Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014889.1 Kokia drynarioides strain JFW-HI SEQ_129932, 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: 229557
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 877 characters in sequence are not A, C, G, or T
Found at i:95 original size:14 final size:14
Alignment explanation
Indices: 51--95 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
41 AACTTGAACT
*
51 CCTAAACCCCAAAA
1 CCTAAACACCAAAA
* * *
65 CCCAAACTCTAAAA
1 CCTAAACACCAAAA
79 CCTAAACACCAAAA
1 CCTAAACACCAAAA
93 CCT
1 CCT
96 TGAACCCCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.11
Consensus pattern (14 bp):
CCTAAACACCAAAA
Found at i:2357 original size:20 final size:20
Alignment explanation
Indices: 2318--2374 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
2308 CGCACGCATG
* *
2318 CACACATGCACATACCCACC
1 CACACATGCACACACACACC
* *
2338 CACACTTGCACTCACACACC
1 CACACATGCACACACACACC
*
2358 CACCCATGCACACACAC
1 CACACATGCACACACAC
2375 TCGCTCACTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.51, G:0.05, T:0.11
Consensus pattern (20 bp):
CACACATGCACACACACACC
Found at i:2385 original size:8 final size:8
Alignment explanation
Indices: 2372--2398 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2362 CATGCACACA
2372 CACTCGCT
1 CACTCGCT
2380 CACTCGCT
1 CACTCGCT
2388 CACTCGCT
1 CACTCGCT
2396 CAC
1 CAC
2399 ATACACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.52, G:0.11, T:0.22
Consensus pattern (8 bp):
CACTCGCT
Found at i:2424 original size:40 final size:42
Alignment explanation
Indices: 2362--2459 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 42
2352 CACACCCACC
* * *
2362 CATGCACACACACTCGCTCACTCGCTCACTCGCTCACATACA
1 CATGCACACACACTCACACACTCACTCACTCGCTCACATACA
*
2404 CATGCACACACA-T-ACACACTCACTCTCTCGCTCACATACA
1 CATGCACACACACTCACACACTCACTCACTCGCTCACATACA
2444 CATGCACACACACTCA
1 CATGCACACACACTCA
2460 TTTTTAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 35 0.70
41 2 0.04
42 13 0.26
ACGTcount: A:0.31, C:0.44, G:0.07, T:0.18
Consensus pattern (42 bp):
CATGCACACACACTCACACACTCACTCACTCGCTCACATACA
Found at i:6388 original size:8 final size:8
Alignment explanation
Indices: 6375--6401 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6365 TGGAATTTAT
6375 AATATAAA
1 AATATAAA
6383 AATATAAA
1 AATATAAA
6391 AATATAAA
1 AATATAAA
6399 AAT
1 AAT
6402 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATATAAA
Found at i:6423 original size:27 final size:26
Alignment explanation
Indices: 6388--6439 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
6378 ATAAAAATAT
*
6388 AAAAATATAAAAATTATTTTTTTATA
1 AAAAATATAAAAATTATTTATTTATA
* *
6414 AAAAATTATATAATTTATTTATTTAT
1 AAAAA-TATAAAAATTATTTATTTAT
6440 TTAATACGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AAAAATATAAAAATTATTTATTTATA
Found at i:6624 original size:23 final size:24
Alignment explanation
Indices: 6593--6637 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6583 TCAACTTTAA
*
6593 AATTGTTAA-AAAAATATTAAAGC
1 AATTATTAAGAAAAATATTAAAGC
*
6616 AATTATTAAGAAAAGTATTAAA
1 AATTATTAAGAAAAATATTAAA
6638 AATACTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (24 bp):
AATTATTAAGAAAAATATTAAAGC
Found at i:10805 original size:20 final size:21
Alignment explanation
Indices: 10767--10805 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
10757 AAATAATCAC
*
10767 TTTTATTTACCTTAAGTTATA
1 TTTTAATTACCTTAAGTTATA
*
10788 TTTTAATTA-CTTACGTTA
1 TTTTAATTACCTTAAGTTA
10806 ACGTGTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTAATTACCTTAAGTTATA
Found at i:13974 original size:4 final size:4
Alignment explanation
Indices: 13965--14004 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
13955 TCAAAGTGAA
* *
13965 CTAT CTAT CTAT CTAT CTAT CCAT CTGT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
14005 ATATTCTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.23, C:0.28, G:0.03, T:0.47
Consensus pattern (4 bp):
CTAT
Found at i:22152 original size:170 final size:172
Alignment explanation
Indices: 21828--22152 Score: 364
Period size: 170 Copynumber: 1.9 Consensus size: 172
21818 GGAGTTTTGT
* *
21828 GGAGTAAAATTTTAGAGGGAAAATATTCAAAAAAATTTGGGAGGGGGGAATGGGTTTGGGTAGAT
1 GGAGTAAAATTTTAGAGGGAAAATATTCAAAAAAATTTGGGA-GGGGAAATGGGTTGGGGTAGAT
* * * * * *
21893 GGAGGATTGGATGGGAGGGAAGTAAAAGTTTCAAGAGGAAAATGAGATATAGTAAAAGTTTTGAG
65 GGAGGAGTGGATGGGAGAGAAGTAAAAATTTCAAGAGGAAAATGAGAAAGAGTAAAAGATTTGAG
* *
21958 GGAAAATGAAGAGTTTTGAGAGTTTTTGAGGAAAATAAATAAG
130 GGAAAATAAAAAGTTTTGAGAGTTTTTGAGGAAAATAAATAAG
*
22001 GGAGTAAAATTTTGGAGGGAAAATATT-AAAAAGAA-TT-GGA-GGGAAATGGGGTTGGGGTAGA
1 GGAGTAAAATTTTAGAGGGAAAATATTCAAAAA-AATTTGGGAGGGGAAAT-GGGTTGGGGTAGA
** *
22062 TGG-GG-GTGAGATGGGA-AGAGAGTAAAAATTTTGAG-GGAAAAAGTGTGAAAGAGTAAAAGAT
64 TGGAGGAGTG-GATGGGAGAGA-AGTAAAAATTTCAAGAGG-AAAA-TGAGAAAGAGTAAAAGAT
*
22123 TTGGGGGAAAAGTAAAAA-TGTTT-AGAGTTT
125 TTGAGGGAAAA-TAAAAAGT-TTTGAGAGTTT
22153 GGAGTAAAAA
Statistics
Matches: 129, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
168 6 0.05
169 31 0.24
170 47 0.36
171 10 0.08
172 7 0.05
173 28 0.22
ACGTcount: A:0.40, C:0.01, G:0.35, T:0.25
Consensus pattern (172 bp):
GGAGTAAAATTTTAGAGGGAAAATATTCAAAAAAATTTGGGAGGGGAAATGGGTTGGGGTAGATG
GAGGAGTGGATGGGAGAGAAGTAAAAATTTCAAGAGGAAAATGAGAAAGAGTAAAAGATTTGAGG
GAAAATAAAAAGTTTTGAGAGTTTTTGAGGAAAATAAATAAG
Found at i:22300 original size:14 final size:14
Alignment explanation
Indices: 22283--22320 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
22273 TTAATTCGAA
22283 TAACTCGATTCGTT
1 TAACTCGATTCGTT
22297 TAACTCGATTCGTT
1 TAACTCGATTCGTT
22311 TAACTCGATT
1 TAACTCGATT
22321 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (14 bp):
TAACTCGATTCGTT
Found at i:23976 original size:37 final size:38
Alignment explanation
Indices: 23906--24003 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 38
23896 AAATGTCTTG
* * * *
23906 AAATCAAAACCCCAAACCAAAACCAAATTTAAAAT-TA
1 AAATCAAAACCCTAAACCAAAATCAAATCTAAAATCCA
* *
23943 AAATCAAAACTCTAAACCAAAATCGAATCTAAAATCCA
1 AAATCAAAACCCTAAACCAAAATCAAATCTAAAATCCA
*
23981 AAA-CTAAAACCCTAAACTAAAAT
1 AAATC-AAAACCCTAAACCAAAAT
24004 TTAAGTTGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 31 0.61
38 20 0.39
ACGTcount: A:0.58, C:0.23, G:0.01, T:0.17
Consensus pattern (38 bp):
AAATCAAAACCCTAAACCAAAATCAAATCTAAAATCCA
Found at i:31095 original size:6 final size:6
Alignment explanation
Indices: 31084--31112 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31074 GATCAGAAGT
31084 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
31113 AATCAGCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:31326 original size:6 final size:6
Alignment explanation
Indices: 31315--31342 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31305 ATTGATGAAT
31315 AGAAGG AGAAGG AGAAGG AGAAGG AGAA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAA
31343 ACATAGGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:31851 original size:2 final size:2
Alignment explanation
Indices: 31844--31877 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31834 CTTAATCCTA
31844 AT AT AT AT AT 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
31878 GAATATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31913 original size:30 final size:30
Alignment explanation
Indices: 31879--31945 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
31869 TATATATATG
31879 AATATTTT-AAAAATATAAAAAAAATACAAA
1 AATATTTTAAAAAATATAAAAAAAATA-AAA
* * *
31909 AATATTTTCAAAAAATATAATAATAATAATA
1 AATATTTT-AAAAAATATAAAAAAAATAAAA
31940 AATATT
1 AATATT
31946 AATATTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.25
31 8 0.25
32 16 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (30 bp):
AATATTTTAAAAAATATAAAAAAAATAAAA
Found at i:31954 original size:19 final size:18
Alignment explanation
Indices: 31921--31962 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
31911 TATTTTCAAA
31921 AAATATAATAATAATAAT
1 AAATATAATAATAATAAT
* *
31939 AAATATTAATATTAATATT
1 AAATA-TAATAATAATAAT
31958 AAATA
1 AAATA
31963 AAAATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATAATAATAATAAT
Found at i:35679 original size:69 final size:69
Alignment explanation
Indices: 35566--35714 Score: 199
Period size: 69 Copynumber: 2.2 Consensus size: 69
35556 AGTGCTGGGG
** * * *
35566 AAACAATAAGCACACACAGTGCAAATCAGTAGGCATACACAGTGCAAATCAGTAGGCATACACAG
1 AAACAATAAGCACACACAGTGCAAATCAGTAAACACACACAGTGCAAATCAGTAAGCACACACAG
35631 TGCA
66 TGCA
* * * *
35635 AAACAATAAGCACACACAGTGCAAATCAGTAAACACATATAGTGCGAATTAGTAAGCACACACAG
1 AAACAATAAGCACACACAGTGCAAATCAGTAAACACACACAGTGCAAATCAGTAAGCACACACAG
*
35700 TGCT
66 TGCA
*
35704 GAACAATAAGC
1 AAACAATAAGC
35715 GCGCTAATGT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.15
Consensus pattern (69 bp):
AAACAATAAGCACACACAGTGCAAATCAGTAAACACACACAGTGCAAATCAGTAAGCACACACAG
TGCA
Found at i:35714 original size:23 final size:23
Alignment explanation
Indices: 35572--35702 Score: 163
Period size: 23 Copynumber: 5.7 Consensus size: 23
35562 GGGGAAACAA
35572 TAAGCACACACAGTGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
* *
35595 TAGGCATACACAGTGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
* * * *
35618 TAGGCATACACAGTGCAAAACAA
1 TAAGCACACACAGTGCAAATCAG
35641 TAAGCACACACAGTGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
* * * * *
35664 TAAACACATATAGTGCGAATTAG
1 TAAGCACACACAGTGCAAATCAG
35687 TAAGCACACACAGTGC
1 TAAGCACACACAGTGC
35703 TGAACAATAA
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 92 1.00
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (23 bp):
TAAGCACACACAGTGCAAATCAG
Found at i:43286 original size:24 final size:28
Alignment explanation
Indices: 43236--43288 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
43226 ATTCAATTAA
43236 TCAGAAAATGTAATAAAATAATAATTATT
1 TCAGAAAA-GTAATAAAATAATAATTATT
43265 TCAGAAAA-TAA-AAAA-AAT-ATTATT
1 TCAGAAAAGTAATAAAATAATAATTATT
43289 CTAGCACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 6 0.25
25 3 0.12
26 4 0.17
27 3 0.12
29 8 0.33
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (28 bp):
TCAGAAAAGTAATAAAATAATAATTATT
Found at i:47232 original size:20 final size:21
Alignment explanation
Indices: 47203--47248 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
47193 GCTTAGAGCT
*
47203 ATTTTGACTTG-TTTAAAATC
1 ATTTTAACTTGATTTAAAATC
*
47223 ATTTTAACTTGATTTTAAAATT
1 ATTTTAACTTGA-TTTAAAATC
47245 ATTT
1 ATTT
47249 CAAACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTTTAACTTGATTTAAAATC
Found at i:47883 original size:16 final size:15
Alignment explanation
Indices: 47848--47882 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47838 AAAACTTAAG
47848 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
47863 AAAAATGAATGTTTT
1 AAAAATGAATATTGT
47878 AAAAA
1 AAAAA
47883 AAAACTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:55911 original size:63 final size:63
Alignment explanation
Indices: 55812--55934 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 63
55802 AGAACTTAAA
* * *
55812 TAAATAAATATAACCAAAATAAATTTATTAATTAGAGATGGGTTTAGGTGATTTTTTTTTTTG
1 TAAATAAATATAACCAAAATAAATTAAATAATTAGAGATGGGTTTAGGTGATGTTTTTTTTTG
*
55875 TAAATAAATATAACCAAAATAAATTAAATAATTAGAGTTGGGTTTAGGTGATGTTTTTTT
1 TAAATAAATATAACCAAAATAAATTAAATAATTAGAGATGGGTTTAGGTGATGTTTTTTT
55935 ACCTCTTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (63 bp):
TAAATAAATATAACCAAAATAAATTAAATAATTAGAGATGGGTTTAGGTGATGTTTTTTTTTG
Found at i:62034 original size:7 final size:6
Alignment explanation
Indices: 62011--62040 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
62001 TCTCCTTTCT
62011 CCCTTC CCCTTC CCCTTCC CCCTTC CCCTT
1 CCCTTC CCCTTC CCCTT-C CCCTTC CCCTT
62041 TGAGAGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:62034 original size:13 final size:12
Alignment explanation
Indices: 62011--62040 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
62001 TCTCCTTTCT
62011 CCCTTCCCCTTC
1 CCCTTCCCCTTC
62023 CCCTTCCCCCTTC
1 CCCTT-CCCCTTC
62036 CCCTT
1 CCCTT
62041 TGAGAGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (12 bp):
CCCTTCCCCTTC
Found at i:64676 original size:13 final size:14
Alignment explanation
Indices: 64645--64677 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
64635 AAAGTAATTT
*
64645 ATTTTCCAGAAATC
1 ATTTTCCAGAAACC
64659 ATTTTCCAG-AACC
1 ATTTTCCAGAAACC
64672 ATTTTC
1 ATTTTC
64678 AGTCAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (14 bp):
ATTTTCCAGAAACC
Found at i:83983 original size:31 final size:31
Alignment explanation
Indices: 83948--84016 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
83938 TTAATATAAT
* * *
83948 ATTTGGTATCTT-AATTTGATAGTTTTTCTTA
1 ATTTGGTA-CTTGAACTTGACAATTTTTCTTA
83979 ATTTGGTACTTGAACTTGACAATTTTTCTTA
1 ATTTGGTACTTGAACTTGACAATTTTTCTTA
84010 ATTTGGT
1 ATTTGGT
84017 TCCTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (31 bp):
ATTTGGTACTTGAACTTGACAATTTTTCTTA
Found at i:84046 original size:59 final size:59
Alignment explanation
Indices: 83976--84111 Score: 155
Period size: 59 Copynumber: 2.3 Consensus size: 59
83966 ATAGTTTTTC
* * * *
83976 TTAATTTGGTACTTGAACTTGACAATTTTTCTTAATTTGGTTCCTAAATTTTTTTGGAT
1 TTAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTGGTACCTAAATTTTTTTGGAT
* ** * * **
84035 TTAATTTGGTACCTAAATTTGGTATTTTTTCCTAATTTGGTACCTAAGTTTTTTTAAAAT
1 TTAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTGGTACCTAAATTTTTTT-GGAT
*
84095 TCAATTTGGTACCTAAA
1 TTAATTTGGTACCTAAA
84112 TTTATTAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 46 0.72
60 18 0.28
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.50
Consensus pattern (59 bp):
TTAATTTGGTACCTAAACTTGACAATTTTTCCTAATTTGGTACCTAAATTTTTTTGGAT
Found at i:84049 original size:28 final size:26
Alignment explanation
Indices: 84007--84114 Score: 90
Period size: 31 Copynumber: 3.8 Consensus size: 26
83997 ACAATTTTTC
*
84007 TTAATTTGGTTCCTAAATTTTTTTGGAT
1 TTAATTTGGTACCTAAATTTTTTT--AT
*
84035 TTAATTTGGTACCTAAATTTGGTATTTTT
1 TTAATTTGGTACCTAAATTT--T-TTTAT
*
84064 TCCTAATTTGGTACCTAAGTTTTTTTAAAAT
1 T--TAATTTGGTACCTAAATTTTTTT---AT
*
84095 TCAATTTGGTACCTAAATTT
1 TTAATTTGGTACCTAAATTT
84115 ATTAAATATT
Statistics
Matches: 66, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
28 22 0.33
29 20 0.30
30 1 0.02
31 23 0.35
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (26 bp):
TTAATTTGGTACCTAAATTTTTTTAT
Found at i:85588 original size:17 final size:17
Alignment explanation
Indices: 85563--85596 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
85553 CTAATTTCGC
*
85563 ACAACCACCTCTTTATA
1 ACAACCACCACTTTATA
*
85580 ACAATCACCACTTTATA
1 ACAACCACCACTTTATA
85597 GTAGCCGAAT
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:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (17 bp):
ACAACCACCACTTTATA
Found at i:88862 original size:17 final size:17
Alignment explanation
Indices: 88827--88862 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
88817 TTTAAAATAA
* *
88827 ATTTAAAAAATATTTAT
1 ATTTAAAAAACATTAAT
88844 ATTTAAAAAACATTAAT
1 ATTTAAAAAACATTAAT
88861 AT
1 AT
88863 AGGTCAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAAAAACATTAAT
Found at i:88863 original size:19 final size:19
Alignment explanation
Indices: 88822--88863 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
88812 ACAAATTTAA
* *
88822 AATAAATTTAAAAAATATT
1 AATATATTTAAAAAACATT
88841 --TATATTTAAAAAACATT
1 AATATATTTAAAAAACATT
88858 AATATA
1 AATATA
88864 GGTCAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 15 0.79
19 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATATTTAAAAAACATT
Found at i:89759 original size:27 final size:27
Alignment explanation
Indices: 89705--89759 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
89695 AAGCTTTGAA
***
89705 TTCTTCTTTTTTTCTTTCTTCTTCTTC
1 TTCTTCTTTTTTTCTTTCTTCAAATTC
* *
89732 TTCTTCTTTTTTTTTTTTTTCAAATTC
1 TTCTTCTTTTTTTCTTTCTTCAAATTC
89759 T
1 T
89760 AATATATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (27 bp):
TTCTTCTTTTTTTCTTTCTTCAAATTC
Found at i:92917 original size:87 final size:87
Alignment explanation
Indices: 92810--93032 Score: 349
Period size: 87 Copynumber: 2.6 Consensus size: 87
92800 ACAATCAATG
* *
92810 TGTCAAAGATTGAAAATGAAAATTGTTTGAATTTTAATTTGTAGATTTAAAAAATATATTTTATA
1 TGTCAAAGATTGAAAATGAAAATTGTTTGAATTTTAATTTGTAGATTTAAAAAATATACTTTAGA
* *
92875 TTTAAGTTGACCTAATA-ATTAA
66 TTCAAATTGACCTAA-AGATTAA
*
92897 TGTCAAAGATCGAAAATGAAAATTGTTTGAATTTTAATTTGTAGATTTAAAAAATATACTTTAGA
1 TGTCAAAGATTGAAAATGAAAATTGTTTGAATTTTAATTTGTAGATTTAAAAAATATACTTTAGA
*
92962 TTCAAATTGATCTAAAGATTAA
66 TTCAAATTGACCTAAAGATTAA
* * *
92984 TGTCAAAGATTGAAAATAAAAACTGTTTGAATTTTAATTTGTAAATTTA
1 TGTCAAAGATTGAAAATGAAAATTGTTTGAATTTTAATTTGTAGATTTA
93033 TAACATTTAA
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
86 1 0.01
87 124 0.99
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.40
Consensus pattern (87 bp):
TGTCAAAGATTGAAAATGAAAATTGTTTGAATTTTAATTTGTAGATTTAAAAAATATACTTTAGA
TTCAAATTGACCTAAAGATTAA
Found at i:93060 original size:23 final size:25
Alignment explanation
Indices: 93039--93097 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
93029 TTTATAACAT
93039 TTAAAAT-TGTTTAATGAAAACAAA
1 TTAAAATGTGTTTAATGAAAACAAA
*
93063 TTAAATTGTGTTTAATGAAAA-AGAA
1 TTAAAATGTGTTTAATGAAAACA-AA
*
93088 TTAAATTGTG
1 TTAAAATGTG
93098 AAAATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (25 bp):
TTAAAATGTGTTTAATGAAAACAAA
Found at i:93080 original size:25 final size:25
Alignment explanation
Indices: 93046--93097 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
93036 CATTTAAAAT
93046 TGTTTAATGAAAACA-AATTAAATTG
1 TGTTTAATGAAAA-AGAATTAAATTG
93071 TGTTTAATGAAAAAGAATTAAATTG
1 TGTTTAATGAAAAAGAATTAAATTG
93096 TG
1 TG
93098 AAAATGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (25 bp):
TGTTTAATGAAAAAGAATTAAATTG
Found at i:93111 original size:24 final size:25
Alignment explanation
Indices: 93051--93112 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
93041 AAAATTGTTT
**
93051 AATGAAAACA-AATTAAATTGTGTTT
1 AATGAAAA-AGAATTAAATTGTGTAA
93076 AATGAAAAAGAATTAAATTGTG-AA
1 AATGAAAAAGAATTAAATTGTGTAA
*
93100 AATGAAAGAGAAT
1 AATGAAAAAGAAT
93113 AAAAATTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (25 bp):
AATGAAAAAGAATTAAATTGTGTAA
Found at i:93235 original size:16 final size:17
Alignment explanation
Indices: 93214--93246 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
93204 TAATGATTAT
93214 TTTAT-AAATTTTTAAA
1 TTTATAAAATTTTTAAA
93230 TTTATAAAATTTTTAAA
1 TTTATAAAATTTTTAAA
93247 ATTAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATAAAATTTTTAAA
Found at i:95871 original size:16 final size:15
Alignment explanation
Indices: 95846--95880 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
95836 CAATTGCAAT
95846 ATAAATATTTTAATA
1 ATAAATATTTTAATA
95861 ATAAGATATTTTAATA
1 ATAA-ATATTTTAATA
95877 ATAA
1 ATAA
95881 TTAATATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATAAATATTTTAATA
Found at i:96128 original size:23 final size:23
Alignment explanation
Indices: 96096--96157 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
96086 AAATTAAAAT
*
96096 ATATTATTAAAATATTAATATA-A
1 ATATTTTTAAAATATTAATA-AGA
*
96119 ATATTTTTAATAATA-TATTAAGA
1 ATATTTTTAA-AATATTAATAAGA
96142 ATATTGTTTAAAATAT
1 ATATT-TTTAAAATAT
96158 AAAGTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 23 0.70
24 9 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
ATATTTTTAAAATATTAATAAGA
Found at i:96133 original size:12 final size:11
Alignment explanation
Indices: 96089--96157 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 11
96079 TATTTATAAA
96089 TTAAAATATATT
1 TTAAAATAT-TT
*
96101 ATTAAAATATTA
1 -TTAAAATATTT
*
96113 ATATAAATATTT
1 TTA-AAATATTT
*
96125 TTAATAATA-TA
1 TTAA-AATATTT
96136 TTAAGAATATTGT
1 TTAA-AATATT-T
96149 TTAAAATAT
1 TTAAAATAT
96158 AAAGTTATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
11 12 0.27
12 20 0.44
13 13 0.29
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TTAAAATATTT
Found at i:96197 original size:17 final size:16
Alignment explanation
Indices: 96175--96228 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
96165 TTATTGTTAA
96175 AATTTATAATATTAAAT
1 AATTTAT-ATATTAAAT
96192 AATTTATATA--AAAT
1 AATTTATATATTAAAT
96206 AA-TTAGTTATATT-AAT
1 AATTTA--TATATTAAAT
96222 AATTTAT
1 AATTTAT
96229 TTTATTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.09
14 6 0.19
15 5 0.16
16 8 0.25
17 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTTATATATTAAAT
Found at i:96590 original size:16 final size:17
Alignment explanation
Indices: 96563--96596 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
96553 AAATAAAAAT
96563 TTTATGTAAAATTTTTA
1 TTTATGTAAAATTTTTA
96580 TTTAT-TAAAATTTTTA
1 TTTATGTAAAATTTTTA
96596 T
1 T
96597 ATAAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTATGTAAAATTTTTA
Found at i:98437 original size:12 final size:13
Alignment explanation
Indices: 98420--98448 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
98410 ATTTCATAAA
98420 TTAAAAATTT-AT
1 TTAAAAATTTAAT
98432 TTAAAAATTTAAT
1 TTAAAAATTTAAT
98445 TTAA
1 TTAA
98449 GACGCCAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAAAATTTAAT
Found at i:100038 original size:22 final size:21
Alignment explanation
Indices: 100013--100053 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
100003 AAATGCATGG
*
100013 AAAATAATTTAAATTTATATGA
1 AAAATAA-TTAAAATTATATGA
*
100035 AAAATGATTAAAATTATAT
1 AAAATAATTAAAATTATAT
100054 CCAGAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAATAATTAAAATTATATGA
Found at i:100514 original size:19 final size:17
Alignment explanation
Indices: 100486--100523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 17
100476 TTAAGATGTT
100486 ATTTTAAAAAATATTTAA
1 ATTTTAAAAAATA-TTAA
100504 ATTTATAAAAAATATTAA
1 ATTT-TAAAAAATATTAA
100522 AT
1 AT
100524 GAAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTTAAAAAATATTAA
Found at i:111839 original size:25 final size:25
Alignment explanation
Indices: 111785--111842 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
111775 CATTTTTATT
* *
111785 AATTT-AATTTTTATTTTCTAATTA
1 AATTTAAATTTTAATTTTCTAAATA
111809 AA-TTAAATTATTAATTTT-TAAATA
1 AATTTAAATT-TTAATTTTCTAAATA
111833 AATTTAAATT
1 AATTTAAATT
111843 GTTTTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 13 0.45
25 14 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTTAAATTTTAATTTTCTAAATA
Found at i:114099 original size:37 final size:37
Alignment explanation
Indices: 114058--114138 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 37
114048 ATTGTAGATA
*
114058 AATATTTTA-TTAATTTAAT-AG-ATTTAATATTAAAGTT
1 AATATTATATTTAATTTAATAAGTA-TT-ATATTAAA-TT
* *
114095 AATATAATATTTATTTTAATAAGTATTATATTAAATT
1 AATATTATATTTAATTTAATAAGTATTATATTAAATT
114132 AATATTA
1 AATATTA
114139 AAATGATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
37 15 0.41
38 17 0.46
39 4 0.11
40 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (37 bp):
AATATTATATTTAATTTAATAAGTATTATATTAAATT
Found at i:122393 original size:44 final size:44
Alignment explanation
Indices: 122343--122433 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
122333 ATAATTGTAA
* * *
122343 ATTAAATTCA-AAATAATTTTAAATGTGTAGTAATCACAATTTCT
1 ATTAAATT-ATAAATAATTTTAAATGTATAATAATCACAAGTTCT
* * *
122387 ATTAAATTATAAATATTTTTATATGTATAATTATCACAAGTTCT
1 ATTAAATTATAAATAATTTTAAATGTATAATAATCACAAGTTCT
122431 ATT
1 ATT
122434 TTACTTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (44 bp):
ATTAAATTATAAATAATTTTAAATGTATAATAATCACAAGTTCT
Found at i:122862 original size:27 final size:29
Alignment explanation
Indices: 122789--122864 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 29
122779 TCATCATGGA
122789 TAATTATCATGTATGAGTTTATTTGGTTG
1 TAATTATCATGTATGAGTTTATTTGGTTG
* * **
122818 TACTCTA--AT-TCTTCGTTTATTT-G-TG
1 TAAT-TATCATGTATGAGTTTATTTGGTTG
122843 TAATTATCATGTATGAGTTTAT
1 TAATTATCATGTATGAGTTTAT
122865 AATTGTAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
24 2 0.06
25 5 0.14
26 3 0.09
27 18 0.51
28 2 0.06
29 3 0.09
30 2 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (29 bp):
TAATTATCATGTATGAGTTTATTTGGTTG
Found at i:123417 original size:15 final size:16
Alignment explanation
Indices: 123381--123420 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
123371 ATAGTAAAAA
123381 AATAATTTTATCATTTT
1 AATAA-TTTATCATTTT
123398 AATAATTTAT-ATTTT
1 AATAATTTATCATTTT
*
123413 TATAATTT
1 AATAATTT
123421 TTAAAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
AATAATTTATCATTTT
Found at i:123805 original size:2 final size:2
Alignment explanation
Indices: 123798--123848 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
123788 TTCAGTTTAG
* * *
123798 CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT TT CT CC CT CT C-
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
123839 CAT CT CT CT C
1 C-T CT CT CT C
123849 GCCATTTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.02, C:0.53, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:128499 original size:32 final size:31
Alignment explanation
Indices: 128433--128500 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
128423 AATACATCAA
* *
128433 TTTATTTATTAAAATAATTATAATTACTTATT
1 TTTATTAATTAAAATAATTAAAATTAC-TATT
*
128465 TTTATTAATTAAAATATAGTTAAAATTA-TCTT
1 TTTATTAATTAAAATA-A-TTAAAATTACTATT
128497 TTTA
1 TTTA
128501 AAATCACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 1 0.03
34 8 0.26
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTATTAATTAAAATAATTAAAATTACTATT
Found at i:128638 original size:203 final size:201
Alignment explanation
Indices: 128229--128622 Score: 632
Period size: 203 Copynumber: 2.0 Consensus size: 201
128219 GAATTTTAAT
*
128229 ATTTATTTATTAAAATAATTAACTACTTATTTTTTTATTAATGAAAATATATTTAAAATTATTTT
1 ATTTATTTATTAAAATAATTAACTACTTA-TTTTTTATTAATGAAAATATAGTTAAAATTATTTT
* * * *
128294 TTAAAAATCACAAATGTTATGCTTAATTTGTACAAGATAGATATAAAATTTATACATTAATTTTG
65 TTAAAAATCACAAATGTTATGCATAATTTGTACAAGACAAATATAAAATTTATACATTAACTTTG
* *
128359 ATTTAATTTGTAATTTGATACATAAATTTTGATTTTGTACAATTATATATATTTTAAAAAAATAA
130 ATTTAATTTGTAATTTGATACATAAATTTTGATTTTATACAATTATACATA-TTTAAAAAAATAA
128424 ATACATCA
194 ATACATCA
* *
128432 ATTTATTTATTAAAATAATTATAATTACTTA-TTTTTATTAATTAAAATATAGTTAAAATTATCT
1 ATTTATTTATTAAAATAA-T-TAACTACTTATTTTTTATTAATGAAAATATAGTTAAAATTAT-T
*
128496 TTTT-AAAATCACAAATGTTATGCATAATTTGTACAAGACAAATATAAAATTTATACGTTAACTT
63 TTTTAAAAATCACAAATGTTATGCATAATTTGTACAAGACAAATATAAAATTTATACATTAACTT
128560 TGATTTAATTTGTAATTTGATACATAAATTTTGATTTTATACAATTATACATA-TTAAAAAAAT
128 TGATTTAATTTGTAATTTGATACATAAATTTTGATTTTATACAATTATACATATTTAAAAAAAT
128623 TTGAGTACAT
Statistics
Matches: 178, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
201 10 0.06
203 153 0.86
204 6 0.03
205 9 0.05
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (201 bp):
ATTTATTTATTAAAATAATTAACTACTTATTTTTTATTAATGAAAATATAGTTAAAATTATTTTT
TAAAAATCACAAATGTTATGCATAATTTGTACAAGACAAATATAAAATTTATACATTAACTTTGA
TTTAATTTGTAATTTGATACATAAATTTTGATTTTATACAATTATACATATTTAAAAAAATAAAT
ACATCA
Found at i:149611 original size:9 final size:9
Alignment explanation
Indices: 149597--149630 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
149587 TTTAAATTTT
149597 GAATTATTC
1 GAATTATTC
*
149606 GAATTAATC
1 GAATTATTC
*
149615 GAATTATTT
1 GAATTATTC
149624 GAATTAT
1 GAATTAT
149631 CTGAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (9 bp):
GAATTATTC
Found at i:155721 original size:3 final size:3
Alignment explanation
Indices: 155710--155761 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
155700 CCTTTTTTTT
* ** *
155710 TTC TCC TTC TTC CCC TTC TTC TCC TTC TTCC TTC TTC TTCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT-C TTC TTC
155757 TTC TT
1 TTC TT
155762 TCTTTCTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (3 bp):
TTC
Found at i:155748 original size:10 final size:10
Alignment explanation
Indices: 155715--155765 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
155705 TTTTTTTCTC
*
155715 CTTCTTCC-C
1 CTTCTTCCTT
*
155724 CTTCTT-CTC
1 CTTCTTCCTT
155733 CTTCTTCCTT
1 CTTCTTCCTT
155743 CTTCTTCCTT
1 CTTCTTCCTT
*
155753 CTTCTTCTTT
1 CTTCTTCCTT
155763 CTT
1 CTT
155766 TCTTTCTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 1 0.03
9 13 0.34
10 24 0.63
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (10 bp):
CTTCTTCCTT
Found at i:155749 original size:13 final size:13
Alignment explanation
Indices: 155723--155761 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
155713 TCCTTCTTCC
*
155723 CCTTCTTCTCCTT
1 CCTTCTTCTTCTT
155736 -CTTCCTTCTTCTT
1 CCTT-CTTCTTCTT
155749 CCTTCTTCTTCTT
1 CCTTCTTCTTCTT
155762 TCTTTCTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
CCTTCTTCTTCTT
Found at i:159798 original size:11 final size:12
Alignment explanation
Indices: 159785--159848 Score: 64
Period size: 12 Copynumber: 5.5 Consensus size: 12
159775 AAACTTAATT
159785 AATTTAATATT-
1 AATTTAATATTA
*
159796 AATTT-TTATT-
1 AATTTAATATTA
*
159806 AATTAAATATTAA
1 AATTTAATATT-A
159819 AATATTAA-ATTA
1 AAT-TTAATATTA
159831 AATTTAATATTA
1 AATTTAATATTA
159843 AATTTA
1 AATTTA
159849 TTAAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 8 0.18
11 13 0.30
12 14 0.32
13 6 0.14
14 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTTAATATTA
Found at i:159807 original size:10 final size:11
Alignment explanation
Indices: 159782--159848 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 11
159772 ATCAAACTTA
159782 ATTAATTTAAT
1 ATTAATTTAAT
*
159793 ATTAATTT-TT
1 ATTAATTTAAT
*
159803 ATTAATTAAAT
1 ATTAATTTAAT
159814 ATTAAAATATTAA-
1 ATT--AAT-TTAAT
159827 ATTAAATTTAAT
1 ATT-AATTTAAT
159839 ATTAAATTTA
1 ATT-AATTTA
159849 TTAAAATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.17
11 16 0.34
12 14 0.30
13 6 0.13
14 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTAATTTAAT
Found at i:159831 original size:34 final size:34
Alignment explanation
Indices: 159788--159856 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 34
159778 CTTAATTAAT
* *
159788 TTAATATTAATTTTTATTAATTAAA-TATTAAAATA
1 TTAATATTAA-ATTTAAT-ATTAAATTATTAAAATA
159823 TTAA-ATTAAATTTAATATTAAATTTATTAAAATA
1 TTAATATTAAATTTAATATTAAA-TTATTAAAATA
159857 ATATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 6 0.20
33 5 0.17
34 15 0.50
35 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
TTAATATTAAATTTAATATTAAATTATTAAAATA
Found at i:159834 original size:25 final size:26
Alignment explanation
Indices: 159806--159862 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
159796 AATTTTTATT
*
159806 AATTAAATATTAAA-ATATTAAATTA
1 AATTAAATATTAAATATATTAAAATA
* *
159831 AATTTAATATTAAATTTATTAAAATA
1 AATTAAATATTAAATATATTAAAATA
159857 ATATTA
1 A-ATTA
159863 TTTTTGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 13 0.50
26 10 0.38
27 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAAATATTAAATATATTAAAATA
Found at i:159856 original size:17 final size:18
Alignment explanation
Indices: 159812--159856 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
159802 TATTAATTAA
159812 ATATTAAAATATTAAATT
1 ATATTAAAATATTAAATT
* *
159830 AAATT-TAATATTAAATT
1 ATATTAAAATATTAAATT
159847 -TATTAAAATA
1 ATATTAAAATA
159857 ATATTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAAAATATTAAATT
Found at i:161746 original size:21 final size:22
Alignment explanation
Indices: 161722--161768 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
161712 CTATCTAAGA
161722 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
161743 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAACAGAATT
161765 AAAA
1 AAAA
161769 GAAATGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:161747 original size:22 final size:23
Alignment explanation
Indices: 161721--161768 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
161711 GCTATCTAAG
161721 AAAAAATAAAAG-AAACAGAATT
1 AAAAAATAAAAGAAAACAGAATT
*
161743 -AAAAATAAAAGAAAATAGAATT
1 AAAAAATAAAAGAAAACAGAATT
161765 AAAA
1 AAAA
161769 GAAATGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 9 0.39
23 3 0.13
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (23 bp):
AAAAAATAAAAGAAAACAGAATT
Found at i:162598 original size:19 final size:19
Alignment explanation
Indices: 162574--162616 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
162564 AAATATAAAT
162574 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
162593 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
162612 TAAAT
1 TAAAT
162617 CCTAATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:165989 original size:17 final size:15
Alignment explanation
Indices: 165946--165996 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
165936 TTAAAATTTT
*
165946 TAAATTCAAAAAATG
1 TAAAATCAAAAAATG
165961 TAAAAT-AAAAAATCG
1 TAAAATCAAAAAAT-G
* *
165976 ATCAAATCAAAAAATA
1 -TAAAATCAAAAAATG
165992 TAAAA
1 TAAAA
165997 ATTTAATCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 7 0.24
15 10 0.34
16 5 0.17
17 7 0.24
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.22
Consensus pattern (15 bp):
TAAAATCAAAAAATG
Found at i:168003 original size:221 final size:221
Alignment explanation
Indices: 167591--168039 Score: 699
Period size: 221 Copynumber: 2.0 Consensus size: 221
167581 AATCGCCAAC
* *
167591 GTTTCGACATTGGGTGGGTCGAGTCCAAATATTGTTGGAATTGCTAAATATTACAAAGGAATAAG
1 GTTTAGACATTGGGTGGGTCGAGTCCAAATATTGTTGGAATTGCTAAATATTACAAAGGAATAAA
* *
167656 AAAGAAATATGGAAAAAAATAAAGAGAAATAAATAATGTAAAGGCAAATAAAAGAATTAAAAATA
66 AAAGAAATATGGAAAAAAATAAAGAGAAAGAAATAATGTAAAGGCAAATAAAAAAATTAAAAATA
* * * *
167721 ACATTTTGATGTAAAATAGGTAACGAAAGAATAACGTAGGTACCAATTGTGATAAAAAAAAATTT
131 ACATTTTGATATAAAATAGGTAACGAAAGAATAACGTAAGTACCAATTGTGAAAAAAAAAAAATT
*
167786 AGTGCCAACTTGGGAAAAAGAATTTT
196 AGTACCAACTTGGGAAAAAGAATTTT
*
167812 GTTTAGACATTGGGTGGGTCGAGTTCAAATATTGTTGGAATTGCTAAATATTAC-AAGAGAATAA
1 GTTTAGACATTGGGTGGGTCGAGTCCAAATATTGTTGGAATTGCTAAATATTACAAAG-GAATAA
167876 AAAAGAAATATGGAAAAAAAAAATAAAGAGAAAGAAATAATGTAAAGGCAAATAAAAAAATTAAA
65 AAAAGAAATATGG---AAAAAAATAAAGAGAAAGAAATAATGTAAAGGCAAATAAAAAAATTAAA
* * * *
167941 AATAATA-TTTGATATAAAAT-GAGTAACGAATGAATAGCGTAAGTACCAATTGTG-ACAAAAAA
127 AATAACATTTTGATATAAAATAG-GTAACGAAAGAATAACGTAAGTACCAATTGTGAAAAAAAAA
168003 AAATTAGTACCAACTTGGGAAAAAGAATTTT
191 AAATTAGTACCAACTTGGGAAAAAGAATTTT
168034 GTTTAG
1 GTTTAG
168040 GTATTAATTT
Statistics
Matches: 209, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
220 3 0.01
221 70 0.33
222 42 0.20
223 41 0.20
224 53 0.25
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (221 bp):
GTTTAGACATTGGGTGGGTCGAGTCCAAATATTGTTGGAATTGCTAAATATTACAAAGGAATAAA
AAAGAAATATGGAAAAAAATAAAGAGAAAGAAATAATGTAAAGGCAAATAAAAAAATTAAAAATA
ACATTTTGATATAAAATAGGTAACGAAAGAATAACGTAAGTACCAATTGTGAAAAAAAAAAAATT
AGTACCAACTTGGGAAAAAGAATTTT
Found at i:169212 original size:29 final size:29
Alignment explanation
Indices: 169142--169213 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
169132 CTACTTTGGC
* * **
169142 CTAATATGATTCTTTTTAATAATGCAGGGA
1 CTAATTTGA-TCTATTTAATAATAAAGGGA
* * *
169172 TTAAATTAATCTATTTAATAATAAAGGGA
1 CTAATTTGATCTATTTAATAATAAAGGGA
169201 CTAATTTGATCTA
1 CTAATTTGATCTA
169214 ACTCCATATA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.40
Consensus pattern (29 bp):
CTAATTTGATCTATTTAATAATAAAGGGA
Found at i:176843 original size:12 final size:11
Alignment explanation
Indices: 176801--176843 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
176791 TGTTACCTGC
176801 AAAAAACAGAG
1 AAAAAACAGAG
*
176812 AAAAAGAAAGAG
1 AAAAA-ACAGAG
176824 AAAAAACAGAG
1 AAAAAACAGAG
176835 AAAAGAACA
1 AAAA-AACA
176844 AAATATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAACAGAG
Found at i:177810 original size:4 final size:4
Alignment explanation
Indices: 177801--177901 Score: 60
Period size: 4 Copynumber: 26.5 Consensus size: 4
177791 TTTGCATACC
* *
177801 TTAT TTAT TTAT TTAT TTA- TAAT TTA- -TAT TTAA TTAT TTAAT TTAAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TT-AT
*
177848 TTAAT TTATT TTAT TTA- TT-T TTCT TTA- TTA- TTA- TTA- TTAT TT-T
1 TT-AT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
177891 TTATT TTAT TT
1 TTA-T TTAT TT
177902 TATGTCGTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
2 2 0.02
3 21 0.26
4 37 0.45
5 22 0.27
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:177827 original size:19 final size:18
Alignment explanation
Indices: 177801--177903 Score: 69
Period size: 19 Copynumber: 5.9 Consensus size: 18
177791 TTTGCATACC
177801 TTATTTATTTA-TTT-AT
1 TTATTTATTTATTTTAAT
*
177817 TTA-TAATTTATATTTAA-
1 TTATTTATTTAT-TTTAAT
*
177834 TTATTTAATTTAATTTAAT
1 TTATTT-ATTTATTTTAAT
**
177853 TTATTTTATTTATTTTTCT
1 TTA-TTTATTTATTTTAAT
177872 TTA-TTA-TTATTATT-AT
1 TTATTTATTTATT-TTAAT
177888 TT-TTTATTTTATTTTA
1 TTATTTA-TTTATTTTA
177904 TGTCGTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
15 6 0.09
16 14 0.21
17 13 0.19
18 12 0.18
19 20 0.29
20 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTATTTATTTTAAT
Found at i:177846 original size:5 final size:5
Alignment explanation
Indices: 177803--177864 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
177793 TGCATACCTT
*
177803 ATTT- ATTT- ATTTA TTTATA ATTTA TATTTA A-TT- ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATT-TA ATTTA -ATTTA ATTTA ATTTA ATTTA ATTTA
*
177851 ATTT- ATTTT ATTTA
1 ATTTA ATTTA ATTTA
177865 TTTTTCTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
3 1 0.02
4 16 0.33
5 23 0.47
6 9 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
ATTTA
Found at i:177869 original size:10 final size:10
Alignment explanation
Indices: 177808--177901 Score: 63
Period size: 10 Copynumber: 9.7 Consensus size: 10
177798 ACCTTATTTA
177808 TTTATTTATT
1 TTTATTTATT
* *
177818 TATAATTTATA
1 T-TTATTTATT
*
177829 TTTAATTA-T
1 TTTATTTATT
* *
177838 TTAATTTAAT
1 TTTATTTATT
*
177848 TTAATTTA-T
1 TTTATTTATT
177857 TTTATTTATT
1 TTTATTTATT
*
177867 TTTCTTTATT
1 TTTATTTATT
*
177877 ATTA-TTATT
1 TTTATTTATT
177886 ATTT-TTTA-T
1 -TTTATTTATT
177895 TTTATTT
1 TTTATTT
177902 TATGTCGTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
8 3 0.05
9 23 0.35
10 32 0.48
11 8 0.12
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATTTATT
Found at i:177899 original size:5 final size:5
Alignment explanation
Indices: 177804--177904 Score: 52
Period size: 5 Copynumber: 20.0 Consensus size: 5
177794 GCATACCTTA
* * * * *
177804 TTTA- TTTA- TTTAT TTATAA TTTAT ATTTA- ATTA- TTTAA TTTAA TTTAA
1 TTTAT TTTAT TTTAT TT-TAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT
177852 TTTAT TTTA- TTTAT TTT-T CTTTAT TATTAT TATTATTT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT -TTTAT T-TTAT T-TTA--T TTTAT TTTAT
177900 TTTAT
1 TTTAT
177905 GTCGTTTATG
Statistics
Matches: 82, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
4 19 0.23
5 40 0.49
6 18 0.22
7 3 0.04
8 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:179545 original size:29 final size:29
Alignment explanation
Indices: 179503--179558 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
179493 CTGTTCCTCT
*
179503 AAACACCACTACTTCATATGTGTATCAGC
1 AAACACCACTACTTCATAGGTGTATCAGC
* *
179532 AAACGCCACTACTTCATCGGTGTATCA
1 AAACACCACTACTTCATAGGTGTATCA
179559 TCAAGTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (29 bp):
AAACACCACTACTTCATAGGTGTATCAGC
Found at i:183447 original size:2 final size:2
Alignment explanation
Indices: 183440--183470 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
183430 TTACTGGTAC
183440 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
183471 GAATGGGGGA
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:189106 original size:25 final size:25
Alignment explanation
Indices: 189078--189125 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
189068 TAATGGTTCG
189078 TAAAT-AATATATAAT-TAATATAAAA
1 TAAATAAAT-TATAATAT-ATATAAAA
189103 TAAATAAATTATAATATATATAA
1 TAAATAAATTATAATATATATAA
189126 GATTATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAATAAATTATAATATATATAAAA
Found at i:189115 original size:16 final size:17
Alignment explanation
Indices: 189096--189137 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
189086 ATATAATTAA
189096 TATAAAATAAATAA-AT
1 TATAAAATAAATAAGAT
* *
189112 TATAATATATATAAGAT
1 TATAAAATAAATAAGAT
189129 TATATAAAT
1 TATA-AAAT
189138 GTATTGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 12 0.57
17 6 0.29
18 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TATAAAATAAATAAGAT
Found at i:191067 original size:31 final size:26
Alignment explanation
Indices: 191002--191070 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 26
190992 ATTGAGGTGT
191002 AAATTAAAGTTAAGTTTATTTAGATA
1 AAATTAAAGTTAAGTTTATTTAGATA
*
191028 AAAGTTAAAGATTAAGGGCTTTATTTGGACTA
1 AAA-TTAAAG-TTAA--G-TTTATTTAGA-TA
191060 AAATTAAAGTT
1 AAATTAAAGTT
191071 TAAAAAGCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 3 0.08
27 6 0.17
28 4 0.11
30 3 0.08
31 15 0.42
32 5 0.14
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (26 bp):
AAATTAAAGTTAAGTTTATTTAGATA
Found at i:197201 original size:18 final size:18
Alignment explanation
Indices: 197178--197215 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
197168 ATGTATTGGT
197178 GATGCATGGGGCTGACTC
1 GATGCATGGGGCTGACTC
197196 GATGCATGGGGCTGACTC
1 GATGCATGGGGCTGACTC
197214 GA
1 GA
197216 ATAGTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.21, G:0.39, T:0.21
Consensus pattern (18 bp):
GATGCATGGGGCTGACTC
Found at i:197290 original size:19 final size:19
Alignment explanation
Indices: 197250--197312 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
197240 AATATAAATT
*
197250 TTAAA-TATGTTTA-TATTA
1 TTAAATTAT-TTTATTATTC
197268 TTAAATTATTTTATTATTC
1 TTAAATTATTTTATTATTC
*
197287 TT-AATATATATTATTAATTC
1 TTAAAT-TATTTTATT-ATTC
197307 -TAAATT
1 TTAAATT
197313 TTGAGAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 12 0.32
19 19 0.50
20 7 0.18
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAAATTATTTTATTATTC
Found at i:201486 original size:21 final size:21
Alignment explanation
Indices: 201462--201503 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
201452 ATATTAATAC
*
201462 TTCTTGAATTTA-AAGTTTAAA
1 TTCTCGAATTTAGAA-TTTAAA
*
201483 TTCTCGAGTTTAGAATTTAAA
1 TTCTCGAATTTAGAATTTAAA
201504 ATAGGGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TTCTCGAATTTAGAATTTAAA
Found at i:216109 original size:24 final size:24
Alignment explanation
Indices: 216082--216129 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
216072 AAGCGTCGAC
*
216082 TAATACGAAAATTGAGAAATTAAT
1 TAATACGAAAATAGAGAAATTAAT
216106 TAATACGAAAATAGAGAAATTAAT
1 TAATACGAAAATAGAGAAATTAAT
216130 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.27
Consensus pattern (24 bp):
TAATACGAAAATAGAGAAATTAAT
Found at i:216356 original size:20 final size:21
Alignment explanation
Indices: 216319--216366 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
216309 CATGTGTTTA
216319 TTAATAATTGTTTCAATTTTT
1 TTAATAATTGTTTCAATTTTT
216340 TTAA-AATT-TTTCTAATTTTT
1 TTAATAATTGTTTC-AATTTTT
*
216360 TTTATAA
1 TTAATAA
216367 AGTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTAATAATTGTTTCAATTTTT
Found at i:217582 original size:7 final size:7
Alignment explanation
Indices: 217538--217605 Score: 75
Period size: 7 Copynumber: 9.9 Consensus size: 7
217528 TTCAAACTTG
*
217538 ATTCTTA
1 ATTCTCA
217545 ATT-TCA
1 ATTCTCA
*
217551 ATTATCA
1 ATTCTCA
*
217558 ATTATCA
1 ATTCTCA
*
217565 ATTATCA
1 ATTCTCA
217572 ATTCTCA
1 ATTCTCA
*
217579 ATTCTTA
1 ATTCTCA
*
217586 ATTCTTA
1 ATTCTCA
217593 ATTCTCA
1 ATTCTCA
217600 ATTCTC
1 ATTCTC
217606 TCAATAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
6 5 0.09
7 51 0.91
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (7 bp):
ATTCTCA
Found at i:220982 original size:125 final size:125
Alignment explanation
Indices: 220760--220999 Score: 356
Period size: 125 Copynumber: 1.9 Consensus size: 125
220750 CTAAAAATGA
* * *
220760 ACCCTCGAAAGTCAAACAAGTCAAAATGATGCAATTAGCCAAGATTGAACCAGTGGGTACCACTA
1 ACCCTCGAAAGTCAAACAAGCCAAAACGATGCAATTAGCCAAGATTGAACCAGAGGGTACCACTA
* *
220825 GAGAAGTATAGATACCTTATGAGAGAAGTACCAACACCTACGAGATGTATAGGTACATCC
66 AAGAAGTATAGATACCTTACGAGAGAAGTACCAACACCTACGAGATGTATAGGTACATCC
* * ***
220885 ACCCTCGAAAGTCAAACAAGCCAAAACGGTGCAATTAGTCAAGATTGAACCAGAGGGTACTTTTA
1 ACCCTCGAAAGTCAAACAAGCCAAAACGATGCAATTAGCCAAGATTGAACCAGAGGGTACCACTA
**
220950 AAGAAGTATA-AGTACCTTACGAGAGAAGTACCAACACCTGGGAGATGTAT
66 AAGAAGTATAGA-TACCTTACGAGAGAAGTACCAACACCTACGAGATGTAT
221000 TGATACATTT
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.01
125 101 0.99
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (125 bp):
ACCCTCGAAAGTCAAACAAGCCAAAACGATGCAATTAGCCAAGATTGAACCAGAGGGTACCACTA
AAGAAGTATAGATACCTTACGAGAGAAGTACCAACACCTACGAGATGTATAGGTACATCC
Done.