Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015001.1 Kokia drynarioides strain JFW-HI SEQ_130045, 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: 675174
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 656 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:32599 original size:45 final size:46
Alignment explanation
Indices: 32518--32609 Score: 168
Period size: 45 Copynumber: 2.0 Consensus size: 46
32508 ATATTCTGAA
32518 TTGATTGATCTAATATCTTTTTTTCATATTGATACTCAACTAATTT
1 TTGATTGATCTAATATCTTTTTTTCATATTGATACTCAACTAATTT
*
32564 TTGATTGATCTAAT-TTTTTTTTTCATATTGATACTCAACTAATTT
1 TTGATTGATCTAATATCTTTTTTTCATATTGATACTCAACTAATTT
32609 T
1 T
32610 CCGTTCAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 31 0.69
46 14 0.31
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (46 bp):
TTGATTGATCTAATATCTTTTTTTCATATTGATACTCAACTAATTT
Found at i:32609 original size:23 final size:23
Alignment explanation
Indices: 32538--32610 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
32528 TAATATCTTT
32538 TTTTCATATTGATACTCAACTAA
1 TTTTCATATTGATACTCAACTAA
* **
32561 TTTT--TGATTGAT-CT-AATTTTTT
1 TTTTCAT-ATTGATACTCAA--CTAA
32583 TTTTCATATTGATACTCAACTAA
1 TTTTCATATTGATACTCAACTAA
32606 TTTTC
1 TTTTC
32611 CGTTCAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 11 0.30
23 16 0.43
24 3 0.08
25 2 0.05
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTTCATATTGATACTCAACTAA
Found at i:32975 original size:19 final size:19
Alignment explanation
Indices: 32953--32996 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
32943 CTATAACAAC
*
32953 ATTTTATTAT-AATAATTAA
1 ATTTTATTATGAA-AATCAA
32972 A-TTTATTATGAAAATCAA
1 ATTTTATTATGAAAATCAA
32990 ATTTTAT
1 ATTTTAT
32997 GTTATTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTTTATTATGAAAATCAA
Found at i:33221 original size:52 final size:52
Alignment explanation
Indices: 33163--33269 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
33153 AGTACTAACA
*
33163 TTTTTTGTGGACTCCAGGTCTACTGGACACATGTCTATGAAGCACATGGTCC
1 TTTTTTGTGGACTCCAGGTCTACTGGACACATGTCTACGAAGCACATGGTCC
*
33215 TTTTTTGTGGACTCCGGGTCTACTGGACACATGTCTACGAAGCACATGGTCC
1 TTTTTTGTGGACTCCAGGTCTACTGGACACATGTCTACGAAGCACATGGTCC
33267 TTT
1 TTT
33270 CTGTTCCTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (52 bp):
TTTTTTGTGGACTCCAGGTCTACTGGACACATGTCTACGAAGCACATGGTCC
Found at i:33379 original size:60 final size:60
Alignment explanation
Indices: 33286--33417 Score: 237
Period size: 60 Copynumber: 2.2 Consensus size: 60
33276 CTGGGACTGA
33286 CATTCTGAGAGGGCTTCAGGCTGCTAGACACTTGTCTGGATGCCCTATAAAGCACGCGAT
1 CATTCTGAGAGGGCTTCAGGCTGCTAGACACTTGTCTGGATGCCCTATAAAGCACGCGAT
*
33346 CATTCTGAGAGGGCTTCAGGCTGCTAGACACTTGTTTGGATGCCCTATAAAGCACGCGAT
1 CATTCTGAGAGGGCTTCAGGCTGCTAGACACTTGTCTGGATGCCCTATAAAGCACGCGAT
*
33406 CCTTCTTGAGAG
1 CATTC-TGAGAG
33418 CTTTTTGGGT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
60 63 0.91
61 6 0.09
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.27
Consensus pattern (60 bp):
CATTCTGAGAGGGCTTCAGGCTGCTAGACACTTGTCTGGATGCCCTATAAAGCACGCGAT
Found at i:33809 original size:35 final size:36
Alignment explanation
Indices: 33770--33838 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
33760 TTTCAACTAA
**
33770 AATAAAAAACATAAATTTTAGTTAAAAAT-TATTTC
1 AATAAAAAACATAAATTTTACATAAAAATCTATTTC
* **
33805 AATAAAACATTTAAATTTTACATAAAAATCTATT
1 AATAAAAAACATAAATTTTACATAAAAATCTATT
33839 ATTTATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (36 bp):
AATAAAAAACATAAATTTTACATAAAAATCTATTTC
Found at i:35066 original size:21 final size:21
Alignment explanation
Indices: 35042--35093 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
35032 ATTTTTACAG
*
35042 TTAAATTTAAAAT-TTAAAATT
1 TTAAATATAAAATATT-AAATT
*
35063 TTAAAAATAAAATGATTAAATT
1 TTAAATATAAAAT-ATTAAATT
35085 TTAAATATA
1 TTAAATATA
35094 TGAAGAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAATATAAAATATTAAATT
Found at i:37447 original size:3 final size:3
Alignment explanation
Indices: 37439--37463 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37429 AGCCATTTTC
37439 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
37464 AATGAAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38294 original size:31 final size:32
Alignment explanation
Indices: 38259--38328 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
38249 TTTTACCCTC
38259 AATTATTCAAAAGTTTTT-ATTTAACTCATTG
1 AATTATTCAAAAGTTTTTCATTTAACTCATTG
* *
38290 AATTATTTAAAAGTTTTTCATTTAATTCATTG
1 AATTATTCAAAAGTTTTTCATTTAACTCATTG
*
38322 AGTTATT
1 AATTATT
38329 AAGGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (32 bp):
AATTATTCAAAAGTTTTTCATTTAACTCATTG
Found at i:39400 original size:93 final size:93
Alignment explanation
Indices: 39241--39427 Score: 329
Period size: 93 Copynumber: 2.0 Consensus size: 93
39231 TTTTACCAAC
* *
39241 AATCTCTGAGCTTTATGGTAAAAGTATTATGTGAAAACGTGAGTCGTAATACCATTGCCCACCCC
1 AATCTCTAAACTTTATGGTAAAAGTATTATGTGAAAACGTGAGTCGTAATACCATTGCCCACCCC
39306 AATTATAAAAAATAAATGAATATTTTCT
66 AATTATAAAAAATAAATGAATATTTTCT
* *
39334 AATCTCTAAACTTTATGGTAAAAGTATTATGTGGAAACGTGAGTCGTAATACCATTGCTCACCCC
1 AATCTCTAAACTTTATGGTAAAAGTATTATGTGAAAACGTGAGTCGTAATACCATTGCCCACCCC
*
39399 AATTATAAAAAATAAATGTATATTTTCT
66 AATTATAAAAAATAAATGAATATTTTCT
39427 A
1 A
39428 TTTATAACCT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (93 bp):
AATCTCTAAACTTTATGGTAAAAGTATTATGTGAAAACGTGAGTCGTAATACCATTGCCCACCCC
AATTATAAAAAATAAATGAATATTTTCT
Found at i:40124 original size:80 final size:80
Alignment explanation
Indices: 40035--40193 Score: 273
Period size: 80 Copynumber: 2.0 Consensus size: 80
40025 TTGTTTGGAC
* * * *
40035 TTTTGTTTTTTATTCTTCATTTATTGTGCTTTGTTTTAGTTTGATTTTACTTTATAGTTGGTCTA
1 TTTTGTTTTTTATTCTTCATTCATTATGCTTTGTGTTAGTTTGATTTTACTTTATAGTTGATCTA
*
40100 ATATGTATGTACTTT
66 ATATGTATATACTTT
40115 TTTTGTTTTTTATTCTTCATTCATTATGCTTTGTGTTAGTTTGATTTTACTTTATAGTTGATCTA
1 TTTTGTTTTTTATTCTTCATTCATTATGCTTTGTGTTAGTTTGATTTTACTTTATAGTTGATCTA
40180 ATATGTATATACTT
66 ATATGTATATACTT
40194 ATGTGTACTT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (80 bp):
TTTTGTTTTTTATTCTTCATTCATTATGCTTTGTGTTAGTTTGATTTTACTTTATAGTTGATCTA
ATATGTATATACTTT
Found at i:47935 original size:13 final size:13
Alignment explanation
Indices: 47917--47943 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47907 ATTATTAAAA
47917 CCGTTAATTGAAC
1 CCGTTAATTGAAC
47930 CCGTTAATTGAAC
1 CCGTTAATTGAAC
47943 C
1 C
47944 ATTAAATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (13 bp):
CCGTTAATTGAAC
Found at i:47948 original size:12 final size:12
Alignment explanation
Indices: 47915--47948 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
47905 TCATTATTAA
47915 AACCGTTAATTG
1 AACCGTTAATTG
47927 AACCCGTTAATTG
1 AA-CCGTTAATTG
*
47940 AACCATTAA
1 AACCGTTAA
47949 ATGACACGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (12 bp):
AACCGTTAATTG
Found at i:48589 original size:5 final size:5
Alignment explanation
Indices: 48519--48577 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
48509 GAGGTATATT
* * **
48519 TTTTA TTTTA TTGT- TTTTA TTTTA ATTTA TTTTAA AATTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA
48569 TTTTA TTTT
1 TTTTA TTTT
48578 TAATTATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
4 3 0.07
5 38 0.86
6 3 0.07
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:50885 original size:29 final size:29
Alignment explanation
Indices: 50819--50889 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
50809 TAAATGTAAA
** **
50819 TTGTTTTAATTATTATAAAGTTATTTATT
1 TTGTTTTAATTATTATAAAGTTATAAAGC
50848 TTGTTTTTAATTATTATAAA-TTATAAAGGC
1 TTG-TTTTAATTATTATAAAGTTATAAA-GC
50878 TTGTTTTAATTA
1 TTGTTTTAATTA
50890 AATTTGTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.58
Consensus pattern (29 bp):
TTGTTTTAATTATTATAAAGTTATAAAGC
Found at i:67165 original size:39 final size:39
Alignment explanation
Indices: 67091--67165 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
67081 CCGATGAGAA
*
67091 AATTTTATAATGAATGTTTAAATTAAATAAGTTAATAAT
1 AATTTTATAATGAATGTTTAAATTAAAAAAGTTAATAAT
* *
67130 AATTTTAT-ATGAAAT-TTTGAATTAAAGAAATTTAAT
1 AATTTTATAATG-AATGTTTAAATTAAA-AAAGTTAAT
67166 TATTGAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 13 0.42
39 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (39 bp):
AATTTTATAATGAATGTTTAAATTAAAAAAGTTAATAAT
Found at i:75754 original size:21 final size:20
Alignment explanation
Indices: 75709--75761 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
75699 TTGTGCTAGC
*
75709 TCTACCAATACAAGTATGATT
1 TCTACCGATACAAGTATGA-T
75730 TCTACCGATACAAGTCATGCA-
1 TCTACCGATACAAGT-ATG-AT
75751 TCTACCGATAC
1 TCTACCGATAC
75762 CAAAAACTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 25 0.86
22 3 0.10
23 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAT
Found at i:79946 original size:16 final size:16
Alignment explanation
Indices: 79909--79939 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
79899 GAAATTTTTG
*
79909 TGTTAAAGGACTAAAA
1 TGTTAAAGGAATAAAA
79925 TGTTAAAGGAATAAA
1 TGTTAAAGGAATAAA
79940 TTTTTAAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
TGTTAAAGGAATAAAA
Found at i:80484 original size:53 final size:53
Alignment explanation
Indices: 80402--80646 Score: 348
Period size: 53 Copynumber: 4.6 Consensus size: 53
80392 GTAAATGTAA
* * *
80402 AAAGGTTCGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATTGCGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTGTGGATT
* *
80455 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCATATTGTAGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTGTGGATT
* * *
80508 AAAGGTCCGATGACTCGGTGTTATCGTGAGTTATATGAATCCGATTGTGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTGTGGATT
** *
80561 AAAGGTCCGATGACTCTGTGTCATTATGAGTTATATGAATCCTATT-AGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTGTGGATT
* * * *
80613 AAAGGTCCGATGATTTTGTGCCATCTTGAGTTAT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
80647 CAAATGTGAA
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
52 34 0.20
53 137 0.80
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTGTGGATT
Found at i:81251 original size:21 final size:21
Alignment explanation
Indices: 81225--81275 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
81215 GTTCATAGTA
81225 GTATCGGTAGTTTGGATACTT
1 GTATCGGTAGTTTGGATACTT
81246 GTATCGGTAGTTTGGATACTT
1 GTATCGGTAGTTTGGATACTT
81267 GTATCGGTA
1 GTATCGGTA
81276 TAAGTTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (21 bp):
GTATCGGTAGTTTGGATACTT
Found at i:82466 original size:12 final size:11
Alignment explanation
Indices: 82449--82486 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
82439 TTTTTTATTT
82449 TATAATATAAAA
1 TATAATA-AAAA
82461 TATAATAAAAA
1 TATAATAAAAA
82472 -ATTAATAAAAA
1 TA-TAATAAAAA
82483 TATA
1 TATA
82487 TCAGGCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 15 0.62
12 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:82477 original size:11 final size:12
Alignment explanation
Indices: 82449--82486 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
82439 TTTTTTATTT
*
82449 TATAATATAAAA
1 TATAATAAAAAA
82461 TATAATAAAAAA
1 TATAATAAAAAA
82473 T-TAAT-AAAAA
1 TATAATAAAAAA
82483 TATA
1 TATA
82487 TCAGGCATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TATAATAAAAAA
Found at i:83665 original size:32 final size:32
Alignment explanation
Indices: 83625--83695 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
83615 CTTTATTTTT
* *
83625 CATTCTCTTCTACTTCTCCTTTTGTTTTCCTC
1 CATTCTCTTCTACGTCTCCTTTTGTTTTCATC
*
83657 CATTCTCTTCTACGTCTCCTTTTGTTTTCATT
1 CATTCTCTTCTACGTCTCCTTTTGTTTTCATC
83689 CATTCTC
1 CATTCTC
83696 CATGTAATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.32, G:0.04, T:0.55
Consensus pattern (32 bp):
CATTCTCTTCTACGTCTCCTTTTGTTTTCATC
Found at i:83988 original size:21 final size:21
Alignment explanation
Indices: 83964--84021 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
83954 TAGTGCAAAC
83964 TTCTACCAATACAAGTGACAA
1 TTCTACCAATACAAGTGACAA
* * * * **
83985 TTCTATCGATATAAGAGACTC
1 TTCTACCAATACAAGTGACAA
*
84006 TTCTACCAAAACAAGT
1 TTCTACCAATACAAGT
84022 CATGCAACAA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (21 bp):
TTCTACCAATACAAGTGACAA
Found at i:86713 original size:92 final size:92
Alignment explanation
Indices: 86604--86784 Score: 281
Period size: 92 Copynumber: 2.0 Consensus size: 92
86594 TGAACCACCT
* *
86604 ATACCGACAATTCAACTACTGATACAATAAAAGTCAGAGAACAACTTGTCTCCTACCCAATACTC
1 ATACCGACAATTCAACTACCGATACAATAAAAGTCAGAGAACAACCTGTCTCCTACCCAATACTC
*
86669 CTACCGATACATGCAATAATTCTATTG
66 CGACCGATACATGCAATAATTCTATTG
* * * ** *
86696 ATACCTACAATTTAACTACCGATACAATACAAGTCAGAGAACAACCTGTCTCCTACCCTGTACTT
1 ATACCGACAATTCAACTACCGATACAATAAAAGTCAGAGAACAACCTGTCTCCTACCCAATACTC
86761 CGACCGATACATGCAATAATTCTA
66 CGACCGATACATGCAATAATTCTA
86785 CCGAAACTAG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 80 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.26
Consensus pattern (92 bp):
ATACCGACAATTCAACTACCGATACAATAAAAGTCAGAGAACAACCTGTCTCCTACCCAATACTC
CGACCGATACATGCAATAATTCTATTG
Found at i:97349 original size:21 final size:21
Alignment explanation
Indices: 97301--97349 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
97291 TAGTGCAGAC
* *
97301 TTCTATCGATACAAGTGACAA
1 TTCTACCGATACAAGAGACAA
*
97322 TTCTACCGATACAAGAGACTA
1 TTCTACCGATACAAGAGACAA
*
97343 TTTTACC
1 TTCTACC
97350 TAAACAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGAGACAA
Found at i:98774 original size:26 final size:26
Alignment explanation
Indices: 98738--98793 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
98728 TCCATGGGTG
*
98738 TTCATCTAACATCTCCTTTCAACTAT
1 TTCATCCAACATCTCCTTTCAACTAT
98764 TTCATCCAACATCTCCTTTCAACTAT
1 TTCATCCAACATCTCCTTTCAACTAT
98790 TTCA
1 TTCA
98794 CAACAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (26 bp):
TTCATCCAACATCTCCTTTCAACTAT
Found at i:103222 original size:19 final size:19
Alignment explanation
Indices: 103187--103225 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
103177 GCTTGACACA
103187 TTGACGAAAATAAAAAAAT
1 TTGACGAAAATAAAAAAAT
*
103206 TTGACTGAAAATGAAAAAAT
1 TTGAC-GAAAATAAAAAAAT
103226 AAACTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.23
Consensus pattern (19 bp):
TTGACGAAAATAAAAAAAT
Found at i:104108 original size:11 final size:11
Alignment explanation
Indices: 104094--104127 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
104084 GTGTCAATTA
104094 TATTAAAAAAT
1 TATTAAAAAAT
*
104105 TATTAAAATAT
1 TATTAAAAAAT
*
104116 TATTAAATAAT
1 TATTAAAAAAT
104127 T
1 T
104128 GAAAAGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAAAAAT
Found at i:109479 original size:23 final size:23
Alignment explanation
Indices: 109404--109500 Score: 88
Period size: 23 Copynumber: 4.2 Consensus size: 23
109394 TGGGCAACAA
* *
109404 AGAGCACACACAGTGCTAAATAG
1 AGAGCACACAAAGTGCTAATTAG
* * * *
109427 AGAGTACACAAAGTACTAATCAA
1 AGAGCACACAAAGTGCTAATTAG
*
109450 AGAGCACACAAAGTGCTGATTAG
1 AGAGCACACAAAGTGCTAATTAG
* **
109473 AGGGCACA-AAACGTGCTAAACAG
1 AGAGCACACAAA-GTGCTAATTAG
109496 AGAGC
1 AGAGC
109501 GCGCTAGTGT
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
22 3 0.05
23 54 0.95
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (23 bp):
AGAGCACACAAAGTGCTAATTAG
Found at i:109480 original size:69 final size:68
Alignment explanation
Indices: 109352--109499 Score: 158
Period size: 69 Copynumber: 2.1 Consensus size: 68
109342 TATACGGAAC
* * *
109352 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAAAGAGCAC-ACACA
1 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCT-GGCAACAAAGAGCACAAAAC-
109416 GTGCT
64 GTGCT
* ** * *
109421 AAATAGAGAGTACACAAAGTACTAATCAAAGAGCACACAAAGTGCT-G-ATTAGAGGGCACAAAA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAAAGAGCACA-AAAGTGCTGGCAACAAAGAGCACAAAA
109484 CGTGCT
63 CGTGCT
109490 AAACAGAGAG
1 AAACAGAGAG
109500 CGCGCTAGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
69 34 0.52
70 15 0.23
71 10 0.15
72 7 0.11
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCTGGCAACAAAGAGCACAAAACGT
GCT
Found at i:109500 original size:46 final size:46
Alignment explanation
Indices: 109399--109500 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
109389 AGTGCTGGGC
* *
109399 AACAAAGAGCACACACAGTGCTAAATAGAGAGTACACAAAGTACTA
1 AACAAAGAGCACACAAAGTGCTAAATAGAGAGCACACAAAGTACTA
* * * * *
109445 ATCAAAGAGCACACAAAGTGCTGATTAGAGGGCACA-AAACGTGCTA
1 AACAAAGAGCACACAAAGTGCTAAATAGAGAGCACACAAA-GTACTA
*
109491 AACAGAGAGC
1 AACAAAGAGC
109501 GCGCTAGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
45 3 0.07
46 43 0.93
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (46 bp):
AACAAAGAGCACACAAAGTGCTAAATAGAGAGCACACAAAGTACTA
Found at i:119718 original size:22 final size:22
Alignment explanation
Indices: 119693--119736 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
119683 CCATATTACT
119693 TTTTAATTTT-TTTAAATATTTA
1 TTTT-ATTTTATTTAAATATTTA
*
119715 TTTTATTTTATTTTAATATTTA
1 TTTTATTTTATTTAAATATTTA
119737 ATAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTTTATTTAAATATTTA
Found at i:123421 original size:20 final size:22
Alignment explanation
Indices: 123398--123444 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
123388 ATTTTGGAAA
123398 TTTTATAAA-TA-TTTTGAATT
1 TTTTATAAATTATTTTTGAATT
*
123418 TTTTA-AAATTATTTTTGTATT
1 TTTTATAAATTATTTTTGAATT
123439 TTTTAT
1 TTTTAT
123445 TGAGGGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.13
20 7 0.30
21 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTTATAAATTATTTTTGAATT
Found at i:135946 original size:55 final size:55
Alignment explanation
Indices: 135885--136026 Score: 212
Period size: 55 Copynumber: 2.6 Consensus size: 55
135875 CGTGCTACAC
*
135885 AACAATCGATTTAAATATATAAACAATCGATTAAAAAAAAACAGTATTCCAACAT
1 AACAATCGATTTAAACATATAAACAATCGATTAAAAAAAAACAGTATTCCAACAT
* * * * *
135940 AACAATCGATTTAAACATATAAACAATCGTTTCAAAAGAAGCAGTATTCCACCAT
1 AACAATCGATTTAAACATATAAACAATCGATTAAAAAAAAACAGTATTCCAACAT
* *
135995 AACAACCGATTTAAACATATAAACTATCGATT
1 AACAATCGATTTAAACATATAAACAATCGATT
136027 TTTGGGAGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (55 bp):
AACAATCGATTTAAACATATAAACAATCGATTAAAAAAAAACAGTATTCCAACAT
Found at i:137782 original size:18 final size:18
Alignment explanation
Indices: 137733--137782 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
137723 ATTTGTTTTT
* *
137733 AAAAATGATTTTTGAAAA
1 AAAAATTATTTTTTAAAA
137751 AAAAATTATTTTTTAAAA
1 AAAAATTATTTTTTAAAA
137769 AAATAA-TATTTTTT
1 AAA-AATTATTTTTT
137783 GGTGTTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
AAAAATTATTTTTTAAAA
Found at i:138347 original size:21 final size:21
Alignment explanation
Indices: 138269--138347 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
138259 AAAAATAATT
* * *
138269 TTATTTTTTCATAAA-TTAAC
1 TTATTTTTTAAAAAACTTAAG
*
138289 TTATCATTTTAAAAAACTTTAAG
1 TTAT-TTTTTAAAAAAC-TTAAG
138312 TTATTTTTTAAAAAACTTAAG
1 TTATTTTTTAAAAAACTTAAG
138333 TTATTTTTTAAAAAA
1 TTATTTTTTAAAAAA
138348 TAGTTCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.08
21 28 0.55
22 11 0.22
23 8 0.16
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (21 bp):
TTATTTTTTAAAAAACTTAAG
Found at i:138947 original size:28 final size:29
Alignment explanation
Indices: 138916--138978 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
138906 CGTATTTTAA
138916 ATTAAAATTTAATTA-GAT-TTTATTTATT
1 ATTAAAATTTAATTATGATATTTA-TTATT
*
138944 ATT-AAATTTATTTATGATATTTATTATT
1 ATTAAAATTTAATTATGATATTTATTATT
138972 A-TAAAAT
1 ATTAAAAT
138979 ATTATCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 11 0.35
28 16 0.52
29 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTAAAATTTAATTATGATATTTATTATT
Found at i:138955 original size:16 final size:15
Alignment explanation
Indices: 138934--138995 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
138924 TTAATTAGAT
138934 TTTATTTATTATTAAA
1 TTTATTTATTA-TAAA
*
138950 TTTATTTATGAT--A
1 TTTATTTATTATAAA
138963 TTTA-TTATTATAAAA
1 TTTATTTATTAT-AAA
138978 TATTATCTTATTATAAA
1 T-TTAT-TTATTATAAA
138995 T
1 T
138996 AAAATAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
12 6 0.16
13 5 0.13
15 3 0.08
16 13 0.34
17 4 0.11
18 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTATTTATTATAAA
Found at i:138989 original size:25 final size:25
Alignment explanation
Indices: 138935--138989 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
138925 TAATTAGATT
** *
138935 TTATTTATTATTAAATTTATTTATG
1 TTATTTATTATTAAAAATATTTATC
*
138960 ATATTTATTATTATAAAATA-TTATC
1 TTATTTATTATTA-AAAATATTTATC
138985 TTATT
1 TTATT
138990 ATAAATAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTATTTATTATTAAAAATATTTATC
Found at i:151609 original size:23 final size:23
Alignment explanation
Indices: 151579--151628 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
151569 ACCCATGTTG
151579 TTATGGTGATGTCTTCTTGGATT
1 TTATGGTGATGTCTTCTTGGATT
151602 TTATGGTGATGTCTTCTTGGATT
1 TTATGGTGATGTCTTCTTGGATT
151625 TTAT
1 TTAT
151629 AACTACATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.08, G:0.24, T:0.54
Consensus pattern (23 bp):
TTATGGTGATGTCTTCTTGGATT
Found at i:159633 original size:36 final size:36
Alignment explanation
Indices: 159586--159654 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
159576 TCATTCAAAA
*
159586 TCACTTCGTAATTTACTAGAGCAACTCAAATGTGGT
1 TCACTTCGTAATTTACCAGAGCAACTCAAATGTGGT
159622 TCACTTCGTAATTTACCAGAGCAACTCAAATGT
1 TCACTTCGTAATTTACCAGAGCAACTCAAATGT
159655 TGTTGAATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (36 bp):
TCACTTCGTAATTTACCAGAGCAACTCAAATGTGGT
Found at i:163986 original size:26 final size:27
Alignment explanation
Indices: 163953--164029 Score: 113
Period size: 26 Copynumber: 2.9 Consensus size: 27
163943 TTTAAATTTA
163953 TCTTTAATAATTGTCTACGAAACTCT-
1 TCTTTAATAATTGTCTACGAAACTCTG
**
163979 TCTTTAATAATTGTCTATAAAAC-CTG
1 TCTTTAATAATTGTCTACGAAACTCTG
*
164005 TCTTTAATAATTATCTACGAAACTC
1 TCTTTAATAATTGTCTACGAAACTC
164030 AAATTTCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 2 0.05
26 41 0.93
27 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (27 bp):
TCTTTAATAATTGTCTACGAAACTCTG
Found at i:164533 original size:18 final size:18
Alignment explanation
Indices: 164501--164552 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
164491 CTAGGATGAG
164501 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
164517 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
164535 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
164553 CAACTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:166217 original size:10 final size:11
Alignment explanation
Indices: 166190--166222 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
166180 ACAAAAAATA
*
166190 ATTTAATAATT
1 ATTTTATAATT
166201 ATTTTATAATT
1 ATTTTATAATT
166212 -TTTTATAATT
1 ATTTTATAATT
166222 A
1 A
166223 AATAACAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTATAATT
Found at i:181911 original size:28 final size:28
Alignment explanation
Indices: 181873--181928 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
181863 GTAGAGTCAG
181873 ATATGAGGTTAAGGAAAATTTAGCCTAT
1 ATATGAGGTTAAGGAAAATTTAGCCTAT
181901 ATATGAGGTTAAGGAAAATTTAGCCTAT
1 ATATGAGGTTAAGGAAAATTTAGCCTAT
181929 CTTTCTCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (28 bp):
ATATGAGGTTAAGGAAAATTTAGCCTAT
Found at i:193320 original size:15 final size:14
Alignment explanation
Indices: 193300--193335 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
193290 TATAAAGTAT
193300 ATATTTAAATTTATA
1 ATATTTAAATTT-TA
*
193315 ATATTTATATTTTA
1 ATATTTAAATTTTA
193329 ATATTTA
1 ATATTTA
193336 TATTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTAAATTTTA
Found at i:193330 original size:14 final size:15
Alignment explanation
Indices: 193300--193339 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
193290 TATAAAGTAT
*
193300 ATATTTAAATTTATA
1 ATATTTATATTTATA
193315 ATATTTATATTT-TA
1 ATATTTATATTTATA
193329 ATATTTATATT
1 ATATTTATATT
193340 AAAATATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTATATTTATA
Found at i:193345 original size:14 final size:14
Alignment explanation
Indices: 193300--193346 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
193290 TATAAAGTAT
*
193300 ATATTTAAATTTATA
1 ATATTTATA-TTATA
*
193315 ATATTTATATTTTA
1 ATATTTATATTATA
*
193329 ATATTTATATTAAA
1 ATATTTATATTATA
193343 ATAT
1 ATAT
193347 AGTTTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTATATTATA
Found at i:194531 original size:6 final size:6
Alignment explanation
Indices: 194522--194584 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 6
194512 TATTAACATT
194522 ATAAAA ATAAAA ATAACAA ATATATAA A-AAAA ATTAAAGA ATAAAA ATTAAAA
1 ATAAAA ATAAAA ATAA-AA ATA-A-AA ATAAAA A-TAAA-A ATAAAA A-TAAAA
194575 A-AAAA A-AAAA
1 ATAAAA ATAAAA
194585 CAAACACTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
5 12 0.24
6 13 0.26
7 19 0.38
8 6 0.12
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:194569 original size:14 final size:13
Alignment explanation
Indices: 194522--194580 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 13
194512 TATTAACATT
194522 ATAAAAA-TAAAA
1 ATAAAAATTAAAA
*
194534 ATAACAAATATATAA
1 ATAA-AAAT-TAAAA
194549 A-AAAAATTAAAGA
1 ATAAAAATTAAA-A
194562 ATAAAAATTAAAA
1 ATAAAAATTAAAA
194575 A-AAAAA
1 ATAAAAA
194581 AAAACAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 12 0.30
13 11 0.28
14 12 0.30
15 5 0.12
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
ATAAAAATTAAAA
Found at i:194575 original size:25 final size:25
Alignment explanation
Indices: 194524--194584 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
194514 TTAACATTAT
194524 AAAAATAAAAATAACAAATATATAAA
1 AAAAATAAAAATAACAAATATA-AAA
194550 AAAAATTAAAGAATAA-AAAT-TAAAA
1 AAAAA-TAAA-AATAACAAATATAAAA
194575 AAAAA-AAAAA
1 AAAAATAAAAA
194585 CAAACACTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
25 8 0.24
26 7 0.21
27 8 0.24
28 5 0.15
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAAATAAAAATAACAAATATAAAA
Found at i:194717 original size:13 final size:13
Alignment explanation
Indices: 194686--194722 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
194676 ATTTGACTTT
194686 TTATA-ATTTGTTA
1 TTATATATTT-TTA
194699 TT-TATATTTTTA
1 TTATATATTTTTA
194711 TTATATATTTTT
1 TTATATATTTTT
194723 TTAAAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTATATATTTTTA
Found at i:205307 original size:19 final size:18
Alignment explanation
Indices: 205266--205308 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
205256 ATATTTATAT
205266 TTATTTTATTTTTTAAAA
1 TTATTTTATTTTTTAAAA
*
205284 ATATTTTATAATTTTT-AAA
1 TTATTTTAT--TTTTTAAAA
205303 TTATTT
1 TTATTT
205309 GTTGAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTATTTTTTAAAA
Found at i:213485 original size:3 final size:3
Alignment explanation
Indices: 213477--213508 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
213467 GGGATTGGAT
213477 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
213509 GGAGCTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:218502 original size:2 final size:2
Alignment explanation
Indices: 218495--218541 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
218485 AGATAAATAA
218495 AT AT AT AT 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 AT AT AT AT
218537 AT AT A
1 AT AT A
218542 ATTTCAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223508 original size:21 final size:20
Alignment explanation
Indices: 223484--223527 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
223474 GGATTTTGAA
*
223484 TTCGAGTTTAAGGTTCAAGGT
1 TTCGAATTTAAGGTTCAA-GT
* *
223505 TTCGAATTTATGGTTTAAGT
1 TTCGAATTTAAGGTTCAAGT
223525 TTC
1 TTC
223528 ATGTTTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (20 bp):
TTCGAATTTAAGGTTCAAGT
Found at i:225198 original size:2 final size:2
Alignment explanation
Indices: 225191--225218 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
225181 TATAACCTAC
225191 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
225219 CTGCATGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:226773 original size:29 final size:30
Alignment explanation
Indices: 226734--226816 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 30
226724 TATCATAATA
*
226734 AAAATATAATTTCATCATTTTTAAAAAATT
1 AAAATATAATTTTATCATTTTTAAAAAATT
* *
226764 AAATTA-AATTTTTAT-ATTTTTTAAAAATT
1 AAAATATAA-TTTTATCATTTTTAAAAAATT
*
226793 AAAATATAATTTTATCATTATTAA
1 AAAATATAATTTTATCATTTTTAA
226817 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 26 0.59
30 18 0.41
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAATATAATTTTATCATTTTTAAAAAATT
Found at i:226773 original size:59 final size:59
Alignment explanation
Indices: 226705--226816 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
226695 TTTTTTATTG
* * *
226705 AAATTAAA-TTGTATATTTTTATCATAATAAAAATATAATTTCATCATTTTTAAAAAATT
1 AAATTAAATTTGTATATTTTT-TAAAAATAAAAATATAATTTCATCATTATTAAAAAATT
* * *
226764 AAATTAAATTTTTATATTTTTTAAAAATTAAAATATAATTTTATCATTATTAA
1 AAATTAAATTTGTATATTTTTTAAAAATAAAAATATAATTTCATCATTATTAA
226817 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 35 0.76
60 11 0.24
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (59 bp):
AAATTAAATTTGTATATTTTTTAAAAATAAAAATATAATTTCATCATTATTAAAAAATT
Found at i:228843 original size:22 final size:22
Alignment explanation
Indices: 228817--228880 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
228807 GATGTTAGTA
*
228817 TTTAATTAATTTTTTAAATAAT
1 TTTAATTAATTTTTAAAATAAT
*
228839 TTTAA-TGATTTTTAAACATAAT
1 TTTAATTAATTTTTAAA-ATAAT
*
228861 TTT-TTTGAATTTTTAAAATA
1 TTTAATT-AATTTTTAAAATA
228881 TAATTAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 9 0.26
22 17 0.49
23 9 0.26
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTAATTAATTTTTAAAATAAT
Found at i:239114 original size:30 final size:30
Alignment explanation
Indices: 239023--239114 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 30
239013 AAATGGGTTG
*
239023 TTTACTAAAATGGTACAAAATATATATTTA
1 TTTACTAAAATGGTACAAAATAAATATTTA
* * * * * * **
239053 TATACCAAATTGGTATCCACA-CACCA-TTA
1 TTTACTAAAATGGTA-CAAAATAAATATTTA
239082 TTTACTAAAATGGTACAAAATAAATATTTA
1 TTTACTAAAATGGTACAAAATAAATATTTA
239112 TTT
1 TTT
239115 TGTACCATTT
Statistics
Matches: 42, Mismatches: 17, Indels: 6
0.65 0.26 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 19 0.45
31 3 0.07
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTACTAAAATGGTACAAAATAAATATTTA
Found at i:239168 original size:16 final size:16
Alignment explanation
Indices: 239147--239195 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
239137 TGATGAGAAT
239147 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
239163 ATTATTTTTAT-A-TA
1 ATTATTTTGATAATTA
*
239177 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
239192 ATTA
1 ATTA
239196 GTTAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:240154 original size:4 final size:4
Alignment explanation
Indices: 240147--240189 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
240137 TTCTTCTTCC
*
240147 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTC
240190 AATTTTCGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:240195 original size:13 final size:11
Alignment explanation
Indices: 240147--240189 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
240137 TTCTTCTTCC
240147 TTCTTTCTTTCT
1 TTCTTTCTTT-T
240159 TTCTTTCTCTTTT
1 TTC-TT-TCTTTT
240172 TTCTTTCTTTT
1 TTCTTTCTTTT
240183 TTCTTTC
1 TTCTTTC
240190 AATTTTCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.45
12 5 0.17
13 6 0.21
14 5 0.17
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:240567 original size:16 final size:16
Alignment explanation
Indices: 240546--240578 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
240536 GTAGCTTTGG
*
240546 TTTCCTCACAGGGTTC
1 TTTCCTCACAAGGTTC
240562 TTTCCTCACAAGGTTC
1 TTTCCTCACAAGGTTC
240578 T
1 T
240579 GATCCCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.39
Consensus pattern (16 bp):
TTTCCTCACAAGGTTC
Found at i:248524 original size:24 final size:24
Alignment explanation
Indices: 248479--248531 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
248469 TAAATATTTT
* * **
248479 AATTAAAGTGATTAAATTAAAAAA
1 AATTAAAATGATAAAAAGAAAAAA
*
248503 AATTAAAATGATAAAAAGAAAATA
1 AATTAAAATGATAAAAAGAAAAAA
248527 AATTA
1 AATTA
248532 TATTTTAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (24 bp):
AATTAAAATGATAAAAAGAAAAAA
Found at i:270874 original size:18 final size:18
Alignment explanation
Indices: 270842--270876 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
270832 TTTTTAATTC
*
270842 TAATTTTTAAGATATTTA
1 TAATTTTTAACATATTTA
*
270860 TAATTTTTTACATATTT
1 TAATTTTTAACATATTT
270877 TTTAAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TAATTTTTAACATATTTA
Found at i:275838 original size:90 final size:90
Alignment explanation
Indices: 275313--275826 Score: 751
Period size: 90 Copynumber: 5.7 Consensus size: 90
275303 TGGACCCATC
* * * ** *
275313 GTTTGTGCATCGACTAGAGCAGGAGAAACAGTTTGCACGCTAGTAGCTGAGCCAGTTGAAGGGAT
1 GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGAT
* *
275378 CCCTGAAGCAGTGGAAGGCTGCAAG
66 CCCTGAAGCAGTAGAACGCTGCAAG
* *
275403 GTTTGTGAATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGGAGGGAT
1 GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGAT
*
275468 CCCTGAAGCAGT-GAAAGGCTGCAAG
66 CCCTGAAGCAGTAG-AACGCTGCAAG
* ** * *
275493 TTTTGCACATTGACTACAGCAGGTGAAATAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGAT
1 GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGAT
275558 CCCTGAAGCAGTAGAACGCTGCAAG
66 CCCTGAAGCAGTAGAACGCTGCAAG
* * * * *
275583 GTTAGTGCATTGACTATAGCAGGTGAAACGGTTTGCATAGTATAAGCTGAGCCAGTTGAAGGGAT
1 GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGAT
*
275648 CCCTGAAGCAGTAGAACGCTGCAAT
66 CCCTGAAGCAGTAGAACGCTGCAAG
* *
275673 GTTTGTGCATTGACTACAGCAGTTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGAT
1 GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGAT
*
275738 CCCTGAAGCAGTAGAACGCTGCAAT
66 CCCTGAAGCAGTAGAACGCTGCAAG
* * * *
275763 GTTTGTGCATTAACAACAGCAGGTGGAACAGTTTGCATACTAGAAGCTAAGCCAGTTGAAGGGA
1 GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
275827 GACCAGAAGC
Statistics
Matches: 386, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
89 1 0.00
90 384 0.99
91 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (90 bp):
GTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGAT
CCCTGAAGCAGTAGAACGCTGCAAG
Found at i:287610 original size:6 final size:6
Alignment explanation
Indices: 287601--287627 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
287591 AGAGAGATGT
287601 GGGTGG GGGTGG GGGTGG GGGTGG GGG
1 GGGTGG GGGTGG GGGTGG GGGTGG GGG
287628 GAGAAGGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGTGG
Found at i:290922 original size:42 final size:42
Alignment explanation
Indices: 290863--291071 Score: 328
Period size: 42 Copynumber: 5.0 Consensus size: 42
290853 TTAAATCATT
* *
290863 ATCTCCATCATCCTTAGCTTTCCTACTAGATGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
290905 ATCTCCATCATCCTTAGCTTTCCTTCTAGAGGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
*
290947 ACCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* *
290989 ATCTCCGTCATCCTTAGCTTTCCTACCAGACGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* *
291031 ATCTCCATCATCCTTAGCTTTCCTACTAGACAACCTAGTAC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTAC
291072 AATTCGCCAT
Statistics
Matches: 154, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 154 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (42 bp):
ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
Found at i:292286 original size:16 final size:15
Alignment explanation
Indices: 292250--292288 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
292240 TATTATAATT
292250 TATAAATATTTGATA
1 TATAAATATTTGATA
*
292265 -ATAAATATTTTATAA
1 TATAAATATTTGAT-A
292280 TATAAATAT
1 TATAAATAT
292289 GAATATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TATAAATATTTGATA
Found at i:292294 original size:36 final size:36
Alignment explanation
Indices: 292227--292297 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
292217 AATATTTTTC
* *
292227 TAATAAATATATATATTATAATTTATAAATATTTGA
1 TAATAAATATATATAATATAATATATAAATATTTGA
* *
292263 TAATAAATATTTTATAATATAA-ATATGAATATTTG
1 TAATAAATA-TATATAATATAATATATAAATATTTG
292298 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (36 bp):
TAATAAATATATATAATATAATATATAAATATTTGA
Found at i:292457 original size:17 final size:17
Alignment explanation
Indices: 292435--292472 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
292425 AAATGCAAAA
292435 AAAAAAAAATCATTTTT
1 AAAAAAAAATCATTTTT
*
292452 AAAAAAAAATTATTTTT
1 AAAAAAAAATCATTTTT
292469 AAAA
1 AAAA
292473 TTTATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAAAAAATCATTTTT
Found at i:294305 original size:20 final size:22
Alignment explanation
Indices: 294272--294311 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
294262 GGAATTTGGA
294272 ATTTTTTATATTTTT-AAAAAC
1 ATTTTTTATATTTTTGAAAAAC
294293 ATTTTTTAT-TTTTTGAAAA
1 ATTTTTTATATTTTTGAAAA
294312 TTAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (22 bp):
ATTTTTTATATTTTTGAAAAAC
Found at i:297601 original size:92 final size:92
Alignment explanation
Indices: 297435--297607 Score: 240
Period size: 92 Copynumber: 1.9 Consensus size: 92
297425 GGTATAGTAT
* *
297435 CATAATAAAACACATATTGATAATTTAGACATTACATTGAATATTTTCAAAGTACAAATATCACA
1 CATAATAAAACAAATATTGATAATTTAGACACTACATTGAATATTTTCAAAGTACAAATATCACA
297500 TCAGATATTTTATGAAGGTACATGTAC
66 TCAGATATTTTATGAAGGTACATGTAC
* *** * *
297527 CATAATAAAAACAAATATTGATAGTTTAGGTGCTACATTGAATA-TTTCAAAGTACAAGTATCAT
1 CATAAT-AAAACAAATATTGATAATTTAGACACTACATTGAATATTTTCAAAGTACAAATATCAC
**
297591 ATTGGATATTTTATGAA
65 ATCAGATATTTTATGAA
297608 AATACAAGCA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
92 39 0.56
93 31 0.44
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (92 bp):
CATAATAAAACAAATATTGATAATTTAGACACTACATTGAATATTTTCAAAGTACAAATATCACA
TCAGATATTTTATGAAGGTACATGTAC
Found at i:301531 original size:20 final size:21
Alignment explanation
Indices: 301492--301532 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
301482 GGAATTTTTT
301492 TAAAAATGAAATAATTTAATTA
1 TAAAAATGAAAT-ATTTAATTA
*
301514 TAAAAATTAAAT-TTTAATT
1 TAAAAATGAAATATTTAATT
301533 CAATGTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAATGAAATATTTAATTA
Found at i:305512 original size:49 final size:49
Alignment explanation
Indices: 305440--305539 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
305430 CCCAATGTTG
305440 TTTTTAACTACGTCCGATAGTTCAATCATAAAAATGATATCAATTCATA
1 TTTTTAACTACGTCCGATAGTTCAATCATAAAAATGATATCAATTCATA
* * * * *
305489 TTTTTAACTACGTTCTATAGTTCAATCATAAAAATGCTATTAGTTCATA
1 TTTTTAACTACGTCCGATAGTTCAATCATAAAAATGATATCAATTCATA
305538 TT
1 TT
305540 CAAAGCACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (49 bp):
TTTTTAACTACGTCCGATAGTTCAATCATAAAAATGATATCAATTCATA
Found at i:333937 original size:23 final size:22
Alignment explanation
Indices: 333872--333952 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 22
333862 AAACTAAAAT
* *
333872 ATAATTA-AAAGTATATATTTAA
1 ATAATTATAAATTA-ATAATTAA
333894 ATAATTATAAATTAATTAATTAA
1 ATAATTATAAATTAA-TAATTAA
*
333917 CATAATATATAAATTGA-AATTGAA
1 -ATAAT-TATAAATTAATAATT-AA
*
333941 ACAATT-TAAATT
1 ATAATTATAAATT
333953 TAAATTTATG
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.12
22 9 0.18
23 19 0.38
24 7 0.14
25 9 0.18
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAATTATAAATTAATAATTAA
Found at i:337178 original size:130 final size:130
Alignment explanation
Indices: 336945--337207 Score: 526
Period size: 130 Copynumber: 2.0 Consensus size: 130
336935 TAAATAGAAA
336945 ATGCTCAATAATGGAAGTTTATGGGACCCTTCTTTAACAATCTGCTTTCTTCATTATCTCAAGGA
1 ATGCTCAATAATGGAAGTTTATGGGACCCTTCTTTAACAATCTGCTTTCTTCATTATCTCAAGGA
337010 TTTGGCAGGAGGGAATCTTGTTCCTATTGAAGGATTGAATTCTCCTTTGTTTGCTCTAGAGGTAT
66 TTTGGCAGGAGGGAATCTTGTTCCTATTGAAGGATTGAATTCTCCTTTGTTTGCTCTAGAGGTAT
337075 ATGCTCAATAATGGAAGTTTATGGGACCCTTCTTTAACAATCTGCTTTCTTCATTATCTCAAGGA
1 ATGCTCAATAATGGAAGTTTATGGGACCCTTCTTTAACAATCTGCTTTCTTCATTATCTCAAGGA
337140 TTTGGCAGGAGGGAATCTTGTTCCTATTGAAGGATTGAATTCTCCTTTGTTTGCTCTAGAGGTAT
66 TTTGGCAGGAGGGAATCTTGTTCCTATTGAAGGATTGAATTCTCCTTTGTTTGCTCTAGAGGTAT
337205 ATG
1 ATG
337208 GTTTTAGGTT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 133 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (130 bp):
ATGCTCAATAATGGAAGTTTATGGGACCCTTCTTTAACAATCTGCTTTCTTCATTATCTCAAGGA
TTTGGCAGGAGGGAATCTTGTTCCTATTGAAGGATTGAATTCTCCTTTGTTTGCTCTAGAGGTAT
Found at i:340011 original size:4 final size:4
Alignment explanation
Indices: 340002--340029 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
339992 GCATTTCTTA
340002 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
340030 CTAAACCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:360192 original size:5 final size:5
Alignment explanation
Indices: 360182--360213 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
360172 AATTGATTCA
*
360182 ACTGC ACTGC ACTGC ACTGC ACTGC GCTGC AC
1 ACTGC ACTGC ACTGC ACTGC ACTGC ACTGC AC
360214 ATCTGATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.41, G:0.22, T:0.19
Consensus pattern (5 bp):
ACTGC
Found at i:361277 original size:23 final size:23
Alignment explanation
Indices: 361204--361352 Score: 123
Period size: 23 Copynumber: 6.5 Consensus size: 23
361194 TATACGGAAC
* *
361204 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
361226 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
361247 GGGCAACAGAGAGCACACACAA-TGCT
1 ---AAACAGAGAGCACACA-AAGTGCT
361273 AAACAGAGAGCACACACAA-TGCT
1 AAACAGAGAGCACACA-AAGTGCT
*
361296 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
361319 GATA-AGAGGGCACA-AAACGTGCT
1 -AAACAGAGAGCACACAAA-GTGCT
361342 AAACAGAGAGC
1 AAACAGAGAGC
361353 GTGCTAGTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
21 17 0.16
22 7 0.07
23 61 0.58
24 1 0.01
25 13 0.12
26 4 0.04
27 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:363544 original size:58 final size:59
Alignment explanation
Indices: 363467--363732 Score: 254
Period size: 59 Copynumber: 4.5 Consensus size: 59
363457 TTTGGGATTA
* * * *
363467 AAAATGGAATTTTTAGACATTCGGGGGTAAAAGGGTAA-TTTTGAGAGTTTCGAGGTCG
1 AAAATGGAATTTCTGGACATTCGGGGGTAAAACGGTAATTTTTGAAAGTTTCGAGGTCG
* * * * * *
363525 AAAATGGAGTTTCTGGACATCCGGGAGCAAAACGGTAATTTTTGAAAGTTTCGAGATAG
1 AAAATGGAATTTCTGGACATTCGGGGGTAAAACGGTAATTTTTGAAAGTTTCGAGGTCG
* * * *
363584 AAAATGGAGTTTCTGGATA-TCTGGGAGCAAAACGGTAATTTTTGAAAGTTTCGAGGTC-
1 AAAATGGAATTTCTGGACATTC-GGGGGTAAAACGGTAATTTTTGAAAGTTTCGAGGTCG
* * ** * * * *
363642 AAAATGGAAATTT-TAGAGATTCGGGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGG-AATTTCTGGACATTCGGGGGTAAAACGGTAATTTTTGAAAGTTTCGAGGTCG
* *
363701 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAA
1 AAAATGGAATTTCTGGACA-TTCGGGGGTAAAA
363733 ATGGAATTTT
Statistics
Matches: 175, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
58 78 0.45
59 97 0.55
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.30
Consensus pattern (59 bp):
AAAATGGAATTTCTGGACATTCGGGGGTAAAACGGTAATTTTTGAAAGTTTCGAGGTCG
Found at i:363675 original size:29 final size:30
Alignment explanation
Indices: 363642--363798 Score: 120
Period size: 29 Copynumber: 5.5 Consensus size: 30
363632 TTTCGAGGTC
363642 AAAATGGAAATTTTAGAGA-TTCGGGGGTA
1 AAAATGGAAATTTTAGAGAGTTCGGGGGTA
*
363671 AAAAT-GAAATTTTTG-GAAGTTTC-GGGGTCA
1 AAAATGGAAATTTTAGAG-AG-TTCGGGGGT-A
* * *
363701 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
1 AAAATGGAAATTTTAGAGAGTTCGGGGGTA
**
363730 AAAATGG-AATTTTAG-GAAGTTTTGGGGTA
1 AAAATGGAAATTTTAGAG-AGTTCGGGGGTA
* * *
363759 AAAATGTAATTTTTA-AAAGTT-GGGGGT-
1 AAAATGGAAATTTTAGAGAGTTCGGGGGTA
363786 AAAAT-GAAATTTT
1 AAAATGGAAATTTT
363799 GGAAAGTTTC
Statistics
Matches: 102, Mismatches: 15, Indels: 25
0.72 0.11 0.18
Matches are distributed among these distances:
26 6 0.06
27 6 0.06
28 21 0.21
29 40 0.39
30 21 0.21
31 8 0.08
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAATGGAAATTTTAGAGAGTTCGGGGGTA
Found at i:363705 original size:117 final size:117
Alignment explanation
Indices: 363495--363717 Score: 254
Period size: 117 Copynumber: 1.9 Consensus size: 117
363485 ATTCGGGGGT
* * * * *
363495 AAAAGGGTAATTTTGAGAGTTTCGAGGTCGAAAATGGAGTTTCTGGACATCCGGGAGCAAAACGG
1 AAAACGGTAATTTTGAAAGTTTCGAGGTCGAAAATGGAATTTCTAGACATCCGGGAGCAAAAAGG
* *
363560 TAATTTTTGAAAGTTTCGAGATAGAAAATGGAGTTTCTGGATATCTGGGAGC
66 AAATTTTTGAAAGTTTCGAGATAGAAAATGGAATTTCTGGATATCTGGGAGC
* * * *
363612 AAAACGGTAATTTTTGAAAGTTTCGAGGTC-AAAATGGAAATTT-TAGAGATTCGGGGGTAAAAA
1 AAAACGGTAA-TTTTGAAAGTTTCGAGGTCGAAAATGG-AATTTCTAGACATCCGGGAGCAAAAA
* * * * *
363675 TGAAATTTTTGGAAGTTTCGGGGTCA-AAAATGGAATTTTTGGA
64 GGAAATTTTTGAAAGTTTCGAGAT-AGAAAATGGAATTTCTGGA
363718 AGTTCGAGGG
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
117 64 0.74
118 23 0.26
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (117 bp):
AAAACGGTAATTTTGAAAGTTTCGAGGTCGAAAATGGAATTTCTAGACATCCGGGAGCAAAAAGG
AAATTTTTGAAAGTTTCGAGATAGAAAATGGAATTTCTGGATATCTGGGAGC
Found at i:363734 original size:59 final size:59
Alignment explanation
Indices: 363620--363811 Score: 234
Period size: 59 Copynumber: 3.3 Consensus size: 59
363610 GCAAAACGGT
* * *
363620 AATTTTTGAAAGTTTCGAGGTC-AAAATGGAAATTTTAG-AGATTCGGGGGTAAAAATGA
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAG-TTCGGGGGTAAAAATGA
* * *
363678 AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGA
* * * *
363737 AATTTTAGGAAGTTTTGGGGT-AAAAATGTAATTTTTAAAAGTT-GGGGGT-AAAATGA
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGA
363793 AA-TTTTGGAAAGTTTCGGG
1 AATTTTTGG-AAGTTTCGGG
363812 ACCTCTAGGG
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
55 5 0.04
56 17 0.15
57 5 0.04
58 39 0.34
59 48 0.41
60 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGA
Found at i:364962 original size:3 final size:3
Alignment explanation
Indices: 364954--365009 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
364944 CCTTTCGGCT
* *
364954 TTA TTA TTA TTA TTA ATA TCTA TTA TTA TTA TTA -TA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
364999 ATA TTAA TTA T
1 TTA TT-A TTA T
365010 AGTTGCCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:365764 original size:16 final size:16
Alignment explanation
Indices: 365743--365790 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
365733 TGGATACTTG
365743 TATTAATTTAAATTTA
1 TATTAATTTAAATTTA
* *
365759 TATTAAATCAAATTTA
1 TATTAATTTAAATTTA
* *
365775 TAATAAATATAAATTT
1 T-ATTAATTTAAATTT
365791 TAAGTAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTAATTTAAATTTA
Found at i:365790 original size:17 final size:16
Alignment explanation
Indices: 365750--365833 Score: 66
Period size: 16 Copynumber: 5.1 Consensus size: 16
365740 TTGTATTAAT
*
365750 TTAAATTTATATTAAA
1 TTAAATTTATAATAAA
*
365766 TCAAATTTATAATAAA
1 TTAAATTTATAATAAA
365782 TATAAATTT-TAAGTAAA
1 T-TAAATTTATAA-TAAA
*
365799 TTTAAACTTA-AAGTAAA
1 -TTAAATTTATAA-TAAA
*
365816 TTTAATTTA-AATTAAA
1 TTAAATTTATAA-TAAA
365832 TT
1 TT
365834 TAAGTTTTGT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
16 33 0.58
17 23 0.40
18 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAATTTATAATAAA
Found at i:367058 original size:18 final size:17
Alignment explanation
Indices: 367037--367079 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
367027 AATGTATTTT
367037 AAATTATATAATATATAA
1 AAATTATATAATATA-AA
* *
367055 AAATAACATAATATAAA
1 AAATTATATAATATAAA
*
367072 ATATTATA
1 AAATTATA
367080 AACTTAAAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:384570 original size:21 final size:22
Alignment explanation
Indices: 384528--384571 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
384518 TTTGTAATAA
*
384528 TTTCATATAATTTTCTAGATTT
1 TTTCATATAATTTTCTAAATTT
*
384550 TTTC-TATAA-TTTCTAAAATT
1 TTTCATATAATTTTCTAAATTT
384570 TT
1 TT
384572 AAGATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTCATATAATTTTCTAAATTT
Found at i:384713 original size:9 final size:9
Alignment explanation
Indices: 384701--384790 Score: 62
Period size: 9 Copynumber: 10.1 Consensus size: 9
384691 ATAACATTTA
384701 ATAATTTTT
1 ATAATTTTT
**
384710 ATAAGCTTT
1 ATAATTTTT
384719 ATAA--TTT
1 ATAATTTTT
*
384726 CTAATTTTT
1 ATAATTTTT
*
384735 ATAGTTTTTT
1 ATA-ATTTTT
384745 ATAATTTTT
1 ATAATTTTT
384754 AT-ATATTTT
1 ATAAT-TTTT
384763 AT-ATTTGTT
1 ATAATTT-TT
* *
384772 ATAATATTA
1 ATAATTTTT
*
384781 ATAATGTTT
1 ATAATTTTT
384790 A
1 A
384791 GATTTGATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
7 6 0.09
8 4 0.06
9 44 0.68
10 11 0.17
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:384719 original size:28 final size:25
Alignment explanation
Indices: 384687--384737 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
384677 TATTAATATA
384687 CTTTATAACATTTAATAATTTTTATAAG
1 CTTTAT-A-ATTT-ATAATTTTTATAAG
*
384715 CTTTATAATTTCTAATTTTTATA
1 CTTTATAATTTATAATTTTTATA
384738 GTTTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 4 0.18
27 1 0.05
28 6 0.27
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (25 bp):
CTTTATAATTTATAATTTTTATAAG
Found at i:384724 original size:18 final size:19
Alignment explanation
Indices: 384688--384725 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
384678 ATTAATATAC
384688 TTTATAACATTTAATAATT
1 TTTATAACATTTAATAATT
384707 TTTATAAGC-TTT-ATAATT
1 TTTATAA-CATTTAATAATT
384725 T
1 T
384726 CTAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 10 0.56
20 1 0.06
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTATAACATTTAATAATT
Found at i:384751 original size:19 final size:18
Alignment explanation
Indices: 384706--384779 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
384696 ATTTAATAAT
**
384706 TTTTATAAGCTTTATA-A
1 TTTTATAATTTTTATATA
* *
384723 -TTTCTAATTTTTATAGTT
1 TTTTATAATTTTTATA-TA
384741 TTTTATAATTTTTATATA
1 TTTTATAATTTTTATATA
384759 TTTTAT-ATTTGTTATAATA
1 TTTTATAATTT-TTAT-ATA
384778 TT
1 TT
384780 AATAATGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 12 0.26
17 4 0.09
18 11 0.24
19 19 0.41
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTATAATTTTTATATA
Found at i:384755 original size:35 final size:37
Alignment explanation
Indices: 384705--384774 Score: 92
Period size: 35 Copynumber: 1.9 Consensus size: 37
384695 CATTTAATAA
384705 TTTTTATAAGCTTTATA-ATTTCTA-ATTT-TTATAGT
1 TTTTTATAAGCTTTATATATTT-TATATTTGTTATAGT
**
384740 TTTTTATAATTTTTATATATTTTATATTTGTTATA
1 TTTTTATAAGCTTTATATATTTTATATTTGTTATA
384775 ATATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 17 0.57
36 8 0.27
37 5 0.17
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (37 bp):
TTTTTATAAGCTTTATATATTTTATATTTGTTATAGT
Found at i:384790 original size:27 final size:26
Alignment explanation
Indices: 384731--384796 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
384721 AATTTCTAAT
* * *
384731 TTTTATAGTTTTTTATAATTTTTATATA
1 TTTTATA-TTTGTTATAATATTAATA-A
384759 TTTTATATTTGTTATAATATTAATAA
1 TTTTATATTTGTTATAATATTAATAA
*
384785 TGTTTAGATTTG
1 T-TTTATATTTG
384797 ATTAATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.06
27 24 0.73
28 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTTATATTTGTTATAATATTAATAA
Found at i:389156 original size:33 final size:33
Alignment explanation
Indices: 389118--389182 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
389108 TAAAACATGT
389118 ACAATGTAAAAATAAATTGAAACTTGTCAACAA
1 ACAATGTAAAAATAAATTGAAACTTGTCAACAA
389151 ACAATGTAAAAATAAATTGAAACTTGTCAACA
1 ACAATGTAAAAATAAATTGAAACTTGTCAACA
389183 TAAATAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (33 bp):
ACAATGTAAAAATAAATTGAAACTTGTCAACAA
Found at i:390819 original size:16 final size:18
Alignment explanation
Indices: 390780--390813 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
390770 TAAGTTTATA
390780 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
390797 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
390814 AATTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:390964 original size:22 final size:22
Alignment explanation
Indices: 390937--390983 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
390927 ATAAAATTAT
*
390937 TAAATA-TTAAAATAATATAATA
1 TAAATATTTAAAA-AATATAAAA
*
390959 TAAATATTTTAAAAATATAAAA
1 TAAATATTTAAAAAATATAAAA
390981 TAA
1 TAA
390984 TATGGACAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATATTTAAAAAATATAAAA
Found at i:390985 original size:32 final size:31
Alignment explanation
Indices: 390926--390986 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
390916 AATAAAAATG
*
390926 TATAAAATTATTAAATATTAAAATAATATAA
1 TATAAAATTATTAAAAATTAAAATAATATAA
390957 TATAAATATT-TTAAAAATATAAAATAATAT
1 TATAAA-ATTATTAAAAAT-TAAAATAATAT
390987 GGACAGGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TATAAAATTATTAAAAATTAAAATAATATAA
Found at i:391626 original size:12 final size:12
Alignment explanation
Indices: 391609--391646 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
391599 CAATATCAAT
*
391609 TCACCATCACCA
1 TCACCATTACCA
391621 TCACCATTACCA
1 TCACCATTACCA
*
391633 TTACCATTACCA
1 TCACCATTACCA
391645 TC
1 TC
391647 CTTGTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (12 bp):
TCACCATTACCA
Found at i:391638 original size:18 final size:18
Alignment explanation
Indices: 391611--391645 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
391601 ATATCAATTC
391611 ACCATCACCATCACCATT
1 ACCATCACCATCACCATT
* *
391629 ACCATTACCATTACCAT
1 ACCATCACCATCACCAT
391646 CCTTGTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (18 bp):
ACCATCACCATCACCATT
Found at i:394278 original size:2 final size:2
Alignment explanation
Indices: 394271--394305 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
394261 TTACAAACAA
394271 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
394306 AAAAAATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:395021 original size:23 final size:22
Alignment explanation
Indices: 394986--395028 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
394976 TCATGAGTAG
394986 AAAATATTATGTAT-AAAATTA
1 AAAATATTATGTATGAAAATTA
395007 AAAATAATGTATGTATGAAAAT
1 AAAAT-AT-TATGTATGAAAAT
395029 CACGTATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 7 0.37
24 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (22 bp):
AAAATATTATGTATGAAAATTA
Found at i:413690 original size:13 final size:13
Alignment explanation
Indices: 413666--413703 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
413656 TTGTTCATTA
413666 TAGAATATATATTT
1 TAGAA-ATATATTT
413680 TAGAAATATATTT
1 TAGAAATATATTT
*
413693 AAG-AATATATT
1 TAGAAATATATT
413704 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 10 0.43
14 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (13 bp):
TAGAAATATATTT
Found at i:414526 original size:12 final size:12
Alignment explanation
Indices: 414504--414538 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
414494 CAGCCCCATT
414504 TTTTATTTTTTTA
1 TTTT-TTTTTTTA
414517 TTTTTTTTTTTA
1 TTTTTTTTTTTA
414529 TTTTTTTTTT
1 TTTTTTTTTT
414539 GTGATTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:418115 original size:18 final size:18
Alignment explanation
Indices: 418083--418118 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
418073 AGGGAGTGTT
**
418083 TTAATTAGATTGATTAAA
1 TTAATTAGAGGGATTAAA
418101 TTAATTAGAGGGATTAAA
1 TTAATTAGAGGGATTAAA
418119 ATAGGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (18 bp):
TTAATTAGAGGGATTAAA
Found at i:421934 original size:16 final size:16
Alignment explanation
Indices: 421913--421946 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
421903 GGGTATAATC
*
421913 GAATTGAGTTAAGTTT
1 GAATTGAGGTAAGTTT
*
421929 GAATTGTGGTAAGTTT
1 GAATTGAGGTAAGTTT
421945 GA
1 GA
421947 GCTAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (16 bp):
GAATTGAGGTAAGTTT
Found at i:423351 original size:38 final size:38
Alignment explanation
Indices: 423299--423383 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
423289 TGTTCGTCTA
423299 ATAACCCAATGAAACTCCTCGTTTCATTTAATCCATTTC
1 ATAA-CCAATGAAACTCCTCGTTTCATTTAATCCATTTC
423338 ATAACCAATGAAACTCCTCGTTTCATTTAATCCATTTC
1 ATAACCAATGAAACTCCTCGTTTCATTTAATCCATTTC
423376 ATAACCAA
1 ATAACCAA
423384 AACCCACTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 42 0.91
39 4 0.09
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (38 bp):
ATAACCAATGAAACTCCTCGTTTCATTTAATCCATTTC
Found at i:428441 original size:21 final size:21
Alignment explanation
Indices: 428415--428456 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
428405 AATAACAACT
* *
428415 TAAAAAAAATAAATAATAAAAA
1 TAAAAACAA-AAATAAGAAAAA
428437 TAAAAACAAAAATAAGAAAA
1 TAAAAACAAAAATAAGAAAA
428457 TAACAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (21 bp):
TAAAAACAAAAATAAGAAAAA
Found at i:428447 original size:12 final size:13
Alignment explanation
Indices: 428419--428451 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
428409 ACAACTTAAA
*
428419 AAAAATAAATAAT
1 AAAAATAAATAAC
428432 AAAAATAAA-AAC
1 AAAAATAAATAAC
428444 AAAAATAA
1 AAAAATAA
428452 GAAAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAATAAC
Found at i:433837 original size:16 final size:18
Alignment explanation
Indices: 433811--433843 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
433801 TAAAATTGAG
433811 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
433828 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
433844 TTAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:433892 original size:26 final size:27
Alignment explanation
Indices: 433845--433907 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
433835 ATTAATTTAT
* *
433845 TAATTAAATAATATTTATTTTGA-AAA
1 TAATAAAATAATATTTAGTTTGATAAA
*
433871 TAA-AAAATAAATATTTGGTTTGATTAAA
1 TAATAAAAT-AATATTTAGTTTGA-TAAA
433899 TAATAAAAT
1 TAATAAAAT
433908 GTTGATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 15 0.50
28 6 0.20
29 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (27 bp):
TAATAAAATAATATTTAGTTTGATAAA
Found at i:440357 original size:32 final size:30
Alignment explanation
Indices: 440316--440381 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
440306 CGTTTGGGTG
* * *
440316 TTTGGTCACTTTGACCCTTAAGATTTTTTTT
1 TTTGGTCACTTTCACACATAAG-TTTTTTTT
*
440347 TTTGGCTCACTTTCATACATAAGTTTTTTTT
1 TTTGG-TCACTTTCACACATAAGTTTTTTTT
440378 TTTG
1 TTTG
440382 TGGTCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (30 bp):
TTTGGTCACTTTCACACATAAGTTTTTTTT
Found at i:440578 original size:19 final size:20
Alignment explanation
Indices: 440531--440581 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
440521 CCACATCAGC
*
440531 AAATGATTTTAAAAGTATTA
1 AAATAATTTTAAAAGTATTA
* *
440551 AAATTATTTTAAAATTATT-
1 AAATAATTTTAAAAGTATTA
440570 AAATAATTTTAA
1 AAATAATTTTAA
440582 TTTTCAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
AAATAATTTTAAAAGTATTA
Found at i:440902 original size:99 final size:99
Alignment explanation
Indices: 440728--440925 Score: 252
Period size: 99 Copynumber: 2.0 Consensus size: 99
440718 TTTGAACCAA
** * * * ** *
440728 ACCATGACTACTTCTCCACTTGGATTTTGAACCAAACCATGGCTTCTTCTTCTTCCATCGTTCTC
1 ACCATGACTACTTCTCCACTTAAATTTTCAACCAAACCATGACGTCTTCTTCTTCCATCACTCAC
* * *
440793 CCAACCCTTCAAGCTTCTCTATTTTAATCTCATT
66 CCAACACTTCAAGATTCTCTATTTCAATCTCATT
* * *
440827 ACCATGGCTACTTCTCCACTTAAATTTTCAATCAAATCATGACGTCTTCTTCTTCCATCACTCAC
1 ACCATGACTACTTCTCCACTTAAATTTTCAACCAAACCATGACGTCTTCTTCTTCCATCACTCAC
**
440892 TTAACACTTCAAGATTCTCTATTTCAATCTCATT
66 CCAACACTTCAAGATTCTCTATTTCAATCTCATT
440926 TCTTAGGAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 83 1.00
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (99 bp):
ACCATGACTACTTCTCCACTTAAATTTTCAACCAAACCATGACGTCTTCTTCTTCCATCACTCAC
CCAACACTTCAAGATTCTCTATTTCAATCTCATT
Found at i:454245 original size:47 final size:47
Alignment explanation
Indices: 454173--454266 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
454163 AAAAGAAATA
454173 ACCTTTCAACACTTTGTTTTCTTTTCTGTTCTTTTTCTCTCATTTTC
1 ACCTTTCAACACTTTGTTTTCTTTTCTGTTCTTTTTCTCTCATTTTC
* *
454220 ACCTTTCAACACTTTGTTTTGTTTTCTTTTCTTTTTCTCTCATTTTC
1 ACCTTTCAACACTTTGTTTTCTTTTCTGTTCTTTTTCTCTCATTTTC
454267 TTACTTTCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.11, C:0.24, G:0.04, T:0.61
Consensus pattern (47 bp):
ACCTTTCAACACTTTGTTTTCTTTTCTGTTCTTTTTCTCTCATTTTC
Found at i:458060 original size:3 final size:3
Alignment explanation
Indices: 458052--458086 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
458042 GGCTAAATAC
* *
458052 TGA TGA TGA TGA TGA TGA TGA GGA TGA TGA GGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
458087 GATGGTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (3 bp):
TGA
Done.