAT-ATTTTTAAAAATT
11282 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 3 0.11
16 10 0.37
17 14 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATTTTTAAAAATT
Found at i:15869 original size:36 final size:36
Alignment explanation
Indices: 15815--15886 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
15805 CCTATGAGAT
*
15815 TAGATTTTCCTAACTTTCTACAGATTTATTTGAGTC
1 TAGATTTTCCTAACTTTCTACAGATTTAATTGAGTC
* *
15851 TAGATTTTCCTGATTTTCTACAGATTTAATTGAGTC
1 TAGATTTTCCTAACTTTCTACAGATTTAATTGAGTC
15887 GATTTATCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (36 bp):
TAGATTTTCCTAACTTTCTACAGATTTAATTGAGTC
Found at i:17796 original size:13 final size:13
Alignment explanation
Indices: 17778--17802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17768 TTATAAATCT
17778 AAAATTTTTAAAA
1 AAAATTTTTAAAA
17791 AAAATTTTTAAA
1 AAAATTTTTAAA
17803 CACGAACCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTTTAAAA
Found at i:17879 original size:7 final size:7
Alignment explanation
Indices: 17867--17896 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
17857 TGCAACGACA
17867 GACTCGC
1 GACTCGC
17874 GACTCGC
1 GACTCGC
17881 GACTCGC
1 GACTCGC
17888 GACTCGC
1 GACTCGC
17895 GA
1 GA
17897 GTTAACTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.40, G:0.30, T:0.13
Consensus pattern (7 bp):
GACTCGC
Found at i:23484 original size:5 final size:6
Alignment explanation
Indices: 23467--23492 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23457 TTTATTAATT
23467 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
23493 TTAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:31434 original size:23 final size:23
Alignment explanation
Indices: 31403--31447 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31393 TCAATTATAA
31403 TATTATTA-TATTAATAATATTTT
1 TATTATTATTATTAA-AATATTTT
* *
31426 TATTTTTATTTTTAAAATATTT
1 TATTATTATTATTAAAATATTT
31448 AAAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTATTATTAAAATATTTT
Found at i:38588 original size:21 final size:21
Alignment explanation
Indices: 38523--38590 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
38513 GCATTACGGA
*
38523 GAAAAATTATATAAAATACAC
1 GAAAAATTATACAAAATACAC
** ***
38544 -AAAAAAAATACTTGA-ACAC
1 GAAAAATTATACAAAATACAC
38563 TGAAAAATTATACAAAATACAC
1 -GAAAAATTATACAAAATACAC
38585 GAAAAA
1 GAAAAA
38591 AATAACTAAG
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 4 0.12
20 9 0.27
21 16 0.48
22 4 0.12
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (21 bp):
GAAAAATTATACAAAATACAC
Found at i:38858 original size:30 final size:32
Alignment explanation
Indices: 38796--38860 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
38786 TAAAATTATA
*
38796 TTTTGTTTAGTATTTATTGTTTTAAGTTATTTG
1 TTTTGTTTAG-ATTTAATGTTTTAAGTTATTTG
38829 TTTTGTTTA-ATTTAAT-TTTTAA-TTGATTTG
1 TTTTGTTTAGATTTAATGTTTTAAGTT-ATTTG
38859 TT
1 TT
38861 ATTTAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (32 bp):
TTTTGTTTAGATTTAATGTTTTAAGTTATTTG
Found at i:38930 original size:23 final size:23
Alignment explanation
Indices: 38838--38923 Score: 100
Period size: 23 Copynumber: 3.6 Consensus size: 23
38828 GTTTTGTTTA
38838 ATTTAATTTTTAATTGATTTGTT
1 ATTTAATTTTTAATTGATTTGTT
* * * *
38861 ATTTAATGTTTTTATTTAGTTGAGTAA
1 ATTTAAT-TTTTAATTGA-TT-TGT-T
38888 ATTTAATTTTTAATTGATTTGTT
1 ATTTAATTTTTAATTGATTTGTT
38911 ATTTAATTTTTAA
1 ATTTAATTTTTAA
38924 GTTATTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 20 0.39
24 10 0.20
25 4 0.08
26 10 0.20
27 7 0.14
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
ATTTAATTTTTAATTGATTTGTT
Found at i:38941 original size:11 final size:11
Alignment explanation
Indices: 38893--38942 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
38883 AGTAAATTTA
38893 ATTTTTAATTG
1 ATTTTTAATTG
* *
38904 ATTTGTTATTTA
1 ATTT-TTAATTG
38916 ATTTTTAAGTT-
1 ATTTTTAA-TTG
38927 ATTTTTAATTG
1 ATTTTTAATTG
38938 ATTTT
1 ATTTT
38943 CTATTTTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.06
11 20 0.61
12 11 0.33
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (11 bp):
ATTTTTAATTG
Found at i:39087 original size:58 final size:57
Alignment explanation
Indices: 39024--39199 Score: 232
Period size: 58 Copynumber: 3.1 Consensus size: 57
39014 ATTTTGTATA
* *
39024 ATTTTTTCTAATAATGCCGCCATTTGATAACCCTCCACTAATATAATATTATTTTTTT
1 ATTTTTTCT-ATAATGTCGTCATTTGATAACCCTCCACTAATATAATATTATTTTTTT
* *
39082 ATTTTTTCCTATGATGTCGTCATTTGATAATCCTCCACTAATATAATATTA-TTTTTT
1 ATTTTTT-CTATAATGTCGTCATTTGATAACCCTCCACTAATATAATATTATTTTTTT
* * ** *
39139 A-TTTTT-TATAGTGTCGTTATTTGATAACCCTTTATTAATATAATATTATTTTTTT
1 ATTTTTTCTATAATGTCGTCATTTGATAACCCTCCACTAATATAATATTATTTTTTT
39194 ATTTTT
1 ATTTTT
39200 AAGATATAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
54 35 0.34
55 7 0.07
56 9 0.09
57 7 0.07
58 44 0.42
59 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.53
Consensus pattern (57 bp):
ATTTTTTCTATAATGTCGTCATTTGATAACCCTCCACTAATATAATATTATTTTTTT
Found at i:39178 original size:54 final size:58
Alignment explanation
Indices: 39044--39199 Score: 230
Period size: 54 Copynumber: 2.8 Consensus size: 58
39034 ATAATGCCGC
*
39044 CATTTGATAACCCTCCACTAATATAATATTATTTTTTTATTTTTTCCTATGATGTCGT
1 CATTTGATAACCCTCCACTAATATAATATTATTTTTTTATTTTTTCATATGATGTCGT
*
39102 CATTTGATAATCCTCCACTAATATAATATTA-TTTTTTATTTTTT-ATA-G-TGTCGT
1 CATTTGATAACCCTCCACTAATATAATATTATTTTTTTATTTTTTCATATGATGTCGT
* ** *
39156 TATTTGATAACCCTTTATTAATATAATATTATTTTTTTATTTTT
1 CATTTGATAACCCTCCACTAATATAATATTATTTTTTTATTTTT
39200 AAGATATAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
54 32 0.36
55 13 0.14
56 2 0.02
57 13 0.14
58 30 0.33
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.54
Consensus pattern (58 bp):
CATTTGATAACCCTCCACTAATATAATATTATTTTTTTATTTTTTCATATGATGTCGT
Found at i:41938 original size:18 final size:19
Alignment explanation
Indices: 41902--41940 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
41892 TCACATCAAC
**
41902 AAATAATTTAAAATTATAA
1 AAATAATTTAAAAAAATAA
41921 AAATAA-TTAAAAAAATAA
1 AAATAATTTAAAAAAATAA
41939 AA
1 AA
41941 TGCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAATTTAAAAAAATAA
Found at i:45684 original size:272 final size:271
Alignment explanation
Indices: 45199--45739 Score: 1028
Period size: 272 Copynumber: 2.0 Consensus size: 271
45189 ATGACCAAGG
*
45199 CATTTTTGAGTTTGGGGTCCCATCCCCATTGTTTTTGCCATTAACAGTGGTAGCAATAATCAACT
1 CATTTTTGAGTTTGGGGTCCCATCCCCATTGTTTTTGCCATTAACAGTGGCAGCAATAATCAACT
45264 TCTTGTCATTCCTATTGGTATTGACACAATTTTTTAGTGGAGAAATACGGAAGGCCTCTGTTTGC
66 TCTTGTCATTCCTATTGGTATTGACACAATTTTTTAGTGGAGAAATACGGAAGGCCTCTGTTTGC
45329 AGATGATTTTAACTGGTTCCATCGTCTTGAATTGCCTACCAGTTTATGGAGCCATTGGCTTAAGG
131 AGATGATTTTAACTGGTTCCATCGTCTTGAATTGCCTACCAGTTTATGGAGCCATTGGCTTAAGG
45394 AATGATTCAGGGAAAATGCCAACCCAAATTACTATTATCTCAACATTTGTGTCGGTGGCTCTCTA
196 AATGATTCAGGGAAAATGCCAACCCAAATTACTATTATCTCAACATTTGTGTCGGTGGCTCTCTA
45459 TTATGCCTCAA
261 TTATGCCTCAA
*
45470 CATTTTTGAGTTTTGGGTCCCATCCCCATTGTTTTTGCCATTAACAGTGGCAGCAATAATCAACT
1 CATTTTTGAGTTTGGGGTCCCATCCCCATTGTTTTTGCCATTAACAGTGGCAGCAATAATCAACT
* *
45535 TGTTGTCATTCCTATTGGTATTGACGCAATTTTTTAGTGGAGAAAATACGGAAGGCCTCTGTTTG
66 TCTTGTCATTCCTATTGGTATTGACACAATTTTTTAGTGGAG-AAATACGGAAGGCCTCTGTTTG
45600 CAGATGATTTTAACTGGTTCCATCGTCTTGAATTGCCTACCAGTTTATGGAGCCATTGGCTTAAG
130 CAGATGATTTTAACTGGTTCCATCGTCTTGAATTGCCTACCAGTTTATGGAGCCATTGGCTTAAG
*
45665 GAATGATTCAGGGAAAATGCTAACCCAAATTACTATTATCTCAACATTTGTGTCGGTGGCTCTCT
195 GAATGATTCAGGGAAAATGCCAACCCAAATTACTATTATCTCAACATTTGTGTCGGTGGCTCTCT
45730 ATTATGCCTC
260 ATTATGCCTC
45740 TTCACTTTGT
Statistics
Matches: 264, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
271 103 0.39
272 161 0.61
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (271 bp):
CATTTTTGAGTTTGGGGTCCCATCCCCATTGTTTTTGCCATTAACAGTGGCAGCAATAATCAACT
TCTTGTCATTCCTATTGGTATTGACACAATTTTTTAGTGGAGAAATACGGAAGGCCTCTGTTTGC
AGATGATTTTAACTGGTTCCATCGTCTTGAATTGCCTACCAGTTTATGGAGCCATTGGCTTAAGG
AATGATTCAGGGAAAATGCCAACCCAAATTACTATTATCTCAACATTTGTGTCGGTGGCTCTCTA
TTATGCCTCAA
Found at i:47321 original size:20 final size:20
Alignment explanation
Indices: 47296--47339 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
47286 ATAACATGCC
47296 AACTATATCTGATCTAGTCT
1 AACTATATCTGATCTAGTCT
47316 AACTATATCTGATCTAGTCT
1 AACTATATCTGATCTAGTCT
47336 AACT
1 AACT
47340 TAATGCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (20 bp):
AACTATATCTGATCTAGTCT
Found at i:48110 original size:18 final size:18
Alignment explanation
Indices: 48060--48110 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
48050 TTATATTTTA
48060 TATTAA-TAATATAAAATAT
1 TATTAATTAATAT--AATAT
* *
48079 TATTATTTATTATAATAT
1 TATTAATTAATATAATAT
48097 TATTAATTAATATA
1 TATTAATTAATATA
48111 TCTTTTGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 17 0.63
19 5 0.19
20 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAATTAATATAATAT
Found at i:50770 original size:25 final size:23
Alignment explanation
Indices: 50734--50857 Score: 101
Period size: 23 Copynumber: 5.3 Consensus size: 23
50724 CACTAGCGCT
50734 CTCTCT-ATTTAGCAC-GTCTCGTG
1 CTCTCTGA-TTAGCACTGTCT-GTG
*
50757 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG--ATTAGCACTGTCTGTG
* * *
50782 CTCTCTGATTAGCACTTTGTATG
1 CTCTCTGATTAGCACTGTCTGTG
* * *
50805 CTCTCTGATTAGCACTTTGTGTA
1 CTCTCTGATTAGCACTGTCTGTG
* *
50828 CTCTCT-ATTTAGCATTGTGTGTG
1 CTCTCTGA-TTAGCACTGTCTGTG
50851 CTCTCTG
1 CTCTCTG
50858 TTGTTCAGCA
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.01
23 65 0.75
25 17 0.20
26 4 0.05
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (23 bp):
CTCTCTGATTAGCACTGTCTGTG
Found at i:50792 original size:23 final size:23
Alignment explanation
Indices: 50754--50857 Score: 129
Period size: 23 Copynumber: 4.4 Consensus size: 23
50744 AGCACGTCTC
50754 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTGTGT
*
50779 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
50802 ATGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
50825 GTACTCTCT-ATTTAGCATTGTGT
1 GTGCTCTCTGA-TTAGCACTGTGT
50848 GTGCTCTCTG
1 GTGCTCTCTG
50858 TTGTTCAGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.01
23 59 0.84
25 10 0.14
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:50898 original size:69 final size:68
Alignment explanation
Indices: 50767--50902 Score: 170
Period size: 69 Copynumber: 2.0 Consensus size: 68
50757 CTCTCTGTTA
50767 TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTATGCTCTCTGATTAGCACTTTGTGTACTCT
1 TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTG-ATGCTCTCTGATTAGCACTTTGTGTACTCT
50832 CTAT
65 CTAT
* * * *
50836 TTAGCATTGTGTGTGCTCTCTGTTGTTCAGCACTTATG-TGCTCTCTG-TTAGTAGTTTG-GTAC
1 TTAGCACTGTGTGTGCTCTCTG--ATT-AGCACTT-TGATGCTCTCTGATTAGCACTTTGTGTAC
50898 TCTCT
62 TCTCT
50903 GTTTGTTTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
69 30 0.51
70 9 0.15
71 11 0.19
72 7 0.12
73 2 0.03
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (68 bp):
TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGATGCTCTCTGATTAGCACTTTGTGTACTCTC
TAT
Found at i:52650 original size:25 final size:26
Alignment explanation
Indices: 52619--52697 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 26
52609 AAAAAAAAAT
52619 ACTCACACCAAATTATAGAATTAAAG
1 ACTCACACCAAATTATAGAATTAAAG
* * ** *
52645 A-TCACATCAGTATATTA-AAAAAAAAAT
1 ACTCACACCA--A-ATTATAGAATTAAAG
52672 ACTCACACCAAATTATAGAATTAAAG
1 ACTCACACCAAATTATAGAATTAAAG
52698 TTTGTATCTA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
25 11 0.29
26 8 0.21
27 8 0.21
28 11 0.29
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.24
Consensus pattern (26 bp):
ACTCACACCAAATTATAGAATTAAAG
Found at i:52654 original size:52 final size:53
Alignment explanation
Indices: 52593--52697 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
52583 CTACTATATA
52593 ATCACATCAGTATATT-AAAAAAAAATACTCACACCAAATTATAGAATTAAAG
1 ATCACATCAGTATATTAAAAAAAAAATACTCACACCAAATTATAGAATTAAAG
52645 ATCACATCAGTATATTAAAAAAAAAATACTCACACCAAATTATAGAATTAAAG
1 ATCACATCAGTATATTAAAAAAAAAATACTCACACCAAATTATAGAATTAAAG
52698 TTTGTATCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 16 0.31
53 36 0.69
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (53 bp):
ATCACATCAGTATATTAAAAAAAAAATACTCACACCAAATTATAGAATTAAAG
Done.