Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015175.1 Kokia drynarioides strain JFW-HI SEQ_130219, 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: 106858
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 424 characters in sequence are not A, C, G, or T
Found at i:8773 original size:93 final size:93
Alignment explanation
Indices: 8614--8790 Score: 300
Period size: 93 Copynumber: 1.9 Consensus size: 93
8604 CAATATATTG
8614 GTAGTCTAAATATCAAATCCATGTAATAATAATTAAACTTGTACATGTAAGCGCCATAAGTACTT
1 GTAGTCTAAATATCAAATCCATGTAATAATAATTAAACTTGTACATGTAAGCGCCATAAGTACTT
*
8679 AAGCTATATTTTATTTTTTAATGAATTA
66 AAGCTATATTGTATTTTTTAATGAATTA
* * * *
8707 GTAGTTTAAATATCATATCCATGTACTAATAATTAAACTTGTACATGTAAGCGTCATAAGTACTT
1 GTAGTCTAAATATCAAATCCATGTAATAATAATTAAACTTGTACATGTAAGCGCCATAAGTACTT
*
8772 AAGCTATCTTGTATTTTTT
66 AAGCTATATTGTATTTTTT
8791 TGTGGACCCT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (93 bp):
GTAGTCTAAATATCAAATCCATGTAATAATAATTAAACTTGTACATGTAAGCGCCATAAGTACTT
AAGCTATATTGTATTTTTTAATGAATTA
Found at i:13806 original size:8 final size:9
Alignment explanation
Indices: 13778--13833 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
13768 AAAAAATTGT
*
13778 TAAAAATAT
1 TAAAAATAA
*
13787 TAAAAATCA
1 TAAAAATAA
13796 TAAAAA-AA
1 TAAAAATAA
13804 TAAAAATATA
1 TAAAAATA-A
*
13814 TAAAAATTA
1 TAAAAATAA
13823 TAAAAA-AA
1 TAAAAATAA
13831 TAA
1 TAA
13834 TGGTTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 11 0.28
9 21 0.52
10 8 0.20
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
TAAAAATAA
Found at i:13807 original size:17 final size:16
Alignment explanation
Indices: 13787--13820 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13777 TTAAAAATAT
13787 TAAAAATCATAAAAAAA
1 TAAAAAT-ATAAAAAAA
*
13804 TAAAAATATATAAAAA
1 TAAAAATATAAAAAAA
13820 T
1 T
13821 TATAAAAAAA
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:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAATATAAAAAAA
Found at i:13809 original size:27 final size:27
Alignment explanation
Indices: 13778--13833 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
13768 AAAAAATTGT
13778 TAAAAATAT-TAAAAATCATAAAAAAA
1 TAAAAATATATAAAAATCATAAAAAAA
*
13804 TAAAAATATATAAAAATTATAAAAAAA
1 TAAAAATATATAAAAATCATAAAAAAA
13831 TAA
1 TAA
13834 TGGTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAAAATATATAAAAATCATAAAAAAA
Found at i:14160 original size:19 final size:19
Alignment explanation
Indices: 14136--14242 Score: 58
Period size: 19 Copynumber: 5.4 Consensus size: 19
14126 CTGGTTCAAG
14136 ATTTTTAAATAATTTTTAT
1 ATTTTTAAATAATTTTTAT
* *
14155 ATTTTTATAATTATTTTCA-
1 ATTTTTA-AATAATTTTTAT
* * *
14174 ATTATATT-AATAAATTTCACA
1 ATT-T-TTAAATAATTTTTA-T
* *
14195 ATATTT-AATAATTTTTAC
1 ATTTTTAAATAATTTTTAT
*
14213 ACATTTTAAATAATGTTTTAT
1 A-TTTTTAAATAAT-TTTTAT
14234 GATTTTTAA
1 -ATTTTTAA
14243 CATTTATTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
18 1 0.01
19 33 0.49
20 17 0.25
21 15 0.22
22 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTTTAAATAATTTTTAT
Found at i:14340 original size:34 final size:35
Alignment explanation
Indices: 14288--14372 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 35
14278 TTAATAACTA
*
14288 TTTACAATTTTTAGTATTTTGCA-AATTGTAAATA-TTT
1 TTTACAA-TTTT--TATTTTGAACAATT-TAAATATTTT
*
14325 TTTACAATTTTTATTTTTAACAATTTAAATATTTT
1 TTTACAATTTTTATTTTGAACAATTTAAATATTTT
14360 TTTAC-ATTTTTAT
1 TTTACAATTTTTAT
14373 ATATTTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 21 0.48
35 12 0.27
36 4 0.09
37 7 0.16
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.59
Consensus pattern (35 bp):
TTTACAATTTTTATTTTGAACAATTTAAATATTTT
Found at i:14341 original size:16 final size:16
Alignment explanation
Indices: 14320--14372 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
14310 AAATTGTAAA
14320 TATTTTTTACAATTTT
1 TATTTTTTACAATTTT
* *
14336 TATTTTTAACAATTTAAA
1 TATTTTTTACAATTT--T
14354 TATTTTTTTAC-ATTTT
1 TA-TTTTTTACAATTTT
14370 TAT
1 TAT
14373 ATATTTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 16 0.53
18 6 0.20
19 7 0.23
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTTTACAATTTT
Found at i:14374 original size:18 final size:18
Alignment explanation
Indices: 14322--14380 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 18
14312 ATTGTAAATA
*
14322 TTTTTTACAATTTT-TA-
1 TTTTTTACATTTTTATAT
* **
14338 TTTTTAACAATTTAAATAT
1 TTTTTTAC-ATTTTTATAT
14357 TTTTTTACATTTTTATAT
1 TTTTTTACATTTTTATAT
14375 ATTTTT
1 -TTTTT
14381 GAAGATTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 10 0.31
19 12 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTTACATTTTTATAT
Found at i:31810 original size:28 final size:29
Alignment explanation
Indices: 31779--31837 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
31769 ATTGAATTGA
* *
31779 ATTTAACTTA-ATTTAATTTGATTTTTTT
1 ATTTAACTTATAATTAATTTGACTTTTTT
* *
31807 ATTTAAGTTATAATTAATTTTACTTTTTT
1 ATTTAACTTATAATTAATTTGACTTTTTT
31836 AT
1 AT
31838 GTAAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (29 bp):
ATTTAACTTATAATTAATTTGACTTTTTT
Found at i:31931 original size:15 final size:15
Alignment explanation
Indices: 31901--31929 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31891 ATTGATTAAT
31901 TTTATTTTCTTAAAA
1 TTTATTTTCTTAAAA
31916 TTTATTTT-TTAAAA
1 TTTATTTTCTTAAAA
31930 ATATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTTTCTTAAAA
Found at i:32222 original size:28 final size:27
Alignment explanation
Indices: 32171--32248 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
32161 TTTTTTACTC
* *
32171 TAAACTCGAACCTTGAACTA-TAAACCA
1 TAAACTCAAACCTCGAA-TATTAAACCA
*
32198 TAACACTCAAACCTCGAATATTAAACCC
1 TAA-ACTCAAACCTCGAATATTAAACCA
*
32226 TAAACATCAAACTTCGAAT-TTAA
1 TAAAC-TCAAACCTCGAATATTAA
32249 GATTTTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
27 11 0.25
28 33 0.75
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (27 bp):
TAAACTCAAACCTCGAATATTAAACCA
Found at i:34494 original size:23 final size:23
Alignment explanation
Indices: 34412--34502 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 23
34402 GCTCTTTGTT
*
34412 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTACTCTCTG
* * * *
34435 ATTAGTACTTTATGTACTCTATG
1 ATTAGCACTGTGTGTACTCTCTG
* *
34458 ATTAGTACTTTGTGTACTCTCTG
1 ATTAGCACTGTGTGTACTCTCTG
* *
34481 TTTAGCACTGTGTGTGCTCTCT
1 ATTAGCACTGTGTGTACTCTCT
34503 ATTGCCCAGC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (23 bp):
ATTAGCACTGTGTGTACTCTCTG
Found at i:34537 original size:21 final size:21
Alignment explanation
Indices: 34424--34549 Score: 76
Period size: 23 Copynumber: 5.5 Consensus size: 21
34414 TAGCACTGTG
34424 TGTGCTCTCTGATTAGTACTTT
1 TGTGCTCTCTGATTAGTAC-TT
* *
34446 ATGTACTCTATGATTAGTACTT
1 -TGTGCTCTCTGATTAGTACTT
* *
34468 TGTGTACTCTCTGTTTAGCACTGT
1 TGTG--CTCTCTGATTAGTACT-T
*
34492 GTGTGCTCTCT-ATTGCCCAGCACTT
1 -TGTGCTCTCTGATT----AGTACTT
34517 ATGTGCTCTCTG-TTAGTACTT
1 -TGTGCTCTCTGATTAGTACTT
*
34538 TGATACTCTCTG
1 TG-TGCTCTCTG
34550 TTTGTTCCGT
Statistics
Matches: 83, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.02
21 17 0.20
22 4 0.05
23 36 0.43
24 1 0.01
25 17 0.20
26 6 0.07
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (21 bp):
TGTGCTCTCTGATTAGTACTT
Found at i:34545 original size:69 final size:69
Alignment explanation
Indices: 34413--34552 Score: 180
Period size: 69 Copynumber: 2.0 Consensus size: 69
34403 CTCTTTGTTA
* *
34413 TTAGCACTGTGTGTGCTCTCTGATTAGTACTTTATGTACTCTATGATTAGTACTTTGTGTACTCT
1 TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTACTCTATGATTAGTACTTTGTATACTCT
34478 CTGT
66 CTGT
* *
34482 TTAGCACTGTGTGTGCTCTCT-ATTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-ATA
1 TTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTATGTACTCTATGATTAGTACTTTGTATA
34543 CTCTCTGT
62 CTCTCTGT
34551 TT
1 TT
34553 GTTCCGTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
68 3 0.05
69 33 0.52
70 11 0.17
71 12 0.19
72 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.45
Consensus pattern (69 bp):
TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTACTCTATGATTAGTACTTTGTATACTCT
CTGT
Found at i:42093 original size:15 final size:14
Alignment explanation
Indices: 42073--42103 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
42063 AGCTTTCCTC
42073 TATTTTTTTTTTATT
1 TATTTTTTTTTT-TT
42088 TATTTTTTTTTTTT
1 TATTTTTTTTTTTT
42102 TA
1 TA
42104 CAATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TATTTTTTTTTTTT
Found at i:43306 original size:3 final size:3
Alignment explanation
Indices: 43298--43324 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43288 TTTTATCCAA
43298 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
43325 GAAACTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53298 original size:10 final size:10
Alignment explanation
Indices: 53279--53310 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
53269 CGTAGCTTGC
53279 TTTTTT-TTT
1 TTTTTTCTTT
53288 TTTTTTCTTT
1 TTTTTTCTTT
53298 TTTTTTCTTT
1 TTTTTTCTTT
53308 TTT
1 TTT
53311 CTTTTAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:53301 original size:17 final size:17
Alignment explanation
Indices: 53278--53315 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
53268 CCGTAGCTTG
53278 CTTTTTTTTT-TTTTTT
1 CTTTTTTTTTCTTTTTT
53294 CTTTTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTT
53311 CTTTT
1 CTTTT
53316 AAGGAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
CTTTTTTTTTCTTTTTT
Found at i:54474 original size:21 final size:21
Alignment explanation
Indices: 54444--54484 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54434 TAAGTACTAG
54444 TTGATCTTAG-CTTTCTTGGGC
1 TTGATCTTAGAC-TTCTTGGGC
*
54465 TTGATGTTAGACTTCTTGGG
1 TTGATCTTAGACTTCTTGGG
54485 TTCTTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46
Consensus pattern (21 bp):
TTGATCTTAGACTTCTTGGGC
Found at i:64847 original size:23 final size:22
Alignment explanation
Indices: 64816--64942 Score: 139
Period size: 23 Copynumber: 5.6 Consensus size: 22
64806 GCTGGGGAAA
64816 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
64838 CTAGTAAGCACACACAGTGCAAT
1 C-AGTAAGCACACACAGTGCAAT
*
64861 CTAGTAAGCACACACAATGCAAT
1 C-AGTAAGCACACACAGTGCAAT
* * * *
64884 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
* *
64907 CAGTAAGCACATGA-AGTGCGAAA
1 CAGTAAGCACA-CACAGTGC-AAT
64930 CAGTAAGCACACA
1 CAGTAAGCACACA
64943 GTGTTGAACA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
22 15 0.17
23 73 0.82
24 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:83067 original size:18 final size:19
Alignment explanation
Indices: 83040--83085 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
83030 TATTTTTAAT
*
83040 TTTTTAAAAATTATAT-AA
1 TTTTTGAAAATTATATAAA
*
83058 TTTTTGAAAATTTTATAAA
1 TTTTTGAAAATTATATAAA
83077 TATTTTGAA
1 T-TTTTGAA
83086 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 14 0.58
19 3 0.12
20 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTTGAAAATTATATAAA
Found at i:83071 original size:27 final size:25
Alignment explanation
Indices: 83025--83077 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
83015 ATCAATTAAC
**
83025 TTATATATTTTTAATTTTTTAAAAA
1 TTATATATTTTTAAAATTTTAAAAA
*
83050 TTATATAATTTTTGAAAATTTTATAAA
1 TTATAT-ATTTTT-AAAATTTTAAAAA
83077 T
1 T
83078 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 6 0.26
27 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTATATATTTTTAAAATTTTAAAAA
Found at i:83073 original size:20 final size:19
Alignment explanation
Indices: 83036--83085 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
83026 TATATATTTT
*
83036 TAATTTTTTAAAAATTATA
1 TAATTTTTGAAAAATTATA
*
83055 TAATTTTTG-AAAATTTTA
1 TAATTTTTGAAAAATTATA
83073 TAAATATTTTGAA
1 T-AAT-TTTTGAA
83086 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 9 0.35
19 11 0.42
20 5 0.19
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
TAATTTTTGAAAAATTATA
Found at i:83087 original size:18 final size:18
Alignment explanation
Indices: 83066--83106 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
83056 AATTTTTGAA
83066 AATTTTATAAA-TATTTTG
1 AATTTTA-AAATTATTTTG
83084 AATTTTAAAATTTATTTTG
1 AATTTTAAAA-TTATTTTG
83103 AATT
1 AATT
83107 GTTTTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 7 0.33
19 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
AATTTTAAAATTATTTTG
Found at i:83225 original size:24 final size:24
Alignment explanation
Indices: 83190--83242 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
83180 TGAATTGTAA
*
83190 AATTTAATTCGACTCAAACTCAAAT
1 AATTTAATTCGAAT-AAACTCAAAT
*
83215 AATTT-ATTCGAATTAACTCAAAT
1 AATTTAATTCGAATAAACTCAAAT
83238 AATTT
1 AATTT
83243 TAATAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 14 0.54
24 7 0.27
25 5 0.19
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (24 bp):
AATTTAATTCGAATAAACTCAAAT
Found at i:85202 original size:18 final size:18
Alignment explanation
Indices: 85179--85251 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 18
85169 TAAAAAATAA
85179 TTTTTATAATATTTTTAG
1 TTTTTATAATATTTTTAG
*
85197 TTTTTATTAA-A-TTTTAA
1 TTTTTA-TAATATTTTTAG
85214 TTATTT-TAATTATTTCTTATG
1 TT-TTTATAA-TATTT-TTA-G
85235 TTTTTA-AATATTGTTTA
1 TTTTTATAATATT-TTTA
85252 TTTATTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
16 3 0.07
17 7 0.16
18 11 0.25
19 12 0.27
20 9 0.20
21 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTTATAATATTTTTAG
Found at i:87222 original size:15 final size:17
Alignment explanation
Indices: 87191--87223 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
87181 TCAATTTAAT
87191 TTAATTATTTAAAATAA
1 TTAATTATTTAAAATAA
87208 TTAATT-TTT-AAATAA
1 TTAATTATTTAAAATAA
87223 T
1 T
87224 AAACAGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTATTTAAAATAA
Found at i:89049 original size:18 final size:19
Alignment explanation
Indices: 89026--89061 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
89016 CTCTTTATAC
89026 TTTTATTTTT-AATTTTTT
1 TTTTATTTTTAAATTTTTT
89044 TTTTATTTTTAAATTTTT
1 TTTTATTTTTAAATTTTT
89062 ATAATGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTAAATTTTTT
Found at i:94559 original size:15 final size:15
Alignment explanation
Indices: 94539--94572 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
94529 AATAACCTGC
94539 CATACAAAACTTCAG
1 CATACAAAACTTCAG
*
94554 CATACAAAACTTCGG
1 CATACAAAACTTCAG
94569 CATA
1 CATA
94573 TCATCCAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (15 bp):
CATACAAAACTTCAG
Found at i:98053 original size:13 final size:15
Alignment explanation
Indices: 98030--98061 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
98020 GAAATTACTA
98030 TTTAAATAATT-AAT
1 TTTAAATAATTAAAT
98044 TTTAAA-AATTAAAT
1 TTTAAATAATTAAAT
98058 TTTA
1 TTTA
98062 CTAACAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAATAATTAAAT
Found at i:100208 original size:15 final size:15
Alignment explanation
Indices: 100188--100218 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
100178 GTCCTTATGA
100188 TGAACTCATAAACTT
1 TGAACTCATAAACTT
100203 TGAACTCATAAACTT
1 TGAACTCATAAACTT
100218 T
1 T
100219 TTACTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (15 bp):
TGAACTCATAAACTT
Found at i:102138 original size:57 final size:56
Alignment explanation
Indices: 102042--102274 Score: 227
Period size: 57 Copynumber: 4.1 Consensus size: 56
102032 CCAACACCTA
* * * ** * *
102042 AAAAATATTTTTTTAGGTGTTTACCACCTAATGATTTACATCACTTTTTTGAAATTT
1 AAAAATATTTTTTTAAGTGTTTATCACCCAATGGCTTACA-CACATTTTTCAAATTT
102099 AAAAATATTTTTTTAAGTGTTTATCACCCAATGGCTTACACCACATTTTTCAAATTT
1 AAAAATATTTTTTTAAGTGTTTATCACCCAATGGCTTACA-CACATTTTTCAAATTT
* * * *
102156 AAAAATATTTTTTTTGAA-TGATTGTCACCCAATGGTCTATAC-CACATTTGTCATATTT
1 AAAAATA-TTTTTTT-AAGTGTTTATCACCCAATGG-CT-TACACACATTTTTCAAATTT
* * * * * * *
102214 AAAAATATTTTTTTGAGTGTTTGTCACCTAATGGCCTACACTATATTTCTCAGATTT
1 AAAAATATTTTTTTAAGTGTTTATCACCCAATGGCTTACAC-ACATTTTTCAAATTT
102271 AAAA
1 AAAA
102275 TTTTTGAGTG
Statistics
Matches: 150, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
55 3 0.02
56 3 0.02
57 94 0.63
58 43 0.29
59 4 0.03
60 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (56 bp):
AAAAATATTTTTTTAAGTGTTTATCACCCAATGGCTTACACACATTTTTCAAATTT
Found at i:102403 original size:57 final size:57
Alignment explanation
Indices: 102314--102497 Score: 230
Period size: 57 Copynumber: 3.2 Consensus size: 57
102304 CACCACTTAA
* *
102314 AAAAATGTGGTGTGAGCCATTGGATGGA-AAACACCTAAACAAATATTTTTAAATATG
1 AAAAATGTGGTGTGAGCCATTGGAT-GACAAACACCTAAAAAAATATTTTTAAATTTG
* *
102371 AAAAAGGTGGTGTGAGCCATTGGATGACAAACACTTAAAAAAATATTTTTAAATTTG
1 AAAAATGTGGTGTGAGCCATTGGATGACAAACACCTAAAAAAATATTTTTAAATTTG
* * * * *
102428 AAAAATATGATGT-AGGTCATTGGTTGGCAAACATCC-AAAAAAATATTTTTAAATTTG
1 AAAAATGTGGTGTGA-GCCATTGGATGACAAACA-CCTAAAAAAATATTTTTAAATTTG
*
102485 AAAAAAGTGGTGT
1 AAAAATGTGGTGT
102498 AACACCTAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
56 3 0.03
57 106 0.96
58 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (57 bp):
AAAAATGTGGTGTGAGCCATTGGATGACAAACACCTAAAAAAATATTTTTAAATTTG
Found at i:103815 original size:33 final size:35
Alignment explanation
Indices: 103734--103829 Score: 124
Period size: 33 Copynumber: 2.8 Consensus size: 35
103724 TGATATTCAA
* *
103734 TTTACTCCCTGTTGACCCAAAGGTTATGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATAAT-CTCAT
* * *
103770 TTTACTCACTGTTGACCTAAAGGTCATAAT-T-GT
1 TTTACTCCCTGTTGACCCAAAGGTCATAATCTCAT
103803 TTTACTCCCTGTTGACCCAAAGGTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCAT
103830 GCCTGTTACC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 26 0.49
34 1 0.02
36 26 0.49
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (35 bp):
TTTACTCCCTGTTGACCCAAAGGTCATAATCTCAT
Found at i:105919 original size:13 final size:13
Alignment explanation
Indices: 105903--105927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105893 TTCGTATTTT
105903 TTTGAGTGTCGGC
1 TTTGAGTGTCGGC
105916 TTTGAGTGTCGG
1 TTTGAGTGTCGG
105928 TCATGGATTG
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:0.08, C:0.12, G:0.40, T:0.40
Consensus pattern (13 bp):
TTTGAGTGTCGGC
Done.