Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013338.1 Kokia drynarioides strain JFW-HI SEQ_128360, 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: 152924
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 260 characters in sequence are not A, C, G, or T
Found at i:4955 original size:28 final size:27
Alignment explanation
Indices: 4924--4984 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
4914 TAATTTTCAG
* *
4924 TTAATGATTGTTTCCTTTAATCCTCCTT
1 TTAATAATTGTTTCCTTCAATCCT-CTT
*
4952 TTAATAATTGTTTCCTTCGATCCTCTT
1 TTAATAATTGTTTCCTTCAATCCTCTT
4979 TTAATA
1 TTAATA
4985 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (27 bp):
TTAATAATTGTTTCCTTCAATCCTCTT
Found at i:10662 original size:28 final size:27
Alignment explanation
Indices: 10631--10691 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
10621 TAATTTTCAG
* *
10631 TTAATGATTGTTTCCTTTAATCCTCCTT
1 TTAATAATTGTTTCCTTCAATCCT-CTT
*
10659 TTAATAATTGTTTCCTTCGATCCTCTT
1 TTAATAATTGTTTCCTTCAATCCTCTT
10686 TTAATA
1 TTAATA
10692 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (27 bp):
TTAATAATTGTTTCCTTCAATCCTCTT
Found at i:11681 original size:201 final size:201
Alignment explanation
Indices: 11336--11879 Score: 939
Period size: 201 Copynumber: 2.7 Consensus size: 201
11326 NNNNNNNNAG
11336 CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
* *
11401 AGAAGTGAACCAAATTCTTCTTCCTGATGATATACAGAGAAGCGAGTTGAAACAAACGACGCGAT
66 AGAAGTGAACCAAATTCATCTTCCTGATGATATACAGAGAAGCGAGTTGAAACAAACGACGCGGT
*
11466 CATCTTCCTGATGAGACACCGAGAAGAAGACTC-AAACGAGGCTCAAAGTGAGCGAAATCTTCAA
131 CATCTTCCTGATGAGACACCGAGAAGAAGAC-CAAAACAAGGCTCAAAGTGAGCGAAATCTTCAA
11530 AACCCAA
195 AACCCAA
11537 CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
* *
11602 AGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGCGAGTTAAAACAAACGACGCGGT
66 AGAAGTGAACCAAATTCATCTTCCTGATGATATACAGAGAAGCGAGTTGAAACAAACGACGCGGT
*
11667 CATCTTCCTGATGAGACATCGAGAAGAAGACCAAAACAAGGCTCAAAGTGAGCGAAATCTTCAAA
131 CATCTTCCTGATGAGACACCGAGAAGAAGACCAAAACAAGGCTCAAAGTGAGCGAAATCTTCAAA
* *
11732 ACTCAG
196 ACCCAA
11738 CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
* * * *
11803 AGAAATGAACCAAATTCATCTTCTTGATGAGATACAGAGAAGCG-GATTGAAACAAGCGACGCGG
66 AGAAGTGAACCAAATTCATCTTCCTGATGATATACAGAGAAGCGAG-TTGAAACAAACGACGCGG
*
11867 TCATTTTCCTGAT
130 TCATCTTCCTGAT
11880 ACCGAGAAGA
Statistics
Matches: 327, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
200 2 0.01
201 325 0.99
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (201 bp):
CTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTG
AGAAGTGAACCAAATTCATCTTCCTGATGATATACAGAGAAGCGAGTTGAAACAAACGACGCGGT
CATCTTCCTGATGAGACACCGAGAAGAAGACCAAAACAAGGCTCAAAGTGAGCGAAATCTTCAAA
ACCCAA
Found at i:12248 original size:11 final size:11
Alignment explanation
Indices: 12236--12296 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
12226 TGTTTAAAAT
*
12236 TTTAAATTTAT
1 TTTAAATTTAA
12247 TTTAAATTTAAA
1 TTTAAATTT-AA
**
12259 TTTATTTTTAA
1 TTTAAATTTAA
12270 TTTAAATTTAA
1 TTTAAATTTAA
*
12281 TTTAAGTTTAAA
1 TTTAAATTT-AA
12293 TTTA
1 TTTA
12297 TTCTCAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 28 0.67
12 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:12256 original size:6 final size:6
Alignment explanation
Indices: 12236--12296 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
12226 TGTTTAAAAT
* * *
12236 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12281 TTTAAG TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
12297 TTCTCAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:12258 original size:17 final size:17
Alignment explanation
Indices: 12203--12310 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
12193 TCGAACTCCC
*
12203 TTTAAATTTATTTT--T
1 TTTAAATTTATTTTAAA
* *
12218 TTTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
12235 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
*
12253 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
* *
12270 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
12287 TTTAAATTTATTCTCAAA
1 TTTAAATTTATT-TTAAA
12305 TTTAAA
1 TTTAAA
12311 ATTGCTAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.16
17 41 0.53
18 24 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:13513 original size:64 final size:65
Alignment explanation
Indices: 13412--13536 Score: 207
Period size: 64 Copynumber: 1.9 Consensus size: 65
13402 ACGCGCTGCA
*
13412 GCGGACCGAGGCGCATGGTGGCAACGCGCAACGGACGG-GACCAGCCCGACCGACAGGAGCGGCC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
* * *
13476 GCGGACCGAGGTGCGTGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACCGGAGC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGC
13537 ATGGCCGACC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
64 35 0.62
65 21 0.38
ACGTcount: A:0.22, C:0.34, G:0.40, T:0.04
Consensus pattern (65 bp):
GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
Found at i:14220 original size:59 final size:59
Alignment explanation
Indices: 14125--14796 Score: 900
Period size: 59 Copynumber: 11.4 Consensus size: 59
14115 TCCCTAAACT
* * *
14125 TTCTAAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
14184 TTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
14242 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
14301 TTCTAAAAATTACCATTTTATCGCCTAACTTCCAAAAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
** * * * *
14360 TTCTAAAAATTATTATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * ** *
14419 TTCAAAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACC
1 TTCTAAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * * * *
14479 TTCTAAAAATTACCATTTTACCCTCGAACTTTCAAGAACCCCA-TTTTGACTCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* ** *
14537 TTCTAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
14596 TTTTAAAAATTACCATTTTACCCCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
14655 TTCTTAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
14714 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
14773 TTC-CAAAACTACCATTTTGCCCCC
1 TTCTAAAAATTACCATTTTACCCCC
14797 GCGCATCCGA
Statistics
Matches: 533, Mismatches: 77, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
58 121 0.23
59 362 0.68
60 50 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:14674 original size:295 final size:294
Alignment explanation
Indices: 14129--14797 Score: 1007
Period size: 295 Copynumber: 2.3 Consensus size: 294
14119 TAAACTTTCT
* * *
14129 AAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACCTTCTAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
* *
14194 TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
66 TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
* * *
14259 TTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTATCG
131 TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
* * *
14324 CCTAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTATTATTTTACCCCTAAAC
196 CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
*
14389 TTCCAAAAATCTCATTTTTAACCTCGAACCTTCA
261 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * *
14423 AAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACCTTCTAAAAA
1 AAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAA
* * * * * *
14488 TTACCATTTTACCCTCGAACTTTCAAGAACCCCATTTTGACTCTGAACCTTCTAAAAATTACTAT
65 TTACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCAT
** *
14553 TTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTTAAAAATTACCATTTTACC
130 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACC
* *
14618 CCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACCTTCTTAAAATTACTATTTTACCCCCAAA
195 CCCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAA
* *
14683 CTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT
260 CTTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * * * * *
14718 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACCTTC-CAAAAC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
*
14782 TACCATTTTGCCCCCG
66 TACCATTTTACCCCCG
14798 CGCATCCGAA
Statistics
Matches: 336, Mismatches: 38, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
293 18 0.05
294 52 0.15
295 266 0.79
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (294 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
Found at i:16560 original size:16 final size:18
Alignment explanation
Indices: 16530--16563 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16520 AAAAATAGTA
16530 ATAAAAAATATAATTTAG
1 ATAAAAAATATAATTTAG
16548 ATAAAAAA-A-AATTTAG
1 ATAAAAAATATAATTTAG
16564 GAAAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAAATATAATTTAG
Found at i:16875 original size:17 final size:18
Alignment explanation
Indices: 16853--16888 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16843 AAATATTTTC
*
16853 TTAAATT-TTATTTTTAT
1 TTAAATTATAATTTTTAT
16870 TTAAATTATAATTTTTAT
1 TTAAATTATAATTTTTAT
16888 T
1 T
16889 ATTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAAATTATAATTTTTAT
Found at i:21048 original size:11 final size:11
Alignment explanation
Indices: 21036--21096 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
21026 TGTTTAAAAT
*
21036 TTTAAATTTAT
1 TTTAAATTTAA
21047 TTTAAATTTAAA
1 TTTAAATTT-AA
**
21059 TTTATTTTTAA
1 TTTAAATTTAA
21070 TTTAAATTTAA
1 TTTAAATTTAA
*
21081 TTTAAGTTTAAA
1 TTTAAATTT-AA
21093 TTTA
1 TTTA
21097 TTCTCAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 28 0.67
12 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:21056 original size:6 final size:6
Alignment explanation
Indices: 21036--21096 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
21026 TGTTTAAAAT
* * *
21036 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
21081 TTTAAG TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
21097 TTCTCAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:21058 original size:17 final size:17
Alignment explanation
Indices: 21003--21110 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
20993 TCGAACTCCC
*
21003 TTTAAATTTATTTT--T
1 TTTAAATTTATTTTAAA
* *
21018 TTTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
21035 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
*
21053 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
* *
21070 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
21087 TTTAAATTTATTCTCAAA
1 TTTAAATTTATT-TTAAA
21105 TTTAAA
1 TTTAAA
21111 ATTGCTAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.16
17 41 0.53
18 24 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:22313 original size:64 final size:65
Alignment explanation
Indices: 22212--22336 Score: 207
Period size: 64 Copynumber: 1.9 Consensus size: 65
22202 ACGCGCTGCA
*
22212 GCGGACCGAGGCGCATGGTGGCAACGCGCAACGGACGG-GACCAGCCCGACCGACAGGAGCGGCC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
* * *
22276 GCGGACCGAGGTGCGTGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACCGGAGC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGC
22337 ATGGCCGACC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
64 35 0.62
65 21 0.38
ACGTcount: A:0.22, C:0.34, G:0.40, T:0.04
Consensus pattern (65 bp):
GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
Found at i:23020 original size:59 final size:59
Alignment explanation
Indices: 22925--23596 Score: 900
Period size: 59 Copynumber: 11.4 Consensus size: 59
22915 TCCCTAAACT
* * *
22925 TTCTAAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
22984 TTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
23042 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
23101 TTCTAAAAATTACCATTTTATCGCCTAACTTCCAAAAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
** * * * *
23160 TTCTAAAAATTATTATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * ** *
23219 TTCAAAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACC
1 TTCTAAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * * * *
23279 TTCTAAAAATTACCATTTTACCCTCGAACTTTCAAGAACCCCA-TTTTGACTCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* ** *
23337 TTCTAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
23396 TTTTAAAAATTACCATTTTACCCCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
23455 TTCTTAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
23514 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
23573 TTC-CAAAACTACCATTTTGCCCCC
1 TTCTAAAAATTACCATTTTACCCCC
23597 GCGCATCCGA
Statistics
Matches: 533, Mismatches: 77, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
58 121 0.23
59 362 0.68
60 50 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:23474 original size:295 final size:294
Alignment explanation
Indices: 22929--23597 Score: 1007
Period size: 295 Copynumber: 2.3 Consensus size: 294
22919 TAAACTTTCT
* * *
22929 AAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACCTTCTAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
* *
22994 TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
66 TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
* * *
23059 TTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTATCG
131 TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
* * *
23124 CCTAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTATTATTTTACCCCTAAAC
196 CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
*
23189 TTCCAAAAATCTCATTTTTAACCTCGAACCTTCA
261 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * *
23223 AAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACCTTCTAAAAA
1 AAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAA
* * * * * *
23288 TTACCATTTTACCCTCGAACTTTCAAGAACCCCATTTTGACTCTGAACCTTCTAAAAATTACTAT
65 TTACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCAT
** *
23353 TTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTTAAAAATTACCATTTTACC
130 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACC
* *
23418 CCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACCTTCTTAAAATTACTATTTTACCCCCAAA
195 CCCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAA
* *
23483 CTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT
260 CTTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * * * * *
23518 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACCTTC-CAAAAC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
*
23582 TACCATTTTGCCCCCG
66 TACCATTTTACCCCCG
23598 CGCATCCGAA
Statistics
Matches: 336, Mismatches: 38, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
293 18 0.05
294 52 0.15
295 266 0.79
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (294 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
Found at i:25360 original size:16 final size:18
Alignment explanation
Indices: 25330--25363 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25320 AAAAATAGTA
25330 ATAAAAAATATAATTTAG
1 ATAAAAAATATAATTTAG
25348 ATAAAAAA-A-AATTTAG
1 ATAAAAAATATAATTTAG
25364 GAAAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAAATATAATTTAG
Found at i:25675 original size:17 final size:18
Alignment explanation
Indices: 25653--25688 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25643 AAATATTTTC
*
25653 TTAAATT-TTATTTTTAT
1 TTAAATTATAATTTTTAT
25670 TTAAATTATAATTTTTAT
1 TTAAATTATAATTTTTAT
25688 T
1 T
25689 ATTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAAATTATAATTTTTAT
Found at i:29857 original size:11 final size:11
Alignment explanation
Indices: 29845--29905 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
29835 TGTTTAAAAT
*
29845 TTTAAATTTAT
1 TTTAAATTTAA
29856 TTTAAATTTAAA
1 TTTAAATTT-AA
**
29868 TTTATTTTTAA
1 TTTAAATTTAA
29879 TTTAAATTTAA
1 TTTAAATTTAA
*
29890 TTTAAGTTTAAA
1 TTTAAATTT-AA
29902 TTTA
1 TTTA
29906 TTCTCAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 28 0.67
12 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:29865 original size:6 final size:6
Alignment explanation
Indices: 29845--29905 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
29835 TGTTTAAAAT
* * *
29845 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
29890 TTTAAG TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
29906 TTCTCAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:29867 original size:17 final size:17
Alignment explanation
Indices: 29812--29919 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
29802 TCGAACTCCC
*
29812 TTTAAATTTATTTT--T
1 TTTAAATTTATTTTAAA
* *
29827 TTTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
29844 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
*
29862 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
* *
29879 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
29896 TTTAAATTTATTCTCAAA
1 TTTAAATTTATT-TTAAA
29914 TTTAAA
1 TTTAAA
29920 ATTGCTAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.16
17 41 0.53
18 24 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:31122 original size:64 final size:65
Alignment explanation
Indices: 31021--31145 Score: 207
Period size: 64 Copynumber: 1.9 Consensus size: 65
31011 ACGCGCTGCA
*
31021 GCGGACCGAGGCGCATGGTGGCAACGCGCAACGGACGG-GACCAGCCCGACCGACAGGAGCGGCC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
* * *
31085 GCGGACCGAGGTGCGTGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACCGGAGC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGC
31146 ATGGCCGACC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
64 35 0.62
65 21 0.38
ACGTcount: A:0.22, C:0.34, G:0.40, T:0.04
Consensus pattern (65 bp):
GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
Found at i:31829 original size:59 final size:59
Alignment explanation
Indices: 31734--32405 Score: 900
Period size: 59 Copynumber: 11.4 Consensus size: 59
31724 TCCCTAAACT
* * *
31734 TTCTAAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
31793 TTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
31851 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
31910 TTCTAAAAATTACCATTTTATCGCCTAACTTCCAAAAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
** * * * *
31969 TTCTAAAAATTATTATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * ** *
32028 TTCAAAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACC
1 TTCTAAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * * * *
32088 TTCTAAAAATTACCATTTTACCCTCGAACTTTCAAGAACCCCA-TTTTGACTCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* ** *
32146 TTCTAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
32205 TTTTAAAAATTACCATTTTACCCCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
32264 TTCTTAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
32323 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
32382 TTC-CAAAACTACCATTTTGCCCCC
1 TTCTAAAAATTACCATTTTACCCCC
32406 GCGCATCCGA
Statistics
Matches: 533, Mismatches: 77, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
58 121 0.23
59 362 0.68
60 50 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:32283 original size:295 final size:294
Alignment explanation
Indices: 31738--32406 Score: 1007
Period size: 295 Copynumber: 2.3 Consensus size: 294
31728 TAAACTTTCT
* * *
31738 AAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACCTTCTAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
* *
31803 TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
66 TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
* * *
31868 TTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTATCG
131 TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
* * *
31933 CCTAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTATTATTTTACCCCTAAAC
196 CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
*
31998 TTCCAAAAATCTCATTTTTAACCTCGAACCTTCA
261 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * *
32032 AAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACCTTCTAAAAA
1 AAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAA
* * * * * *
32097 TTACCATTTTACCCTCGAACTTTCAAGAACCCCATTTTGACTCTGAACCTTCTAAAAATTACTAT
65 TTACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCAT
** *
32162 TTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTTAAAAATTACCATTTTACC
130 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACC
* *
32227 CCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACCTTCTTAAAATTACTATTTTACCCCCAAA
195 CCCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAA
* *
32292 CTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT
260 CTTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * * * * *
32327 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACCTTC-CAAAAC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
*
32391 TACCATTTTGCCCCCG
66 TACCATTTTACCCCCG
32407 CGCATCCGAA
Statistics
Matches: 336, Mismatches: 38, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
293 18 0.05
294 52 0.15
295 266 0.79
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (294 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
Found at i:34169 original size:16 final size:18
Alignment explanation
Indices: 34139--34172 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34129 AAAAATAGTA
34139 ATAAAAAATATAATTTAG
1 ATAAAAAATATAATTTAG
34157 ATAAAAAA-A-AATTTAG
1 ATAAAAAATATAATTTAG
34173 GAAAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAAATATAATTTAG
Found at i:34484 original size:17 final size:18
Alignment explanation
Indices: 34462--34497 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34452 AAATATTTTC
*
34462 TTAAATT-TTATTTTTAT
1 TTAAATTATAATTTTTAT
34479 TTAAATTATAATTTTTAT
1 TTAAATTATAATTTTTAT
34497 T
1 T
34498 ATTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAAATTATAATTTTTAT
Found at i:38666 original size:11 final size:11
Alignment explanation
Indices: 38654--38714 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
38644 TGTTTAAAAT
*
38654 TTTAAATTTAT
1 TTTAAATTTAA
38665 TTTAAATTTAAA
1 TTTAAATTT-AA
**
38677 TTTATTTTTAA
1 TTTAAATTTAA
38688 TTTAAATTTAA
1 TTTAAATTTAA
*
38699 TTTAAGTTTAAA
1 TTTAAATTT-AA
38711 TTTA
1 TTTA
38715 TTCTCAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 28 0.67
12 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:38674 original size:6 final size:6
Alignment explanation
Indices: 38654--38714 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
38644 TGTTTAAAAT
* * *
38654 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
38699 TTTAAG TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
38715 TTCTCAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:38676 original size:17 final size:17
Alignment explanation
Indices: 38621--38728 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
38611 TCGAACTCCC
*
38621 TTTAAATTTATTTT--T
1 TTTAAATTTATTTTAAA
* *
38636 TTTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
38653 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
*
38671 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
* *
38688 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
38705 TTTAAATTTATTCTCAAA
1 TTTAAATTTATT-TTAAA
38723 TTTAAA
1 TTTAAA
38729 ATTGCTAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.16
17 41 0.53
18 24 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:39931 original size:64 final size:65
Alignment explanation
Indices: 39830--39954 Score: 207
Period size: 64 Copynumber: 1.9 Consensus size: 65
39820 ACGCGCTGCA
*
39830 GCGGACCGAGGCGCATGGTGGCAACGCGCAACGGACGG-GACCAGCCCGACCGACAGGAGCGGCC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
* * *
39894 GCGGACCGAGGTGCGTGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACCGGAGC
1 GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGC
39955 ATGGCCGACC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
64 35 0.62
65 21 0.38
ACGTcount: A:0.22, C:0.34, G:0.40, T:0.04
Consensus pattern (65 bp):
GCGGACCGAGGCGCATGGTGGCAACACGCAACGGACGGCGACCAGCCCGACCGACAGGAGCGGCC
Found at i:40638 original size:59 final size:59
Alignment explanation
Indices: 40543--41214 Score: 900
Period size: 59 Copynumber: 11.4 Consensus size: 59
40533 TCCCTAAACT
* * *
40543 TTCTAAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
40602 TTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
40660 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
40719 TTCTAAAAATTACCATTTTATCGCCTAACTTCCAAAAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
** * * * *
40778 TTCTAAAAATTATTATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * ** *
40837 TTCAAAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACC
1 TTCTAAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * * * *
40897 TTCTAAAAATTACCATTTTACCCTCGAACTTTCAAGAACCCCA-TTTTGACTCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* ** *
40955 TTCTAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
41014 TTTTAAAAATTACCATTTTACCCCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
41073 TTCTTAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
41132 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
41191 TTC-CAAAACTACCATTTTGCCCCC
1 TTCTAAAAATTACCATTTTACCCCC
41215 GCGCATCCGA
Statistics
Matches: 533, Mismatches: 77, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
58 121 0.23
59 362 0.68
60 50 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:41092 original size:295 final size:294
Alignment explanation
Indices: 40547--41215 Score: 1007
Period size: 295 Copynumber: 2.3 Consensus size: 294
40537 TAAACTTTCT
* * *
40547 AAAAATTATCATTTTACCCCCAAACTTTCAAAAATCACATTTTTGACCCCGAACCTTCTAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
* *
40612 TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
66 TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
* * *
40677 TTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTATCG
131 TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
* * *
40742 CCTAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTATTATTTTACCCCTAAAC
196 CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
*
40807 TTCCAAAAATCTCATTTTTAACCTCGAACCTTCA
261 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * *
40841 AAAATATTACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAAACCTTCTAAAAA
1 AAAA-ATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAA
* * * * * *
40906 TTACCATTTTACCCTCGAACTTTCAAGAACCCCATTTTGACTCTGAACCTTCTAAAAATTACTAT
65 TTACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCAT
** *
40971 TTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTTAAAAATTACCATTTTACC
130 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACC
* *
41036 CCCAAACTTCCAAGAACCCCATTTTTGACCCCGAACCTTCTTAAAATTACTATTTTACCCCCAAA
195 CCCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAA
* *
41101 CTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT
260 CTTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
* * * * * *
41136 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACTCCGAACCTTC-CAAAAC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
*
41200 TACCATTTTGCCCCCG
66 TACCATTTTACCCCCG
41216 CGCATCCGAA
Statistics
Matches: 336, Mismatches: 38, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
293 18 0.05
294 52 0.15
295 266 0.79
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (294 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGACCCCGAACCTTCTAAAAAT
TACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTGACCCCGAACCTTCTAAAAATTACCATT
TTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCC
CCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTCTAAAAATTACTATTTTACCCCCAAAC
TTCCAAAAATCCCATTTTTAACCTCGAACCTTCA
Found at i:42978 original size:16 final size:18
Alignment explanation
Indices: 42948--42981 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42938 AAAAATAGTA
42948 ATAAAAAATATAATTTAG
1 ATAAAAAATATAATTTAG
42966 ATAAAAAA-A-AATTTAG
1 ATAAAAAATATAATTTAG
42982 GAAAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAAATATAATTTAG
Found at i:43293 original size:17 final size:18
Alignment explanation
Indices: 43271--43306 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43261 AAATATTTTC
*
43271 TTAAATT-TTATTTTTAT
1 TTAAATTATAATTTTTAT
43288 TTAAATTATAATTTTTAT
1 TTAAATTATAATTTTTAT
43306 T
1 T
43307 ATTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAAATTATAATTTTTAT
Found at i:48432 original size:29 final size:29
Alignment explanation
Indices: 48390--48447 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
48380 ACTTTGTCTT
48390 TTCCAAAACAAAACTTAAATGAAACTATC
1 TTCCAAAACAAAACTTAAATGAAACTATC
48419 TTCCAAAACAAAACTTAAATGAAACTATC
1 TTCCAAAACAAAACTTAAATGAAACTATC
48448 CCTAGTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.21, G:0.03, T:0.24
Consensus pattern (29 bp):
TTCCAAAACAAAACTTAAATGAAACTATC
Found at i:50396 original size:15 final size:15
Alignment explanation
Indices: 50373--50405 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
50363 ATTTGAAGTT
50373 ATTGATTGGATTTGA
1 ATTGATTGGATTTGA
*
50388 ATTGGTTGGATTTGA
1 ATTGATTGGATTTGA
50403 ATT
1 ATT
50406 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGATTGGATTTGA
Found at i:50547 original size:43 final size:43
Alignment explanation
Indices: 50500--50752 Score: 238
Period size: 43 Copynumber: 5.9 Consensus size: 43
50490 AAAAGCACCA
* * *
50500 CTAAAAACCATGTTTTATAGCGGCATTTGTGGGAAAAATGCTG
1 CTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAATGCTG
* * * * * *
50543 CTAAAAACCAT-TCTCCATAACGGCGTTTATGGGTAAAACGCTG
1 CTAAAGACCATGT-TCTATAGCGGCGTTTGTGGGAAAAATGCTG
* ** * * * *
50586 CTAAAGATCATGTTCTATAGTAGCGTTTGTGTGTAAAGTGCCG
1 CTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAATGCTG
* * *
50629 TTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGTTG
1 CTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAATGCTG
* * ** *
50672 CTAAAGACCATGTTCTATAGCGGCATTTGTGAGAAAAGCGCCG
1 CTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAATGCTG
* * * *
50715 CTAAAGCCCATGTTCTATAACGGCGTTTATGAGAAAAA
1 CTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAA
50753 CGTCGTTAAA
Statistics
Matches: 171, Mismatches: 37, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
42 1 0.01
43 169 0.99
44 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (43 bp):
CTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAATGCTG
Found at i:50615 original size:86 final size:84
Alignment explanation
Indices: 50508--50775 Score: 268
Period size: 86 Copynumber: 3.1 Consensus size: 84
50498 CACTAAAAAC
* * * * * * *
50508 CATGTTTTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCAT-TCTCCATAACGGCGTTTA
1 CATGTTCTATAGCAGCATTTGTGAGAAAAGTGCCGCTAAAGACCATGT-TCTATAACGGCGTTTA
50572 TGGGTAAAACGCTGCTAAAGAT
65 TGGG-AAAACG-TGCTAAAGAT
* * * * * * *
50594 CATGTTCTATAGTAGCGTTTGTGTGTAAAGTGCCGTTAAAGACCATGTTCTATAGCGGCGTTTGT
1 CATGTTCTATAGCAGCATTTGTGAGAAAAGTGCCGCTAAAGACCATGTTCTATAACGGCGTTTAT
* *
50659 GGGAAAAGTGTTGCTAAAGAC
66 GGGAAAA-CG-TGCTAAAGAT
* * *
50680 CATGTTCTATAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGCCCATGTTCTATAACGGCGTTTAT
1 CATGTTCTATAGCAGCATTTGTGAGAAAAGTGCCGCTAAAGACCATGTTCTATAACGGCGTTTAT
* *
50745 GAGAAAAACGTCGTTAAAGAT
66 G-GGAAAACGT-GCTAAAGAT
*
50766 CATATTCTAT
1 CATGTTCTAT
50776 CACATAAACG
Statistics
Matches: 147, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
85 5 0.03
86 136 0.93
87 6 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (84 bp):
CATGTTCTATAGCAGCATTTGTGAGAAAAGTGCCGCTAAAGACCATGTTCTATAACGGCGTTTAT
GGGAAAACGTGCTAAAGAT
Found at i:50719 original size:129 final size:129
Alignment explanation
Indices: 50501--50733 Score: 308
Period size: 129 Copynumber: 1.8 Consensus size: 129
50491 AAAGCACCAC
*
50501 TAAAAACCATGTTTTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCATTCTCCATAACGG
1 TAAAAACCATGTTCTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCATTCTCCATAACGG
* * * *
50566 CGTTTATGGGTAAAACGCTGCTAAAGATCATGTTCTATAGTAGCGTTTGTGTGTAAAGTGCCGT
66 CATTTATGAGTAAAACGCCGCTAAAGACCATGTTCTATAGTAGCGTTTGTGTGTAAAGTGCCGT
* * * * * * *
50630 TAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGTTGCTAAAGACCATGT-TCTATAGCG
1 TAAAAACCATGTTCTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCAT-TCTCCATAACG
* *
50694 GCATTTGTGAG-AAAAGCGCCGCTAAAGCCCATGTTCTATA
65 GCATTTATGAGTAAAA-CGCCGCTAAAGACCATGTTCTATA
50734 ACGGCGTTTA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
128 4 0.05
129 83 0.94
130 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (129 bp):
TAAAAACCATGTTCTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCATTCTCCATAACGG
CATTTATGAGTAAAACGCCGCTAAAGACCATGTTCTATAGTAGCGTTTGTGTGTAAAGTGCCGT
Found at i:50760 original size:129 final size:129
Alignment explanation
Indices: 50501--50775 Score: 293
Period size: 129 Copynumber: 2.1 Consensus size: 129
50491 AAAGCACCAC
* *
50501 TAAAAACCATGTTTTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCATTCTCCATAACGG
1 TAAAGACCATGTTCTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCATTCTCCATAACGG
* * * * ** * * * **
50566 CGTTTATGGGTAAAACGCTGCTAAAGATCATGTTCTATAGTAGCGTTTGTGTGTAAAGTGCCGT
66 CATTTATGAGTAAAACGCCGCTAAAGACCATGTTCTATAACAGCGTTTATGAGAAAAACGCCGT
* * * * * *
50630 TAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGTTGCTAAAGACCATGT-TCTATAGCG
1 TAAAGACCATGTTCTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCAT-TCTCCATAACG
* * * *
50694 GCATTTGTGAG-AAAAGCGCCGCTAAAGCCCATGTTCTATAACGGCGTTTATGAGAAAAACGTCG
65 GCATTTATGAGTAAAA-CGCCGCTAAAGACCATGTTCTATAACAGCGTTTATGAGAAAAACGCCG
50758 T
129 T
* *
50759 TAAAGATCATATTCTAT
1 TAAAGACCATGTTCTAT
50776 CACATAAACG
Statistics
Matches: 119, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
128 4 0.03
129 114 0.96
130 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (129 bp):
TAAAGACCATGTTCTATAGCGGCATTTGTGGGAAAAATGCTGCTAAAAACCATTCTCCATAACGG
CATTTATGAGTAAAACGCCGCTAAAGACCATGTTCTATAACAGCGTTTATGAGAAAAACGCCGT
Found at i:50763 original size:43 final size:43
Alignment explanation
Indices: 50482--50775 Score: 211
Period size: 43 Copynumber: 6.8 Consensus size: 43
50472 GTTAGTGGCA
* ** * * * *
50482 TTTGTGGGAAAAGCACCACTAAAAACCATGTTTTATAGCGGCA
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCG
* * * *
50525 TTTGTGGGAAAAATGC-T-GCTAAAAACCAT-TCTCCATAACGGCG
1 TTTGTGAG-AAAA-GCGTCGCTAAAGACCATGT-TCTATAGCGGCG
* * * **
50568 TTTATGGGTAAAA-CG-CTGCTAAAGATCATGTTCTATAGTAGCG
1 TTTGTGAG-AAAAGCGTC-GCTAAAGACCATGTTCTATAGCGGCG
* * * * *
50611 TTTGTGTGTAAAGTGCCGTTAAAGACCATGTTCTATAGCGGCG
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCG
* * * *
50654 TTTGTGGGAAAAGTGTTGCTAAAGACCATGTTCTATAGCGGCA
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCG
* * *
50697 TTTGTGAGAAAAGCGCCGCTAAAGCCCATGTTCTATAACGGCG
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCG
* * * * *
50740 TTTATGAGAAAAACGTCGTTAAAGATCATATTCTAT
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTAT
50776 CACATAAACG
Statistics
Matches: 200, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.00
42 4 0.02
43 187 0.94
44 6 0.03
45 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (43 bp):
TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCG
Found at i:51648 original size:22 final size:23
Alignment explanation
Indices: 51623--51682 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
51613 GATAAATCTT
51623 ACTAAAA-ATATTTAAAAATAAA
1 ACTAAAAGATATTTAAAAATAAA
* * *
51645 ACTAAGAATATAATTAATAATAAA
1 ACTAA-AAGATATTTAAAAATAAA
51669 A-TATAAAGATATTT
1 ACTA-AAAGATATTT
51683 TAATTAGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 15 0.48
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (23 bp):
ACTAAAAGATATTTAAAAATAAA
Found at i:56652 original size:1 final size:1
Alignment explanation
Indices: 56646--56675 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
56636 TAAAATTAAC
56646 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
56676 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56690 original size:1 final size:1
Alignment explanation
Indices: 56686--56723 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
56676 NNNNNNNNNN
56686 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
56724 CCAAACAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:62719 original size:3 final size:3
Alignment explanation
Indices: 62711--62736 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
62701 AAGAACACCA
62711 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
62737 TTGTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:71478 original size:2 final size:2
Alignment explanation
Indices: 71471--71497 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71461 CACTCGTGAT
71471 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
71498 TTGTTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:71587 original size:27 final size:27
Alignment explanation
Indices: 71557--71620 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 27
71547 ACCCATGGCT
71557 CTCCACCCTTCGGTTGAACCATGCATC
1 CTCCACCCTTCGGTTGAACCATGCATC
71584 CTCCACCACCCTTCGGTTGAACCATGCATC
1 CT---CCACCCTTCGGTTGAACCATGCATC
71614 CTCCACC
1 CTCCACC
71621 ACCCTTTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 7 0.21
30 27 0.79
ACGTcount: A:0.19, C:0.45, G:0.12, T:0.23
Consensus pattern (27 bp):
CTCCACCCTTCGGTTGAACCATGCATC
Found at i:81471 original size:2 final size:2
Alignment explanation
Indices: 81464--81495 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
81454 GGAGTGCATT
81464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81496 AAGCTGCATT
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):
TA
Found at i:81999 original size:8 final size:8
Alignment explanation
Indices: 81962--82009 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
81952 TTGTTTATAC
81962 ATATGTTAT
1 ATATG-TAT
*
81971 ACATGTAT
1 ATATGTAT
*
81979 ATATATAT
1 ATATGTAT
81987 ATATGTAT
1 ATATGTAT
81995 ATATGTAT
1 ATATGTAT
*
82003 GTATGTA
1 ATATGTA
82010 ATTATTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 30 0.88
9 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (8 bp):
ATATGTAT
Found at i:82003 original size:12 final size:12
Alignment explanation
Indices: 81963--82006 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
81953 TGTTTATACA
*
81963 TATGTTATACATG
1 TATG-TATATATG
* *
81976 TATATATATATA
1 TATGTATATATG
81988 TATGTATATATG
1 TATGTATATATG
82000 TATGTAT
1 TATGTAT
82007 GTAATTATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 23 0.88
13 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (12 bp):
TATGTATATATG
Found at i:95811 original size:20 final size:20
Alignment explanation
Indices: 95786--95828 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
95776 ATTATATTCA
*
95786 TTATTTTAAATATAAAATAT
1 TTATTTTAAACATAAAATAT
* *
95806 TTATTTTACACATAAAATTT
1 TTATTTTAAACATAAAATAT
95826 TTA
1 TTA
95829 ATTAATTAAA
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:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTTAAACATAAAATAT
Found at i:108210 original size:14 final size:15
Alignment explanation
Indices: 108193--108229 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
108183 ATATTCAAAC
108193 AATAATAACAA-AAT
1 AATAATAACAATAAT
*
108207 AATAATAATAATAAT
1 AATAATAACAATAAT
108222 -ATAATAAC
1 AATAATAAC
108230 GAAACGGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAACAATAAT
Found at i:108215 original size:17 final size:17
Alignment explanation
Indices: 108193--108228 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
108183 ATATTCAAAC
108193 AATAATAACAAAATAAT
1 AATAATAACAAAATAAT
* *
108210 AATAATAATAATATAAT
1 AATAATAACAAAATAAT
108227 AA
1 AA
108229 CGAAACGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATAACAAAATAAT
Found at i:122219 original size:23 final size:23
Alignment explanation
Indices: 122165--122221 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
122155 AATTTTTAAC
122165 AATATAA-ATAAATGAAATTTTT
1 AATATAATATAAATGAAATTTTT
* * * *
122187 AATAAAAATATCAATTAACTTTTT
1 AAT-ATAATATAAATGAAATTTTT
122211 AATATAATATA
1 AATATAATATA
122222 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 3 0.11
23 9 0.33
24 15 0.56
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATAATATAAATGAAATTTTT
Found at i:124047 original size:62 final size:60
Alignment explanation
Indices: 123909--124052 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
123899 TTAATCTGAT
** *
123909 TAAAAAAA-TCAAA-TTTTTGAGTGTTGGCCATGCAATGGCCGACACCCCATTTTCTCGG
1 TAAAAAAATTCAAATTTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCATATTCTCGG
* * * * *
123967 GAAAAAAATTCAATTTTTTTTTGTGTTGGTCTTGCAATGGCCGACACCCCCTATTCTCGG
1 TAAAAAAATTCAAATTTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCATATTCTCGG
124027 ATAAAAAAATTTCAAATTTTTTTTGT
1 -TAAAAAAA-TTCAAATTTTTTTTGT
124053 AATGGCCGAC
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
58 7 0.10
59 4 0.06
60 39 0.54
61 7 0.10
62 15 0.21
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (60 bp):
TAAAAAAATTCAAATTTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCATATTCTCGG
Found at i:131296 original size:29 final size:31
Alignment explanation
Indices: 131243--131310 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
131233 TCATATACAG
* * **
131243 TTTTAATTTGATATGCAATTTTATATGT-AAA
1 TTTTGATTTGATA-GCAATTATATACATAAAA
131274 TTTTGATTTGATA-CAATTATATACATAAAA
1 TTTTGATTTGATAGCAATTATATACATAAAA
131304 TTTTGAT
1 TTTTGAT
131311 GGTTGTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 10 0.31
30 10 0.31
31 12 0.38
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (31 bp):
TTTTGATTTGATAGCAATTATATACATAAAA
Found at i:134328 original size:43 final size:43
Alignment explanation
Indices: 134280--134372 Score: 186
Period size: 43 Copynumber: 2.2 Consensus size: 43
134270 TTTTTGTCAA
134280 ATAACAATTCATTCAAGATAAAAGGAAGACTCAATCACCATAC
1 ATAACAATTCATTCAAGATAAAAGGAAGACTCAATCACCATAC
134323 ATAACAATTCATTCAAGATAAAAGGAAGACTCAATCACCATAC
1 ATAACAATTCATTCAAGATAAAAGGAAGACTCAATCACCATAC
134366 ATAACAA
1 ATAACAA
134373 CCAAGAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (43 bp):
ATAACAATTCATTCAAGATAAAAGGAAGACTCAATCACCATAC
Found at i:135890 original size:42 final size:40
Alignment explanation
Indices: 135809--135890 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
135799 CACGGGCTGT
* * *
135809 CACATGGGCGTGTATCAAGGTGTGTGTATACTGTTTTAGG
1 CACATGGACATGTATCAAGGTGTGTGTATACTGTCTTAGG
* *
135849 CACATGGACATGTATCAGGGTGTGTGTGCATATTGTCTTAGG
1 CACATGGACATGTATCAAGGTGTGTGT--ATACTGTCTTAGG
135891 GAACATGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 24 0.69
42 11 0.31
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (40 bp):
CACATGGACATGTATCAAGGTGTGTGTATACTGTCTTAGG
Found at i:136833 original size:23 final size:23
Alignment explanation
Indices: 136652--136847 Score: 193
Period size: 23 Copynumber: 8.4 Consensus size: 23
136642 CGAAATACTT
136652 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
136678 AACAGTAAGCACACACAGTG-TA
1 AACAGTAAGCACACAAAGTGCGA
* * *
136700 ATCCAGTAGGCACACACAGTGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
* * * * *
136723 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
136745 AATCAGTAGGCACACAAGGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
136769 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
136792 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
136815 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
136838 AACAGTAAGC
1 AACAGTAAGC
136848 GTGCTAGTGT
Statistics
Matches: 149, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
22 20 0.13
23 108 0.72
24 3 0.02
26 14 0.09
27 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:138878 original size:40 final size:40
Alignment explanation
Indices: 138793--138895 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
138783 TGAAATGATT
** * * *
138793 CAGTGACACTGTAAACACTATAATATTATAACTTAACCGA
1 CAGTGACACTGTAAACACTGCAAGATTACAACTAAACCGA
* * * *
138833 AAGTGACACTGTAAACACTGCAAGGTTACCACTAAACTGA
1 CAGTGACACTGTAAACACTGCAAGATTACAACTAAACCGA
138873 CAGTGACACTGTAAACACTGCAA
1 CAGTGACACTGTAAACACTGCAA
138896 CTTGTCATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (40 bp):
CAGTGACACTGTAAACACTGCAAGATTACAACTAAACCGA
Found at i:138999 original size:29 final size:29
Alignment explanation
Indices: 138957--139016 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
138947 ACGGAAGGGA
*
138957 GTATCATGTCTGCATCTATAACTGTATTT
1 GTATCATGTCTGCATCCATAACTGTATTT
* *
138986 GTATCGTGTCTGCATCCGTAACTGTATTT
1 GTATCATGTCTGCATCCATAACTGTATTT
139015 GT
1 GT
139017 GACATGACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (29 bp):
GTATCATGTCTGCATCCATAACTGTATTT
Found at i:139028 original size:17 final size:17
Alignment explanation
Indices: 139006--139062 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
138996 TGCATCCGTA
139006 ACTGTATTTGTGACATG
1 ACTGTATTTGTGACATG
139023 ACTGTATTTGT-A-AT-
1 ACTGTATTTGTGACATG
139037 --TGTATCTT-TGACATG
1 ACTGTAT-TTGTGACATG
139052 ACTGTATTTGT
1 ACTGTATTTGT
139063 AACTGTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
12 6 0.18
13 3 0.09
14 2 0.06
15 2 0.06
16 3 0.09
17 17 0.52
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (17 bp):
ACTGTATTTGTGACATG
Found at i:139035 original size:29 final size:29
Alignment explanation
Indices: 139003--139093 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
138993 GTCTGCATCC
139003 GTAACTGTATTTGTGACATGACTGTATTT
1 GTAACTGTATTTGTGACATGACTGTATTT
*
139032 GTAATTGTATCTT-TGACATGACTGTATTT
1 GTAACTGTAT-TTGTGACATGACTGTATTT
* * * *
139061 GTAACTGTATCTGTGGCATGAGTGTATCT
1 GTAACTGTATTTGTGACATGACTGTATTT
139090 GTAA
1 GTAA
139094 TCGTATCTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 51 0.94
30 2 0.04
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (29 bp):
GTAACTGTATTTGTGACATGACTGTATTT
Found at i:139099 original size:29 final size:29
Alignment explanation
Indices: 139009--139103 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
138999 ATCCGTAACT
* *
139009 GTATTTGTGACATGACTGTATTTGTAATT
1 GTATCTGTGACATGACTGTATTTGTAATC
*
139038 GTATCTTTGACATGACTGTATTTGTAA-C
1 GTATCTGTGACATGACTGTATTTGTAATC
* * *
139066 TGTATCTGTGGCATGAGTGTATCTGTAATC
1 -GTATCTGTGACATGACTGTATTTGTAATC
139096 GTATCTGT
1 GTATCTGT
139104 ATTATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 56 0.98
30 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (29 bp):
GTATCTGTGACATGACTGTATTTGTAATC
Found at i:150116 original size:13 final size:13
Alignment explanation
Indices: 150098--150123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150088 ATAATATATT
150098 TATTAATTAAAAA
1 TATTAATTAAAAA
150111 TATTAATTAAAAA
1 TATTAATTAAAAA
150124 ATCACAATTA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:150125 original size:14 final size:14
Alignment explanation
Indices: 150098--150182 Score: 52
Period size: 14 Copynumber: 5.9 Consensus size: 14
150088 ATAATATATT
150098 TATTAATT-AAAAA
1 TATTAATTAAAAAA
150111 TATTAATTAAAAAA
1 TATTAATTAAAAAA
* ***
150125 TCA-CAATTATCTAA
1 T-ATTAATTAAAAAA
150139 TCATCTAA-TAAAAAA
1 T-AT-TAATTAAAAAA
150154 -ATTAATATATTAAAAA
1 TATTAAT-TA--AAAAA
150170 TATTAATTAAAAA
1 TATTAATTAAAAA
150183 TATAAAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.05
13 10 0.18
14 22 0.40
15 5 0.09
16 9 0.16
17 6 0.11
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
TATTAATTAAAAAA
Found at i:152586 original size:4 final size:4
Alignment explanation
Indices: 152577--152639 Score: 65
Period size: 4 Copynumber: 15.5 Consensus size: 4
152567 AAATAAACGG
* * *
152577 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
152627 G-AA GAAG GAAA GA
1 GAAA GAAA GAAA GA
152640 TATGTAATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 39 0.78
5 8 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:152599 original size:17 final size:16
Alignment explanation
Indices: 152577--152639 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
152567 AAATAAACGG
152577 GAAAGAAAGAAAGGAAA
1 GAAAG-AAGAAAGGAAA
152594 GAAAGAAAGAAAGG-AA
1 GAAAG-AAGAAAGGAAA
*
152610 G-AAG--GAGAGGAAA
1 GAAAGAAGAAAGGAAA
152623 GAAAGAAG-AAGGAAA
1 GAAAGAAGAAAGGAAA
152638 GA
1 GA
152640 TATGTAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 5 0.12
13 3 0.08
14 3 0.08
15 11 0.28
16 4 0.10
17 14 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAAGAAGAAAGGAAA
Found at i:152605 original size:25 final size:26
Alignment explanation
Indices: 152577--152638 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
152567 AAATAAACGG
152577 GAAAGAAAGAAAGGA-AAGAAAGAAA
1 GAAAGAAAGAAAGGAGAAGAAAGAAA
* *
152602 GAAAGGAAG-AAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGGAGAAGAAAGAAA
*
152627 G-AAGAAGGAAAG
1 GAAAGAAAGAAAG
152639 ATATGTAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (26 bp):
GAAAGAAAGAAAGGAGAAGAAAGAAA
Found at i:152612 original size:29 final size:27
Alignment explanation
Indices: 152579--152636 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
152569 ATAAACGGGA
152579 AAGAAAGAAAGGAAAGAAAGAAAGAAAGG
1 AAGAAAGAAAGGAAAGAAAG-AAG-AAGG
* *
152608 AAGAAGGAGAGGAAAGAAAGAAGAAGG
1 AAGAAAGAAAGGAAAGAAAGAAGAAGG
152635 AA
1 AA
152637 AGATATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
28 3 0.11
29 18 0.67
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAGGAAAGAAAGAAGAAGG
Done.