Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011464.1 Kokia drynarioides strain JFW-HI SEQ_126448, 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: 106138
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 85 characters in sequence are not A, C, G, or T
Found at i:389 original size:41 final size:41
Alignment explanation
Indices: 300--616 Score: 313
Period size: 41 Copynumber: 7.8 Consensus size: 41
290 TAACGGCGTT
* * *
300 TTTCACATAAGCGTCGCTAATGCA-CTGACCTTT---GGCGC
1 TTTCCCATAAGCGCCGCTATTG-ATCTGACCTTTAGCGGCGC
** *
338 TTTTACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * *
379 TTTCCCATAAGCGTCGCTATTGATATGACCTTTAGCGACGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* *
420 TTTCTCATAAGC-CCGCTATTGATCTGACCTTTAGCGACGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * *
460 -TTCCTCATAAGCACCGTTATTGCTCTGACCTTTAGCGGCGC
1 TTTCC-CATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
*** * * *
501 TTGATCATAAGCACCGCTATTGATCTGACCTTTAGTGGTGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * * * * *
542 TTGCCTATAAGCGTCGGTATTGATATGACCTTTAGCAGCGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * *
583 TTTCTCATAAGCGTCGCTATTGCTCTGACCTTTA
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTA
617 ACAGTGCTTA
Statistics
Matches: 232, Mismatches: 40, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
38 28 0.12
39 3 0.01
40 33 0.14
41 167 0.72
42 1 0.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (41 bp):
TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
Found at i:563 original size:82 final size:81
Alignment explanation
Indices: 333--616 Score: 356
Period size: 82 Copynumber: 3.5 Consensus size: 81
323 ACTGACCTTT
* *
333 GGCGCTTT-TACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCGCT
1 GGCGCTTTCT-CATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC-TTCCTATAAGCGTCGCT
397 ATTGATATGACCTTTAGC
64 ATTGATATGACCTTTAGC
* * ** *
415 GACGCTTTCTCATAAGC-CCGCTATTGATCTGACCTTTAGCGACGCTTCCTCATAAGCACCGTTA
1 GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGCTTCCT-ATAAGCGTCGCTA
* *
479 TTGCTCTGACCTTTAGC
65 TTGATATGACCTTTAGC
** * * * *
496 GGCGCTTGATCATAAGCACCGCTATTGATCTGACCTTTAGTGGTGCTTGCCTATAAGCGTCGGTA
1 GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGCTT-CCTATAAGCGTCGCTA
561 TTGATATGACCTTTAGC
65 TTGATATGACCTTTAGC
* * *
578 AGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACCTTTA
1 GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTA
617 ACAGTGCTTA
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 4 0.02
81 65 0.38
82 99 0.58
83 4 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (81 bp):
GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGCTTCCTATAAGCGTCGCTAT
TGATATGACCTTTAGC
Found at i:3531 original size:17 final size:18
Alignment explanation
Indices: 3510--3552 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3500 TATAAGAATG
3510 GAAATGCAACT-AT-AAT
1 GAAATGCAACTAATAAAT
3526 GAAAATGC-ACTAATAAAT
1 G-AAATGCAACTAATAAAT
3544 GAAATGCAA
1 GAAATGCAA
3553 TGACAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 14 0.61
18 5 0.22
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (18 bp):
GAAATGCAACTAATAAAT
Found at i:3566 original size:18 final size:18
Alignment explanation
Indices: 3545--3581 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3535 CTAATAAATG
3545 AAATGCAATGACAAATAA
1 AAATGCAATGACAAATAA
* *
3563 AAATGTAATGACAACTAA
1 AAATGCAATGACAAATAA
3581 A
1 A
3582 TAAGATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:4072 original size:18 final size:16
Alignment explanation
Indices: 4049--4095 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
4039 CCCTTAATTC
4049 TCTTTCTCATGTCCTTCT
1 TCTTTCTCATG--CTTCT
4067 TCTTTCTC-TGCTTCT
1 TCTTTCTCATGCTTCT
* *
4082 TCTTCCTCAAGCTT
1 TCTTTCTCATGCTT
4096 GTCCTACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 2 0.08
18 8 0.31
ACGTcount: A:0.06, C:0.34, G:0.06, T:0.53
Consensus pattern (16 bp):
TCTTTCTCATGCTTCT
Found at i:9197 original size:3 final size:3
Alignment explanation
Indices: 9189--9221 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
9179 AATATAAGTA
9189 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9222 AATAAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11477 original size:49 final size:49
Alignment explanation
Indices: 11406--11512 Score: 162
Period size: 49 Copynumber: 2.2 Consensus size: 49
11396 CTGGATGAGT
*
11406 AAAAT-TTTGATATATTATGTATAGTTAAGTCTACTGTACATGCCGTCA
1 AAAATATTTGATATATTATGTATAGCTAAGTCTACTGTACATGCCGTCA
* * *
11454 AAAATATTTGATATATTATGTATAGCTAAGTTTAGTGTACATGCTGTCA
1 AAAATATTTGATATATTATGTATAGCTAAGTCTACTGTACATGCCGTCA
11503 ATAAATATTT
1 A-AAATATTT
11513 AGGTTGAGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 5 0.09
49 40 0.75
50 8 0.15
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (49 bp):
AAAATATTTGATATATTATGTATAGCTAAGTCTACTGTACATGCCGTCA
Found at i:24732 original size:13 final size:14
Alignment explanation
Indices: 24714--24743 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24704 GTGAACGCAA
24714 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
24727 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
24741 TCA
1 TCA
24744 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:27294 original size:12 final size:12
Alignment explanation
Indices: 27279--27314 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27269 CTTCTTTTTA
27279 TTCTCTTCTTCC
1 TTCTCTTCTTCC
27291 TTCTCTTCTT-C
1 TTCTCTTCTTCC
27302 TTC-CTT-TTCC
1 TTCTCTTCTTCC
27312 TTC
1 TTC
27315 AGCTGGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 4 0.17
12 10 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:54208 original size:10 final size:10
Alignment explanation
Indices: 54195--54234 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
54185 AAAAAATCAC
54195 AAAAAGAAAG
1 AAAAAGAAAG
*
54205 AAAATGAAAG
1 AAAAAGAAAG
54215 AAAAAGAAACG
1 AAAAAGAAA-G
54226 AGAAAAGAA
1 A-AAAAGAA
54235 TAGGAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 2 0.08
12 7 0.27
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:56842 original size:24 final size:24
Alignment explanation
Indices: 56805--56861 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
56795 AATCTTTTAG
*
56805 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTCTTTATTTGTTTCAA
*
56829 TTAAACTTTCTTTATTTGTTTCAA
1 TTAAACTCTCTTTATTTGTTTCAA
*
56853 TCAAACTCT
1 TTAAACTCT
56862 AATTAGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (24 bp):
TTAAACTCTCTTTATTTGTTTCAA
Found at i:73673 original size:10 final size:11
Alignment explanation
Indices: 73660--73707 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
73650 AAAAATTCAC
73660 AAAAAG-AAAG
1 AAAAAGAAAAG
73670 AAAAAG-AAAG
1 AAAAAGAAAAG
*
73680 AAGAAGAAAAG
1 AAAAAGAAAAG
73691 AGAAAAGAAAAG
1 A-AAAAGAAAAG
73703 AAAAA
1 AAAAA
73708 TATTGTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 15 0.44
11 9 0.26
12 10 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:73694 original size:17 final size:16
Alignment explanation
Indices: 73661--73707 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
73651 AAAATTCACA
73661 AAAAG-AAAGAAAAAG
1 AAAAGAAAAGAAAAAG
73676 -AAAGAAGAAGAAAAGAG
1 AAAAGAA-AAGAAAA-AG
73693 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
73708 TATTGTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 8 0.29
17 9 0.32
18 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:77461 original size:24 final size:24
Alignment explanation
Indices: 77434--77490 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
77424 AATCTTTCGG
77434 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
77458 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
77482 TCAAACTCT
1 TTAAACTCT
77491 AATTAATTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:78079 original size:235 final size:236
Alignment explanation
Indices: 77662--78134 Score: 840
Period size: 235 Copynumber: 2.0 Consensus size: 236
77652 GAGGTTTAGT
*
77662 TTTCATCTCCATCTTTTGTACTCTTTATTCTTTTGCCATTATAGTAAAATTATTTTTGCTCGTGG
1 TTTCATCTCCATCTTTTGTACTCTTTATTCTTTTGCCATTATAGTAAAATTATTTTTGCCCGTGG
*
77727 TTTTTTATCCTCTTCGAAGGAGTTTTTTCATGTTAAATTTGTGTGTTCAATTTCTTAATTTCTTC
66 TTTTTTATCCTCTTCGAAGGAGTTTTTTCATGTTAAATTTGTGTGTTCAAATTCTTAATTTCTTC
* * * * *
77792 CACTGATTTTATTTTTTCGGTACTTAATCAGGTCAATCCCCAATAGTAAGCCAACTATGGAATCT
131 CACTGATTTTAATTTTTCGATACTTAATCAGGTCAATCCCCAACAGTAAGCCAACTATGAAATCC
77857 ATTACAATTCTCTCCAACTTCCATTTGGTTATTGTTATAGG
196 ATTACAATTCTCTCCAACTTCCATTTGGTTATTGTTATAGG
*
77898 TTTCGTCTCCATCTTTTGTACTCTTTATTCTTTTGCCATTATAGTAAAATTATTTTTGCCCGTGG
1 TTTCATCTCCATCTTTTGTACTCTTTATTCTTTTGCCATTATAGTAAAATTATTTTTGCCCGTGG
* *
77963 -TTTTTATCCTCTTTGGAGGAGTTTTTTCATGTTAAATTTGTGTGTTCAAATTCTTAATTTCTTC
66 TTTTTTATCCTCTTCGAAGGAGTTTTTTCATGTTAAATTTGTGTGTTCAAATTCTTAATTTCTTC
*
78027 CACTGATTTTAATTTTTCGATACTTAATCGGGTCAATCCCCAACAGTAAGCCAACTATGAAATCC
131 CACTGATTTTAATTTTTCGATACTTAATCAGGTCAATCCCCAACAGTAAGCCAACTATGAAATCC
78092 ATTACAATTCTCTCCAACTTCCATTTGGTTATTGTTATAGG
196 ATTACAATTCTCTCCAACTTCCATTTGGTTATTGTTATAGG
78133 TT
1 TT
78135 GTAACAATCC
Statistics
Matches: 226, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
235 163 0.72
236 63 0.28
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (236 bp):
TTTCATCTCCATCTTTTGTACTCTTTATTCTTTTGCCATTATAGTAAAATTATTTTTGCCCGTGG
TTTTTTATCCTCTTCGAAGGAGTTTTTTCATGTTAAATTTGTGTGTTCAAATTCTTAATTTCTTC
CACTGATTTTAATTTTTCGATACTTAATCAGGTCAATCCCCAACAGTAAGCCAACTATGAAATCC
ATTACAATTCTCTCCAACTTCCATTTGGTTATTGTTATAGG
Found at i:78859 original size:20 final size:20
Alignment explanation
Indices: 78809--78882 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
78799 GAAAAGTTTG
* *
78809 AAATAATTTTAAAATCAAGTTA
1 AAATAATTTT-AAA-CATGTCA
*
78831 AAATGATTTTAAACATGTCA
1 AAATAATTTTAAACATGTCA
*
78851 AAATAA-TTTGAACTATGTCA
1 AAATAATTTTAAAC-ATGTCA
*
78871 AAATCATTTTAA
1 AAATAATTTTAA
78883 CACTTCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 6 0.14
20 21 0.49
21 7 0.16
22 9 0.21
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (20 bp):
AAATAATTTTAAACATGTCA
Found at i:79077 original size:20 final size:22
Alignment explanation
Indices: 79054--79093 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
79044 ACTTTAGCGG
79054 TATCGATA-ATTT-CTAAAACA
1 TATCGATACATTTGCTAAAACA
79074 TATCGATACATTTGCTAAAA
1 TATCGATACATTTGCTAAAA
79094 AACGACACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (22 bp):
TATCGATACATTTGCTAAAACA
Found at i:85867 original size:19 final size:19
Alignment explanation
Indices: 85843--85881 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
85833 CATACGAAAG
85843 AAAGATTTCTTCATGACAT
1 AAAGATTTCTTCATGACAT
85862 AAAGATTTCTTCATGACAT
1 AAAGATTTCTTCATGACAT
85881 A
1 A
85882 GAAAAATATT
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:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (19 bp):
AAAGATTTCTTCATGACAT
Found at i:89230 original size:12 final size:13
Alignment explanation
Indices: 89213--89245 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
89203 GTGAATTGAG
89213 TTAGTTTTTA-TT
1 TTAGTTTTTAGTT
89225 TTAGTTTTTAGTT
1 TTAGTTTTTAGTT
89238 TTAGTTTT
1 TTAGTTTT
89246 CATGAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (13 bp):
TTAGTTTTTAGTT
Found at i:98558 original size:20 final size:20
Alignment explanation
Indices: 98508--98612 Score: 70
Period size: 20 Copynumber: 5.2 Consensus size: 20
98498 GAAAAGTTTG
*
98508 AAATAATTTTAAAATCAAGTTA
1 AAATAATTTT-AAA-CAAGTCA
* *
98530 AAATGATTTTAAACATGTCA
1 AAATAATTTTAAACAAGTCA
*
98550 AAATAA-TTTGAACTAAGTCA
1 AAATAATTTTAAAC-AAGTCA
* **
98570 AAATCATTTT-AACACTTCA
1 AAATAATTTTAAACAAGTCA
* **
98589 AAGTGTTTTTCAAACAAGTCA
1 AAATAATTTT-AAACAAGTCA
98610 AAA
1 AAA
98613 CAGCTCTAGG
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
19 17 0.27
20 23 0.36
21 15 0.23
22 9 0.14
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (20 bp):
AAATAATTTTAAACAAGTCA
Found at i:99943 original size:18 final size:18
Alignment explanation
Indices: 99918--99967 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
99908 AAGAGGAAGG
99918 ACAAAAAGTACAATTTAA
1 ACAAAAAGTACAATTTAA
*
99936 AGAAAAAGTACAATTTAA
1 ACAAAAAGTACAATTTAA
*
99954 CCAAAAAGTACAAT
1 ACAAAAAGTACAAT
99968 GAGTTGTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (18 bp):
ACAAAAAGTACAATTTAA
Found at i:101043 original size:6 final size:6
Alignment explanation
Indices: 101032--101061 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
101022 AAAATCATTC
101032 ATAAAT ATAAAT ATAAAT ATATAAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATA-AAT ATAAA
101062 GTCTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:101068 original size:14 final size:13
Alignment explanation
Indices: 101032--101074 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
101022 AAAATCATTC
101032 ATAAATATA-AAT
1 ATAAATATATAAT
101044 ATAAATATATAAT
1 ATAAATATATAAT
*
101057 ATAAAGTCTATAAT
1 ATAAA-TATATAAT
101071 -TAAA
1 ATAAA
101075 ATAAAATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 12 0.43
14 7 0.25
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
ATAAATATATAAT
Found at i:102311 original size:29 final size:29
Alignment explanation
Indices: 102279--102348 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
102269 TATCGATCAA
* *
102279 CGGTCAACGGTCGGTCAATGGTCAACGGT
1 CGGTCAACGGTCGATCAATGATCAACGGT
**
102308 CGGTCAATAGTCGATCAATGATCAACGGT
1 CGGTCAACGGTCGATCAATGATCAACGGT
*
102337 CGATCAACGGTC
1 CGGTCAACGGTC
102349 AAACCTGAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (29 bp):
CGGTCAACGGTCGATCAATGATCAACGGT
Found at i:102315 original size:18 final size:18
Alignment explanation
Indices: 102275--102315 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
102265 CAACTATCGA
*
102275 TCAACGGTCAACGGTCGG
1 TCAATGGTCAACGGTCGG
102293 TCAATGGTCAACGGTCGG
1 TCAATGGTCAACGGTCGG
102311 TCAAT
1 TCAAT
102316 AGTCGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (18 bp):
TCAATGGTCAACGGTCGG
Found at i:102350 original size:18 final size:18
Alignment explanation
Indices: 102271--102350 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 18
102261 CAGTCAACTA
102271 TCGATCAACGGTCAACGG
1 TCGATCAACGGTCAACGG
* *
102289 TCGGTCAATGGTCAACGG
1 TCGATCAACGGTCAACGG
*
102307 TCGGTCAA---T--A--G
1 TCGATCAACGGTCAACGG
* *
102318 TCGATCAATGATCAACGG
1 TCGATCAACGGTCAACGG
102336 TCGATCAACGGTCAA
1 TCGATCAACGGTCAA
102351 ACCTGAATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
11 8 0.16
13 1 0.02
14 1 0.02
15 1 0.02
16 1 0.02
18 38 0.76
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (18 bp):
TCGATCAACGGTCAACGG
Found at i:102424 original size:17 final size:17
Alignment explanation
Indices: 102399--102443 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
102389 GGATTGATTT
*
102399 GGGTT-TTGGGTTTTAA
1 GGGTTATTGGGTATTAA
102415 GGGTTATTGGGTATTAA
1 GGGTTATTGGGTATTAA
102432 GGGTTATTGGGT
1 GGGTTATTGGGT
102444 CACTTATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (17 bp):
GGGTTATTGGGTATTAA
Done.