Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 21 of 202
Found at i:6275049 original size:7 final size:8
Alignment explanation
Indices: 6275032--6275089 Score: 53
Period size: 8 Copynumber: 6.5 Consensus size: 8
6275022 AAAATATTTT
6275032 AAAATTAA
1 AAAATTAA
6275040 AAAATTAA
1 AAAATTAA
6275048 AAAGTATTTTAA
1 AAA--A--TTAA
*
6275060 AAATTTAA
1 AAAATTAA
6275068 AAAATTTAA
1 AAAA-TTAA
6275077 AAAATTTAA
1 AAAA-TTAA
6275086 AAAA
1 AAAA
6275090 AGTTGTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 18 0.42
9 17 0.40
10 1 0.02
12 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (8 bp):
AAAATTAA
Found at i:6275065 original size:9 final size:9
Alignment explanation
Indices: 6275018--6275089 Score: 78
Period size: 9 Copynumber: 8.0 Consensus size: 9
6275008 AAAAAAGTAT
6275018 TTTAAAAATA
1 TTTAAAAA-A
*
6275028 TTT-TAAAA
1 TTTAAAAAA
6275036 -TTAAAAAA
1 TTTAAAAAA
6275044 -TTAAAAAGTA
1 TTTAAAAA--A
*
6275054 TTTTAAAAA
1 TTTAAAAAA
6275063 TTTAAAAAA
1 TTTAAAAAA
6275072 TTTAAAAAA
1 TTTAAAAAA
6275081 TTTAAAAAA
1 TTTAAAAAA
6275090 AGTTGTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
7 2 0.04
8 12 0.22
9 30 0.56
10 4 0.07
11 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:6275109 original size:77 final size:78
Alignment explanation
Indices: 6274983--6275132 Score: 207
Period size: 77 Copynumber: 1.9 Consensus size: 78
6274973 ACCAAAATTT
*
6274983 ATTTAAAAAATTAAAACAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTAA
1 ATTTAAAAAATTAAAACAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAA
6275048 AAAGTATTTTAAAA
66 AAA-TATTTTAAAA
* ** * *
6275062 ATTTAAAAAATT-TAA-AAAATTTAAAAAAAGT-TGTTTAAAAGTTTTTTAAAATTAAAAAAATA
1 ATTTAAAAAATTAAAACAAAAAATAAAAAAAGTAT-TTTAAAAATATTTTAAAATTAAAAAAATA
6275124 AAAATATTT
65 AAAATATTT
6275133 ATTATATTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
76 6 0.09
77 44 0.69
78 2 0.03
79 12 0.19
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (78 bp):
ATTTAAAAAATTAAAACAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAA
AAATATTTTAAAA
Found at i:6277816 original size:12 final size:11
Alignment explanation
Indices: 6277785--6277848 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
6277775 ATTTTTTAAA
6277785 TTTTAAAATAC
1 TTTTAAAATAC
6277796 TTTTAAAATAC
1 TTTTAAAATAC
*
6277807 TTTTTTAAAT--
1 -TTTTAAAATAC
6277817 TTTT--AA-A-
1 TTTTAAAATAC
6277824 TTTTAAAATA-
1 TTTTAAAATAC
6277834 TTTTAAAATAC
1 TTTTAAAATAC
6277845 TTTT
1 TTTT
6277849 TTAATTTTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
7 6 0.13
9 6 0.13
10 11 0.24
11 15 0.33
12 8 0.17
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:6277871 original size:38 final size:39
Alignment explanation
Indices: 6277770--6277869 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
6277760 ATAATAAATA
6277770 TTTTT-ATTTTTTAAATTTTAAAATACTTTTAAAATACT
1 TTTTTAATTTTTTAAATTTTAAAATACTTTTAAAATACT
*
6277808 TTTTTAAATTTTTAAATTTTAAAATA-TTTTAAAATACT
1 TTTTTAATTTTTTAAATTTTAAAATACTTTTAAAATACT
*
6277846 TTTTTAATTTTGTTTAATTTTAAA
1 TTTTTAATTTT-TTAAATTTTAAA
6277870 TAAAATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 27 0.47
39 30 0.53
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (39 bp):
TTTTTAATTTTTTAAATTTTAAAATACTTTTAAAATACT
Found at i:6278175 original size:21 final size:21
Alignment explanation
Indices: 6278149--6278212 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
6278139 TTCTTAAAAG
6278149 TATTTTTTAATTTTCTTTTTA
1 TATTTTTTAATTTTCTTTTTA
**
6278170 TA-TTTTTAAACTTCTTATTT-
1 TATTTTTTAATTTTCTT-TTTA
*
6278190 TAATTTTTATAATTTTTTTTTTA
1 T-ATTTTT-TAATTTTCTTTTTA
6278213 ACTTTTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 13 0.39
21 6 0.18
22 7 0.21
23 7 0.21
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTTTTTAATTTTCTTTTTA
Found at i:6278213 original size:21 final size:21
Alignment explanation
Indices: 6278150--6278218 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
6278140 TCTTAAAAGT
*
6278150 ATTTTT-TAATTTTCTTTTTA
1 ATTTTTATAATTTTTTTTTTA
* *
6278170 TATTTTTA-AACTTCTTATTTTA
1 -ATTTTTATAA-TTTTTTTTTTA
6278192 ATTTTTATAATTTTTTTTTTA
1 ATTTTTATAATTTTTTTTTTA
*
6278213 ACTTTT
1 ATTTTT
6278219 CTTGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 29 0.74
22 10 0.26
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTTATAATTTTTTTTTTA
Found at i:6289139 original size:3 final size:3
Alignment explanation
Indices: 6289133--6289186 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
6289123 TTGCTACTAC
6289133 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6289181 TAT TAT
1 TAT TAT
6289187 CATGACCAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6290734 original size:6 final size:6
Alignment explanation
Indices: 6290720--6290755 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
6290710 TTTTATTTTG
*
6290720 GCTGCT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
6290756 CTTATTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.33, T:0.47
Consensus pattern (6 bp):
GCTGTT
Found at i:6309744 original size:42 final size:42
Alignment explanation
Indices: 6309697--6309777 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
6309687 TGTGAGAAAA
6309697 AAATGAAAAAAAAAAGAGACAATAAGTAAAATATAAAATGGT
1 AAATGAAAAAAAAAAGAGACAATAAGTAAAATATAAAATGGT
6309739 AAATGAAAAAAAAAAGAGACAATAAGTAAAATATAAAAT
1 AAATGAAAAAAAAAAGAGACAATAAGTAAAATATAAAAT
6309778 AGTATTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.16
Consensus pattern (42 bp):
AAATGAAAAAAAAAAGAGACAATAAGTAAAATATAAAATGGT
Found at i:6315436 original size:12 final size:12
Alignment explanation
Indices: 6315419--6315443 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6315409 TGTTAGTTTG
6315419 TTATTATTTCTA
1 TTATTATTTCTA
6315431 TTATTATTTCTA
1 TTATTATTTCTA
6315443 T
1 T
6315444 ATTCATTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTATTTCTA
Found at i:6323604 original size:19 final size:20
Alignment explanation
Indices: 6323562--6323612 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6323552 AAAAAAACTA
* *
6323562 AAATAAGAAAT-TTAAGAAT
1 AAATAATAAATATTAAAAAT
6323581 AAATAATAAATATTAAAAAT
1 AAATAATAAATATTAAAAAT
6323601 -AATAACTAAATA
1 AAATAA-TAAATA
6323613 AAGAAACGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AAATAATAAATATTAAAAAT
Found at i:6324211 original size:6 final size:6
Alignment explanation
Indices: 6324160--6324193 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
6324150 ATTCAAGCAA
6324160 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
6324194 GCAGATCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6329215 original size:18 final size:18
Alignment explanation
Indices: 6329189--6329231 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
6329179 CCCAATGATT
6329189 GCCACCACCTTCTTCTTC
1 GCCACCACCTTCTTCTTC
*
6329207 GCCAGCACCTTCTTCTTC
1 GCCACCACCTTCTTCTTC
*
6329225 ACCACCA
1 GCCACCA
6329232 ACCATGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.28
Consensus pattern (18 bp):
GCCACCACCTTCTTCTTC
Found at i:6329975 original size:3 final size:3
Alignment explanation
Indices: 6329967--6330004 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6329957 TCTTAATACT
6329967 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
6330005 TAATACTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6330090 original size:19 final size:21
Alignment explanation
Indices: 6330066--6330104 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6330056 CTAAAACAAA
*
6330066 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
6330085 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
6330105 ATCAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:6330175 original size:3 final size:3
Alignment explanation
Indices: 6330167--6330191 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6330157 CCGCAGCAAC
6330167 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
6330192 TTTTTTTGAT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:6330293 original size:27 final size:27
Alignment explanation
Indices: 6330263--6330347 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
6330253 CCAAACAATA
6330263 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
**
6330290 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* *
6330317 TGGCACCTTTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
6330344 TGGC
1 TGGC
6330348 GTGACCAAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:6330439 original size:27 final size:28
Alignment explanation
Indices: 6330404--6330474 Score: 128
Period size: 27 Copynumber: 2.6 Consensus size: 28
6330394 TTTGTTTTTT
6330404 TATATATTTTGGTAAATAAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
6330431 TATATATTTTGGTAAATAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
6330459 TA-ATATTTTGGTAAAT
1 TATATATTTTGGTAAAT
6330475 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 38 0.88
28 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAGTTA
Found at i:6330762 original size:24 final size:24
Alignment explanation
Indices: 6330726--6330771 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
6330716 TGGAAATTTA
* *
6330726 AATAATGATACATAATAAATTTTG
1 AATAATAAAACATAATAAATTTTG
**
6330750 AATAATAAAACATGGTAAATTT
1 AATAATAAAACATAATAAATTT
6330772 ATATAATATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (24 bp):
AATAATAAAACATAATAAATTTTG
Found at i:6331507 original size:6 final size:6
Alignment explanation
Indices: 6331496--6331524 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6331486 AAAGAAACAC
6331496 AGAGAA AGAGAA AGAGAA AGA-AA AGAGAA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA
6331525 CCACCTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:6331878 original size:26 final size:27
Alignment explanation
Indices: 6331849--6331899 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
6331839 CCACATTAGC
*
6331849 TGGGCTAGGTTAATTGGGT-TTTGGTT
1 TGGGCTAGGTTAAGTGGGTATTTGGTT
6331875 TGGGCTAGGTTAAGTGGGTATTTGG
1 TGGGCTAGGTTAAGTGGGTATTTGG
6331900 GATCTGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.14, C:0.04, G:0.41, T:0.41
Consensus pattern (27 bp):
TGGGCTAGGTTAAGTGGGTATTTGGTT
Found at i:6331997 original size:23 final size:23
Alignment explanation
Indices: 6331971--6332016 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
6331961 ACTGATGGAC
6331971 TTTTA-ATAATTTTATT-TTTATTT
1 TTTTATAT-ATTTT-TTGTTTATTT
6331994 TTTTATATATTTTTTGTTTATTT
1 TTTTATATATTTTTTGTTTATTT
6332017 ATTTGATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.10
23 17 0.81
24 2 0.10
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTATATATTTTTTGTTTATTT
Found at i:6337439 original size:97 final size:97
Alignment explanation
Indices: 6337289--6337483 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
6337279 TGTGAGACAT
6337289 CATGAACATTATTTTGTCCTTTATAGAAACAAAGCACAACCCACTAAACCCAAGCCAATATAGGC
1 CATGAACATTATTTTGTCCTTTATAGAAACAAAGCACAACCCACTAAACCCAAGCCAATATAGGC
6337354 TTCTTTGTGATCTATTAATATATATGTATAGA
66 TTCTTTGTGATCTATTAATATATATGTATAGA
6337386 CATGAACATTATTTTGTCCTTTATAGAAACAAAGCACAACCCACTAAACCCAAGCCAATATAGGC
1 CATGAACATTATTTTGTCCTTTATAGAAACAAAGCACAACCCACTAAACCCAAGCCAATATAGGC
6337451 TTCTTTGTGATCTATTAATATATATGTATAGA
66 TTCTTTGTGATCTATTAATATATATGTATAGA
6337483 C
1 C
6337484 TTGTTTGTTC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (97 bp):
CATGAACATTATTTTGTCCTTTATAGAAACAAAGCACAACCCACTAAACCCAAGCCAATATAGGC
TTCTTTGTGATCTATTAATATATATGTATAGA
Found at i:6342478 original size:40 final size:40
Alignment explanation
Indices: 6342433--6342518 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
6342423 GCGTTATACT
* *
6342433 TTCTGTTTGACGTGTTTTAGG-TGGATCAACTCTTATGAGC
1 TTCTGTTTGACATATTTT-GGTTGGATCAACTCTTATGAGC
* * *
6342473 TTCTGTTTGGCATATTTTGGTTGGATTAGCTCTTATGAGC
1 TTCTGTTTGACATATTTTGGTTGGATCAACTCTTATGAGC
6342513 TTCTGT
1 TTCTGT
6342519 CTGGTGTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.05
40 38 0.95
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.47
Consensus pattern (40 bp):
TTCTGTTTGACATATTTTGGTTGGATCAACTCTTATGAGC
Found at i:6344988 original size:12 final size:12
Alignment explanation
Indices: 6344971--6345003 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
6344961 CTAGCACACG
6344971 CCCGTGTGGCCA
1 CCCGTGTGGCCA
6344983 CCCGTGTGGCCA
1 CCCGTGTGGCCA
6344995 CCCGTGTGG
1 CCCGTGTGG
6345004 TCACAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.39, G:0.36, T:0.18
Consensus pattern (12 bp):
CCCGTGTGGCCA
Found at i:6356456 original size:24 final size:24
Alignment explanation
Indices: 6356422--6356469 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6356412 TTTCTAGAAG
* *
6356422 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
6356446 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
6356470 TTAACTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:6358970 original size:10 final size:10
Alignment explanation
Indices: 6358937--6358977 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
6358927 AAAGAGTTAT
6358937 TAAAAAT-TA
1 TAAAAATATA
*
6358946 T-AGAATATA
1 TAAAAATATA
6358955 -AAAAATATA
1 TAAAAATATA
6358964 TAAAAATATA
1 TAAAAATATA
6358974 TAAA
1 TAAA
6358978 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.15
9 10 0.37
10 13 0.48
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
TAAAAATATA
Found at i:6358973 original size:19 final size:19
Alignment explanation
Indices: 6358949--6358988 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6358939 AAAATTATAG
*
6358949 AATATAAAAAATATATAAA
1 AATATAAAAAATAAATAAA
* *
6358968 AATATATAAATTAAATAAA
1 AATATAAAAAATAAATAAA
6358987 AA
1 AA
6358989 GAATACGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATAAAAAATAAATAAA
Found at i:6359168 original size:21 final size:22
Alignment explanation
Indices: 6359127--6359168 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6359117 TAATATCAAC
*
6359127 TAAAAATTAACATAAACACAGG
1 TAAAAATTAACATAAAAACAGG
*
6359149 TAAAAATTAAGA-AAAAACAG
1 TAAAAATTAACATAAAAACAG
6359169 ATGAAGACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.17
Consensus pattern (22 bp):
TAAAAATTAACATAAAAACAGG
Found at i:6370892 original size:21 final size:21
Alignment explanation
Indices: 6370860--6370900 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6370850 AGGCTCGAGG
6370860 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
6370881 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
6370901 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:6380038 original size:3 final size:3
Alignment explanation
Indices: 6380030--6380087 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
6380020 TAATCCCCAT
6380030 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6380077 TTA TTA TTA TT
1 TTA TTA TTA TT
6380088 GTATTTTCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6380401 original size:32 final size:34
Alignment explanation
Indices: 6380360--6380424 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
6380350 ATGATTTACC
*
6380360 AATACATACACTTATACA-TTTTTTAT-TTTATA
1 AATACATACACATATACATTTTTTTATATTTATA
*
6380392 AATATATACACATATACATTTTTTTATATTTAT
1 AATACATACACATATACATTTTTTTATATTTAT
6380425 TTTATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 16 0.55
33 8 0.28
34 5 0.17
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (34 bp):
AATACATACACATATACATTTTTTTATATTTATA
Found at i:6388689 original size:43 final size:43
Alignment explanation
Indices: 6388625--6388873 Score: 354
Period size: 43 Copynumber: 5.8 Consensus size: 43
6388615 GCGTCACTAA
* *
6388625 CTTTAGCGGCGCTTTGCTCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* **
6388668 CTTTAGCGGTGCTTTTTTCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
6388711 CTTTAGCGGCGCTTATCCCACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * **
6388754 CTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* ***
6388797 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
*
6388840 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
6388874 AACATGACTT
Statistics
Matches: 181, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 181 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:6388783 original size:129 final size:129
Alignment explanation
Indices: 6388625--6388873 Score: 390
Period size: 129 Copynumber: 1.9 Consensus size: 129
6388615 GCGTCACTAA
* **
6388625 CTTTAGCGGCGCTTTGCTCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTTTCACA
1 CTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTTTCACA
* *
6388690 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACAAATGCCGCTAAAGACCAAGAC
66 AACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* * * ** *
6388754 CTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGACCTTTAGCGGCACTTTTTTTACA
1 CTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTTTCACA
*
6388819 AACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAA
66 AACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTATCCCACAAACGCCGCTAAA
6388874 AACATGACTT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 108 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (129 bp):
CTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTTTCACA
AACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:6392639 original size:41 final size:40
Alignment explanation
Indices: 6392579--6392814 Score: 274
Period size: 41 Copynumber: 5.8 Consensus size: 40
6392569 CAAAATATTT
* * *
6392579 TTAGCGGCGCTTCTCCAAAAACGCCGCTACAGACCCCAGCA
1 TTAGCGGCCCTTAT-CAAAAACGCCGCTAAAGACCCCAGCA
* *
6392620 TTAGCGGCACCTTATCAAAAACGCCGCTAAAGATCCCGGCA
1 TTAGCGGC-CCTTATCAAAAACGCCGCTAAAGACCCCAGCA
*
6392661 TTAGCGGCGCTTTATCAAAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGC-CCTTATCAAAAACGCCGCTAAAGACCCCAGCA
* *
6392702 TTAGCGGCGCTTCTACAAAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCCCTTAT-CAAAAACGCCGCTAAAGACCCCAGCA
* * * *
6392743 TTAGCGGCGCTTTTCAAAAAACGTCGCTAAAGATCCCAGCA
1 TTAGCGGCCCTTATC-AAAAACGCCGCTAAAGACCCCAGCA
* * * *
6392784 TTAGCAGCGCTTCTACAAAAATGCCGCTAAA
1 TTAGCGGCCCTTAT-CAAAAACGCCGCTAAA
6392815 TCCCCCAAAG
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
40 4 0.02
41 163 0.95
42 5 0.03
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (40 bp):
TTAGCGGCCCTTATCAAAAACGCCGCTAAAGACCCCAGCA
Found at i:6392821 original size:82 final size:81
Alignment explanation
Indices: 6392579--6392814 Score: 339
Period size: 82 Copynumber: 2.9 Consensus size: 81
6392569 CAAAATATTT
* * * *
6392579 TTAGCGGCGCTTCTCCAAAAACGCCGCTACAGACCCCAGCATTAGCGGCACCT-TATCAAAAACG
1 TTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTA-CAAAAACG
* *
6392643 CCGCTAAAGATCCCGGCA
64 CCGCTAAAGACCCCAGCA
6392661 TTAGCGGCGCTTTATCAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACAAAAACGC
1 TTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACAAAAACGC
6392726 CGCTAAAGACCCCAGCA
65 CGCTAAAGACCCCAGCA
* * * *
6392743 TTAGCGGCGCTTTTCAAAAAACGTCGCTAAAGATCCCAGCATTAGCAGCGCTTCTACAAAAATGC
1 TTAGCGGCGCTTTTC-AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACAAAAACGC
6392808 CGCTAAA
65 CGCTAAA
6392815 TCCCCCAAAG
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
81 3 0.02
82 136 0.96
83 2 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (81 bp):
TTAGCGGCGCTTTTCAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACAAAAACGCC
GCTAAAGACCCCAGCA
Found at i:6392821 original size:123 final size:123
Alignment explanation
Indices: 6392579--6392814 Score: 368
Period size: 123 Copynumber: 1.9 Consensus size: 123
6392569 CAAAATATTT
* *
6392579 TTAGCGGCGCTTCTCCAAAAACGCCGCTACAGACCCCAGCATTAGCGGCACCTTATCAAAAACGC
1 TTAGCGGCGCTTCTACAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCACCTTATCAAAAACGC
* *
6392644 CGCTAAAGATCCCGGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGACCCCAGCA
66 CGCTAAAGATCCCAGCATTAGCAGCGCTTTATCAAAAACGCCGCTAAAGACCCCAGCA
* *
6392702 TTAGCGGCGCTTCTACAAAAACGCCGCTAAAGACCCCAGCATTAGCGGC-GCTTTTCAAAAAACG
1 TTAGCGGCGCTTCTACAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCACCTTATC-AAAAACG
* *
6392766 TCGCTAAAGATCCCAGCATTAGCAGCGCTTCTA-CAAAAATGCCGCTAAA
65 CCGCTAAAGATCCCAGCATTAGCAGCGCTT-TATCAAAAACGCCGCTAAA
6392815 TCCCCCAAAG
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
122 5 0.05
123 96 0.93
124 2 0.02
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (123 bp):
TTAGCGGCGCTTCTACAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCACCTTATCAAAAACGC
CGCTAAAGATCCCAGCATTAGCAGCGCTTTATCAAAAACGCCGCTAAAGACCCCAGCA
Found at i:6392908 original size:40 final size:40
Alignment explanation
Indices: 6392854--6392990 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 40
6392844 GGGCTTTGGT
6392854 TTTTTA-CGGCGTTTTTCCT-AAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCGTTTTT--TGAAAAACGCCGCTAATGCTCGA
*
6392893 TTTTTAGCGGTGTTTTTTGAAAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTTGAAAAACGCCGCTAATGCTCGA
* * ** *
6392933 TCTTTAGTGGCGATTTTCTT--AAAGTGCCACTAATGCTCGA
1 TTTTTAGCGGCG-TTTT-TTGAAAAACGCCGCTAATGCTCGA
* *
6392973 TTTTTACCGGCATTTTTT
1 TTTTTAGCGGCGTTTTTT
6392991 ATCCAAACGC
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
38 3 0.04
39 29 0.35
40 44 0.54
41 4 0.05
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTGAAAAACGCCGCTAATGCTCGA
Found at i:6399215 original size:19 final size:20
Alignment explanation
Indices: 6399179--6399226 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
6399169 AAAAGCAAAT
6399179 AAAATAAAAATTAGAAAACA
1 AAAATAAAAATTAGAAAACA
* *
6399199 AAAATTAAACTTA-AAAACA
1 AAAATAAAAATTAGAAAACA
6399218 AAAATAAAA
1 AAAATAAAA
6399227 TGCAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAATAAAAATTAGAAAACA
Found at i:6400375 original size:30 final size:30
Alignment explanation
Indices: 6400330--6400434 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
6400320 CATGAGCGTA
* *
6400330 TGGCTAGCCCGTGTGGCTCAGACGAGCATG
1 TGGCTAGCCTGTGTGGCTCACACGAGCATG
* *
6400360 TGGCCAGCCTGTGTGGCTCACACGGGCATG
1 TGGCTAGCCTGTGTGGCTCACACGAGCATG
* *
6400390 TGGCTAGCCCT-TGTAGCTCACACGATCATG
1 TGGCTAG-CCTGTGTGGCTCACACGAGCATG
* *
6400420 TGGCTTGCCCGTGTG
1 TGGCTAGCCTGTGTG
6400435 AAAATGCTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.03
30 57 0.92
31 3 0.05
ACGTcount: A:0.14, C:0.29, G:0.33, T:0.24
Consensus pattern (30 bp):
TGGCTAGCCTGTGTGGCTCACACGAGCATG
Found at i:6401532 original size:3 final size:3
Alignment explanation
Indices: 6401524--6401651 Score: 114
Period size: 3 Copynumber: 42.7 Consensus size: 3
6401514 TAATAGAACA
* * * * * * *
6401524 AGT AGT AGT AGA AGT AGT AGT AGC AGT AGT AGT AGC AGC AGC AGC AGC
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
* * * *
6401572 AGC AGT AGT AGT AGT AGT AGT AGT AGC AGT AGC AGT AGC AGT AAG-
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT -AGT
* * *
6401617 AGT AGT AGT AGT AGC AGT AGC AGT AGC AGT AGT AG
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AG
6401652 GAATTCAATC
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.02
3 101 0.96
4 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.34, T:0.21
Consensus pattern (3 bp):
AGT
Found at i:6401540 original size:12 final size:12
Alignment explanation
Indices: 6401524--6401651 Score: 136
Period size: 12 Copynumber: 10.7 Consensus size: 12
6401514 TAATAGAACA
*
6401524 AGTAGTAGTAGA
1 AGTAGTAGTAGC
6401536 AGTAGTAGTAGC
1 AGTAGTAGTAGC
6401548 AGTAGTAGTAGCAGC
1 AGTAGTAGT---AGC
* * *
6401563 AGCAGCAGCAGC
1 AGTAGTAGTAGC
*
6401575 AGTAGTAGTAGT
1 AGTAGTAGTAGC
6401587 AGTAGTAGTAGC
1 AGTAGTAGTAGC
*
6401599 AGTAGCAGTAGC
1 AGTAGTAGTAGC
*
6401611 AGTA--AG-AGT
1 AGTAGTAGTAGC
6401620 AGTAGTAGTAGC
1 AGTAGTAGTAGC
*
6401632 AGTAGCAGTAGC
1 AGTAGTAGTAGC
6401644 AGTAGTAG
1 AGTAGTAG
6401652 GAATTCAATC
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
9 6 0.06
10 2 0.02
11 2 0.02
12 77 0.80
15 9 0.09
ACGTcount: A:0.35, C:0.10, G:0.34, T:0.21
Consensus pattern (12 bp):
AGTAGTAGTAGC
Found at i:6423746 original size:44 final size:43
Alignment explanation
Indices: 6423679--6423764 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 43
6423669 TGTTTTTAGT
6423679 TTTCCACTTAAACCCTGATTAGTGTAAGTTATTTTAATATTAA
1 TTTCCACTTAAACCCTGATTAGTGTAAGTTATTTTAATATTAA
* *
6423722 TTTCTCACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTA
1 TTTC-CACTTAAACCCTGATTAGTGTAAGTTATTTTAATATTA
6423765 TTTGACCTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 4 0.10
44 36 0.90
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (43 bp):
TTTCCACTTAAACCCTGATTAGTGTAAGTTATTTTAATATTAA
Found at i:6424294 original size:24 final size:24
Alignment explanation
Indices: 6424267--6424324 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
6424257 TGGGCCTATG
6424267 TGGCCCAAAATCCGGAATAAATAA
1 TGGCCCAAAATCCGGAATAAATAA
6424291 TGGCCCAAAATCCGGAATAAATAA
1 TGGCCCAAAATCCGGAATAAATAA
6424315 TGGCCCAAAA
1 TGGCCCAAAA
6424325 CAATGTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (24 bp):
TGGCCCAAAATCCGGAATAAATAA
Found at i:6425258 original size:12 final size:12
Alignment explanation
Indices: 6425236--6425316 Score: 85
Period size: 12 Copynumber: 6.8 Consensus size: 12
6425226 TTTCTTTAGT
6425236 TTATT-TTATTA
1 TTATTGTTATTA
**
6425247 ACATTGTTATTA
1 TTATTGTTATTA
*
6425259 TTATTATTATTA
1 TTATTGTTATTA
6425271 TTATTGTTATTA
1 TTATTGTTATTA
*
6425283 TTATTGTTATTG
1 TTATTGTTATTA
*
6425295 TTA-TATTATATA
1 TTATTGTTAT-TA
*
6425307 TTATTATTAT
1 TTATTGTTAT
6425317 ATCTACATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
11 8 0.14
12 44 0.76
13 6 0.10
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:6425261 original size:3 final size:3
Alignment explanation
Indices: 6425253--6425316 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
6425243 ATTAACATTG
* * *
6425253 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTG TTA TTG TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6425300 TTA TATA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA T
6425317 ATCTACATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6425457 original size:34 final size:34
Alignment explanation
Indices: 6425419--6425483 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
6425409 ATTATCTTGT
**
6425419 TTTCATAATTTTCACATACATATATATTTTTATA
1 TTTCATAATTTAAACATACATATATATTTTTATA
* * *
6425453 TTTCATGATTTAAACATGCATGTATATTTTT
1 TTTCATAATTTAAACATACATATATATTTTT
6425484 TGTATGTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (34 bp):
TTTCATAATTTAAACATACATATATATTTTTATA
Found at i:6441163 original size:34 final size:36
Alignment explanation
Indices: 6441125--6441201 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 36
6441115 TTAAAAATAT
6441125 ATATTTTTTAATTAATATA-TTTTTAATA-TTTTTA
1 ATATTTTTTAATTAATATATTTTTTAATATTTTTTA
* ** *
6441159 ATATTTTTTTATTTTTATATTTTTTTATATTTTTTA
1 ATATTTTTTAATTAATATATTTTTTAATATTTTTTA
*
6441195 AAATTTT
1 ATATTTT
6441202 AATTTTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 16 0.44
35 8 0.22
36 12 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (36 bp):
ATATTTTTTAATTAATATATTTTTTAATATTTTTTA
Found at i:6441171 original size:26 final size:26
Alignment explanation
Indices: 6441142--6441193 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
6441132 TTAATTAATA
6441142 TATTTTTA-ATATTTTTAATATTTTTT
1 TATTTTTATAT-TTTTTAATATTTTTT
*
6441168 TATTTTTATATTTTTTTATATTTTTT
1 TATTTTTATATTTTTTAATATTTTTT
6441194 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (26 bp):
TATTTTTATATTTTTTAATATTTTTT
Found at i:6441178 original size:16 final size:16
Alignment explanation
Indices: 6441124--6441191 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
6441114 TTTAAAAATA
* **
6441124 TATATTTTTTAATTAA
1 TATATTTTTTTATTTT
*
6441140 TATATTTTTAATATTTT
1 TATATTTTT-TTATTTT
6441157 TAATATTTTTTTATTTT
1 T-ATATTTTTTTATTTT
6441174 TATATTTTTTTATATTT
1 TATATTTTTTTAT-TTT
6441191 T
1 T
6441192 TTAAAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
16 21 0.48
17 15 0.34
18 8 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATATTTTTTTATTTT
Found at i:6441193 original size:9 final size:9
Alignment explanation
Indices: 6441140--6441194 Score: 69
Period size: 9 Copynumber: 6.2 Consensus size: 9
6441130 TTTTAATTAA
6441140 TATATTTTT
1 TATATTTTT
*
6441149 AATATTTTT
1 TATATTTTT
*
6441158 AATATTTTT
1 TATATTTTT
6441167 T-TA-TTTT
1 TATATTTTT
6441174 TATATTTTTT
1 TATA-TTTTT
6441184 TATATTTTT
1 TATATTTTT
6441193 TA
1 TA
6441195 AAATTTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 5 0.12
8 4 0.10
9 24 0.59
10 8 0.20
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TATATTTTT
Found at i:6442635 original size:43 final size:42
Alignment explanation
Indices: 6442530--6442658 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 42
6442520 TGTGGGTTTA
* *
6442530 TACTTCGATTTAGCCGATGATACACTTATGTGCCAGTATATT
1 TACTTCGATTTATCCGATGATACACTTGTGTGCCAGTATATT
* * *
6442572 TGCTTC-ATTTTATCCAATGATACACTGTGTGTGTC--TATATGAT
1 TACTTCGA-TTTATCCGATGATACACT-TGTGTGCCAGTATAT--T
*
6442615 TACTTCGATTTATCCGATGATGCACTATGTGTGCCAGTATATT
1 TACTTCGATTTATCCGATGATACACT-TGTGTGCCAGTATATT
6442658 T
1 T
6442659 CTTTCGGTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
41 6 0.09
42 21 0.30
43 37 0.53
44 1 0.01
45 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (42 bp):
TACTTCGATTTATCCGATGATACACTTGTGTGCCAGTATATT
Found at i:6451291 original size:59 final size:60
Alignment explanation
Indices: 6451152--6451302 Score: 139
Period size: 59 Copynumber: 2.5 Consensus size: 60
6451142 GTTTAACTCC
* * * * * *
6451152 AAAAAAGTT-TAGACCCCAATGTGGGAACAATTGCAAGTTTAGGAACTAACTTAGACCCCC
1 AAAAAAGTTCAAG-CCCCAATATGAGAACAATTGCAAGTTCAGGAACTAACTTAGACACCA
* * * * * *
6451212 CAAAATGTTCAAACCTCAATATGAGAACAATTGTCACGTTCAGGGACTAACTT-GA-ACCA
1 AAAAAAGTTCAAGCCCCAATATGAGAACAATTG-CAAGTTCAGGAACTAACTTAGACACCA
6451271 AAAAAAGTTCAAGCCCCAATAT-AGGAACAATT
1 AAAAAAGTTCAAGCCCCAATATGA-GAACAATT
6451303 ACCTAATTCA
Statistics
Matches: 72, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
58 1 0.01
59 28 0.39
60 26 0.36
61 17 0.24
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (60 bp):
AAAAAAGTTCAAGCCCCAATATGAGAACAATTGCAAGTTCAGGAACTAACTTAGACACCA
Found at i:6452268 original size:24 final size:24
Alignment explanation
Indices: 6452235--6452281 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
6452225 GCCCATCACT
* *
6452235 CACACGCAGCGCAACCTCATGTAC
1 CACACCCAGCGCAACCGCATGTAC
*
6452259 CACACCCAGCGCCACCGCATGTA
1 CACACCCAGCGCAACCGCATGTA
6452282 TCAAATCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.45, G:0.17, T:0.11
Consensus pattern (24 bp):
CACACCCAGCGCAACCGCATGTAC
Found at i:6452828 original size:2 final size:2
Alignment explanation
Indices: 6452821--6452852 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6452811 AACCAATTTC
6452821 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
6452853 CATTTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6454834 original size:21 final size:21
Alignment explanation
Indices: 6454801--6454845 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
6454791 ATACATGAAT
6454801 AATTTAAATATATATAATAATA
1 AATTTAAATATATATAATAA-A
*
6454823 AATTTAAA-ATATATATTAAA
1 AATTTAAATATATATAATAAA
6454843 AAT
1 AAT
6454846 AAAAAATGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 10 0.45
22 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAAATATATATAATAAA
Found at i:6454836 original size:23 final size:23
Alignment explanation
Indices: 6454801--6454848 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6454791 ATACATGAAT
*
6454801 AATTTAAATATATA-TAATAATA
1 AATTTAAATATATATTAAAAATA
6454823 AATTTAAAATATATATTAAAAATA
1 AATTT-AAATATATATTAAAAATA
6454847 AA
1 AA
6454849 AAATGCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 9 0.39
24 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTAAATATATATTAAAAATA
Found at i:6457029 original size:12 final size:12
Alignment explanation
Indices: 6457012--6457056 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
6457002 ATCCAACCCG
6457012 TTCAATTGTCTA
1 TTCAATTGTCTA
* *
6457024 TTCAATTGGTTTG
1 TTCAATT-GTCTA
6457037 TTCAATTGTCTA
1 TTCAATTGTCTA
6457049 TTCAATTG
1 TTCAATTG
6457057 GTTTTTAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (12 bp):
TTCAATTGTCTA
Found at i:6457045 original size:25 final size:25
Alignment explanation
Indices: 6457011--6457060 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6457001 GATCCAACCC
6457011 GTTCAATTGTCTATTCAATTGGTTT
1 GTTCAATTGTCTATTCAATTGGTTT
6457036 GTTCAATTGTCTATTCAATTGGTTT
1 GTTCAATTGTCTATTCAATTGGTTT
6457061 TTAGCTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (25 bp):
GTTCAATTGTCTATTCAATTGGTTT
Found at i:6459759 original size:114 final size:115
Alignment explanation
Indices: 6459543--6459761 Score: 245
Period size: 114 Copynumber: 1.9 Consensus size: 115
6459533 AATCATTTGA
* * **
6459543 AAAAGGAATAGTTGCTTTTGATGACAATTTCTTTTTTATAATTCTGTTTTTGGTGCTTTTTTTTT
1 AAAAGGAATAGTTGCTTTTGATGACAATTTCTTTTTTATAATTCTGGTTCTGGTGCTTTTGCTTT
**
6459608 CTGAAGTTGAGAAATTTGTTGATTGAATTGTGTTTGTGTTCTTGGTTTCTC
66 CTGAAGTTGAGAAATTTGTTGATT-AATTGTAATTGTGTTCTTGGTTTCTC
* *
6459659 AAAA-GAAT-GTTGC-TTTGATGACAATTTCTTATTATTCT-ATTCTGGGTTCTGGTTCTTTCTG
1 AAAAGGAATAGTTGCTTTTGATGACAATTTCTT-TT-TTATAATTCT-GGTTCTGGTGCTTT-TG
*
6459720 CTTT-T-AAGTTGAGAATTTTGTTGCTATT-ATTGTAATTGTGTT
62 CTTTCTGAAGTTGAGAAATTTGTTG--ATTAATTGTAATTGTGTT
6459762 ATAGCCAATT
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
113 17 0.19
114 41 0.47
115 19 0.22
116 11 0.12
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.52
Consensus pattern (115 bp):
AAAAGGAATAGTTGCTTTTGATGACAATTTCTTTTTTATAATTCTGGTTCTGGTGCTTTTGCTTT
CTGAAGTTGAGAAATTTGTTGATTAATTGTAATTGTGTTCTTGGTTTCTC
Found at i:6475617 original size:92 final size:90
Alignment explanation
Indices: 6475384--6475645 Score: 269
Period size: 93 Copynumber: 2.8 Consensus size: 90
6475374 ACAAGTCACT
* *
6475384 GCATCTTCACTAAATTAAGATTCAAGAGGAAGTGCTTCAGTTTGGTTTGGTTTTGGACTCCACTA
1 GCATCTTCACTAAA-T-AGA-TCAAGAGGAAGTGCTTCAGTTTGGTTTTGTTTTGGACT-CACTG
*
6475449 ATCCTTTGAAAACATCAAAAGATACATCA
62 ATCCTTTGAAAGCATCAAAAGATACATCA
* * **
6475478 -CATCTTCACTAGATAAAGGTTCATA-AGGAAGCACTTCAGTTTGGTTTTGTTTTGGACTCAGCT
1 GCATCTTCACTA-A-ATA-GATCA-AGAGGAAGTGCTTCAGTTTGGTTTTGTTTTGGACTCA-CT
* * *
6475541 GATCCCTTGAAAGCAT-AAAAGGTGCATCGCA
61 GATCCTTTGAAAGCATCAAAAGATACAT--CA
* ** *
6475572 GCATCTTCACTAAATAGATCACGAGGAAGTGCTTCAACTTGGTTTTGTTTTGGACTCAAATGATC
1 GCATCTTCACTAAATAGATCAAGAGGAAGTGCTTCAGTTTGGTTTTGTTTTGGACTC-ACTGATC
6475637 CTTTGAAAG
65 CTTTGAAAG
6475646 TACTAAAAAA
Statistics
Matches: 139, Mismatches: 19, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
92 58 0.42
93 63 0.45
94 6 0.04
95 12 0.09
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (90 bp):
GCATCTTCACTAAATAGATCAAGAGGAAGTGCTTCAGTTTGGTTTTGTTTTGGACTCACTGATCC
TTTGAAAGCATCAAAAGATACATCA
Found at i:6475828 original size:15 final size:15
Alignment explanation
Indices: 6475808--6475839 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6475798 CTCGCTAGTC
6475808 GGTTCATGTTTGAAA
1 GGTTCATGTTTGAAA
*
6475823 GGTTCATGTTTGGAA
1 GGTTCATGTTTGAAA
6475838 GG
1 GG
6475840 ACAACTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.34, T:0.38
Consensus pattern (15 bp):
GGTTCATGTTTGAAA
Found at i:6477867 original size:6 final size:6
Alignment explanation
Indices: 6477856--6477903 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
6477846 AGCTGAACCC
6477856 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
6477904 ATCTTAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:6478181 original size:37 final size:37
Alignment explanation
Indices: 6478140--6478212 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
6478130 TCTTAAAAGA
*
6478140 ACATGACAAGTTAACTT-AAGAGTTCATATCTAATTTG
1 ACATGACAAGTTAA-TTCAAGAGTTAATATCTAATTTG
** *
6478177 ACATGGTAAGTTAATTCAATAGTTAATATCTAATTT
1 ACATGACAAGTTAATTCAAGAGTTAATATCTAATTT
6478213 AACTTATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.06
37 29 0.94
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (37 bp):
ACATGACAAGTTAATTCAAGAGTTAATATCTAATTTG
Found at i:6486243 original size:13 final size:13
Alignment explanation
Indices: 6486225--6486250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6486215 TCCTTTTACT
6486225 ATATATTTTGTAG
1 ATATATTTTGTAG
6486238 ATATATTTTGTAG
1 ATATATTTTGTAG
6486251 GTATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATATATTTTGTAG
Found at i:6486946 original size:20 final size:20
Alignment explanation
Indices: 6486893--6486964 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
6486883 AAATATTAAA
*
6486893 TTAA-ATTAAA-TAATTATC
1 TTAATATTAAATTTATTATC
* *
6486911 TTAATAGT-ATTTTATTAAT-
1 TTAATATTAAATTTATT-ATC
6486930 TTAATATTAAATTTATTATC
1 TTAATATTAAATTTATTATC
6486950 TTAATATTAAATTTA
1 TTAATATTAAATTTA
6486965 ATTTAATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.11
19 15 0.34
20 24 0.55
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (20 bp):
TTAATATTAAATTTATTATC
Found at i:6487021 original size:62 final size:59
Alignment explanation
Indices: 6486950--6487066 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 59
6486940 ATTTATTATC
* * *
6486950 TTAATATTAAATTTAATT-TAATGTTTATCTTATAGATAAATATTCTATTTATTTAATAAGAT
1 TTAATATTAAATTT-ATTATAATATTTATC--A-AGATAAATATTATATTAATTTAATAAGAT
6487012 TTAATATTAAATTTATTATAATATTTATCAAGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTATTATAATATTTATCAAGATAAATATTATATTAATTTAATA
6487067 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
59 23 0.45
60 1 0.02
61 3 0.06
62 24 0.47
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTATTATAATATTTATCAAGATAAATATTATATTAATTTAATAAGAT
Found at i:6491632 original size:20 final size:22
Alignment explanation
Indices: 6491607--6491655 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
6491597 ACTTTTTTAT
6491607 ATTTTCATA-ACTTTATA-ACA
1 ATTTTCATATACTTTATATACA
*
6491627 ATTTTC-TATATTTTATATACA
1 ATTTTCATATACTTTATATACA
*
6491648 TTTTTCAT
1 ATTTTCAT
6491656 GATTTTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 13 0.54
21 8 0.33
22 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTCATATACTTTATATACA
Found at i:6491660 original size:21 final size:19
Alignment explanation
Indices: 6491607--6491661 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
6491597 ACTTTTTTAT
*
6491607 ATTTTCATAACTTTATAACA
1 ATTTTCAT-ATTTTATAACA
6491627 ATTTTCTATATTTTATATACA
1 ATTTTC-ATATTTTATA-ACA
*
6491648 TTTTTCATGATTTT
1 ATTTTCAT-ATTTT
6491662 TACATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTCATATTTTATAACA
Found at i:6493361 original size:20 final size:21
Alignment explanation
Indices: 6493318--6493362 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
6493308 TTTTGAGCAA
*
6493318 TTTAAATTTTTTTTTATGTTC
1 TTTAAATTTCTTTTTATGTTC
6493339 TTTAAACTTTCTTTTT-T-TTC
1 TTTAAA-TTTCTTTTTATGTTC
6493359 TTTA
1 TTTA
6493363 TTTTCCGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTAAATTTCTTTTTATGTTC
Found at i:6499040 original size:22 final size:22
Alignment explanation
Indices: 6499015--6499057 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6499005 ATAAGTTCCT
*
6499015 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
6499037 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
6499058 GAATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:6513278 original size:20 final size:18
Alignment explanation
Indices: 6513250--6513290 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6513240 TAAAAGATAG
6513250 ATAAAATT-AA-T-AACT
1 ATAAAATTAAATTAAACT
6513265 ATAAAATTAAATTAAACT
1 ATAAAATTAAATTAAACT
6513283 ATAAAATT
1 ATAAAATT
6513291 TAAAACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 1 0.04
18 12 0.52
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAATTAAATTAAACT
Found at i:6513835 original size:31 final size:31
Alignment explanation
Indices: 6513800--6513867 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6513790 ATTTGATTTG
* *
6513800 ATTATACATATTAAAATTTGATTTTAAATT-A
1 ATTATACAAATAAAAATTTGATTTT-AATTCA
*
6513831 ATTATATAAATAAAAATTTGATTTTAATTCA
1 ATTATACAAATAAAAATTTGATTTTAATTCA
6513862 ATTATA
1 ATTATA
6513868 AATCTTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTATACAAATAAAAATTTGATTTTAATTCA
Found at i:6513924 original size:93 final size:93
Alignment explanation
Indices: 6513816--6513996 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
6513806 CATATTAAAA
* * * *
6513816 TTTGATTTTAAATTAATTATATAAATAAAAATTTGA-TTTTAATTCAATTATAAATCTTTAGAAA
1 TTTGATTTCAAATTAATTATAAAAAT-AAAATTTGAGTTTTAATTCAATTATAAACCATTAGAAA
*
6513880 AACAAATAAGTTATGTTATTTAATAATTT
65 AACAAATAAGTTAAGTTATTTAATAATTT
* * * * *
6513909 TTTGATTTCGAATTAATTATAAAAATAAAATTTTAGTTTTGATTCAATTATAAACCATTATAAAT
1 TTTGATTTCAAATTAATTATAAAAATAAAATTTGAGTTTTAATTCAATTATAAACCATTAGAAAA
*
6513974 ATAAATAAGTTAAGTTATTTAAT
66 ACAAATAAGTTAAGTTATTTAAT
6513997 GACTTAGGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
92 8 0.11
93 68 0.89
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (93 bp):
TTTGATTTCAAATTAATTATAAAAATAAAATTTGAGTTTTAATTCAATTATAAACCATTAGAAAA
ACAAATAAGTTAAGTTATTTAATAATTT
Found at i:6520670 original size:34 final size:34
Alignment explanation
Indices: 6520610--6520676 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
6520600 TCACTATAAT
*
6520610 CAAATAGTGATAATGCAACTATAATAACAACAACA
1 CAAATAGTGATAAT-CAACAATAATAACAACAACA
*
6520645 CAAATAGATGATAAT-AACAATAATAATAACAA
1 CAAATAG-TGATAATCAACAATAATAACAACAA
6520677 TTATGACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 15 0.52
35 7 0.24
36 7 0.24
ACGTcount: A:0.58, C:0.13, G:0.07, T:0.21
Consensus pattern (34 bp):
CAAATAGTGATAATCAACAATAATAACAACAACA
Found at i:6520785 original size:21 final size:21
Alignment explanation
Indices: 6520746--6520785 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6520736 TTTAAAGGGC
*
6520746 AAAAATGTAAATAATAAAATT
1 AAAAATGTAAATAACAAAATT
6520767 AAAAATGCTAAA-AACAAAA
1 AAAAATG-TAAATAACAAAA
6520786 ATACACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAATGTAAATAACAAAATT
Found at i:6522295 original size:16 final size:15
Alignment explanation
Indices: 6522272--6522303 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
6522262 AATTAATGGA
6522272 TTTTTTATTTTTGTT
1 TTTTTTATTTTTGTT
6522287 TTTTATTATTTTTGTT
1 TTTT-TTATTTTTGTT
6522303 T
1 T
6522304 AGGCCGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.84
Consensus pattern (15 bp):
TTTTTTATTTTTGTT
Found at i:6525860 original size:29 final size:30
Alignment explanation
Indices: 6525811--6525895 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
6525801 TTTTATGTGT
*
6525811 AATTTAATACATG-AACTTTGATTTGGTGC
1 AATTTGATACATGAAACTTTGATTTGGTGC
*
6525840 AATTTGATACATGAAAC-TTGAATTGTGGTTC
1 AATTTGATACATGAAACTTTG-ATT-TGGTGC
* *
6525871 -ATATGTATACATTAAACTTTGATTT
1 AATTTG-ATACATGAAACTTTGATTT
6525896 TAGTTAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
29 15 0.32
30 11 0.23
31 18 0.38
32 3 0.06
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (30 bp):
AATTTGATACATGAAACTTTGATTTGGTGC
Found at i:6528409 original size:32 final size:31
Alignment explanation
Indices: 6528363--6528463 Score: 150
Period size: 32 Copynumber: 3.2 Consensus size: 31
6528353 AAAAATATTT
* *
6528363 AAAA-TATTTTAAAAATAATTTAAAATTACA
1 AAAATTATTTTAAAAATATTTTAAAATTAAA
6528393 AAAATTATTTTAAAAAATATTTTAAAATTAAA
1 AAAATTATTTT-AAAAATATTTTAAAATTAAA
*
6528425 AAAAGTATTTTAAAAATATTTTAAAATTTAAA
1 AAAATTATTTTAAAAATATTTTAAAA-TTAAA
6528457 AAAATTA
1 AAAATTA
6528464 AAAAAGTATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.06
31 21 0.33
32 39 0.61
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (31 bp):
AAAATTATTTTAAAAATATTTTAAAATTAAA
Found at i:6528441 original size:21 final size:19
Alignment explanation
Indices: 6528341--6528439 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 19
6528331 TTAATTTAAA
*
6528341 ATTTAAAAATT-AAAAAAT
1 ATTTTAAAATTAAAAAAAT
* **
6528359 ATTTAAAATATTTTAAAAAT
1 ATTTTAAA-ATTAAAAAAAT
* *
6528379 AATTTAAAATTACAAAAAT
1 ATTTTAAAATTAAAAAAAT
*
6528398 -TATT----TT-AAAAAAT
1 ATTTTAAAATTAAAAAAAT
6528411 ATTTTAAAATTAAAAAAAGT
1 ATTTTAAAATTAAAAAAA-T
6528431 ATTTTAAAA
1 ATTTTAAAA
6528440 ATATTTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
13 6 0.10
14 5 0.08
18 12 0.19
19 18 0.29
20 22 0.35
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
ATTTTAAAATTAAAAAAAT
Found at i:6528480 original size:40 final size:41
Alignment explanation
Indices: 6528416--6528501 Score: 138
Period size: 40 Copynumber: 2.1 Consensus size: 41
6528406 AAAATATTTT
* * *
6528416 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAA
1 AAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAAA
6528457 AAAATT-AAAAAAGTATGTAAAAAATATTTTAAAATTAAAA
1 AAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAAA
6528497 AAAAT
1 AAAAT
6528502 AAATATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 36 0.86
41 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (41 bp):
AAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAAA
Found at i:6530292 original size:19 final size:20
Alignment explanation
Indices: 6530254--6530298 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6530244 TAATTACTAT
*
6530254 AAAAATTTATTAACACAATA
1 AAAAATTTATAAACACAATA
*
6530274 AAAAATTTCTAAACA-AATA
1 AAAAATTTATAAACACAATA
6530293 ACAAAA
1 A-AAAA
6530299 AATCGTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATTTATAAACACAATA
Found at i:6531156 original size:2 final size:2
Alignment explanation
Indices: 6531149--6531182 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6531139 ATGAATAAGC
*
6531149 AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6531183 GCTTGGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6531392 original size:19 final size:21
Alignment explanation
Indices: 6531348--6531392 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
6531338 AAATTTATAA
*
6531348 AATATACATAAATTAGTTTTAT
1 AATATACATAAATTA-TTTTAC
6531370 AATATA-ATAAATT-TTTTAC
1 AATATACATAAATTATTTTAC
6531389 AATA
1 AATA
6531393 ACCATCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATACATAAATTATTTTAC
Found at i:6533209 original size:18 final size:18
Alignment explanation
Indices: 6533172--6533214 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6533162 GAATAGGTTT
6533172 TTAATTAAATAAATTTAA
1 TTAATTAAATAAATTTAA
* *
6533190 TTGATTAAA-AATTTTAAA
1 TTAATTAAATAAATTT-AA
6533208 TTAATTA
1 TTAATTA
6533215 CATATTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAATAAATTTAA
Found at i:6536339 original size:17 final size:17
Alignment explanation
Indices: 6536306--6536340 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6536296 TCCTCTATGT
* *
6536306 TAGAATAAATATTAAAA
1 TAGAATAAAAATCAAAA
6536323 TAGAATAAAAATCAAAA
1 TAGAATAAAAATCAAAA
6536340 T
1 T
6536341 CAAATAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
TAGAATAAAAATCAAAA
Found at i:6540987 original size:20 final size:20
Alignment explanation
Indices: 6540962--6541004 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6540952 CAAATCCAAC
6540962 CTCGAACCTCAAATCCTGAA
1 CTCGAACCTCAAATCCTGAA
** *
6540982 CTCGAACCTTGAATCTTGAA
1 CTCGAACCTCAAATCCTGAA
6541002 CTC
1 CTC
6541005 AGGGTTCGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.26
Consensus pattern (20 bp):
CTCGAACCTCAAATCCTGAA
Found at i:6542144 original size:13 final size:13
Alignment explanation
Indices: 6542123--6542161 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
6542113 TCTATTATTT
*
6542123 AATATTTTTTTTA
1 AATAATTTTTTTA
6542136 AATAATTTTTTTA
1 AATAATTTTTTTA
6542149 AA-AATTGTTTTTA
1 AATAATT-TTTTTA
6542162 GTGAAACAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
AATAATTTTTTTA
Found at i:6545467 original size:16 final size:16
Alignment explanation
Indices: 6545446--6545513 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
6545436 TTTGGTTCGC
6545446 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
6545462 TGTATTGGATTAGATG
1 TGTATTGGATTAGAGG
6545478 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6545494 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6545510 TGTA
1 TGTA
6545514 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6545578 original size:44 final size:45
Alignment explanation
Indices: 6545494--6545584 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
6545484 GGATTAGAGG
* * *
6545494 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
6545539 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
6545583 TG
1 TG
6545585 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:6545766 original size:16 final size:16
Alignment explanation
Indices: 6545729--6545770 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6545719 TTAATCATAT
6545729 TTAAACATA-ATTATAA
1 TTAAA-ATATATTATAA
*
6545745 TT-AAATATATTTTAA
1 TTAAAATATATTATAA
6545760 TTAAAATATAT
1 TTAAAATATAT
6545771 AATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6545776 original size:18 final size:17
Alignment explanation
Indices: 6545735--6545778 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
6545725 ATATTTAAAC
6545735 ATAATTATAATTAAATAT
1 ATAATT-TAATTAAATAT
6545753 AT--TTTAATTAAAATAT
1 ATAATTTAATT-AAATAT
6545769 ATAATTTAAT
1 ATAATTTAAT
6545779 ATCTCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
18 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATTTAATTAAATAT
Found at i:6545922 original size:18 final size:17
Alignment explanation
Indices: 6545901--6545935 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6545891 TTATTATTAA
*
6545901 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6545919 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6545936 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6555647 original size:13 final size:13
Alignment explanation
Indices: 6555629--6555653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6555619 TTTAATCAAC
6555629 ACTAAAAAAAAAA
1 ACTAAAAAAAAAA
6555642 ACTAAAAAAAAA
1 ACTAAAAAAAAA
6555654 TATTTTAAAT
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
ACTAAAAAAAAAA
Found at i:6561727 original size:17 final size:18
Alignment explanation
Indices: 6561689--6561732 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
6561679 TATTTTCAAG
*
6561689 AAAATATAATAATAAATTA
1 AAAATAT-ATAATAAATAA
6561708 AAAATATATAA-AAATAA
1 AAAATATATAATAAATAA
6561725 AAAATATA
1 AAAATATA
6561733 GTTGGCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 4 0.17
19 7 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATATATAATAAATAA
Found at i:6561835 original size:25 final size:24
Alignment explanation
Indices: 6561807--6561855 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
6561797 ATTTAAATTT
*
6561807 TATATTAATATTAAATAAATATAAA
1 TATATTAATACTAAATAAA-ATAAA
6561832 TATATTAATACTAAATAAAATAAA
1 TATATTAATACTAAATAAAATAAA
6561856 AATCCCCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATTAATACTAAATAAAATAAA
Found at i:6561836 original size:19 final size:20
Alignment explanation
Indices: 6561814--6561853 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
6561804 TTTTATATTA
6561814 ATATTAA-A-TAAATATAAAT
1 ATATTAATACTAAATA-AAAT
6561833 ATATTAATACTAAATAAAAT
1 ATATTAATACTAAATAAAAT
6561853 A
1 A
6561854 AAAATCCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATTAATACTAAATAAAAT
Found at i:6562196 original size:10 final size:10
Alignment explanation
Indices: 6562181--6562223 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
6562171 TTTGAAATAT
6562181 TTTAATATAA
1 TTTAATATAA
6562191 TTTAATATTTAA
1 TTTAATA--TAA
*
6562203 TATTAATTTAA
1 T-TTAATATAA
6562214 TTTAATATAA
1 TTTAATATAA
6562224 AACATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 15 0.54
11 4 0.14
12 4 0.14
13 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAATATAA
Found at i:6562199 original size:18 final size:18
Alignment explanation
Indices: 6562176--6562214 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6562166 AAATATTTGA
6562176 AATATTTTAATA-TAATTT
1 AATA-TTTAATATTAATTT
6562194 AATATTTAATATTAATTT
1 AATATTTAATATTAATTT
6562212 AAT
1 AAT
6562215 TTAATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTTAATATTAATTT
Found at i:6562345 original size:29 final size:29
Alignment explanation
Indices: 6562313--6562398 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
6562303 TAAATTATAT
6562313 ATTATTTTATTAAATTATATTTAATAACA
1 ATTATTTTATTAAATTATATTTAATAACA
* **
6562342 ATTA---TATTAAAATATGA-TTAA-AGTA
1 ATTATTTTATTAAATTAT-ATTTAATAACA
*
6562367 TTTATTATTATTAAATTATATTTAATAACA
1 ATTATT-TTATTAAATTATATTTAATAACA
6562397 AT
1 AT
6562399 CCTATTAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 13
0.67 0.13 0.21
Matches are distributed among these distances:
25 5 0.12
26 14 0.33
27 1 0.02
28 1 0.02
29 18 0.43
30 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (29 bp):
ATTATTTTATTAAATTATATTTAATAACA
Found at i:6562350 original size:26 final size:26
Alignment explanation
Indices: 6562320--6562409 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 26
6562310 TATATTATTT
6562320 TATTAAATTATATTTAATAACAATTA
1 TATTAAATTATATTTAATAACAATTA
* * ***
6562346 TATTAAAATATGATTAAAGTATTTATTA
1 TATTAAATTAT-ATTTAA-TAACAATTA
**
6562374 TTATTAAATTATATTTAATAACAATCC
1 -TATTAAATTATATTTAATAACAATTA
6562401 TATTAAATT
1 TATTAAATT
6562410 TTAATAACAA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
26 19 0.39
27 9 0.18
28 11 0.22
29 10 0.20
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
TATTAAATTATATTTAATAACAATTA
Found at i:6562395 original size:55 final size:56
Alignment explanation
Indices: 6562283--6562407 Score: 171
Period size: 55 Copynumber: 2.2 Consensus size: 56
6562273 AATATAAAAT
* * *
6562283 AATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTATATTTAATAAC
1 AATTATATTAA-AATATGATTAAAGTATATATTA-TTTATTAAATTATATTTAATAAC
*
6562341 AATTATATTAAAATATGATTAAAGTATTTATTA-TTATTAAATTATATTTAATAAC
1 AATTATATTAAAATATGATTAAAGTATATATTATTTATTAAATTATATTTAATAAC
**
6562396 AATCCTATTAAA
1 AATTATATTAAA
6562408 TTTTAATAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 32 0.52
57 18 0.30
58 11 0.18
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (56 bp):
AATTATATTAAAATATGATTAAAGTATATATTATTTATTAAATTATATTTAATAAC
Found at i:6562987 original size:22 final size:22
Alignment explanation
Indices: 6562956--6563006 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
6562946 TAAACCTTTT
* *
6562956 TTTTGTTGTTGTTTTACTGTCA
1 TTTTGCTGTTGTTTTACTATCA
* *
6562978 TTTTGCTGTTTTTTTTCTATCA
1 TTTTGCTGTTGTTTTACTATCA
6563000 TTTTGCT
1 TTTTGCT
6563007 ATTATATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.08, C:0.12, G:0.14, T:0.67
Consensus pattern (22 bp):
TTTTGCTGTTGTTTTACTATCA
Found at i:6566379 original size:21 final size:21
Alignment explanation
Indices: 6566355--6566404 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6566345 TTTACCTAAG
*
6566355 ATATAAATTGAATTGAATTGA
1 ATATAAATTGAATTAAATTGA
* *
6566376 ATATGAATTGTATTAAATTGA
1 ATATAAATTGAATTAAATTGA
*
6566397 GT-TAAATT
1 ATATAAATT
6566405 TACTTGTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (21 bp):
ATATAAATTGAATTAAATTGA
Found at i:6568572 original size:21 final size:18
Alignment explanation
Indices: 6568544--6568600 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
6568534 CTTTACACCA
6568544 CATTGTGGATAAACCACT
1 CATTGTGGATAAACCACT
**
6568562 CATCGTTGTGGACGAACCACT
1 CA---TTGTGGATAAACCACT
6568583 CATTGTGGATAAACCACT
1 CATTGTGGATAAACCACT
6568601 AGTAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 16 0.50
21 16 0.50
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (18 bp):
CATTGTGGATAAACCACT
Found at i:6568785 original size:22 final size:22
Alignment explanation
Indices: 6568755--6568833 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 22
6568745 TTTCTATTAT
*
6568755 AGTGTAGATAAACCACTCAAAC
1 AGTGCAGATAAACCACTCAAAC
*
6568777 AGTGCAGATAAAATCTACTCAAAC
1 AGTGCAGAT-AAA-CCACTCAAAC
* **
6568801 GGTGTGGATAAACCACTC-AAC
1 AGTGCAGATAAACCACTCAAAC
* *
6568822 GGTGCATATAAA
1 AGTGCAGATAAA
6568834 TTGTTCAACT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.26
22 13 0.28
23 6 0.13
24 15 0.33
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (22 bp):
AGTGCAGATAAACCACTCAAAC
Found at i:6571355 original size:13 final size:13
Alignment explanation
Indices: 6571337--6571362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6571327 TCCATTCAAC
6571337 TTTGACCTTATAA
1 TTTGACCTTATAA
6571350 TTTGACCTTATAA
1 TTTGACCTTATAA
6571363 GCTGAGGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTGACCTTATAA
Found at i:6574382 original size:109 final size:108
Alignment explanation
Indices: 6574187--6574513 Score: 489
Period size: 109 Copynumber: 3.0 Consensus size: 108
6574177 TGGATTAAGA
* * *
6574187 TTTAAGAGGATATTTGGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGT
** * *
6574250 TTTCTCGAATTTTCGAACGCAAAACATTGCCTTATTTTGAAAT
66 TTTCTCGAATTCCCAAACGCAAAACATTGCCTTACTTTGAAAT
* *
6574293 TTCTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCGCATTAGGGCAGG
1 TT-TAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACG
*
6574358 TTTTCTCAAATTCCCAAACGCAAAACATTGCCTTACTTTGAAAAT
65 TTTTCTCGAATTCCCAAACGCAAAACATTGCCTTACTTTG-AAAT
**
6574403 TTTAAAATTATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGT
*
6574468 TTTCTCGAA-TCTCCAAACGCAAAACATTGTCTTACTTTGAAAT
66 TTTCTCGAATTC-CCAAACGCAAAACATTGCCTTACTTTGAAAT
6574511 TTT
1 TTT
6574514 TTTTAAAAGG
Statistics
Matches: 200, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
106 2 0.01
107 29 0.14
108 9 0.05
109 154 0.77
110 6 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (108 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGT
TTTCTCGAATTCCCAAACGCAAAACATTGCCTTACTTTGAAAT
Found at i:6575840 original size:12 final size:12
Alignment explanation
Indices: 6575823--6575873 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
6575813 TATATATATT
6575823 AAAATAAAAAGA
1 AAAATAAAAAGA
*
6575835 AAAATAAATAGA
1 AAAATAAAAAGA
* *
6575847 GTAAA-AAGAAGTA
1 -AAAATAAAAAG-A
6575860 AAAATAAAAAGA
1 AAAATAAAAAGA
6575872 AA
1 AA
6575874 CCCTTAGATC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 21 0.70
13 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (12 bp):
AAAATAAAAAGA
Found at i:6576635 original size:88 final size:88
Alignment explanation
Indices: 6576516--6576773 Score: 356
Period size: 88 Copynumber: 2.9 Consensus size: 88
6576506 GATTTGTGGT
* * * * * * **
6576516 TTAAATTTACTTCACTACTACCTTGGGAAGATAAGATTCACCGTCTTTGATCCCCTCCACTACTG
1 TTAAATATACTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
*
6576581 CTTAGGGAGACAGGA-CTAATGGC
66 CTTAGGGAGACAGAATC-AATGGC
* * * *
6576604 TTAAATATATTTTTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATGTGCTCCACTACTG
1 TTAAATATACTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
*
6576669 CTTAGGGAGATAGAATCAATGGC
66 CTTAGGGAGACAGAATCAATGGC
*
6576692 TTAAATATGCTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
1 TTAAATATACTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
*
6576757 CTTAGGGAGATAGAATC
66 CTTAGGGAGACAGAATC
6576774 TGCAATCTTC
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
88 150 0.99
89 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (88 bp):
TTAAATATACTTCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTG
CTTAGGGAGACAGAATCAATGGC
Found at i:6576665 original size:42 final size:42
Alignment explanation
Indices: 6576617--6576753 Score: 120
Period size: 42 Copynumber: 3.2 Consensus size: 42
6576607 AATATATTTT
*
6576617 TCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATGTGC
1 TCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATGTAC
* ** *
6576659 TCCACTACTGCTTAGGG-AGAT-AGAATCA--ATGGCTTAAATATGCTTC
1 TCCACTA-T-CTT-GGGAAGATAAGATTCACCAT--CTT--CGATG-TAC
*
6576705 TCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTAC
1 TCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATGTAC
6576747 TCCACTA
1 TCCACTA
6576754 CTGCTTAGGG
Statistics
Matches: 74, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
41 2 0.03
42 16 0.22
43 15 0.20
44 14 0.19
45 16 0.22
46 9 0.12
47 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (42 bp):
TCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATGTAC
Found at i:6576791 original size:44 final size:44
Alignment explanation
Indices: 6576734--6576945 Score: 161
Period size: 44 Copynumber: 4.8 Consensus size: 44
6576724 AAGATTCACC
* *
6576734 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGAATCTGCA
*
6576778 ATCTTCAACCTACTCCACTACCGCTTAGGGAGATA-AGA-CT--A
1 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGA-ATCTGCA
* * * * * *
6576819 ATGGCTTAAATATGCTTCTCCACTA-T-CTT-GGGAAGATAAGATTC-ACC
1 AT--CTT-CA-A-CCTACTCCACTACTGCTTAGGG-AGAT-AGAATCTGCA
* * * * *
6576866 ATCTTCGATCTGCTCCACTACTACTTAGGGAGACAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGAATCTGCA
*
6576910 ATCTTCAACCTACTTCACTACTGCTTAGGGAGATAG
1 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAG
6576946 GACTAGTGGC
Statistics
Matches: 129, Mismatches: 23, Indels: 32
0.70 0.12 0.17
Matches are distributed among these distances:
41 3 0.02
42 10 0.08
43 16 0.12
44 78 0.60
45 8 0.06
46 12 0.09
47 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGAATCTGCA
Found at i:6576869 original size:132 final size:132
Alignment explanation
Indices: 6576658--6576957 Score: 512
Period size: 132 Copynumber: 2.3 Consensus size: 132
6576648 CTTCGATGTG
*
6576658 CTCCACTACTGCTTAGGGAGAT-AGAATCAATGGCTTAAATATGCTTCTCCACTATCTTGGGAAG
1 CTCCACTACTGCTTAGGGAGATAAGACT-AATGGCTTAAATATGCTTCTCCACTATCTTGGGAAG
* *
6576722 ATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGAATCTGCAATCTTCAAC
65 ATAAGATTCACCATCTTCGATCTACTCCACTACTACTTAGGGAGACAGAATCTGCAATCTTCAAC
6576787 CTA
130 CTA
*
6576790 CTCCACTACCGCTTAGGGAGATAAGACTAATGGCTTAAATATGCTTCTCCACTATCTTGGGAAGA
1 CTCCACTACTGCTTAGGGAGATAAGACTAATGGCTTAAATATGCTTCTCCACTATCTTGGGAAGA
*
6576855 TAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGAGACAGAATCTGCAATCTTCAACC
66 TAAGATTCACCATCTTCGATCTACTCCACTACTACTTAGGGAGACAGAATCTGCAATCTTCAACC
6576920 TA
131 TA
* * *
6576922 CTTCACTACTGCTTAGGGAGATAGGACTAGTGGCTT
1 CTCCACTACTGCTTAGGGAGATAAGACTAATGGCTT
6576958 CCCCGATCTA
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
132 154 0.97
133 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGAGATAAGACTAATGGCTTAAATATGCTTCTCCACTATCTTGGGAAGA
TAAGATTCACCATCTTCGATCTACTCCACTACTACTTAGGGAGACAGAATCTGCAATCTTCAACC
TA
Found at i:6586490 original size:43 final size:43
Alignment explanation
Indices: 6586429--6586516 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
6586419 GTTCTTCTCT
*
6586429 TGGCCTAAGGATGTTATCATTAATCATTTTACTCTGCCACTCA
1 TGGCCTAAGGATGTTATCATTAATCATTTTACTCTGCCACCCA
*
6586472 TGGCCTAAGGATGTTATCATTAATCCTTTTACTCTGCCACCCA
1 TGGCCTAAGGATGTTATCATTAATCATTTTACTCTGCCACCCA
6586515 TG
1 TG
6586517 ATATTCCGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (43 bp):
TGGCCTAAGGATGTTATCATTAATCATTTTACTCTGCCACCCA
Found at i:6587722 original size:16 final size:16
Alignment explanation
Indices: 6587701--6587735 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6587691 TTTTATAATG
**
6587701 AAATGCCATGTAGTCA
1 AAATGCCATCCAGTCA
6587717 AAATGCCATCCAGTCA
1 AAATGCCATCCAGTCA
6587733 AAA
1 AAA
6587736 CAAAACAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (16 bp):
AAATGCCATCCAGTCA
Found at i:6588988 original size:109 final size:109
Alignment explanation
Indices: 6588667--6588988 Score: 518
Period size: 109 Copynumber: 3.0 Consensus size: 109
6588657 GATTTAAGAG
* * *
6588667 GATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACTCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTCGA
* * *
6588732 ATTTCCAAACGCAAAACATTACCTTATTTTGAAAGTTTTAAAAA
66 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTTAAAAA
* *
6588776 GATATTTGGCTATTTGGTCGAACAAGAAAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTTGA
1 GATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTCGA
* * * *
6588841 ATTTTCAAACGCAAAACATTGCCTCACTTTGAACTTTTTAAAAT
66 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTTAAAAA
6588885 GATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTCGA
1 GATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTCGA
* *
6588950 ATCTCCAAACGCAAAACATTGCCTTACTTTGAATTTTTT
66 ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTT
6588989 TTAAAAGGAT
Statistics
Matches: 195, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 195 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (109 bp):
GATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTCGA
ATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTTAAAAA
Found at i:6589242 original size:14 final size:14
Alignment explanation
Indices: 6589225--6589255 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6589215 AAGTAAAAGT
*
6589225 AAAAATAAAACTAA
1 AAAAATAAAAATAA
6589239 AAAAATAAAAATAA
1 AAAAATAAAAATAA
6589253 AAA
1 AAA
6589256 TAAAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:6589242 original size:20 final size:20
Alignment explanation
Indices: 6589206--6589261 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
6589196 TAATAATGAG
6589206 AATAAAAA-AAAGTAAAAGTAAA
1 AATAAAAATAAA--AAAA-TAAA
*
6589228 AATAAAACTAAAAAAATAAA
1 AATAAAAATAAAAAAATAAA
6589248 AATAAAAATAAAAA
1 AATAAAAATAAAAA
6589262 TCTATGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.55
21 4 0.13
22 7 0.23
23 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (20 bp):
AATAAAAATAAAAAAATAAA
Found at i:6589248 original size:6 final size:6
Alignment explanation
Indices: 6589212--6589262 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
6589202 TGAGAATAAA
* *
6589212 AAAAAGT AAAAGT AAAAAT AAAACTAA AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAA-T AAAAAT AAAAAT AAAA--AT AAAAAT AAAAAT AAAAAT AAAAAT
6589263 CTATGTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 29 0.76
7 4 0.11
8 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Done.