Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000811.1 Kokia drynarioides strain JFW-HI SEQ_111892, 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: 108639
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:4214 original size:94 final size:93
Alignment explanation
Indices: 4032--4221 Score: 265
Period size: 94 Copynumber: 2.0 Consensus size: 93
4022 AAGAACTAAA
* ** * *
4032 AGGCTTAAATAGAATTATTTAATGTTTCGAAGGGGCTCGAGGGTTAAAATTTTTGTAATTAGATA
1 AGGCTTAAATAGAATTATTTAATGTTTCAAAAAGGCTCGAGAGTTAAAATTTTAGTAATTAGATA
* * *
4097 GCCAAAATTGAAATGCTCTAAAAGTTAG
66 ACCAAAATTGAAATACTCTAAAAGCTAG
* *
4125 AGGCTTAAATAGAATTATTTAATGTTTCAAAAAGGCTTGA-AGTTTAAATTTTCCAGTAATTAGA
1 AGGCTTAAATAGAATTATTTAATGTTTCAAAAAGGCTCGAGAGTTAAAATTTT--AGTAATTAGA
4189 TAACCAAAATTGAAATACTCTAAAAGCTAG
64 TAACCAAAATTGAAATACTCTAAAAGCTAG
4219 AGG
1 AGG
4222 ACCATCGGTG
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 10 0.12
93 36 0.42
94 39 0.46
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (93 bp):
AGGCTTAAATAGAATTATTTAATGTTTCAAAAAGGCTCGAGAGTTAAAATTTTAGTAATTAGATA
ACCAAAATTGAAATACTCTAAAAGCTAG
Found at i:5001 original size:21 final size:21
Alignment explanation
Indices: 4977--5016 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4967 ACTGTTGGAA
*
4977 GAGGAAGAGGAGGAGGAAGTG
1 GAGGAAGAAGAGGAGGAAGTG
4998 GAGGAAGAAGAGGAGGAAG
1 GAGGAAGAAGAGGAGGAAG
5017 AGTCGGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.55, T:0.03
Consensus pattern (21 bp):
GAGGAAGAAGAGGAGGAAGTG
Found at i:5015 original size:12 final size:12
Alignment explanation
Indices: 4980--5017 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4970 GTTGGAAGAG
*
4980 GAAGAGGAGGAG
1 GAAGAGGAGGAA
*
4992 GAAGTGGAGGAA
1 GAAGAGGAGGAA
5004 GAAGAGGAGGAA
1 GAAGAGGAGGAA
5016 GA
1 GA
5018 GTCGGAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.03
Consensus pattern (12 bp):
GAAGAGGAGGAA
Found at i:7935 original size:18 final size:19
Alignment explanation
Indices: 7899--7936 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
7889 CTTTTAAAAT
*
7899 ATATATTTTTTATTGAATG
1 ATATATTTTTTACTGAATG
*
7918 ATATTTTTTTTACT-AATG
1 ATATATTTTTTACTGAATG
7936 A
1 A
7937 CCGGAAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (19 bp):
ATATATTTTTTACTGAATG
Found at i:11563 original size:28 final size:28
Alignment explanation
Indices: 11531--11585 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
11521 GTTTAAAAGG
*
11531 TATTTTTAGATGGTGAGATAAAACATAA
1 TATTTTTAGATAGTGAGATAAAACATAA
* *
11559 TATTTTTAGGTAGTGAGATAAAGCATA
1 TATTTTTAGATAGTGAGATAAAACATA
11586 TTTAAGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (28 bp):
TATTTTTAGATAGTGAGATAAAACATAA
Found at i:18287 original size:26 final size:26
Alignment explanation
Indices: 18236--18288 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
18226 TTCTATGGTT
* *
18236 TAGAAAATTCTAAAAAGATATGAAAA
1 TAGAAAATTCTAAAAAAATATCAAAA
18262 TAGAAAATTCTAATAAAAAT-TCAAAA
1 TAGAAAATTCTAA-AAAAATATCAAAA
18288 T
1 T
18289 TCAAAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (26 bp):
TAGAAAATTCTAAAAAAATATCAAAA
Found at i:18294 original size:26 final size:26
Alignment explanation
Indices: 18239--18295 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
18229 TATGGTTTAG
* * *
18239 AAAATTCTAAAAAGATATGAAAATAG
1 AAAATTCTAAAAAAATATCAAAATAC
*
18265 AAAATTCTAATAAAAAT-TCAAAATTC
1 AAAATTCTAA-AAAAATATCAAAATAC
18291 AAAAT
1 AAAAT
18296 CATTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26
Consensus pattern (26 bp):
AAAATTCTAAAAAAATATCAAAATAC
Found at i:26426 original size:17 final size:18
Alignment explanation
Indices: 26390--26436 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
26380 AAAATTTAAA
26390 AATATTTTTATAATTCTTT
1 AATA-TTTTATAATTCTTT
*
26409 AATATTTTA-AATTTTTT
1 AATATTTTATAATTCTTT
26426 AATAATTTTAT
1 AAT-ATTTTAT
26437 TTTTTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 11 0.44
19 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTTTATAATTCTTT
Found at i:27787 original size:26 final size:27
Alignment explanation
Indices: 27756--27807 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
27746 TTGTATTCAA
* * *
27756 TTATCACTTTTATA-TTTAATTTTTTT
1 TTATCAATTTGATACTTTAAGTTTTTT
27782 TTATCAATTTGATACTTTAAGTTTTT
1 TTATCAATTTGATACTTTAAGTTTTT
27808 AATCCGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (27 bp):
TTATCAATTTGATACTTTAAGTTTTTT
Found at i:28582 original size:11 final size:10
Alignment explanation
Indices: 28534--28583 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
28524 TAAAAATGTG
28534 GAAAATTAAA
1 GAAAATTAAA
*
28544 -AAAA-AAAA
1 GAAAATTAAA
*
28552 G-AAATAAAA
1 GAAAATTAAA
28561 GAAAATTAAA
1 GAAAATTAAA
28571 GAAAACTTAAA
1 GAAAA-TTAAA
28582 GA
1 GA
28584 TAGGCCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 6 0.18
9 9 0.26
10 12 0.35
11 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (10 bp):
GAAAATTAAA
Found at i:45476 original size:25 final size:26
Alignment explanation
Indices: 45438--45490 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
45428 AAAATTGAGA
* *
45438 TTTTTTTTAATTTTTTAATTTTCTTTC
1 TTTTTTTT-ATTTTTTAAATTTATTTC
45465 TTTTTTTT-TTTTTTAAATTTATTTC
1 TTTTTTTTATTTTTTAAATTTATTTC
45490 T
1 T
45491 GGAAAACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.67
27 8 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTTTTATTTTTTAAATTTATTTC
Found at i:47664 original size:28 final size:28
Alignment explanation
Indices: 47567--47722 Score: 70
Period size: 28 Copynumber: 5.6 Consensus size: 28
47557 TAATGCCATG
* * **
47567 TACAGCTCGGGTAGAGCTATGATCTGCT
1 TACATCTCGGTTAGAGCTATGATCTATT
* * * *
47595 TACGTCTCGTTTAGAGCGTAT-AGC-ATG
1 TACATCTCGGTTAGAGC-TATGATCTATT
* *
47622 TACAACTCAAG-TAGAGCTATGATCTATT
1 TACATCTC-GGTTAGAGCTATGATCTATT
* * * *
47650 TACATCTCGGTTAGAG-TGTAATGCCATG
1 TACATCTCGGTTAGAGCTATGAT-CTATT
* * *
47678 TACAGCTC-GTGTAGAGCTATGACCTACT
1 TACATCTCGGT-TAGAGCTATGATCTATT
* *
47706 TACATCTTGATTAGAGC
1 TACATCTCGGTTAGAGC
47723 ATAATGCCAT
Statistics
Matches: 89, Mismatches: 30, Indels: 18
0.65 0.22 0.13
Matches are distributed among these distances:
26 3 0.03
27 21 0.24
28 58 0.65
29 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (28 bp):
TACATCTCGGTTAGAGCTATGATCTATT
Found at i:47692 original size:111 final size:112
Alignment explanation
Indices: 47549--47754 Score: 308
Period size: 111 Copynumber: 1.8 Consensus size: 112
47539 TACGTCACGT
* * * * *
47549 TTAGAGCGTAATGCCATGTACAGCTCGGGTAGAGCTATGATCTGCTTACGTCTCGTTTAGAGCGT
1 TTAGAGCGTAATGCCATGTACAGCTCGGGTAGAGCTATGACCTACTTACATCTCGATTAGAGCAT
47614 -ATAG-CATGTACAACTCAAGTAGAGCTATGATCTATTTACATCTCGG
66 AAT-GCCATGTACAACTCAAGTAGAGCTATGATCTATTTACATCTCGG
* * *
47660 TTAGAGTGTAATGCCATGTACAGCTCGTGTAGAGCTATGACCTACTTACATCTTGATTAGAGCAT
1 TTAGAGCGTAATGCCATGTACAGCTCGGGTAGAGCTATGACCTACTTACATCTCGATTAGAGCAT
*
47725 AATGCCATGTACAGCTCAAGTAGAGCTATG
66 AATGCCATGTACAACTCAAGTAGAGCTATG
47755 TTTTGCTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 58 0.69
112 26 0.31
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (112 bp):
TTAGAGCGTAATGCCATGTACAGCTCGGGTAGAGCTATGACCTACTTACATCTCGATTAGAGCAT
AATGCCATGTACAACTCAAGTAGAGCTATGATCTATTTACATCTCGG
Found at i:47776 original size:56 final size:56
Alignment explanation
Indices: 47456--47782 Score: 307
Period size: 56 Copynumber: 5.9 Consensus size: 56
47446 TCATTGAAGG
* * * ** *
47456 ACAGCTCGAGTGGAGCTATGATTTGCTTACGTCTTAGTTAGAGCATAATGCCATGA
1 ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAATGCCATGT
* * * * * * * * *
47512 ACAGTTTAGGTAAAGCTTTGATATGCTTACGTCACGTTTAGAGCGTAATGCCATGT
1 ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAATGCCATGT
** * *
47568 ACAGCTCGGGTAGAGCTATGATCTGCTTACGTCTCGTTTAGAGCGT-ATAG-CATGT
1 ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAAT-GCCATGT
* ** * **
47623 ACAACTCAAGTAGAGCTATGATCTATTTACATCTCGGTTAGAGTGTAATGCCATGT
1 ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAATGCCATGT
** * * * * *
47679 ACAGCTCGTGTAGAGCTATGACCTACTTACATCTTGATTAGAGCATAATGCCATGT
1 ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAATGCCATGT
* * **
47735 ACAGCTCAAGTAGAGCTATGTTTTGCTTTTGTCTCGGTTAGAGCATAA
1 ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAA
47783 GGCTATGGAA
Statistics
Matches: 219, Mismatches: 49, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
55 46 0.21
56 173 0.79
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (56 bp):
ACAGCTCAAGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCATAATGCCATGT
Found at i:49275 original size:18 final size:18
Alignment explanation
Indices: 49254--49307 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
49244 TAATTGATAT
*
49254 GGAGGATATATTTGAGGA
1 GGAGGATACATTTGAGGA
* * *
49272 GGAGGATACATTGGTGGT
1 GGAGGATACATTTGAGGA
*
49290 GGAGGATGCATTTGAGGA
1 GGAGGATACATTTGAGGA
49308 TGATATGACA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.43, T:0.26
Consensus pattern (18 bp):
GGAGGATACATTTGAGGA
Found at i:53846 original size:20 final size:22
Alignment explanation
Indices: 53806--53848 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53796 ACTCAGGCAG
*
53806 AAATTAAACACTTCTTTAAGAC
1 AAATTAAACACTACTTTAAGAC
53828 AAATTAAACAC-AC-TTAAGAC
1 AAATTAAACACTACTTTAAGAC
53848 A
1 A
53849 CACAATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (22 bp):
AAATTAAACACTACTTTAAGAC
Found at i:63224 original size:17 final size:17
Alignment explanation
Indices: 63208--63239 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
63198 TTTTTCTTGT
63208 TAGTT-CATTTGCATTG
1 TAGTTGCATTTGCATTG
63224 TAGTTGCATTTGCATT
1 TAGTTGCATTTGCATT
63240 CTTATTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (17 bp):
TAGTTGCATTTGCATTG
Found at i:76819 original size:6 final size:6
Alignment explanation
Indices: 76810--76859 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
76800 TTTGAGAATG
* *
76810 AGAAAA AG-AAA AGAAAA A-AAAA AGAAAA AGAGAG AG-AAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
76855 AGAAA
1 AGAAA
76860 TATTGCTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 13 0.35
6 24 0.65
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:76824 original size:17 final size:16
Alignment explanation
Indices: 76804--76854 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
76794 ATAAAATTTG
76804 AGAATGAGAAAAAGAAA
1 AGAA-GAGAAAAAGAAA
* *
76821 AGAAAAAAAAAAGAAA
1 AGAAGAGAAAAAGAAA
76837 A-AGAGAGAGAAAAGAAA
1 AGA-AGAGA-AAAAGAAA
76854 A
1 A
76855 AGAAATATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 14 0.50
17 13 0.46
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
AGAAGAGAAAAAGAAA
Found at i:76826 original size:11 final size:11
Alignment explanation
Indices: 76810--76859 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
76800 TTTGAGAATG
76810 AGAAAAAGAAA
1 AGAAAAAGAAA
*
76821 AGAAAAAAAAA
1 AGAAAAAGAAA
*
76832 AGAAAAAG-AG
1 AGAAAAAGAAA
76842 AGAGAAAAGAAAA
1 AGA-AAAAG-AAA
76855 AGAAA
1 AGAAA
76860 TATTGCTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.12
11 22 0.69
12 2 0.06
13 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:79559 original size:51 final size:51
Alignment explanation
Indices: 79483--79667 Score: 223
Period size: 51 Copynumber: 3.6 Consensus size: 51
79473 CTATAAACGA
79483 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * *
79534 AAAGGTCTGGTGACTAAGTGTCATCGTGAGTAAATGAATTCATGATGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * * * *
79585 AAAGGTCTGATGACTCAGTGTTATCATGAGT--ATGAATTCCTATACGGAAT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATT
*
79635 AAGAGGTCTGATGAC-AATATGTCATCGTGAGTA
1 AA-AGGTCTGATGACTAA-GTGTCATCGTGAGTA
79668 TGAATGAGTT
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
49 5 0.04
50 10 0.09
51 97 0.87
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:79659 original size:102 final size:101
Alignment explanation
Indices: 79483--79667 Score: 248
Period size: 102 Copynumber: 1.8 Consensus size: 101
79473 CTATAAACGA
* * * * *
79483 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCTGGTGAC
1 AAAGGTCTGATGACTAAGTGTCATCATGAGT-AATGAATCCTATACGGAATAAAGGTCTGATGAC
*
79548 TAAGTGTCATCGTGAGTAAATGAATTCATGATGGATT
65 TAAATGTCATCGTGAGTAAATGAATTCATGATGGATT
* *
79585 AAAGGTCTGATGACTCAGTGTTATCATGAGT-ATGAATTCCTATACGGAATAAGAGGTCTGATGA
1 AAAGGTCTGATGACTAAGTGTCATCATGAGTAATGAA-TCCTATACGGAATAA-AGGTCTGATGA
79649 C-AATATGTCATCGTGAGTA
64 CTAA-ATGTCATCGTGAGTA
79668 TGAATGAGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 5 0.07
101 14 0.19
102 53 0.74
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (101 bp):
AAAGGTCTGATGACTAAGTGTCATCATGAGTAATGAATCCTATACGGAATAAAGGTCTGATGACT
AAATGTCATCGTGAGTAAATGAATTCATGATGGATT
Found at i:95403 original size:26 final size:26
Alignment explanation
Indices: 95353--95404 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
95343 TATTAATTAC
* *
95353 ATTAATTAAAAATATAATATTTAAAA
1 ATTAATTAAAAATATAACATGTAAAA
95379 ATTAATTAAAAAT-TAAACATGTAAAA
1 ATTAATTAAAAATAT-AACATGTAAAA
95405 TCAAATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
ATTAATTAAAAATATAACATGTAAAA
Found at i:96606 original size:19 final size:19
Alignment explanation
Indices: 96584--96636 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
96574 TTAGAAGTTA
96584 ATAAAAACAATAAAATTTT
1 ATAAAAACAATAAAATTTT
***
96603 ATAAAATGTATAAAA-TTT
1 ATAAAAACAATAAAATTTT
96621 ATTAAAAACAA-AAAAT
1 A-TAAAAACAATAAAAT
96637 AGAAAAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAAACAATAAAATTTT
Found at i:96862 original size:9 final size:9
Alignment explanation
Indices: 96848--96944 Score: 56
Period size: 10 Copynumber: 10.4 Consensus size: 9
96838 AATAAATTAT
96848 TTTTATAAA
1 TTTTATAAA
96857 TTTTATAGAA
1 TTTTATA-AA
*
96867 TTTTAT-GA
1 TTTTATAAA
*
96875 TTTTAATGAA
1 TTTT-ATAAA
*
96885 TTTCTATTAA
1 TTT-TATAAA
96895 TTTTATAAAA
1 TTTTAT-AAA
* ***
96905 TTTAATTGT
1 TTTTATAAA
96914 TTTTAT-AA
1 TTTTATAAA
96922 TTTTAATAAA
1 TTTT-ATAAA
96932 TTTT-TATAA
1 TTTTATA-AA
96941 TTTT
1 TTTT
96945 TTTATTTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
8 11 0.16
9 25 0.36
10 32 0.46
11 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:96878 original size:28 final size:28
Alignment explanation
Indices: 96846--96900 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
96836 ATAATAAATT
*
96846 ATTTTTATAAATTT-TATAGAATTTTATG
1 ATTTTAATAAATTTCTAT-GAATTTTATG
* *
96874 ATTTTAATGAATTTCTATTAATTTTAT
1 ATTTTAATAAATTTCTATGAATTTTAT
96901 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (28 bp):
ATTTTAATAAATTTCTATGAATTTTATG
Found at i:96899 original size:47 final size:47
Alignment explanation
Indices: 96843--96944 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 47
96833 AAAATAATAA
* * * *
96843 ATTATTTTTAT-AAATTTTATAGAATTTTATGATTTTAATGAATTTCT
1 ATTAATTTTATAAAATTTAATAG-ATTTTATAATTTTAATAAATTTCT
* * *
96890 ATTAATTTTATAAAATTTAATTGTTTTTATAATTTTAATAAATTTTT
1 ATTAATTTTATAAAATTTAATAGATTTTATAATTTTAATAAATTTCT
96937 A-TAATTTT
1 ATTAATTTT
96945 TTTATTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
46 7 0.15
47 31 0.66
48 9 0.19
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (47 bp):
ATTAATTTTATAAAATTTAATAGATTTTATAATTTTAATAAATTTCT
Found at i:96945 original size:9 final size:9
Alignment explanation
Indices: 96846--96961 Score: 72
Period size: 9 Copynumber: 12.4 Consensus size: 9
96836 ATAATAAATT
96846 ATTTTTATA
1 ATTTTTATA
*
96855 AATTTTATA
1 ATTTTTATA
* *
96864 GAATTTTATG
1 -ATTTTTATA
*
96874 ATTTTAATGA
1 ATTTTTAT-A
*
96884 ATTTCTATTA
1 ATTTTTA-TA
96894 A-TTTTATAA
1 ATTTTTAT-A
* * *
96903 AATTTAATT
1 ATTTTTATA
*
96912 GTTTTTATA
1 ATTTTTATA
*
96921 ATTTTAATAA
1 ATTTTTAT-A
96931 ATTTTTATA
1 ATTTTTATA
*
96940 ATTTTTTTA
1 ATTTTTATA
*
96949 TTTTTTATA
1 ATTTTTATA
96958 ATTT
1 ATTT
96962 CAAAATGCAA
Statistics
Matches: 80, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
8 1 0.01
9 50 0.62
10 28 0.35
11 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:96945 original size:10 final size:10
Alignment explanation
Indices: 96913--96961 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
96903 AATTTAATTG
96913 TTTTTATAA-
1 TTTTTATAAT
* *
96922 TTTTAATAAA
1 TTTTTATAAT
96932 TTTTTATAAT
1 TTTTTATAAT
96942 TTTTT-T-AT
1 TTTTTATAAT
96950 TTTTTATAAT
1 TTTTTATAAT
96960 TT
1 TT
96962 CAAAATGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 7 0.21
9 10 0.29
10 17 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:98129 original size:26 final size:24
Alignment explanation
Indices: 98068--98129 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
98058 TTAATGTTTC
*
98068 TTTATAATTCTTTTATTTTTAAATT
1 TTTA-AATTATTTTATTTTTAAATT
*
98093 TTT-AATATATTTTATTATTATTAATT
1 TTTAAAT-TATTTTATT-TT-TAAATT
98119 TTTAAATTATT
1 TTTAAATTATT
98130 AATAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 3 0.10
24 8 0.26
25 5 0.16
26 12 0.39
27 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTAAATTATTTTATTTTTAAATT
Found at i:104178 original size:11 final size:11
Alignment explanation
Indices: 104159--104209 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
104149 AAAAAATCTA
*
104159 TTTTGTTGTTG
1 TTTTATTGTTG
*
104170 TTTTATTGTTA
1 TTTTATTGTTG
*
104181 TTTTCTTGTTG
1 TTTTATTGTTG
* *
104192 TTTCACTGTTG
1 TTTTATTGTTG
104203 TTTTATT
1 TTTTATT
104210 ATATTTTTGC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.71
Consensus pattern (11 bp):
TTTTATTGTTG
Found at i:104201 original size:22 final size:22
Alignment explanation
Indices: 104157--104206 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
104147 CAAAAAAATC
* * *
104157 TATTTTGTTGTTGTTTTATTGT
1 TATTTTCTTGTTGTTTCACTGT
104179 TATTTTCTTGTTGTTTCACTGT
1 TATTTTCTTGTTGTTTCACTGT
*
104201 TGTTTT
1 TATTTT
104207 ATTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.70
Consensus pattern (22 bp):
TATTTTCTTGTTGTTTCACTGT
Found at i:107585 original size:6 final size:6
Alignment explanation
Indices: 107574--107659 Score: 58
Period size: 6 Copynumber: 15.0 Consensus size: 6
107564 GACTCAACAG
* * * * *
107574 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTG AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
107619 -ATTTGA ATTTTA AATTT- -ATTATA AATTTA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA
107660 TTTAAATAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
4 7 0.11
5 9 0.15
6 40 0.65
7 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:107634 original size:17 final size:17
Alignment explanation
Indices: 107574--107653 Score: 106
Period size: 17 Copynumber: 4.7 Consensus size: 17
107564 GACTCAACAG
107574 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
107591 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
* *
107608 AATTTGAATTTATTTGA
1 AATTTAAATTTATTTTA
* *
107625 ATTTTAAATTTATTATA
1 AATTTAAATTTATTTTA
107642 AATTTAAATTTA
1 AATTTAAATTTA
107654 AATTTATTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:107688 original size:13 final size:13
Alignment explanation
Indices: 107670--107695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
107660 TTTAAATAAT
107670 GTCCAATTACAAA
1 GTCCAATTACAAA
107683 GTCCAATTACAAA
1 GTCCAATTACAAA
107696 TCAGGCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:108319 original size:3 final size:3
Alignment explanation
Indices: 108299--108366 Score: 50
Period size: 3 Copynumber: 22.3 Consensus size: 3
108289 AATGGCATTG
* * * * *
108299 ATA ATA ATTA ATG TTA ATA ATA ATA GTA ATA ATA AGTT AT- TTA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
108345 ATA ATA AGT- ATA ATA ATA ATA A
1 ATA ATA A-TA ATA ATA ATA ATA A
108367 AAAAGAATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:108333 original size:15 final size:14
Alignment explanation
Indices: 108313--108366 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
108303 TAATTAATGT
108313 TAATAATAATAGTAA
1 TAATAATAATA-TAA
* *
108328 TAATAAGTTATTTAA
1 TAATAA-TAATATAA
108343 TAATAATAAGTATAA
1 TAATAATAA-TATAA
108358 TAATAATAA
1 TAATAATAA
108367 AAAAGAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 28 0.85
16 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (14 bp):
TAATAATAATATAA
Done.