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 43 of 202
Found at i:12840830 original size:14 final size:15
Alignment explanation
Indices: 12840807--12840839 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12840797 ATCGACGCTT
*
12840807 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
12840821 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
12840836 TTCC
1 TTCC
12840840 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Found at i:12844790 original size:4 final size:4
Alignment explanation
Indices: 12844781--12844809 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
12844771 TAGGCACCTA
12844781 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
12844810 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:12845120 original size:23 final size:20
Alignment explanation
Indices: 12845072--12845120 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 20
12845062 TTTTTCAAAA
*
12845072 AATATAATAATAAATTTAAT
1 AATATAATAATAAATTAAAT
12845092 ATATATATATATATAAATATAAAT
1 A-ATATA-ATA-ATAAAT-TAAAT
12845116 AATAT
1 AATAT
12845121 TGTTGACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 3 0.12
23 10 0.42
24 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAATAATAAATTAAAT
Found at i:12845206 original size:31 final size:29
Alignment explanation
Indices: 12845039--12845200 Score: 106
Period size: 29 Copynumber: 5.6 Consensus size: 29
12845029 AAATTCAAAG
*
12845039 AAATATATAAAAATACATAAATATTTTTCAA
1 AAATATATAAAAATAAATAAATA-TTTT-AA
* * * *
12845070 AAA-ATATAATAATAAATTTAATA-TATAT
1 AAATATATAAAAATAAA-TAAATATTTTAA
* *
12845098 ATATATATAAATATAAAT-AATATTGTTGACA
1 AAATATATAAAAATAAATAAATATT-TT-A-A
** *
12845129 AAA-A-ATAGTAATATAT-AA-ATTTTAA
1 AAATATATAAAAATAAATAAATATTTTAA
12845154 AAATATATAAAAATAAATAAATATTTTCAA
1 AAATATATAAAAATAAATAAATATTTT-AA
*
12845184 AAA-ATATAATAATAAAT
1 AAATATATAAAAATAAAT
12845201 TTAAATTTTA
Statistics
Matches: 101, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
25 4 0.04
26 2 0.02
27 15 0.15
28 10 0.10
29 42 0.42
30 18 0.18
31 10 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATATATAAAAATAAATAAATATTTTAA
Found at i:12848803 original size:67 final size:67
Alignment explanation
Indices: 12848695--12848831 Score: 265
Period size: 67 Copynumber: 2.0 Consensus size: 67
12848685 ACTTTCGGCA
12848695 TCTTCATCACAATAGCTACTCAACTCCCACACCGAAGTCGCAACGATAACTAGAAATCATCCACG
1 TCTTCATCACAATAGCTACTCAACTCCCACACCGAAGTCGCAACGATAACTAGAAATCATCCACG
12848760 CT
66 CT
*
12848762 TCTTCATCACAATAGCTACTCAACTCCCACACTGAAGTCGCAACGATAACTAGAAATCATCCACG
1 TCTTCATCACAATAGCTACTCAACTCCCACACCGAAGTCGCAACGATAACTAGAAATCATCCACG
12848827 CT
66 CT
12848829 TCT
1 TCT
12848832 AAAACTTTGG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.23
Consensus pattern (67 bp):
TCTTCATCACAATAGCTACTCAACTCCCACACCGAAGTCGCAACGATAACTAGAAATCATCCACG
CT
Found at i:12853014 original size:5 final size:6
Alignment explanation
Indices: 12852997--12853021 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12852987 ATATTAAATG
12852997 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
12853022 TTGAGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:12857184 original size:26 final size:26
Alignment explanation
Indices: 12857155--12857207 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
12857145 CTTTCTAAAT
*
12857155 TCCTATTTACACTACAATAATTTTTA
1 TCCTATTTACACCACAATAATTTTTA
*
12857181 TCCTATTTACACCATAATAATTTTTA
1 TCCTATTTACACCACAATAATTTTTA
12857207 T
1 T
12857208 AATCTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (26 bp):
TCCTATTTACACCACAATAATTTTTA
Found at i:12859608 original size:25 final size:25
Alignment explanation
Indices: 12859574--12859624 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12859564 AATATGCCCC
12859574 AGAAATATGACTTCTTTTAGCCAAA
1 AGAAATATGACTTCTTTTAGCCAAA
12859599 AGAAATATGACTTCTTTTAGCCAAA
1 AGAAATATGACTTCTTTTAGCCAAA
12859624 A
1 A
12859625 TTGTTTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (25 bp):
AGAAATATGACTTCTTTTAGCCAAA
Found at i:12864491 original size:67 final size:67
Alignment explanation
Indices: 12864376--12864503 Score: 202
Period size: 67 Copynumber: 1.9 Consensus size: 67
12864366 AGTAAGTAGC
* ** *
12864376 TTCACACGGCCTAGCACATGGGCGTGTGGCTTGGCCGTGTGTCACAAGTCAGTATGCTCACCATT
1 TTCACACGGCCTAGAACATGGGCGTGTGGCTTGGCCGTGTAACACAAGTCAGTAAGCTCACCATT
12864441 TT
66 TT
* *
12864443 TTCACACGGCCTAGAATATGGGCGTGTGGCTTGGCCGTGTAACCCAAGTCAGTAAGCTCAC
1 TTCACACGGCCTAGAACATGGGCGTGTGGCTTGGCCGTGTAACACAAGTCAGTAAGCTCAC
12864504 TAGTTTGGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (67 bp):
TTCACACGGCCTAGAACATGGGCGTGTGGCTTGGCCGTGTAACACAAGTCAGTAAGCTCACCATT
TT
Found at i:12866714 original size:272 final size:272
Alignment explanation
Indices: 12866228--12866771 Score: 1043
Period size: 272 Copynumber: 2.0 Consensus size: 272
12866218 AACCTTGTGC
*
12866228 AGTGCTCTGATGTCTTAGGGTGGCAATGGAATAGTTTGCCTAAACCTGAATTGTCAAATCACTCA
1 AGTGCTCTGATGTCTTAGGGTGGCAATGAAATAGTTTGCCTAAACCTGAATTGTCAAATCACTCA
*
12866293 ATCGAATTCTTGCATTTCCACCATGGTGTACACTATCAATGGTGTAACACTCTTAACCCATCTCT
66 ATCGAATTCTTGCATTTCCACCATGGTGTACACTATCAATGGTGTAACACTCCTAACCCATCTCT
12866358 GTCGCCAGATTGGGGTCACAAGGTATTACGATAACAATTTAAACATTTAACATTACCTACAAATA
131 GTCGCCAGATTGGGGTCACAAGGTATTACGATAACAATTTAAACATTTAACATTACCTACAAATA
*
12866423 AATATTCAAAAACTCATTTTTAAACATCAATTACATACCATATTATTGCCCATTCTAAACCTAAC
196 AATATTCAAAAACTCATTTTTAAACATCAATTACATACCATATGATTGCCCATTCTAAACCTAAC
*
12866488 CAATATGCCATT
261 CAATATGACATT
12866500 AGTGCTCTGATGTCTTAGGGTGGCAATGAAATAGTTTGCCTAAACCTGAATTGTCAAATCACTCA
1 AGTGCTCTGATGTCTTAGGGTGGCAATGAAATAGTTTGCCTAAACCTGAATTGTCAAATCACTCA
*
12866565 ATTGAATTCTTGCATTTCCACCATGGTGTACACTATCAATGGTGTAACACTCCTAACCCATCTCT
66 ATCGAATTCTTGCATTTCCACCATGGTGTACACTATCAATGGTGTAACACTCCTAACCCATCTCT
12866630 GTCGCCAGATTGGGGTCACAAGGTATTACGATAACAATTTAAACATTTAACATTACCTACAAATA
131 GTCGCCAGATTGGGGTCACAAGGTATTACGATAACAATTTAAACATTTAACATTACCTACAAATA
12866695 AATATTCAAAAACTCATTTTTAAACATCAATTACATACCATATGATTGCCCATTCTAAACCTAAC
196 AATATTCAAAAACTCATTTTTAAACATCAATTACATACCATATGATTGCCCATTCTAAACCTAAC
12866760 CAATATGACATT
261 CAATATGACATT
12866772 CAAAGGCACC
Statistics
Matches: 267, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
272 267 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (272 bp):
AGTGCTCTGATGTCTTAGGGTGGCAATGAAATAGTTTGCCTAAACCTGAATTGTCAAATCACTCA
ATCGAATTCTTGCATTTCCACCATGGTGTACACTATCAATGGTGTAACACTCCTAACCCATCTCT
GTCGCCAGATTGGGGTCACAAGGTATTACGATAACAATTTAAACATTTAACATTACCTACAAATA
AATATTCAAAAACTCATTTTTAAACATCAATTACATACCATATGATTGCCCATTCTAAACCTAAC
CAATATGACATT
Found at i:12870907 original size:30 final size:29
Alignment explanation
Indices: 12870871--12870950 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
12870861 CTATCAAAAA
* *
12870871 ATTTTTCTTCTCTCAATTTCTCCTAACAT
1 ATTTTTCTTCTCTCATTTTCTCCCAACAT
* *
12870900 CATTTTTCTTCTCCCATTTTCCCCCAACAT
1 -ATTTTTCTTCTCTCATTTTCTCCCAACAT
*
12870930 ATTTTTCTCCTCTCATTTTCT
1 ATTTTTCTTCTCTCATTTTCT
12870951 TTCCAACACT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.16, C:0.33, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTTTCTTCTCTCATTTTCTCCCAACAT
Found at i:12872552 original size:17 final size:17
Alignment explanation
Indices: 12872511--12872552 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
12872501 CATTATTTAT
12872511 GAAA-ATTATAAGTTGA
1 GAAAGATTATAAGTTGA
*
12872527 -TAAGAATTATAAGTTGA
1 GAAAG-ATTATAAGTTGA
12872544 GAAAGATTA
1 GAAAGATTA
12872553 ATTTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (17 bp):
GAAAGATTATAAGTTGA
Found at i:12877702 original size:19 final size:19
Alignment explanation
Indices: 12877678--12877715 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12877668 AAAGTTAATA
12877678 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
12877697 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
12877716 GTGACAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:12879335 original size:23 final size:24
Alignment explanation
Indices: 12879289--12879336 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
12879279 GTAAACTCAA
*
12879289 GACATATTTAAAATGCTCAGGTTAT
1 GACATATTTAAAA-GCTCAAGTTAT
12879314 GACATATTTAAAA-CTCAAGTTAT
1 GACATATTTAAAAGCTCAAGTTAT
12879337 TGATGTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
25 13 0.59
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (24 bp):
GACATATTTAAAAGCTCAAGTTAT
Found at i:12879892 original size:12 final size:13
Alignment explanation
Indices: 12879875--12879907 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
12879865 AATAAAAAAA
12879875 TTATAAATTTT-T
1 TTATAAATTTTGT
12879887 TTATAAATTTTGT
1 TTATAAATTTTGT
12879900 TTATAAAT
1 TTATAAAT
12879908 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
TTATAAATTTTGT
Found at i:12885706 original size:8 final size:8
Alignment explanation
Indices: 12885695--12885723 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12885685 AGAAATGGTA
12885695 GAATGGAG
1 GAATGGAG
12885703 GAATGGAG
1 GAATGGAG
12885711 GAATGGAG
1 GAATGGAG
12885719 GAATG
1 GAATG
12885724 AAATGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.48, T:0.14
Consensus pattern (8 bp):
GAATGGAG
Found at i:12893355 original size:18 final size:18
Alignment explanation
Indices: 12893332--12893382 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
12893322 AATCTATATA
12893332 TATGT-ATATTTATTTTTT
1 TATGTAATATTT-TTTTTT
12893350 TATGTACATATTTTTTTTT
1 TATGTA-ATATTTTTTTTT
* **
12893369 CAACTAATATTTTT
1 TATGTAATATTTTT
12893383 CTCATGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 13 0.46
19 9 0.32
20 6 0.21
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (18 bp):
TATGTAATATTTTTTTTT
Found at i:12893360 original size:28 final size:27
Alignment explanation
Indices: 12893303--12893360 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
12893293 TATATTTTTC
*
12893303 ATATGTAATTATTTTTTTAAATCTATAT
1 ATATGTAATTATTTTTTT-AATCTACAT
*
12893331 ATATGTATATTTATTTTTTT-ATGTACAT
1 ATATGTA-A-TTATTTTTTTAATCTACAT
12893359 AT
1 AT
12893361 TTTTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 15 0.58
29 1 0.04
30 10 0.38
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (27 bp):
ATATGTAATTATTTTTTTAATCTACAT
Found at i:12893420 original size:26 final size:29
Alignment explanation
Indices: 12893389--12893452 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 29
12893379 TTTTCTCATG
12893389 TTTATATATATACATA-TATTT-ATT-TT
1 TTTATATATATACATATTATTTAATTATT
* *
12893415 TTTATA-ATGTAGATATTATTTAATTATT
1 TTTATATATATACATATTATTTAATTATT
12893443 TTTA-ATATAT
1 TTTATATATAT
12893453 TTTACGTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.23
26 11 0.35
27 4 0.13
28 9 0.29
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTATATATATACATATTATTTAATTATT
Found at i:12896242 original size:18 final size:18
Alignment explanation
Indices: 12896219--12896256 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12896209 TGATGTCTAA
12896219 AAGATAAAACTTTGAAAC
1 AAGATAAAACTTTGAAAC
12896237 AAGATAAAACTTTGAAAC
1 AAGATAAAACTTTGAAAC
12896255 AA
1 AA
12896257 TTTTAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (18 bp):
AAGATAAAACTTTGAAAC
Found at i:12896502 original size:21 final size:22
Alignment explanation
Indices: 12896478--12896519 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12896468 TGCTTTTGGT
12896478 ATCAATA-CTTT-TTGAAAAATA
1 ATCAATACCTTTCTT-AAAAATA
12896499 ATCAATACCTTTCTTAAAAAT
1 ATCAATACCTTTCTTAAAAAT
12896520 GATACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
ATCAATACCTTTCTTAAAAATA
Found at i:12897716 original size:7 final size:7
Alignment explanation
Indices: 12897704--12897745 Score: 75
Period size: 7 Copynumber: 5.9 Consensus size: 7
12897694 GACAATACAA
12897704 AGGGTTT
1 AGGGTTT
12897711 AGGGTTT
1 AGGGTTT
12897718 AGGGTTTT
1 AGGG-TTT
12897726 AGGGTTT
1 AGGGTTT
12897733 AGGGTTT
1 AGGGTTT
12897740 AGGGTT
1 AGGGTT
12897746 AAAAAGCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:12897728 original size:15 final size:14
Alignment explanation
Indices: 12897704--12897745 Score: 75
Period size: 15 Copynumber: 2.9 Consensus size: 14
12897694 GACAATACAA
12897704 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
12897718 AGGGTTTTAGGGTTT
1 AGGG-TTTAGGGTTT
12897733 AGGGTTTAGGGTT
1 AGGGTTTAGGGTT
12897746 AAAAAGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (14 bp):
AGGGTTTAGGGTTT
Found at i:12897732 original size:22 final size:22
Alignment explanation
Indices: 12897704--12897745 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12897694 GACAATACAA
12897704 AGGGTTTAGGGTTTAGGGTTTT
1 AGGGTTTAGGGTTTAGGGTTTT
12897726 AGGGTTTAGGGTTTAGGGTT
1 AGGGTTTAGGGTTTAGGGTT
12897746 AAAAAGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (22 bp):
AGGGTTTAGGGTTTAGGGTTTT
Found at i:12899835 original size:45 final size:45
Alignment explanation
Indices: 12899784--12899922 Score: 188
Period size: 45 Copynumber: 3.1 Consensus size: 45
12899774 AACAGATACA
* * *
12899784 CGGTGGAATCAGCACATAGCAACCACCTTCATAATCAATGGTACC
1 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACC
** *
12899829 CGGTGGAATCAGCACACAACAGTCACCTTTATAATCAATGATACC
1 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACC
* * * *
12899874 AGGAGGAATCAACACACAACAACCACCTTTATAATCAATGGTACT
1 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACC
12899919 CGGT
1 CGGT
12899923 ACACGTAGTA
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.21
Consensus pattern (45 bp):
CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACC
Found at i:12915189 original size:25 final size:25
Alignment explanation
Indices: 12915161--12915264 Score: 136
Period size: 25 Copynumber: 3.9 Consensus size: 25
12915151 TCATCACTGC
*
12915161 TTCTTTGATCCTCTGCTGGTGCTGG
1 TTCTTTGTTCCTCTGCTGGTGCTGG
*
12915186 TTCTCTGTTCTTCTGCTGGTGCTGGTGCTGG
1 TTCTTTGTTC--CT-C---TGCTGGTGCTGG
12915217 TTCTTTGTTCCTCTGCTGGTGCTGG
1 TTCTTTGTTCCTCTGCTGGTGCTGG
12915242 TTCTTTGTTCCTCTGCTGGTGCT
1 TTCTTTGTTCCTCTGCTGGTGCT
12915265 TTGTTCCTCT
Statistics
Matches: 70, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
25 43 0.61
27 2 0.03
28 2 0.03
29 2 0.03
31 21 0.30
ACGTcount: A:0.01, C:0.24, G:0.28, T:0.47
Consensus pattern (25 bp):
TTCTTTGTTCCTCTGCTGGTGCTGG
Found at i:12915209 original size:31 final size:31
Alignment explanation
Indices: 12915174--12915242 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
12915164 TTTGATCCTC
*
12915174 TGCTGGTGCTGGTTCTCTGTTCTTCTGCTGG
1 TGCTGGTGCTGGTTCTCTGTTCCTCTGCTGG
*
12915205 TGCTGGTGCTGGTTCTTTGTTCCTCTGCTGG
1 TGCTGGTGCTGGTTCTCTGTTCCTCTGCTGG
12915236 TGCTGGT
1 TGCTGGT
12915243 TCTTTGTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.00, C:0.22, G:0.33, T:0.45
Consensus pattern (31 bp):
TGCTGGTGCTGGTTCTCTGTTCCTCTGCTGG
Found at i:12915235 original size:19 final size:19
Alignment explanation
Indices: 12915236--12915274 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12915226 CCTCTGCTGG
*
12915236 TGCTGGTTCTTTGTTCCTC
1 TGCTGGTGCTTTGTTCCTC
12915255 TGCTGGTGCTTTGTTCCTC
1 TGCTGGTGCTTTGTTCCTC
12915274 T
1 T
12915275 TCTCCACCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.23, T:0.51
Consensus pattern (19 bp):
TGCTGGTGCTTTGTTCCTC
Found at i:12916980 original size:43 final size:43
Alignment explanation
Indices: 12916883--12917064 Score: 291
Period size: 43 Copynumber: 4.3 Consensus size: 43
12916873 GAAATCTGAT
*
12916883 TTAGGTAAAAGAAGTGGG-GAAAA-AAAAAGAAGAAGATAGCAA
1 TTAGGTAAAAGAAG-GGGAAAAAAGAAAAAGAAGAAGATAGCAA
12916925 TTAGGTAAAAGAAGGGGGAAAAAAAGAAAAA-AAGAAGATAGCAA
1 TTAGGTAAAAGAA-GGGG-AAAAAAGAAAAAGAAGAAGATAGCAA
12916969 TTAGGT-AAAGAAGGGGAAAAAAGAAAAAGAAGAAGATAGCAA
1 TTAGGTAAAAGAAGGGGAAAAAAGAAAAAGAAGAAGATAGCAA
12917011 TTAGGTAAAAGAAGGGGAAAAAAGAAAAAGAAGAAGATAGCAA
1 TTAGGTAAAAGAAGGGGAAAAAAGAAAAAGAAGAAGATAGCAA
*
12917054 TCAGGTAAAAG
1 TTAGGTAAAAG
12917065 GAGGAGGCGT
Statistics
Matches: 132, Mismatches: 2, Indels: 11
0.91 0.01 0.08
Matches are distributed among these distances:
41 12 0.09
42 39 0.30
43 53 0.40
44 23 0.17
45 5 0.04
ACGTcount: A:0.59, C:0.03, G:0.28, T:0.10
Consensus pattern (43 bp):
TTAGGTAAAAGAAGGGGAAAAAAGAAAAAGAAGAAGATAGCAA
Found at i:12918406 original size:18 final size:18
Alignment explanation
Indices: 12918383--12918448 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
12918373 AAAATATGAG
*
12918383 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
12918401 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
*
12918419 ACATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
12918437 AAATGATGTTCA
1 AAATGATGTTCA
12918449 AACTGATGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:12919025 original size:72 final size:72
Alignment explanation
Indices: 12918871--12919043 Score: 233
Period size: 72 Copynumber: 2.4 Consensus size: 72
12918861 AACAACAATG
* * * * *
12918871 CTAAACTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTA
1 CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTTA
12918936 TTTATGT
66 TTTATGT
* * *
12918943 GT-AATCTAGTTTTATTAAAAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTT
1 CTAAAT-TAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTT
*
12919007 ATTT-TTT
65 ATTTATGT
12919014 ACTAAATTAGTTTTATCAATAGTTGTTTAT
1 -CTAAATTAGTTTTATCAATAGTTGTTTAT
12919044 ATGTGATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
71 4 0.05
72 79 0.92
73 3 0.03
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (72 bp):
CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTTA
TTTATGT
Found at i:12921108 original size:13 final size:13
Alignment explanation
Indices: 12921087--12921150 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
12921077 ACACTCAAAA
*
12921087 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
* *
12921100 TTCTCAAAATCAC
1 TTTTCAAAAGCAC
* *
12921113 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
12921126 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
12921139 TTTTCAAAAGCA
1 TTTTCAAAAGCA
12921151 ATGAAGAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:12921798 original size:21 final size:21
Alignment explanation
Indices: 12921773--12921812 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12921763 TTTTACTTTA
*
12921773 TTTTTCTTC-TTCTTCTTCCT
1 TTTTTTTTCTTTCTTCTTCCT
*
12921793 TTTTTTTTCTTTCTTTTTCC
1 TTTTTTTTCTTTCTTCTTCC
12921813 ACATTTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTTCTTTCTTCTTCCT
Found at i:12923166 original size:12 final size:12
Alignment explanation
Indices: 12923149--12923174 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12923139 ATGGAAATAA
12923149 TTATATGAAGTG
1 TTATATGAAGTG
12923161 TTATATGAAGTG
1 TTATATGAAGTG
12923173 TT
1 TT
12923175 TACATGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (12 bp):
TTATATGAAGTG
Found at i:12928163 original size:23 final size:22
Alignment explanation
Indices: 12928122--12928164 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12928112 CCTAAACTCC
* *
12928122 CAAACCTTTTTACTTTTCCCCT
1 CAAAACTTTTTACTCTTCCCCT
12928144 CAAAACTTTTTACTCCTTCCC
1 CAAAACTTTTTACT-CTTCCC
12928165 ACTTTCCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (22 bp):
CAAAACTTTTTACTCTTCCCCT
Found at i:12928336 original size:30 final size:31
Alignment explanation
Indices: 12928300--12928359 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
12928290 AAACCTTTTA
12928300 TTTTCCCCTAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCTAAAATTTTTACTCCCTTCCCAC
*
12928330 TTTTCCCCTAAAATTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAATTTTTACTCCCTTCCCA
12928360 TCCCACCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCTAAAATTTTTACTCCCTTCCCAC
Found at i:12928511 original size:20 final size:19
Alignment explanation
Indices: 12928473--12928511 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12928463 TATTCCTCAA
* *
12928473 AACTTTTTATTTTCCCCCT
1 AACTTTTTATTCTCACCCT
12928492 AACTTTTTACTTCTCACCCT
1 AACTTTTTA-TTCTCACCCT
12928512 TTACTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (19 bp):
AACTTTTTATTCTCACCCT
Found at i:12929130 original size:5 final size:5
Alignment explanation
Indices: 12929120--12929145 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12929110 CTCGAAAATT
12929120 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
12929146 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12934638 original size:16 final size:16
Alignment explanation
Indices: 12934617--12934650 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12934607 TGGAGCCGAC
12934617 AAGTTAGAGGAACCAA
1 AAGTTAGAGGAACCAA
**
12934633 AAGTTAGATTAACCAA
1 AAGTTAGAGGAACCAA
12934649 AA
1 AA
12934651 AAAGAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AAGTTAGAGGAACCAA
Found at i:12944733 original size:2 final size:2
Alignment explanation
Indices: 12944726--12944756 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12944716 ATACTAAAGT
12944726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12944757 GCATGTATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12947327 original size:61 final size:59
Alignment explanation
Indices: 12947216--12947880 Score: 294
Period size: 61 Copynumber: 10.9 Consensus size: 59
12947206 ATCCAATGCT
* ** * **
12947216 CAAATAAATTCAGCAATATATATTCATATACGAACCAAATTCGGCAATGTATATCTATATA
1 CAAATAAATTCAGCAATGTATAACCATATACGAATC-AATTCGAAAATGTATATC-ATATA
* * *
12947277 CAAAAAAAATCAGCAATGTATAACCATATATGAATCAAGTTCGAAAATGTATAATCATATA
1 CAAATAAATTCAGCAATGTATAACCATATACGAATCAA-TTCGAAAATGTAT-ATCATATA
* *
12947338 CAAATTAAATTTAGCAATGTATAACCATATACGAATCAATTCGACAACT-TATATCCATATA
1 CAAA-TAAATTCAGCAATGTATAACCATATACGAATCAATTCGA-AAATGTATAT-CATATA
* * * * ** * * *
12947399 CAATTCAATTTCAACAATGTATAACCATGTAAAAATTAATTTC-AGCAATATATAATCATATA
1 CAAAT-AAATTCAGCAATGTATAACCATATACGAATCAA-TTCGA-AAATGTAT-ATCATATA
* * * * *
12947461 CAAATCAATTCGGCAACT-TATATCCATATAC-AATTCAATTTC-AACAATGTATAACCATGTA
1 CAAATAAATTCAGCAA-TGTATAACCATATACGAA-TCAA-TTCGAA-AATGTAT-ATCATATA
* * * * * * *
12947522 CAAATTAATTTCAGCAATATATAATCATATACAAATCAATTCGGCAACT-AATATCCATATA
1 CAAA-TAAATTCAGCAATGTATAACCATATACGAATCAATTC-GAAAATGTATAT-CATATA
* * * * * * * *
12947583 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTC-AGCAATATATAATCATATA
1 CAAAT-AAATTCAGCAATGTATAACCATATACGAATCAA-TTCGA-AAATGTAT-ATCATATA
* * * * * * * *
12947645 CAAATCAATTCGGCAACT-TATATCCATATACAAATTATTTC-AACAATGTATAACCATGTA
1 CAAATAAATTCAGCAA-TGTATAACCATATACGAATCAATTCGAA-AATGTAT-ATCATATA
* * * * * * * *
12947705 CAAATTAATTTCAGCAATGTACAATCATATACAAATCAATTCGGCAACT-TATACCCATATG
1 CAAA-TAAATTCAGCAATGTATAACCATATACGAATCAATTC-GAAAATGTATA-TCATATA
* * ** * * *
12947766 CAAATCAATTTC-GACAATGTATAACCATGTAAAAATTAATTTC-AGCAATGTACAATCATATA
1 CAAAT-AAATTCAG-CAATGTATAACCATATACGAATCAA-TTCGA-AAATGTA-TATCATATA
* * * * * *
12947828 CAAATCAATTCGGCAACT-TATACCCATATGCAAATCAATTTCGACAATGTATA
1 CAAATAAATTCAGCAA-TGTATAACCATATACGAATCAA-TTCGAAAATGTATA
12947881 ACTATGAACA
Statistics
Matches: 464, Mismatches: 101, Indels: 79
0.72 0.16 0.12
Matches are distributed among these distances:
60 35 0.08
61 305 0.66
62 115 0.25
63 9 0.02
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (59 bp):
CAAATAAATTCAGCAATGTATAACCATATACGAATCAATTCGAAAATGTATATCATATA
Found at i:12947328 original size:31 final size:31
Alignment explanation
Indices: 12947291--12947882 Score: 205
Period size: 31 Copynumber: 19.3 Consensus size: 31
12947281 AAAAATCAGC
*
12947291 AATGTATAACCATATATGAATCAAGTTCGA-A
1 AATGTATAACCATATACGAATCAA-TTCGACA
* * * *
12947322 AATGTATAATCATATACAAATTAAATT-TAGC-
1 AATGTATAACCATATACGAA-TCAATTCGA-CA
12947353 AATGTATAACCATATACGAATCAATTCGACA
1 AATGTATAACCATATACGAATCAATTCGACA
* * *
12947384 ACT-TATATCCATATAC-AATTCAATTTCAAC-
1 AATGTATAACCATATACGAA-TCAA-TTCGACA
* ** *
12947414 AATGTATAACCATGTAAAAATTAATTTC-AGC-
1 AATGTATAACCATATACGAATCAA-TTCGA-CA
* * * *
12947445 AATATATAATCATATACAAATCAATTCGGCA
1 AATGTATAACCATATACGAATCAATTCGACA
* * *
12947476 ACT-TATATCCATATAC-AATTCAATTTCAAC-
1 AATGTATAACCATATACGAA-TCAA-TTCGACA
* * *
12947506 AATGTATAACCATGTACAAATTAATTTC-AGC-
1 AATGTATAACCATATACGAATCAA-TTCGA-CA
* * * *
12947537 AATATATAATCATATACAAATCAATTCGGCA
1 AATGTATAACCATATACGAATCAATTCGACA
* * * *
12947568 ACT-AATATCCATATAC-AATTCAATTTCAAC-
1 AATGTATAACCATATACGAA-TCAA-TTCGACA
* * *
12947598 AATGTATAACCATGTACAAATTAATTTC-AGC-
1 AATGTATAACCATATACGAATCAA-TTCGA-CA
* * * *
12947629 AATATATAATCATATACAAATCAATTCGGCA
1 AATGTATAACCATATACGAATCAATTCGACA
* * * * * *
12947660 ACT-TATATCCATATACAAATTATTTCAAC-
1 AATGTATAACCATATACGAATCAATTCGACA
* * *
12947689 AATGTATAACCATGTACAAATTAATTTC-AGC-
1 AATGTATAACCATATACGAATCAA-TTCGA-CA
* * * *
12947720 AATGTACAATCATATACAAATCAATTCGGCA
1 AATGTATAACCATATACGAATCAATTCGACA
* * * *
12947751 ACT-TATACCCATATGCAAATCAATTTCGAC-
1 AATGTATAACCATATACGAATCAA-TTCGACA
* ** *
12947781 AATGTATAACCATGTAAAAATTAATTTC-AGC-
1 AATGTATAACCATATACGAATCAA-TTCGA-CA
* * * *
12947812 AATGTACAATCATATACAAATCAATTCGGCA
1 AATGTATAACCATATACGAATCAATTCGACA
* * * *
12947843 ACT-TATACCCATATGCAAATCAATTTCGAC-
1 AATGTATAACCATATACGAATCAA-TTCGACA
12947873 AATGTATAAC
1 AATGTATAAC
12947883 TATGAACAAT
Statistics
Matches: 428, Mismatches: 95, Indels: 76
0.71 0.16 0.13
Matches are distributed among these distances:
29 8 0.02
30 156 0.36
31 255 0.60
32 9 0.02
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (31 bp):
AATGTATAACCATATACGAATCAATTCGACA
Found at i:12947396 original size:92 final size:91
Alignment explanation
Indices: 12947295--12947912 Score: 841
Period size: 92 Copynumber: 6.7 Consensus size: 91
12947285 ATCAGCAATG
* * * * * *
12947295 TATAACCATATATGAATCAAGTTCGAA-AATGTATAATCATATACAAATTAAATTT-AGCAATGT
1 TATATCCATATA-AAATCAATTTC-AACAATGTATAACCATGTACAAATT-AATTTCAGCAATAT
* * *
12947358 ATAACCATATACGAATCAATTCGACAACT
63 ATAATCATATACAAATCAATTCGGCAACT
* *
12947387 TATATCCATATACAATTCAATTTCAACAATGTATAACCATGTAAAAATTAATTTCAGCAATATAT
1 TATATCCATATA-AAATCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
12947452 AATCATATACAAATCAATTCGGCAACT
65 AATCATATACAAATCAATTCGGCAACT
*
12947479 TATATCCATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
1 TATATCCATATA-AAATCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
12947544 AATCATATACAAATCAATTCGGCAACT
65 AATCATATACAAATCAATTCGGCAACT
* *
12947571 AATATCCATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
1 TATATCCATATA-AAATCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
12947636 AATCATATACAAATCAATTCGGCAACT
65 AATCATATACAAATCAATTCGGCAACT
* * *
12947663 TATATCCATATACAAAT-TATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATGTAC
1 TATATCCATATA-AAATCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
12947727 AATCATATACAAATCAATTCGGCAACT
65 AATCATATACAAATCAATTCGGCAACT
* * * * * *
12947754 TATACCCATATGCAAATCAATTTCGACAATGTATAACCATGTAAAAATTAATTTCAGCAATGTAC
1 TATATCCATAT-AAAATCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATAT
12947819 AATCATATACAAATCAATTCGGCAACT
65 AATCATATACAAATCAATTCGGCAACT
* * * * * *
12947846 TATACCCATATGCAAATCAATTTCGACAATGTATAACTATGAAC-AATTCGAA-TTCGGCAATAT
1 TATATCCATAT-AAAATCAATTTCAACAATGTATAACCATGTACAAATT--AATTTCAGCAATAT
12947909 ATAA
63 ATAA
12947913 AACAATCAAA
Statistics
Matches: 490, Mismatches: 30, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
91 96 0.20
92 392 0.80
93 2 0.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (91 bp):
TATATCCATATAAAATCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATATA
ATCATATACAAATCAATTCGGCAACT
Found at i:12947785 original size:275 final size:276
Alignment explanation
Indices: 12947300--12947912 Score: 896
Period size: 275 Copynumber: 2.2 Consensus size: 276
12947290 CAATGTATAA
** * * * *
12947300 CCATATATGAATCAAGTTCGAA-AATGTATAATCATATACAAATTAAATTT-AGCAATGTATAAC
1 CCATATACAAATCAATTTC-AACAATGTATAACCATGTACAAATTAAATTTCAGCAATATATAAC
*
12947363 CATATACGAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATG
65 CATATACAAATCAATTCGACAACTTATATCCATATACAATT-AATTTCAACAATGTATAACCATG
* *
12947428 TAAAAATTAATTTCAGCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACA
129 TAAAAATTAATTTCAGCAATATACAATCATATACAAATCAATTCGGCAACTTATACCCATATACA
* * *
12947493 ATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATATAATCATATACAAAT
194 AATCAATTTCAACAATGTATAACCATGTAAAAATTAATTTCAGCAATATACAATCATATACAAAT
*
12947558 CAATTCGGCAACTAATAT
259 CAATTCGGCAACTAATAC
* *
12947576 CCATATACAATTCAATTTCAACAATGTATAACCATGTACAAATT-AATTTCAGCAATATATAATC
1 CCATATACAAATCAATTTCAACAATGTATAACCATGTACAAATTAAATTTCAGCAATATATAACC
*
12947640 ATATACAAATCAATTCGGCAACTTATATCCATATACAAATT-ATTTCAACAATGTATAACCATGT
66 ATATACAAATCAATTCGACAACTTATATCCATATAC-AATTAATTTCAACAATGTATAACCATGT
* * *
12947704 ACAAATTAATTTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATACCCATATGCAA
130 AAAAATTAATTTCAGCAATATACAATCATATACAAATCAATTCGGCAACTTATACCCATATACAA
* *
12947769 ATCAATTTCGACAATGTATAACCATGTAAAAATTAATTTCAGCAATGTACAATCATATACAAATC
195 ATCAATTTCAACAATGTATAACCATGTAAAAATTAATTTCAGCAATATACAATCATATACAAATC
*
12947834 AATTCGGCAACTTATAC
260 AATTCGGCAACTAATAC
* * * * * *
12947851 CCATATGCAAATCAATTTCGACAATGTATAACTATGAAC-AATTCGAA-TTCGGCAATATATAA
1 CCATATACAAATCAATTTCAACAATGTATAACCATGTACAAATT-AAATTTCAGCAATATATAA
12947913 AACAATCAAA
Statistics
Matches: 304, Mismatches: 28, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
274 4 0.01
275 213 0.70
276 83 0.27
277 4 0.01
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (276 bp):
CCATATACAAATCAATTTCAACAATGTATAACCATGTACAAATTAAATTTCAGCAATATATAACC
ATATACAAATCAATTCGACAACTTATATCCATATACAATTAATTTCAACAATGTATAACCATGTA
AAAATTAATTTCAGCAATATACAATCATATACAAATCAATTCGGCAACTTATACCCATATACAAA
TCAATTTCAACAATGTATAACCATGTAAAAATTAATTTCAGCAATATACAATCATATACAAATCA
ATTCGGCAACTAATAC
Found at i:12947926 original size:25 final size:26
Alignment explanation
Indices: 12947887--12947936 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
12947877 TATAACTATG
* *
12947887 AACAATTCGAATTCGGCAATATATAA
1 AACAATTCAAATTCGACAATATATAA
*
12947913 AACAA-TCAAATTCGACAATGTATA
1 AACAATTCAAATTCGACAATATATA
12947937 TCTATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (26 bp):
AACAATTCAAATTCGACAATATATAA
Found at i:12956305 original size:31 final size:31
Alignment explanation
Indices: 12956263--12956766 Score: 214
Period size: 31 Copynumber: 16.4 Consensus size: 31
12956253 AATCAATATA
* *
12956263 TATATTCATATACGAACCAAATTCGGCAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* * * *
12956294 TATATCTATATACAAAT-AAAATCGACAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* * *
12956324 TATAACCATATACGAATCAAGTTCGACAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* * *
12956355 TATAAT-CATATACAAATTAAATTCAGCAATG
1 TAT-ATCCATATACGAATCAAATTCGGCAATG
*
12956386 TATAACCATATACGAATC-AATTCGGCAACT-
1 TATATCCATATACGAATCAAATTCGGCAA-TG
* **
12956416 TATATCCATATAC-AATTCAATTTCAACAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * ** *
12956447 TATAACCATGTACAAATTAATTTTAGCAATA
1 TATATCCATATACGAATCAAATTCGGCAATG
*
12956478 TATAAT-CATATACAAATC-AATTCGGCAACT-
1 TAT-ATCCATATACGAATCAAATTCGGCAA-TG
* ****
12956508 TATATCCATATAC-AATTCAATTTAAAAAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * * *
12956539 TATAACCATGTACAAATTAATTTCAGCAATT
1 TATATCCATATACGAATCAAATTCGGCAATG
* **
12956570 TATATCCATATAC-AATTCAATTTCAACAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * * * *
12956601 TATAACCATGTACAAATTAATTTCAGCGATA
1 TATATCCATATACGAATCAAATTCGGCAATG
* *
12956632 TATAAT-CATATACAAATC-AATTCGACAACT-
1 TAT-ATCCATATACGAATCAAATTCGGCAA-TG
* ***
12956662 TATATCCATATAC-AATTCAATTTCAATAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * *
12956693 TATAACCATGTACAAATTAAATTCAGCAATA
1 TATATCCATATACGAATCAAATTCGGCAATG
* * *
12956724 TATAAT-TATATACAAATC-AATTCGACAACT-
1 TAT-ATCCATATACGAATCAAATTCGGCAA-TG
12956754 TATATCCATATAC
1 TATATCCATATAC
12956767 AATTTAATTT
Statistics
Matches: 362, Mismatches: 84, Indels: 55
0.72 0.17 0.11
Matches are distributed among these distances:
29 12 0.03
30 108 0.30
31 230 0.64
32 12 0.03
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (31 bp):
TATATCCATATACGAATCAAATTCGGCAATG
Found at i:12956354 original size:61 final size:58
Alignment explanation
Indices: 12956269--12956881 Score: 268
Period size: 61 Copynumber: 10.0 Consensus size: 58
12956259 TATATATATT
* *
12956269 CATATACGAACCAAATTCGGCAATGTATATCTATATACAAATAAAATCGACAATGTATAAC
1 CATATACGAATC-AATTCGGCAATGTATATC-ATATACAAATAAATTC-ACAATGTATAAC
*
12956330 CATATACGAATCAAGTTCGACAATGTATAATCATATACAAATTAAATTCAGCAATGTATAAC
1 CATATACGAATCAA-TTCGGCAATGTAT-ATCATATACAAA-TAAATTCA-CAATGTATAAC
* *
12956392 CATATACGAATCAATTCGGCAACT-TATATCCATATACAATTCAATTTCAACAATGTATAAC
1 CATATACGAATCAATTCGGCAA-TGTATAT-CATATACAAAT-AAATTC-ACAATGTATAAC
* * * ** * * * *
12956453 CATGTACAAATTAATTTTAGCAATATATAATCATATACAAATCAATTCGGCAACT-TATATC
1 CATATACGAATCAA-TTCGGCAATGTAT-ATCATATACAAATAAATTC-ACAA-TGTATAAC
**** * * * * *
12956514 CATATAC-AATTCAATTTAAAAAATGTATAACCATGTACAAATTAATTTCAGCAATTTATATC
1 CATATACGAA-TCAA-TTCGGCAATGTAT-ATCATATACAAA-TAAATTCA-CAATGTATAAC
** * * * * * *
12956576 CATATAC-AATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCGATATATAAT
1 CATATACGAA-TCAA-TTCGGCAATGTAT-ATCATATACAAA-TAAATTCA-CAATGTATAAC
* * * * *
12956638 CATATACAAATCAATTCGACAACT-TATATCCATATACAATTCAATTTCAATAATGTATAAC
1 CATATACGAATCAATTCGGCAA-TGTATAT-CATATACAAAT-AAATTC-ACAATGTATAAC
* * * * * * * *
12956699 CATGTACAAATTAAATTCAGCAATATATAATTATATACAAATCAATTCGACAACT-TATATC
1 CATATACGAA-TCAATTCGGCAATGTAT-ATCATATACAAATAAATTC-ACAA-TGTATAAC
* *** * * * * * *
12956760 CATATAC-AATTTAATTTCAAAAATGTATAACCATGTACAGATTAATTTCAGCAATGTACAAT
1 CATATACGAA-TCAA-TTCGGCAATGTAT-ATCATATACA-AATAAATTCA-CAATGTATAAC
* * ** * *
12956822 CATATACAAATCAATTAGGCAACATATATCTATATGCAAATCAATTTCGACAATGTATAA
1 CATATACGAATCAATTCGGCAATGTATATC-ATATACAAAT-AAATTC-ACAATGTATAA
12956882 TTATAAACAA
Statistics
Matches: 440, Mismatches: 79, Indels: 66
0.75 0.14 0.11
Matches are distributed among these distances:
60 19 0.04
61 229 0.52
62 184 0.42
63 8 0.02
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (58 bp):
CATATACGAATCAATTCGGCAATGTATATCATATACAAATAAATTCACAATGTATAAC
Found at i:12956588 original size:154 final size:153
Alignment explanation
Indices: 12956319--12956778 Score: 590
Period size: 154 Copynumber: 3.0 Consensus size: 153
12956309 ATAAAATCGA
* * * * * *
12956319 CAATGTATAACCATATACGAATCAAGTTCGACAA-TGTATAAT-CATATACAAATT-AAATTCAG
1 CAATATATAATCATATACAAATCAA-TTCGACAACT-TAT-ATCCATATAC-AATTCAATTTAAA
* * * * * *
12956381 CAATGTATAACCATATACGAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAAT
62 AAATGTATAACCATGTACAAATTAATTCAGCAATTTATATCCATATACAATTCAATTTCAACAAT
*
12956446 GTATAACCATGTACAAATTAATTTTAG
127 GTATAACCATGTACAAATTAATTTCAG
*
12956473 CAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTAAAAAAT
1 CAATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTAAAAAAT
12956538 GTATAACCATGTACAAATTAATTTCAGCAATTTATATCCATATACAATTCAATTTCAACAATGTA
66 GTATAACCATGTACAAATTAA-TTCAGCAATTTATATCCATATACAATTCAATTTCAACAATGTA
12956603 TAACCATGTACAAATTAATTTCAG
130 TAACCATGTACAAATTAATTTCAG
* * *
12956627 CGATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAATAAT
1 CAATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTAAAAAAT
* * * *
12956692 GTATAACCATGTACAAATTAAATTCAGCAATATATAAT-TATATACAAATCAA-TTCGACAACT-
66 GTATAACCATGTACAAATT-AATTCAGCAATTTAT-ATCCATATACAATTCAATTTCAACAA-TG
* * *
12956754 TATATCCATATACAATTTAATTTCA
128 TATAACCATGTACAAATTAATTTCA
12956779 AAAATGTATA
Statistics
Matches: 274, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
152 6 0.02
153 72 0.26
154 192 0.70
155 4 0.01
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (153 bp):
CAATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTAAAAAAT
GTATAACCATGTACAAATTAATTCAGCAATTTATATCCATATACAATTCAATTTCAACAATGTAT
AACCATGTACAAATTAATTTCAG
Found at i:12956684 original size:92 final size:92
Alignment explanation
Indices: 12956260--12956881 Score: 491
Period size: 92 Copynumber: 6.8 Consensus size: 92
12956250 ATTAATCAAT
* * * * * * ** *
12956260 ATATATATTCATATACGAACCAAATTCGGCAA-TGTATATCTATATACAAAT-AAAATCGACAAT
1 ATATATAATCATATACAAATC-AATTCGACAACT-TATATCCATATACAATTCAATTTCAACAAT
* * * *
12956323 GTATAACCATATACGAATCAAGTTC-GACA
64 GTATAACCATGTACAAATTAATTTCAG-CA
* * * **
12956352 ATGTATAATCATATACAAATTAAATTC-AGCAA-TGTATAACCATATACGAA-TCAA-TTCGGCA
1 ATATATAATCATATACAAA-TCAATTCGA-CAACT-TATATCCATATAC-AATTCAATTTCAACA
* * *
12956413 ACT-TATATCCATATAC-AATTCAATTTCAACA
62 A-TGTATAACCATGTACAAATT-AATTTCAGCA
* * * * ** * **
12956444 ATGTATAACCATGTACAAATTAATTTTAGCAA-TATATAAT-CATATACAAATCAA-TTCGGCAA
1 ATATATAATCATATACAAATCAATTCGA-CAACT-TAT-ATCCATATACAATTCAATTTCAACAA
* * * **
12956506 CT-TATATCCATATAC-AATTCAATTTAAAAA
63 -TGTATAACCATGTACAAATT-AATTTCAGCA
* * * * *
12956536 ATGTATAACCATGTACAAATTAATTTC-AGCAATTTATATCCATATACAATTCAATTTCAACAAT
1 ATATATAATCATATACAAATCAA-TTCGA-CAACTTATATCCATATACAATTCAATTTCAACAAT
*
12956600 GTATAACCATGTACAAATTAATTTCAGCG
64 GTATAACCATGTACAAATTAATTTCAGCA
*
12956629 ATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAATAATGT
1 ATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGT
*
12956694 ATAACCATGTACAAATTAAATTCAGCA
66 ATAACCATGTACAAATTAATTTCAGCA
* * *
12956721 ATATATAATTATATACAAATCAATTCGACAACTTATATCCATATACAATTTAATTTCAAAAATGT
1 ATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGT
*
12956786 ATAACCATGTACAGATTAATTTCAGCA
66 ATAACCATGTACAAATTAATTTCAGCA
* * * * * * * * *
12956813 ATGTACAATCATATACAAATCAATTAGGCAACATATATCTATATGCAAATCAATTTCGACAATGT
1 ATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGT
12956878 ATAA
66 ATAA
12956882 TTATAAACAA
Statistics
Matches: 456, Mismatches: 57, Indels: 34
0.83 0.10 0.06
Matches are distributed among these distances:
91 12 0.03
92 388 0.85
93 52 0.11
94 4 0.01
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (92 bp):
ATATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGT
ATAACCATGTACAAATTAATTTCAGCA
Found at i:12956763 original size:246 final size:245
Alignment explanation
Indices: 12956319--12956837 Score: 806
Period size: 246 Copynumber: 2.1 Consensus size: 245
12956309 ATAAAATCGA
* * * *
12956319 CAATGTATAACCATATACGAATCAAGTTCGACAATGTATAATCATATACAAATTAAATTCAGCAA
1 CAATGTATATCCATATAC-AATCAATTTCAACAATGTATAACCATATACAAATTAAATTCAGCAA
* * *
12956384 TGTATAACCATATACGAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTA
65 TATATAACCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGTA
* * *
12956449 TAACCATGTACAAATTAATTTTAGCAATATATAATCATATACAAATCAATTCGGCAACTTATATC
130 TAACCATGTACAAATTAAATTCAGCAATATATAATCATATACAAATCAATTCGACAACTTATATC
12956514 CATATACAATTCAATTTAAAAAATGTATAACCATGTACAAATTAATTTCAG
195 CATATACAATTCAATTTAAAAAATGTATAACCATGTACAAATTAATTTCAG
* * * *
12956565 CAATTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCGA
1 CAATGTATATCCATATACAA-TCAATTTCAACAATGTATAACCATATACAAATTAAATTCAGCAA
* *
12956630 TATATAATCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAATAATGTA
65 TATATAACCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGTA
*
12956695 TAACCATGTACAAATTAAATTCAGCAATATATAATTATATACAAATCAATTCGACAACTTATATC
130 TAACCATGTACAAATTAAATTCAGCAATATATAATCATATACAAATCAATTCGACAACTTATATC
* * *
12956760 CATATACAATTTAATTTCAAAAATGTATAACCATGTACAGATTAATTTCAG
195 CATATACAATTCAATTTAAAAAATGTATAACCATGTACAAATTAATTTCAG
*
12956811 CAATGTACAAT-CATATACAAATCAATT
1 CAATGTA-TATCCATATAC-AATCAATT
12956838 AGGCAACATA
Statistics
Matches: 248, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
245 2 0.01
246 242 0.98
247 4 0.02
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (245 bp):
CAATGTATATCCATATACAATCAATTTCAACAATGTATAACCATATACAAATTAAATTCAGCAAT
ATATAACCATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCAACAATGTAT
AACCATGTACAAATTAAATTCAGCAATATATAATCATATACAAATCAATTCGACAACTTATATCC
ATATACAATTCAATTTAAAAAATGTATAACCATGTACAAATTAATTTCAG
Found at i:12956915 original size:26 final size:25
Alignment explanation
Indices: 12956886--12956936 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12956876 GTATAATTAT
*
12956886 AAACAATTCGAATTCGGAAATATATA
1 AAACAA-TCAAATTCGGAAATATATA
* *
12956912 AAACAATCAAATTCGGCAATGTATA
1 AAACAATCAAATTCGGAAATATATA
12956937 TCTATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (25 bp):
AAACAATCAAATTCGGAAATATATA
Found at i:12962051 original size:2 final size:2
Alignment explanation
Indices: 12962044--12962088 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12962034 TAATGTGTCA
12962044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12962086 AT A
1 AT A
12962089 CATGAAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12968165 original size:13 final size:13
Alignment explanation
Indices: 12968149--12968178 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12968139 AGTGTTGTGA
*
12968149 AAAAATATTTTTG
1 AAAAATACTTTTG
12968162 AAAAATACTTTTG
1 AAAAATACTTTTG
12968175 AAAA
1 AAAA
12968179 GTTTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (13 bp):
AAAAATACTTTTG
Found at i:12968404 original size:30 final size:31
Alignment explanation
Indices: 12968353--12968463 Score: 92
Period size: 33 Copynumber: 3.5 Consensus size: 31
12968343 AACTTATTGA
12968353 AAATA-TTTT-AATATATGAAATATAAATTTT
1 AAATATTTTTAAATATAT-AAATATAAATTTT
12968383 AAATATTTTTAAATA-ATAAATATTAATTATTTGT
1 AAATATTTTTAAATATATAAATA-TAA--ATTT-T
*
12968417 AAA-ATTTAATTAGAATATATAAAT-TATATTTT
1 AAATATTT--TTA-AATATATAAATATAAATTTT
12968449 AAATA--TTTAAATATA
1 AAATATTTTTAAATATA
12968464 ATCATTAAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 24
0.73 0.01 0.26
Matches are distributed among these distances:
28 6 0.09
29 3 0.04
30 10 0.14
31 10 0.14
32 8 0.12
33 13 0.19
34 4 0.06
35 5 0.07
36 4 0.06
37 6 0.09
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
AAATATTTTTAAATATATAAATATAAATTTT
Found at i:12968408 original size:24 final size:23
Alignment explanation
Indices: 12968353--12968419 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
12968343 AACTTATTGA
* *
12968353 AAATATTTTAATATATG-AAATAT
1 AAATA-TTAAATATTTGTAAATAT
* *
12968376 AAATTTTAAATATTTTTAAATAAT
1 AAATATTAAATATTTGTAAAT-AT
*
12968400 AAATATTAATTATTTGTAAA
1 AAATATTAAATATTTGTAAA
12968420 ATTTAATTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 8 0.23
23 8 0.23
24 19 0.54
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
AAATATTAAATATTTGTAAATAT
Found at i:12968473 original size:33 final size:32
Alignment explanation
Indices: 12968378--12968473 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 32
12968368 TGAAATATAA
12968378 ATTTTAAATATTTTTAAATAATAAATATT-AATTAT
1 ATTTTAAATA--TTTAAAT-AT-AATATTAAATTAT
* * *
12968413 -TTGTAAA-ATTTAATTAGAATATATAAATTAT
1 ATTTTAAATATTTAAATATAATAT-TAAATTAT
12968444 ATTTTAAATATTTAAATATAATCATTAAAT
1 ATTTTAAATATTTAAATATAAT-ATTAAAT
12968474 ATTTATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
29 5 0.10
30 2 0.04
31 12 0.24
32 6 0.12
33 17 0.34
34 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (32 bp):
ATTTTAAATATTTAAATATAATATTAAATTAT
Found at i:12968491 original size:21 final size:19
Alignment explanation
Indices: 12968425--12968492 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
12968415 GTAAAATTTA
*
12968425 ATTAGAATATATAAATTATAT
1 ATTA-AATATTTAAATTA-AT
*
12968446 TTTAAATATTTAAATATAAT
1 ATTAAATATTTAAAT-TAAT
12968466 CATTAAATATTTATAATTAGAT
1 -ATTAAATATTTA-AATTA-AT
12968488 ATTAA
1 ATTAA
12968493 CACATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 12 0.30
21 23 0.57
22 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTAAATATTTAAATTAAT
Found at i:12973435 original size:20 final size:20
Alignment explanation
Indices: 12973401--12973442 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12973391 AACTATTTAA
** *
12973401 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
12973421 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
12973441 AT
1 AT
12973443 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:12983469 original size:27 final size:27
Alignment explanation
Indices: 12983431--12983485 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12983421 AATACTTAGG
12983431 AAAGAATTCACCTAGATTTCATCTGTT
1 AAAGAATTCACCTAGATTTCATCTGTT
12983458 AAAGAATTCACCTAGATTTCATCTGTT
1 AAAGAATTCACCTAGATTTCATCTGTT
12983485 A
1 A
12983486 TTATCAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (27 bp):
AAAGAATTCACCTAGATTTCATCTGTT
Found at i:12985063 original size:21 final size:22
Alignment explanation
Indices: 12985039--12985081 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12985029 AAAAATATTT
12985039 TTATAT-AAAT-TTAATTATAAA
1 TTATATAAAATATTAA-TATAAA
12985060 TTATATAAAATATTAATATAAA
1 TTATATAAAATATTAATATAAA
12985082 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATATAAAATATTAATATAAA
Found at i:12985730 original size:11 final size:11
Alignment explanation
Indices: 12985714--12985744 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12985704 CCACCCGTAT
12985714 TAATTTTTATA
1 TAATTTTTATA
12985725 TAATTTTTATA
1 TAATTTTTATA
12985736 TAATTTTTA
1 TAATTTTTA
12985745 AATATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:12985902 original size:30 final size:30
Alignment explanation
Indices: 12985866--12985928 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12985856 ACTTAACAAG
12985866 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
12985896 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
12985926 CAA
1 CAA
12985929 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:12988239 original size:23 final size:22
Alignment explanation
Indices: 12988176--12988235 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
12988166 AGGAAGTAAA
12988176 ATAAAA-ATA-AAAACATATGT
1 ATAAAATATATAAAACATATGT
*
12988196 ATAAAATATATATAAGCATATGT
1 ATAAAATATATA-AAACATATGT
**
12988219 ATACTATATATAAAACA
1 ATAAAATATATAAAACA
12988236 ATATATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 3 0.09
22 5 0.15
23 19 0.58
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
ATAAAATATATAAAACATATGT
Found at i:12988299 original size:18 final size:18
Alignment explanation
Indices: 12988278--12988316 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12988268 GAATATAAAA
12988278 ATAAAAATAAAAATAATG
1 ATAAAAATAAAAATAATG
* *
12988296 ATAATAATAATAATAATG
1 ATAAAAATAAAAATAATG
12988314 ATA
1 ATA
12988317 CAAGATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAAAAATAAAAATAATG
Found at i:12988312 original size:12 final size:12
Alignment explanation
Indices: 12988272--12988311 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
12988262 GTGCATGAAT
*
12988272 ATAAAAATAAAA
1 ATAAAAATAATA
*
12988284 ATAAAAATAATG
1 ATAAAAATAATA
*
12988296 ATAATAATAATA
1 ATAAAAATAATA
12988308 ATAA
1 ATAA
12988312 TGATACAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:12988819 original size:19 final size:19
Alignment explanation
Indices: 12988791--12988862 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 19
12988781 AATCATATCT
*
12988791 TCTAAAATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12988810 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
* * *
12988829 CCTAAGATTACAAATCATA
1 TCTAAGATTGCATATCATA
12988848 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
12988863 TCTTGAAGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:13000063 original size:9 final size:9
Alignment explanation
Indices: 13000049--13000143 Score: 138
Period size: 9 Copynumber: 10.4 Consensus size: 9
13000039 TTTGGTTAAA
13000049 AATTACCCG
1 AATTACCCG
13000058 AATTACCCG
1 AATTACCCG
13000067 AATTACCCG
1 AATTACCCG
13000076 AATTACCCG
1 AATTACCCG
*
13000085 AATTAACCG
1 AATTACCCG
*
13000094 AATTAACCG
1 AATTACCCG
13000103 AATTACCCG
1 AATTACCCG
13000112 AATTA-CCG
1 AATTACCCG
*
13000120 AAAAATACCCG
1 --AATTACCCG
13000131 AATTACCCG
1 AATTACCCG
13000140 AATT
1 AATT
13000144 TTTTTATTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
8 3 0.04
9 69 0.87
10 4 0.05
11 3 0.04
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:13000301 original size:13 final size:13
Alignment explanation
Indices: 13000283--13000312 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
13000273 TTTTAGTTTT
13000283 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
13000296 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
13000309 ATTG
1 ATTG
13000313 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:13005920 original size:16 final size:17
Alignment explanation
Indices: 13005879--13005921 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
13005869 ATATTTTTAC
13005879 TTTATAC-ATTTTAGAT
1 TTTATACAATTTTAGAT
13005895 TTT-T-CAATTTTA-AT
1 TTTATACAATTTTAGAT
13005909 TTTATACAATTTT
1 TTTATACAATTTT
13005922 CTAATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 10 0.42
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATACAATTTTAGAT
Found at i:13009943 original size:18 final size:18
Alignment explanation
Indices: 13009920--13009958 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
13009910 AAAGAATAGT
13009920 TTTTCATATCAGTAACAC
1 TTTTCATATCAGTAACAC
13009938 TTTTCATATCAGTAACAC
1 TTTTCATATCAGTAACAC
13009956 TTT
1 TTT
13009959 AGAACCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTCATATCAGTAACAC
Found at i:13016660 original size:14 final size:14
Alignment explanation
Indices: 13016641--13016667 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13016631 CTTAAAAAAT
13016641 TTAAGTTTGATTTA
1 TTAAGTTTGATTTA
13016655 TTAAGTTTGATTT
1 TTAAGTTTGATTT
13016668 TAAACTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
TTAAGTTTGATTTA
Found at i:13023504 original size:332 final size:332
Alignment explanation
Indices: 13022898--13023566 Score: 1320
Period size: 332 Copynumber: 2.0 Consensus size: 332
13022888 TTAATTTGCA
13022898 AAATTATTAAAGTGTTAGGGTTTTTCCATGGATGAGTATAGTTGAATTATAAAGTTTTATGGTAG
1 AAATTATTAAAGTGTTAGGGTTTTTCCATGGATGAGTATAGTTGAATTATAAAGTTTTATGGTAG
13022963 AAAATGAAAGGTTGTTGATATATAAACAACTTTTGTAAAGAAAATTTTGATGAAATTATGATTTA
66 AAAATGAAAGGTTGTTGATATATAAACAACTTTTGTAAAGAAAATTTTGATGAAATTATGATTTA
13023028 GGGACTAAATTGAAAATATGGAAAATTTATGGAAAAATTTTGAATTTTTTGAAATACATAAGCTG
131 GGGACTAAATTGAAAATATGGAAAATTTATGGAAAAATTTTGAATTTTTTGAAATACATAAGCTG
13023093 CTATGGATATGTATGAAAATTGGCTTGAAATAAGATTAAATTGTATGAATTTCATTTTCCGAGCC
196 CTATGGATATGTATGAAAATTGGCTTGAAATAAGATTAAATTGTATGAATTTCATTTTCCGAGCC
13023158 TAAAGACAAAATCATAATTAATTAAAAGTATAGGGGCAAAATAGTAATTTTGCCAAAGATATGTA
261 TAAAGACAAAATCATAATTAATTAAAAGTATAGGGGCAAAATAGTAATTTTGCCAAAGATATGTA
13023223 TTGGACT
326 TTGGACT
13023230 AAATTATTAAAGTGTTAGGGTTTTTCCATGGATGAGTATAGTTGAATTATAAAGTTTTATGGTAG
1 AAATTATTAAAGTGTTAGGGTTTTTCCATGGATGAGTATAGTTGAATTATAAAGTTTTATGGTAG
13023295 AAAATGAAAGGTTGTTGATATATAAACAACTTTTGTAAAGAAAATTTTGATGAAATTATGATTTA
66 AAAATGAAAGGTTGTTGATATATAAACAACTTTTGTAAAGAAAATTTTGATGAAATTATGATTTA
13023360 GGGACTAAATTGAAAATATGGAAAATTTATGGAAAAATTTTGAATTTTTTGAAATACATAAGCTG
131 GGGACTAAATTGAAAATATGGAAAATTTATGGAAAAATTTTGAATTTTTTGAAATACATAAGCTG
*
13023425 CTATGGATATGTATGAAAATTGGCTTGAAATAATATTAAATTGTATGAATTTCATTTTCCGAGCC
196 CTATGGATATGTATGAAAATTGGCTTGAAATAAGATTAAATTGTATGAATTTCATTTTCCGAGCC
13023490 TAAAGACAAAATCATAATTAATTAAAAGTATAGGGGCAAAATAGTAATTTTGCCAAAGATATGTA
261 TAAAGACAAAATCATAATTAATTAAAAGTATAGGGGCAAAATAGTAATTTTGCCAAAGATATGTA
13023555 TTGGACT
326 TTGGACT
*
13023562 GAATT
1 AAATT
13023567 GAATGTGAAT
Statistics
Matches: 335, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
332 335 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (332 bp):
AAATTATTAAAGTGTTAGGGTTTTTCCATGGATGAGTATAGTTGAATTATAAAGTTTTATGGTAG
AAAATGAAAGGTTGTTGATATATAAACAACTTTTGTAAAGAAAATTTTGATGAAATTATGATTTA
GGGACTAAATTGAAAATATGGAAAATTTATGGAAAAATTTTGAATTTTTTGAAATACATAAGCTG
CTATGGATATGTATGAAAATTGGCTTGAAATAAGATTAAATTGTATGAATTTCATTTTCCGAGCC
TAAAGACAAAATCATAATTAATTAAAAGTATAGGGGCAAAATAGTAATTTTGCCAAAGATATGTA
TTGGACT
Found at i:13023921 original size:25 final size:25
Alignment explanation
Indices: 13023893--13023980 Score: 99
Period size: 25 Copynumber: 3.5 Consensus size: 25
13023883 ATGGCTCTCT
*
13023893 TGAGCTTCCCGA-TAATTGGTTCGCA
1 TGAGCTTCCCGATTTA-TGGTTCGCA
* *
13023918 TGAGTTTCCCAATTTATGGCTT-GCA
1 TGAGCTTCCCGATTTATGG-TTCGCA
*
13023943 TGAGCTTCCCGATTTATGGCTCGCA
1 TGAGCTTCCCGATTTATGGTTCGCA
*
13023968 TGAGCTTCTCGAT
1 TGAGCTTCCCGAT
13023981 ATACAACTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.02
25 48 0.91
26 4 0.08
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGATTTATGGTTCGCA
Found at i:13024021 original size:25 final size:25
Alignment explanation
Indices: 13023942--13024059 Score: 71
Period size: 25 Copynumber: 4.8 Consensus size: 25
13023932 TATGGCTTGC
** *
13023942 ATGAGCTTCCCGATT-TATGGCTCGC
1 ATGAGCTTCCCG-TTATACAGCTCGA
* * * * *
13023967 ATGAGCTTCTCGATATACAACTTGT
1 ATGAGCTTCCCGTTATACAGCTCGA
*
13023992 TTGAGCTTCCCGTTATACAGCTC-A
1 ATGAGCTTCCCGTTATACAGCTCGA
* * **
13024016 CATGAGCTTCTCATTATATGGCTCGA
1 -ATGAGCTTCCCGTTATACAGCTCGA
*
13024042 AAGAGCTTCCCGTT-TACA
1 ATGAGCTTCCCGTTATACA
13024060 TACTTGTATG
Statistics
Matches: 67, Mismatches: 23, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
24 3 0.04
25 63 0.94
26 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATACAGCTCGA
Found at i:13026163 original size:24 final size:25
Alignment explanation
Indices: 13026136--13026196 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
13026126 GTGCTTTCTA
*
13026136 ATTAAGTGCTCTTCGGAGCTTCCC-
1 ATTAAGTGCTCTTCGGAGCTACCCG
* *
13026160 ATTAAGTTCTCTTTGGAGCTACCCG
1 ATTAAGTGCTCTTCGGAGCTACCCG
*
13026185 ATAAAG-GCTCTT
1 ATTAAGTGCTCTT
13026197 TTGTAAGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
ATTAAGTGCTCTTCGGAGCTACCCG
Found at i:13033377 original size:24 final size:24
Alignment explanation
Indices: 13033350--13033425 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
13033340 TGCTTTCTAA
13033350 TTAAGTGCTCTTCGGAGCTTCCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
*
13033374 TTAAGTGCTCTTCGGAGCTACCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
* * *
13033398 ATATAG-GCTCTTTGTGAGCTTCCTG
1 TTA-AGTGCTCTTCG-GAGCTTCCCG
13033423 TTA
1 TTA
13033426 TTAAGCTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 32 0.73
25 12 0.27
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.36
Consensus pattern (24 bp):
TTAAGTGCTCTTCGGAGCTTCCCG
Found at i:13038334 original size:12 final size:12
Alignment explanation
Indices: 13038317--13038344 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13038307 AAAACCTAAT
13038317 TAACCACACAAC
1 TAACCACACAAC
13038329 TAACCACACAAC
1 TAACCACACAAC
13038341 TAAC
1 TAAC
13038345 TTCTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.39, G:0.00, T:0.11
Consensus pattern (12 bp):
TAACCACACAAC
Found at i:13045425 original size:48 final size:48
Alignment explanation
Indices: 13045354--13045445 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
13045344 TTCTTTGCTT
* *
13045354 AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTTACAATAATAAAGGATTCAACAGC
*
13045402 AAAAACGCCTAAGTCGGCCTAACTTACAATAATAAAGGATTCAA
1 AAAAACGCCTAAGTCAGCCTAACTTACAATAATAAAGGATTCAA
13045446 TAGAATTCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTTACAATAATAAAGGATTCAACAGC
Found at i:13045485 original size:11 final size:11
Alignment explanation
Indices: 13045469--13045510 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
13045459 AGGCACCCAC
*
13045469 GAAGAACAGCA
1 GAAGAACAACA
13045480 GAAGAACAACA
1 GAAGAACAACA
*
13045491 GAAGAACGA-A
1 GAAGAACAACA
13045501 GTAAGAACAA
1 G-AAGAACAA
13045511 ACGTTGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 2 0.07
11 25 0.93
ACGTcount: A:0.60, C:0.14, G:0.24, T:0.02
Consensus pattern (11 bp):
GAAGAACAACA
Found at i:13045685 original size:17 final size:17
Alignment explanation
Indices: 13045663--13045726 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
13045653 CATCAAAGGC
*
13045663 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
13045680 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
13045699 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
13045716 TACAATTAGAA
1 TACAATTAGAA
13045727 CTTTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 21 0.55
19 11 0.29
20 3 0.08
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:13045712 original size:36 final size:36
Alignment explanation
Indices: 13045664--13045734 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
13045654 ATCAAAGGCT
13045664 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
* *
13045700 ACAATTAGAAGCTGTATACAATTAGAACTTTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
13045735 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:13051512 original size:29 final size:30
Alignment explanation
Indices: 13051453--13051510 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13051443 TCCGAGCCTT
* *
13051453 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATATAATTATGAAAAAGTTTA
* *
13051483 GGGGCAAAATTATAATTTTGAAAAAGTT
1 GGGGCAAAAATATAATTATGAAAAAGTT
13051511 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATATAATTATGAAAAAGTTTA
Found at i:13051961 original size:50 final size:50
Alignment explanation
Indices: 13051848--13052146 Score: 382
Period size: 50 Copynumber: 5.8 Consensus size: 50
13051838 ATTTGGGTAA
* *
13051848 AGAGATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* *
13051904 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
13051954 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
13052004 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
13052054 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * * *
13052104 AGAACATCTCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
13052147 TGTTATTATC
Statistics
Matches: 220, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 143 0.65
51 32 0.15
52 1 0.00
53 4 0.02
55 2 0.01
56 38 0.17
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:13053682 original size:17 final size:17
Alignment explanation
Indices: 13053660--13053705 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
13053650 ATGTAGATAC
13053660 GTATATAAAATATATAA
1 GTATATAAAATATATAA
* *
13053677 GTATAT-ATATATGTAA
1 GTATATAAAATATATAA
13053693 GT-TATGAAAATAT
1 GTATAT-AAAATAT
13053706 GTATGTGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
GTATATAAAATATATAA
Found at i:13074457 original size:15 final size:15
Alignment explanation
Indices: 13074415--13074467 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
13074405 TTATATACTT
*
13074415 TTAATTAAA-TCTAA
1 TTAATTAAACTTTAA
* *
13074429 TTAATCATAA-TTTAT
1 TTAATTA-AACTTTAA
13074444 TTAATTAAACTTTAA
1 TTAATTAAACTTTAA
13074459 TTAATTAAA
1 TTAATTAAA
13074468 AATTAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 8 0.25
15 24 0.75
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTAAACTTTAA
Found at i:13075405 original size:33 final size:35
Alignment explanation
Indices: 13075367--13075463 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
13075357 ATGGTTATAT
13075367 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
13075400 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
*
13075435 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
13075464 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
32 7 0.14
33 25 0.49
34 5 0.10
35 11 0.22
36 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (35 bp):
TTAAATATTTAAAATATATTTTATATATTGCTTAA
Found at i:13075676 original size:26 final size:25
Alignment explanation
Indices: 13075647--13075712 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
13075637 TAAACTAAAC
13075647 TTTTCAAAAGTATTTCTCAAAAGCAA
1 TTTTCAAAAGTATTT-TCAAAAGCAA
* * *
13075673 TTTTC-CACGTCACTTTTCAAAAGCAC
1 TTTTCAAAAGT-A-TTTTCAAAAGCAA
*
13075699 TTTTTAAAAGTATT
1 TTTTCAAAAGTATT
13075713 GCCAAACTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
25 5 0.16
26 20 0.65
27 6 0.19
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (25 bp):
TTTTCAAAAGTATTTTCAAAAGCAA
Found at i:13075699 original size:13 final size:13
Alignment explanation
Indices: 13075645--13075708 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
13075635 TTTAAACTAA
*
13075645 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
13075658 A-TTTCTCAAAAGC
1 ACTTT-TCAAAAGC
* * *
13075671 AATTTTC-CACGTC
1 ACTTTTCAAAAG-C
13075684 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
13075697 ACTTTTTAAAAG
1 ACTTTTCAAAAG
13075709 TATTGCCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
12 5 0.12
13 30 0.75
14 5 0.12
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:13078725 original size:12 final size:12
Alignment explanation
Indices: 13078708--13078742 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
13078698 TTTTCACAAT
13078708 AAAATATTAATA
1 AAAATATTAATA
*
13078720 AAAATA-TAATT
1 AAAATATTAATA
13078731 AAAATATTAATA
1 AAAATATTAATA
13078743 TTATAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATATTAATA
Found at i:13091897 original size:25 final size:26
Alignment explanation
Indices: 13091868--13091916 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
13091858 AAAAGAAAAA
*
13091868 AAATAG-AACAACGTGCCACAAGAGT
1 AAATAGAAAAAACGTGCCACAAGAGT
*
13091893 AAATAGAAAAAACGTGCCATAAGA
1 AAATAGAAAAAACGTGCCACAAGA
13091917 ATATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (26 bp):
AAATAGAAAAAACGTGCCACAAGAGT
Found at i:13108446 original size:19 final size:17
Alignment explanation
Indices: 13108413--13108447 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
13108403 AAGCTCGAAT
13108413 TTGACTTGATTGATAAC
1 TTGACTTGATTGATAAC
13108430 TTGAGCTTGACTTGATAA
1 TTGA-CTTGA-TTGATAA
13108448 TTATCGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (17 bp):
TTGACTTGATTGATAAC
Found at i:13111183 original size:13 final size:13
Alignment explanation
Indices: 13111165--13111190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13111155 AGAATTCAAG
13111165 TATGTACTTTTAT
1 TATGTACTTTTAT
13111178 TATGTACTTTTAT
1 TATGTACTTTTAT
13111191 CCTTGCATTT
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:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TATGTACTTTTAT
Found at i:13114637 original size:18 final size:18
Alignment explanation
Indices: 13114614--13114648 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13114604 GAAGATATAA
13114614 TTTTAT-ATTAATATTTAT
1 TTTTATAATTAA-ATTTAT
13114632 TTTTATAATTAAATTTA
1 TTTTATAATTAAATTTA
13114649 AATAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATAATTAAATTTAT
Found at i:13121909 original size:2 final size:2
Alignment explanation
Indices: 13121902--13121932 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13121892 GGCCAAAGCT
13121902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13121933 TAGATTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13122808 original size:46 final size:46
Alignment explanation
Indices: 13122741--13122833 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
13122731 ATGAAAATGA
*
13122741 AAACCAACTAAGCATACCTGCTCCAACTCGCTCTCACTCTACCCCC
1 AAACCAACCAAGCATACCTGCTCCAACTCGCTCTCACTCTACCCCC
13122787 AAACCAACCAAGCATACCTGCTCCAACTCGCTCTCACTCTACCCCC
1 AAACCAACCAAGCATACCTGCTCCAACTCGCTCTCACTCTACCCCC
13122833 A
1 A
13122834 CTTGCTCCAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.29, C:0.46, G:0.06, T:0.18
Consensus pattern (46 bp):
AAACCAACCAAGCATACCTGCTCCAACTCGCTCTCACTCTACCCCC
Found at i:13127349 original size:3 final size:3
Alignment explanation
Indices: 13127341--13127379 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
13127331 AAGGACCCAA
* * *
13127341 ATT ATT ATT ATT ATT ATC ATT AGT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13127380 TTTACAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:13129201 original size:50 final size:48
Alignment explanation
Indices: 13129134--13129331 Score: 189
Period size: 51 Copynumber: 4.0 Consensus size: 48
13129124 AAAGTGAAAG
* * *
13129134 TGATGGTCACGTGTGTAGTACTATATGTAGGCTACTACGTGTACCAGAA
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA
* * * *
13129183 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
* * * *
13129232 TAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATA
1 T-G-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CCGA-A
* * * *
13129285 GTGATGGTCACATGTGTAGTACTATGTACAGGTTACTATGTGAACCG
1 -TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
13129332 GTATCATTAA
Statistics
Matches: 119, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
49 7 0.06
50 38 0.32
51 68 0.57
52 3 0.03
53 2 0.02
54 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (48 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
Found at i:13129255 original size:101 final size:102
Alignment explanation
Indices: 13129140--13129324 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
13129130 AAAGTGATGG
* *
13129140 TCACGTGTGTAGTACTATATGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
*
13129203 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTACAGGCTACTATGCGTACCGGATAGCTTCGA
* * *
13129241 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
*
13129306 CTATGTACAGGTTACTATG
66 CTATGTACAGGCTACTATG
13129325 TGAACCGGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 38 0.51
102 33 0.44
103 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTACAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:13129407 original size:44 final size:42
Alignment explanation
Indices: 13129328--13129424 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 42
13129318 TACTATGTGA
*
13129328 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGC-ATGTGCTGAAT-CC
*
13129371 ACCGGATATCATTGATTACAAAGGGTGGTTGC-TGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCATGTGCTGAATCC
13129415 ACCGTGTATC
1 ACCG-GTATC
13129425 TGTTATTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
43 5 0.11
44 28 0.60
45 5 0.11
46 9 0.19
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCATGTGCTGAATCC
Found at i:13129569 original size:16 final size:16
Alignment explanation
Indices: 13129548--13129579 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13129538 TGATTGAAAG
*
13129548 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
13129564 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
13129580 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:13131779 original size:16 final size:16
Alignment explanation
Indices: 13131758--13131789 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13131748 GTTTTGTTGC
*
13131758 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
13131774 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
13131790 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:13132075 original size:51 final size:51
Alignment explanation
Indices: 13132008--13132207 Score: 237
Period size: 51 Copynumber: 3.9 Consensus size: 51
13131998 TTAATGATAT
* * *
13132008 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATC
* *
13132059 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATC
* * * * *
13132110 CGGTACGCATAGTAGCCTGCACATAGTACTACATATGCGACCTATCA-T-TC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATC
* *
13132160 TGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
13132208 TTCACTTTCA
Statistics
Matches: 124, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
49 4 0.03
50 40 0.32
51 77 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATC
Found at i:13132183 original size:101 final size:102
Alignment explanation
Indices: 13132015--13132199 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
13132005 TATCGGTTCA
* *
13132015 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
13132080 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
13132117 CATAGTAGCCTGCACATAGTACTACATATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTAC
13132180 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
13132200 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 39 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:13137263 original size:2 final size:2
Alignment explanation
Indices: 13137256--13137282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13137246 AGCCATGCAA
13137256 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
13137283 TATATATAAG
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13154212 original size:34 final size:35
Alignment explanation
Indices: 13154137--13154202 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
13154127 CCGAAAAAAG
13154137 AAAAAAGAAGGAATAGAGAAAGCGAATAAGAAACA
1 AAAAAAGAAGGAATAGAGAAAGCGAATAAGAAACA
* *
13154172 AAAAAAGAAAGGAA-ATAGAAAG-GAGTAAGAA
1 AAAAAAG-AAGGAATAGAGAAAGCGAATAAGAA
13154203 TGAAGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 14 0.50
36 6 0.21
ACGTcount: A:0.67, C:0.03, G:0.24, T:0.06
Consensus pattern (35 bp):
AAAAAAGAAGGAATAGAGAAAGCGAATAAGAAACA
Found at i:13154779 original size:21 final size:21
Alignment explanation
Indices: 13154735--13154776 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
13154725 AAATCAAGAA
* *
13154735 AAAAAGAAAAAAGAAAAAGGG
1 AAAAACAAAAAACAAAAAGGG
13154756 AAAAACAATAAAACAAAAAGG
1 AAAAACAA-AAAACAAAAAGG
13154777 AAACAAAAAA
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:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAACAAAAAACAAAAAGGG
Found at i:13155249 original size:42 final size:42
Alignment explanation
Indices: 13155190--13155495 Score: 364
Period size: 42 Copynumber: 7.3 Consensus size: 42
13155180 AAGGGAAACA
* **
13155190 TTCATTGCATTTAGAGGCCCAAGTGTGGAACTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
13155232 TTCATTGCATTTAGAGGCTCGGGCGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
13155274 TTCATTGCATTTAGAGGCCTAGG-GTAGAGGTCCATTTACGTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTAC-TT
* * *
13155316 TT-ATTACATTTAGAGGCCTAGGTGTGGAGTTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
13155357 TTCATTGCATTTAAAGGCCCAGATGTGTGGAGTTCCATTGACTT
1 TTCATTGCATTTAGAGGCCCAG--GTGTGGAGGTCCATTTACTT
* * * *
13155401 TTCATTACATTTAGAGGTCTAGGTGTGGAGGTCCATCTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
13155443 TTCATTACATTTAAAGGCTCAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
13155485 TTCATTGCATT
1 TTCATTGCATT
13155496 GTATATGAAG
Statistics
Matches: 228, Mismatches: 31, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
41 39 0.17
42 152 0.67
44 37 0.16
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:13155939 original size:3 final size:3
Alignment explanation
Indices: 13155931--13156041 Score: 114
Period size: 3 Copynumber: 36.7 Consensus size: 3
13155921 AAGGGCCCAA
* ** * * * * *
13155931 ATT ATT ATT ATT ATT ATT ATT ATT ACT GCT ACT ACT ACT ATT ACT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
13155979 ATT ATGA AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13156025 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
13156042 CATTTTTTAC
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 94 0.99
4 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:13156160 original size:3 final size:3
Alignment explanation
Indices: 13156154--13156179 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13156144 GTTAAAAAAA
13156154 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
13156180 GCATTCTAGT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:13156538 original size:24 final size:23
Alignment explanation
Indices: 13156511--13156579 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
13156501 AACTATTTCG
13156511 AAATAAAGTTTTGATTTTTAAGAA
1 AAATAAAGTTTTGATTTTTAA-AA
**
13156535 AAATAGTGATTTT--TTTTTAAAA
1 AAATAAAG-TTTTGATTTTTAAAA
* * *
13156557 AGAGAAAGTTTAGATTTTTAAAA
1 AAATAAAGTTTTGATTTTTAAAA
13156580 TAAAAATATG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 3 0.09
22 6 0.17
23 16 0.46
24 6 0.17
25 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (23 bp):
AAATAAAGTTTTGATTTTTAAAA
Found at i:13156608 original size:149 final size:148
Alignment explanation
Indices: 13156397--13156699 Score: 455
Period size: 149 Copynumber: 2.0 Consensus size: 148
13156387 AAAATTTTGA
* *
13156397 TTTTTTTTAAAAGGAGAAAGTTTAGATTTTTAAAATAAAATATGTTTTTTTAGTCATATTAAAGG
1 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATATGTGTTTTTAGTCATATTAAAGG
*
13156462 A-AAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAGTTTTGAT
66 ACAAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATCTCG-AATAAAGTTTTGAT
*
13156526 TTTTAAGAAAAATAGTGAT
130 TTTTAAGAAAAATAGAGAT
* *
13156545 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTAGTCTTTTTAAAG
1 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAT-AAAATATGTGTTTTTAGTCATATTAAAG
* * * ****
13156610 GACAAAGTTTAAATTTTTAAAATAAAGTTTTGATCTTTTTCAACTATCTCGAATTTTTTTTTGAT
65 GACAAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATCTCGAATAAAGTTTTGAT
*
13156675 TTTTAAGAAAAGTAGAGAT
130 TTTTAAGAAAAATAGAGAT
13156694 TTTTTT
1 TTTTTT
13156700 AAAGAAAACT
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
148 35 0.25
149 60 0.43
150 44 0.32
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.46
Consensus pattern (148 bp):
TTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATATGTGTTTTTAGTCATATTAAAGG
ACAAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATCTCGAATAAAGTTTTGATT
TTTAAGAAAAATAGAGAT
Found at i:13156626 original size:52 final size:51
Alignment explanation
Indices: 13156400--13156635 Score: 157
Period size: 52 Copynumber: 4.7 Consensus size: 51
13156390 ATTTTGATTT
*
13156400 TTTTTAAAAGGAGAAAGTTTAGATTTTTAAAAT-AAAATATGTTTTTTTAGTC
1 TTTTT-AAAGGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTA-TC
* * * * * * ** * * *
13156452 ATATTAAAGGA-AAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAAC
1 TTTTTAAAGGAGAAAGTTTAGATTTTTAAAATAAAAATATG-TGTTTTT-ATC
** * * * *
13156504 TATTTCGAA--ATAAAGTTTTGATTTTT--AAGAAAAATA-GTGATTTT-T-
1 T-TTTTAAAGGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTATC
* *
13156549 TTTTAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTAGTC
1 TTTTTAAAGGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTA-TC
* *
13156601 TTTTTAAAGGACAAAGTTTAAATTTTTAAAATAAA
1 TTTTTAAAGGAGAAAGTTTAGATTTTTAAAATAAA
13156636 GTTTTGATCT
Statistics
Matches: 135, Mismatches: 36, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
44 5 0.04
45 1 0.01
46 15 0.11
48 14 0.10
49 8 0.06
50 22 0.16
51 13 0.10
52 52 0.39
53 5 0.04
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (51 bp):
TTTTTAAAGGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTATC
Found at i:13156735 original size:150 final size:147
Alignment explanation
Indices: 13156395--13156731 Score: 443
Period size: 149 Copynumber: 2.3 Consensus size: 147
13156385 GAAAAATTTT
* *
13156395 GATTTTTTTTAAAAGGAGAAAGTTTAGATTTTTAAAAT-AAAATATGTTTTTTTAGTCATATTAA
1 GATTTTTTTTAAAA-GAGAAACTTTAGATTTTTAAAATAAAAATATGTGTTTTTAGTCATATTAA
*
13156459 AGGAAAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAGTTTTG
65 AGGAAAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATCTCGAAATAAAGTTTTG
*
13156524 ATTTTTAAGAAAAATAGT
130 ATTTTTAAGAAAAATAGA
* * *
13156542 GATTTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATGTGTTTTTAGTCTTTTTA
1 GA-TTTTTTTT-AAAAGAGAAACTTTAGATTTTTAAAATAAAAATATGTGTTTTTAGTCATATTA
* * * ****
13156607 AAGGACAAAGTTTAAATTTTTAAAATAAAGTTTTGATCTTTTTCAACTATCTCG-AATTTTTTTT
64 AAGGA-AAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATCTCGAAATAAAGTTT
*
13156671 TGATTTTTAAGAAAAGTAGA
128 TGATTTTTAAGAAAAATAGA
*
13156691 GA-TTTTTTT-AAAGA-AAACTTT-GATTTTGCAAAATAAAAATA
1 GATTTTTTTTAAAAGAGAAACTTTAGATTTT-TAAAATAAAAATA
13156732 AAAAATTCTA
Statistics
Matches: 170, Mismatches: 15, Indels: 13
0.86 0.08 0.07
Matches are distributed among these distances:
143 6 0.04
144 18 0.11
145 5 0.03
147 9 0.05
148 31 0.18
149 57 0.34
150 44 0.26
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (147 bp):
GATTTTTTTTAAAAGAGAAACTTTAGATTTTTAAAATAAAAATATGTGTTTTTAGTCATATTAAA
GGAAAAATTTAAATTCTTAAAACAAAGTTTTGATCTTTTTCAACTATCTCGAAATAAAGTTTTGA
TTTTTAAGAAAAATAGA
Found at i:13161947 original size:17 final size:18
Alignment explanation
Indices: 13161925--13161964 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
13161915 AAGAAAGTAA
13161925 TAAAAATATATAAG-ATT
1 TAAAAATATATAAGAATT
* *
13161942 TAAAAATATGTTAGAATT
1 TAAAAATATATAAGAATT
13161960 TAAAA
1 TAAAA
13161965 TAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (18 bp):
TAAAAATATATAAGAATT
Found at i:13166301 original size:20 final size:20
Alignment explanation
Indices: 13166273--13166322 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
13166263 TATTGATCCA
*
13166273 GTATCGATACT-TTTCTTAAG
1 GTATCGATA-TATTTCCTAAG
*
13166293 GTATTGATATATTTCCTAAG
1 GTATCGATATATTTCCTAAG
13166313 GTATCGATAT
1 GTATCGATAT
13166323 TCCTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (20 bp):
GTATCGATATATTTCCTAAG
Found at i:13168087 original size:14 final size:13
Alignment explanation
Indices: 13168070--13168108 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
13168060 TGAGACCATA
13168070 AAAACTTTTAATTT
1 AAAAC-TTTAATTT
*
13168084 AAAACTTTAAATT
1 AAAACTTTAATTT
13168097 AAAA-TTTAATTT
1 AAAACTTTAATTT
13168109 CACCAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 7 0.30
13 11 0.48
14 5 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAACTTTAATTT
Found at i:13171892 original size:20 final size:20
Alignment explanation
Indices: 13171856--13171893 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13171846 TTAATTACCT
*
13171856 TAAAATGAATTTCAAAAAAA
1 TAAAATGAATCTCAAAAAAA
13171876 TAAAACTGAATCT-AAAAA
1 TAAAA-TGAATCTCAAAAA
13171894 TAATTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (20 bp):
TAAAATGAATCTCAAAAAAA
Found at i:13172626 original size:21 final size:21
Alignment explanation
Indices: 13172581--13172627 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
13172571 TTAGATATAT
* *
13172581 TATAATATGAAATTTATATAT
1 TATAATATGAAATTTAGATAG
13172602 TATAATATGAAATTTAGGAT-G
1 TATAATATGAAATTTA-GATAG
13172623 TATAA
1 TATAA
13172628 ATTCATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (21 bp):
TATAATATGAAATTTAGATAG
Found at i:13172626 original size:26 final size:21
Alignment explanation
Indices: 13172575--13172617 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13172565 GATAGCTTAG
13172575 ATATATTATAATATGAAATTT
1 ATATATTATAATATGAAATTT
13172596 ATATATTATAATATGAAATTT
1 ATATATTATAATATGAAATTT
13172617 A
1 A
13172618 GGATGTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATATTATAATATGAAATTT
Found at i:13181573 original size:8 final size:8
Alignment explanation
Indices: 13181560--13181585 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
13181550 ATGAATTCGA
13181560 ATTGTTTG
1 ATTGTTTG
13181568 ATTGTTTG
1 ATTGTTTG
13181576 ATTGTTTG
1 ATTGTTTG
13181584 AT
1 AT
13181586 CTATAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTGTTTG
Done.