Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011205.1 Kokia drynarioides strain JFW-HI SEQ_126182, 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: 127379
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:2843 original size:6 final size:6
Alignment explanation
Indices: 2809--2870 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
2799 TAATAGGGAT
* * * *
2809 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
2856 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
2871 TGATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:7014 original size:23 final size:22
Alignment explanation
Indices: 6964--7015 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
6954 AGGAACTGAA
** *
6964 ATTAAATTGTAATTTTTACGAT
1 ATTAAATTGTAATTTTTAAAAG
*
6986 AATAAATGTGTAATTTTTAAAAG
1 ATTAAAT-TGTAATTTTTAAAAG
7009 ATTAAAT
1 ATTAAAT
7016 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (22 bp):
ATTAAATTGTAATTTTTAAAAG
Found at i:11877 original size:22 final size:22
Alignment explanation
Indices: 11851--11905 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
11841 CCCACAATAA
11851 ACACACACATATATATATATAT
1 ACACACACATATATATATATAT
*
11873 ACACACATATATATATATATAT
1 ACACACACATATATATATATAT
11895 AC-CACAACATA
1 ACACAC-ACATA
11906 GTTTCCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
ACACACACATATATATATATAT
Found at i:11878 original size:20 final size:20
Alignment explanation
Indices: 11853--11893 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11843 CACAATAAAC
11853 ACACACATATATATATATAT
1 ACACACATATATATATATAT
11873 ACACACATATATATATATAT
1 ACACACATATATATATATAT
11893 A
1 A
11894 TACCACAACA
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:0.15, G:0.00, T:0.34
Consensus pattern (20 bp):
ACACACATATATATATATAT
Found at i:12808 original size:17 final size:17
Alignment explanation
Indices: 12788--12833 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
12778 TTAAAAAAAA
12788 AATTTTAAATTTTTTTT
1 AATTTTAAATTTTTTTT
12805 AATTTTAAA-TTTTTTT
1 AATTTTAAATTTTTTTT
*
12821 ATTTTTTAAATTT
1 A-ATTTTAAATTT
12834 ACGTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.31
17 16 0.62
18 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
AATTTTAAATTTTTTTT
Found at i:13971 original size:21 final size:21
Alignment explanation
Indices: 13946--13985 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
13936 TCCTCAACAT
13946 TTAT-ATTTATTTTTAATTTGA
1 TTATAATTT-TTTTTAATTTGA
13967 TTATAATTTTTTTTAATTT
1 TTATAATTTTTTTTAATTT
13986 ATGTGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTATAATTTTTTTTAATTTGA
Found at i:14566 original size:18 final size:18
Alignment explanation
Indices: 14543--14581 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14533 GATTTAAAAT
*
14543 TTAATTACATTTAGTAAA
1 TTAATTACATTGAGTAAA
**
14561 TTAATTTTATTGAGTAAA
1 TTAATTACATTGAGTAAA
14579 TTA
1 TTA
14582 CACTCATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (18 bp):
TTAATTACATTGAGTAAA
Found at i:15705 original size:21 final size:21
Alignment explanation
Indices: 15664--15714 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
15654 GCTTACACAA
15664 ATTCAGGCTTTGTTGCTGTGT
1 ATTCAGGCTTTGTTGCTGTGT
*
15685 TTTCAGGCTTTG-TGCTGGTGT
1 ATTCAGGCTTTGTTGCT-GTGT
*
15706 ATTCGGGCT
1 ATTCAGGCT
15715 ATATGCCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.08, C:0.16, G:0.31, T:0.45
Consensus pattern (21 bp):
ATTCAGGCTTTGTTGCTGTGT
Found at i:16881 original size:50 final size:50
Alignment explanation
Indices: 16826--16925 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
16816 GCCATGAAGG
* **
16826 TTTATTTAAATATGTGAGTTTATTAGTTATTTCGGGCTAGGGGTGTCACA
1 TTTATTGAAATATGTGAGTTTATTAGTTATTTCGGGCTAAAGGTGTCACA
** *
16876 TTTATTGGTATATGTGAGTTTGTTAGTTATTTCGGGCTAAAGGTGTCACA
1 TTTATTGAAATATGTGAGTTTATTAGTTATTTCGGGCTAAAGGTGTCACA
16926 GTTGAAGCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (50 bp):
TTTATTGAAATATGTGAGTTTATTAGTTATTTCGGGCTAAAGGTGTCACA
Found at i:18958 original size:18 final size:18
Alignment explanation
Indices: 18918--18960 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18908 GTTCTATGTA
18918 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
18936 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
18954 TAATTAA
1 TAATTAA
18961 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:19315 original size:6 final size:6
Alignment explanation
Indices: 19295--19361 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
19285 TTTAAGGTTA
* ** *
19295 TAAATT T-ATTT TAAATT TAAATT T-GTTT TAAAATT TAAATT T-AATA
1 TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
*
19341 TAAATA TAAATT TAAAATT TA
1 TAAATT TAAATT T-AAATT TA
19362 TTATAAATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 11 0.23
6 28 0.58
7 9 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:19330 original size:18 final size:17
Alignment explanation
Indices: 19276--19354 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
19266 ACTCATTTTA
*
19276 AAATTTATTTTTAAGGTTAT
1 AAATTTA-TTTTAA-ATT-T
19296 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
19313 AAATTTGTTTTAAAATTT
1 AAATTTATTTT-AAATTT
* * *
19331 AAATTTAATATAAATAT
1 AAATTTATTTTAAATTT
19348 AAATTTA
1 AAATTTA
19355 AAATTTATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
17 23 0.44
18 16 0.31
19 6 0.12
20 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:19350 original size:24 final size:24
Alignment explanation
Indices: 19325--19371 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19315 ATTTGTTTTA
19325 AAATTT-AAATTTAATATAAATAT
1 AAATTTAAAATTTAATATAAATAT
*
19348 AAATTTAAAATTTATTATAAATAT
1 AAATTTAAAATTTAATATAAATAT
19372 TGAAAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATTTAAAATTTAATATAAATAT
Found at i:21271 original size:30 final size:30
Alignment explanation
Indices: 21206--21338 Score: 100
Period size: 29 Copynumber: 4.5 Consensus size: 30
21196 CTAAATTGTT
* *
21206 CAAAAATTA-CATTTTT-ACCTCCGAATTTT
1 CAAAAATTACCATTTTTGACCT-CAAATTTC
** **
21235 TTAAAATT-CCATTTTTGACCTCTATTTTTC
1 CAAAAATTACCATTTTTGACCTC-AAATTTC
* *
21265 CAAAAATTACCA-TTTT-ACACTCGAACTTC
1 CAAAAATTACCATTTTTGAC-CTCAAATTTC
*
21294 CAAAAAAT-CCATTTTTGACCTCAAACTTT-
1 CAAAAATTACCATTTTTGACCTCAAA-TTTC
21323 CAAAAATTACCATTTT
1 CAAAAATTACCATTTT
21339 ACCCCTAGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
28 3 0.04
29 42 0.53
30 31 0.39
31 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (30 bp):
CAAAAATTACCATTTTTGACCTCAAATTTC
Found at i:21281 original size:59 final size:57
Alignment explanation
Indices: 21204--21341 Score: 161
Period size: 59 Copynumber: 2.4 Consensus size: 57
21194 CCCTAAATTG
* *** * * **
21204 TTCAAAAATTA-CATTTTTACCTCCGAATTTTTTAAAATTCCATTTTTGACCTCTATTT
1 TTCAAAAATTACCA-TTTTACCT-CGAACTTCCAAAAAATCCATTTTTGACCTCAAACT
21262 TTCCAAAAATTACCATTTTACACTCGAACTTCCAAAAAATCCATTTTTGACCTCAAACT
1 TT-CAAAAATTACCATTTTAC-CTCGAACTTCCAAAAAATCCATTTTTGACCTCAAACT
21321 TTCAAAAATTACCATTTTACC
1 TTCAAAAATTACCATTTTACC
21342 CCTAGATGCC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
57 1 0.01
58 20 0.29
59 44 0.64
60 4 0.06
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (57 bp):
TTCAAAAATTACCATTTTACCTCGAACTTCCAAAAAATCCATTTTTGACCTCAAACT
Found at i:21425 original size:58 final size:56
Alignment explanation
Indices: 21265--21429 Score: 135
Period size: 58 Copynumber: 2.9 Consensus size: 56
21255 TCTATTTTTC
* *
21265 CAAAAATTACCATTTTACACTCGA-ACTTCCAAAAA--ATCCATTTTTGA-CCTCAAACTTT
1 CAAAAATTACCATTTTAC-CCCGAGA-TGCCAAAAATTAT-CA-TTTT-ACCCT-AAACTTT
* * **
21323 CAAAAATTACCATTTTACCCCTAGATGCCAAAAATTTTGTTTTTAACCCTAAACTTT
1 CAAAAATTACCATTTTACCCCGAGATGCCAAAAATTATCATTTT-ACCCTAAACTTT
*
21380 CTCAAAATTACCATTTTACCTCCGAG-TGTCC-AAAATTATCATTTTACCCT
1 C-AAAAATTACCATTTTACC-CCGAGATG-CCAAAAATTATCATTTTACCCT
21430 TGGGTATCCA
Statistics
Matches: 88, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
57 29 0.33
58 52 0.59
59 7 0.08
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (56 bp):
CAAAAATTACCATTTTACCCCGAGATGCCAAAAATTATCATTTTACCCTAAACTTT
Found at i:27021 original size:7 final size:7
Alignment explanation
Indices: 27009--27079 Score: 56
Period size: 7 Copynumber: 9.6 Consensus size: 7
26999 AGATACAATG
27009 AAGAAAA
1 AAGAAAA
27016 AAGAAAAA
1 AAG-AAAA
27024 AAGAAGAA
1 AAGAA-AA
27032 GAA-AGAAA
1 -AAGA-AAA
*
27040 AAGAAGA
1 AAGAAAA
27047 AAGAAAA
1 AAGAAAA
27054 TAGAGAAAA
1 -A-AGAAAA
*
27063 ATGAAAA
1 AAGAAAA
27070 AA-AAAA
1 AAGAAAA
27076 AAGA
1 AAGA
27080 GAGGTCGAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
6 6 0.12
7 22 0.42
8 15 0.29
9 9 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:27061 original size:13 final size:13
Alignment explanation
Indices: 27013--27053 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
27003 ACAATGAAGA
27013 AAAAAGAA-AAA-
1 AAAAAGAAGAAAG
*
27024 AAGAAGAAGAAAG
1 AAAAAGAAGAAAG
27037 AAAAAGAAGAAAG
1 AAAAAGAAGAAAG
27050 AAAA
1 AAAA
27054 TAGAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 7 0.27
12 3 0.12
13 16 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAAAG
Found at i:27072 original size:10 final size:9
Alignment explanation
Indices: 27012--27077 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
27002 TACAATGAAG
27012 AAAAAAG-A
1 AAAAAAGAA
27020 AAAAAAGAA
1 AAAAAAGAA
*
27029 GAAGAAAGAA
1 -AAAAAAGAA
*
27039 AAAGAAGAA
1 AAAAAAGAA
*
27048 AGAAAATAGAG
1 A-AAAA-AGAA
*
27059 AAAAATGAA
1 AAAAAAGAA
27068 AAAAAA-AA
1 AAAAAAGAA
27076 AA
1 AA
27078 GAGAGGTCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
8 11 0.24
9 16 0.35
10 15 0.33
11 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:27082 original size:24 final size:23
Alignment explanation
Indices: 27013--27082 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
27003 ACAATGAAGA
* *
27013 AAAAAGAAAAAAAGAAGAAGAAAG
1 AAAAAGAAAAAAA-AAAAAGAGAG
* *
27037 AAAAAGAAGAAAGAAAATAGAGA-
1 AAAAAGAA-AAAAAAAAAAGAGAG
*
27060 AAAATGAAAAAAAAAAAAGAGAG
1 AAAAAGAAAAAAAAAAAAGAGAG
27083 GTCGAGGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 12 0.32
23 7 0.19
24 14 0.38
25 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAAAAAAAAAAGAGAG
Found at i:28634 original size:50 final size:50
Alignment explanation
Indices: 28409--28655 Score: 202
Period size: 50 Copynumber: 4.9 Consensus size: 50
28399 TGAAGACATG
* * *
28409 AAGGGAAAGATCTAAGATCGCAACGACTGATCCAGTACCACAAAGATACAA
1 AAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAGATACAA
* * *
28460 AAGGGAAA-AGTCTAAGTCGCAACGGTGGA-CC-GTATACCTCAGAAG--ACAA
1 AAGGGAAAGA-TCTAAGCCGCAACGGCGGATCCAG--TACCACA-AAGATACAA
* * * * **
28509 GAAGGGAAAGATTTAAGCCTCAACGGCGAATCTAGTACCATGAAG--ACATA
1 -AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGATACA-A
* *
28559 AAGGGAAAGATCTAAGGCTGTAACGGCGGATCCAGTACCACAAAGATACAA
1 AAGGGAAAGATCTAA-GCCGCAACGGCGGATCCAGTACCACAAAGATACAA
* * * * *
28610 AAAGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCACGAAGAT
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAT
28656 TTGAAGGAGA
Statistics
Matches: 156, Mismatches: 28, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
48 1 0.01
49 26 0.17
50 93 0.60
51 32 0.21
52 4 0.03
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (50 bp):
AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGATACAA
Found at i:28668 original size:50 final size:48
Alignment explanation
Indices: 28509--28675 Score: 145
Period size: 50 Copynumber: 3.4 Consensus size: 48
28499 CAGAAGACAA
* * * *
28509 GAAGGGAAAGATTTAAGCCTCAACGGCGAATCTAGTACCATGAAGACAT
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA-TT
* * * * * * *
28558 AAAGGGAAAGATCTAAGGCTGTAACGGCGGATCCAGTACCACAAAGATACA
1 GAAGGGAAAGATTTAA-GCCGCAACGGCGAATCCAGTACCACGAAGAT--T
* * *
28609 AAAAGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATTT
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA-TT
*
28658 GAAGGAGAAAGGTTTAAG
1 GAAGG-GAAAGATTTAAG
28676 TCGAAATGGC
Statistics
Matches: 92, Mismatches: 21, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
49 17 0.18
50 61 0.66
51 14 0.15
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.16
Consensus pattern (48 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATT
Found at i:28697 original size:150 final size:149
Alignment explanation
Indices: 28392--28688 Score: 339
Period size: 150 Copynumber: 2.0 Consensus size: 149
28382 TACAAGTCTC
* *
28392 AGTACCATGAAGACATGAAGGGAAAGATCTAAGATCGCAACGACTGATCCAGTACCACAAAGATA
1 AGTACCATGAAGACATAAAGGGAAAGATCTAAGATCGCAACGACGGATCCAGTACCACAAAGATA
* * * * *
28457 CAAAAGGGAAAAGTCTAAGTCGCAACGGTGGACCGTATACCTCAGAAGACAAGAAGGGAAAGATT
66 CAAAAAGGAAAAGTCTAAGCCGCAACGGCGAACCG-ATACCACAGAAGACAAGAAGGGAAAGATT
** *
28522 TAAGCCTCAACGGCGAATCT
130 TAAGCCGAAACGGCAAATCT
* * *
28542 AGTACCATGAAGACATAAAGGGAAAGATCTAAG-GCTGTAACGGCGGATCCAGTACCACAAAGAT
1 AGTACCATGAAGACATAAAGGGAAAGATCTAAGATC-GCAACGACGGATCCAGTACCACAAAGAT
* * ***
28606 ACAAAAAGGAAAGGTTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGATTTGAAGGAGAAAG
65 ACAAAAAGGAAAAGTCTAAGCCGCAACGGCGAA-CCGA-TACCACAGAAGACAAGAAGG-GAAAG
* * *
28669 GTTTAAGTCGAAATGGCAAA
127 ATTTAAGCCGAAACGGCAAA
28689 CTCGGTACCT
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
149 12 0.10
150 108 0.89
151 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (149 bp):
AGTACCATGAAGACATAAAGGGAAAGATCTAAGATCGCAACGACGGATCCAGTACCACAAAGATA
CAAAAAGGAAAAGTCTAAGCCGCAACGGCGAACCGATACCACAGAAGACAAGAAGGGAAAGATTT
AAGCCGAAACGGCAAATCT
Found at i:28968 original size:101 final size:101
Alignment explanation
Indices: 28783--28977 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 101
28773 ACTACAATGA
* * * * *
28783 CAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACGTCAATTCCTATCCT
1 CAAGTCTTTATCTCTCTAAAGTTGCAGTAAGAGAAAAATGAAGCTTTAACATCAAATCCTATCCT
* * ** *
28848 CTTGAAGTTATAGTAAAGTTGGATTAAAAACAATAG
66 CCTGAAGTTACAACAAAGTTGGAATAAAAACAATAG
* * *
28884 CAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGAAAAATGAAGCTTTAACATCAAATCTTATCTT
1 CAAGTCTTTATCTCTCTAAAGTTGCAGTAAGAGAAAAATGAAGCTTTAACATCAAATCCTATCCT
* *
28949 CCTGAAGTTGCAACGAAGTTGGAATAAAA
66 CCTGAAGTTACAACAAAGTTGGAATAAAA
28978 CTACATCAAC
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (101 bp):
CAAGTCTTTATCTCTCTAAAGTTGCAGTAAGAGAAAAATGAAGCTTTAACATCAAATCCTATCCT
CCTGAAGTTACAACAAAGTTGGAATAAAAACAATAG
Found at i:29106 original size:39 final size:38
Alignment explanation
Indices: 29044--29175 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
29034 TCATCAACTA
* * * *
29044 ATCTATTACCTCGAGCTTGGGGCAGATTGTAACCATTTG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAACCA-TTG
* *
29083 ATCTTTTACCCCGAGCCTAGGGCAAATCATCGTCAACCA---
1 ATCTCTTACCCCGAGCCTAGGGCAGAT--T-GT-AACCATTG
* * *
29122 ATCTCTTACCCTGAGCC-AGGGCAGATTATATCCATTCG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAACCATT-G
29160 ATCTCTTACCCCGAGC
1 ATCTCTTACCCCGAGC
29176 TTGGGGTAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
34 4 0.05
35 1 0.01
36 1 0.01
38 23 0.31
39 37 0.50
41 1 0.01
42 2 0.03
43 5 0.07
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATTGTAACCATTG
Found at i:29163 original size:77 final size:78
Alignment explanation
Indices: 29063--29226 Score: 195
Period size: 77 Copynumber: 2.1 Consensus size: 78
29053 CTCGAGCTTG
* * * * * *
29063 GGGCAGATTGTAACCATTTGATCTTTTACCCCGAGCCTAGGGCAAATCATCGTCAACCAATCTCT
1 GGGCAGATTATAACCATTCGATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAACCAATCTCC
*
29128 TACCCTGAGC-CA
66 TACCCCGAGCACA
* * * * **
29140 GGGCAGATTATATCCATTCGATCTCTTACCCCGAGCTTGGGGTAGGTCACCATCAACCAATCTCC
1 GGGCAGATTATAACCATTCGATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAACCAATCTCC
*
29205 TACCCCGATCACA
66 TACCCCGAGCACA
29218 GGGCAGATT
1 GGGCAGATT
29227 GCGATTATCC
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
77 61 0.85
78 11 0.15
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (78 bp):
GGGCAGATTATAACCATTCGATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAACCAATCTCC
TACCCCGAGCACA
Found at i:29658 original size:191 final size:192
Alignment explanation
Indices: 29247--29830 Score: 710
Period size: 194 Copynumber: 3.0 Consensus size: 192
29237 ATAAATAAGT
* * *
29247 GAGGCAGTCATCTTCTTGATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAATCTTCGAA
1 GAGGCAGTCAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* * * *
29312 CCGCAGCTTCTTGATGAGATACTGAGAAGTAGGGCGAAGCAATAAAAATGTTAGCTTCCTGATGA
66 CCCCAGCTTCTTGATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGGTTAGCTTCC---TGA
* **
29377 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTATAGAGAAGCGGATTGAAAC-AAGT
128 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTATAGAGAAGCGGATTGAAACAAACA
* * *
29441 GAGGCAGTCAGCTTCCTGATGAGATACAGAGAAGTATACTAACTTAATGCGAACAAATCTTTGAA
1 GAGGCAGTCAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* * *
29506 CCCCAACTTCCTGATGAGATATTGAGAAGCAGGGTGAAGCAATAAAAAGGTTAGCTTCCTGAGAT
66 CCCCAGCTTCTTGATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGGTTAGCTTCCTGAGAT
*
29571 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACT-GAGAAGCGGATCGAAACAAACA
131 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTA-TAGAGAAGCGGATTGAAACAAACA
* * ** * *
29633 G-GGTAGTTATTTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGTGAGTAAAT
1 GAGGCAGTCAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATG--CGA----A-CAAAT
* * * *
29697 CTTCGAATCCCAGCTTCTTGATGAGA-AGCTGAGAAACA-GGTCAAAGCAATAAAATGGTTAGCT
59 CTTCGAACCCCAGCTTCTTGATGAGATA-CTGAGAAGCAGGGT-GAAGCAATAAAAAGGTTAGCT
* * * *
29760 TTCTGATGAAATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTATAGAGAAACGGATTG
122 TCCTGA-G--ATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTATAGAGAAGCGGATTG
29825 AAACAA
184 AAACAA
29831 GCGATGCGGT
Statistics
Matches: 337, Mismatches: 38, Indels: 23
0.85 0.10 0.06
Matches are distributed among these distances:
191 99 0.29
192 4 0.01
193 3 0.01
194 111 0.33
197 5 0.01
198 58 0.17
199 1 0.00
200 1 0.00
201 55 0.16
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (192 bp):
GAGGCAGTCAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
CCCCAGCTTCTTGATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGGTTAGCTTCCTGAGAT
ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTATAGAGAAGCGGATTGAAACAAACA
Found at i:30208 original size:17 final size:17
Alignment explanation
Indices: 30186--30225 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
30176 ACTCATTTTA
* *
30186 AAATTTATTTTAAGGTT
1 AAATTTATATTAAAGTT
*
30203 AAATTTATATTAAATTT
1 AAATTTATATTAAAGTT
30220 AAATTT
1 AAATTT
30226 GTTAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
AAATTTATATTAAAGTT
Found at i:30232 original size:25 final size:22
Alignment explanation
Indices: 30204--30271 Score: 57
Period size: 25 Copynumber: 2.9 Consensus size: 22
30194 TTTAAGGTTA
30204 AATTTATATTAAATTTAAATTTGTT
1 AATTTATATTAAATTTAAA--T-TT
* *
30229 AATTTA-AGTTTAATATAAATTT
1 AATTTATA-TTAAATTTAAATTT
30251 AGATTTATATCTAAATTTAAA
1 A-ATTTATAT-TAAATTTAAA
30272 ACTTATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
22 3 0.09
23 7 0.20
24 10 0.29
25 15 0.43
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (22 bp):
AATTTATATTAAATTTAAATTT
Found at i:30251 original size:17 final size:19
Alignment explanation
Indices: 30229--30284 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 19
30219 TAAATTTGTT
30229 AATTTAAG-TTTA-ATATA
1 AATTTAAGATTTATATATA
*
30246 AATTT-AGATTTATATCTA
1 AATTTAAGATTTATATATA
* *
30264 AATTTAAAACTTAT-TATA
1 AATTTAAGATTTATATATA
30282 AAT
1 AAT
30285 ATTGAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 2 0.06
17 9 0.28
18 15 0.47
19 6 0.19
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
AATTTAAGATTTATATATA
Found at i:32147 original size:30 final size:28
Alignment explanation
Indices: 32111--32215 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 28
32101 CCTTGAAGGT
*
32111 CCCTAAACTATCCAAAGATTACATTTTTA
1 CCCTAAACTTTCCAAA-ATTACATTTTTA
* *
32140 CCCCTAAACTTTTCAAAATTCCATTTTTAA
1 -CCCTAAACTTTCCAAAATTACATTTTT-A
**
32170 CCCTAATTTTTCCAAAAATTACCA-TTTTA
1 CCCTAAACTTTCC-AAAATTA-CATTTTTA
32199 CCCTCAAAC-TTCCAAAA
1 CCCT-AAACTTTCCAAAA
32216 ACTCCATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.06
29 29 0.47
30 27 0.44
31 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTACATTTTTA
Found at i:32173 original size:29 final size:29
Alignment explanation
Indices: 32111--32209 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 29
32101 CCTTGAAGGT
* * * *
32111 CCCTAAACTATCCAAAGATTACATTTTTAC
1 CCCTAAACTTTTCAAA-ATTCCATTTTTAA
32141 CCCTAAACTTTTCAAAATTCCATTTTTAA
1 CCCTAAACTTTTCAAAATTCCATTTTTAA
*
32170 CCCT-AATTTTTCCAAAAATTACCA-TTTT-A
1 CCCTAAACTTTT-C-AAAATT-CCATTTTTAA
32199 CCCTCAAACTT
1 CCCT-AAACTT
32210 CCAAAAACTC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
28 6 0.10
29 21 0.36
30 24 0.41
31 7 0.12
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTTCAAAATTCCATTTTTAA
Found at i:32257 original size:58 final size:58
Alignment explanation
Indices: 32186--32318 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 58
32176 TTTTTCCAAA
* *
32186 AATTACCATTTTACCCTCAAACTTCCAAAAACTCCA-TTTTGATCCCGAACTTTAAAAT
1 AATTACCATTTTACCCTCAAA-TGCCAAAAACTCCATTTTTAATCCCGAACTTTAAAAT
* * * * * ***
32244 AATTATCATTTTACCCTCGAATGCCTAAAATTCCATTTTTAATCCTGAACTTTCCCGA-
1 AATTACCATTTTACCCTCAAATGCCAAAAACTCCATTTTTAATCCCGAACTTT-AAAAT
32302 AATTACCATTTTACCCT
1 AATTACCATTTTACCCT
32319 TGAGTGTCTA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 11 0.18
58 50 0.81
59 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (58 bp):
AATTACCATTTTACCCTCAAATGCCAAAAACTCCATTTTTAATCCCGAACTTTAAAAT
Found at i:32359 original size:28 final size:28
Alignment explanation
Indices: 32301--32359 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
32291 AACTTTCCCG
* * *
32301 AAATTACCATTTTACCCTTGAGTGTCTA
1 AAATTACCATTTTACCCTCGAGTATCCA
* *
32329 AAATTACCATTTTGCCCTCGGGTATCCA
1 AAATTACCATTTTACCCTCGAGTATCCA
32357 AAA
1 AAA
32360 ATCACATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTACCCTCGAGTATCCA
Found at i:36701 original size:23 final size:23
Alignment explanation
Indices: 36643--36729 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
36633 TTCAAAACAT
* *
36643 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
** *
36667 TGTTCACAAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
36690 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
36713 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
36730 ATGAACATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.61
24 17 0.33
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:36740 original size:23 final size:23
Alignment explanation
Indices: 36696--36741 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
36686 TTAATGTTCG
* *
36696 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
36719 TGAACATGTTC-ATGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
36742 CAAATGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:38391 original size:8 final size:9
Alignment explanation
Indices: 38373--38399 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38363 GTCTTTTTAT
38373 AATTTTAAA
1 AATTTTAAA
38382 AATTTTAAA
1 AATTTTAAA
38391 AATTTTAAA
1 AATTTTAAA
38400 TTAATATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTTTAAA
Found at i:39704 original size:35 final size:35
Alignment explanation
Indices: 39664--39736 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
39654 CTCCTAAAAT
39664 AATAGAGGGGGAGAAGAGAGGGGATGCGTATAATA
1 AATAGAGGGGGAGAAGAGAGGGGATGCGTATAATA
39699 AATAGAGGGGGAGAAGAGAGGGGATGCGTATAATA
1 AATAGAGGGGGAGAAGAGAGGGGATGCGTATAATA
39734 AAT
1 AAT
39737 GAAAAAACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.41, C:0.03, G:0.41, T:0.15
Consensus pattern (35 bp):
AATAGAGGGGGAGAAGAGAGGGGATGCGTATAATA
Found at i:42352 original size:11 final size:11
Alignment explanation
Indices: 42336--42380 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
42326 GACAAGACCT
42336 TTTTAAATTTA
1 TTTTAAATTTA
42347 TTTTAAATTTA
1 TTTTAAATTTA
* *
42358 GATTTAAATTCA
1 -TTTTAAATTTA
*
42370 TCTTAAATTTA
1 TTTTAAATTTA
42381 AATTTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:42392 original size:23 final size:23
Alignment explanation
Indices: 42337--42386 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
42327 ACAAGACCTT
* * *
42337 TTTAAATTTATTTTAAATTTAGA
1 TTTAAATTCATCTTAAATTTAAA
42360 TTTAAATTCATCTTAAATTTAAA
1 TTTAAATTCATCTTAAATTTAAA
42383 TTTA
1 TTTA
42387 TTTTCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTAAATTCATCTTAAATTTAAA
Found at i:43131 original size:3 final size:3
Alignment explanation
Indices: 43123--43158 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
43113 ATTAAATGAT
* *
43123 TAA TAA TAA TAA TAA TAA TAG TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43159 AAAAAAAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:44061 original size:30 final size:30
Alignment explanation
Indices: 44016--44388 Score: 219
Period size: 30 Copynumber: 12.5 Consensus size: 30
44006 AAACTGTTCT
* *
44016 AAAATTACA-TTTTGACCCTCGTACTTCCA
1 AAAATTCCATTTTTGACCCTCGAACTTCCA
44045 AAAATTCCATTTTTGACCCTCGAACTTCCA
1 AAAATTCCATTTTTGACCCTCGAACTTCCA
* *
44075 AAAATTCCATTTTT-AACCTCAAAACTTCCA
1 AAAATTCCATTTTTGACCCTC-GAACTTCCA
**
44105 AAAATTATATTTTT-ACCCTCGAAC-TCCTA
1 AAAATTCCATTTTTGACCCTCGAACTTCC-A
* * *
44134 AAAATTCCATTTTTAACCCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCTC-GAACTTCCA
* * **
44165 AAAATTACATTTTT-ACCC-CTTAACTTTTTAA
1 AAAATTCCATTTTTGACCCTC-GAAC--TTCCA
*
44196 AAAATTCCA-TTTTGA-CCTTGAAACTTCCA
1 AAAATTCCATTTTTGACCCTCG-AACTTCCA
*
44225 AAAATTACCA-TTTTG-CCCCCGAA-TGTCCA
1 AAAATT-CCATTTTTGACCCTCGAACT-TCCA
* * *
44254 AAAATTTCATTTTTAACCC-CGAAACTTTCA
1 AAAATTCCATTTTTGACCCTCG-AACTTCCA
*
44284 AAAATTACC-CTTTT-ACCC-CTGAA-TATCCA
1 AAAATT-CCATTTTTGACCCTC-GAACT-TCCA
* * * **
44313 AAAATTTCATTTTTTA-TCTCGATTTTCCTA
1 AAAATTCCATTTTTGACCCTCGAACTTCC-A
* *
44343 AAAATTACCA-TTTT-ACCCCCTGGA-TGTCCA
1 AAAATT-CCATTTTTGACCCTC-GAACT-TCCA
44373 AAAATTCCATTTTTGA
1 AAAATTCCATTTTTGA
44389 TCTCGATTTT
Statistics
Matches: 273, Mismatches: 39, Indels: 62
0.73 0.10 0.17
Matches are distributed among these distances:
28 8 0.03
29 90 0.33
30 131 0.48
31 41 0.15
32 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCTCGAACTTCCA
Found at i:44125 original size:59 final size:58
Alignment explanation
Indices: 44038--44326 Score: 280
Period size: 59 Copynumber: 4.8 Consensus size: 58
44028 TGACCCTCGT
* *
44038 ACTTCCAAAAATTCCATTTTTGACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCAAA
1 ACTTCCAAAAATTACATTTTT-ACCC-CGAACTTCCAAAAATTCCATTTTTAACCCCAAA
*
44098 ACTTCCAAAAATTATATTTTTACCCTCGAAC-TCCTAAAAATTCCATTTTTAACCCCCAAA
1 ACTTCCAAAAATTACATTTTTACCC-CGAACTTCC-AAAAATTCCATTTTTAA-CCCCAAA
* ** * ***
44158 ACTTCCAAAAATTACATTTTTACCCCTTAACTTTTTAAAAAATTCCA-TTTTGACCTTGAA
1 ACTTCCAAAAATTACATTTTTACCCC-GAAC--TTCCAAAAATTCCATTTTTAACCCCAAA
** * *
44218 ACTTCCAAAAATTACCATTTTGCCCCCGAA-TGTCCAAAAATTTCATTTTTAACCCCGAA
1 ACTTCCAAAAATTA-CATTTTTACCCCGAACT-TCCAAAAATTCCATTTTTAACCCCAAA
* ** *
44277 ACTTTCAAAAATTACCCTTTTACCCCTGAA-TATCCAAAAATTTCATTTTT
1 ACTTCCAAAAATTACATTTTTACCCC-GAACT-TCCAAAAATTCCATTTTT
44327 TATCTCGATT
Statistics
Matches: 193, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.01
58 21 0.11
59 73 0.38
60 72 0.37
61 15 0.08
62 10 0.05
63 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
ACTTCCAAAAATTACATTTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCCCAAA
Found at i:44375 original size:60 final size:59
Alignment explanation
Indices: 44220--44398 Score: 220
Period size: 59 Copynumber: 3.0 Consensus size: 59
44210 ACCTTGAAAC
* * * *
44220 TTCCAAAAATTACCATTTTGCCCCC-GAATGTCCAAAAATTTCATTTTTAACCCCGAAACT
1 TTCCAAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTTCATTTTTAATCTCG--ATT
* * *
44280 TT-CAAAAATTACCCTTTTA-CCCCTGAATATCCAAAAATTTCATTTTTTATCTCGATT
1 TTCCAAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTTCATTTTTAATCTCGATT
* * *
44337 TTCCTAAAAATTACCATTTTACCCCCTGGATGTCCAAAAATTCCATTTTTGATCTCGATT
1 TTCC-AAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTTCATTTTTAATCTCGATT
44397 TT
1 TT
44399 TTTAAAAGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
57 4 0.04
58 5 0.05
59 56 0.54
60 38 0.37
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (59 bp):
TTCCAAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTTCATTTTTAATCTCGATT
Found at i:44405 original size:60 final size:60
Alignment explanation
Indices: 44224--44418 Score: 214
Period size: 59 Copynumber: 3.3 Consensus size: 60
44214 TGAAACTTCC
* * * * *** *
44224 AAAAATTACCATTTTGCCCCC-GAATGTCCAAAAATTTCATTTTTAACCCCGAAACTTTC
1 AAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATTTTTTT
* * * * **
44283 AAAAATTACCCTTTTA-CCCCTGAATATCCAAAAATTTCATTTTTTATCTCGATTTTCCT
1 AAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATTTTTTT
* *
44342 AAAAATTACCATTTTACCCCCTGGATGTCCAAAAATTCCATTTTTGATCTCGATTTTTTT
1 AAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATTTTTTT
* *
44402 AAAAGTTACCGTTTTAC
1 AAAAATTACCATTTTAC
44419 GTCCAGGTGT
Statistics
Matches: 113, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
58 4 0.04
59 57 0.50
60 52 0.46
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATTTTTTT
Found at i:44444 original size:59 final size:60
Alignment explanation
Indices: 44220--44445 Score: 194
Period size: 59 Copynumber: 3.8 Consensus size: 60
44210 ACCTTGAAAC
* * * * * * *
44220 TTCC-AAAAATTACCATTTTGCCCCC-GAATGTCCAAAAATTTCATTTTTAACCCCGAAACT
1 TTCCTAAAAATTACCATTTTACCCCCAGGATGTCCAAAAATTCCATTTTTGATCTCG--ATT
* * * * * *
44280 TT-C-AAAAATTACCCTTTTA-CCCCTGAATATCCAAAAATTTCATTTTTTATCTCGATT
1 TTCCTAAAAATTACCATTTTACCCCCAGGATGTCCAAAAATTCCATTTTTGATCTCGATT
*
44337 TTCCTAAAAATTACCATTTTACCCCCTGGATGTCCAAAAATTCCATTTTTGATCTCGATT
1 TTCCTAAAAATTACCATTTTACCCCCAGGATGTCCAAAAATTCCATTTTTGATCTCGATT
** * * ** **
44397 TTTTTAAAAGTTACCGTTTTACGTCCAGG-TGTTTAAAAATTCCATTTTT
1 TTCCTAAAAATTACCATTTTACCCCCAGGATGTCCAAAAATTCCATTTTT
44446 AACCCCGAAC
Statistics
Matches: 141, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
57 4 0.03
58 5 0.04
59 74 0.52
60 58 0.41
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (60 bp):
TTCCTAAAAATTACCATTTTACCCCCAGGATGTCCAAAAATTCCATTTTTGATCTCGATT
Found at i:50988 original size:28 final size:28
Alignment explanation
Indices: 50956--51052 Score: 137
Period size: 28 Copynumber: 3.5 Consensus size: 28
50946 TTTAGGTCCC
50956 TTAAAAGTTGATAAAAAAAATTAGACTT
1 TTAAAAGTTGATAAAAAAAATTAGACTT
*
50984 TTAAAAGTTGGTAAAAAAAATTAGACTT
1 TTAAAAGTTGATAAAAAAAATTAGACTT
* *
51012 TTAAAA---GCTAAAAAAAATTAGACCCT
1 TTAAAAGTTGATAAAAAAAATTAGA-CTT
51038 TTAAAAGTTGATAAA
1 TTAAAAGTTGATAAA
51053 TTTTTAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
25 15 0.25
26 8 0.13
28 33 0.54
29 5 0.08
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30
Consensus pattern (28 bp):
TTAAAAGTTGATAAAAAAAATTAGACTT
Found at i:60112 original size:17 final size:17
Alignment explanation
Indices: 60065--60134 Score: 52
Period size: 18 Copynumber: 4.0 Consensus size: 17
60055 ATTTAATCAA
* *
60065 TAAAATTTTAAATAAATT
1 TAAAATTATAAATATA-T
*
60083 TATAAAATA-AAATATAT
1 TA-AAATTATAAATATAT
* *
60100 TAGAATTTTAAATATTAT
1 TAAAATTATAAATA-TAT
*
60118 TAAAATTATATATATAT
1 TAAAATTATAAATATAT
60135 ACATATATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
16 3 0.08
17 11 0.28
18 22 0.55
19 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAAATTATAAATATAT
Found at i:60131 original size:2 final size:2
Alignment explanation
Indices: 60124--60156 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
60114 TTATTAAAAT
*
60124 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60157 GAAATTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60679 original size:21 final size:21
Alignment explanation
Indices: 60640--60681 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60630 TGCGACATTA
**
60640 CCAAGGTATATTGCAACTTTG
1 CCAAGGTATATCACAACTTTG
*
60661 CCAAGGTATATCACGACTTTG
1 CCAAGGTATATCACAACTTTG
60682 AAAGCAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
CCAAGGTATATCACAACTTTG
Found at i:62616 original size:313 final size:313
Alignment explanation
Indices: 62044--62673 Score: 1242
Period size: 313 Copynumber: 2.0 Consensus size: 313
62034 TGTTGTTCTT
62044 TACTGGAAGAGTATTTAATAGATAAGTTAGGTAACATAGCAGTTTCATCAAAAATAACATCTCTG
1 TACTGGAAGAGTATTTAATAGATAAGTTAGGTAACATAGCAGTTTCATCAAAAATAACATCTCTG
62109 CTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTCACACCAGCCTTAAAACC
66 CTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTCACACCAGCCTTAAAACC
62174 AAGAAAAACACATTTAATGGATCTTGGTTCCAATTTTCCATTATCAACATGAGCATAAGCAGGAC
131 AAGAAAAACACATTTAATGGATCTTGGTTCCAATTTTCCATTATCAACATGAGCATAAGCAGGAC
*
62239 ATCCAAAAATCTTTATATTAGAATAATCAGCAGGATTACCAAACCATATCTCTTGTGGAGTCTTT
196 ATCCAAAAATCTTTATATTAGAATAATCAGCAGGATTACCAAACCATATCTCTTGTGAAGTCTTT
*
62304 TTCTCAATGGCAACGGATGGAGATCGGTTGATCAAAAAACATGCAGTAGAGGC
261 TTCTCAATGGCAACGGATGGAGATCGGTTGATCAAAAAACATGCAGTAAAGGC
62357 TACTGGAAGAGTATTTAATAGATAAGTTAGGTAACATAGCAGTTTCATCAAAAATAACATCTCTG
1 TACTGGAAGAGTATTTAATAGATAAGTTAGGTAACATAGCAGTTTCATCAAAAATAACATCTCTG
62422 CTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTCACACCAGCCTTAAAACC
66 CTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTCACACCAGCCTTAAAACC
62487 AAGAAAAACACATTTAATGGATCTTGGTTCCAATTTTCCATTATCAACATGAGCATAAGCAGGAC
131 AAGAAAAACACATTTAATGGATCTTGGTTCCAATTTTCCATTATCAACATGAGCATAAGCAGGAC
62552 ATCCAAAAATCTTTATATTAGAATAATCAGCAGGATTACCAAACCATATCTCTTGTGAAGTCTTT
196 ATCCAAAAATCTTTATATTAGAATAATCAGCAGGATTACCAAACCATATCTCTTGTGAAGTCTTT
62617 TTCTCAATGGCAACGGATGGAGATCGGTTGATCAAAAAACATGCAGTAAAGGC
261 TTCTCAATGGCAACGGATGGAGATCGGTTGATCAAAAAACATGCAGTAAAGGC
62670 TACT
1 TACT
62674 TCAGCCTAAA
Statistics
Matches: 315, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
313 315 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (313 bp):
TACTGGAAGAGTATTTAATAGATAAGTTAGGTAACATAGCAGTTTCATCAAAAATAACATCTCTG
CTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTCACACCAGCCTTAAAACC
AAGAAAAACACATTTAATGGATCTTGGTTCCAATTTTCCATTATCAACATGAGCATAAGCAGGAC
ATCCAAAAATCTTTATATTAGAATAATCAGCAGGATTACCAAACCATATCTCTTGTGAAGTCTTT
TTCTCAATGGCAACGGATGGAGATCGGTTGATCAAAAAACATGCAGTAAAGGC
Found at i:66443 original size:175 final size:175
Alignment explanation
Indices: 66152--66510 Score: 637
Period size: 175 Copynumber: 2.1 Consensus size: 175
66142 AAATAATATT
* *
66152 AGTTTTCGTAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTCATTTTAGTCC
1 AGTTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTAATTTTAGTCC
* * *
66217 CTTTATTCGAAATATTTGTTTATTTTGGTGTATAATATCAAATCAAAATCAGATTTCACATTCTT
66 CTATATTCGAAATATTTGTATATTTTGGTATATAATATCAAATCAAAATCAGATTTCACATTCTT
66282 TCATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAAC
131 TCATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAAC
66327 AGTTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTAATTTTAGTCC
1 AGTTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTAATTTTAGTCC
* *
66392 CTATATTCGAAATATTTGTATATTTTGGTATATAGTATCGAATCAAAATCAGATTTCACATTCTT
66 CTATATTCGAAATATTTGTATATTTTGGTATATAATATCAAATCAAAATCAGATTTCACATTCTT
* *
66457 TCATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTCAT
131 TCATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAAC
66502 AGTTTTCGC
1 AGTTTTCGC
66511 TTTGTTCAAT
Statistics
Matches: 175, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (175 bp):
AGTTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTAATTTTAGTCC
CTATATTCGAAATATTTGTATATTTTGGTATATAATATCAAATCAAAATCAGATTTCACATTCTT
TCATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAAC
Found at i:71275 original size:13 final size:13
Alignment explanation
Indices: 71257--71283 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
71247 TTTGTAGTAA
71257 TCAAATGTGTAGG
1 TCAAATGTGTAGG
71270 TCAAATGTGTAGG
1 TCAAATGTGTAGG
71283 T
1 T
71284 GTTGAAGATT
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:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (13 bp):
TCAAATGTGTAGG
Found at i:77705 original size:201 final size:201
Alignment explanation
Indices: 77360--77760 Score: 694
Period size: 201 Copynumber: 2.0 Consensus size: 201
77350 TATGCGTACA
* * * *
77360 AATATATTACATGGTTATAATACGATACATATTTATTTTTAGGTCTCATACGAGGTTATGAAAGT
1 AATATATTACATGGTTATAATACGATACATATTCATTTTCAGGTCTCATACGAGCTTAAGAAAGT
* * *
77425 TTTTTTGTTAATTCGATGTTGAATTAGAATCAAATCGTAAAGTTTGCAAAATAACGAGTTGATGT
66 TCTTTTGTTAACTCGATGTTGAATTAGAATCAAATCGTAAAGTTTGCAAAAAAACGAGTTGATGT
* *
77490 CGCAACTTCGAGGTTCCTCATCGCGATGCAAGTTACTGACTAGGTCTTATTGCGACGACAAGAGT
131 CGCAACTTCGAGGTTCCTCATCGCGATGCAAGTTACTGACTAAGTCTTATCGCGACGACAAGAGT
77555 CCAACG
196 CCAACG
**
77561 AATATATTACATGGTTATAATGTGATACATATTCATTTTCAGGTCTCATACGAGCTTAAGAAAGT
1 AATATATTACATGGTTATAATACGATACATATTCATTTTCAGGTCTCATACGAGCTTAAGAAAGT
77626 TCTTTTGTTAACTCGATGTTGAATTAGAATCAAATCGTAAAGTTTGCAAAAAAACGAGTTGATGT
66 TCTTTTGTTAACTCGATGTTGAATTAGAATCAAATCGTAAAGTTTGCAAAAAAACGAGTTGATGT
*
77691 CGTAACTTCGAGGTTCCTCATCGCGATGCAAGTTACTGACTAAGTCTTATCGCGACGACAAGAGT
131 CGCAACTTCGAGGTTCCTCATCGCGATGCAAGTTACTGACTAAGTCTTATCGCGACGACAAGAGT
77756 CCAAC
196 CCAAC
77761 AGCGCAACGT
Statistics
Matches: 188, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 188 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (201 bp):
AATATATTACATGGTTATAATACGATACATATTCATTTTCAGGTCTCATACGAGCTTAAGAAAGT
TCTTTTGTTAACTCGATGTTGAATTAGAATCAAATCGTAAAGTTTGCAAAAAAACGAGTTGATGT
CGCAACTTCGAGGTTCCTCATCGCGATGCAAGTTACTGACTAAGTCTTATCGCGACGACAAGAGT
CCAACG
Found at i:79407 original size:29 final size:29
Alignment explanation
Indices: 79375--79459 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 29
79365 TTTAATGTGT
79375 AATTATATACATGAACTTTAATTTGGTGC
1 AATTATATACATGAACTTTAATTTGGTGC
* * * *
79404 AATTATACACGTGAATTTCTAATTGTGGTTC
1 AATTATATACATGAACTT-TAATT-TGGTGC
*
79435 ACA-TGTATACATGAAGCTTTAATTT
1 A-ATTATATACATGAA-CTTTAATTT
79460 TGATTTAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
29 15 0.34
30 6 0.14
31 20 0.45
32 3 0.07
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (29 bp):
AATTATATACATGAACTTTAATTTGGTGC
Found at i:80885 original size:21 final size:20
Alignment explanation
Indices: 80861--80908 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
80851 AAAGTAATGG
*
80861 CAAAAAGTGGGAAAACAACAA
1 CAAAAA-TGGAAAAACAACAA
* *
80882 CAAAACATGGAAAAATAACAG
1 CAAAA-ATGGAAAAACAACAA
80903 CAAAAA
1 CAAAAA
80909 CAACATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.65, C:0.15, G:0.15, T:0.06
Consensus pattern (20 bp):
CAAAAATGGAAAAACAACAA
Found at i:93141 original size:6 final size:6
Alignment explanation
Indices: 93127--93184 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
93117 TTTAATTTAT
* * *
93127 TTTAAA TTTAGA TTT-AT TTTAAA -TTAAA GTT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
93173 TTTAAA TTTAAA
1 TTTAAA TTTAAA
93185 AAAGTTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 10 0.23
6 30 0.70
7 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:93143 original size:17 final size:16
Alignment explanation
Indices: 93117--93176 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
93107 CGGACTCATT
93117 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
93133 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
* * *
93150 TTAAAGTTAATCTTAAA
1 TTTAA-TTTATTTTAAA
93167 TTTAAATTTA
1 TTT-AATTTA
93177 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.14
17 29 0.81
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:93171 original size:12 final size:11
Alignment explanation
Indices: 93120--93183 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
93110 ACTCATTTTT
*
93120 AATTTATTTTA
1 AATTTAATTTA
93131 AATTTAGATTT-
1 AATTTA-ATTTA
* *
93142 ATTTTAAATTA
1 AATTTAATTTA
*
93153 AAGTTAATCTTA
1 AATTTAAT-TTA
93165 AATTTAAATTTA
1 AATTT-AATTTA
93177 AATTTAA
1 AATTTAA
93184 AAAAGTTCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.07
11 18 0.43
12 18 0.43
13 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:93201 original size:34 final size:33
Alignment explanation
Indices: 93129--93201 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 33
93119 TAATTTATTT
* * * *
93129 TAAATTTAGATTTATTTTAAATTAAAGTTAATCT
1 TAAATTTAAATTTAATTTAAA-TAAAGTTAAACA
93163 TAAATTTAAATTTAAATTTAAA-AAAGTTCAAACA
1 TAAATTTAAATTT-AATTTAAATAAAGTT-AAACA
93197 TAAAT
1 TAAAT
93202 GTCCAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 6 0.18
34 20 0.61
35 7 0.21
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (33 bp):
TAAATTTAAATTTAATTTAAATAAAGTTAAACA
Found at i:94996 original size:29 final size:29
Alignment explanation
Indices: 94948--95173 Score: 210
Period size: 29 Copynumber: 7.7 Consensus size: 29
94938 GAGGTCTCTA
* *
94948 AACTTTTAAAAATTCTATTTTTACCCCCG
1 AACTTTCAAAAATTCCATTTTTACCCCCG
* *
94977 AACTTTCAAAAATCCCATTTTTAACCCCG
1 AACTTTCAAAAATTCCATTTTTACCCCCG
*
95006 AAACTTTCAAAAATTCTATTTTTACCCCCG
1 -AACTTTCAAAAATTCCATTTTTACCCCCG
* **
95036 AACATTC-AAAA-TCTCATTTTTGACCCCAA
1 AACTTTCAAAAATTC-CATTTTT-ACCCCCG
* **
95065 AAC-TTCGAAAAATTCTATTTTTACCTTCG
1 AACTTTC-AAAAATTCCATTTTTACCCCCG
* *
95094 AACTTTCAAAAATGCCATTTTTGA-CCTCG
1 AACTTTCAAAAATTCCATTTTT-ACCCCCG
* * *
95123 AAACTTCCAAAAATTCCATTTTTACCCTCA
1 -AACTTTCAAAAATTCCATTTTTACCCCCG
95153 AACTTTC-AAAATCTCCATTTT
1 AACTTTCAAAAAT-TCCATTTT
95174 CGACATCGAA
Statistics
Matches: 163, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.01
28 18 0.11
29 77 0.47
30 64 0.39
31 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
AACTTTCAAAAATTCCATTTTTACCCCCG
Found at i:95044 original size:59 final size:58
Alignment explanation
Indices: 94947--95193 Score: 298
Period size: 59 Copynumber: 4.2 Consensus size: 58
94937 AGAGGTCTCT
* *
94947 AAACTTTTAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTAACCCCG
1 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTTC-AAAATCCCATTTTTGACCCCG
* * *
95006 AAACTTTCAAAAATTCTATTTTTACCCCCGAACATTCAAAATCTCATTTTTGACCCCA
1 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTTCAAAATCCCATTTTTGACCCCG
** * *
95064 AAAC-TTCGAAAAATTCTATTTTTACCTTCGAACTTTCAAAAATGCCATTTTTGACCTCG
1 AAACTTTC-AAAAATTCTATTTTTACCCCCGAACTTTC-AAAATCCCATTTTTGACCCCG
* * * * * **
95123 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAATCTCCATTTTCGACATCG
1 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTTCAAAATC-CCATTTTTGACCCCG
*
95182 AAACTCTCAAAA
1 AAACTTTCAAAA
95194 TTGCCCTTTT
Statistics
Matches: 163, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.02
58 53 0.33
59 105 0.64
60 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTTCAAAATCCCATTTTTGACCCCG
Found at i:104608 original size:21 final size:21
Alignment explanation
Indices: 104582--104621 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
104572 ATACGAAGCA
104582 TGTTTTTTTATATTATTTTCT
1 TGTTTTTTTATATTATTTTCT
* *
104603 TGTTTTTTTTTATTGTTTT
1 TGTTTTTTTATATTATTTT
104622 GTTATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (21 bp):
TGTTTTTTTATATTATTTTCT
Found at i:104611 original size:11 final size:11
Alignment explanation
Indices: 104592--104644 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
104582 TGTTTTTTTA
*
104592 TATTATTTTCT
1 TATTTTTTTCT
*
104603 TGTTTTTTT-T
1 TATTTTTTTCT
* *
104613 TATTGTTTTGT
1 TATTTTTTTCT
*
104624 TATTATTTTCT
1 TATTTTTTTCT
104635 TATTTTTTTC
1 TATTTTTTTC
104645 ACTATTTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 8 0.24
11 26 0.76
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (11 bp):
TATTTTTTTCT
Found at i:107704 original size:23 final size:23
Alignment explanation
Indices: 107670--107727 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
107660 ACGCTAGCGC
*
107670 GCTTACTGTTTCACACTTTGTGT
1 GCTTACTATTTCACACTTTGTGT
*
107693 GCTTACTATTTCGCACTTTGTGT
1 GCTTACTATTTCACACTTTGTGT
*
107716 GCCTACTGATTT
1 GCTTACT-ATTT
107728 GCGCTATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (23 bp):
GCTTACTATTTCACACTTTGTGT
Found at i:107759 original size:22 final size:22
Alignment explanation
Indices: 107683--107811 Score: 143
Period size: 22 Copynumber: 5.8 Consensus size: 22
107673 TACTGTTTCA
* *
107683 CACTTTGTGTGCTTACT-ATTTCG
1 CACTGTGTGTGCCTACTGA-TT-G
*
107706 CACTTTGTGTGCCTACTGATTTG
1 CACTGTGTGTGCCTACTGA-TTG
* * ** *
107729 CGCTATGTGCCCCTATTGATTG
1 CACTGTGTGTGCCTACTGATTG
107751 CACTGTGTGTGCCTACTGATTG
1 CACTGTGTGTGCCTACTGATTG
107773 CACTGTGTGTGCCTACTGATTG
1 CACTGTGTGTGCCTACTGATTG
*
107795 CACTGTGTGTGCTTACT
1 CACTGTGTGTGCCTACT
107812 CTTTCCCTAG
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
22 58 0.62
23 31 0.33
24 4 0.04
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (22 bp):
CACTGTGTGTGCCTACTGATTG
Found at i:114790 original size:23 final size:23
Alignment explanation
Indices: 114760--114813 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
114750 ACGCTAGCGC
*
114760 GCTTACTGTTTCTCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
114783 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
114806 GCCTACTG
1 GCTTACTG
114814 ATTTGCGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.26, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:114827 original size:23 final size:22
Alignment explanation
Indices: 114779--114881 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 22
114769 TTCTCACTTC
* * *
114779 GTGTGCTTACTGTTTCGCACTTT
1 GTGTGCCTACTGATT-GCACTGT
* *
114802 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTGT
* * *
114825 GTGCGTCTACTGATTGCAATGT
1 GTGTGCCTACTGATTGCACTGT
114847 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
*
114870 GTGTGCTTACTG
1 GTGTGCCTACTG
114882 TTTCCTCAGC
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
22 16 0.25
23 47 0.72
24 2 0.03
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:114881 original size:45 final size:46
Alignment explanation
Indices: 114779--114881 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
114769 TTCTCACTTC
* * * *
114779 GTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGATTTGCGCTAT
1 GTGTGCTTACTGATTCGCAATGTGTGTGCCTACTGATTTGCACTAT
* *
114825 GTGCG-TCTACTGATT-GCAATGTGTGTGCCTACTGGA-TTGCACTGT
1 GTGTGCT-TACTGATTCGCAATGTGTGTGCCTACT-GATTTGCACTAT
114870 GTGTGCTTACTG
1 GTGTGCTTACTG
114882 TTTCCTCAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
45 33 0.70
46 14 0.30
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (46 bp):
GTGTGCTTACTGATTCGCAATGTGTGTGCCTACTGATTTGCACTAT
Found at i:116767 original size:206 final size:204
Alignment explanation
Indices: 116394--117057 Score: 943
Period size: 206 Copynumber: 3.2 Consensus size: 204
116384 CGATTATCCA
* * * *
116394 TAAACAAACGATGCAGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAGTCAAACCCACGCT
1 TAAACAAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
* * * * *
116459 CGATGTGAGTAAATCTTCGAACACCAGCTTCTTCATGAGATACTGAGAAGCAGGTTGAAGCAATA
66 CGATGTGAGCAAATCTTCGAAC-CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATA
*
116524 AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAG
130 AAACGGTTAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAG
116589 AGAAGCGGAT
195 AGAAGCGGAT
* *
116599 TGAAACAAGCAATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
1 T-AAACAAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
*
116664 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGACGAGATACTGAGAAGCAGGTCGAAGTAAT
65 TCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAAT
*
116729 AAAACGGTTAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTTCTGATGAGATACA
129 AAAACGGTTAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACA
* * *
116794 AAGAAGCGAAC
194 GAGAAGCGGAT
116805 TATAACAAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
1 TA-AACAAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * *
116870 TCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAAGTCGAAGTAAT
65 TCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAAT
* * ** * * *
116935 AAAACGGTTAGCTTCCTGGTGAGATAC-GGGGAAGTGAACCAAAACCATCTTCCTGATGAAACAC
129 AAAACGGTTAGCTTCCTGATGAGATACTGAGG-AGTGAACCAAATTCGTCTTCCTGATGAGATAC
*
116999 AGAGAAGTGGAT
193 AGAGAAGCGGAT
* *** ** *
117011 CAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTGAGAAGAAG
1 -TAAACAAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
117058 GTCAAGTCAA
Statistics
Matches: 411, Mismatches: 43, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
205 5 0.01
206 404 0.98
207 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (204 bp):
TAAACAAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
CGATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAA
AACGGTTAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
GAAGCGGAT
Found at i:117396 original size:6 final size:6
Alignment explanation
Indices: 117382--117445 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
117372 TTTAATTTAT
* *
117382 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
117428 TTTAAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA
117446 AAAGTCCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
4 2 0.04
5 5 0.11
6 37 0.79
7 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:117398 original size:17 final size:17
Alignment explanation
Indices: 117375--117445 Score: 97
Period size: 17 Copynumber: 4.1 Consensus size: 17
117365 GCCCCTGTTT
117375 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
117392 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
117409 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
117426 AATTTAATTTTAAAATTA
1 AATTT-ATTTTAAATTTA
117444 AA
1 AA
117446 AAAGTCCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 34 0.74
18 12 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:118191 original size:31 final size:31
Alignment explanation
Indices: 118141--118210 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
118131 TTAATGACAT
* *
118141 TAATAATAATAAACAGTTTTCTTAATAATCA
1 TAATAATAATAAACAGTTTTCATAATAATAA
* *
118172 TAAATAATAATAAA-TGTTTTGATAATAATAA
1 T-AATAATAATAAACAGTTTTCATAATAATAA
118203 TAATAATA
1 TAATAATA
118211 TTAATAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.21
31 15 0.44
32 12 0.35
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (31 bp):
TAATAATAATAAACAGTTTTCATAATAATAA
Found at i:118199 original size:3 final size:3
Alignment explanation
Indices: 118193--118227 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
118183 AAATGTTTTG
*
118193 ATA ATA ATA ATA ATA ATA TTA ATA ATTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA A
118228 AGAAAACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:119219 original size:29 final size:29
Alignment explanation
Indices: 119184--119468 Score: 250
Period size: 29 Copynumber: 9.8 Consensus size: 29
119174 AAGGTCCCGA
*
119184 AACTTCCAAAAAATTCCGTTTTT-CCCTCG
1 AACTTCC-AAAAATTCCATTTTTACCCTCG
*
119213 AACTTCCAAAAATCCCATTTTTAACCCT-G
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
119242 AAACTTCCAAAAATTCCA-TTTTACCCCCT
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
119271 AACTTCCAAAAA-TCTCATTTTTAACCC-CG
1 AACTTCCAAAAATTC-CATTTTT-ACCCTCG
* **
119300 AACTTCCCAAAATTATATTTTTACCC-CTG
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
*
119329 AACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
119358 AAACTTCCAAAAATTCCATTTTTTCCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
119388 AAGTTCC-GAAATCTCCATTTTTAACCTCG
1 AACTTCCAAAAAT-TCCATTTTTACCCTCG
* *
119417 AAAC-TCTAAAAATTACC-CTTTTACCCTCG
1 -AACTTCCAAAAATT-CCATTTTTACCCTCG
*
119446 AA-TATCTAAAAATTCCATTTTTA
1 AACT-TCCAAAAATTCCATTTTTA
119469 AACCCTAAAT
Statistics
Matches: 211, Mismatches: 25, Indels: 40
0.76 0.09 0.14
Matches are distributed among these distances:
27 2 0.01
28 44 0.21
29 104 0.49
30 61 0.29
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:119275 original size:58 final size:58
Alignment explanation
Indices: 119182--119496 Score: 295
Period size: 58 Copynumber: 5.4 Consensus size: 58
119172 TGAAGGTCCC
* *
119182 GAAACTTCCAAAAAATTCCGTTTTTCCCTCGAACTTCCAAAAATCCCATTTTTAACCCT
1 GAAACTTCC-AAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCT
* * * *
119241 GAAACTTCCAAAAATTCCATTTTACCCCCTAACTTCCAAAAATCTCATTTTTAACCCC
1 GAAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCT
* ** *
119299 G-AACTTCCCAAAATTATATTTTTACCC-CTGAACTTCCAAAAATCCCATTTTTGA-CCT
1 GAAACTTCCAAAAATTCCA-TTTTACCCTC-GAACTTCCAAAAATCCCATTTTTAACCCT
* * *
119356 CGAAACTTCCAAAAATTCCATTTTTTCCCTCGAAGTTCC-GAAATCTCCATTTTTAA-CCT
1 -GAAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATC-CCATTTTTAACCCT
* * * *
119415 CGAAAC-TCTAAAAATTACCCTTTTACCCTCGAA-TATCTAAAAATTCCATTTTTAAACCCT
1 -GAAACTTCCAAAAATT-CCATTTTACCCTCGAACT-TCCAAAAATCCCATTTTT-AACCCT
* *
119475 -AAATTTTCCCAAAATTACCATT
1 GAAA-CTTCCAAAAATT-CCATT
119497 ATGCCCCTCG
Statistics
Matches: 213, Mismatches: 30, Indels: 25
0.79 0.11 0.09
Matches are distributed among these distances:
57 18 0.08
58 114 0.54
59 64 0.30
60 17 0.08
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (58 bp):
GAAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCT
Found at i:119611 original size:32 final size:32
Alignment explanation
Indices: 119575--119643 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
119565 TTTGCACTTA
*
119575 ATTTTAAAATTTATTATGCACTTGTATTTTGC
1 ATTTTAAAATTTATTATGCACTCGTATTTTGC
119607 ATTTTAAAATTTATTATGCACTCGTATTTTGC
1 ATTTTAAAATTTATTATGCACTCGTATTTTGC
119639 ATTTT
1 ATTTT
119644 TGATTTTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTTTAAAATTTATTATGCACTCGTATTTTGC
Found at i:125152 original size:20 final size:20
Alignment explanation
Indices: 125127--125164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
125117 AAATCTTTAG
125127 TTATTTATTATTTTGAATAT
1 TTATTTATTATTTTGAATAT
* *
125147 TTATTTTTTGTTTTGAAT
1 TTATTTATTATTTTGAAT
125165 TTTCTTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTATTTATTATTTTGAATAT
Done.