Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014620.1 Kokia drynarioides strain JFW-HI SEQ_129659, 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: 168405
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
Found at i:951 original size:23 final size:23
Alignment explanation
Indices: 925--972 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
915 GCGCTATCTA
*
925 TTTAGCATTGTGTGTGCTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
*
948 TTTAGCACTGTGTGTGTTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
971 TT
1 TT
973 ACCCAGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.50
Consensus pattern (23 bp):
TTTAGCACTGTGTGTGCTCTCTG
Found at i:5647 original size:24 final size:24
Alignment explanation
Indices: 5620--5668 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5610 CTAATTTTTG
5620 TTCAATCATCCATTAACATATTTC
1 TTCAATCATCCATTAACATATTTC
5644 TTCAATCATCCATTAACATATTTC
1 TTCAATCATCCATTAACATATTTC
5668 T
1 T
5669 CTGCAACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (24 bp):
TTCAATCATCCATTAACATATTTC
Found at i:20004 original size:93 final size:93
Alignment explanation
Indices: 19856--20192 Score: 514
Period size: 93 Copynumber: 3.6 Consensus size: 93
19846 CTGGAGCTGG
* *
19856 ACAGGAGAGAGGTACTTCATTGGCGTCTAAGGCCGAACACGAGAGTGATGAAGAGAAAAGACGAC
1 ACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGAGAAAAGACGAC
19921 GGAGTTATGCCGCTGCTGCTGGACATCC
66 GGAGTTATGCCGCTGCTGCTGGACATCC
* *
19949 ACAGGAGAGAGGTATTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATGAAGAGAAAAGACGAC
1 ACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGAGAAAAGACGAC
20014 GGAGTTATGCCGCTGCTGCTGGACATCC
66 GGAGTTATGCCGCTGCTGCTGGACATCC
*
20042 ACAGGAGAGAGGTA-TTCCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGAGAAAGGACGA
1 ACAGGAGAGAGGTACTT-CAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGAGAAAAGACGA
* * *
20106 CGGAGTTATGCTGCTGCTGCTGGGCATCA
65 CGGAGTTATGCCGCTGCTGCTGGACATCC
* * * * *
20135 ACAAGAGAGAGGTGCTTCAATGGAGTCCAAGGGCAGCAAACACGAGAGTGATAAAGAG
1 ACAGGAGAGAGGTACTTCAATGGCGTCTAA-GGC--CGAACACGAGAGTGATAAAGAG
20193 CAAGGACGTC
Statistics
Matches: 227, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.01
93 199 0.88
94 5 0.02
96 21 0.09
ACGTcount: A:0.32, C:0.19, G:0.33, T:0.16
Consensus pattern (93 bp):
ACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGAGAAAAGACGAC
GGAGTTATGCCGCTGCTGCTGGACATCC
Found at i:29706 original size:13 final size:12
Alignment explanation
Indices: 29682--29719 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
29672 ATTTAAATCT
29682 AATTTAATTTAA
1 AATTTAATTTAA
29694 AATTTAGATTTAA
1 AATTTA-ATTTAA
29707 AATTTAATTTAA
1 AATTTAATTTAA
29719 A
1 A
29720 TCCACCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
AATTTAATTTAA
Found at i:43657 original size:12 final size:12
Alignment explanation
Indices: 43642--43666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43632 ATTTCCATTT
43642 AGATTTTGATCA
1 AGATTTTGATCA
43654 AGATTTTGATCA
1 AGATTTTGATCA
43666 A
1 A
43667 ATTATATAAC
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
AGATTTTGATCA
Found at i:49247 original size:25 final size:25
Alignment explanation
Indices: 49188--49247 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
49178 TAATTTGGTA
* *
49188 TATTTAGA-AATAAATATATTAATT
1 TATTTAGATATTAAATAAATTAATT
**
49212 TATTTTTATATTAAATAAATATAA-T
1 TATTTAGATATTAAATAAAT-TAATT
49237 TATTTAGATAT
1 TATTTAGATAT
49248 GTAATATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 6 0.21
25 19 0.68
26 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
TATTTAGATATTAAATAAATTAATT
Found at i:51679 original size:37 final size:36
Alignment explanation
Indices: 51613--51696 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 36
51603 AAATCAAAAC
*
51613 CATGAAATCCACTCAAAACCATTTCCATTTTCAATTT
1 CATGAAATCCACCCAAAACCATTTCCATTTT-AATTT
* * * * *
51650 TATGAAGTCCACCCAAAGCTATTTTCATTTTAATTT
1 CATGAAATCCACCCAAAACCATTTCCATTTTAATTT
51686 CATGAAATCCA
1 CATGAAATCCA
51697 AAACCAGCAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 14 0.36
37 25 0.64
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (36 bp):
CATGAAATCCACCCAAAACCATTTCCATTTTAATTT
Found at i:53790 original size:21 final size:20
Alignment explanation
Indices: 53753--53791 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
53743 AAAACTTAAA
*
53753 AATATTTTATTTAAAAAAGT
1 AATATTTTATCTAAAAAAGT
*
53773 AATATTTTTATCTCAAAAA
1 AATA-TTTTATCTAAAAAA
53792 TGTTATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
AATATTTTATCTAAAAAAGT
Found at i:58047 original size:14 final size:15
Alignment explanation
Indices: 58024--58056 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
58014 TACTATATGA
*
58024 TTTTATTTAATATT-
1 TTTTAATTAATATTC
58038 TTTTAATTAATATTC
1 TTTTAATTAATATTC
58053 TTTT
1 TTTT
58057 GCTAATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATTAATATTC
Found at i:58907 original size:27 final size:28
Alignment explanation
Indices: 58884--58937 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
58874 ATATTTATTT
*
58884 ATTTTTTA-ATATTTAATAATTTTATAC
1 ATTTTTTATATATTGAATAATTTTATAC
* *
58911 ATTTTTTATTTATTGAATATTTTTATA
1 ATTTTTTATATATTGAATAATTTTATA
58938 TAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
ATTTTTTATATATTGAATAATTTTATAC
Found at i:59458 original size:2 final size:2
Alignment explanation
Indices: 59451--59478 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59441 GTGTAAACAT
59451 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
59479 ACCATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82252 original size:12 final size:12
Alignment explanation
Indices: 82219--82253 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
82209 ATTTTGGTCT
82219 TTTTTATTGTTA
1 TTTTTATTGTTA
**
82231 TTTTGGTTGTTA
1 TTTTTATTGTTA
82243 TTTTTATTGTT
1 TTTTTATTGTT
82254 TAGATGTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.74
Consensus pattern (12 bp):
TTTTTATTGTTA
Found at i:82316 original size:22 final size:22
Alignment explanation
Indices: 82273--82316 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
82263 TTTTTATACG
* ***
82273 TTTTTACTATTATTTCGTTATT
1 TTTTTAATATTATTTAAATATT
82295 TTTTTAATATTATTTAAATATT
1 TTTTTAATATTATTTAAATATT
82317 ATAGAACTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTTAATATTATTTAAATATT
Found at i:90526 original size:46 final size:47
Alignment explanation
Indices: 90450--90596 Score: 155
Period size: 46 Copynumber: 3.2 Consensus size: 47
90440 TACGAAACAA
* * *
90450 ACAGAGAGTACA-AAAGTACTAA-CAGAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAATCAAAGAGCACACACAGTGCTAAT
*
90495 -CAGATAGCACACAAAGTGCTAATCAAAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAATCAAAGAGCACACACAGTGCTAAT
* *
90541 AACAGAGAGCACAC--AGTGCTAATAACAGAGAGCACGAGAC-GTGCTAA-
1 -ACAGAGAGCACACAAAGTGCTAAT--CAAAGAGCAC-ACACAGTGCTAAT
90588 ACAGAGAGC
1 ACAGAGAGC
90597 GCGCTAGTGA
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
44 9 0.10
45 9 0.10
46 40 0.45
48 27 0.31
49 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (47 bp):
ACAGAGAGCACACAAAGTGCTAATCAAAGAGCACACACAGTGCTAAT
Found at i:90530 original size:25 final size:23
Alignment explanation
Indices: 90451--90596 Score: 140
Period size: 23 Copynumber: 6.3 Consensus size: 23
90441 ACGAAACAAA
* * *
90451 CAGAGAGTACA-AAAGTACTAA-
1 CAGAGAGCACACACAGTGCTAAT
90472 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
* *
90495 CAGATAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
*
90518 CAAAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
90541 AACAGAGAG--CACACAGTGCTAAT
1 --CAGAGAGCACACACAGTGCTAAT
* *
90564 AACAGAGAGCACGAGAC-GTGCTAAA
1 --CAGAGAGCAC-ACACAGTGCTAAT
90589 CAGAGAGC
1 CAGAGAGC
90597 GCGCTAGTGA
Statistics
Matches: 107, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
21 10 0.09
22 8 0.07
23 72 0.67
25 14 0.13
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACACAGTGCTAAT
Found at i:99857 original size:18 final size:18
Alignment explanation
Indices: 99834--99869 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
99824 ACTTACCTCA
*
99834 ATGTCACAGTTTGTGCAT
1 ATGTCACAGTTTGCGCAT
99852 ATGTCACAGTTTGCGCAT
1 ATGTCACAGTTTGCGCAT
99870 TCTTTCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (18 bp):
ATGTCACAGTTTGCGCAT
Found at i:100044 original size:23 final size:23
Alignment explanation
Indices: 100018--100096 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
100008 TGCTGGGTAA
100018 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
100041 CAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
100064 AACAGAGAGTACACACAGTGCTAAT
1 --CAGAGAGCACACAAAGTGCTAAT
100089 CAGAGAGC
1 CAGAGAGC
100097 GCGCTAGTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 29 0.59
25 20 0.41
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:100049 original size:48 final size:48
Alignment explanation
Indices: 99983--100096 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
99973 GAGAGTACCG
* * * **
99983 AAGTACTAAACAGAGAGCACA-TAAGTGCTGGGTAACAGAGAGCACACA
1 AAGTGCTAATCAGAGAGCACACGAAGTGCT-AATAACAGAGAGCACACA
*
100031 AAGTGCTAATCAGAGAGCACACGAAGTGCTAATAACAGAGAGTACACA
1 AAGTGCTAATCAGAGAGCACACGAAGTGCTAATAACAGAGAGCACACA
*
100079 CAGTGCTAATCAGAGAGC
1 AAGTGCTAATCAGAGAGC
100097 GCGCTAGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 51 0.88
49 7 0.12
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (48 bp):
AAGTGCTAATCAGAGAGCACACGAAGTGCTAATAACAGAGAGCACACA
Found at i:106357 original size:20 final size:19
Alignment explanation
Indices: 106332--106397 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
106322 GAAAAGCTTC
106332 TACCAAAATATCTAAGGATT
1 TACCAAAATATCTAA-GATT
* * *
106352 TACCAATATTTCTAAAACTT
1 TACCAAAATATCTAAGA-TT
106372 TACCAAAATATCTAAAGATT
1 TACCAAAATATCT-AAGATT
106392 TACCAA
1 TACCAA
106398 TATTTATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.89
21 3 0.08
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (19 bp):
TACCAAAATATCTAAGATT
Found at i:106392 original size:40 final size:42
Alignment explanation
Indices: 106323--106402 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 42
106313 AAAGCTTAGG
*
106323 AAAAGCTTCTACCAAAATATCTAAGGATTTACCAATATTTCT
1 AAAAGCTTCTACCAAAATATCTAAAGATTTACCAATATTTCT
106365 AAAA-CTT-TACCAAAATATCTAAAGATTTACCAATATTT
1 AAAAGCTTCTACCAAAATATCTAAAGATTTACCAATATTT
106403 ATATATTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 30 0.81
41 3 0.08
42 4 0.11
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (42 bp):
AAAAGCTTCTACCAAAATATCTAAAGATTTACCAATATTTCT
Found at i:112382 original size:21 final size:20
Alignment explanation
Indices: 112344--112382 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
112334 TAAAAATAGC
* *
112344 TTAATTTTTTAATTTATATA
1 TTAATTTTTCAATATATATA
112364 TTAATATTTTCAATATATA
1 TTAAT-TTTTCAATATATA
112383 AAAAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTTTTCAATATATATA
Found at i:113696 original size:16 final size:16
Alignment explanation
Indices: 113652--113704 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
113642 CTCTAAAATG
113652 ATAA-ATTTTTAATTT
1 ATAATATTTTTAATTT
113667 A-AAT-TGTTTATAATTT
1 ATAATAT-TTT-TAATTT
*
113683 ATAATATTTTTAATTA
1 ATAATATTTTTAATTT
113699 ATAATA
1 ATAATA
113705 GTAAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 18 0.56
17 6 0.19
18 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATAATATTTTTAATTT
Found at i:114482 original size:20 final size:20
Alignment explanation
Indices: 114451--114488 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
114441 TATAAATTTT
114451 TTAAAAATATA-TAAAAAAC
1 TTAAAAATATATTAAAAAAC
114470 TTAAAATATATATTAAAAA
1 TTAAAA-ATATATTAAAAA
114489 TTCAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAAATATATTAAAAAAC
Found at i:114859 original size:25 final size:27
Alignment explanation
Indices: 114819--114881 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
114809 AAAATCAAAG
114819 ATTTGAATATACATAAATTTAATATTT
1 ATTTGAATATACATAAATTTAATATTT
* *
114846 -TTTGAATAT-TATAAATTTAATGTTT
1 ATTTGAATATACATAAATTTAATATTT
*
114871 ATTTCAATATA
1 ATTTGAATATA
114882 GATTGTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (27 bp):
ATTTGAATATACATAAATTTAATATTT
Found at i:122433 original size:28 final size:30
Alignment explanation
Indices: 122402--122468 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
122392 AATTTATTTT
122402 ATTTCAAAAAATTACAA-AAAATTATT-AA
1 ATTTCAAAAAATTACAATAAAATTATTAAA
* * *
122430 ATTT-TAAAAATTTCAATTAAATTATTAAA
1 ATTTCAAAAAATTACAATAAAATTATTAAA
122459 ATATTCAAAA
1 AT-TTCAAAA
122469 TGGTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 10 0.32
28 12 0.39
29 4 0.13
30 2 0.06
31 3 0.10
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (30 bp):
ATTTCAAAAAATTACAATAAAATTATTAAA
Found at i:122460 original size:20 final size:21
Alignment explanation
Indices: 122425--122466 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
122415 ACAAAAAATT
122425 ATTAAATTTTAAAAAT-TTCA
1 ATTAAATTTTAAAAATATTCA
122445 ATTAAATTATT-AAAATATTCA
1 ATTAAATT-TTAAAAATATTCA
122466 A
1 A
122467 AATGGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAATTTTAAAAATATTCA
Found at i:125649 original size:15 final size:16
Alignment explanation
Indices: 125622--125667 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
125612 GAGAGATTTC
125622 TTTGGCAAACAATTAT
1 TTTGGCAAACAATTAT
125638 TTTGGC-AACAATTAT
1 TTTGGCAAACAATTAT
* * *
125653 GTTAGCAAATAATTA
1 TTTGGCAAACAATTA
125668 CCGAATTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (16 bp):
TTTGGCAAACAATTAT
Found at i:134067 original size:17 final size:18
Alignment explanation
Indices: 134047--134080 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
134037 AAAAAATTCA
*
134047 AATTTAAGAA-AATAAAC
1 AATTTAAAAACAATAAAC
134064 AATTTAAAAACAATAAA
1 AATTTAAAAACAATAAA
134081 TTATAGGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTTAAAAACAATAAAC
Found at i:138129 original size:12 final size:11
Alignment explanation
Indices: 138109--138151 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
138099 GAAGAGAATG
138109 AAAAATAAAAA
1 AAAAATAAAAA
*
138120 AAAAATTAAAA
1 AAAAATAAAAA
* *
138131 GAATATAAAAGA
1 AAAAATAAAA-A
138143 AAAAATAAA
1 AAAAATAAA
138152 TTGTTCAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:139700 original size:30 final size:32
Alignment explanation
Indices: 139642--139706 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
139632 TTAATAATAA
* * *
139642 AAAAAATTATATTTTAACTTTTTTAAAATGAT
1 AAAAAATTATATTTTAAATCTTTAAAAATGAT
*
139674 AAAAAATTA-A-TTTAAATCTTTAAAAATTAT
1 AAAAAATTATATTTTAAATCTTTAAAAATGAT
139704 AAA
1 AAA
139707 TATATAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.66
31 1 0.03
32 9 0.31
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (32 bp):
AAAAAATTATATTTTAAATCTTTAAAAATGAT
Found at i:141117 original size:19 final size:19
Alignment explanation
Indices: 141093--141157 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
141083 CAAATTATTT
141093 TAAAATTATTTTTAAAATA
1 TAAAATTATTTTTAAAATA
*
141112 TAAAATTA---TTAATATTA
1 TAAAATTATTTTTAA-AATA
* * *
141129 TTATATTATTTTTTAAATA
1 TAAAATTATTTTTAAAATA
141148 TAAAATTATT
1 TAAAATTATT
141158 AAATAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
16 4 0.11
17 9 0.26
19 19 0.54
20 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAAATTATTTTTAAAATA
Found at i:142619 original size:25 final size:25
Alignment explanation
Indices: 142585--142636 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
142575 CGAAGTACTT
*
142585 AACAGAAGCGCATAAGTGCTGGGGA
1 AACAAAAGCGCATAAGTGCTGGGGA
142610 AACAAAAGCGCATAAGTGCTGGGGA
1 AACAAAAGCGCATAAGTGCTGGGGA
142635 AA
1 AA
142637 AGTAGGCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.33, T:0.12
Consensus pattern (25 bp):
AACAAAAGCGCATAAGTGCTGGGGA
Found at i:142670 original size:22 final size:23
Alignment explanation
Indices: 142637--142692 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
142627 GCTGGGGAAA
* *
142637 AGTAGGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGATGAAC
142660 AG-AAGCACACACAGTGATGAAC
1 AGTAAGCACACACAGTGATGAAC
142682 AGTAAGCACAC
1 AGTAAGCACAC
142693 TAGCATTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.11
Consensus pattern (23 bp):
AGTAAGCACACACAGTGATGAAC
Found at i:145422 original size:17 final size:16
Alignment explanation
Indices: 145378--145413 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
145368 AAATAAAAAA
* *
145378 TAAAAAATGAATATTG
1 TAAAAAATGGATGTTG
145394 TAAAAAATGGATGTTG
1 TAAAAAATGGATGTTG
145410 TAAA
1 TAAA
145414 TATATGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
TAAAAAATGGATGTTG
Found at i:145504 original size:19 final size:18
Alignment explanation
Indices: 145464--145496 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
145454 TTGTTCTCTC
145464 TTTT-TTTTTCAGTTTTA
1 TTTTATTTTTCAGTTTTA
145481 TTTTATTTTT-AGTTTT
1 TTTTATTTTTCAGTTTT
145497 TAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTCAGTTTTA
Found at i:150484 original size:25 final size:27
Alignment explanation
Indices: 150447--150498 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
150437 CCTTCAAAGA
*
150447 AAAACTATGAAAAATATGAATA-AAAT
1 AAAACTATGAAAAATATAAATATAAAT
*
150473 AAAATTAT-AAAAATATAAATATAAAT
1 AAAACTATGAAAAATATAAATATAAAT
150499 TTCGAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (27 bp):
AAAACTATGAAAAATATAAATATAAAT
Found at i:158262 original size:26 final size:26
Alignment explanation
Indices: 158224--158278 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
158214 AAAAATATAC
*
158224 AGAAAACAGGTTCAACTTCAATCAAT
1 AGAAAACACGTTCAACTTCAATCAAT
158250 AGAAAACACGTTCAACTTCAATCAAT
1 AGAAAACACGTTCAACTTCAATCAAT
158276 AGA
1 AGA
158279 CATAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (26 bp):
AGAAAACACGTTCAACTTCAATCAAT
Found at i:161413 original size:20 final size:21
Alignment explanation
Indices: 161378--161423 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
161368 ATTAAACTGT
*
161378 ATATTAATATATTTTGTATAA
1 ATATTAATATATTTTGAATAA
*
161399 ATATTTATA-ATTTTGAATAA
1 ATATTAATATATTTTGAATAA
161419 ATATT
1 ATATT
161424 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
ATATTAATATATTTTGAATAA
Found at i:162465 original size:25 final size:25
Alignment explanation
Indices: 162436--162486 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
162426 TAAATTATAT
162436 ATTTTTAT--AATTGTAAAA-ATGTAA
1 ATTTTTATAAAATT-TAAAAGAT-TAA
162460 ATTTTTATAAAATTTAAAAGATTAA
1 ATTTTTATAAAATTTAAAAGATTAA
162485 AT
1 AT
162487 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (25 bp):
ATTTTTATAAAATTTAAAAGATTAA
Found at i:163656 original size:16 final size:17
Alignment explanation
Indices: 163622--163656 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
163612 ATAAACTTTG
163622 AAAATATACATATGAAAA
1 AAAATATACATAT-AAAA
*
163640 AAAATATATATATAAAA
1 AAAATATACATATAAAA
163657 GTTGTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATACATATAAAA
Found at i:165178 original size:29 final size:29
Alignment explanation
Indices: 165097--165177 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
165087 AATTTCAAAA
165097 TTATACATG-AATTATGATTTAATGTGCAATT
1 TTATACATGAAATT-TGATTT--TGTGCAATT
* * *
165128 GTATATATGAACTTTGATTTTGTGCAATT
1 TTATACATGAAATTTGATTTTGTGCAATT
165157 TTATACATGAAAATTTGATTT
1 TTATACATG-AAATTTGATTT
165178 GATCCAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 16 0.38
30 10 0.24
31 13 0.31
32 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (29 bp):
TTATACATGAAATTTGATTTTGTGCAATT
Found at i:165843 original size:25 final size:24
Alignment explanation
Indices: 165815--165868 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
165805 TTATTAATAT
*
165815 ATATTATTTTTT-ATTAATTATATTA
1 ATATTATTTTTTAAATAA-TAT-TTA
165840 ATATTATTTTTTAAATAATATTTA
1 ATATTATTTTTTAAATAATATTTA
165864 ATATT
1 ATATT
165869 TATAGGCACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATATTATTTTTTAAATAATATTTA
Done.