Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 1 of 128
Found at i:3283 original size:4 final size:4
Alignment explanation
Indices: 3274--3331 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
3264 CTCCCTCAGA
3274 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3322 ATGT ATGT AT
1 ATGT ATGT AT
3332 AACTGGATTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:7218 original size:4 final size:4
Alignment explanation
Indices: 7209--7234 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
7199 ATTTCATAAG
7209 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
7235 ATTTTGTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:11487 original size:30 final size:28
Alignment explanation
Indices: 11453--11512 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
11443 CATTTAGATA
11453 ATTTTTAAAATTTAAAAAAATATAAAAATT
1 ATTTTTAAAA-TT-AAAAAATATAAAAATT
* *
11483 ATTTTTAAAATTAAAAATTATTAAAATT
1 ATTTTTAAAATTAAAAAATATAAAAATT
11511 AT
1 AT
11513 AAAATGTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 16 0.57
29 2 0.07
30 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTTTAAAATTAAAAAATATAAAAATT
Found at i:13351 original size:17 final size:17
Alignment explanation
Indices: 13329--13362 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13319 TATTCTTATC
*
13329 ATTAATATTTATTTTTA
1 ATTAATATTTATATTTA
*
13346 ATTAATTTTTATATTTA
1 ATTAATATTTATATTTA
13363 TCCTAGCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTAATATTTATATTTA
Found at i:16424 original size:25 final size:25
Alignment explanation
Indices: 16390--16442 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
16380 TTTTCACTAG
16390 TTGTGAAGGGCTCCAAATTAA-GCCT
1 TTGTGAAGGGCTCCAAA-TAATGCCT
16415 TTGTGAAGGGCTCCAAATAATGCCT
1 TTGTGAAGGGCTCCAAATAATGCCT
16440 TTG
1 TTG
16443 AAAATAGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (25 bp):
TTGTGAAGGGCTCCAAATAATGCCT
Found at i:24608 original size:2 final size:2
Alignment explanation
Indices: 24601--24631 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24591 ATTTTGTTTT
24601 TA TA TA TA TA TA 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 T
24632 TGGCTCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25575 original size:1 final size:1
Alignment explanation
Indices: 25571--25595 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
25561 CGCCCCCCCC
25571 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
25596 GCTACTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26739 original size:12 final size:12
Alignment explanation
Indices: 26722--26746 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26712 TTAATTACTA
26722 TTGTTGTTGTCG
1 TTGTTGTTGTCG
26734 TTGTTGTTGTCG
1 TTGTTGTTGTCG
26746 T
1 T
26747 ACAGCAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.32, T:0.60
Consensus pattern (12 bp):
TTGTTGTTGTCG
Found at i:33831 original size:95 final size:97
Alignment explanation
Indices: 33664--33860 Score: 292
Period size: 95 Copynumber: 2.0 Consensus size: 97
33654 GAAATTGAAT
* *
33664 ATATAATTATAATTATTTAAATGCTCGCTCCTAGCTCTTATTACCATTGTAAAAGTTTTGCTTGT
1 ATATAATTATAATTATTTAAA--CTCGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGT
*
33729 GTTATAAAGTTATATATATAATT-TTTTTTCCAAA
64 GTTATAAACTTATATATA-AATTATTTTTTCCAAA
* *
33763 ATATAATTATAATTATTTAAA-T-GCTCCTAGATTTTATTACTATTGTAAAAGTTTTACTTGTGT
1 ATATAATTATAATTATTTAAACTCGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGT
*
33826 TATAAACTTATATATAATTTATTTTTTCCAAA
66 TATAAACTTATATATAAATTATTTTTTCCAAA
33858 ATA
1 ATA
33861 AGTTTTTTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
94 3 0.03
95 66 0.73
96 1 0.01
99 21 0.23
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (97 bp):
ATATAATTATAATTATTTAAACTCGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGT
TATAAACTTATATATAAATTATTTTTTCCAAA
Found at i:36594 original size:82 final size:83
Alignment explanation
Indices: 36492--36656 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
36482 GACTAAATGT
36492 ATTTTCCAATTTGTTAATTTAATAATTAGTTTTTTATTCTTGAAATATTAATTAATTAAAATAAA
1 ATTTTCCAATTTGTTAATTTAATAATTAGTTTTTTATTCTTGAAATATTAATTAATTAAAATAAA
36557 TTTAATTAATTTTCTCAA
66 TTTAATTAATTTTCTCAA
36575 ATTTTCCAA-TTGTTAATTTAATAATTAGTTTTTTATTCTTGAAATATTAATTAATTAAAATAAA
1 ATTTTCCAATTTGTTAATTTAATAATTAGTTTTTTATTCTTGAAATATTAATTAATTAAAATAAA
36639 TTTAATTAATTTTCTCAA
66 TTTAATTAATTTTCTCAA
36657 TTAAAATATT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 73 0.89
83 9 0.11
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (83 bp):
ATTTTCCAATTTGTTAATTTAATAATTAGTTTTTTATTCTTGAAATATTAATTAATTAAAATAAA
TTTAATTAATTTTCTCAA
Found at i:38210 original size:34 final size:34
Alignment explanation
Indices: 38167--38237 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
38157 TATTCGAATG
* *
38167 CATAAGACATTTCAACCCAGAAATGCCTGAATCC
1 CATAAGACATCTCAACCCAGAAATGCCTAAATCC
38201 CATAAGACATCTCAACCCAGAAATGCCTAAATCC
1 CATAAGACATCTCAACCCAGAAATGCCTAAATCC
38235 CAT
1 CAT
38238 CCAAAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (34 bp):
CATAAGACATCTCAACCCAGAAATGCCTAAATCC
Found at i:40223 original size:21 final size:21
Alignment explanation
Indices: 40197--40251 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
40187 AATAGCGGTG
*
40197 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
40218 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
**
40239 GCAATGAGATTAG
1 GCGGTGAGATTAG
40252 AAACAGCGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:43612 original size:6 final size:6
Alignment explanation
Indices: 43601--43633 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
43591 TTTGCAACCC
*
43601 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAG
43634 AAGAAGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:43639 original size:18 final size:18
Alignment explanation
Indices: 43601--43641 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43591 TTTGCAACCC
*
43601 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGAG
43619 AAGGGGAAGGGG-AAGAAG
1 AAGGGGAAGGGGAAAG-AG
43637 AAGGG
1 AAGGG
43642 TAGCCAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGAG
Found at i:50914 original size:14 final size:14
Alignment explanation
Indices: 50871--50915 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
50861 AATAGTAAAA
*
50871 TAATATTTAGAATA
1 TAATATTTAGAATT
50885 TAATATTTAGAGATT
1 TAATATTTAGA-ATT
*
50900 TAATATTTATAATT
1 TAATATTTAGAATT
50914 TA
1 TA
50916 GGATTAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (14 bp):
TAATATTTAGAATT
Found at i:58522 original size:6 final size:6
Alignment explanation
Indices: 58511--58542 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
58501 AAGGTCCGGA
58511 TGCGGG TGCGGG TGCGGG TGCGGG TGCGGG TG
1 TGCGGG TGCGGG TGCGGG TGCGGG TGCGGG TG
58543 TGGGCGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.66, T:0.19
Consensus pattern (6 bp):
TGCGGG
Found at i:71225 original size:36 final size:36
Alignment explanation
Indices: 71084--71229 Score: 220
Period size: 36 Copynumber: 4.1 Consensus size: 36
71074 TGGGCTGGGG
*
71084 CTGGGACTGGGGCTGCGAATTCGAGGCTGACTTAGA
1 CTGGGGCTGGGGCTGCGAATTCGAGGCTGACTTAGA
* * *
71120 TTCGGGCTGGGGCTGCGAATTCGATGCTGACTTAGA
1 CTGGGGCTGGGGCTGCGAATTCGAGGCTGACTTAGA
* *
71156 CTTGGGCTGGGGCTGCGAATTCGAGGCTGACTTGGA
1 CTGGGGCTGGGGCTGCGAATTCGAGGCTGACTTAGA
* *
71192 CTGGGGCTGGGGCTGCGAATTCGAGGCTTACTTGGA
1 CTGGGGCTGGGGCTGCGAATTCGAGGCTGACTTAGA
71228 CT
1 CT
71230 AGAAGAAGGG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.16, C:0.20, G:0.39, T:0.25
Consensus pattern (36 bp):
CTGGGGCTGGGGCTGCGAATTCGAGGCTGACTTAGA
Found at i:73403 original size:4 final size:4
Alignment explanation
Indices: 73394--73420 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
73384 AACCATCAAA
73394 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
73421 AATATAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:76752 original size:14 final size:14
Alignment explanation
Indices: 76735--76764 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
76725 TTTTTTTAAA
76735 ATTATAATAATGTT
1 ATTATAATAATGTT
*
76749 ATTATAATAATTTT
1 ATTATAATAATGTT
76763 AT
1 AT
76765 CTTTTCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTATAATAATGTT
Found at i:76833 original size:24 final size:22
Alignment explanation
Indices: 76790--76837 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
76780 ATATACCTTT
76790 AAATAAAATAATTCAAAAATCAA
1 AAATAAAATAATTCAAAAAT-AA
*
76813 AAATCAAATGAATT-AATAAATAA
1 AAATAAAAT-AATTCAA-AAATAA
76836 AA
1 AA
76838 TATTTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAAATAATTCAAAAATAA
Found at i:77090 original size:9 final size:9
Alignment explanation
Indices: 77076--77105 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
77066 CGCGACTCAC
77076 TCTTCTTCA
1 TCTTCTTCA
77085 TCTTCTTCA
1 TCTTCTTCA
77094 TCTTCTTCA
1 TCTTCTTCA
77103 TCT
1 TCT
77106 GCCCACATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:78649 original size:18 final size:18
Alignment explanation
Indices: 78625--78667 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
78615 GGATGAACCA
78625 GAAGAAGATGATGAAGGG
1 GAAGAAGATGATGAAGGG
* * *
78643 GATGAAGATGGTGAATGG
1 GAAGAAGATGATGAAGGG
78661 GAAGAAG
1 GAAGAAG
78668 CAGATGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (18 bp):
GAAGAAGATGATGAAGGG
Found at i:81830 original size:4 final size:4
Alignment explanation
Indices: 81821--81926 Score: 77
Period size: 4 Copynumber: 26.5 Consensus size: 4
81811 TTTCTTAATA
* * * * * * *
81821 ACAT ACAT ACAT ACAT GCAT GCAT GCAT GCAT ACAT ACAC ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* ** * ** * *
81869 ACAC ACGC ACAC ACGC ACAC GCAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
81917 ACAT ACAT AC
1 ACAT ACAT AC
81927 CCACTGTCCA
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 92 1.00
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (4 bp):
ACAT
Found at i:84948 original size:25 final size:26
Alignment explanation
Indices: 84898--84951 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
84888 TATACAGATC
*
84898 AAAGACAGTGAACCCAATTATGAAAA
1 AAAGACACTGAACCCAATTATGAAAA
*
84924 AAAGACACTGAGCCC-ATTATGAAAA
1 AAAGACACTGAACCCAATTATGAAAA
84949 AAA
1 AAA
84952 TGGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.15
Consensus pattern (26 bp):
AAAGACACTGAACCCAATTATGAAAA
Found at i:98975 original size:22 final size:21
Alignment explanation
Indices: 98950--98990 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
98940 AAGGAAAGAA
*
98950 TTAGAAGTAAGAATGCAAAAAT
1 TTAGAA-TAAAAATGCAAAAAT
98972 TTAGAATAAAAATGCAAAA
1 TTAGAATAAAAATGCAAAA
98991 TCATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.22
Consensus pattern (21 bp):
TTAGAATAAAAATGCAAAAAT
Found at i:105418 original size:31 final size:31
Alignment explanation
Indices: 105383--105443 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
105373 TAGCCCAATG
*
105383 ACTTAAAT-AAAATCTTTCAAATAGTTTAGTA
1 ACTTAAATGAAAA-CTTTCAAATAATTTAGTA
*
105414 ACTTAAATGAAAACTTTCAAGTAATTTAGT
1 ACTTAAATGAAAACTTTCAAATAATTTAGT
105444 GAATATTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCAAATAATTTAGTA
Found at i:113259 original size:129 final size:126
Alignment explanation
Indices: 112876--113279 Score: 546
Period size: 129 Copynumber: 3.2 Consensus size: 126
112866 GCTAGCATGG
* * * * *
112876 ATATAATTCATGTTGTGGACAACTAGGAATCTTAAAAGATGTAGCTTTAGATCAATTTGTGGTGT
1 ATATAATTCATGGTGTGAACAACTAAGAACCTT-AAAGATGTAGCTTTAGATCAATTTGGGGTGT
*
112941 AATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAT--AT-AC
65 AATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAATAAC
* * * *
113000 ATATAATTCATGGCGTGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTA
1 ATATAATTCATGGTGTGAACAACTAAGAACCTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
* * * *
113064 ATATAACATTCAATCAAGATAAGCTAGCATGAAAAAGTGTCGATATAGACACACATACATAAAC
66 ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAG--ACATATAAAT-AAC
* * ***
113128 ATATAATTCAAGGTTTGAACAACTAAGAGTGTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
1 ATATAATTCATGGTGTGAACAACTAAGAACCTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
*
113193 ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAAAATAC
66 ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAATA-AC
*
113255 ACATAATTCATGGTGTGAACAACTA
1 ATATAATTCATGGTGTGAACAACTA
113280 GGAATCTGAA
Statistics
Matches: 244, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
122 74 0.30
123 9 0.04
124 24 0.10
126 3 0.01
127 31 0.13
128 21 0.09
129 82 0.34
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (126 bp):
ATATAATTCATGGTGTGAACAACTAAGAACCTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAATAAC
Found at i:116029 original size:12 final size:12
Alignment explanation
Indices: 116012--116040 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
116002 TAGATAGTGA
116012 CACATGACATGC
1 CACATGACATGC
116024 CACATGACATGC
1 CACATGACATGC
116036 CACAT
1 CACAT
116041 ATACCTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (12 bp):
CACATGACATGC
Found at i:119465 original size:4 final size:4
Alignment explanation
Indices: 119458--119490 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
119448 AGGTAGAAGA
119458 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
119491 AGGAGTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:124444 original size:26 final size:26
Alignment explanation
Indices: 124401--124453 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
124391 ATAGATAAAA
**
124401 TTTATATTTATATTTTTATCTTTATC
1 TTTATATTTATATTTTTAAATTTATC
*
124427 TTTATTTTTAT-TTATTTAAATTTATC
1 TTTATATTTATATT-TTTAAATTTATC
124453 T
1 T
124454 CTCAATCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATATTTATATTTTTAAATTTATC
Found at i:125982 original size:275 final size:276
Alignment explanation
Indices: 125476--126031 Score: 1098
Period size: 275 Copynumber: 2.0 Consensus size: 276
125466 CTAAAATATA
125476 TATTT-ATAATGGAATTTAAAATAAAATAATATTTAATTTTATATAAAATTTTAATAAATTTATT
1 TATTTAATAATGGAATTTAAAATAAAATAATATTTAATTTTATATAAAATTTTAATAAATTTATT
125540 GTATACGTATTCTCACCTAAATTGTCTAGTATTACATTTTTTTTAAGTAAATCTAATATAGTCCA
66 GTATACGTATTCTCACCTAAATTGTCTAGTATTACATTTTTTTTAAGTAAATCTAATATAGTCCA
125605 TTCACTAATCTCCAAATATGTCAATGTCATGTGTCATCTAAGCTTCCTGGAAATTTCTCCATATC
131 TTCACTAATCTCCAAATATGTCAATGTCATGTGTCATCTAAGCTTCCTGGAAATTTCTCCATATC
125670 TAGTCTGAGACTTGTCAAGTGTTTAATTAATACCCACATATATATATGTGTCAAATTGAAAGTTT
196 TAGTCTGAGACTTGTCAAGTGTTTAATTAATACCCACATATATATATGTGTCAAATTGAAAGTTT
125735 GGTCCTTCTAGTATGC
261 GGTCCTTCTAGTATGC
125751 TATTTAATAATGGAA-TTAAAATAAAATAATATTTAATTTTATATAAAATTTTAATAAATTTATT
1 TATTTAATAATGGAATTTAAAATAAAATAATATTTAATTTTATATAAAATTTTAATAAATTTATT
125815 GTATACGTATTCTCACCTAAATTGTCTAGTATTACATTTTTTTTAAGTAAATCTAATATAGTCCA
66 GTATACGTATTCTCACCTAAATTGTCTAGTATTACATTTTTTTTAAGTAAATCTAATATAGTCCA
125880 TTCACTAATCTCCAAATATGTCAATGTCATGTGTCATCTAAGCTTCCTGGAAATTTCTCCATATC
131 TTCACTAATCTCCAAATATGTCAATGTCATGTGTCATCTAAGCTTCCTGGAAATTTCTCCATATC
125945 TAGTCTGAGACTTGTCAAGTGTTTAATTAATACCCACATATATATATGTGTCAAATTGAAAGTTT
196 TAGTCTGAGACTTGTCAAGTGTTTAATTAATACCCACATATATATATGTGTCAAATTGAAAGTTT
126010 GGTCCTTCTAGTATGC
261 GGTCCTTCTAGTATGC
126026 TATTTA
1 TATTTA
126032 TTTGAATTTG
Statistics
Matches: 280, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
275 271 0.97
276 9 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (276 bp):
TATTTAATAATGGAATTTAAAATAAAATAATATTTAATTTTATATAAAATTTTAATAAATTTATT
GTATACGTATTCTCACCTAAATTGTCTAGTATTACATTTTTTTTAAGTAAATCTAATATAGTCCA
TTCACTAATCTCCAAATATGTCAATGTCATGTGTCATCTAAGCTTCCTGGAAATTTCTCCATATC
TAGTCTGAGACTTGTCAAGTGTTTAATTAATACCCACATATATATATGTGTCAAATTGAAAGTTT
GGTCCTTCTAGTATGC
Found at i:134540 original size:13 final size:13
Alignment explanation
Indices: 134522--134552 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
134512 TTATAAAAAT
134522 TTATGATCAATAA
1 TTATGATCAATAA
134535 TTATGATCAATAA
1 TTATGATCAATAA
*
134548 GTATG
1 TTATG
134553 GACATAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (13 bp):
TTATGATCAATAA
Found at i:134746 original size:14 final size:15
Alignment explanation
Indices: 134701--134748 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
134691 ACTAGAAAAT
*
134701 TTATAAAACTTTAT-
1 TTATAAAGCTTTATA
*
134715 TTATAAAGGTTATATA
1 TTATAAAGCTT-TATA
134731 TTAT-AAGCTTTATA
1 TTATAAAGCTTTATA
134745 TTAT
1 TTAT
134749 TCTTGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 17 0.59
15 8 0.28
16 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAAAGCTTTATA
Found at i:138160 original size:36 final size:36
Alignment explanation
Indices: 138108--138178 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
138098 AGCTTCTGTG
138108 TCATCTTATACAAGACCATCCTCTCCCATTACTCGA
1 TCATCTTATACAAGACCATCCTCTCCCATTACTCGA
* *
138144 TCATCTTATACCAGACCATCCTCTCCTATTACTCG
1 TCATCTTATACAAGACCATCCTCTCCCATTACTCG
138179 CTCGCCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.37, G:0.06, T:0.32
Consensus pattern (36 bp):
TCATCTTATACAAGACCATCCTCTCCCATTACTCGA
Found at i:149336 original size:20 final size:19
Alignment explanation
Indices: 149290--149336 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
149280 ACAAATATTT
149290 AATTTT-TATATTTAAATA
1 AATTTTATATATTTAAATA
* * *
149308 TAGTTTATATATTCTAATTA
1 AATTTTATATATT-TAAATA
149328 AATTTTATA
1 AATTTTATA
149337 AATAATTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTATATATTTAAATA
Found at i:149590 original size:13 final size:13
Alignment explanation
Indices: 149568--149639 Score: 99
Period size: 13 Copynumber: 5.5 Consensus size: 13
149558 CAAATGTCTC
*
149568 AAAAGCACTTTTG
1 AAAAGCACTTCTG
* *
149581 AAAAGTACTTCTC
1 AAAAGCACTTCTG
149594 AAAAGCACTTCTG
1 AAAAGCACTTCTG
*
149607 AAAAGCACTTCTC
1 AAAAGCACTTCTG
*
149620 AAAAGCACTTCTC
1 AAAAGCACTTCTG
149633 AAAAGCA
1 AAAAGCA
149640 ATGAAGAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24
Consensus pattern (13 bp):
AAAAGCACTTCTG
Found at i:149593 original size:26 final size:26
Alignment explanation
Indices: 149564--149639 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
149554 CACTCAAATG
* *
149564 TCTCAAAAGCACTTTTGAAAAGTACT
1 TCTCAAAAGCACTTCTGAAAAGCACT
149590 TCTCAAAAGCACTTCTGAAAAGCACT
1 TCTCAAAAGCACTTCTGAAAAGCACT
*
149616 TCTCAAAAGCACTTCTCAAAAGCA
1 TCTCAAAAGCACTTCTGAAAAGCA
149640 ATGAAGAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (26 bp):
TCTCAAAAGCACTTCTGAAAAGCACT
Found at i:170527 original size:20 final size:19
Alignment explanation
Indices: 170486--170531 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
170476 GTATTATATT
*
170486 AAATATTTATCTAATGTTC
1 AAATATTTATCCAATGTTC
*
170505 AAATATTTATCCCAATTTTC
1 AAATATTTAT-CCAATGTTC
170525 AAA-ATTT
1 AAATATTT
170532 TGTATGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (19 bp):
AAATATTTATCCAATGTTC
Found at i:171581 original size:19 final size:19
Alignment explanation
Indices: 171550--171589 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
171540 ATATGTCATA
*
171550 TTAATAAATAATTTAAAAT
1 TTAATAAATAATTCAAAAT
171569 TTAA-AAATAAATTCAAAAT
1 TTAATAAAT-AATTCAAAAT
171588 TT
1 TT
171590 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATAAATAATTCAAAAT
Found at i:180965 original size:19 final size:21
Alignment explanation
Indices: 180927--180967 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
180917 TTAATAGTTC
180927 AATAATTTGAATAAATTTTTTA
1 AATAATTTGAAT-AATTTTTTA
180949 AATAATTT-AAT-ATTTTTTA
1 AATAATTTGAATAATTTTTTA
180968 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATAATTTGAATAATTTTTTA
Found at i:185049 original size:17 final size:17
Alignment explanation
Indices: 185029--185073 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
185019 GCCTTATCAG
185029 TAATATTAATTTATAAA
1 TAATATTAATTTATAAA
*
185046 TAATATT-A-TCATAAA
1 TAATATTAATTTATAAA
185061 TAAT-TTAAGTTTA
1 TAATATTAA-TTTA
185074 ATCAACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 1 0.04
17 9 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TAATATTAATTTATAAA
Found at i:185693 original size:34 final size:34
Alignment explanation
Indices: 185629--185693 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
185619 TGTATAAAAA
* *
185629 AAATTAAAATTTCATATATATATTTTTTTACACT
1 AAATTAAAATTTCATATATATATATATTTACACT
185663 AAATTAAAAATTT-ATATATATATATATTTAC
1 AAATT-AAAATTTCATATATATATATATTTAC
185694 TTTTTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (34 bp):
AAATTAAAATTTCATATATATATATATTTACACT
Found at i:194731 original size:47 final size:47
Alignment explanation
Indices: 194678--194771 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
194668 GTACATGTTG
194678 GGAAAAAACAGAGGGCGCAGAACATGCATATCAAAATAAACTAACCT
1 GGAAAAAACAGAGGGCGCAGAACATGCATATCAAAATAAACTAACCT
194725 GGAAAAAACAGAGGGCGCAGAACATGCATATCAAAATAAACTAACCT
1 GGAAAAAACAGAGGGCGCAGAACATGCATATCAAAATAAACTAACCT
194772 CAAAAGAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (47 bp):
GGAAAAAACAGAGGGCGCAGAACATGCATATCAAAATAAACTAACCT
Found at i:201420 original size:24 final size:24
Alignment explanation
Indices: 201373--201421 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
201363 CGGTGTTTCT
*
201373 CATTAATTGCTCTTCGGAGATACC
1 CATTAATTGCTCTTCAGAGATACC
* * *
201397 CATTAATTGCTTTTTAGAGCTACC
1 CATTAATTGCTCTTCAGAGATACC
201421 C
1 C
201422 GTTATAGGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (24 bp):
CATTAATTGCTCTTCAGAGATACC
Found at i:205723 original size:13 final size:13
Alignment explanation
Indices: 205691--205732 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
205681 TCTCTTGATG
* *
205691 AATGAAAACAAAA
1 AATGAAAATAATA
*
205704 AACGAAAATAATA
1 AATGAAAATAATA
205717 AATG-AAATAATA
1 AATGAAAATAATA
205729 AATG
1 AATG
205733 CTGGAGATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.17
Consensus pattern (13 bp):
AATGAAAATAATA
Found at i:212188 original size:31 final size:31
Alignment explanation
Indices: 212143--212296 Score: 96
Period size: 31 Copynumber: 4.6 Consensus size: 31
212133 AAATTGAATC
212143 AAATTAAAATTTTATGTATAAAATTACACAAT
1 AAATTAAAA-TTTATGTATAAAATTACACAAT
*
212175 AAATCAAAATTTATGTATAGTTTTAATATTTATCAC-AT
1 AAATTAAAATTTATGTATA-----AA-A-TTA-CACAAT
* * * * * *
212213 TATTTATTAATTTAT-TGATAAAAATAAAAGAAT
1 AAATTA-AAATTTATGT-AT-AAAATTACACAAT
*
212246 CAAATTAAATTTTATGTATAAAATTACACAAT
1 -AAATTAAAATTTATGTATAAAATTACACAAT
*
212278 AAATCAAAATTTATGTATA
1 AAATTAAAATTTATGTATA
212297 GTTTTAATAT
Statistics
Matches: 91, Mismatches: 17, Indels: 29
0.66 0.12 0.21
Matches are distributed among these distances:
31 27 0.30
32 19 0.21
33 12 0.13
34 6 0.07
35 2 0.02
36 2 0.02
37 1 0.01
38 9 0.10
39 12 0.13
40 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (31 bp):
AAATTAAAATTTATGTATAAAATTACACAAT
Found at i:212264 original size:103 final size:104
Alignment explanation
Indices: 212138--212344 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 104
212128 TATAAAAATT
212138 GAATCAAATTAAAATTTTATGTATAAAATTACACAATAAATCAAAATTTATGTATAGTTTTAATA
1 GAATCAAATTAAAATTTTATGTATAAAATTACACAATAAATCAAAATTTATGTATAGTTTTAATA
212203 TTTATCACATTATTTATTAATTTATTGATAAAAATAAAA
66 TTTATCACATTATTTATTAATTTATTGATAAAAATAAAA
212242 GAATCAAATT-AAATTTTATGTATAAAATTACACAATAAATCAAAATTTATGTATAGTTTTAATA
1 GAATCAAATTAAAATTTTATGTATAAAATTACACAATAAATCAAAATTTATGTATAGTTTTAATA
212306 TTTATCACATTATTTATTAATTTATTGATAAAAATAAAA
66 TTTATCACATTATTTATTAATTTATTGATAAAAATAAAA
212345 AAACAATTTA
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 93 0.90
104 10 0.10
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (104 bp):
GAATCAAATTAAAATTTTATGTATAAAATTACACAATAAATCAAAATTTATGTATAGTTTTAATA
TTTATCACATTATTTATTAATTTATTGATAAAAATAAAA
Found at i:233029 original size:98 final size:99
Alignment explanation
Indices: 232894--233094 Score: 395
Period size: 98 Copynumber: 2.0 Consensus size: 99
232884 TAAGTCCCAA
232894 AATTATTGTTTTAGAATTTTTTTAAAAATTTTAACTTTTTTTTACATATTCTTTAGAATTTTTTA
1 AATTATTGTTTTAGAATTTTTTTAAAAATTTTAACTTTTTTTTACATATTCTTTAGAATTTTTTA
232959 GAATTTATACTTTTTTAAATTTTATTAAAAATAT
66 GAATTTATACTTTTTTAAATTTTATTAAAAATAT
232993 AATTATTGTTTTA-AATTTTTTTAAAAATTTTAACTTTTTTTTACATATTCTTTAGAATTTTTTA
1 AATTATTGTTTTAGAATTTTTTTAAAAATTTTAACTTTTTTTTACATATTCTTTAGAATTTTTTA
233057 GAATTTATACTTTTTTAAATTTTATTAAAAATAT
66 GAATTTATACTTTTTTAAATTTTATTAAAAATAT
233091 AATT
1 AATT
233095 TTTAGAATTT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 89 0.87
99 13 0.13
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (99 bp):
AATTATTGTTTTAGAATTTTTTTAAAAATTTTAACTTTTTTTTACATATTCTTTAGAATTTTTTA
GAATTTATACTTTTTTAAATTTTATTAAAAATAT
Found at i:233123 original size:19 final size:20
Alignment explanation
Indices: 233094--233146 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
233084 AAAATATAAT
*
233094 TTTTAGAATTTTTAGAAAT-A
1 TTTT-GAATTTTTAAAAATCA
233114 TTTTGAATTTTTAAAAATCA
1 TTTTGAATTTTTAAAAATCA
233134 TTTTGAATCTTTT
1 TTTTGAAT-TTTT
233147 TTGTAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 13 0.43
21 4 0.13
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATCA
Found at i:233754 original size:24 final size:24
Alignment explanation
Indices: 233727--233772 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
233717 TTATAAAAGT
*
233727 AAGAGATCAATTTGTTAAATTTCA
1 AAGAGAACAATTTGTTAAATTTCA
*
233751 AAGATAACAATTTGTTAAATTT
1 AAGAGAACAATTTGTTAAATTT
233773 GAATATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (24 bp):
AAGAGAACAATTTGTTAAATTTCA
Found at i:239989 original size:26 final size:25
Alignment explanation
Indices: 239947--239995 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
239937 TTTTAAAAAG
*
239947 TAATTTTTATAGCATGAGATTTTTA
1 TAATTTTTATAGCATGAAATTTTTA
*
239972 TAATTTTTATAGTTATGAAATTTT
1 TAATTTTTATAG-CATGAAATTTT
239996 GAAAGGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (25 bp):
TAATTTTTATAGCATGAAATTTTTA
Found at i:240271 original size:12 final size:12
Alignment explanation
Indices: 240254--240279 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
240244 AAATAGAATT
240254 AAATTATTGAAG
1 AAATTATTGAAG
240266 AAATTATTGAAG
1 AAATTATTGAAG
240278 AA
1 AA
240280 TGATACAAAT
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AAATTATTGAAG
Found at i:246531 original size:5 final size:5
Alignment explanation
Indices: 246523--246561 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
246513 TTAAGTTAAA
* *
246523 TATAT TATAT TATAT TATAT CATAT TATAC TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
246562 GAGTAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:246549 original size:20 final size:20
Alignment explanation
Indices: 246524--246561 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
246514 TAAGTTAAAT
*
246524 ATATTATATTATATTATATC
1 ATATTATACTATATTATATC
246544 ATATTATACTATATTATA
1 ATATTATACTATATTATA
246562 GAGTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATACTATATTATATC
Found at i:251798 original size:221 final size:222
Alignment explanation
Indices: 251407--251850 Score: 881
Period size: 221 Copynumber: 2.0 Consensus size: 222
251397 AAACAAAGAA
251407 ATATTATAAAATAATTATTTAATATTTAATTTTATATTTTTTTATTATCAGTTGATTAATGTAAA
1 ATATTATAAAATAATTATTTAATATTTAATTTTATATTTTTTTATTATCAGTTGATTAATGTAAA
251472 TTTTGAAACACCTAAGAATTTAAGATGGTTAGATTTTTCCCTAACTACTAATGTAATTTACATTC
66 TTTTGAAACACCTAAGAATTTAAGATGGTTAGATTTTTCCCTAACTACTAATGTAATTTACATTC
251537 TTTTCTTTTTAATTATTGCATCGTTTTAATTAAGTAGAAGTGTTCATAGTTTGAAGGTCTAGGAT
131 TTTTCTTTTTAATTATTGCATCGTTTTAATTAAGTAGAAGTGTTCATAGTTTGAAGGTCTAGGAT
251602 GAGTTTGAATGAGCAGTGAAGTGCGGT
196 GAGTTTGAATGAGCAGTGAAGTGCGGT
251629 ATATTAT-AAATAATTATTTAATATTTAATTTTATATTTTTTTATTATCAGTTGATTAATGTAAA
1 ATATTATAAAATAATTATTTAATATTTAATTTTATATTTTTTTATTATCAGTTGATTAATGTAAA
251693 TTTTGAAACACCTAAGAATTTAAGATGGTTAGATTTTTCCCTAACTACTAATGTAATTTACATTC
66 TTTTGAAACACCTAAGAATTTAAGATGGTTAGATTTTTCCCTAACTACTAATGTAATTTACATTC
251758 TTTTCTTTTTAATTATTGCATCGTTTTAATTAAGTAGAAGTGTTCATAGTTTGAAGGTCTAGGAT
131 TTTTCTTTTTAATTATTGCATCGTTTTAATTAAGTAGAAGTGTTCATAGTTTGAAGGTCTAGGAT
251823 GAGTTTGAATGAGCAGTGAAGTGCGGT
196 GAGTTTGAATGAGCAGTGAAGTGCGGT
251850 A
1 A
251851 CGGTTAATTT
Statistics
Matches: 222, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
221 215 0.97
222 7 0.03
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (222 bp):
ATATTATAAAATAATTATTTAATATTTAATTTTATATTTTTTTATTATCAGTTGATTAATGTAAA
TTTTGAAACACCTAAGAATTTAAGATGGTTAGATTTTTCCCTAACTACTAATGTAATTTACATTC
TTTTCTTTTTAATTATTGCATCGTTTTAATTAAGTAGAAGTGTTCATAGTTTGAAGGTCTAGGAT
GAGTTTGAATGAGCAGTGAAGTGCGGT
Found at i:254627 original size:30 final size:28
Alignment explanation
Indices: 254579--254648 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 28
254569 TTTTTATAAA
*
254579 AATTTA-AACATTTCAAATATGTTTTATT
1 AATTTATAAGATTTCAAATATGTTTTA-T
* *
254607 AATTTTATAAGATTTTAAATATTTTTTAT
1 AA-TTTATAAGATTTCAAATATGTTTTAT
*
254636 AATTTATCAGATT
1 AATTTATAAGATT
254649 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.33
29 7 0.19
30 17 0.47
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
AATTTATAAGATTTCAAATATGTTTTAT
Found at i:254654 original size:30 final size:31
Alignment explanation
Indices: 254588--254661 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 31
254578 AAATTTAAAC
*
254588 ATTTCAAATATGTTTTATTAATTTTATAAGAT
1 ATTT-AAATATTTTTTATTAATTTTATAAGAT
*
254620 -TTTAAATATTTTTTA-TAA-TTTATCAGATT
1 ATTTAAATATTTTTTATTAATTTTATAAGA-T
*
254649 ATTTAAAAATTTT
1 ATTTAAATATTTT
254662 ATAAGTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 8 0.22
29 4 0.11
30 22 0.59
31 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (31 bp):
ATTTAAATATTTTTTATTAATTTTATAAGAT
Found at i:267695 original size:49 final size:49
Alignment explanation
Indices: 267623--267722 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
267613 TTGTCATTTT
*
267623 GCTGTCTTGGTTTTCATAGCTATCGATTGGTGTGATCATCAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
* *
267672 GCTGTCTTGGTTTTTATAGCTATCAATTGGTGTGATCATTAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
267721 GC
1 GC
267723 ATTCATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (49 bp):
GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
Found at i:278745 original size:22 final size:21
Alignment explanation
Indices: 278705--278745 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
278695 CTGAAAAAAA
* *
278705 AGGGTTATGAACCGCAAAATT
1 AGGGTTATGAACAGAAAAATT
278726 AGGGATTATGAACAGAAAAA
1 AGGG-TTATGAACAGAAAAA
278746 GACCCTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (21 bp):
AGGGTTATGAACAGAAAAATT
Found at i:282135 original size:3 final size:3
Alignment explanation
Indices: 282127--282162 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
282117 ATGAAAACTT
*
282127 TGA TGA TGA TGA TGA TGA TGA AGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
282163 GAGATATGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:282355 original size:15 final size:15
Alignment explanation
Indices: 282335--282363 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
282325 AGCTTTTTGC
282335 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
282350 TTTATTTTTTATTT
1 TTTATTTTTTATTT
282364 GCATGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTATTTTTTATTTT
Found at i:284872 original size:2 final size:2
Alignment explanation
Indices: 284865--284899 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
284855 TTCCAAAAGC
284865 TA TA TA TA TA TA TA TA 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 TA T
284900 GCAANNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:293593 original size:13 final size:13
Alignment explanation
Indices: 293575--293600 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293565 ATTAGAGAGG
293575 AATATGTATATAT
1 AATATGTATATAT
293588 AATATGTATATAT
1 AATATGTATATAT
293601 CATTTGTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AATATGTATATAT
Found at i:294172 original size:27 final size:25
Alignment explanation
Indices: 294124--294175 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
294114 ATAAATAATT
*
294124 TAAAAATTATAAATATTCAAAAAAA
1 TAAAAATTATAAACATTCAAAAAAA
*
294149 TAAAAAGTTCATAAACATTTAAAAAAA
1 TAAAAA-TT-ATAAACATTCAAAAAAA
294176 AATCATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 15 0.65
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAAAATTATAAACATTCAAAAAAA
Found at i:294692 original size:25 final size:24
Alignment explanation
Indices: 294658--294704 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
294648 ACATTATAAG
* *
294658 TCATTTAATTATGGATTATTTTTTA
1 TCATTCAATTATGAATT-TTTTTTA
294683 TCATTCAATTATGAATTTTTTT
1 TCATTCAATTATGAATTTTTTT
294705 AAAATTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (24 bp):
TCATTCAATTATGAATTTTTTTTA
Found at i:320643 original size:28 final size:28
Alignment explanation
Indices: 320582--320645 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
320572 GAAACCGAAC
* *
320582 TAAATTTTATTTTTTATTTAATATATAA
1 TAAATTTTATTTTTTATATAATATAAAA
*
320610 TTAATTTTACTTTTTTATGAT-ATA-AAAA
1 TAAATTTTA-TTTTTTAT-ATAATATAAAA
320638 TAAATTTT
1 TAAATTTT
320646 TATATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 18 0.60
29 11 0.37
30 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TAAATTTTATTTTTTATATAATATAAAA
Found at i:321637 original size:24 final size:25
Alignment explanation
Indices: 321610--321661 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
321600 CGTTCCCATG
*
321610 TAAATATTAAAATATAAATTAG-TA
1 TAAATATTAAAATAAAAATTAGATA
*
321634 TAAATATTAATATAAAAATTAGATA
1 TAAATATTAAAATAAAAATTAGATA
321659 TAA
1 TAA
321662 TGATAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
TAAATATTAAAATAAAAATTAGATA
Found at i:321765 original size:16 final size:16
Alignment explanation
Indices: 321744--321776 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
321734 TTAAATTTTA
321744 TAATTTTTTAGAAATT
1 TAATTTTTTAGAAATT
321760 TAATTTTTTAGAAATT
1 TAATTTTTTAGAAATT
321776 T
1 T
321777 GAGTTGTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TAATTTTTTAGAAATT
Found at i:325031 original size:12 final size:12
Alignment explanation
Indices: 325014--325039 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
325004 TCCACCTTGA
325014 AATAAACTGTGC
1 AATAAACTGTGC
325026 AATAAACTGTGC
1 AATAAACTGTGC
325038 AA
1 AA
325040 AATGCCTTGA
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (12 bp):
AATAAACTGTGC
Found at i:326943 original size:21 final size:21
Alignment explanation
Indices: 326919--326971 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
326909 ATTAAAAATT
326919 TTAAAATTTTCGAGGCACTAA
1 TTAAAATTTTCGAGGCACTAA
*
326940 TTAAAATTTTCGAGGCGCTAA
1 TTAAAATTTTCGAGGCACTAA
326961 TTAAAATTTTC
1 TTAAAATTTTC
326972 AAATATTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (21 bp):
TTAAAATTTTCGAGGCACTAA
Found at i:327071 original size:21 final size:21
Alignment explanation
Indices: 327034--327077 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
327024 AAAAACTTTT
* *
327034 AAAATTTGAAGAGTTTATTAA
1 AAAATTTCAAGAGTTTATGAA
327055 AAAATTTCAA-AGCTTTATGAA
1 AAAATTTCAAGAG-TTTATGAA
327076 AA
1 AA
327078 CTTAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (21 bp):
AAAATTTCAAGAGTTTATGAA
Found at i:340834 original size:2 final size:2
Alignment explanation
Indices: 340827--340872 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
340817 AGTATGGGTC
* * *
340827 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
340869 AT AT
1 AT AT
340873 TTTAGAAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
AT
Found at i:343397 original size:94 final size:95
Alignment explanation
Indices: 343236--343425 Score: 373
Period size: 94 Copynumber: 2.0 Consensus size: 95
343226 ATTCAAATTA
343236 TTTCTTCTTTTCTTTTTATTAATTTTGTTGAAAGCAAATACAACTTTTAGATAAAAACTATATTT
1 TTTCTTCTTTTCTTTTTATTAATTTTGTTGAAAGCAAATACAACTTTTAGATAAAAACTATATTT
343301 ATCTCTTAAATATATATAT-TATATAAAAT
66 ATCTCTTAAATATATATATATATATAAAAT
343330 TTTCTTCTTTTCTTTTTATTAATTTTGTTGAAAGCAAATACAACTTTTAGATAAAAACTATATTT
1 TTTCTTCTTTTCTTTTTATTAATTTTGTTGAAAGCAAATACAACTTTTAGATAAAAACTATATTT
343395 ATCTCTTAAATATATATATATATATAAAAT
66 ATCTCTTAAATATATATATATATATAAAAT
343425 T
1 T
343426 GATAATTCAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 84 0.88
95 11 0.12
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (95 bp):
TTTCTTCTTTTCTTTTTATTAATTTTGTTGAAAGCAAATACAACTTTTAGATAAAAACTATATTT
ATCTCTTAAATATATATATATATATAAAAT
Found at i:349744 original size:20 final size:19
Alignment explanation
Indices: 349719--349764 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
349709 CGAAAAATGA
349719 TTTTTGGAAAATGGAATAGT
1 TTTTTGGAAAATGGAATA-T
* **
349739 TTTTTGAAAAATGTTATAT
1 TTTTTGGAAAATGGAATAT
349758 TTTTTGG
1 TTTTTGG
349765 TGTTTGATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (19 bp):
TTTTTGGAAAATGGAATAT
Found at i:360729 original size:37 final size:34
Alignment explanation
Indices: 360688--360756 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 34
360678 TTATTTAAAT
360688 TTAATTAA-TATTAATTAATTATAAAGATTATTAATTA
1 TTAATTAATTATT-ATTAA--ATAAA-ATTATTAATTA
*
360725 TTAATTAATTATTTTTAAATAAAATTATTAAT
1 TTAATTAATTATTATTAAATAAAATTATTAAT
360757 ATTTATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 9 0.30
35 5 0.17
37 12 0.40
38 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
TTAATTAATTATTATTAAATAAAATTATTAATTA
Found at i:360750 original size:27 final size:26
Alignment explanation
Indices: 360720--360770 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
360710 AAAGATTATT
*
360720 AATTATTAATTAATTATTTTTAAATAA
1 AATTATTAA-TAATTATTTATAAATAA
*
360747 AATTATTAATATTTATTTATAAAT
1 AATTATTAATAATTATTTATAAAT
360771 CTTCGACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTATTAATAATTATTTATAAATAA
Found at i:360869 original size:57 final size:57
Alignment explanation
Indices: 360805--360977 Score: 346
Period size: 57 Copynumber: 3.0 Consensus size: 57
360795 AATGATGATA
360805 TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
1 TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
360862 TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
1 TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
360919 TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
1 TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
360976 TC
1 TC
360978 ATATGATTAG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 116 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (57 bp):
TCGTACTATTATTTATGTGTATGAAACTTATACACTAACGACCCATCAAATATTTTT
Found at i:378951 original size:2 final size:2
Alignment explanation
Indices: 378946--378979 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
378936 TAAAACACAC
*
378946 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378980 TTGTGTGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:387446 original size:16 final size:16
Alignment explanation
Indices: 387425--387474 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
387415 TGAAAAGGAT
387425 ATTGAAAAAATAGAAA
1 ATTGAAAAAATAGAAA
* *
387441 ATTGAAAGAATAGGGAA
1 ATTGAAAAAATA-GAAA
387458 A-T-AAAAAGATAGAAA
1 ATTGAAAAA-ATAGAAA
387473 AT
1 AT
387475 ATAAATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.30
16 15 0.56
17 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (16 bp):
ATTGAAAAAATAGAAA
Found at i:389354 original size:30 final size:31
Alignment explanation
Indices: 389320--389386 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
389310 CTTAACACCC
* * * *
389320 AGTGATTTAAAT-AAATTTTTTGAATAGTTT
1 AGTGACTTAAATGAAAATTTTTAAAAAGTTT
389350 AGTGACTTAAATGAAAATTTTTAAAAAGTTT
1 AGTGACTTAAATGAAAATTTTTAAAAAGTTT
389381 AGTGAC
1 AGTGAC
389387 CATTTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (31 bp):
AGTGACTTAAATGAAAATTTTTAAAAAGTTT
Found at i:393376 original size:20 final size:20
Alignment explanation
Indices: 393347--393385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
393337 ATACCCTTCA
*
393347 AAATTTTTAAAAATTAAATT
1 AAATTCTTAAAAATTAAATT
*
393367 AAATTCTTAAAACTTAAAT
1 AAATTCTTAAAAATTAAAT
393386 AGCAAGATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTCTTAAAAATTAAATT
Found at i:395601 original size:156 final size:157
Alignment explanation
Indices: 395335--395647 Score: 619
Period size: 156 Copynumber: 2.0 Consensus size: 157
395325 GAGTCGAGTG
395335 ACAAAACCCAAGAATCAGCATATATACTAGGGGATGGAAAAATTTACATTTAGACCCTTTTAAAA
1 ACAAAACCCAAGAATCAGCATATATACTAGGGGATGGAAAAATTTACATTTAGACCCTTTTAAAA
395400 TTGATAAAAATTTAAATTAGTAAAGGTAAAATTGCACTTTAGCCCCCTAAAAATGATAAAAGTTT
66 TTGATAAAAATTTAAATTAGTAAAGGTAAAATTGCACTTTAGCCCCCTAAAAATGATAAAAGTTT
395465 GATTTAATCCTTT-AAAATTATAAAGA
131 GATTTAATCCTTTAAAAATTATAAAGA
395491 ACAAAACCCAAGAATCAGCATATATACTAGGGGATGGAAAAATTTACATTTAGACCCTTTTAAAA
1 ACAAAACCCAAGAATCAGCATATATACTAGGGGATGGAAAAATTTACATTTAGACCCTTTTAAAA
395556 TTGATAAAAATTTAAATTAGTAAAGGTAAAATTGCACTTTAGCCCCCTAAAAATGATAAAAGTTT
66 TTGATAAAAATTTAAATTAGTAAAGGTAAAATTGCACTTTAGCCCCCTAAAAATGATAAAAGTTT
395621 GATTTAATCCTTTAAAAATTATAAAGA
131 GATTTAATCCTTTAAAAATTATAAAGA
395648 TATAGATATT
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 143 0.92
157 13 0.08
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (157 bp):
ACAAAACCCAAGAATCAGCATATATACTAGGGGATGGAAAAATTTACATTTAGACCCTTTTAAAA
TTGATAAAAATTTAAATTAGTAAAGGTAAAATTGCACTTTAGCCCCCTAAAAATGATAAAAGTTT
GATTTAATCCTTTAAAAATTATAAAGA
Found at i:396595 original size:15 final size:17
Alignment explanation
Indices: 396565--396597 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
396555 TCATGACATA
396565 ATATCATTGAGGAATGC
1 ATATCATTGAGGAATGC
396582 ATATCA-TG-GGAATGC
1 ATATCATTGAGGAATGC
396597 A
1 A
396598 GCAGGGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (17 bp):
ATATCATTGAGGAATGC
Found at i:398332 original size:24 final size:24
Alignment explanation
Indices: 398300--398348 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
398290 GCATTGCTGA
398300 TTGCCTGATTGTACTATGTAAATG
1 TTGCCTGATTGTACTATGTAAATG
398324 TTGCCTGATTGTACTATGTAAATG
1 TTGCCTGATTGTACTATGTAAATG
398348 T
1 T
398349 AGTTATCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (24 bp):
TTGCCTGATTGTACTATGTAAATG
Found at i:406446 original size:25 final size:25
Alignment explanation
Indices: 406416--406467 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
406406 TTATTTACAC
406416 TTAGGAATTGATTCTGCTTCTCTTA
1 TTAGGAATTGATTCTGCTTCTCTTA
406441 TTAGGAATTGATTCTGCTTCTCTTA
1 TTAGGAATTGATTCTGCTTCTCTTA
406466 TT
1 TT
406468 CTACTTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (25 bp):
TTAGGAATTGATTCTGCTTCTCTTA
Found at i:417088 original size:69 final size:70
Alignment explanation
Indices: 416942--417118 Score: 223
Period size: 69 Copynumber: 2.5 Consensus size: 70
416932 ATCAGTAAAA
*
416942 CTAGCTAAATCTTACATTAATTTACAAAACATTAATCGACAAAACCCCGAAAAAAAGTAGTAAAT
1 CTAGCTAAATATTACATTAA-TTACAAAACATTAATCGACAAAACCCC-AAAAAAAGTAGTAAAT
417007 CGAGCTC
64 CGAGCTC
* * * * *
417014 GTAGCTAAATATTCCATTAATTACAGAACATTAGTCGATC-AAACCCC-AGAAAAGTAGTAAATC
1 CTAGCTAAATATTACATTAATTACAAAACATTAATCGA-CAAAACCCCAAAAAAAGTAGTAAATC
417077 GAGCTC
65 GAGCTC
* * *
417083 CTAGCTAAATTTTACATTAATTTCCCAAACATTAAT
1 CTAGCTAAATATTACATTAA-TTACAAAACATTAAT
417119 TGATAAACCC
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
69 38 0.42
70 11 0.12
71 23 0.26
72 18 0.20
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (70 bp):
CTAGCTAAATATTACATTAATTACAAAACATTAATCGACAAAACCCCAAAAAAAGTAGTAAATCG
AGCTC
Found at i:423021 original size:31 final size:30
Alignment explanation
Indices: 422949--423027 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
422939 TTTTTTCGGT
* *
422949 CTAATTTGGTACCCAAACTTGACATGTTTTC
1 CTAA-TTGGTACCTAAACTTGACATGTTCTC
422980 CTAATGTGGTACCTAAACTTGACACT-TTCTC
1 CTAAT-TGGTACCTAAACTTGACA-TGTTCTC
* *
423011 TTAAGTTGGTACTTAAA
1 CTAA-TTGGTACCTAAA
423028 ACTTTTTGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 38 0.93
32 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (30 bp):
CTAATTGGTACCTAAACTTGACATGTTCTC
Found at i:434309 original size:22 final size:22
Alignment explanation
Indices: 434269--434315 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
434259 TTAATATATT
*
434269 ATTTTTATTTGTACTTTGATAAA
1 ATTTTTATTTGTACATTGA-AAA
*
434292 ATTTTTATTT-TAGATTGAAAA
1 ATTTTTATTTGTACATTGAAAA
434313 ATT
1 ATT
434316 GATCTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
ATTTTTATTTGTACATTGAAAA
Found at i:439124 original size:21 final size:22
Alignment explanation
Indices: 439077--439124 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
439067 AATTTAATTT
*
439077 AAAAGAAAAAAAGTGATTGTCA
1 AAAAGAAAAAAAGTGATTATCA
* * *
439099 TAAAG-AAAAATGTGATTATTA
1 AAAAGAAAAAAAGTGATTATCA
439120 AAAAG
1 AAAAG
439125 TTGCTAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAAGAAAAAAAGTGATTATCA
Found at i:441661 original size:60 final size:60
Alignment explanation
Indices: 441547--441663 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 60
441537 AATTATTTTT
* *
441547 TTAAAATCGATAATCATTGGGTAATGATGATGAGTGATATCGCCGGACAGGTTGGCGGCA
1 TTAAAATCGATAATCATTGGGTAATGATGAGGAGTGATATCGCCGGACAAGTTGGCGGCA
*
441607 TTAAAATCGATAATCATTGGGTAATGATGAGGGGTGATATCGCC-GATCAAGTTGGCG
1 TTAAAATCGATAATCATTGGGTAATGATGAGGAGTGATATCGCCGGA-CAAGTTGGCG
441664 ACACCGATAG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
59 2 0.04
60 51 0.96
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (60 bp):
TTAAAATCGATAATCATTGGGTAATGATGAGGAGTGATATCGCCGGACAAGTTGGCGGCA
Found at i:446082 original size:19 final size:19
Alignment explanation
Indices: 446054--446092 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
446044 ATTTAAACTT
446054 TCATTCCATTTCATAATCA
1 TCATTCCATTTCATAATCA
* *
446073 TCATTTCATTTCATATTCA
1 TCATTCCATTTCATAATCA
446092 T
1 T
446093 TTAACATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (19 bp):
TCATTCCATTTCATAATCA
Found at i:446112 original size:28 final size:29
Alignment explanation
Indices: 446075--446166 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 29
446065 CATAATCATC
446075 ATTT-CATTTCATATTCATTTAACATTTA
1 ATTTACATTTCATATTCATTTAACATTTA
* * * *
446103 ATTTA-TTTTCATGTTTA-TT-ACAAATTA
1 ATTTACATTTCATATTCATTTAAC-ATTTA
*
446130 CA-TTACATTTCATATTCATTTAACATTTC
1 -ATTTACATTTCATATTCATTTAACATTTA
446159 ATTT-CATT
1 ATTTACATT
446167 AATTTTTTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
26 2 0.04
27 9 0.19
28 28 0.58
29 7 0.15
30 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTTACATTTCATATTCATTTAACATTTA
Found at i:446176 original size:18 final size:19
Alignment explanation
Indices: 446155--446195 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
446145 TCATTTAACA
*
446155 TTTCATTT-CATTAATTTT
1 TTTCATTTAAATTAATTTT
*
446173 TTTCATTTAAATTTATTTT
1 TTTCATTTAAATTAATTTT
446192 TTTC
1 TTTC
446196 CTAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCATTTAAATTAATTTT
Found at i:446368 original size:21 final size:21
Alignment explanation
Indices: 446326--446368 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
446316 TATCAGGGTC
*
446326 ATTTAAAATTTTTCATATTTT
1 ATTTAAAATTTTTCATAATTT
*
446347 ATTTAAATTTTTTC-TAAATTT
1 ATTTAAAATTTTTCAT-AATTT
446368 A
1 A
446369 AATATCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAAATTTTTCATAATTT
Found at i:449152 original size:18 final size:18
Alignment explanation
Indices: 449129--449185 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
449119 TGTACTTTCA
449129 AATATTTATACCCATCAT
1 AATATTTATACCCATCAT
* *
449147 AATATTTAGATTCACGATTCA-
1 AATATTT--ATAC-CCA-TCAT
449168 AATATTTATACCCATCAT
1 AATATTTATACCCATCAT
449186 TATGGGGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
17 3 0.10
18 9 0.30
19 3 0.10
20 3 0.10
21 9 0.30
22 3 0.10
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (18 bp):
AATATTTATACCCATCAT
Found at i:450820 original size:17 final size:18
Alignment explanation
Indices: 450776--450820 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
450766 CACATGCACG
450776 TTTTAAAATACACATGTT
1 TTTTAAAATACACATGTT
*
450794 TTTCAAAATACACAT-TT
1 TTTTAAAATACACATGTT
*
450811 TTTTATAATA
1 TTTTAAAATA
450821 GATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTTAAAATACACATGTT
Found at i:456491 original size:3 final size:3
Alignment explanation
Indices: 456483--456538 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
456473 ACATTATAAA
456483 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
456531 TCT TCT TC
1 TCT TCT TC
456539 ACTGTACAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:459860 original size:43 final size:43
Alignment explanation
Indices: 459807--460033 Score: 339
Period size: 43 Copynumber: 5.3 Consensus size: 43
459797 AAAAAAAATA
*
459807 CCGCTAAAGACCAAGTCCTTTAGCGGCGCTTTTCCCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* *
459850 CCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAAAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* * * *
459893 CCGCCAGAGACCAAGACCTTTAGCGGCG-TTTTCCCAAAAACA
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
**
459935 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* * *
459978 TCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
460021 CCGCTAAAGACCA
1 CCGCTAAAGACCA
460034 CNNNNNNNNN
Statistics
Matches: 163, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 39 0.24
43 124 0.76
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (43 bp):
CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
Found at i:459948 original size:128 final size:128
Alignment explanation
Indices: 459800--460033 Score: 387
Period size: 128 Copynumber: 1.8 Consensus size: 128
459790 TTTTAGAAAA
* * *
459800 AAAAATACCGCTAAAGACCAAGTCCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATG
1 AAAAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCATG
*
459865 ACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCCAGAGACCAAGACCTTTAGCGGCGTTTTCCC
66 ACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCCAAAGACCAAGACCTTTAGCGGCGTTTTCCC
* * *
459928 AAAAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACGTCGCTATAGACCATG
1 AAAAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCATG
* *
459993 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA
66 ACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCCAAAGACCA
460034 CNNNNNNNNN
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
128 97 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (128 bp):
AAAAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCATG
ACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCCAAAGACCAAGACCTTTAGCGGCGTTTTCCC
Found at i:459953 original size:85 final size:86
Alignment explanation
Indices: 459814--460033 Score: 334
Period size: 85 Copynumber: 2.6 Consensus size: 86
459804 ATACCGCTAA
* *
459814 AGACCAAGTCCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
1 AGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC
*
459879 TTTTCCCAAAAACGCCGCCAG
66 TTTTACCAAAAACGCCGCCAG
* *
459900 AGACCAAGACCTTTAGCGGCG-TTTTCCCAAAAACACCGCTAAAGACCAAGACCTTTAGCGGCGC
1 AGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC
* * * * *
459964 TTTTATCACAAACGTCGCTAT
66 TTTTACCAAAAACGCCGCCAG
*
459985 AGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA
1 AGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA
460034 CNNNNNNNNN
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
85 75 0.62
86 45 0.38
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (86 bp):
AGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC
TTTTACCAAAAACGCCGCCAG
Found at i:460826 original size:23 final size:23
Alignment explanation
Indices: 460776--460827 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
460766 GTTAGGTGTC
* *
460776 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
460799 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
460822 AGTATG
1 AGTATG
460828 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:462653 original size:41 final size:41
Alignment explanation
Indices: 462590--462870 Score: 363
Period size: 41 Copynumber: 6.9 Consensus size: 41
462580 AATATTTTTT
* *
462590 GCGGCGCTT-TTCTAAAAACGCCGCTAAAG-CCCTGAGCATTA
1 GCGGCGCTTCCTC-AAAAACGCCGCTAAAGACCC-AAGCATTA
* *
462631 GCAGCGCTTCCTCAAAACCGCCGCTAAAGACCCAAGCATTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAAGCATTA
*
462672 GCGGCGCTTCCTCAAAAACGCCGCTAAAGACACAAGCATTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAAGCATTA
* *
462713 GAGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAATCATTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAAGCATTA
* *
462754 GCGGCGATTCTTCAAAAACGCCGCTAAAGACCCAAGCATTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAAGCATTA
** *
462795 GCGGCGCTTTTTCAAAAACGCCGCTAAA-ACCCTGAGCATTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAAGACCC-AAGCATTA
* * *
462836 GTGGCGCTT-CTGAAAAAACGCCGCTAAAGTCCCAA
1 GCGGCGCTTCCT-CAAAAACGCCGCTAAAGACCCAA
462871 AAACTCACAA
Statistics
Matches: 213, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
40 5 0.02
41 200 0.94
42 8 0.04
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAAGCATTA
Found at i:467397 original size:7 final size:7
Alignment explanation
Indices: 467385--467409 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
467375 ACAAACAATC
467385 TTAAATA
1 TTAAATA
467392 TTAAATA
1 TTAAATA
467399 TTAAATA
1 TTAAATA
467406 TTAA
1 TTAA
467410 TAATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAATA
Found at i:468238 original size:79 final size:79
Alignment explanation
Indices: 468107--468271 Score: 303
Period size: 79 Copynumber: 2.1 Consensus size: 79
468097 TTTTATTTTT
468107 TATATTTAGTAGGTCAATTGAGGCGTGTTTTCCGACTTTGGAGGTGGAATGGCTTCACAATATTT
1 TATATTTAGTAGGTCAATTGAGGCGTGTTTTCCGACTTTGGAGGTGGAATGGCTTCACAATATTT
*
468172 TATTCGGCTCAGCC
66 AATTCGGCTCAGCC
468186 TATATTTAGTAGGTCAATTGAGGCGTGTTTTCCGACTTTGGAGGTGGAATGGCTTCACAATATTT
1 TATATTTAGTAGGTCAATTGAGGCGTGTTTTCCGACTTTGGAGGTGGAATGGCTTCACAATATTT
*
468251 AATTGGGCTCAGCC
66 AATTCGGCTCAGCC
*
468265 TTTATTT
1 TATATTT
468272 GTTTGTTTTC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (79 bp):
TATATTTAGTAGGTCAATTGAGGCGTGTTTTCCGACTTTGGAGGTGGAATGGCTTCACAATATTT
AATTCGGCTCAGCC
Found at i:468303 original size:17 final size:17
Alignment explanation
Indices: 468277--468312 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
468267 TATTTGTTTG
468277 TTTTCTTAAAA-TATTT
1 TTTTCTTAAAATTATTT
468293 TTTTACTTAAAATTATTT
1 TTTT-CTTAAAATTATTT
468311 TT
1 TT
468313 GAGAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 7 0.39
18 7 0.39
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCTTAAAATTATTT
Found at i:469919 original size:12 final size:11
Alignment explanation
Indices: 469896--469929 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
469886 ATAGAAACCC
469896 AAAATAAAATA
1 AAAATAAAATA
469907 AAAATAGAAATA
1 AAAATA-AAATA
469919 AAAATATAAAT
1 AAAATA-AAAT
469930 TAAAGTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:480613 original size:22 final size:22
Alignment explanation
Indices: 480577--480632 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
480567 AAGATAATAA
* *
480577 AATAATAAAATATAT-TATTTT
1 AATAATTAAATTTATATATTTT
480598 -AT-ATTAATATTTATATATTTT
1 AATAATTAA-ATTTATATATTTT
480619 AATAATTAAATTTA
1 AATAATTAAATTTA
480633 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.14
20 7 0.24
21 6 0.21
22 7 0.24
23 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATAATTAAATTTATATATTTT
Found at i:481460 original size:13 final size:13
Alignment explanation
Indices: 481439--481463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
481429 ATTTATTGTT
481439 AATATTTAATTTC
1 AATATTTAATTTC
481452 AATATTTAATTT
1 AATATTTAATTT
481464 TTTATTTTGT
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTAATTTC
Found at i:486138 original size:14 final size:15
Alignment explanation
Indices: 486121--486153 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
486111 AATAAATTTG
486121 TTTCT-AAAAATCAT
1 TTTCTGAAAAATCAT
*
486135 TTTCTGAAAAGTCAT
1 TTTCTGAAAAATCAT
486150 TTTC
1 TTTC
486154 GACCCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTCTGAAAAATCAT
Found at i:487110 original size:45 final size:43
Alignment explanation
Indices: 487047--487198 Score: 196
Period size: 43 Copynumber: 3.5 Consensus size: 43
487037 GCAGCGTTTA
* *
487047 CAAAAATAAACGCTGCTAAAGGTCATGTTCTTTAGCGGCGCTT
1 CAAAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTT
*
487090 CAAAAAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGGGCTT
1 C--AAAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTT
* * *
487135 CAAAAAAAAACGTCGCTAAAGGTCATGTTCTTTAGTGGCGATT
1 CAAAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTT
* ** *
487178 CTACGACAAACGCCGCTAAAG
1 CAAAAAAAAACGCCGCTAAAG
487199 AACATGACAT
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
43 55 0.58
45 40 0.42
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
CAAAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTT
Found at i:487154 original size:43 final size:42
Alignment explanation
Indices: 487047--487174 Score: 184
Period size: 45 Copynumber: 2.9 Consensus size: 42
487037 GCAGCGTTTA
*
487047 CAAAAATAAACGCTGCTAAAGGTCATGTTCTTTAGCGGCGCTT
1 CAAAAAAAAACGC-GCTAAAGGTCATGTTCTTTAGCGGCGCTT
*
487090 CAAAAAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGGGCTT
1 C--AAAAAAAAACG-CGCTAAAGGTCATGTTCTTTAGCGGCGCTT
*
487135 CAAAAAAAAACGTCGCTAAAGGTCATGTTCTTTAGTGGCG
1 CAAAAAAAAACG-CGCTAAAGGTCATGTTCTTTAGCGGCG
487175 ATTCTACGAC
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
43 37 0.48
45 39 0.51
46 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (42 bp):
CAAAAAAAAACGCGCTAAAGGTCATGTTCTTTAGCGGCGCTT
Found at i:487255 original size:43 final size:42
Alignment explanation
Indices: 487099--487252 Score: 123
Period size: 43 Copynumber: 3.6 Consensus size: 42
487089 TCAAAAAAAA
* * * * * * * *
487099 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGGGCTTCAAAAAA
1 AAACGTCGCTAAAGATCATGTTCTTTAGTGGCGATAC-ACAAC
* * *
487142 AAACGTCGCTAAAGGTCATGTTCTTTAGTGGCGATTCTACGAC
1 AAACGTCGCTAAAGATCATGTTCTTTAGTGGCGATAC-ACAAC
* * *
487185 AAACGCCGCTAAAGAACATG-ACATTTAGTGGCGCATAC-CAAC
1 AAACGTCGCTAAAGATCATGTTC-TTTAGTGGCG-ATACACAAC
*
487227 AAACGTCGCTAAAGCTCATGTTCTTT
1 AAACGTCGCTAAAGATCATGTTCTTT
487253 TAGCGGAGCC
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 24 0.27
43 63 0.70
44 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (42 bp):
AAACGTCGCTAAAGATCATGTTCTTTAGTGGCGATACACAAC
Found at i:487768 original size:21 final size:21
Alignment explanation
Indices: 487744--487785 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
487734 ATTTCTTTTG
487744 AACCTCTACTTCTCC-CGCTGC
1 AACCTCTACTTC-CCTCGCTGC
*
487765 AACCTCTGCTTCCCTCGCTGC
1 AACCTCTACTTCCCTCGCTGC
487786 CGCCTCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.12, C:0.48, G:0.12, T:0.29
Consensus pattern (21 bp):
AACCTCTACTTCCCTCGCTGC
Found at i:488951 original size:9 final size:9
Alignment explanation
Indices: 488934--489045 Score: 82
Period size: 9 Copynumber: 13.2 Consensus size: 9
488924 TAAGTATAAT
*
488934 TAAGCTATG
1 TAAGTTATG
488943 TAAGTTATG
1 TAAGTTATG
488952 TAAGTTATG
1 TAAGTTATG
488961 T-A-TTATG
1 TAAGTTATG
488968 TAAGTTATG
1 TAAGTTATG
488977 T-A-TTATG
1 TAAGTTATG
*
488984 -AATATTATG
1 TAA-GTTATG
*
488993 TAAGTTGTG
1 TAAGTTATG
489002 -AA-TTATG
1 TAAGTTATG
**
489009 TAAGTGCTG
1 TAAGTTATG
489018 T-A-TTATG
1 TAAGTTATG
489025 ATCAA-TTATG
1 -T-AAGTTATG
489035 TAAGTTATG
1 TAAGTTATG
489044 TA
1 TA
489046 TTGTCGAAAC
Statistics
Matches: 83, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
7 19 0.23
8 11 0.13
9 45 0.54
10 8 0.10
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:488967 original size:25 final size:24
Alignment explanation
Indices: 488939--489010 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 24
488929 ATAATTAAGC
488939 TATGTAAGTTATGTAAGTTATGTAT
1 TATGTAAGTTATGTAA-TTATGTAT
488964 TATGTAAGTTATGT-ATTATGAATAT
1 TATGTAAGTTATGTAATTATG--TAT
*
488989 TATGTAAGTTGTG-AATTATGTA
1 TATGTAAGTTATGTAATTATGTA
489011 AGTGCTGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 7 0.16
24 1 0.02
25 35 0.81
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (24 bp):
TATGTAAGTTATGTAATTATGTAT
Found at i:488968 original size:16 final size:16
Alignment explanation
Indices: 488947--488983 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
488937 GCTATGTAAG
488947 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
488963 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
488979 TTATG
1 TTATG
488984 AATATTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:488992 original size:41 final size:41
Alignment explanation
Indices: 488939--489047 Score: 141
Period size: 41 Copynumber: 2.6 Consensus size: 41
488929 ATAATTAAGC
*
488939 TATG-TAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAT
1 TATGATAA-TTATGTAAGTTATGTATTATGTAAGTGATGTAT
* * *
488980 TATGA-ATATTATGTAAGTTGTGAATTATGTAAGTGCTGTAT
1 TATGATA-ATTATGTAAGTTATGTATTATGTAAGTGATGTAT
489021 TATGATCAATTATGTAAGTTATGTATT
1 TATGAT-AATTATGTAAGTTATGTATT
489048 GTCGAAACCA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 39 0.67
42 18 0.31
43 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (41 bp):
TATGATAATTATGTAAGTTATGTATTATGTAAGTGATGTAT
Found at i:489022 original size:16 final size:16
Alignment explanation
Indices: 488947--489024 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 16
488937 GCTATGTAAG
*
488947 TTATGTAAGTTATGTA
1 TTATGTAAGTTGTGTA
*
488963 TTATGTAAGTTATGTA
1 TTATGTAAGTTGTGTA
488979 TTATG-AA------TA
1 TTATGTAAGTTGTGTA
*
488988 TTATGTAAGTTGTGAA
1 TTATGTAAGTTGTGTA
489004 TTATGTAAG-TGCTGTA
1 TTATGTAAGTTG-TGTA
489020 TTATG
1 TTATG
489025 ATCAATTATG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
9 7 0.13
10 2 0.04
15 4 0.08
16 39 0.75
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTGTGTA
Found at i:492259 original size:85 final size:85
Alignment explanation
Indices: 492107--492375 Score: 234
Period size: 98 Copynumber: 3.0 Consensus size: 85
492097 CCCAGTTGGC
* * * * ** ** **
492107 AAGACTTGATGCGATATGCTCTACTGCAACTTCAGAGAGATAAGATCGGTT-TCTTCTGTCTATT
1 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATCTT-AATCTGCT
*
492171 CCACTGTGATCTTAGGGAGAT
65 CCACTGTAATCTTAGGGAGAT
* *
492192 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCATTTATCTTAATCCGCTC
1 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATCTTAATCTGCTC
* *
492257 CACTGTAATCTCAGGGAAAT
66 CACTGTAATCTTAGGGAGAT
* *
492277 AAGATTTCTAGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA
1 AAGA---C------C--T-G-ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTA
* *
492342 TTTTAATCTGCTCCACTGTAATCATAGGGAGAT
53 TCTTAATCTGCTCCACTGTAATCTTAGGGAGAT
492375 A
1 A
492376 GGATTACTAG
Statistics
Matches: 147, Mismatches: 23, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
85 69 0.47
86 4 0.03
88 1 0.01
94 1 0.01
96 1 0.01
98 71 0.48
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (85 bp):
AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATCTTAATCTGCTC
CACTGTAATCTTAGGGAGAT
Found at i:492371 original size:98 final size:98
Alignment explanation
Indices: 492197--492395 Score: 310
Period size: 98 Copynumber: 2.0 Consensus size: 98
492187 GAGATAAGAC
492197 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCATTTATCTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCATTTATCTTAATCCGCTCCACTG
* *
492262 TAATCTCAGGGAAATAAGATTTCTAGTTTCAAT
66 TAATCTCAGGGAAATAAGATTACTAGCTTCAAT
* * * *
492295 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCATTTATCTTAATCCGCTCCACTG
* *
492360 TAATCAT-AGGGAGATAGGATTACTAGCTTCAAT
66 TAATC-TCAGGGAAATAAGATTACTAGCTTCAAT
492393 CTG
1 CTG
492396 CTCCGCTGTA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 91 0.99
99 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (98 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCATTTATCTTAATCCGCTCCACTG
TAATCTCAGGGAAATAAGATTACTAGCTTCAAT
Done.