Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015075.1 Kokia drynarioides strain JFW-HI SEQ_130119, 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: 164298
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:16077 original size:19 final size:20
Alignment explanation
Indices: 16031--16077 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
16021 AATGAAAATT
*
16031 TTTGAATAATTTATTGATTA
1 TTTGAATAATTTATTGATAA
* *
16051 TTT-TATAATTTTTTGA-AA
1 TTTGAATAATTTATTGATAA
16069 TTTGAATAA
1 TTTGAATAA
16078 CATAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 4 0.18
19 15 0.68
20 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTGAATAATTTATTGATAA
Found at i:23505 original size:22 final size:21
Alignment explanation
Indices: 23462--23505 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
23452 TTTAAAGTAA
* * *
23462 AAATATCTTTATATTAATAAT
1 AAATATCTTTAAAGTAAAAAT
23483 AAATATCCTTTAAAGTAAAAAT
1 AAATAT-CTTTAAAGTAAAAAT
23505 A
1 A
23506 TTTTAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATCTTTAAAGTAAAAAT
Found at i:36908 original size:4 final size:4
Alignment explanation
Indices: 36899--36950 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
36889 TCCTGGACAA
*
36899 AAAT AAAT AAAT AAAT AAAT AAGAT AGAA- AAAT AAAAT AAA- AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT A-AAT AAAT -AAAT AAAT AAAT AAAT
36948 AAA
1 AAA
36951 AATAATTGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
3 5 0.12
4 28 0.67
5 8 0.19
6 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:41851 original size:28 final size:28
Alignment explanation
Indices: 41820--41879 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
41810 AAATGAGACT
41820 TTTTAGATACCCGAGGGAAAAATGGTAA
1 TTTTAGATACCCGAGGGAAAAATGGTAA
* * * *
41848 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTAGATACCCGAGGGAAAAATGGTAA
41876 TTTT
1 TTTT
41880 GGGAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (28 bp):
TTTTAGATACCCGAGGGAAAAATGGTAA
Found at i:42026 original size:30 final size:30
Alignment explanation
Indices: 42000--42268 Score: 215
Period size: 29 Copynumber: 9.2 Consensus size: 30
41990 TTATTTTCAA
*
42000 AAGTTTCGGGGTTAAAAATGGAATTTTTGG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTAG
*
42030 AAG-TTCAGGG-TAAAAATGGAATTTTTAG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTAG
* *
42058 AAG-TTCGGGGTCAAAAATGAAATTTTTAG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTAG
* * *
42087 AAGTTT-GGGGGTAAAAATGAAATTTTTGG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTAG
* * * *
42116 ATG-TTCGAGG-TAAAAATGTG-ATTTTCAA
1 AAGTTTCGGGGTTAAAAATG-GAATTTTTAG
** *
42144 AAGTTTTAGGGTTAAAAAATGGAATTTTTGG
1 AAGTTTCGGGGTT-AAAAATGGAATTTTTAG
*
42175 AAGTTT-GAGGGGTAAAAATGTG-ATTTTTA-
1 AAGTTTCG-GGGTTAAAAATG-GAATTTTTAG
*
42204 AGAGTTTCGAGGTTAAAAATGGAATTTTT--
1 A-AGTTTCGGGGTTAAAAATGGAATTTTTAG
* *
42233 AAG-TTCGAGGG-TAAAAATGTAATTTTTGG
1 AAGTTTCG-GGGTTAAAAATGGAATTTTTAG
42262 ACAGTTT
1 A-AGTTT
42269 AGGGACCTTC
Statistics
Matches: 193, Mismatches: 28, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
27 19 0.10
28 47 0.24
29 58 0.30
30 43 0.22
31 26 0.13
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAGTTTCGGGGTTAAAAATGGAATTTTTAG
Found at i:42074 original size:57 final size:57
Alignment explanation
Indices: 42004--42272 Score: 246
Period size: 57 Copynumber: 4.6 Consensus size: 57
41994 TTTCAAAAGT
* *
42004 TTCGGGGTTAAAAATGGAATTTTTGGAAG-TTCAGGGTAAAAATGGAATTTTTAGAAG
1 TTCGGGG-TAAAAATGGAATTTTTAGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAG
* ** * *
42061 TTCGGGGTCAAAAATGAAATTTTTAGAAGTTTGGGGGTAAAAATGAAATTTTTGGATG
1 TTCGGGGT-AAAAATGGAATTTTTAGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAG
* * * *
42119 TTCGAGGTAAAAATGTG-ATTTTCAAAAGTTTTAGGGTTAAAAAATGGAATTTTTGGAAG
1 TTCGGGGTAAAAATG-GAATTTTTAGAAGTTTCAGGG-T-AAAAATGGAATTTTTGGAAG
* *
42178 TTTGAGGGGTAAAAATGTG-ATTTTTA-AGAGTTTCGAGGTTAAAAATGGAATTTTT--AAG
1 -TT-CGGGGTAAAAATG-GAATTTTTAGA-AGTTTC-AGGGTAAAAATGGAATTTTTGGAAG
* *
42236 TTCGAGGGTAAAAATGTAATTTTTGGACAGTTT-AGGG
1 TTCG-GGGTAAAAATGGAATTTTTAGA-AGTTTCAGGG
42273 ACCTTCAGGG
Statistics
Matches: 175, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
56 5 0.03
57 66 0.38
58 40 0.23
59 18 0.10
60 18 0.10
61 25 0.14
62 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (57 bp):
TTCGGGGTAAAAATGGAATTTTTAGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAG
Found at i:42113 original size:58 final size:57
Alignment explanation
Indices: 41955--42268 Score: 233
Period size: 58 Copynumber: 5.4 Consensus size: 57
41945 ATCGAGATAT
* * * * ** * *
41955 AAAATATAATTTTTGGACA-TTCGGGGGTAAAAAAGTTATTTTCAAAAGTTTCGGGGTTA
1 AAAATGTAATTTTTAGA-AGTTTGGGGGTAAAAATGGAATTTTTAGAAG-TTCGGGG-TA
* * **
42014 AAAATGGAATTTTTGGAAG-TTCAGGGTAAAAATGGAATTTTTAGAAGTTCGGGGTCA
1 AAAATGTAATTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTCGGGGT-A
* * * * *
42071 AAAATGAAATTTTTAGAAGTTTGGGGGTAAAAATGAAATTTTTGGATGTTCGAGGTA
1 AAAATGTAATTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTCGGGGTA
* * * * * * *
42128 AAAATGTGATTTTCAAAAGTTTTAGGGTTAAAAAATGGAATTTTTGGAAGTTTGAGGGGTA
1 AAAATGTAATTTTTAGAAG-TTTGGGGGT-AAAAATGGAATTTTTAGAAG-TT-CGGGGTA
* * *
42189 AAAATGTGATTTTTA-AGAGTTTCGAGGTTAAAAATGGAATTTTT--AAGTTCGAGGGTA
1 AAAATGTAATTTTTAGA-AGTTT-GGGGGTAAAAATGGAATTTTTAGAAGTTCG-GGGTA
*
42246 AAAATGTAATTTTTGGACAGTTT
1 AAAATGTAATTTTTAGA-AGTTT
42269 AGGGACCTTC
Statistics
Matches: 209, Mismatches: 35, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
56 2 0.01
57 61 0.29
58 67 0.32
59 33 0.16
60 21 0.10
61 25 0.12
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTCGGGGTA
Found at i:42163 original size:31 final size:30
Alignment explanation
Indices: 41978--42259 Score: 137
Period size: 30 Copynumber: 9.7 Consensus size: 30
41968 TGGACATTCG
* * *
41978 GGGGTAAAAAAGTTATTTTCAAAAGTTTCG-
1 GGGGTAAAAATGTGATTTTTAAAAGTTT-GA
* ** *
42008 GGGTTAAAAATG-GAATTTTTGGAAG-TTCA
1 GGGGTAAAAATGTG-ATTTTTAAAAGTTTGA
* *
42037 -GGGTAAAAATG-GAATTTTTAGAAG-TT-C
1 GGGGTAAAAATGTG-ATTTTTAAAAGTTTGA
** *
42064 GGGGTCAAAAATGAAATTTTTAGAAGTTTG-
1 GGGGT-AAAAATGTGATTTTTAAAAGTTTGA
** ** * *
42094 GGGGTAAAAATGAAATTTTTGGATGTTCGA
1 GGGGTAAAAATGTGATTTTTAAAAGTTTGA
* *
42124 --GGTAAAAATGTGATTTTCAAAAGTTTTA
1 GGGGTAAAAATGTGATTTTTAAAAGTTTGA
* **
42152 GGGTTAAAAAATG-GAATTTTTGGAAGTTTGA
1 GGGGT-AAAAATGTG-ATTTTTAAAAGTTTGA
*
42183 GGGGTAAAAATGTGATTTTTAAGAGTTTCGA
1 GGGGTAAAAATGTGATTTTTAAAAGTTT-GA
* *
42214 -GGTTAAAAATG-GAATTTTT--AAGTTCGA
1 GGGGTAAAAATGTG-ATTTTTAAAAGTTTGA
*
42241 -GGGTAAAAATGTAATTTTT
1 GGGGTAAAAATGTGATTTTT
42260 GGACAGTTTA
Statistics
Matches: 200, Mismatches: 36, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
27 18 0.09
28 52 0.26
29 42 0.21
30 62 0.31
31 26 0.13
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
GGGGTAAAAATGTGATTTTTAAAAGTTTGA
Found at i:43966 original size:17 final size:17
Alignment explanation
Indices: 43940--44038 Score: 76
Period size: 17 Copynumber: 5.8 Consensus size: 17
43930 TTTTGTAATT
* *
43940 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAGTA
43957 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
** *
43974 AATTTAAACTCAAAAGTG
1 AATTTAAA-TTTAAAGTA
*
43992 AATTTAAATTTAGAA-CA
1 AATTTAAATTTA-AAGTA
* **
44009 AATTCAAGCTTAAAGTA
1 AATTTAAATTTAAAGTA
*
44026 AA-TTAAAGTTAAA
1 AATTTAAATTTAAA
44039 ATTTGGACTC
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
16 10 0.16
17 37 0.59
18 16 0.25
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:45626 original size:21 final size:20
Alignment explanation
Indices: 45602--45651 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
45592 AAGGAAAATT
*
45602 AAAGAAATAGAATTAAAAAGA
1 AAAGAAACAGAATT-AAAAGA
*
45623 AAAGAAAACAGAATTGAAAGA
1 AAAG-AAACAGAATTAAAAGA
45644 AATAGAAA
1 AA-AGAAA
45652 ATAGGGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAGAAACAGAATTAAAAGA
Found at i:47971 original size:20 final size:20
Alignment explanation
Indices: 47947--47992 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
47937 TATTAAAAAT
* *
47947 ATTTTTTTATGATTTGTATA
1 ATTTTTTAATAATTTGTATA
* *
47967 CTTTTTTAATAATTTTTATA
1 ATTTTTTAATAATTTGTATA
47987 ATTTTT
1 ATTTTT
47993 GAATTTAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
ATTTTTTAATAATTTGTATA
Found at i:52307 original size:10 final size:10
Alignment explanation
Indices: 52292--52323 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
52282 GAGATAGAAT
52292 ATCGAATTTG
1 ATCGAATTTG
52302 ATCGAATTTG
1 ATCGAATTTG
*
52312 ATCGAATCTG
1 ATCGAATTTG
52322 AT
1 AT
52324 TGTAGTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (10 bp):
ATCGAATTTG
Found at i:53015 original size:20 final size:20
Alignment explanation
Indices: 52990--53041 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
52980 AACATGTGTC
52990 AAAAATTATAAAAAATCAAT
1 AAAAATTATAAAAAATCAAT
* ** *
53010 AAAAATTATTAAATTTTAAT
1 AAAAATTATAAAAAATCAAT
53030 AAAAA-TATAAAA
1 AAAAATTATAAAA
53042 TACTTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTATAAAAAATCAAT
Found at i:53048 original size:20 final size:20
Alignment explanation
Indices: 52990--53048 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
52980 AACATGTGTC
** *
52990 AAAAATTATAAAAAATCAAT
1 AAAAATTATAAAATCTTAAT
* *
53010 AAAAATTATTAAATTTTAAT
1 AAAAATTATAAAATCTTAAT
53030 AAAAA-TATAAAATACTTAA
1 AAAAATTATAAAAT-CTTAA
53049 AATTTATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTATAAAATCTTAAT
Found at i:53082 original size:10 final size:10
Alignment explanation
Indices: 53069--53183 Score: 57
Period size: 10 Copynumber: 11.9 Consensus size: 10
53059 AATTTAGAAA
53069 AAAAATATAT
1 AAAAATATAT
* *
53079 AAAAGT-TGT
1 AAAAATATAT
53088 -AAAA-ATA-
1 AAAAATATAT
53095 AAAAAT-TAT
1 AAAAATATAT
53104 -AAAATATAT
1 AAAAATATAT
* *
53113 AGAAATATAGA
1 AAAAATATA-T
*
53124 AAAAATTTAT
1 AAAAATATAT
* *
53134 AAAATTTTAT
1 AAAAATATAT
* *
53144 ATAAAATCGTAA
1 A-AAAAT-ATAT
53156 AAAAAT-TAT
1 AAAAATATAT
53165 AAAAATATA-
1 AAAAATATAT
53174 AATAAATATA
1 AA-AAATATA
53184 AAATTTGTAA
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
8 15 0.19
9 15 0.19
10 31 0.39
11 16 0.20
12 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:53165 original size:31 final size:30
Alignment explanation
Indices: 53094--53183 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
53084 TTGTAAAAAT
53094 AAAAAATTATAAAATATATAGAAATATAGA
1 AAAAAATTATAAAATATATAGAAATATAGA
* * * *
53124 AAAAATTTATAAAATTTTATATAAA-ATCGTA
1 AAAAAATTATAAAA-TATATAGAAATATAG-A
* *
53155 AAAAAATTATAAAAATATAAATAAATATA
1 AAAAAATTAT-AAAATATATAGAAATATA
53184 AAATTTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
30 16 0.33
31 26 0.54
32 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAAATTATAAAATATATAGAAATATAGA
Found at i:53434 original size:23 final size:23
Alignment explanation
Indices: 53407--53454 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
53397 CTTTTTATGA
53407 TTTTATAAATTTTACAATTTTTT
1 TTTTATAAATTTTACAATTTTTT
* * * *
53430 TTTTATGATTTTTATAGTTTTTT
1 TTTTATAAATTTTACAATTTTTT
53453 TT
1 TT
53455 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTATAAATTTTACAATTTTTT
Found at i:67473 original size:21 final size:21
Alignment explanation
Indices: 67447--67496 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
67437 GATTATGTAA
*
67447 TTTGGATTTATAATCTTTATG
1 TTTGGATTTATAAACTTTATG
*
67468 TTTGGATTTCTAAACTTTATG
1 TTTGGATTTATAAACTTTATG
67489 TTTGGATT
1 TTTGGATT
67497 ATGCTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (21 bp):
TTTGGATTTATAAACTTTATG
Found at i:71231 original size:15 final size:15
Alignment explanation
Indices: 71211--71249 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
71201 GCACATCAAA
*
71211 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
71226 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
71240 CAAGAATTAA
1 CAAGAATTAA
71250 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:71761 original size:13 final size:13
Alignment explanation
Indices: 71740--71773 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
71730 ACAATATAAT
71740 AATAATAATCCTA
1 AATAATAATCCTA
*
71753 AATATTAATCCTA
1 AATAATAATCCTA
*
71766 AAAAATAA
1 AATAATAA
71774 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:73602 original size:69 final size:69
Alignment explanation
Indices: 73491--73628 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
73481 TTTTGAAATG
*
73491 GAAAGTTTGGGAGAGAATACATTCACTCTTATCCAGAATAAGATACTCTTTTAATGCAAAGACTC
1 GAAAGTTTGGGAGAGAATACATTCACTCTTATCCAGAATAAGATACTCTCTTAATGCAAAGACTC
73556 AGGT
66 AGGT
73560 GAAAGTTTGGGAGAGAATACATTCACTCTTATCCAGAATAAGATACTCTCTTAATGCAAAGACTC
1 GAAAGTTTGGGAGAGAATACATTCACTCTTATCCAGAATAAGATACTCTCTTAATGCAAAGACTC
73625 AGGT
66 AGGT
73629 ATATTTTCAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (69 bp):
GAAAGTTTGGGAGAGAATACATTCACTCTTATCCAGAATAAGATACTCTCTTAATGCAAAGACTC
AGGT
Found at i:79629 original size:154 final size:154
Alignment explanation
Indices: 79345--79656 Score: 597
Period size: 154 Copynumber: 2.0 Consensus size: 154
79335 GACTCAGTAA
*
79345 GAATAGATGGCCAATCTTTTGGCGAGGCAGTGTATTTAGCTGAAACAATTGATCCCATGATTTCT
1 GAATAGATGGCCAATCTTTTGGCGAGGCAGTGTATTTAGCTAAAACAATTGATCCCATGATTTCT
* *
79410 TTTCAATGCTACAAGGTAATGAATAATGGGTTGGGTTGTGTAGGATGAGTTCATGCCTTGTCTTA
66 TTTCAATGCTACAAGGTAATGAATAATGGGTTGGGTTGTGTAGGATGAATTCATGCCTTGCCTTA
79475 AAGGTATACTAATGGAACCCAACT
131 AAGGTATACTAATGGAACCCAACT
79499 GAATAGATGGCCAATCTTTTGGCGAGGCAGTGTATTTAGCTAAAACAATTGATCCCATGATTTCT
1 GAATAGATGGCCAATCTTTTGGCGAGGCAGTGTATTTAGCTAAAACAATTGATCCCATGATTTCT
79564 TTTCAATGCTACAAGGTAATGAATAATGGGTTGGGTTGTGTAGGATGAATTCATGCCTTGCCTTA
66 TTTCAATGCTACAAGGTAATGAATAATGGGTTGGGTTGTGTAGGATGAATTCATGCCTTGCCTTA
79629 AAGGTATACTAATGGAACCCAACT
131 AAGGTATACTAATGGAACCCAACT
79653 GAAT
1 GAAT
79657 CTACAACACC
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (154 bp):
GAATAGATGGCCAATCTTTTGGCGAGGCAGTGTATTTAGCTAAAACAATTGATCCCATGATTTCT
TTTCAATGCTACAAGGTAATGAATAATGGGTTGGGTTGTGTAGGATGAATTCATGCCTTGCCTTA
AAGGTATACTAATGGAACCCAACT
Found at i:85693 original size:26 final size:27
Alignment explanation
Indices: 85639--85705 Score: 127
Period size: 26 Copynumber: 2.5 Consensus size: 27
85629 GATTCTGAAA
85639 CACGGATTTATTCCCTCAAATGTAGCT
1 CACGGATTTATTCCCTCAAATGTAGCT
85666 CACGGATTTATTCCCTC-AATGTAGCT
1 CACGGATTTATTCCCTCAAATGTAGCT
85692 CACGGATTTATTCC
1 CACGGATTTATTCC
85706 TTGTTTTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 23 0.57
27 17 0.43
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (27 bp):
CACGGATTTATTCCCTCAAATGTAGCT
Found at i:88135 original size:18 final size:19
Alignment explanation
Indices: 88092--88141 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
88082 GATAAATTAA
*
88092 ATTTTTTT-ATTAATTTTT
1 ATTTTTTTAATTAATATTT
* *
88110 AGTATTTTAATTAA-ATTT
1 ATTTTTTTAATTAATATTT
*
88128 ATTTTTTTATTTAA
1 ATTTTTTTAATTAA
88142 CAATTTCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAATTAATATTT
Found at i:89604 original size:17 final size:17
Alignment explanation
Indices: 89563--89605 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
89553 TCAACAAATT
89563 ATTTTAAACTTAAAAAA
1 ATTTTAAACTTAAAAAA
*
89580 ATAATTAAAC-TAAAAAA
1 AT-TTTAAACTTAAAAAA
89597 CATTTTAAA
1 -ATTTTAAA
89606 AAATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTTTAAACTTAAAAAA
Found at i:90920 original size:22 final size:22
Alignment explanation
Indices: 90877--90920 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
90867 AAAATTATTT
*
90877 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
90899 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
90921 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:92589 original size:13 final size:13
Alignment explanation
Indices: 92571--92617 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
92561 AGAGAAAAAG
92571 TTATTTTAATTTT
1 TTATTTTAATTTT
92584 TTA-TTTAATTTT
1 TTATTTTAATTTT
*
92596 TTAATCTTTAAATTT
1 TT-AT-TTTAATTTT
*
92611 ATATTTT
1 TTATTTT
92618 TTATTAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 2 0.07
15 9 0.31
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTTAATTTT
Found at i:94155 original size:38 final size:38
Alignment explanation
Indices: 94100--94173 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
94090 CATGTATATC
*
94100 CAACACAACCTCGAGGCGTGACCTCTAAGGGTTCCCCT
1 CAACACAACCTCAAGGCGTGACCTCTAAGGGTTCCCCT
94138 CAACACAACCTCAAGGCGTGACCTCTAAGGGTTCCC
1 CAACACAACCTCAAGGCGTGACCTCTAAGGGTTCCC
94174 TTCTATATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.36, G:0.20, T:0.18
Consensus pattern (38 bp):
CAACACAACCTCAAGGCGTGACCTCTAAGGGTTCCCCT
Found at i:96922 original size:22 final size:24
Alignment explanation
Indices: 96869--96922 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
96859 TAAAATTATT
96869 AATAATATATTTTTGTATATTTAA
1 AATAATATATTTTTGTATATTTAA
* *
96893 ATTTATATATTTTT-T-TA-TTAA
1 AATAATATATTTTTGTATATTTAA
96914 CAATAATAT
1 -AATAATAT
96923 TAATATCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 1 0.04
24 12 0.48
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
AATAATATATTTTTGTATATTTAA
Found at i:97353 original size:13 final size:13
Alignment explanation
Indices: 97335--97359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97325 TAAAAACGCT
97335 ACCAACCAACCAA
1 ACCAACCAACCAA
97348 ACCAACCAACCA
1 ACCAACCAACCA
97360 GCAATGACCC
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (13 bp):
ACCAACCAACCAA
Found at i:99013 original size:20 final size:20
Alignment explanation
Indices: 98985--99022 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
98975 TTTTTGGTTA
98985 TTTTGGTTTCAACTTGAAGC
1 TTTTGGTTTCAACTTGAAGC
* *
99005 TTTTTGTTTGAACTTGAA
1 TTTTGGTTTCAACTTGAA
99023 AAACCTTGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTTGGTTTCAACTTGAAGC
Found at i:102779 original size:7 final size:7
Alignment explanation
Indices: 102767--102792 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
102757 ACAATTATAC
102767 TTGAATT
1 TTGAATT
102774 TTGAATT
1 TTGAATT
102781 TTGAATT
1 TTGAATT
102788 TTGAA
1 TTGAA
102793 AAAGTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (7 bp):
TTGAATT
Found at i:106780 original size:16 final size:17
Alignment explanation
Indices: 106749--106780 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
106739 CCTTTATTAG
106749 CAAAATAAAGAAAAACA
1 CAAAATAAAGAAAAACA
106766 CAAAATAAA-AAAAAC
1 CAAAATAAAGAAAAAC
106781 CCTTACACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.78, C:0.12, G:0.03, T:0.06
Consensus pattern (17 bp):
CAAAATAAAGAAAAACA
Found at i:111980 original size:8 final size:8
Alignment explanation
Indices: 111967--111991 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
111957 TCTTAATATG
111967 ATGTGTTT
1 ATGTGTTT
111975 ATGTGTTT
1 ATGTGTTT
111983 ATGTGTTT
1 ATGTGTTT
111991 A
1 A
111992 AACTTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (8 bp):
ATGTGTTT
Found at i:112547 original size:20 final size:21
Alignment explanation
Indices: 112507--112548 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
112497 GAGAATTAAA
* *
112507 AAAAATTAAAATATATTAATT
1 AAAAATAAAAATATATAAATT
112528 AAAAATAAAAATATA-AAATT
1 AAAAATAAAAATATATAAATT
112548 A
1 A
112549 TTTGTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATAAAAATATATAAATT
Found at i:122519 original size:61 final size:58
Alignment explanation
Indices: 122431--122821 Score: 267
Period size: 61 Copynumber: 6.5 Consensus size: 58
122421 GAAAAAAAAA
* *
122431 TTTGGTGTTGG-CTATTGCAA-GGCCGACACTCCTTTTTAATCTGATAAAAAAAATCAAATT
1 TTTGGTGTTGGTC-A-TGCAATGGTCGACACTCCTTTTT--TCAGATAAAAAAAATCAAATT
* * * * * *
122491 TTTGGATGTTGGTCATGCAATGATCGACAACCACCTTTTTGTCAAAT-AAAAAATTTAATTT
1 TTTGG-TGTTGGTCATGCAATGGTCGAC-A-CTCCTTTTT-TCAGATAAAAAAAATCAAATT
* * * **
122552 TTTGGTATTGGCCATGAAATGG-CTGACACT-CTTATTTATTTGATAAAAAAAATCAAATT
1 TTTGGTGTTGGTCATGCAATGGTC-GACACTCCTT-TTT-TCAGATAAAAAAAATCAAATT
* * * * * *
122611 TTTGGGTGTTAGCCATGCAATGGCCAACACTCCTTTTTTTCAAATAAAAAAATTTCAAATTT
1 TTT-GGTGTTGGTCATGCAATGGTCGACACTCC-TTTTTTCAGATAAAAAAA-ATCAAA-TT
** ** * *
122673 TTTTATGTTAATCATGCAATGGTCGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTT
1 TTTGGTGTTGGTCATGCAATGGTCGACACTCCTTTTTTCAGATAAAAAAA-ATC-AAA-TT
* * *
122734 TTTGGTGTTGGTCATGCCATGGGCGACAC-CCTCTTTTT--GTAAAATAAAAAATCAAATTT
1 TTTGGTGTTGGTCATGCAATGGTCGACACTCCT-TTTTTCAG-ATAA-AAAAAATCAAA-TT
*
122793 TTTTGTGTTGGTCATGCAATGGTCGACAC
1 TTTGGTGTTGGTCATGCAATGGTCGACAC
122822 CCCCCTTTTT
Statistics
Matches: 265, Mismatches: 48, Indels: 37
0.76 0.14 0.11
Matches are distributed among these distances:
57 3 0.01
58 7 0.03
59 49 0.18
60 86 0.32
61 99 0.37
62 13 0.05
63 8 0.03
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (58 bp):
TTTGGTGTTGGTCATGCAATGGTCGACACTCCTTTTTTCAGATAAAAAAAATCAAATT
Found at i:122717 original size:120 final size:119
Alignment explanation
Indices: 122446--122869 Score: 375
Period size: 120 Copynumber: 3.5 Consensus size: 119
122436 TGTTGGCTAT
* * *
122446 TGCAA-GGCCGACACTCCTTTTTAATCTGATAAAAAAAATCAAATTTTTGGATGTTGGTCATGCA
1 TGCAATGGTCGACACCCCTTTTT-ATCTGATAAAAAAAATCAAATTTTTGGGTGTTGGTCATGCA
* * * *
122510 ATGATCGACAAC-CACCTTTTTGTCAAATAAAAAATTT--AATTTTTTGGTATTGGCCA
65 ATG---GACAACAC-CCTTTTTTTCAAATAAAAAATTTCAAATTTTTTTGTGTTGGTCA
* * * * *
122566 TGAAATGG-CTGACA-CTCTTATTTATTTGATAAAAAAAATCAAATTTTTGGGTGTTAGCCATGC
1 TGCAATGGTC-GACACCCCTT-TTTATCTGATAAAAAAAATCAAATTTTTGGGTGTTGGTCATGC
* * **
122629 AATGGCCAACACTCCTTTTTTTCAAATAAAAAAATTTCAAATTTTTTTATGTTAATCA
64 AATGGACAACAC-CCTTTTTTTCAAAT-AAAAAATTTCAAATTTTTTTGTGTTGGTCA
* * *
122687 TGCAATGGTCGACACCCCTTTTT-TCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGC
1 TGCAATGGTCGACACCCCTTTTTATCTGATAAAAAAA-ATC-AAATTTTTGGGTGTTGGTCATGC
* * * *
122751 CATGGGCGACACCCTCTTTTTGTAAAATAAAAAA--TCAAATTTTTTTGTGTTGGTCA
64 AATGGACAACACCCT-TTTTT-TCAAATAAAAAATTTCAAATTTTTTTGTGTTGGTCA
* * *
122807 TGCAATGGTCGACACCCCCCTTTT-TGTGA-AATAAAAAATTCAAAATTTTTTTGGTGTTGGTCA
1 TGCAATGGTCGACA-CCCCTTTTTATCTGATAA-AAAAAA-TC-AAA-TTTTTGGGTGTTGGTCA
122870 CGTCATGACC
Statistics
Matches: 252, Mismatches: 35, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
117 5 0.02
118 14 0.06
119 9 0.04
120 94 0.37
121 63 0.25
122 62 0.25
123 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (119 bp):
TGCAATGGTCGACACCCCTTTTTATCTGATAAAAAAAATCAAATTTTTGGGTGTTGGTCATGCAA
TGGACAACACCCTTTTTTTCAAATAAAAAATTTCAAATTTTTTTGTGTTGGTCA
Found at i:122721 original size:59 final size:61
Alignment explanation
Indices: 122474--122869 Score: 316
Period size: 60 Copynumber: 6.5 Consensus size: 61
122464 TTTTAATCTG
* * *
122474 ATAAAAAAAATC-AAA-TTTTTGGATGTTGGTCATGCAATGATCGACAACCACCTTTTTGTCAA
1 ATAAAAAAATTCAAAATTTTTTTG-TGTTGGTCATGCAATGGTCGAC-ACC-CCTTTTTGTCAA
* * * * * * * ***
122536 AT-AAAAAATT--TAATTTTTTGGTATTGGCCATGAAATGG-CTGACA-CTCTTATTTATTTG
1 ATAAAAAAATTCAAAATTTTTTTGTGTTGGTCATGCAATGGTC-GACACCCCTT-TTTGTCAA
* ** * * * * * *
122594 ATAAAAAAAATC-AAATTTTTGGGTGTTAGCCATGCAATGGCCAACACTCCTTTTTTTCAA
1 ATAAAAAAATTCAAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCTTTTTGTCAA
* ** *
122654 ATAAAAAAATTTC-AAATTTTTTTATGTTAATCATGCAATGGTCGACACCCCTTTTT-TCAG
1 ATAAAAAAA-TTCAAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCTTTTTGTCAA
* * * *
122714 ATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCCATGGGCGACACCCTCTTTTTGTAAA
1 ATAAAAAAA-TTCAAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCC-CTTTTTGTCAA
*
122777 AT-AAAAAA-TC-AAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCCCTTTTTGTGAA
1 ATAAAAAAATTCAAAATTTTTTTGTGTTGGTCATGCAATGGTCGACA--CCCCTTTTTGTCAA
122837 AT-AAAAAATTCAAAATTTTTTTGGTGTTGGTCA
1 ATAAAAAAATTCAAAATTTTTTT-GTGTTGGTCA
122870 CGTCATGACC
Statistics
Matches: 272, Mismatches: 46, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
57 3 0.01
58 7 0.03
59 40 0.15
60 93 0.34
61 91 0.33
62 24 0.09
63 14 0.05
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (61 bp):
ATAAAAAAATTCAAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCTTTTTGTCAA
Found at i:122771 original size:122 final size:120
Alignment explanation
Indices: 122593--122895 Score: 346
Period size: 122 Copynumber: 2.5 Consensus size: 120
122583 TTATTTATTT
* * * * * * *
122593 GATAAAAAAAATC-AAATTTTTGGGTGTTAGCCATGCAATGGCCAACACTCCT-TTTTTTCAAAT
1 GATAAAAAAATTCAAAATTTTTTGGTGTTGGTCATGCCATGGCCGACAC-CCTCTTTTTTAAAAT
122656 AAAAAAATTTCAAATTTTTTTATGTTAATCATGCAATGGTCGACA-CCCCTTTTT-TCA
65 -AAAAAA--TCAAATTTTTTTATGTTAATCATGCAATGGTCGACACCCCCTTTTTGTCA
*
122713 GATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCCATGGGCGACACCCTCTTTTTGTAAAA
1 GATAAAAAAA-TTCAAAATTTTTTGGTGTTGGTCATGCCATGGCCGACACCCTCTTTTT-TAAAA
* ** *
122778 TAAAAAATCAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCCCTTTTTGTGA
64 TAAAAAATCAAATTTTTTTATGTTAATCATGCAATGGTCGACA-CCCCCTTTTTGTCA
* * * * *
122836 AAT-AAAAAATTCAAAATTTTTTTGGTGTTGGTCACGTCATGACCGACACCCCCTTTTTTA
1 GATAAAAAAATTCAAAA-TTTTTTGGTGTTGGTCATGCCATGGCCGACACCCTCTTTTTTA
122896 TTTGGTAAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
120 43 0.27
121 14 0.09
122 91 0.58
123 9 0.06
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (120 bp):
GATAAAAAAATTCAAAATTTTTTGGTGTTGGTCATGCCATGGCCGACACCCTCTTTTTTAAAATA
AAAAATCAAATTTTTTTATGTTAATCATGCAATGGTCGACACCCCCTTTTTGTCA
Found at i:122905 original size:63 final size:60
Alignment explanation
Indices: 122477--122926 Score: 252
Period size: 61 Copynumber: 7.4 Consensus size: 60
122467 TAATCTGATA
* ** * *
122477 AAAAAAATCAAA--TTTTTGGATGTTGGTCATGCAATGATCGACAACCACCTTTTTGT-CAAAT
1 AAAAAATTCAAATTTTTTTGG-TGTTGGTCATGC-ATGGCCGAC-ACCCCCTTTTT-TATAAAT
* * * * * ***
122538 AAAAAATT-TAA-TTTTTTGGTATTGGCCATGAAATGGCTGACACTCTTATTTATTTGAT-AA-
1 AAAAAATTCAAATTTTTTTGGTGTTGGTCATG-CATGGCCGACAC-CCCCTTT-TTT-ATAAAT
* * * * *
122598 AAAAAA-TCAAA-TTTTTGGGTGTTAGCCATGCAATGGCCAACA-CTCCTTTTTT-TCAAAT
1 AAAAAATTCAAATTTTTTTGGTGTTGGTCATGC-ATGGCCGACACCCCCTTTTTTAT-AAAT
* ** * *
122656 AAAAAAATTTCAAATTTTTTT-ATGTTAATCATGCAATGGTCGACA-CCCCTTTTTTCAGATAA-
1 -AAAAAA-TTCAAATTTTTTTGGTGTTGGTCATGC-ATGGCCGACACCCCCTTTTTT-ATA-AAT
* * * *
122718 AAAAATTTCAAAATTTTTTGGTGTTGGTCATGCCATGGGCGACACCCTCTTTTTGTA-AAAT
1 AAAAAATTCAAATTTTTTTGGTGTTGGTCATG-CATGGCCGACACCCCCTTTTT-TATAAAT
* * *
122779 AAAAAA-TCAAATTTTTTT-GTGTTGGTCATGCAATGGTCGACACCCCCCTTTTTGTGAAAT
1 AAAAAATTCAAATTTTTTTGGTGTTGGTCATGC-ATGGCCGACACCCCCTTTTTTAT-AAAT
* * ***
122839 AAAAAATTCAAAATTTTTTTGGTGTTGGTCACGTCATGACCGACACCCCCTTTTTTATTTGGT
1 AAAAAATTC-AAATTTTTTTGGTGTTGGTCATG-CATGGCCGACACCCCCTTTTTTA-TAAAT
*
122902 AAAAAATT-AAATTTTTTTAGTGTTG
1 AAAAAATTCAAATTTTTTTGGTGTTG
122927 ACCATGTAAT
Statistics
Matches: 307, Mismatches: 51, Indels: 62
0.73 0.12 0.15
Matches are distributed among these distances:
55 1 0.00
57 5 0.02
58 7 0.02
59 38 0.12
60 89 0.29
61 98 0.32
62 26 0.08
63 41 0.13
64 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (60 bp):
AAAAAATTCAAATTTTTTTGGTGTTGGTCATGCATGGCCGACACCCCCTTTTTTATAAAT
Found at i:122917 original size:122 final size:120
Alignment explanation
Indices: 122642--122925 Score: 313
Period size: 122 Copynumber: 2.3 Consensus size: 120
122632 GGCCAACACT
* *
122642 CCTTTTTTTCAAATAAAAAAATTTCAAATTTTTTTATGTTAATCATGCAATGGTCGACACCCCTT
1 CCTTTTTGTAAAAT-AAAAAA-TT-AAATTTTTTTATGTTAATCATGCAATGGTCGACACCCCTT
* * **
122707 TTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCCATGGGCGACACCC
63 TTTTCAAATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCACGCCATGACCGACACCC
* * * **
122765 TCTTTTTGTAAAATAAAAAATCAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCCCTTT
1 CCTTTTTGTAAAATAAAAAATTAAATTTTTTTATGTTAATCATGCAATGGTCGACA--CCCCTTT
* *
122830 TTGTGAAAT-AAAAAA-TTCAAAATTTTTTTGGTGTTGGTCACGTCATGACCGACACCC
64 TT-TCAAATAAAAAAATTTCAAAA-TTTTTTGGTGTTGGTCACGCCATGACCGACACCC
***
122887 CCTTTTT-TATTTGGTAAAAAATTAAATTTTTTTAGTGTT
1 CCTTTTTGTA--AAATAAAAAATTAAATTTTTTTA-TGTT
122926 GACCATGTAA
Statistics
Matches: 135, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
120 31 0.23
121 10 0.07
122 57 0.42
123 33 0.24
124 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (120 bp):
CCTTTTTGTAAAATAAAAAATTAAATTTTTTTATGTTAATCATGCAATGGTCGACACCCCTTTTT
TCAAATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCACGCCATGACCGACACCC
Found at i:123780 original size:17 final size:17
Alignment explanation
Indices: 123760--123814 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
123750 AAAAAATAAT
123760 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
*
123777 AATTAGAA-A-ATA--A
1 AATTAGAATATACAGGA
*
123790 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
123807 AATTAGAA
1 AATTAGAA
123815 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
15 4 0.13
16 1 0.03
17 16 0.53
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.24
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:123800 original size:30 final size:30
Alignment explanation
Indices: 123752--123829 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
123742 AAATTTTCAA
*
123752 AAAATAATAATTAGAATATACAGGAAATTAG
1 AAAATAA-AATTAAAATATACAGGAAATTAG
123783 AAAATAAAATTAAAATATACAGGAAATTAG
1 AAAATAAAATTAAAATATACAGGAAATTAG
* *
123813 AAATTAAATTTAAAATA
1 AAAATAAAATTAAAATA
123830 AAAACAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 37 0.84
31 7 0.16
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.27
Consensus pattern (30 bp):
AAAATAAAATTAAAATATACAGGAAATTAG
Found at i:123840 original size:30 final size:30
Alignment explanation
Indices: 123776--123857 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
123766 AATATACAGG
* * * * **
123776 AAATTAGAAAATAAAATTAAAATATACAGG
1 AAATTAGAAATTAAATTTAAAATAAAAACA
123806 AAATTAGAAATTAAATTTAAAATAAAAACA
1 AAATTAGAAATTAAATTTAAAATAAAAACA
*
123836 AAATTACAAATTAAATTTAAAA
1 AAATTAGAAATTAAATTTAAAA
123858 AGTAAATGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATTAGAAATTAAATTTAAAATAAAAACA
Found at i:127806 original size:119 final size:122
Alignment explanation
Indices: 127656--128203 Score: 378
Period size: 119 Copynumber: 4.6 Consensus size: 122
127646 AGGAGAAGTT
* *
127656 GGTGTCGGTCATTACAT-AGCCAACACCAAAAAATTTTAATTTTTTACCAAAT-AAAAA-GAGGT
1 GGTGTCGGTCATTGCATGA-CCAACACAAAAAAATTTTAATTTTTTACCAAATAAAAAAGGAGGT
* * * * * *
127718 GTCGACCATGGCAT-GACAAATACCAAAAAAATTTGAATTTTTTATTTTA-TAAAAGGG
65 GTCGACCATGGCATGGAC-AACACAAAAAAAATTCGAATTTTTTATCTGACAAAAAGGG
* * * * *
127775 GGTGTCGGTAATTGCATGACCAATACAAAAAAA--TTGATTTTTTACCAGATAAAAAAGGGGGTG
1 GGTGTCGGTCATTGCATGACCAACACAAAAAAATTTTAATTTTTTACCAAATAAAAAAGGAGGTG
* *
127838 TCGGCCATGGCATGGTCAACACAAAAAAAATTCGAATTTTTTATCTGACAAAAAGGG
66 TCGACCATGGCATGGACAACACAAAAAAAATTCGAATTTTTTATCTGACAAAAAGGG
* * * *
127895 AGTGTCGGCCATAGCATGACCAACACAAAAAAATTTTGAAATTTTTTTATC---TGAAAAAAGGA
1 GGTGTCGGTCATTGCATGACCAACACAAAAAAATTTT--AA-TTTTTTACCAAAT-AAAAAAGGA
* *** * * * *
127957 -GTGTCAACCATTATATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGGG
62 GGTGTCGACCATGGCATGGACAACACAAAAAAAATTCG-AA-TTTTTTATCTGACAAAAAGGG
*** * ** * * * * *
128018 GGTGTCAACCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGAT-AAATAGG-GGT
1 GGTGTCGGTCATTGCATGACCAACACAAAAAAATTTTA-ATTTTTTACCAAATAAAAAAGGAGGT
* ** * *
128081 GTCGGCCATTTCATGG-CTAACAC-CAAAAAATT-GAATTTTTTATCTAACAAAAA-GG
65 GTCGACCATGGCATGGAC-AACACAAAAAAAATTCGAATTTTTTATCTGACAAAAAGGG
*** * ** * * * * *
128136 GGTGTCAACCATTGCATGGCCAACACTCAAAAATTTGATTTTTTTTATCAGATTAAAAAGG-GGT
1 GGTGTCGGTCATTGCATGACCAACACAAAAAAATTTTA-ATTTTTTACCAAATAAAAAAGGAGGT
128200 GTCG
65 GTCG
128204 GCCGTTGCAA
Statistics
Matches: 357, Mismatches: 51, Indels: 42
0.79 0.11 0.09
Matches are distributed among these distances:
117 15 0.04
118 70 0.20
119 90 0.25
120 39 0.11
121 18 0.05
122 56 0.16
123 47 0.13
124 14 0.04
125 8 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (122 bp):
GGTGTCGGTCATTGCATGACCAACACAAAAAAATTTTAATTTTTTACCAAATAAAAAAGGAGGTG
TCGACCATGGCATGGACAACACAAAAAAAATTCGAATTTTTTATCTGACAAAAAGGG
Found at i:127900 original size:61 final size:58
Alignment explanation
Indices: 127656--128222 Score: 429
Period size: 60 Copynumber: 9.4 Consensus size: 58
127646 AGGAGAAGTT
* * * * * * ** *
127656 GGTGTCGGTCATTACATAGCCAACACCAAAAAATTTTAATTTTTTACCAAATAAAAAGA
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTGA-AAAAAGG
* * * * * * * *
127715 GGTGTCGACCATGGCATGACAAATACCAAAAAAATTTGAATTTTTTATTTTATAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACA-CAAAAAAATTTGAATTTTTTATCTGA-AAAAAGG
** * * * *
127775 GGTGTCGGTAATTGCATGACCAATACAAAAAAA-TTG-ATTTTTTACCAGATAAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTG--AAAAAA-GG
* * *
127834 GGTGTCGGCCATGGCATGGTCAACACAAAAAAAATTCGAATTTTTTATCTGACAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACAC-AAAAAAATTTGAATTTTTTATCTGA-AAAAAGG
* *
127894 GAGTGTCGGCCATAGCATGACCAACACAAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
1 G-GTGTCGGCCATTGCATGGCCAACACAAAAAAA-TTTG-AA-TTTTTTATCTGAAAAAAGG
* ** ** *
127956 AGTGTCAACCATTATATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACA-CAAAAAAATTTG-AA-TTTTTTATCTGAAAAAA-GG
** ** * * *
128018 GGTGTCAACCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGATAAATAGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTGA-ATTTTTTATCTGA-AAAAAGG
* * * *
128078 GGTGTCGGCCATTTCATGGCTAACACCAAAAAA-TTGAATTTTTTATCTAACAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTGA-AAAAAGG
** ** * *
128136 GGTGTCAACCATTGCATGGCCAACACTCAAAAATTTGATTTTTTTTATCAGATTAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTGA-ATTTTTTATCTGA--AAAAAGG
* * *
128197 GGTGTCGGCCGTTGCAAGGCCTACAC
1 GGTGTCGGCCATTGCATGGCCAACAC
128223 TAAATTTTTT
Statistics
Matches: 408, Mismatches: 81, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
57 8 0.02
58 50 0.12
59 56 0.14
60 116 0.28
61 116 0.28
62 50 0.12
63 12 0.03
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (58 bp):
GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTGAAAAAAGG
Found at i:129065 original size:16 final size:16
Alignment explanation
Indices: 129034--129077 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
129024 ACTAGTTAGT
129034 TATAAAAATA-AATTA
1 TATAAAAATATAATTA
* *
129049 TGTAAAAATATATTTA
1 TATAAAAATATAATTA
*
129065 TAAAAAAATATAA
1 TATAAAAATATAA
129078 AACAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TATAAAAATATAATTA
Found at i:130472 original size:12 final size:12
Alignment explanation
Indices: 130455--130480 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
130445 AATTTGTTTG
130455 TTGTTTTAATAT
1 TTGTTTTAATAT
130467 TTGTTTTAATAT
1 TTGTTTTAATAT
130479 TT
1 TT
130481 TTAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:130506 original size:26 final size:24
Alignment explanation
Indices: 130475--130522 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
130465 ATTTGTTTTA
*
130475 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
130501 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
130523 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:132103 original size:14 final size:13
Alignment explanation
Indices: 132084--132113 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
132074 TAACAACGGT
132084 ATTAATTTTAATCA
1 ATTAATTTTAAT-A
132098 ATTAATTTTAATA
1 ATTAATTTTAATA
132111 ATT
1 ATT
132114 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTAATTTTAATA
Found at i:132253 original size:24 final size:24
Alignment explanation
Indices: 132204--132260 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
132194 AATTTATTAA
* * *
132204 ATGTTGTATGTTAATTGTGTATAT
1 ATGTTGTTTTTTAATTGTGTAAAT
132228 ATGTTGTTTTTTAATTGAT-TAAAT
1 ATGTTGTTTTTTAATTG-TGTAAAT
132252 AT-TT-TTTTT
1 ATGTTGTTTTT
132261 AAGAGTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 21 0.72
25 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (24 bp):
ATGTTGTTTTTTAATTGTGTAAAT
Found at i:136771 original size:162 final size:162
Alignment explanation
Indices: 136504--137308 Score: 1520
Period size: 162 Copynumber: 5.0 Consensus size: 162
136494 AAGAACCACT
* * * *
136504 AACTCGTTCACTAGTGTCCAAAATGGCGTTAAAATCCCCAGCCAAAATCTAAGGCCCCGTAACCC
1 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
*
136569 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTATCATGTGGACTCGCATAA
66 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
136634 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
131 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
136666 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
1 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
136731 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
66 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
136796 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
131 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
* * *
136828 AACTCATTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAAGCCCCATAACCC
1 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
136893 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
66 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
136958 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
131 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
*
136990 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCATAACCC
1 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
137055 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
66 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
137120 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
131 ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
*
137152 AACTCGCTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
1 AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
137217 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
66 TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
137282 ACAAAAGAACAGTAGAAAGAACCAGAG
131 ACAAAAGAACAGTAGAAAGAACCAGAG
137309 TAATTTTATT
Statistics
Matches: 631, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 631 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.19
Consensus pattern (162 bp):
AACTCGTTCACTATTGTCCAAAATAGCGTTAAAATCCCCAACCAAAATCCAAGGCCCCGTAACCC
TTGAGGACAAAGAACCCAAAGTCTGCCAAAATTGCTTCCGTTTAGTACCATGTGGACTCGCATAA
ACAAAAGAACAGTAGAAAGAACCAGAGCAACC
Found at i:139610 original size:22 final size:22
Alignment explanation
Indices: 139585--139634 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
139575 TAAAAAGTAT
* *
139585 ATAAAATTTAAAACATTAAAAA
1 ATAAAATTAAAAAAATTAAAAA
*
139607 ATAAAATTAAAAAAATTAAAAC
1 ATAAAATTAAAAAAATTAAAAA
139629 ATAAAA
1 ATAAAA
139635 AATTTAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
ATAAAATTAAAAAAATTAAAAA
Found at i:139611 original size:15 final size:15
Alignment explanation
Indices: 139593--139637 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
139583 ATATAAAATT
139593 TAAAACATTAAAAAA
1 TAAAACATTAAAAAA
139608 T-AAA-ATTAAAAAAA
1 TAAAACATT-AAAAAA
139622 TTAAAACA-TAAAAAA
1 -TAAAACATTAAAAAA
139637 T
1 T
139638 TTAGTTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.12
14 10 0.38
15 8 0.31
16 4 0.15
17 1 0.04
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAAACATTAAAAAA
Found at i:139638 original size:15 final size:15
Alignment explanation
Indices: 139587--139638 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
139577 AAAAGTATAT
*
139587 AAAATTTAAAACATTA
1 AAAAATTAAAACA-TA
*
139603 AAAAA-TAAAA-TTAA
1 AAAAATTAAAACAT-A
139617 AAAAATTAAAACATA
1 AAAAATTAAAACATA
139632 AAAAATT
1 AAAAATT
139639 TAGTTAACAG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.03
14 6 0.20
15 18 0.60
16 5 0.17
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATTAAAACATA
Found at i:156066 original size:16 final size:16
Alignment explanation
Indices: 156047--156077 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
156037 TCCTTTTCAT
156047 TTTTTA-TATTTTATA
1 TTTTTAGTATTTTATA
156062 TTTTTAGTATTTTATA
1 TTTTTAGTATTTTATA
156078 CTAAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTAGTATTTTATA
Found at i:158176 original size:27 final size:27
Alignment explanation
Indices: 158107--158186 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
158097 TTGGTGACTA
*
158107 AAAAGAAAAATTCAAATAGTTGGGTGAC
1 AAAA-AAAAATCCAAATAGTTGGGTGAC
*
158135 -AAAAAAAA-CCGAATAGTTGGGTGAC
1 AAAAAAAAATCCAAATAGTTGGGTGAC
* * *
158160 AAAAAAAAATCCTAATAATTAGGTGAC
1 AAAAAAAAATCCAAATAGTTGGGTGAC
158187 TACTAGTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 15 0.33
26 13 0.29
27 17 0.38
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (27 bp):
AAAAAAAAATCCAAATAGTTGGGTGAC
Found at i:160957 original size:8 final size:8
Alignment explanation
Indices: 160944--160975 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
160934 GTTATTTAAT
160944 TTTCTTGG
1 TTTCTTGG
160952 TTTCTTGG
1 TTTCTTGG
160960 TTTCTTGG
1 TTTCTTGG
160968 TTTCTTGG
1 TTTCTTGG
160976 ACCTAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.00, C:0.12, G:0.25, T:0.62
Consensus pattern (8 bp):
TTTCTTGG
Found at i:161455 original size:17 final size:17
Alignment explanation
Indices: 161433--161472 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
161423 ACATAATTTG
161433 AATTTATCT-TAAAATTA
1 AATTTAT-TATAAAATTA
*
161450 AATTTATTATAAATTTA
1 AATTTATTATAAAATTA
161467 AATTTA
1 AATTTA
161473 AAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATTATAAAATTA
Found at i:161467 original size:23 final size:23
Alignment explanation
Indices: 161441--161486 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
161431 TGAATTTATC
161441 TTAAAATT-AAATTTATTATAAAT
1 TTAAAATTAAAATTTATT-TAAAT
*
161464 TTAAATTTAAAATTTATTTAAAT
1 TTAAAATTAAAATTTATTTAAAT
161487 AATGTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAAATTAAAATTTATTTAAAT
Found at i:163466 original size:29 final size:28
Alignment explanation
Indices: 163429--163554 Score: 112
Period size: 29 Copynumber: 4.3 Consensus size: 28
163419 CCTAAACCAT
163429 TTTTTACCCT-AAATTTTCTAAAAATTACA
1 TTTTTACCCTCAAA-TTTC-AAAAATTACA
* * **
163458 TTTTCACCCTCAAACTTTCCAAAATCCCA
1 TTTTTACCCTCAAA-TTTCAAAAATTACA
*
163487 TTTTTAACCTCAAATTTCCAAAAATTACA
1 TTTTTACCCTCAAATTT-CAAAAATTACA
* *
163516 TTTTTACCCCCAAACTTTCCAAAA-TACCA
1 TTTTTACCCTCAAA-TTTCAAAAATTA-CA
163545 TTTTTGACCC
1 TTTTT-ACCC
163555 GAATTCTCTA
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.06
29 60 0.76
30 14 0.18
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (28 bp):
TTTTTACCCTCAAATTTCAAAAATTACA
Found at i:163516 original size:58 final size:58
Alignment explanation
Indices: 163424--163549 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
163414 TAACTCCTAA
* * *
163424 ACCATTTTTTACCCTAAATTTTCTAAAAATTACATTTTCACCCTCAAACTTTCCAAAAT
1 ACCA-TTTTTAACCTAAATTTTCCAAAAATTACATTTTCACCCCCAAACTTTCCAAAAT
* *
163483 CCCATTTTTAACCTCAAA-TTTCCAAAAATTACATTTTTACCCCCAAACTTTCCAAAAT
1 ACCATTTTTAACCT-AAATTTTCCAAAAATTACATTTTCACCCCCAAACTTTCCAAAAT
163541 ACCATTTTT
1 ACCATTTTT
163550 GACCCGAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 54 0.90
59 6 0.10
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (58 bp):
ACCATTTTTAACCTAAATTTTCCAAAAATTACATTTTCACCCCCAAACTTTCCAAAAT
Found at i:163576 original size:58 final size:56
Alignment explanation
Indices: 163424--163583 Score: 178
Period size: 58 Copynumber: 2.8 Consensus size: 56
163414 TAACTCCTAA
* * *
163424 ACCATTTTTTACCCTAAATTTTCTAAAAATTACATTTTCACCCTCAAACTTTCCAAAAT
1 ACCATTTTTAACCC-AAA-TTTCT-AAAATTACATTTTTACCCCCAAACTTTCCAAAAT
* *
163483 CCCATTTTTAACCTCAAATTTCCAAAAATTACATTTTTACCCCCAAACTTTCCAAAAT
1 ACCATTTTTAACC-CAAATTT-CTAAAATTACATTTTTACCCCCAAACTTTCCAAAAT
* * *
163541 ACCATTTTTGACCCGAATTCTCTAAAATTGCCA-TTTTACCCCC
1 ACCATTTTTAACCCAAATT-TCTAAAATT-ACATTTTTACCCCC
163584 GAATGTCTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
57 22 0.25
58 49 0.56
59 15 0.17
60 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (56 bp):
ACCATTTTTAACCCAAATTTCTAAAATTACATTTTTACCCCCAAACTTTCCAAAAT
Found at i:163636 original size:30 final size:30
Alignment explanation
Indices: 163592--163696 Score: 74
Period size: 30 Copynumber: 3.5 Consensus size: 30
163582 CCGAATGTCT
* * *
163592 AAAAATTTCGATTTTGACTCCGAGCCTTCC
1 AAAAATTACCATTTTGACTCCAAGCCTTCC
* * *
163622 AAAAATTACCATTTT-ACCCCTCAA--ATGTCT
1 AAAAATTACCATTTTGA-CTC-CAAGCCT-TCC
**
163652 AAAAATT-CCGATTTTGACTGTAAGCCTTCC
1 AAAAATTACC-ATTTTGACTCCAAGCCTTCC
163682 AAAAATTACCATTTT
1 AAAAATTACCATTTT
163697 ACCCCCCGAG
Statistics
Matches: 56, Mismatches: 11, Indels: 16
0.67 0.13 0.19
Matches are distributed among these distances:
29 6 0.11
30 44 0.79
31 6 0.11
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (30 bp):
AAAAATTACCATTTTGACTCCAAGCCTTCC
Found at i:163664 original size:60 final size:59
Alignment explanation
Indices: 163564--163702 Score: 215
Period size: 60 Copynumber: 2.3 Consensus size: 59
163554 CGAATTCTCT
* * * *
163564 AAAATTGCCATTTTACCCCCGAATGTCTAAAAATTTCGATTTTGACTCCGAGCCTTCCA
1 AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCGATTTTGACTCCAAGCCTTCCA
**
163623 AAAATTACCATTTTACCCCTCAAATGTCTAAAAATTCCGATTTTGACTGTAAGCCTTCCA
1 AAAATTACCATTTTACCCC-CAAATGTCTAAAAATTCCGATTTTGACTCCAAGCCTTCCA
163683 AAAATTACCATTTTACCCCC
1 AAAATTACCATTTTACCCCC
163703 CGAGTGTCAT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
59 19 0.26
60 54 0.74
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCGATTTTGACTCCAAGCCTTCCA
Found at i:163745 original size:29 final size:30
Alignment explanation
Indices: 163679--163746 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
163669 CTGTAAGCCT
* **
163679 TCCAAAAATTACCATTTTACCCCCCGAGTG
1 TCCAAAAATTACCATTTTACCACCCGAGCA
* *
163709 T-CATAAATTACCGTTTTA-CACCCGAGCA
1 TCCAAAAATTACCATTTTACCACCCGAGCA
163737 TCCAAAAATT
1 TCCAAAAATT
163747 CATATTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.26
29 22 0.71
30 1 0.03
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTACCACCCGAGCA
Done.