Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014959.1 Kokia drynarioides strain JFW-HI SEQ_130003, 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: 119183
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 58 characters in sequence are not A, C, G, or T
Found at i:5809 original size:15 final size:16
Alignment explanation
Indices: 5789--5823 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5779 TTAAGATGTC
*
5789 ATAAAAACTAAT-TTA
1 ATAAAAAATAATATTA
5804 ATAAAAAATAATATTA
1 ATAAAAAATAATATTA
5820 ATAA
1 ATAA
5824 TTAAACCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAAAATAATATTA
Found at i:6473 original size:22 final size:22
Alignment explanation
Indices: 6396--6500 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
6386 TTAAAATAGT
*
6396 AGTAAAATTAATAACAAAATAAT
1 AGTAAAA-TAATAACAAAATAAC
* * *
6419 AGTTATATAATATCCAAACAATAAC
1 AGTAAAATAATA-AC-AA-AATAAC
* *
6444 AATAAAATAATAACAACATAAC
1 AGTAAAATAATAACAAAATAAC
* * * *
6466 AGTGAAATGACAACAAAACAAC
1 AGTAAAATAATAACAAAATAAC
*
6488 AGTAAAACAATAA
1 AGTAAAATAATAA
6501 AGATTTTTTT
Statistics
Matches: 60, Mismatches: 19, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
22 35 0.58
23 8 0.13
24 3 0.05
25 14 0.23
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.20
Consensus pattern (22 bp):
AGTAAAATAATAACAAAATAAC
Found at i:23315 original size:2 final size:2
Alignment explanation
Indices: 23310--23343 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
23300 TCAAAAACGA
* *
23310 CT CT CT TT CT CT CC CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23344 GGTGTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28249 original size:99 final size:98
Alignment explanation
Indices: 28066--28246 Score: 240
Period size: 99 Copynumber: 1.8 Consensus size: 98
28056 ATAATTGCAG
* *
28066 TTACATCCTTGAGTCTTAAGTTCAATTCTTCTATTACTTATATTTGTAATTTTTCATGTTGCTTC
1 TTACATCCTTGAGTCTCAAGTTCAATTCTTCTATTACATATATTTGTAATTTTTCATGTTGCTTC
28131 AAGTTTTTTAAAATTTTAATTAATGTTTTTTAAC
66 AAGTTTTTTAAAA-TTTAATTAATGTTTTTTAAC
* * * *
28165 TTACATCCTTGAGTCTCGAGTTCAATTCTTCTACTACTCACATGTATTTTTTA-TTTT-ATGTTG
1 TTACATCCTTGAGTCTCAAGTTCAATTCTTCTA-T--T-ACATATATTTGTAATTTTTCATGTTG
*
28228 CTTCAAGTTTTTTTAAATT
62 CTTCAAGTTTTTTAAAATT
28247 AATATTTTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
99 31 0.44
100 3 0.04
101 22 0.31
102 5 0.07
103 10 0.14
ACGTcount: A:0.24, C:0.14, G:0.09, T:0.52
Consensus pattern (98 bp):
TTACATCCTTGAGTCTCAAGTTCAATTCTTCTATTACATATATTTGTAATTTTTCATGTTGCTTC
AAGTTTTTTAAAATTTAATTAATGTTTTTTAAC
Found at i:28373 original size:16 final size:16
Alignment explanation
Indices: 28354--28404 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
28344 TTCATATTGC
28354 TTTAATTTTTTTTATT
1 TTTAATTTTTTTTATT
** *
28370 TTTAA-TTAATGTATT
1 TTTAATTTTTTTTATT
28385 TTT-ATTTTTTATTATT
1 TTTAATTTTTT-TTATT
28401 TTTA
1 TTTA
28405 TAAACATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
14 1 0.04
15 13 0.50
16 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTAATTTTTTTTATT
Found at i:28405 original size:16 final size:16
Alignment explanation
Indices: 28381--28487 Score: 53
Period size: 16 Copynumber: 6.8 Consensus size: 16
28371 TTAATTAATG
28381 TATTTTTATTTTTTAT
1 TATTTTTATTTTTTAT
****
28397 TATTTTTATAAACATAT
1 TATTTTTAT-TTTTTAT
* *
28414 TA-ATGTATTTTTT-T
1 TATTTTTATTTTTTAT
* *
28428 TATTTCATATTGTTTCA-
1 TATTT-TTATT-TTTTAT
*
28445 -ATTTTTATTTTTAAT
1 TATTTTTATTTTTTAT
*
28460 TATTTTTATTTTTAAT
1 TATTTTTATTTTTTAT
*
28476 TA-ATTTATTTTT
1 TATTTTTATTTTT
28488 ATAAACATAT
Statistics
Matches: 68, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
14 7 0.10
15 15 0.22
16 38 0.56
17 8 0.12
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (16 bp):
TATTTTTATTTTTTAT
Found at i:28465 original size:15 final size:16
Alignment explanation
Indices: 28445--28488 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
28435 TATTGTTTCA
28445 ATTTTTATTTTTAATT
1 ATTTTTATTTTTAATT
28461 ATTTTTATTTTTAATT
1 ATTTTTATTTTTAATT
*
28477 A-ATTTATTTTTA
1 ATTTTTATTTTTA
28489 TAAACATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTATTTTTAATT
Found at i:28489 original size:84 final size:85
Alignment explanation
Indices: 28326--28506 Score: 239
Period size: 84 Copynumber: 2.2 Consensus size: 85
28316 TTTATTTTTA
*
28326 ATTAATGTA-TTTTTTTATTTCATATTGCTTTAATTTTTTTTATTTTTAATTAATGTATTTTTAT
1 ATTAATGTATTTTTTTTATTTCATATTGCTTTAA--TTTTTTATTTTTAATTAATGTATTTTTAA
**
28390 TTTTTATTATTTTTATAAACAT
64 TTAATATTATTTTTATAAACAT
* *
28412 ATTAATGTATTTTTTTTATTTCATATTG-TTTCAA-TTTTTATTTTTAATTATTTTTATTTTTAA
1 ATTAATGTATTTTTTTTATTTCATATTGCTTT-AATTTTTTATTTTTAATTA-ATGTATTTTTAA
28475 TTAAT-TTATTTTTATAAACAT
64 TTAATATTATTTTTATAAACAT
28496 ATT-AT-TATTTT
1 ATTAATGTATTTT
28507 CATTCAAGTA
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
82 6 0.07
83 2 0.02
84 35 0.40
85 12 0.14
86 12 0.14
87 20 0.23
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (85 bp):
ATTAATGTATTTTTTTTATTTCATATTGCTTTAATTTTTTATTTTTAATTAATGTATTTTTAATT
AATATTATTTTTATAAACAT
Found at i:28622 original size:14 final size:14
Alignment explanation
Indices: 28578--28632 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
28568 TAATGCTAAG
*
28578 AAATT-TATTATAT
1 AAATTATATAATAT
**
28591 AAATTATATCTTAT
1 AAATTATATAATAT
*
28605 -AATTTTATAATAT
1 AAATTATATAATAT
28618 AAATTATATAA-AT
1 AAATTATATAATAT
28631 AA
1 AA
28633 GACGATAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 19 0.56
14 15 0.44
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTATATAATAT
Found at i:32752 original size:20 final size:21
Alignment explanation
Indices: 32729--32771 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
32719 GTTTTTTTTT
*
32729 TTTA-ATTTTGAAAATTTTAA
1 TTTATATTTTGAAAATTCTAA
*
32749 TTTATTTTTTGAAAATTCTAA
1 TTTATATTTTGAAAATTCTAA
32770 TT
1 TT
32772 AAGCCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTATATTTTGAAAATTCTAA
Found at i:32898 original size:30 final size:30
Alignment explanation
Indices: 32755--32900 Score: 84
Period size: 31 Copynumber: 4.8 Consensus size: 30
32745 TTAATTTATT
* * *
32755 TTTTGAAAATTCTAATT-AAGCCTTTTAAAAA
1 TTTTGAAAATTTTAATTAAATCC--TCAAAAA
* * * * *
32786 TTTTGAAGATTTTAATCAGGATTCTCAAAAT
1 TTTTGAAAATTTTAATTA-AATCCTCAAAAA
* * * *
32817 TTTTAAAAATTCTT-ATT-AGTCTTACTAAAA
1 TTTTGAAAATT-TTAATTAAATCCT-CAAAAA
32847 TTTAT-AAAAGTTTTAATTAAATCCTCAAAAA
1 TTT-TGAAAA-TTTTAATTAAATCCTCAAAAA
*
32878 TTTTGAAAATTTTTATTAAATCC
1 TTTTGAAAATTTTAATTAAATCC
32901 CTTAGAATTT
Statistics
Matches: 85, Mismatches: 21, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
29 2 0.02
30 27 0.32
31 48 0.56
32 6 0.07
33 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (30 bp):
TTTTGAAAATTTTAATTAAATCCTCAAAAA
Found at i:37784 original size:17 final size:16
Alignment explanation
Indices: 37752--37802 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 16
37742 GGGAGAACAA
37752 AAAAAAAAATGGAAAAG
1 AAAAAAAAA-GGAAAAG
*
37769 AAGAACAAAAGGAAAAG
1 AA-AAAAAAAGGAAAAG
37786 AAAAAAAAAGGAGAAAG
1 AAAAAAAAAGGA-AAAG
37803 TTAAACGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 9 0.30
17 15 0.50
18 6 0.20
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAG
Found at i:52450 original size:19 final size:20
Alignment explanation
Indices: 52407--52455 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
52397 TATAATCAAA
*
52407 ATAATTTAAAATTTAAAGATC
1 ATAATTTAAAA-TTAAAAATC
52428 --AATTTAAAA-TAAAAATC
1 ATAATTTAAAATTAAAAATC
52445 ATAATTTAAAA
1 ATAATTTAAAA
52456 ATATTTGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
19 18 0.72
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAATTTAAAATTAAAAATC
Found at i:53327 original size:31 final size:31
Alignment explanation
Indices: 53269--53327 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
53259 TATTTTTTAA
* * * *
53269 TTAAATTTGACCCTTAATTTTTTAAAAAGAT
1 TTAAATTTGACCATCAATATTTAAAAAAGAT
53300 TTAAATTTGACCATCAATATTTAAAAAA
1 TTAAATTTGACCATCAATATTTAAAAAA
53328 AATCGAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
TTAAATTTGACCATCAATATTTAAAAAAGAT
Found at i:54332 original size:25 final size:25
Alignment explanation
Indices: 54303--54352 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54293 ACATATATTT
* *
54303 TATATTTATAAAAAATTATGTAAAA
1 TATATTTATAAAAAACTATATAAAA
54328 TATATTTATAAAAAACTATATAAAA
1 TATATTTATAAAAAACTATATAAAA
54353 ATAAATAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
TATATTTATAAAAAACTATATAAAA
Found at i:56773 original size:29 final size:30
Alignment explanation
Indices: 56741--56810 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
56731 GAATTATGCT
56741 TTTTGTAAATTTAA-AATTTAATTTTTATA-
1 TTTT-TAAATTTAAGAATTTAATTTTTATAC
** *
56770 TTTTTATTTTTAAGAATTTAATTTTTTTAC
1 TTTTTAAATTTAAGAATTTAATTTTTATAC
56800 TTTTTAAATTT
1 TTTTTAAATTT
56811 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 7 0.21
29 18 0.53
30 9 0.26
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTTTAAATTTAAGAATTTAATTTTTATAC
Found at i:56803 original size:23 final size:23
Alignment explanation
Indices: 56770--56819 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
56760 AATTTTTATA
56770 TTTTTA-TTTTTAAGAATTTAATT
1 TTTTTACTTTTTAA-AATTTAATT
*
56793 TTTTTACTTTTTAAATTTTAATT
1 TTTTTACTTTTTAAAATTTAATT
56816 TTTT
1 TTTT
56820 ATTTAACTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTACTTTTTAAAATTTAATT
Found at i:57006 original size:23 final size:23
Alignment explanation
Indices: 56975--57033 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 23
56965 AATTAAACTT
*
56975 AAATATTAAATT-TTAAAAATTA
1 AAATATTAAATTCTTAAAAATAA
56997 AAATAATTAAATTCTTAAAAATAA
1 AAAT-ATTAAATTCTTAAAAATAA
57021 AAATATATAAATT
1 AAATAT-TAAATT
57034 AAATTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 4 0.12
23 10 0.30
24 19 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATATTAAATTCTTAAAAATAA
Found at i:57318 original size:36 final size:33
Alignment explanation
Indices: 57268--57343 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 33
57258 ATTTTAAAAT
* * * *
57268 TATATACAAGTTTTGATTTAATGTGTAATATTTTA
1 TATATAAAAATTTTGATTT--TGTATAATATTATA
57303 TAATATAAAAATTTTGATTTTGTATAATATTATA
1 T-ATATAAAAATTTTGATTTTGTATAATATTATA
57337 TATATAA
1 TATATAA
57344 TTTTGATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 6 0.17
34 13 0.36
35 1 0.03
36 16 0.44
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (33 bp):
TATATAAAAATTTTGATTTTGTATAATATTATA
Found at i:57726 original size:41 final size:41
Alignment explanation
Indices: 57680--57758 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
57670 CGTTAAATAA
* *
57680 CAAAACAATATACACACACCC-AGACACATGCTCGTGTGCCT
1 CAAAACAACATACACACACCCTA-ACACATGCCCGTGTGCCT
*
57721 CAAAACAGCATACACACACCCTAACACATGCCCGTGTG
1 CAAAACAACATACACACACCCTAACACATGCCCGTGTG
57759 TCAACCTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (41 bp):
CAAAACAACATACACACACCCTAACACATGCCCGTGTGCCT
Found at i:57812 original size:55 final size:55
Alignment explanation
Indices: 57712--57859 Score: 201
Period size: 55 Copynumber: 2.7 Consensus size: 55
57702 GACACATGCT
* *
57712 CGTGTGCCTCAAAACAG--CATACACACACCCTAACACATGCCCGTGTGTCAACC
1 CGTGTGCCTCAAAACAGTATATACACACACCCTGACACATGCCCGTGTGTCAACC
* * * *
57765 TGTGTGCCTCAAAACAGTATATACACACACACTGACACATGCTCGTGTGTCAGCC
1 CGTGTGCCTCAAAACAGTATATACACACACCCTGACACATGCCCGTGTGTCAACC
* * *
57820 CGTGTACCTCAAAATAGTATACACACACACCCTGACACAT
1 CGTGTGCCTCAAAACAGTATATACACACACCCTGACACAT
57860 AGTCGGGTGT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 16 0.20
55 66 0.80
ACGTcount: A:0.32, C:0.33, G:0.15, T:0.20
Consensus pattern (55 bp):
CGTGTGCCTCAAAACAGTATATACACACACCCTGACACATGCCCGTGTGTCAACC
Found at i:57999 original size:6 final size:6
Alignment explanation
Indices: 57988--58025 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
57978 GCAAAAATGT
57988 AAAAAC AAAAAC AAAAAC AAAAAC -AAAA- AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
58026 GGGGTTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:76026 original size:4 final size:4
Alignment explanation
Indices: 76017--76081 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
76007 AATAAACAGA
* * * *
76017 AAAG AAAG AAAG AAAAG AAAG AAAG AGAG GAAG AAGG AGAG AAAAG AAAG
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG
* *
76067 -AAG AAGG AAAT AAAG
1 AAAG AAAG AAAG AAAG
76082 GTAATGTGTT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
3 3 0.07
4 36 0.78
5 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:76032 original size:13 final size:13
Alignment explanation
Indices: 76014--76068 Score: 65
Period size: 13 Copynumber: 4.0 Consensus size: 13
76004 GCAAATAAAC
76014 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
76027 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
* *
76040 AGAGAGGAAGAAGGAG
1 AGA-A--AAGAAAGAA
76056 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
76069 GAAGGAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 23 0.66
14 1 0.03
15 1 0.03
16 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:76051 original size:29 final size:27
Alignment explanation
Indices: 76018--76075 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
76008 ATAAACAGAA
76018 AAGAAAGAAAGAAAAGAAAGAAAGAGAGG
1 AAGAAAGAAAGAAAAGAAAG-AAGA-AGG
* *
76047 AAGAAGGAGAGAAAAGAAAGAAGAAGG
1 AAGAAAGAAAGAAAAGAAAGAAGAAGG
76074 AA
1 AA
76076 ATAAAGGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 4 0.15
29 18 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAGAAAAGAAAGAAGAAGG
Found at i:76166 original size:19 final size:19
Alignment explanation
Indices: 76121--76166 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
76111 ATATGATATC
*
76121 TTTTTAAAATCTTATTTTA
1 TTTTTAAAATCTTATTTAA
*
76140 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCTTATTTAA
76160 TTTTTAA
1 TTTTTAA
76167 CAGATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTAAAATCTTATTTAA
Found at i:77193 original size:80 final size:79
Alignment explanation
Indices: 77060--77218 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 79
77050 TGCTGGAAGT
*
77060 TGACGGAAGGTTGCAAGTGGCGGGTGCAAGCTGCATTTATCCAAAAGTCGCAGATGTGGGAGATA
1 TGACGGAAGGCTGCAAGTGGCGGGTGCAAGCTGCATTTATCCAAAAGTCGCAGATGTGGGAGATA
77125 AGAAAAATTGATGG
66 AGAAAAATTGATGG
77139 NTGACGGAAGGCTGCAAGTGGCGGGTGCAAGCTGCATTTATCCAAAAGTCGCAGATGTGGGAGAT
1 -TGACGGAAGGCTGCAAGTGGCGGGTGCAAGCTGCATTTATCCAAAAGTCGCAGATGTGGGAGAT
77204 AAGAAAAATTGATGG
65 AAGAAAAATTGATGG
77219 GCCTCACACA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.21
Consensus pattern (79 bp):
TGACGGAAGGCTGCAAGTGGCGGGTGCAAGCTGCATTTATCCAAAAGTCGCAGATGTGGGAGATA
AGAAAAATTGATGG
Found at i:79501 original size:28 final size:28
Alignment explanation
Indices: 79458--79540 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 28
79448 CTCTCCTTAA
*
79458 TCAA-TCTAGTGCTTACAATTTAGAGTT
1 TCAAGTCTAGTGTTTACAATTTAGAGTT
*
79485 TCAAGTCTAGTGTTTACGATTTA-AGATT
1 TCAAGTCTAGTGTTTACAATTTAGAG-TT
* * *
79513 TTAAGTTTAGGGTTT-CAAGTTTAG-GTT
1 TCAAGTCTAGTGTTTACAA-TTTAGAGTT
79540 T
1 T
79541 TAGGGTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 11 0.24
28 35 0.76
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (28 bp):
TCAAGTCTAGTGTTTACAATTTAGAGTT
Found at i:79796 original size:21 final size:21
Alignment explanation
Indices: 79770--79814 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
79760 TAGGGTCCAT
* * *
79770 TTGCCCCGGAGGAGTAGAGTA
1 TTGCCCAGGAGGAATAAAGTA
79791 TTGCCCAGGAGGAATAAAGTA
1 TTGCCCAGGAGGAATAAAGTA
79812 TTG
1 TTG
79815 TGGTGGCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (21 bp):
TTGCCCAGGAGGAATAAAGTA
Found at i:79942 original size:45 final size:45
Alignment explanation
Indices: 79808--79943 Score: 164
Period size: 45 Copynumber: 3.0 Consensus size: 45
79798 GGAGGAATAA
* * * * **
79808 AGTATTGTGGTGGCTCGTCAAACTCAGCCTGATATCCTTCCCTTG
1 AGTATTGCGGTGGCTCATCAAACTGAGGCTGATATCCTTAGCTTG
* * * * *
79853 AGTATTGCGGCGACTCCTCAAATTGAGGCTGATATCATTAGCTTG
1 AGTATTGCGGTGGCTCATCAAACTGAGGCTGATATCCTTAGCTTG
*
79898 AGTATTGCGGTGGCTCATCAAACTGAGGCTGATATCCTTGGCTTG
1 AGTATTGCGGTGGCTCATCAAACTGAGGCTGATATCCTTAGCTTG
79943 A
1 A
79944 TGAGCTATGC
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (45 bp):
AGTATTGCGGTGGCTCATCAAACTGAGGCTGATATCCTTAGCTTG
Found at i:81866 original size:16 final size:16
Alignment explanation
Indices: 81845--81893 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
81835 CGATGGGGAT
81845 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
81861 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
81875 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
81890 ATTA
1 ATTA
81894 GTTAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:82396 original size:20 final size:21
Alignment explanation
Indices: 82371--82412 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
82361 ACTTACTACG
82371 ACTAAC-AACAAAATAAAATT
1 ACTAACTAACAAAATAAAATT
* *
82391 ACTAACTAGCAAAATTAAATT
1 ACTAACTAACAAAATAAAATT
82412 A
1 A
82413 AAGTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (21 bp):
ACTAACTAACAAAATAAAATT
Found at i:82508 original size:16 final size:16
Alignment explanation
Indices: 82487--82525 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
82477 CTATAACAAC
*
82487 ATTAAATAACAAATTA
1 ATTAAAAAACAAATTA
*
82503 ATTAAAAAATAAATTA
1 ATTAAAAAACAAATTA
*
82519 AATAAAA
1 ATTAAAA
82526 CAAAAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAAAACAAATTA
Found at i:82583 original size:12 final size:12
Alignment explanation
Indices: 82568--82592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82558 AAATTAAAAT
82568 ATTTTAAAATTA
1 ATTTTAAAATTA
82580 ATTTTAAAATTA
1 ATTTTAAAATTA
82592 A
1 A
82593 CCAAACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:83591 original size:3 final size:3
Alignment explanation
Indices: 83583--83607 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
83573 GCATATACCA
83583 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
83608 ATGACTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:83703 original size:20 final size:21
Alignment explanation
Indices: 83678--83716 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
83668 ACTTCAACAA
83678 TTATAAAAATT-TAATTTATC
1 TTATAAAAATTATAATTTATC
*
83698 TTATAAAATTTATAATTTA
1 TTATAAAAATTATAATTTA
83717 AAAAAGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAAAAATTATAATTTATC
Found at i:84572 original size:27 final size:26
Alignment explanation
Indices: 84542--84646 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
84532 TTTCCAATTA
84542 TTAAGGGCCCAAACTTTTTTTTAACTT
1 TTAAGGGCCCAAA-TTTTTTTTAACTT
* * *
84569 TTAAAGGCCGAAAGTTTTTTACTAACTT
1 TTAAGGGCCCAAA-TTTTTT-TTAACTT
*
84597 TTAAGGGATCCTC-AATTTTTTTTGAGCTT
1 TTAAGGG--CC-CAAATTTTTTTT-AACTT
* *
84626 TTAAGGGTCTAAATTTTTTTT
1 TTAAGGGCCCAAATTTTTTTT
84647 TTACCAACTT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
27 28 0.45
28 13 0.21
29 17 0.27
30 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (26 bp):
TTAAGGGCCCAAATTTTTTTTAACTT
Found at i:84689 original size:33 final size:31
Alignment explanation
Indices: 84637--84697 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
84627 TAAGGGTCTA
84637 AATTTTTTTTTTACCAACTTTTAAGGAATTT
1 AATTTTTTTTTTACCAACTTTTAAGGAATTT
84668 AATTTTTTTTTT-CTCTAAACTTTTAAGGAA
1 AATTTTTTTTTTAC-C--AACTTTTAAGGAA
84698 CCGAAAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 1 0.04
31 13 0.48
33 13 0.48
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.54
Consensus pattern (31 bp):
AATTTTTTTTTTACCAACTTTTAAGGAATTT
Found at i:86127 original size:2 final size:2
Alignment explanation
Indices: 86120--86152 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86110 AAAACACTTA
86120 AT 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 AT A
86153 AATAAATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92890 original size:18 final size:18
Alignment explanation
Indices: 92867--92901 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
92857 TTTTTGACGA
92867 TTTTTT-CGCTGTAATTTC
1 TTTTTTCCGCT-TAATTTC
92885 TTTTTTCCGCTTAATTT
1 TTTTTTCCGCTTAATTT
92902 GAATTATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.63
Consensus pattern (18 bp):
TTTTTTCCGCTTAATTTC
Found at i:100607 original size:10 final size:10
Alignment explanation
Indices: 100592--100629 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
100582 AGGACTTTAT
100592 GAACACTACA
1 GAACACTACA
100602 GAACACTA-A
1 GAACACTACA
100611 TGAACACTACA
1 -GAACACTACA
100622 GAACACTA
1 GAACACTA
100630 ACACCCATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 24 0.92
11 1 0.04
ACGTcount: A:0.50, C:0.26, G:0.11, T:0.13
Consensus pattern (10 bp):
GAACACTACA
Found at i:100615 original size:20 final size:20
Alignment explanation
Indices: 100590--100630 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
100580 AAAGGACTTT
100590 ATGAACACTACAGAACACTA
1 ATGAACACTACAGAACACTA
100610 ATGAACACTACAGAACACTA
1 ATGAACACTACAGAACACTA
100630 A
1 A
100631 CACCCATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.24, G:0.10, T:0.15
Consensus pattern (20 bp):
ATGAACACTACAGAACACTA
Found at i:101012 original size:2 final size:2
Alignment explanation
Indices: 101005--101038 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
100995 CTGCAAACAG
101005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101039 CATAGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109653 original size:3 final size:3
Alignment explanation
Indices: 109634--109668 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
109624 GCAGGAGGGG
* *
109634 GGT GAT GGT GAT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
109669 AGAGTATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.00, G:0.63, T:0.31
Consensus pattern (3 bp):
GGT
Done.