Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013828.1 Kokia drynarioides strain JFW-HI SEQ_128856, 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: 163701
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:3954 original size:195 final size:193
Alignment explanation
Indices: 3556--4002 Score: 528
Period size: 195 Copynumber: 2.3 Consensus size: 193
3546 GAAACCGACG
* *
3556 CGATGGCTGATGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCA
1 CGATGGCTGAGGTA-CGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCA
* * * *
3621 GGAAAAGAGAAAAGGATCTAGGAATGTATTACAGGCCCTACGATGGTTGAGATTTATGCATAAGT
65 GGAAAAGAGAAAAGGATCTA-GAATGGATTACAGACCCTACGATGGTAGAGATCTATGCATAAGT
* * * *
3686 GCATATTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAGTTATATGCACAAATATCGTAA
129 GCATACTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAGTTATATACACAAACACCGTAA
* * * *
3751 CAATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGATATCTTGTGTGAGCAGCATCGTGACTC-
1 CGATGGCTGAGGTA-CGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCA
* * * * * *
3815 GGGAAAGAGATATGGATCCTA-AATGGATTATAGACCCTACGATGGCTAG-GA-CTATGCTTTA-
65 GGAAAAGAGAAAAGGAT-CTAGAATGGATTACAGACCCTACGATGG-TAGAGATCTATGCATAAG
* *
3876 TGCATACTCTCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTTATAGTACAGACAAGCAC
128 TGCATACTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAG-TTATA-TAC--ACAAACAC
3941 CGTAA
189 CGTAA
* * *
3946 TGATGGCTG-GTGTACAGCATACGTTGCGAGTCCTTGACAGCTCGTGTGAGCAGCATC
1 CGATGGCTGAG-GTAC-GCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATC
4003 TAGTATTGGT
Statistics
Matches: 214, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
191 43 0.20
192 12 0.06
193 25 0.12
194 18 0.08
195 116 0.54
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (193 bp):
CGATGGCTGAGGTACGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCAG
GAAAAGAGAAAAGGATCTAGAATGGATTACAGACCCTACGATGGTAGAGATCTATGCATAAGTGC
ATACTCTCGACAGCTCGTGTGAGCAGCATCATTAAGGAACAGTTATATACACAAACACCGTAA
Found at i:12121 original size:15 final size:13
Alignment explanation
Indices: 12085--12114 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12075 ATCCTTCCTT
*
12085 TTTTTCTATTTTA
1 TTTTTCTCTTTTA
12098 TTTTTCTCTTTTA
1 TTTTTCTCTTTTA
12111 TTTT
1 TTTT
12115 ATGCTCTTCA
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:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTCTTTTA
Found at i:15906 original size:21 final size:20
Alignment explanation
Indices: 15868--15911 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
15858 ATTTATTTTA
*
15868 AAAGTTCAAATACAAAATTCC
1 AAAGTCCAAATACAAAA-TCC
* *
15889 AAAGTCCAAATCCGAAATCC
1 AAAGTCCAAATACAAAATCC
15909 AAA
1 AAA
15912 TTTTACAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.52, C:0.23, G:0.07, T:0.18
Consensus pattern (20 bp):
AAAGTCCAAATACAAAATCC
Found at i:17252 original size:30 final size:29
Alignment explanation
Indices: 17198--17431 Score: 177
Period size: 30 Copynumber: 7.9 Consensus size: 29
17188 CTCCAGAGGT
* * * *
17198 CCCCGAACTTTCCAGAAATCATATTTTGA
1 CCCCAAACTTTTCAAAAATCACATTTTGA
* *
17227 CTCCCAAACTTTTCAAAAATTATATTTTGA
1 C-CCCAAACTTTTCAAAAATCACATTTTGA
*** * * *
17257 CCTTGAAC-TTTCTAAAAATTACAATTTAA
1 CCCCAAACTTTTC-AAAAATCACATTTTGA
* * *
17286 CCCTTAAAATTTAT-AAAAATAACA-TTTGA
1 CCC-CAAACTTT-TCAAAAATCACATTTTGA
17315 CCTCCAAACTTTTCAAAAATCACATTTTGA
1 CC-CCAAACTTTTCAAAAATCACATTTTGA
* *
17345 CCCCCTAACTTCTCAAAAATCACATTTTGA
1 -CCCCAAACTTTTCAAAAATCACATTTTGA
* * * *
17375 CCCACGAACTTTTCCAAAATTACATTTTAA
1 CCC-CAAACTTTTCAAAAATCACATTTTGA
* *
17405 CCTCAAACTTTTCTAAAATCACATTTT
1 CCCCAAACTTTTCAAAAATCACATTTT
17432 TTACTCCTAA
Statistics
Matches: 166, Mismatches: 29, Indels: 20
0.77 0.13 0.09
Matches are distributed among these distances:
28 5 0.03
29 65 0.39
30 91 0.55
31 4 0.02
32 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCCAAACTTTTCAAAAATCACATTTTGA
Found at i:17426 original size:59 final size:58
Alignment explanation
Indices: 17198--17431 Score: 186
Period size: 59 Copynumber: 4.0 Consensus size: 58
17188 CTCCAGAGGT
* * * * * * * *
17198 CCCCGAACTTTCCAGAAATCATATTTTGACTCCCAAACTTTTCAAAAATTATATTTTGA
1 CCCCGAACTTTTCAAAAATTACATTTTAAC-CTCAAACTTTTCAAAAATCACATTTTGA
** * * * *
17257 CCTTGAAC-TTTCTAAAAATTACAATTTAACCCTTAAAATTTAT-AAAAATAACA-TTTGA
1 CCCCGAACTTTTC-AAAAATTACATTTTAA-CCTCAAACTTT-TCAAAAATCACATTTTGA
* * * * * *
17315 CCTCCAAACTTTTCAAAAATCACATTTTGACCCCCTAACTTCTCAAAAATCACATTTTGA
1 CC-CCGAACTTTTCAAAAATTACATTTT-AACCTCAAACTTTTCAAAAATCACATTTTGA
* *
17375 CCCACGAACTTTTCCAAAATTACATTTTAACCTCAAACTTTTCTAAAATCACATTTT
1 CCC-CGAACTTTTCAAAAATTACATTTTAACCTCAAACTTTTCAAAAATCACATTTT
17432 TTACTCCTAA
Statistics
Matches: 133, Mismatches: 33, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
58 11 0.08
59 87 0.65
60 35 0.26
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (58 bp):
CCCCGAACTTTTCAAAAATTACATTTTAACCTCAAACTTTTCAAAAATCACATTTTGA
Found at i:17445 original size:60 final size:59
Alignment explanation
Indices: 17300--17455 Score: 149
Period size: 60 Copynumber: 2.6 Consensus size: 59
17290 TAAAATTTAT
* * * * *
17300 AAAAATAACA-TTTGACCTCCAAACTTTTCAAAAATCACATTTTGACCCCCTAACTTCTC
1 AAAAATCACATTTTGA-CTCCAAACTTTTCCAAAATTACATTTTGAACCCCAAACTTCTC
* *
17359 AAAAATCACATTTTGAC-CCACGAACTTTTCCAAAATTACATTTT-AACCTCAAACTTTTC
1 AAAAATCACATTTTGACTCCA--AACTTTTCCAAAATTACATTTTGAACCCCAAACTTCTC
* *
17418 TAAAATCACATTTTTTACTCCTAAAC-TTTCCTAAAATT
1 AAAAATCACA-TTTTGACTCC-AAACTTTTCC-AAAATT
17456 GAATTTTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
58 3 0.04
59 35 0.43
60 40 0.49
61 2 0.02
62 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAAATCACATTTTGACTCCAAACTTTTCCAAAATTACATTTTGAACCCCAAACTTCTC
Found at i:17475 original size:31 final size:31
Alignment explanation
Indices: 17318--17475 Score: 89
Period size: 30 Copynumber: 5.2 Consensus size: 31
17308 CATTTGACCT
* * * *
17318 CCAAACTTTTCAAAAATCACA-TTTTGACCC
1 CCAAACTTTCCTAAAATCACATTTTTAACTC
* * *
17348 CCTAAC-TTCTCAAAAATCACA-TTTTGAC-C
1 CCAAACTTTC-CTAAAATCACATTTTTAACTC
* *
17377 CACGAACTTTTCC-AAAATTACA-TTTTAAC-C
1 C-CAAAC-TTTCCTAAAATCACATTTTTAACTC
* * *
17407 TCAAACTTTTCTAAAATCACATTTTTTACTC
1 CCAAACTTTCCTAAAATCACATTTTTAACTC
* * *
17438 CTAAACTTTCCTAAAATTGA-ATTTTTAATTC
1 CCAAACTTTCCTAAAA-TCACATTTTTAACTC
17469 CCAAACT
1 CCAAACT
17476 CATCCAAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
28 4 0.04
29 16 0.16
30 48 0.47
31 30 0.29
32 5 0.05
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (31 bp):
CCAAACTTTCCTAAAATCACATTTTTAACTC
Found at i:17580 original size:29 final size:30
Alignment explanation
Indices: 17529--17600 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
17519 CATTTTACCT
*
17529 TCAAA-TTTCCAAAATTCACATTTTCGA-CC
1 TCAAATTTTCCAAAATTCACATTTT-AATCC
* *
17558 TCAAATTTTCCAAAGTTTA-ATTTTAATCC
1 TCAAATTTTCCAAAATTCACATTTTAATCC
17587 -CAAATTTTCCAAAA
1 TCAAATTTTCCAAAA
17601 ATTTCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 14 0.38
29 12 0.32
30 11 0.30
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
TCAAATTTTCCAAAATTCACATTTTAATCC
Found at i:17594 original size:28 final size:30
Alignment explanation
Indices: 17559--17622 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
17549 TTTTCGACCT
* * *
17559 CAAATTTTCC-AAAGTTT-AATTTTAATCC
1 CAAATTTTCCAAAAATTTCAAATTTAACCC
17587 CAAATTTTCCAAAAATTTCAAATTTAACCC
1 CAAATTTTCCAAAAATTTCAAATTTAACCC
17617 CAAATT
1 CAAATT
17623 CCTCGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 10 0.32
29 6 0.19
30 15 0.48
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.38
Consensus pattern (30 bp):
CAAATTTTCCAAAAATTTCAAATTTAACCC
Found at i:23424 original size:3 final size:3
Alignment explanation
Indices: 23416--23474 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
23406 GGGTATTAAG
*
23416 GAA GAA GAA GAA GAAA GAA -AA GAA GAA -TA GAAA GAA GAA -AA GGAA
1 GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA G-AA GAA GAA GAA -GAA
*
23461 GAA AAA GAA GAA GA
1 GAA GAA GAA GAA GA
23475 TGTTACCCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
2 5 0.11
3 34 0.74
4 7 0.15
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:23473 original size:21 final size:21
Alignment explanation
Indices: 23413--23474 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
23403 TATGGGTATT
*
23413 AAGGAAGAAGAAGAAGAAAGAA
1 AAGGAAGAAAAAGAAG-AAGAA
*
23435 AA-GAAG-AATAGAAAGAAGAA
1 AAGGAAGAAAAAG-AAGAAGAA
23455 AAGGAAGAAAAAGAAGAAGA
1 AAGGAAGAAAAAGAAGAAGA
23475 TGTTACCCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 10 0.29
21 18 0.53
22 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (21 bp):
AAGGAAGAAAAAGAAGAAGAA
Found at i:37375 original size:24 final size:24
Alignment explanation
Indices: 37347--37410 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
37337 AAACTATATG
*
37347 AAACCCAAAGATGGAAGGTTT-AAT
1 AAACCCAAAGATGGAA-GTTTCAAC
* *
37371 AAACCAAAATGATTGAAGTTTCAAC
1 AAACCCAAA-GATGGAAGTTTCAAC
*
37396 AAACCCAAAAATGGA
1 AAACCCAAAGATGGA
37411 TGTGAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 16 0.50
25 16 0.50
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (24 bp):
AAACCCAAAGATGGAAGTTTCAAC
Found at i:37457 original size:90 final size:91
Alignment explanation
Indices: 37236--37532 Score: 293
Period size: 92 Copynumber: 3.2 Consensus size: 91
37226 AAGACTCAAC
*
37236 ATGCTTGGGAAGCTTTATGAAACCCAAAGATGTG-AGCTTTAAGAAACCACAAATGGAGTAAGCT
1 ATGCTT-GGAAGCTTTATGAAACCCAAAGATG-GAAGGTTTAAGAAACCACAAATGGAGTAAGCT
*
37300 TAAGAATACCCATAAAAGGAGGTGAAAT
64 TAACAATACCCATAAAAGGAGGTGAAAT
* * * * *
37328 ATGCTTGGAAAACTATATGAAACCCAAAGATGGAAGGTTTAATAAACCA-AAAT-GATTGAAGTT
1 ATGCTTGG-AAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGT-AAGCT
*
37391 TCAACAA-ACCCA-AAAATGGATGTGAAAT
64 T-AACAATACCCATAAAA-GGAGGTGAAAT
* * * * * *
37419 GTAG-TTGGAAGCTTTATGAAATCCAAATATGGAAGGTTTAAGAAACAACAAACGGAGGAAGCTT
1 AT-GCTTGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGTAAGC-T
* *
37483 TAAGAA-ACCCATAAATGGAGGTGAAAT
64 TAACAATACCCATAAAAGGAGGTGAAAT
* **
37510 GTGCTTAGGAAAATTTATGAAAC
1 ATGCTT-GGAAGCTTTATGAAAC
37533 TTGATAGAAA
Statistics
Matches: 168, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
90 42 0.25
91 61 0.36
92 65 0.39
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (91 bp):
ATGCTTGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACCACAAATGGAGTAAGCTTA
ACAATACCCATAAAAGGAGGTGAAAT
Found at i:37499 original size:91 final size:90
Alignment explanation
Indices: 37237--37532 Score: 305
Period size: 91 Copynumber: 3.2 Consensus size: 90
37227 AGACTCAACA
* * *
37237 TGCTTGGGAAGCTTTATGAAACCCAAAGATGTG-AGCTTTAAGAAACCACAAATGGAGTAAGC-T
1 TGCTT-GGAAGCTTTATGAAACCCAAAGATG-GAAGGTTTAAGAAA-CACAAAAGGAGGAAGCTT
* *
37300 TAAGAATACCCATAAAAGGAGGTGAAATA
63 TAAGAA-ACCCATAAATGGAGGTGAAATG
* * * * *
37329 TGCTTGGAAAACTATATGAAACCCAAAGATGGAAGGTTTAATAAAC-CAAAATGATTGAAG-TTT
1 TGCTTGG-AAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACACAAAAGGA-GGAAGCTTT
* * *
37392 CAACAAACCCAAAAATGGATGTGAAATG
64 -AAGAAACCCATAAATGGAGGTGAAATG
* * *
37420 TAG-TTGGAAGCTTTATGAAATCCAAATATGGAAGGTTTAAGAAACAACAAACGGAGGAAGCTTT
1 T-GCTTGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAAC-ACAAAAGGAGGAAGCTTT
37484 AAGAAACCCATAAATGGAGGTGAAATG
64 AAGAAACCCATAAATGGAGGTGAAATG
**
37511 TGCTTAGGAAAATTTATGAAAC
1 TGCTT-GGAAGCTTTATGAAAC
37533 TTGATAGAAA
Statistics
Matches: 166, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
90 40 0.24
91 63 0.38
92 63 0.38
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (90 bp):
TGCTTGGAAGCTTTATGAAACCCAAAGATGGAAGGTTTAAGAAACACAAAAGGAGGAAGCTTTAA
GAAACCCATAAATGGAGGTGAAATG
Found at i:38155 original size:33 final size:32
Alignment explanation
Indices: 38106--38169 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
38096 GTTGGAGAAA
38106 ATTTTTTTAAATCCTTTAAAAATTGGTAAAAAAT
1 ATTTTTTTAAATCCTTTAAAAATT--TAAAAAAT
*
38140 ATTTTTTTATA-CCTTTAAAAATTTAAAAAA
1 ATTTTTTTAAATCCTTTAAAAATTTAAAAAA
38170 AAAAAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 7 0.24
33 12 0.41
34 10 0.34
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTTTTTTAAATCCTTTAAAAATTTAAAAAAT
Found at i:38171 original size:34 final size:34
Alignment explanation
Indices: 38106--38172 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
38096 GTTGGAGAAA
***
38106 ATTTTTTTAAATCCTTTAAAAATTGGTAAAAAAT
1 ATTTTTTTAAATCCTTTAAAAATTAAAAAAAAAT
*
38140 ATTTTTTTATA-CCTTTAAAAATTTAAAAAAAAA
1 ATTTTTTTAAATCCTTTAAAAA-TTAAAAAAAAA
38173 AAAAAGTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (34 bp):
ATTTTTTTAAATCCTTTAAAAATTAAAAAAAAAT
Found at i:39543 original size:27 final size:27
Alignment explanation
Indices: 39512--39565 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
39502 GCAAAATCAA
39512 TAAGAGATTAATTGATGAAAATTCCAG
1 TAAGAGATTAATTGATGAAAATTCCAG
39539 TAAGAGATTAATTGATGAAAATTCCAG
1 TAAGAGATTAATTGATGAAAATTCCAG
39566 GTTGAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (27 bp):
TAAGAGATTAATTGATGAAAATTCCAG
Found at i:43905 original size:18 final size:18
Alignment explanation
Indices: 43893--43927 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43883 GCTGCATACG
43893 AGCATGTGACTGCATCTA
1 AGCATGTGACTGCATCTA
*
43911 AGTATGTGACTGCATCT
1 AGCATGTGACTGCATCT
43928 GATCGTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
AGCATGTGACTGCATCTA
Found at i:48486 original size:2 final size:2
Alignment explanation
Indices: 48479--48506 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48469 CTTAATTATG
48479 CT CT CT CT 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
48507 AACAGATCAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:51537 original size:87 final size:87
Alignment explanation
Indices: 51374--51565 Score: 201
Period size: 87 Copynumber: 2.2 Consensus size: 87
51364 CCCAAACAGT
* * * * *
51374 TAAGTTTATGGATGAACCACCAGTATTTGCAGATAAAACGCCAGTTGGTTGTGGATGCATAACAT
1 TAAGTTTATGGATGAACCACCAGTATTTGCAAATAAAACACCAGTAGGTTGTGAATGCACAACAT
51439 ATTTGTCGATAAAAGCTACCAG
66 ATTTGTCGATAAAAGCTACCAG
* * * *
51461 TAAGTTTGTGGATGAACTACCAGTGA-TTGCAAAT-AAACTACTAGTAGGTTGTGAATGCACAAT
1 TAAGTTTATGGATGAACCACCAGT-ATTTGCAAATAAAAC-ACCAGTAGGTTGTGAATGCACAAC
* * **
51524 GTATTTG-CAGATAACAGCTGTCAG
64 ATATTTGTC-GATAAAAGCTACCAG
* *
51548 TAAATTTATGGATAAACC
1 TAAGTTTATGGATGAACC
51566 GCTAGTGCTA
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
86 5 0.06
87 79 0.93
88 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (87 bp):
TAAGTTTATGGATGAACCACCAGTATTTGCAAATAAAACACCAGTAGGTTGTGAATGCACAACAT
ATTTGTCGATAAAAGCTACCAG
Found at i:58479 original size:18 final size:17
Alignment explanation
Indices: 58433--58481 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
58423 ACTGCAATGC
* *
58433 AAATGTACTAACAAATA
1 AAATGTAATGACAAATA
* *
58450 AAATGCAGTGACAAATAA
1 AAATGTAATGACAAAT-A
58468 AAATGTAATGACAA
1 AAATGTAATGACAA
58482 CTAAGTGCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (17 bp):
AAATGTAATGACAAATA
Found at i:58591 original size:20 final size:19
Alignment explanation
Indices: 58566--58614 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
58556 TTGGCTTTCT
58566 TCTTCTTCTTCTTTGGGCGC
1 TCTTCTTCTTCTTTGGGC-C
* *
58586 TCTTCTTCTGCTTTGTGCC
1 TCTTCTTCTTCTTTGGGCC
*
58605 TCTTTTTCTT
1 TCTTCTTCTT
58615 GTCTTTCCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.00, C:0.29, G:0.14, T:0.57
Consensus pattern (19 bp):
TCTTCTTCTTCTTTGGGCC
Found at i:58935 original size:27 final size:28
Alignment explanation
Indices: 58886--58943 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
58876 TGTCGGGGCA
**
58886 TCTTCCTTCTCTTCATTTTTTTCC-TCT
1 TCTTCCTTCTCTTCATTAATTTCCTTCT
58913 TCTTCCTTCTCTTC-TTCAATTTCCTTCT
1 TCTTCCTTCTCTTCATT-AATTTCCTTCT
58941 TCT
1 TCT
58944 CCTCAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 19 0.70
28 6 0.22
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.60
Consensus pattern (28 bp):
TCTTCCTTCTCTTCATTAATTTCCTTCT
Found at i:60280 original size:101 final size:101
Alignment explanation
Indices: 60157--60360 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
60147 AATAACTGAA
60157 AAAAGAGAACGAGAGAGTTTTGTAGAAAAGTGTGAAGACAATGAAGAAGATGGTCGCAGTAGCAA
1 AAAAGAGAACGAGAGAGTTTTGTAGAAAAGTGTGAAGACAATGAAGAAGATGGTCGCAGTAGCAA
60222 TGGTGGTAGTGAGTGGAAGAAGAAAAATGACAGAAT
66 TGGTGGTAGTGAGTGGAAGAAGAAAAATGACAGAAT
* *
60258 AAAAGAGAACGAGAGGGTTTTGTAGAAAAGTGTGAAGACAATGAAGAAGATGGTTGCAGTAGCAA
1 AAAAGAGAACGAGAGAGTTTTGTAGAAAAGTGTGAAGACAATGAAGAAGATGGTCGCAGTAGCAA
*
60323 TGGTGGTTGTGAGTGGAAGAAGAAAAATGACAGAAT
66 TGGTGGTAGTGAGTGGAAGAAGAAAAATGACAGAAT
60359 AA
1 AA
60361 GGGTTTTATA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.19
Consensus pattern (101 bp):
AAAAGAGAACGAGAGAGTTTTGTAGAAAAGTGTGAAGACAATGAAGAAGATGGTCGCAGTAGCAA
TGGTGGTAGTGAGTGGAAGAAGAAAAATGACAGAAT
Found at i:60651 original size:13 final size:13
Alignment explanation
Indices: 60635--60659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60625 TGAAAATAAA
60635 AAGCAAAAATTAG
1 AAGCAAAAATTAG
60648 AAGCAAAAATTA
1 AAGCAAAAATTA
60660 TAATGACATT
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:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (13 bp):
AAGCAAAAATTAG
Found at i:69637 original size:23 final size:22
Alignment explanation
Indices: 69606--69649 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
69596 AAAGAAATAA
*
69606 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
69628 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
69650 GAAACATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:80444 original size:23 final size:22
Alignment explanation
Indices: 80413--80456 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
80403 AAAGAAATAA
*
80413 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
80435 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
80457 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:84068 original size:29 final size:29
Alignment explanation
Indices: 84026--84085 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
84016 ATCATGGAGG
84026 TTGAACTTTTTGACATGTGGGGTATCGAC
1 TTGAACTTTTTGACATGTGGGGTATCGAC
84055 TTGAACTTTTTGACATGTGGGGTATCGAC
1 TTGAACTTTTTGACATGTGGGGTATCGAC
84084 TT
1 TT
84086 TATGGGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (29 bp):
TTGAACTTTTTGACATGTGGGGTATCGAC
Found at i:94385 original size:15 final size:15
Alignment explanation
Indices: 94353--94381 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
94343 GAAGAAAAAA
94353 AAGAAGATGAAAGAG
1 AAGAAGATGAAAGAG
94368 AAGAAGA-GAAAGAG
1 AAGAAGATGAAAGAG
94382 GAAGTTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (15 bp):
AAGAAGATGAAAGAG
Found at i:94821 original size:16 final size:17
Alignment explanation
Indices: 94800--94835 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
94790 GTCATCACAT
*
94800 TTTTA-TTGTCAGTGCA
1 TTTTATTTGTCAATGCA
94816 TTTTATTTGTCAATGCA
1 TTTTATTTGTCAATGCA
94833 TTT
1 TTT
94836 GCATTGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (17 bp):
TTTTATTTGTCAATGCA
Found at i:106135 original size:18 final size:19
Alignment explanation
Indices: 106108--106151 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
106098 CGACATTATT
106108 AAGGAAAAAGG-AAAAATC
1 AAGGAAAAAGGAAAAAATC
*
106126 AAGGACAAAGGAAAAAATC
1 AAGGAAAAAGGAAAAAATC
106145 AAAGGAA
1 -AAGGAA
106152 GCATCGACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.66, C:0.07, G:0.23, T:0.05
Consensus pattern (19 bp):
AAGGAAAAAGGAAAAAATC
Found at i:122657 original size:29 final size:29
Alignment explanation
Indices: 122624--122682 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
122614 GTTTCAACAC
122624 TTGGTTAAACTTCCACTGCGTCTTAAGCA
1 TTGGTTAAACTTCCACTGCGTCTTAAGCA
122653 TTGGTTAAACTTCCACTGCGTCTTAAGCA
1 TTGGTTAAACTTCCACTGCGTCTTAAGCA
122682 T
1 T
122683 CAGCTTACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (29 bp):
TTGGTTAAACTTCCACTGCGTCTTAAGCA
Found at i:124119 original size:21 final size:21
Alignment explanation
Indices: 124093--124136 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
124083 TCTTCTTCTA
124093 TCTCAAAAGGTTCATTCAACC
1 TCTCAAAAGGTTCATTCAACC
124114 TCTCAAAAGGTTCATTCAACC
1 TCTCAAAAGGTTCATTCAACC
124135 TC
1 TC
124137 AAGGTTTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (21 bp):
TCTCAAAAGGTTCATTCAACC
Found at i:127406 original size:30 final size:27
Alignment explanation
Indices: 127371--127428 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
127361 TAATAATAGT
* *
127371 AAAATTATATTTTATTTCTTTTAAAAGATA
1 AAAATT-TAATTTAATT-TTTTAAAA-ATA
127401 AAAATTTAATTTAATTTTTTAAAAATA
1 AAAATTTAATTTAATTTTTTAAAAATA
127428 A
1 A
127429 TAAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 8 0.31
29 8 0.31
30 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATTTAATTTAATTTTTTAAAAATA
Found at i:127433 original size:29 final size:31
Alignment explanation
Indices: 127360--127439 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 31
127350 AAATTTTAAA
* * * *
127360 TTAATAATAGTAAAATTATATTTTATTTCTT
1 TTAAAAATAATAAAATTATAATTTAATTCTT
127391 TTAAAAGAT-A-AAAATT-TAATTTAATT-TT
1 TTAAAA-ATAATAAAATTATAATTTAATTCTT
*
127419 TTAAAAATAATAAAAATATAA
1 TTAAAAATAATAAAATTATAA
127440 ATTATTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.05
28 9 0.22
29 13 0.32
30 9 0.22
31 5 0.12
32 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (31 bp):
TTAAAAATAATAAAATTATAATTTAATTCTT
Found at i:127483 original size:22 final size:22
Alignment explanation
Indices: 127430--127485 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
127420 TAAAAATAAT
*
127430 AAAAATATAAATTATTAAAATA
1 AAAAATATATATTATTAAAATA
* **
127452 ATAAAA-ATATATTTTTATTATA
1 A-AAAATATATATTATTAAAATA
127474 AAAAATATATAT
1 AAAAATATATAT
127486 AATTTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATATATTATTAAAATA
Found at i:128494 original size:20 final size:19
Alignment explanation
Indices: 128469--128525 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
128459 TATTTTTTTA
128469 TTTTAACATTTTTTATATAT
1 TTTTAACATTTTTTATAT-T
128489 TTTTAA-ATTTTATTATATT
1 TTTTAACATTTT-TTATATT
*
128508 TTATAAAACATTTTTTAT
1 TT-T-TAACATTTTTTAT
128526 CATCTTCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.25
20 13 0.41
21 6 0.19
22 5 0.16
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAACATTTTTTATATT
Found at i:128499 original size:18 final size:19
Alignment explanation
Indices: 128479--128514 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
128469 TTTTAACATT
128479 TTTTA-TATATTTT-TAAA
1 TTTTATTATATTTTATAAA
128496 TTTTATTATATTTTATAAA
1 TTTTATTATATTTTATAAA
128515 ACATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATTATATTTTATAAA
Found at i:140514 original size:15 final size:15
Alignment explanation
Indices: 140494--140523 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
140484 TTAATATGGG
140494 TTATATTTAAATAAT
1 TTATATTTAAATAAT
*
140509 TTATATTTATATAAT
1 TTATATTTAAATAAT
140524 AAATATGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTTAAATAAT
Found at i:142631 original size:31 final size:31
Alignment explanation
Indices: 142540--142631 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 31
142530 TAGCATCGAA
** * *
142540 TTTAATAACCCAATGACTTAAATGAAAAATT
1 TTTAATAACTAAATGACTAAAATGAAAACTT
* * *
142571 TTTAATAACTCAATGACTAAATTG-TAACTT
1 TTTAATAACTAAATGACTAAAATGAAAACTT
** *
142601 TTTTTTAATTAAATGACTAAAATGAAAACTT
1 TTTAATAACTAAATGACTAAAATGAAAACTT
142632 ATCTATAATT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 23 0.47
31 26 0.53
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (31 bp):
TTTAATAACTAAATGACTAAAATGAAAACTT
Found at i:146129 original size:41 final size:41
Alignment explanation
Indices: 146081--146160 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
146071 TCTTATTGTA
* *
146081 TTTTTAATTTGTTTGTTATTTTACGAATTGTTTTAATATCG
1 TTTTTAATTTATTTGTTATTTTAAGAATTGTTTTAATATCG
* * *
146122 TTTTTAATTTATTTGTTGTTTTAATATTTGTTTTAATAT
1 TTTTTAATTTATTTGTTATTTTAAGAATTGTTTTAATAT
146161 TTTTAAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (41 bp):
TTTTTAATTTATTTGTTATTTTAAGAATTGTTTTAATATCG
Found at i:146152 original size:12 final size:12
Alignment explanation
Indices: 146137--146162 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
146127 AATTTATTTG
146137 TTGTTTTAATAT
1 TTGTTTTAATAT
146149 TTGTTTTAATAT
1 TTGTTTTAATAT
146161 TT
1 TT
146163 TTAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:146188 original size:26 final size:24
Alignment explanation
Indices: 146157--146204 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
146147 ATTTGTTTTA
*
146157 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
146183 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
146205 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:148337 original size:4 final size:4
Alignment explanation
Indices: 148320--148358 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
148310 AGAAAAGGGA
*
148320 TATG TATA TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
148359 AAGTTTGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:151915 original size:22 final size:21
Alignment explanation
Indices: 151885--151948 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
151875 AAAATACATG
151885 AATATAAATAATTAAATGAAGAC
1 AATA-AAATAATTAAAT-AAGAC
* *
151908 AATCAAATACAATT-AATAACAC
1 AAT-AAA-ATAATTAAATAAGAC
151930 AATAAAATAA-TAAATAAGA
1 AATAAAATAATTAAATAAGA
151949 GTAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 3 0.09
22 7 0.21
23 8 0.24
24 6 0.18
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (21 bp):
AATAAAATAATTAAATAAGAC
Found at i:152351 original size:35 final size:32
Alignment explanation
Indices: 152274--152374 Score: 85
Period size: 35 Copynumber: 2.9 Consensus size: 32
152264 GATAATAACA
152274 ATAAATACAAATGAAATAAAAAAAATAAAAGAG
1 ATAAATA-AAATGAAATAAAAAAAATAAAAGAG
* * *
152307 ATAACAATAAAATGACATGAAAATAAATAACAATAGG
1 AT-A-AATAAAATGAAAT-AAAAAAAATAA-AAGA-G
**
152344 ATAAATAAACAAAAAATAAATAAAAATAAAA
1 ATAAATAAA-ATGAAATAAA-AAAAATAAAA
152375 ATTAAATGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
33 2 0.04
34 9 0.17
35 25 0.46
36 15 0.28
37 3 0.06
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (32 bp):
ATAAATAAAATGAAATAAAAAAAATAAAAGAG
Found at i:152362 original size:15 final size:15
Alignment explanation
Indices: 152326--152381 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
152316 AAATGACATG
152326 AAAATAAAT-AACAA
1 AAAATAAATAAACAA
**
152340 TAGGATAAATAAACAA
1 -AAAATAAATAAACAA
*
152356 AAAATAAATAAAAATA
1 AAAATAAATAAACA-A
152372 AAAATTAAAT
1 AAAA-TAAAT
152382 GCTAAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 18 0.55
16 10 0.30
17 5 0.15
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:152461 original size:19 final size:19
Alignment explanation
Indices: 152437--152494 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
152427 TTAGGCATGA
152437 AAATAAATGACAAATAAAT
1 AAATAAATGACAAATAAAT
** * *
152456 AAATAAACAAAAAATCAAT
1 AAATAAATGACAAATAAAT
*
152475 AAATTAAATGTCAAAATAAA
1 AAA-TAAATGAC-AAATAAA
152495 CAACTTAATA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 18 0.64
20 4 0.14
21 6 0.21
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (19 bp):
AAATAAATGACAAATAAAT
Found at i:152470 original size:15 final size:15
Alignment explanation
Indices: 152436--152477 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
152426 ATTAGGCATG
*
152436 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
152450 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
152466 AAAATCAATAAA
1 AAAATAAATAAA
152478 TTAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:152604 original size:49 final size:49
Alignment explanation
Indices: 152534--152945 Score: 250
Period size: 49 Copynumber: 8.4 Consensus size: 49
152524 CGCCGTTATA
* * * * *** *
152534 ACTTCAATCTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTCGTTATG
1 ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAAATCCACCGTTACG
* * **
152583 ACTTTAATCTATCCCTCTTCGATTTTAAGGTG-TAAGATCTACCATGGCG
1 ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAA-ATCCACCGTTACG
* * * * ** * *
152632 GCTTCAATCTTTCCCTCTTTGATTTTAAGGTGTTAGGTCCATCGTTGC-
1 ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAAATCCACCGTTACG
* * * * ** *
152680 AGCTTTAACCTATCCCTTTTCAATTTTAAGGTG-TAAGATCCATCAATGCGG
1 A-CTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAA-ATCCACCGTTAC-G
* * * *
152731 A-TTTAATCTTTTCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACG
1 ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAAATCCACCGTTACG
* *
152779 ATTTTAATCTA-CCTCTCTTCGATTTTAA-GT-TATAAGAT-CAGCTGTTACG
1 ACTTTAATCTATCC-CTCTTCGATTTTAAGGTGT-TAA-ATCCA-CCGTTACG
* * ** * * *
152828 ACTTTAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCATTACA
1 ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAAATCCACCGTTACG
* * * * *
152877 ACTTTAACCTATCCCTCTTCAATTTTAAGGTG-TAAGATTCACCATTGCG
1 ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAA-ATCCACCGTTACG
*
152926 GCTTTAATCT-TGCCCTCTTC
1 ACTTTAATCTAT-CCCTCTTC
152946 AACTCTAGGA
Statistics
Matches: 277, Mismatches: 68, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
47 1 0.00
48 17 0.06
49 246 0.89
50 11 0.04
51 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (49 bp):
ACTTTAATCTATCCCTCTTCGATTTTAAGGTGTTAAATCCACCGTTACG
Found at i:152687 original size:98 final size:99
Alignment explanation
Indices: 152539--152945 Score: 418
Period size: 98 Copynumber: 4.2 Consensus size: 99
152529 TTATAACTTC
* * *** * *
152539 AATCTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTCGTTA-TGACTTTAATCTATCCCTCTTC
1 AATCTTTCCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACAGACTTTAACCTATCCCTCTTC
* *
152603 GATTTTAAGGTGTAAGATCTACCATGGCGGCTTC
66 AATTTTAAGGTGTAAGATCTACCATGGCGGCTTT
* * * * * *
152637 AATCTTTCCCTCTTTGATTTTAAGGTGTTAGGTCCATCGTTGCAG-CTTTAACCTATCCCTTTTC
1 AATCTTTCCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACAGACTTTAACCTATCCCTCTTC
* * *
152701 AATTTTAAGGTGTAAGATCCATCAAT-GCGGATTT
66 AATTTTAAGGTGTAAGATCTA-CCATGGCGGCTTT
* * *
152735 AATCTTTTCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTAC-GATTTTAATCTA-CCTCTCTT
1 AATCTTTCCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACAGACTTTAACCTATCC-CTCTT
* * * * * *
152798 CGATTTTAAGTTATAAGATC-AGC-TGTTACGACTTT
65 CAATTTTAAGGTGTAAGATCTACCATG--GCGGCTTT
* * *
152833 AATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCATTACA-ACTTTAACCTATCCCTCTTC
1 AATCTTTCCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACAGACTTTAACCTATCCCTCTTC
*
152897 AATTTTAAGGTGTAAGAT-TCACCATTGCGGCTTT
66 AATTTTAAGGTGTAAGATCT-ACCATGGCGGCTTT
*
152931 AATCTTGCCCTCTTC
1 AATCTTTCCCTCTTC
152946 AACTCTAGGA
Statistics
Matches: 250, Mismatches: 47, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
95 1 0.00
97 4 0.02
98 236 0.94
99 8 0.03
100 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (99 bp):
AATCTTTCCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACAGACTTTAACCTATCCCTCTTC
AATTTTAAGGTGTAAGATCTACCATGGCGGCTTT
Found at i:152884 original size:196 final size:196
Alignment explanation
Indices: 152539--152945 Score: 523
Period size: 196 Copynumber: 2.1 Consensus size: 196
152529 TTATAACTTC
* *** *
152539 AATCTTTCCCTTTTCGATTTTAGGGTGTTAAATCTGTCGTTATGACTTTAATCTATCCCTCTTCG
1 AATCTTTCCCTCTTCGATTTTAGGGTGTTAAATCCACCGTTACGACTTTAATCTATCCCTCTTCG
* * * *
152604 ATTTTAAGGTGTAAGATCTACCATGGCGGCTTCAATCTTTCCCTCTTTGATTTTAAGGTGTTAGG
66 ATTTTAAGGTATAAGATCTACCATGACGACTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGG
* * * * * *
152669 TCCATCGTTGCAGCTTTAACCTATCCCTTTTCAATTTTAAGGTGTAAGATCCATCAATGCGGATT
131 TCCACCATTACAACTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCACCAATGCGGATT
152734 T
196 T
* * *
152735 AATCTTTTCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACGATTTTAATCTA-CCTCTCTTC
1 AATCTTTCCCTCTTCGATTTTAGGGTGTTAAATCCACCGTTACGACTTTAATCTATCC-CTCTTC
* * * *
152799 GATTTTAAGTTATAAGATC-AGC-TGTTACGACTTTAATCTTTCCCTCTTCGATTTTAGGGTGTT
65 GATTTTAAGGTATAAGATCTACCATG--ACGACTTCAATCTTTCCCTCTTCGATTTTAAGGTGTT
* * *
152862 AGGTCCGCCATTACAACTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGATTCACCATTGCGG
128 AGGTCCACCATTACAACTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCACCAATGCGG
*
152927 CTTT
193 ATTT
*
152931 AATCTTGCCCTCTTC
1 AATCTTTCCCTCTTC
152946 AACTCTAGGA
Statistics
Matches: 180, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
194 2 0.01
195 4 0.02
196 174 0.97
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (196 bp):
AATCTTTCCCTCTTCGATTTTAGGGTGTTAAATCCACCGTTACGACTTTAATCTATCCCTCTTCG
ATTTTAAGGTATAAGATCTACCATGACGACTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGG
TCCACCATTACAACTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCACCAATGCGGATT
T
Found at i:152947 original size:49 final size:48
Alignment explanation
Indices: 152584--152945 Score: 285
Period size: 49 Copynumber: 7.4 Consensus size: 48
152574 GTCGTTATGA
* *
152584 CTTTAATCTATCCCTCTTCGATTTTAAGGTGTAAGATCTACCATGGCGG
1 CTTTAATCT-TCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
* * * * * * *
152633 CTTCAATCTTTCCCTCTTTGATTTTAAGGTGTTAGGTCCATCGTTGCAG
1 CTTTAATC-TTCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
* * * * *
152682 CTTTAACCTATCCCTTTTCAATTTTAAGGTGTAAGATCCATCAATGCGG
1 CTTTAATCT-TCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
* * * * * * *
152731 ATTTAATCTTTTCCTCTTCGATTTTAGGGTGTTAGATCCACCGTTACGA
1 CTTTAATC-TTCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
* * * * ** * *
152780 TTTTAATCTACCTCTCTTCGATTTTAAGTTATAAGAT-CAGCTGTTACGA
1 CTTTAATCTTCC-CTCTTCGATTTTAAGGTGTAAGATCCA-CCATTGCGG
* * * * * **
152829 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCATTACAA
1 CTTTAATC-TTCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
* * *
152878 CTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGATTCACCATTGCGG
1 CTTTAATCT-TCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
152927 CTTTAATCTTGCCCTCTTC
1 CTTTAATCTT-CCCTCTTC
152946 AACTCTAGGA
Statistics
Matches: 243, Mismatches: 61, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
48 7 0.03
49 230 0.95
50 6 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (48 bp):
CTTTAATCTTCCCTCTTCGATTTTAAGGTGTAAGATCCACCATTGCGG
Found at i:153996 original size:3 final size:3
Alignment explanation
Indices: 153988--154015 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
153978 CTCTTTTTTG
153988 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
154016 GTGCTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:159333 original size:264 final size:264
Alignment explanation
Indices: 158849--159371 Score: 771
Period size: 264 Copynumber: 2.0 Consensus size: 264
158839 ATGCAGTCAA
* * **
158849 CCCCATCATGAACTTAAGAGGATCCAATTTTGATATCAACCAAGTTGTACGGTATAAAATGTATT
1 CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGTACGGTATAAAATATACG
* * * *
158914 GCCTCAACCTTCGCGTAGTCCAGACTAAAACGCAACATAATTTCTCGATTGGCGAATATCTTATC
66 GCCTCAACCTTCGAGTAGTCCAGACCAAAACACAACACAATTTCTCGATTGGCGAATATCTTATC
** * * *
158979 TTGCATTCAGTGAACTTCTTGTTGAGATAATAAATTGCTCTTTCTTTTTTTCCTAACTCATCATG
131 TCACACTCAGTGAACTTCTTGCTAAGATAATAAATTGCTCTTTCTTTTTTTCCTAACTCATCATG
* *
159044 TTGGCCCAATACGCATCCCATAGAGTTTTCAAATACGACTAAGTACAA-GATCAAAGGTTTATCA
196 TTGGCCCAATACGCATCCAATAGAGTGTTCAAATACGACTAAGTA-AAGGATCAAAGGTTTATCA
159108 GTCGG
260 GTCGG
* * *
159113 CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGTATGGTATAACATATGCG
1 CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGTACGGTATAAAATATACG
* * * * * *
159178 GCTTCAACCTTTGAGTATTCCATACCAAAGCACAACACAATTTCTCGATTGGTGAATATCTTATC
66 GCCTCAACCTTCGAGTAGTCCAGACCAAAACACAACACAATTTCTCGATTGGCGAATATCTTATC
* *
159243 TCACACTCAGTGAACTTCTTGCTAAGAT-ATAAATTGCTGTTTCTTTTTTTCCTAACTCATTATG
131 TCACACTCAGTGAACTTCTTGCTAAGATAATAAATTGCTCTTTCTTTTTTTCCTAACTCATCATG
*
159307 TTGGCCCAGTACGCATCCAAATAGAGTGTTCAAATACGACTAAGTAAAGGATCAAAGGTTTATCA
196 TTGGCCCAATACGCATCC-AATAGAGTGTTCAAATACGACTAAGTAAAGGATCAAAGGTTTATCA
159372 AGATTTGGTG
Statistics
Matches: 230, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
263 53 0.23
264 177 0.77
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (264 bp):
CCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAACCAAGTTGTACGGTATAAAATATACG
GCCTCAACCTTCGAGTAGTCCAGACCAAAACACAACACAATTTCTCGATTGGCGAATATCTTATC
TCACACTCAGTGAACTTCTTGCTAAGATAATAAATTGCTCTTTCTTTTTTTCCTAACTCATCATG
TTGGCCCAATACGCATCCAATAGAGTGTTCAAATACGACTAAGTAAAGGATCAAAGGTTTATCAG
TCGG
Found at i:159822 original size:334 final size:333
Alignment explanation
Indices: 159087--160082 Score: 1543
Period size: 334 Copynumber: 3.0 Consensus size: 333
159077 TACGACTAAG
* *
159087 TACAAGATCAAAGGTTTATCAGTCGGCCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
1 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
* * * * * *
159152 CCAAGTTGTATGGTATAACATATGCGGCTTCAACCTTTGAGTATTCCATACCAAAGCACAACACA
66 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
* * *
159217 ATTTCTCGATTGGTGAATATCTTATCTCACACTCAGTGAACTTCTTGCTAAGAT-ATAAATTGCT
131 ATTTCTCGATTGGTGAATATCTTATCTCGCATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
* * * * *
159281 GTTTCTTTTTTTCCTAACTCATTATGTTGGCCCAGTACGCATCCAAATAGAGTGTTCAAATACGA
196 CTTTCTTTTTTTTCTAACTCATCATGTTGGCCAAGTACGCATCCAAATAGAGTTTTCAAATACGA
* * * *
159346 CTAAGTAAAGGATCAAAGGTTTATCAAGATTTGGTGGCA-T---ATTGGAGCGTTAGACAAGTAA
261 CTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAA
*
159407 TGTTTAAT
326 TGTTTAAC
*
159415 TACAGGATCAAAGGTTTATCAGTTGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
1 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
* *
159480 CCAAGTTGTAAGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACAAA
66 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
* *
159545 ATTTCTCGATTGGTGAATATCTTATCTCGCATTCGGTGAACTTCTTGTTGAGATAATAAATTGCT
131 ATTTCTCGATTGGTGAATATCTTATCTCGCATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
* * *
159610 CTTTCTTTTTTTTCATGACTCATCATGTTAGCCAAGTACGCTTCCAAATAGAGTTTTCAAATACG
196 CTTTCTTTTTTTTC-TAACTCATCATGTTGGCCAAGTACGCATCCAAATAGAGTTTTCAAATACG
*
159675 ACTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGAAGCGTTGGACAAATA
260 ACTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATA
159740 ATGTTTAAC
325 ATGTTTAAC
*
159749 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATAAA
1 TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
* * * *
159814 CAAAGTTGTATGGTATAACATGTACTACCTCAACCTTCGAGTATTCCATACCAAAGTGTAACACA
66 CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
* * * * *
159879 ATTTCTCAATTGGCGAATATCTTATCTCGCGTTCAGTGAACTTATTGCTGAGATAATAAATTACT
131 ATTTCTCGATTGGTGAATATCTTATCTCGCATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
* * *
159944 CTTTCTTTTTTTTCTAACTCATCATGTTGGCCTAGTACACATCCAAATAGAGTTTTCAAATATGA
196 CTTTCTTTTTTTTCTAACTCATCATGTTGGCCAAGTACGCATCCAAATAGAGTTTTCAAATACGA
* *
160009 CTAAGTACGGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGTACAAATAA
261 CTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAA
160074 TGTTTAAC
326 TGTTTAAC
160082 T
1 T
160083 TTTTCAAAGG
Statistics
Matches: 608, Mismatches: 54, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
328 168 0.28
329 22 0.04
330 82 0.13
331 1 0.00
333 116 0.19
334 219 0.36
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (333 bp):
TACAGGATCAAAGGTTTATCAGTCGACCCCATCATGAACTTAAGAGGATCCAATTTTGAAATCAA
CCAAGTTGTATGGTATAACATGTACTGCCTCAACCTTCGAGTATTCCATACCAAAGCGCAACACA
ATTTCTCGATTGGTGAATATCTTATCTCGCATTCAGTGAACTTCTTGCTGAGATAATAAATTGCT
CTTTCTTTTTTTTCTAACTCATCATGTTGGCCAAGTACGCATCCAAATAGAGTTTTCAAATACGA
CTAAGTACAGGATCAAAGGTTTATCAGGATTTGGTGGCATTAAAATTGGAGCGTTGGACAAATAA
TGTTTAAC
Done.