Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011849.1 Kokia drynarioides strain JFW-HI SEQ_126845, 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: 57736
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:1788 original size:3 final size:3
Alignment explanation
Indices: 1780--1817 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1770 AATTAAACAT
1780 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1818 TGGGTTGCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:7238 original size:18 final size:17
Alignment explanation
Indices: 7206--7239 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
7196 AGTATTTGTG
*
7206 ATTCTATTGTATTTATT
1 ATTCTATTCTATTTATT
7223 ATTCTAATTCTATTTAT
1 ATTCT-ATTCTATTTAT
7240 AAACTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTCTATTCTATTTATT
Found at i:9205 original size:15 final size:16
Alignment explanation
Indices: 9177--9207 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9167 ATTACACGAG
9177 TGAAAATTACATATAT
1 TGAAAATTACATATAT
9193 TGAAAATTA-ATATAT
1 TGAAAATTACATATAT
9208 AACAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
TGAAAATTACATATAT
Found at i:10386 original size:26 final size:26
Alignment explanation
Indices: 10337--10387 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
10327 ATATTCAGCC
** **
10337 TTTTATTTTATTTTGATATTTAAATT
1 TTTTATTCCATTTTGATACCTAAATT
10363 TTTTATTCCATTTTGATACCTAAAT
1 TTTTATTCCATTTTGATACCTAAAT
10388 CATTTATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTTATTCCATTTTGATACCTAAATT
Found at i:10393 original size:26 final size:26
Alignment explanation
Indices: 10346--10395 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
10336 CTTTTATTTT
** **
10346 ATTTTGATATTTAAATTTTTTATTCC
1 ATTTTGATACCTAAATCATTTATTCC
10372 ATTTTGATACCTAAATCATTTATT
1 ATTTTGATACCTAAATCATTTATT
10396 TGTTTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.56
Consensus pattern (26 bp):
ATTTTGATACCTAAATCATTTATTCC
Found at i:14402 original size:15 final size:15
Alignment explanation
Indices: 14382--14411 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14372 AACTATAATG
14382 GAATGATAGTTTAGA
1 GAATGATAGTTTAGA
14397 GAATGATAGTTTAGA
1 GAATGATAGTTTAGA
14412 AATTACTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
GAATGATAGTTTAGA
Found at i:15379 original size:18 final size:17
Alignment explanation
Indices: 15338--15441 Score: 78
Period size: 17 Copynumber: 6.4 Consensus size: 17
15328 CCAAACTCAT
* *
15338 TTTAAATTTAATTTATGA
1 TTTAAATTTATTTTA-AA
*
15356 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
15373 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
15390 TTT--A---A-TTTAAG
1 TTTAAATTTATTTTAAA
15401 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
15419 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
15436 TTTAAA
1 TTTAAA
15442 ATAAATAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
11 8 0.12
12 1 0.01
13 1 0.01
15 1 0.01
16 1 0.01
17 30 0.43
18 27 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:15381 original size:6 final size:6
Alignment explanation
Indices: 15370--15441 Score: 62
Period size: 6 Copynumber: 12.5 Consensus size: 6
15360 ATTTGTTTTA
* * **
15370 AAATTT AAATTT -ATTTT AAATTT -AATTT AAGTTT AAATTT ATTTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
15416 AAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT AAATTT AAATT-T AAATTT AAA
15442 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 36 0.71
7 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:15387 original size:11 final size:11
Alignment explanation
Indices: 15371--15440 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
15361 TTTGTTTTAA
15371 AATTTAAATTT
1 AATTTAAATTT
*
15382 ATTTTAAATTT
1 AATTTAAATTT
*
15393 AATTTAAGTTT
1 AATTTAAATTT
**
15404 AAATTTATTTTT
1 -AATTTAAATTT
*
15416 AAATTTAAAATT
1 -AATTTAAATTT
15428 -ATTATAAATTT
1 AATT-TAAATTT
15439 AA
1 AA
15441 AATAAATAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
10 3 0.06
11 25 0.53
12 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:15389 original size:46 final size:46
Alignment explanation
Indices: 15336--15440 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
15326 ACCCAAACTC
* * *
15336 ATTTTAAATTTAATTTATGATTAAATTTGTTTTAAAATTTAAATTT
1 ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATT
* *
15382 ATTTTAAATTTAATTTAAGTTTAAATTTATTTTTAAATTTAAAATT
1 ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATT
*
15428 ATTATAAATTTAA
1 ATTTTAAATTTAA
15441 AATAAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (46 bp):
ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATT
Found at i:15423 original size:29 final size:29
Alignment explanation
Indices: 15338--15423 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
15328 CCAAACTCAT
** **
15338 TTTAAATTT-AATTTATGATTAAATTTGT
1 TTTAAATTTAAATTTATTTTTAAATTTAA
15366 TTTAAAATTTAAATTTA-TTTTAAATTTAA
1 TTT-AAATTTAAATTTATTTTTAAATTTAA
*
15395 TTTAAGTTTAAATTTATTTTTAAATTTAA
1 TTTAAATTTAAATTTATTTTTAAATTTAA
15424 AATTATTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 15 0.30
29 29 0.58
30 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTAAATTTAAATTTATTTTTAAATTTAA
Found at i:15772 original size:13 final size:13
Alignment explanation
Indices: 15754--15780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15744 AAAAATGTAC
15754 ATTTACTTGTATA
1 ATTTACTTGTATA
15767 ATTTACTTGTATA
1 ATTTACTTGTATA
15780 A
1 A
15781 GACAAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTACTTGTATA
Found at i:16134 original size:3 final size:3
Alignment explanation
Indices: 16128--16169 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
16118 TATTAATAGG
* * *
16128 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA CAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16170 ATTATGGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:16215 original size:13 final size:14
Alignment explanation
Indices: 16199--16238 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
16189 TTAATATTTT
16199 TAATTA-TAATAAA
1 TAATTATTAATAAA
16212 TAA-TATTAAT-AA
1 TAATTATTAATAAA
16224 TAAATTATTAATAAA
1 T-AATTATTAATAAA
16239 AAAAGAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.22
13 9 0.39
14 7 0.30
15 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTATTAATAAA
Found at i:16225 original size:16 final size:14
Alignment explanation
Indices: 16204--16237 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
16194 ATTTTTAATT
16204 ATAATAAATAATATTA
1 ATAATAAAT--TATTA
16220 ATAATAAATTATTA
1 ATAATAAATTATTA
16234 ATAA
1 ATAA
16238 AAAAAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAAATTATTA
Found at i:17282 original size:30 final size:30
Alignment explanation
Indices: 17216--17624 Score: 323
Period size: 29 Copynumber: 13.9 Consensus size: 30
17206 CTAAACTGTT
* * *
17216 CAAAAATTACA-TTTTAACCCTCG-AGCTTC
1 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
* *
17245 CAAAAATTTCATTTTTTACCTCGAAACTTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
* * *
17275 CACAAATTCCA-TTTTCACCCTTG-AACTTC
1 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
*
17304 CAAAAATTCCATTTTTGACCTCGAAAGTTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
*
17334 CAAAAATTCCA-TTTT-ACCCCCG-AACTTC
1 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
* *
17362 CAAAAATTCCA-TTTTGACCTTGAAACTTT
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
* * * *
17391 CAAAAATTTCATTTTT-ACCCCCAAACTTT
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
* * *
17420 AAAAAATTCTATTTTTGACCTCAAAACTTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
17450 CAAAAATTCCATTTTT-ACCCTCG-AACTTC
1 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
* ** * *
17479 AAAAAATTCCATTTTCAACCCCAAAACTTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
* *
17509 CAAAAATTCTATTTTTGACCTCG-AACCTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTC
* * *
17538 TAAAATTTCCATTTTTGACC-CTGAAACTTT
1 CAAAAATTCCATTTTTGACCTC-GAAACTTC
* *
17568 CACAAATTACCA-TTTTG-CCATCG-GA-TGTC
1 CAAAAATT-CCATTTTTGACC-TCGAAACT-TC
*
17597 CAAAAACTT-CATTTTCGACCTCGAAACT
1 CAAAAA-TTCCATTTTTGACCTCGAAACT
17625 CTCAAAATTA
Statistics
Matches: 303, Mismatches: 53, Indels: 46
0.75 0.13 0.11
Matches are distributed among these distances:
28 28 0.09
29 150 0.50
30 120 0.40
31 5 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (30 bp):
CAAAAATTCCATTTTTGACCTCGAAACTTC
Found at i:17311 original size:59 final size:59
Alignment explanation
Indices: 17216--17624 Score: 418
Period size: 59 Copynumber: 7.0 Consensus size: 59
17206 CTAAACTGTT
* * * * *
17216 CAAAAATTACATTTTAACCCTCGAGCTTCCAAAAATTTCATTTTTTACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
* * * *
17275 CACAAATTCCATTTTCACCCTTGAACTTCCAAAAATTCCATTTTTGACCTCGAAAGTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
* * *
17334 CAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATTCCA-TTTTGACCTTGAAACTTT
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
* * * ** * *
17391 CAAAAATTTCATTTTTACCCCCAAACTTTAAAAAATTCTATTTTTGACCTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
* ** * *
17450 CAAAAATTCCATTTTTACCCTCGAACTTCAAAAAATTCCATTTTCAACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
* * * * *
17509 CAAAAATTCTATTTTTGA-CCTCGAACCTCTAAAATTTCCATTTTTGACC-CTGAAACTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGACCTC-GAAACTTC
* * * * *
17568 CACAAATTACCA-TTTTGCCATCGGA-TGTCCAAAAACTT-CATTTTCGACCTCGAAACT
1 CAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAA-TTCCATTTTTGACCTCGAAACT
17625 CTCAAAATTA
Statistics
Matches: 293, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
57 25 0.09
58 50 0.17
59 212 0.72
60 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
Found at i:20775 original size:24 final size:24
Alignment explanation
Indices: 20718--20775 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
20708 ATAACATCCA
*
20718 AACAACAAAAATAACAACCAAAAT
1 AACAACAAAAATAACAACCAAAAC
** *
20742 AGTAGCAAAAATAACAA-CAAAAC
1 AACAACAAAAATAACAACCAAAAC
20765 AACAACAAAAA
1 AACAACAAAAA
20776 CAATGATGTG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACAACCAAAAC
Found at i:20778 original size:12 final size:12
Alignment explanation
Indices: 20718--20775 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
20708 ATAACATCCA
20718 AACAACAAAAAT
1 AACAACAAAAAT
*
20730 AACAACCAAAAT
1 AACAACAAAAAT
** *
20742 AGTAGCAAAAAT
1 AACAACAAAAAT
*
20754 AACAAC-AAAAC
1 AACAACAAAAAT
20765 AACAACAAAAA
1 AACAACAAAAA
20776 CAATGATGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:22022 original size:12 final size:12
Alignment explanation
Indices: 21999--22038 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
21989 AGCATTATCA
21999 AACAACAAAAAT
1 AACAACAAAAAT
* *
22011 AGCAACATAAAT
1 AACAACAAAAAT
*
22023 AACAACAAAAAC
1 AACAACAAAAAT
22035 AACA
1 AACA
22039 CATGGTCGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:24664 original size:22 final size:22
Alignment explanation
Indices: 24636--24678 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24626 CGTTGAGCTT
*
24636 CAATGTTGCGACATTCTAGGTC
1 CAATGTTACGACATTCTAGGTC
* *
24658 CAATGTTACGACTTTGTAGGT
1 CAATGTTACGACATTCTAGGT
24679 AGTTTACTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (22 bp):
CAATGTTACGACATTCTAGGTC
Found at i:27189 original size:18 final size:18
Alignment explanation
Indices: 27168--27208 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
27158 TTTTTTAAAA
*
27168 AAAATTATGATTTTTATT-
1 AAAATTATAATTTTT-TTG
27186 AAAA-TATAATTTTTTTG
1 AAAATTATAATTTTTTTG
27203 AAAATT
1 AAAATT
27209 TTTAACCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
AAAATTATAATTTTTTTG
Found at i:28009 original size:13 final size:13
Alignment explanation
Indices: 27987--28016 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27977 CAAATCCCAC
*
27987 TATAGTAATATTT
1 TATAGAAATATTT
28000 TATAGAAATATTT
1 TATAGAAATATTT
28013 TATA
1 TATA
28017 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TATAGAAATATTT
Found at i:37806 original size:14 final size:13
Alignment explanation
Indices: 37792--37842 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
37782 TTGAATAATA
37792 AATTTTAATTGAT
1 AATTTTAATTGAT
37805 AAATTTTAAATT-AT
1 -AATTTT-AATTGAT
* *
37819 -TTTTTAATTTAT
1 AATTTTAATTGAT
37831 AATTTTAATTGA
1 AATTTTAATTGA
37843 AAGCAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.13
12 6 0.19
13 9 0.29
14 8 0.26
15 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (13 bp):
AATTTTAATTGAT
Found at i:49991 original size:33 final size:33
Alignment explanation
Indices: 49954--50021 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
49944 AGTATTCCAA
* *
49954 AACAACATTTTTCCTTTGATTAGGGACATATAT
1 AACAACATTTTTCCTTTCATTAGGGACACATAT
49987 AACAACATTTTTCCTTTCATTAGGGACACATAT
1 AACAACATTTTTCCTTTCATTAGGGACACATAT
50020 AA
1 AA
50022 GTACCATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (33 bp):
AACAACATTTTTCCTTTCATTAGGGACACATAT
Found at i:50971 original size:37 final size:37
Alignment explanation
Indices: 50930--51003 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
50920 TAAGCCTTTT
50930 TGTTGTAAGTACTACAAGAGTTTTGAACTATAGTTTA
1 TGTTGTAAGTACTACAAGAGTTTTGAACTATAGTTTA
50967 TGTTGTAAGTACTACAAGAGTTTTGAACTATAGTTTA
1 TGTTGTAAGTACTACAAGAGTTTTGAACTATAGTTTA
51004 ATTTCTCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (37 bp):
TGTTGTAAGTACTACAAGAGTTTTGAACTATAGTTTA
Found at i:51342 original size:10 final size:11
Alignment explanation
Indices: 51320--51350 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
51310 TTCTGACTTT
51320 GAAAAATTATA
1 GAAAAATTATA
51331 GAAAAATT-TA
1 GAAAAATTATA
51341 GAAAAATTAT
1 GAAAAATTAT
51351 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:51807 original size:23 final size:23
Alignment explanation
Indices: 51781--51905 Score: 162
Period size: 23 Copynumber: 5.3 Consensus size: 23
51771 ACACTAGCGC
51781 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
51804 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
51827 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
51852 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
51875 GCTCTCTGATTAGCATTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
51898 GCTCTCTG
1 GCTCTCTG
51906 TTGCCCAGCA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
22 3 0.03
23 65 0.75
25 16 0.18
26 3 0.03
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:51851 original size:48 final size:46
Alignment explanation
Indices: 51781--51907 Score: 193
Period size: 48 Copynumber: 2.7 Consensus size: 46
51771 ACACTAGCGC
*
51781 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTTAGCAC-TCTGCGT
* *
51827 GCTCTCTGTTATTAGCATTGTGTGTGCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCATTGTGTGTGCTCTCTGTTTAGCACTCTGCGT
51875 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTT
1 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTT
51908 GCCCAGCACT
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
46 33 0.44
47 2 0.03
48 40 0.53
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.44
Consensus pattern (46 bp):
GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTTAGCACTCTGCGT
Found at i:51924 original size:48 final size:45
Alignment explanation
Indices: 51781--51926 Score: 184
Period size: 48 Copynumber: 3.1 Consensus size: 45
51771 ACACTAGCGC
* * *
51781 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTTAGCACTTAT-GT
*
51827 GCTCTCTGTTATTAGCATTGTGTGTGCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCATTGTGTGTGCTCTCTGTTTAGCAC-TTATGT
*
51875 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTGCCCAGCACTTATGT
1 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTT---TAGCACTTATGT
51923 GCTC
1 GCTC
51927 ACTGTTTGTT
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
46 33 0.37
48 49 0.55
49 7 0.08
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (45 bp):
GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTTAGCACTTATGT
Found at i:51924 original size:71 final size:71
Alignment explanation
Indices: 51781--51933 Score: 175
Period size: 71 Copynumber: 2.2 Consensus size: 71
51771 ACACTAGCGC
* * ** *
51781 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCATT
1 GCTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTACCAGCACT
*
51846 GTGTGT
66 GTATGT
* * * *
51852 GCTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCATTGTGT-GTGCTCTCTGTTGCCCAGCA
1 GCTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCA-CGTCTCGTGCTCTCTGTT-ACCAGCA
51916 CT-TATGT
64 CTGTATGT
*
51923 GCTCACTGTTT
1 GCTCTCTGTTT
51934 GTTCCGTATA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
71 61 0.88
72 8 0.12
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (71 bp):
GCTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTACCAGCACT
GTATGT
Found at i:52723 original size:23 final size:23
Alignment explanation
Indices: 52689--52774 Score: 120
Period size: 23 Copynumber: 3.7 Consensus size: 23
52679 GCTGGGAAAA
*
52689 CAGTAAGCACACACAGTGCAAAT
1 CAGTAGGCACACACAGTGCAAAT
*
52712 CAGTAGGTACACACAGTGCAAAAT
1 CAGTAGGCACACACAGTGC-AAAT
*
52736 -AGTAGGCACACACAGTGCAAAA
1 CAGTAGGCACACACAGTGCAAAT
*
52758 CAGTAAGCACACACAGT
1 CAGTAGGCACACACAGT
52775 AAGCACACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.05
23 49 0.88
24 4 0.07
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (23 bp):
CAGTAGGCACACACAGTGCAAAT
Found at i:52746 original size:46 final size:46
Alignment explanation
Indices: 52685--52774 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
52675 AAGTGCTGGG
* * *
52685 AAAACAGTAAGCACACACAGTGCAAATCAGTAGGTACACACAGTGC
1 AAAACAGTAAGCACACACAGTGCAAAACAGTAAGCACACACAGTGC
* *
52731 AAAATAGTAGGCACACACAGTGCAAAACAGTAAGCACACACAGT
1 AAAACAGTAAGCACACACAGTGCAAAACAGTAAGCACACACAGT
52775 AAGCACACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (46 bp):
AAAACAGTAAGCACACACAGTGCAAAACAGTAAGCACACACAGTGC
Found at i:52775 original size:13 final size:12
Alignment explanation
Indices: 52688--52783 Score: 53
Period size: 13 Copynumber: 8.1 Consensus size: 12
52678 TGCTGGGAAA
52688 ACAGTAAGCACAC
1 ACAGT-AGCACAC
52701 ACAGT-GCA-A-
1 ACAGTAGCACAC
*
52710 ATCAGTAGGTACAC
1 A-CAGTA-GCACAC
*
52724 ACAGT-GCA-AA
1 ACAGTAGCACAC
*
52734 ATAGTAGGCACAC
1 ACAGTA-GCACAC
*
52747 ACAGT-GCA-AA
1 ACAGTAGCACAC
52757 ACAGTAAGCACAC
1 ACAGT-AGCACAC
52770 ACAGTAAGCACAC
1 ACAGT-AGCACAC
52783 A
1 A
52784 TAGTGCAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
9 1 0.02
10 16 0.25
11 8 0.12
12 8 0.12
13 30 0.47
14 1 0.02
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (12 bp):
ACAGTAGCACAC
Found at i:55046 original size:16 final size:16
Alignment explanation
Indices: 55025--55055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55015 AAAATTTACA
*
55025 ATGTATGTATTAAATT
1 ATGTATCTATTAAATT
55041 ATGTATCTATTAAAT
1 ATGTATCTATTAAAT
55056 AACAATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (16 bp):
ATGTATCTATTAAATT
Done.