Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013009.1 Kokia drynarioides strain JFW-HI SEQ_128027, 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: 42989
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:148 original size:17 final size:17
Alignment explanation
Indices: 123--203 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
113 TAAATAGATT
*
123 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
141 TAAATTTAAATTTTTAAG
1 TAAATTTAAA-TTTAAAA
*
159 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
176 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
193 TGAATTTAAAT
1 TAAATTTAAAT
204 CCTGTTGGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 34 0.65
18 18 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:178 original size:35 final size:34
Alignment explanation
Indices: 123--202 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 34
113 TAAATAGATT
* * * *
123 TAAACTTTAAATTTATAATAAATTTAAATTTTTAAG
1 TAAA-TTTAAACTTAAAATAAATTT-AATTTTAAAA
159 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
1 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
*
193 TGAATTTAAA
1 TAAATTTAAA
203 TCCTGTTGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 17 0.44
35 18 0.46
36 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
Found at i:1047 original size:13 final size:13
Alignment explanation
Indices: 1029--1054 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1019 TTGTATGCAA
1029 TTGTTATATTTTT
1 TTGTTATATTTTT
1042 TTGTTATATTTTT
1 TTGTTATATTTTT
1055 CTAAATGCGT
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTGTTATATTTTT
Found at i:3064 original size:6 final size:6
Alignment explanation
Indices: 3055--3170 Score: 82
Period size: 6 Copynumber: 20.0 Consensus size: 6
3045 GATTTATTTC
* * **
3055 TAAATT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** * *
3102 TAAATT T-GTTT TAAATT T-AATT T-AGTT TAAATT TGAAA-- TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
* *
3146 TAAACTT AAAATT TAAAAT TAAATT
1 TAAA-TT TAAATT TAAATT TAAATT
3171 CAAAGTCCAT
Statistics
Matches: 83, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
4 2 0.02
5 17 0.20
6 56 0.67
7 8 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:3077 original size:17 final size:17
Alignment explanation
Indices: 3041--3140 Score: 67
Period size: 17 Copynumber: 5.4 Consensus size: 17
3031 TTAGATTAGT
* *
3041 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTT-TAAA
3059 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
3076 TTTAAATTTAAATTCATTTTTAAA
1 TTTAAATTT--A--C---TTTAAA
**
3100 TTTAAATTTGTTTTAAA
1 TTTAAATTTACTTTAAA
*
3117 TTT-AATTTAGTTTAAA
1 TTTAAATTTACTTTAAA
3133 TTTGAAAT
1 TTT-AAAT
3141 AATTTTAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
16 14 0.21
17 22 0.33
18 14 0.21
19 1 0.01
21 1 0.01
24 15 0.22
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:3115 original size:41 final size:40
Alignment explanation
Indices: 3041--3125 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
3031 TTAGATTAGT
* *
3041 TTTAGATTTATTTCTAAATTTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTT-AA
* **
3082 TTTAAATTCATTTTTAAATTTAAATTTGTTTTAAATTTAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAA
3122 TTTA
1 TTTA
3126 GTTTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 6 0.15
41 33 0.85
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (40 bp):
TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAA
Found at i:3959 original size:13 final size:13
Alignment explanation
Indices: 3919--3983 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
3909 TCATTAACAT
3919 TAATATTAATTACAA
1 TAATATTAA-TA-AA
* *
3934 TATTAATAATAAA
1 TAATATTAATAAA
*
3947 TAATATTACTAAA
1 TAATATTAATAAA
*
3960 TAACATTAAT-AA
1 TAATATTAATAAA
*
3972 TAATAATAATAA
1 TAATATTAATAA
3984 TATTAATAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 10 0.25
13 21 0.52
14 2 0.05
15 7 0.17
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATATTAATAAA
Found at i:4025 original size:3 final size:3
Alignment explanation
Indices: 3932--4005 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
3922 TATTAATTAC
* * * * *
3932 AAT ATT AAT AAT AAAT AAT ATT ACT AAAT AAC ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* * *
3979 AAT AAT ATT AAT AAT AAC AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
4006 GAATTTATTA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
3 49 0.91
4 5 0.09
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5179 original size:29 final size:28
Alignment explanation
Indices: 5068--5403 Score: 112
Period size: 30 Copynumber: 11.4 Consensus size: 28
5058 GAAGGTCTCT
**
5068 AAACTGTCCAGAAATTATATTTTGACCCTC
1 AAACT-TCCA-AAATTCCATTTTGACCCTC
** *
5098 AAACTTCTCCAAAATTATATTCTTAACCCT-
1 AAAC-T-TCCAAAATTCCATT-TTGACCCTC
** * *
5128 AAACTTTTTGAAAATTACATTTTTACCCTC
1 AAAC--TTCCAAAATTCCATTTTGACCCTC
5158 AAACTTCCAAAATTCCATTTTTGA-CCTC
1 AAACTTCCAAAATTCCA-TTTTGACCCTC
* ** *
5186 GATTTTCCAAAATTTACCATTTT-ACCCTT
1 AAACTTCCAAAA-TT-CCATTTTGACCCTC
5215 AAACTTCCAAAAAATTCCATTTTTGACCC-C
1 AAACTTCC--AAAATTCCA-TTTTGACCCTC
***
5245 GATTTTTCCAAAAATTACCA-TTT-ACCCTC
1 -AAACTTCC-AAAATT-CCATTTTGACCCTC
* * * * *
5274 GAATTTCCAAAAATTCCATTTTTAACCTT
1 AAACTTCC-AAAATTCCATTTTGACCCTC
**** *
5303 GGTTTTCCCAAAAATTACCATTTT-ACCCCC
1 AAACTT-CC-AAAATT-CCATTTTGACCCTC
* * *
5333 GAACTTCCAAAAATTCCATTTTTAACCTC
1 AAACTTCC-AAAATTCCATTTTGACCCTC
** *
5362 GATTCTTCCTAAAATTACCATTTT-ATCCTC
1 -AAACTTCC-AAAATT-CCATTTTGACCCTC
5392 AAACTTCCAAAA
1 AAACTTCCAAAA
5404 ATTTTATTTT
Statistics
Matches: 241, Mismatches: 43, Indels: 46
0.73 0.13 0.14
Matches are distributed among these distances:
27 3 0.01
28 54 0.22
29 60 0.25
30 80 0.33
31 44 0.18
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (28 bp):
AAACTTCCAAAATTCCATTTTGACCCTC
Found at i:5248 original size:59 final size:58
Alignment explanation
Indices: 5138--5653 Score: 506
Period size: 59 Copynumber: 8.7 Consensus size: 58
5128 AAACTTTTTG
*
5138 AAAATTA-CATTTTTACCCTCAAACTTCC-AAAATTCCATTTTTGACCTCGATTTTCCA
1 AAAATTACCA-TTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTTTCCA
* * * *
5195 AAATTTACCATTTTACCCTTAAACTTCCAAAAAATTCCATTTTTGACCCCGATTTTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCC-AAAAATTCCATTTTTAACCTCGA-TTTTCCA
* * * *
5255 AAAATTACCA-TTTACCCTCGAATTTCCAAAAATTCCATTTTTAACCTTGGTTTTCCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTTT-CCA
* * *
5313 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCGATTCTTCCT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATT-TTCCA
* ** * *
5372 AAAATTACCATTTTATCCTCAAACTTCCAAAAATTTTATTTTTGATCC-CGATTTTTTTCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTT-AACCTCGA--TTTTCCA
* * * * *
5432 AAAATTAGCATTTTACCCTCGAACTTCCAAAAATTCCTTTTTTCAAACCCCGATTCTTCCC
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTT--AACCTCGATT-TTCCA
* * * * * * *
5493 AAAATTACCATTTTATCGTTAAACTTCCAAAAATTTCATTTTTTATCTCGATTTTTTTCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGA--TTTTCCA
* * * * *
5553 AAAATTACCATTTTACCCTCGAA-TGT-CTAAAATTCTATTTTTAACCTCGAACTTTCCC
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTAACCTCG-ATTTTCCA
* *
5611 AAAATTACCATTTTACCCTC-GAGTGTCCAAAAATTACCATTTT
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATT-CCATTTT
5654 GCCCTCGAGT
Statistics
Matches: 378, Mismatches: 61, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
57 28 0.07
58 61 0.16
59 147 0.39
60 93 0.25
61 46 0.12
62 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTTTCCA
Found at i:5466 original size:29 final size:29
Alignment explanation
Indices: 5138--5661 Score: 258
Period size: 29 Copynumber: 17.8 Consensus size: 29
5128 AAACTTTTTG
*
5138 AAAATTA-CATTTTTACCCTCAAACTTCC-
1 AAAATTACCA-TTTTACCCTCGAACTTCCA
**
5166 AAAATT-CCATTTTTGA-CCTCGATTTTCCA
1 AAAATTACCA-TTTT-ACCCTCGAACTTCCA
* **
5195 AAATTTACCATTTTACCCTTAAACTTCCAA
1 AAAATTACCATTTTACCCTCGAACTTCC-A
**
5225 AAAATT-CCATTTTTGACCC-CGATTTTTCCA
1 AAAATTACCA-TTTT-ACCCTCGA-ACTTCCA
*
5255 AAAATTACCA-TTTACCCTCGAATTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
* * ***
5283 AAAATT-CCATTTTTAACCTTGGTTTTCCCA
1 AAAATTACCA-TTTTACCCTCGAACTT-CCA
*
5313 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
* * *
5342 AAAATT-CCATTTTTAACCTCGATTCTTCCT
1 AAAATTACCA-TTTTACCCTCGA-ACTTCCA
* *
5372 AAAATTACCATTTTATCCTCAAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
** * ** *
5401 AAAATT-TTATTTTTGATCC-CGATTTTTTTCA
1 AAAATTACCA-TTTT-ACCCTCGA--ACTTCCA
*
5432 AAAATTAGCATTTTACCCTCGAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
* * *
5461 AAAATT-CCTTTTTTCAAACCC-CGATTCTTCCC
1 AAAATTACC-ATTTT---ACCCTCGA-ACTTCCA
* * **
5493 AAAATTACCATTTTATCGTTAAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
* * ** *
5522 AAAATT-TCATTTTTTA-TCTCGATTTTTTTCA
1 AAAATTACCA--TTTTACCCTCGA--ACTTCCA
*
5553 AAAATTACCATTTTACCCTCGAA-TGT-CT
1 AAAATTACCATTTTACCCTCGAACT-TCCA
* * *
5581 AAAATT-CTATTTTTAACCTCGAACTTTCCC
1 AAAATTACCA-TTTTACCCTCGAAC-TTCCA
*
5611 AAAATTACCATTTTACCCTCG-AGTGTCCA
1 AAAATTACCATTTTACCCTCGAACT-TCCA
*
5640 AAAATTACCATTTTGCCCTCGA
1 AAAATTACCATTTTACCCTCGA
5662 GTATCCAAAA
Statistics
Matches: 376, Mismatches: 75, Indels: 88
0.70 0.14 0.16
Matches are distributed among these distances:
27 5 0.01
28 67 0.18
29 129 0.34
30 97 0.26
31 54 0.14
32 22 0.06
33 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.39
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACTTCCA
Found at i:5662 original size:29 final size:29
Alignment explanation
Indices: 5551--5681 Score: 133
Period size: 29 Copynumber: 4.6 Consensus size: 29
5541 CGATTTTTTT
*
5551 CAAAAATTACCATTTTACCCTCGAATGT-
1 CAAAAATTACCATTTTACCCTCGAGTGTC
* * * * *
5579 CTAAAATT-CTATTTTTAACCTCGAACTTTC
1 CAAAAATTACCA-TTTTACCCTCG-AGTGTC
*
5609 CCAAAATTACCATTTTACCCTCGAGTGTC
1 CAAAAATTACCATTTTACCCTCGAGTGTC
* *
5638 CAAAAATTACCATTTTGCCCTCGAGTATC
1 CAAAAATTACCATTTTACCCTCGAGTGTC
*
5667 CAAAAATCA-CATTTT
1 CAAAAATTACCATTTT
5682 CAAACCCCGA
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
27 2 0.02
28 23 0.27
29 41 0.48
30 17 0.20
31 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAGTGTC
Found at i:17335 original size:48 final size:49
Alignment explanation
Indices: 17231--17343 Score: 167
Period size: 49 Copynumber: 2.3 Consensus size: 49
17221 GCTGCAGCTC
* * **
17231 TCAGCACCACGAA-ACATGAAGGGAAAGATCTAAGCCGTAACGGCGGAT
1 TCAGTACCACGAAGACATGAAGGAAAAGATCTAAGCCGTAACAACGGAT
*
17279 TCAGTACCATGAAGACATGAAGGAAAAGATCTAAGCCGTAACAACGGA-
1 TCAGTACCACGAAGACATGAAGGAAAAGATCTAAGCCGTAACAACGGAT
17327 TCAGTACCACGAAGACA
1 TCAGTACCACGAAGACA
17344 CAAGGGAAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 27 0.47
49 31 0.53
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (49 bp):
TCAGTACCACGAAGACATGAAGGAAAAGATCTAAGCCGTAACAACGGAT
Found at i:17403 original size:13 final size:13
Alignment explanation
Indices: 17385--17413 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17375 TAGTACCTCA
17385 GAAGACGTGAAGG
1 GAAGACGTGAAGG
17398 GAAGACGTGAAGG
1 GAAGACGTGAAGG
17411 GAA
1 GAA
17414 AGATCTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.45, T:0.07
Consensus pattern (13 bp):
GAAGACGTGAAGG
Found at i:17493 original size:111 final size:108
Alignment explanation
Indices: 17289--17506 Score: 310
Period size: 111 Copynumber: 2.0 Consensus size: 108
17279 TCAGTACCAT
** *
17289 GAAGACATGAAGGAAAAGATCTAAGCCGTAACAACGGATCAGTACCACGAAGACACAAGGGAAGG
1 GAAGACATGAAGGAAAAGATCTAAGCCACAACAACGGATCAGTACCACAAAGACACAAGGGAAGG
* * *
17354 TTTAAGTTGCAATGGCGAACCTAGTACCTCAGAAGACGTGAAGG
66 TTTAAGTCGCAATGGCAAACCTAGTACCTCAG-AGACATGAAGG
* * ** *
17398 GAAGACGTGAAGGGAAAGATCTAAGCCACAACGGCGGATCCAGTACCACAAAGACACCAGGGAAA
1 GAAGACATGAAGGAAAAGATCTAAGCCACAACAACGGAT-CAGTACCACAAAGACACAAGGG-AA
17463 GGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAG
64 GGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAG
17507 AGAAAGATCT
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
109 33 0.34
110 29 0.30
111 34 0.35
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (108 bp):
GAAGACATGAAGGAAAAGATCTAAGCCACAACAACGGATCAGTACCACAAAGACACAAGGGAAGG
TTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAGG
Found at i:17569 original size:57 final size:57
Alignment explanation
Indices: 17497--17711 Score: 266
Period size: 57 Copynumber: 3.9 Consensus size: 57
17487 AGTACCTCAG
* * *
17497 AGACATGAAGAGAAAGATCTAAGCCGCAACGGTGGATTCAGTACCGCAAAGATACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACGA
* * *
17554 AGACATGAAGGGAAAGATCTAAGCTGCAATGGCGGATCTAGTACCGCAAAGATACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACGA
* * *
17611 GGACATGAAGGGATAGATTTAAGCCGCAACGGCGGATCCAGTA-C-C------ACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACGA
* * *
17660 AGACATGAAGGGAAAAATCTAAGCCGCAATGGCGGATCCAATACCGCAAAGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGA
17712 CACAAAGGGA
Statistics
Matches: 133, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
49 41 0.31
50 1 0.01
51 1 0.01
55 1 0.01
56 1 0.01
57 88 0.66
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (57 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACGA
Found at i:17737 original size:49 final size:49
Alignment explanation
Indices: 17618--17739 Score: 145
Period size: 49 Copynumber: 2.5 Consensus size: 49
17608 CGAGGACATG
* * * **
17618 AAGGGATAGATTTAAGCCGCAACGGCGGATCCAGTACCACGAAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGGATCCAATACCACAAAGACACA
* * * *
17667 AAGGGAAAAATCTAAGCCGCAATGGCGGATCCAATACCGCAAAGACACA
1 AAGGGAAAGATTTAAGCCGCAACGGCGGATCCAATACCACAAAGACACA
* *
17716 AAGGGAAAGGTTTAAGTCGCAACG
1 AAGGGAAAGATTTAAGCCGCAACG
17740 ACAAACCTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.13
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGGATCCAATACCACAAAGACACA
Found at i:18249 original size:6 final size:6
Alignment explanation
Indices: 18240--18360 Score: 99
Period size: 6 Copynumber: 20.7 Consensus size: 6
18230 GATTTATTTC
* * **
18240 TAAATT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** * *
18287 TAAATT T-GTTT TAAATT TAAATT T-AGTT TAAATT TGAAA-- TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
* *
18332 TAAACT TAAATTT TAAAAT TAAATT TAAA
1 TAAATT TAAA-TT TAAATT TAAATT TAAA
18361 GTCCATTTAC
Statistics
Matches: 88, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
4 2 0.02
5 12 0.14
6 66 0.75
7 8 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:18262 original size:17 final size:17
Alignment explanation
Indices: 18261--18344 Score: 98
Period size: 17 Copynumber: 4.9 Consensus size: 17
18251 TTACTTTAAA
*
18261 TTTAAATTTAAATTCATT
1 TTTAAATTTAAATTTA-T
*
18279 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTAT
*
18296 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
18313 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
18330 TTTAAACTTAAATTT
1 TTTAAATTTAAATTT
18345 TAAAATTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 3 0.05
17 36 0.64
18 17 0.30
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:18300 original size:41 final size:41
Alignment explanation
Indices: 18226--18311 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
18216 TTAGATTAGT
* *
18226 TTTAGATTTATTTCTAAATTTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
* **
18267 TTTAAATTCATTTTTAAATTTAAATTTGTTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
18308 TTTA
1 TTTA
18312 GTTTAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
Found at i:18345 original size:13 final size:13
Alignment explanation
Indices: 18327--18357 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18317 AATTTGAAAT
*
18327 AATTTTAAACTTA
1 AATTTTAAAATTA
18340 AATTTTAAAATTA
1 AATTTTAAAATTA
18353 AATTT
1 AATTT
18358 AAAGTCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTAAAATTA
Found at i:19144 original size:28 final size:28
Alignment explanation
Indices: 19112--19175 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
19102 TCATTAACAT
* *
19112 TAATATTAAT-TACAATATTAATAATAAA
1 TAATATTAATAAACAACATTAATAAT-AA
* *
19140 TAATATTACTAAATAACATTAATAATAA
1 TAATATTAATAAACAACATTAATAATAA
19168 TAATATTA
1 TAATATTA
19176 TTATTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (28 bp):
TAATATTAATAAACAACATTAATAATAA
Found at i:19152 original size:13 final size:13
Alignment explanation
Indices: 19112--19237 Score: 58
Period size: 13 Copynumber: 9.2 Consensus size: 13
19102 TCATTAACAT
19112 TAATATTAATTACAA
1 TAATATTAA-TA-AA
* *
19127 TATTAATAATAAA
1 TAATATTAATAAA
*
19140 TAATATTACTAAA
1 TAATATTAATAAA
*
19153 TAACATTAATAATAA
1 TAATATTAAT-A-AA
* *
19168 TAATATT-ATTAT
1 TAATATTAATAAA
*
19180 TATTATTAATAACA
1 TAATATTAATAA-A
* * *
19194 GTAATAATGAATTTAT
1 -TAAT-ATTAA-TAAA
*
19210 TAATAATAATAAA
1 TAATATTAATAAA
*
19223 TAATA-TAACAAA
1 TAATATTAATAAA
19235 TAA
1 TAA
19238 AATCGAATAA
Statistics
Matches: 82, Mismatches: 22, Indels: 17
0.68 0.18 0.14
Matches are distributed among these distances:
12 16 0.20
13 30 0.37
14 8 0.10
15 22 0.27
16 4 0.05
17 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (13 bp):
TAATATTAATAAA
Found at i:20283 original size:59 final size:57
Alignment explanation
Indices: 20196--20522 Score: 261
Period size: 59 Copynumber: 5.6 Consensus size: 57
20186 TTATACTTTG
* ** *
20196 ACCCTCAAACTTCTCTAAAATTATATTTTTAACCCTAAACTTTTTGAAAAATTA-CATTTT
1 ACCCTCAAACTTC-CAAAAATTCCATTTTTAACCCT-GA-TTTTT-AAAAATTACCATTTT
* * * * * *
20256 ACCC-CTAAACTTTCC-AAAATTCCATTTTTGACCCCGATTTATCCAAAATTTACCAATTA
1 ACCCTC-AAAC-TTCCAAAAATTCCATTTTTAACCCTGATTT-T-TAAAAATTACCATTTT
*
20315 ACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTGATTTTCCTAAAAATTACCATTTT
1 ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGATTTT--TAAAAATTACCATTTT
* * ** * *
20374 ACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCGATTCTTCCCAAAATTACTAGTTT
1 ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGATT-TT-TAAAAATTACCATTTT
* * * * *
20433 ACTCTCAAACTTCCAAAAATTTCATTTTTTATCTTGATTTTTTCAAAAA-TACCATTTT
1 ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGA-TTTTT-AAAAATTACCATTTT
* *
20491 ACCCCCAAA-TGT-CTAAAATTCCATTTTTAACC
1 ACCCTCAAACT-TCCAAAAATTCCATTTTTAACC
20523 TCGAACTTTC
Statistics
Matches: 217, Mismatches: 38, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
57 20 0.09
58 29 0.13
59 151 0.70
60 14 0.06
61 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (57 bp):
ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGATTTTTAAAAATTACCATTTT
Found at i:20300 original size:29 final size:29
Alignment explanation
Indices: 20266--20424 Score: 139
Period size: 30 Copynumber: 5.4 Consensus size: 29
20256 ACCCCTAAAC
*
20266 TTTCC-AAAATTCCATTTTTGACCCCGAT
1 TTTCCAAAAATTCCATTTTTAACCCCGAT
* * *
20294 TTATCCAAAATTTACCA--ATTAACCCTCGAA
1 TT-TCCAAAAATT-CCATTTTTAACCC-CGAT
* *
20324 CTTCCAAAAATTCCATTTTTAACCCTGAT
1 TTTCCAAAAATTCCATTTTTAACCCCGAT
*
20353 TTTCCTAAAAATTACCA-TTTT-ACCCTCGAA
1 TTTCC-AAAAATT-CCATTTTTAACCC-CGAT
*
20383 CTTCCAAAAATTCCATTTTTAACCCCGAT
1 TTTCCAAAAATTCCATTTTTAACCCCGAT
*
20412 TCTTCCCAAAATT
1 T-TTCCAAAAATT
20425 ACTAGTTTAC
Statistics
Matches: 103, Mismatches: 16, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
28 8 0.08
29 42 0.41
30 47 0.46
31 6 0.06
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTCCAAAAATTCCATTTTTAACCCCGAT
Found at i:20346 original size:30 final size:30
Alignment explanation
Indices: 20312--20461 Score: 141
Period size: 30 Copynumber: 5.1 Consensus size: 30
20302 AATTTACCAA
20312 TTAACCCTCGAACTTCCAAAAATTCCATTT
1 TTAACCCTCGAACTTCCAAAAATTCCATTT
**
20342 TTAACCCT-GATTTTCCTAAAAATTACCA-TT
1 TTAACCCTCGAACTTCC-AAAAATT-CCATTT
20372 TT-ACCCTCGAACTTCCAAAAATTCCATTT
1 TTAACCCTCGAACTTCCAAAAATTCCATTT
* * * *
20401 TTAACCC-CGATTCTTCCCAAAATTAC-TAGT
1 TTAACCCTCGA-ACTTCCAAAAATTCCAT-TT
* * *
20431 TT-ACTCTCAAACTTCCAAAAATTTCATTT
1 TTAACCCTCGAACTTCCAAAAATTCCATTT
20460 TT
1 TT
20462 TATCTTGATT
Statistics
Matches: 97, Mismatches: 14, Indels: 19
0.75 0.11 0.15
Matches are distributed among these distances:
28 3 0.03
29 44 0.45
30 47 0.48
31 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.37
Consensus pattern (30 bp):
TTAACCCTCGAACTTCCAAAAATTCCATTT
Found at i:20393 original size:118 final size:118
Alignment explanation
Indices: 20196--20542 Score: 345
Period size: 118 Copynumber: 2.9 Consensus size: 118
20186 TTATACTTTG
* ** * *
20196 ACCCTCAAACTTCTCTAAAATTATATTTTTAACCCTAAACTTTT-TGAAAAATTA-CATTTTACC
1 ACCCTCAAACTTC-CAAAAATTCCATTTTTAACCCT-GA-TTTTCTCAAAAATTACCATTTTACC
*
20259 CCTAAACTTTCCAAAATTCCATTTTTGACCCCGATT-TAT-CCAAAATTTACCAATTA
63 CCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTCT-TCCCAAAA-TTACCAATTA
*
20315 ACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTGATTTTC-CTAAAAATTACCATTTTA-CCC
1 ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGATTTTCTC-AAAAATTACCATTTTACCCC
* * * *
20378 TCGAAC-TTCCAAAAATTCCATTTTTAACCCCGATTCTTCCCAAAATTACTAGTTT
65 T-AAACTTTCC-AAAATTCCATTTTTAACCCCGATTCTTCCCAAAATTACCAATTA
* * * * * * *
20433 ACTCTCAAACTTCCAAAAATTTCATTTTTTATCTTGATTTTTTCAAAAA-TACCATTTTACCCCC
1 ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGATTTTCTCAAAAATTACCATTTTACCCCT
* * * *
20497 AAA-TGTCTAAAATTCCATTTTTAACCTCGA-ACTTTCCCAAAATTAC
66 AAACTTTCCAAAATTCCATTTTTAACCCCGATTC-TTCCCAAAATTAC
20543 TATTTTGCCC
Statistics
Matches: 193, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
115 1 0.01
116 38 0.20
117 31 0.16
118 103 0.53
119 20 0.10
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.37
Consensus pattern (118 bp):
ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGATTTTCTCAAAAATTACCATTTTACCCCT
AAACTTTCCAAAATTCCATTTTTAACCCCGATTCTTCCCAAAATTACCAATTA
Found at i:23162 original size:792 final size:794
Alignment explanation
Indices: 21615--23167 Score: 1881
Period size: 792 Copynumber: 2.0 Consensus size: 794
21605 TTATACCGCA
* * * * *
21615 GTTTCAAATTAATAAAAAAATATTTTTTTTCTAAAATAGTTGGATTACAGGGTGGTTAGACCCTT
1 GTTTCAAATGAAT-AAAAAATATATTTTTTCTAAAATAGTCGGATTACAGGGTGGTCAAACCCTT
*
21680 ACCTAGCTGTCAATTGAAACATCAATTGCGCAAAAAAATTCAAATTTTAATATTTTTTATGTGAT
65 ACCTAGCTGTCAATTGAAACATCAATTGCGCAAAAAAATTCAAATTTTAATATTTTTTATCTGAT
* * * *
21745 CTTCTCCCTTCAGTCCATCAAATCCAGTGCCCAACAACATCACGTCACATGACACTTTAATAAAT
130 CTACTCCCTTCAGTCCATCAAACCCAGTCCCCAACAACAGCACGTCACATGACACTTTAATAAAT
* * * *
21810 TCTTTTTGTCTGAAATTGACTCTCAGGTGACAGTTTCAAACTTCGATATTTTAAAATTGAAAATA
195 TCTTTTTGTCTGAAATTGACTCTCAGGAGACAGTTACAAACTTCGAGATTCTAAAATTGAAAATA
* * *
21875 AAATTACGAAAGTATCCAATGTAAATCTATATGATTGTCACCTTCATCTCTCCCACAAAAATATT
260 AAATTACGAAAATATCCAATGTAAATCTATATGACTGTCACCTCCATCTCTCCCACAAAAATATT
* *
21940 CTCACAATTTCTTCTCTATTTAAACTACTCTCCATTTTGTTGAAGTAAGTTTGCTTTTCTTAGCT
325 CTCACAATTTCTTCTCTATTTAAACCACTCTCCATTTTGTTAAAGTAAGTTTGCTTTTCTTAGCT
*
22005 TTTTTTAAATATATTTTTTAATTTAGTTAATTTTCACTATCAAAGGCAATAATATTATTTGAATG
390 TTTTTTAAATATATTTTTTAATTTAGTTAAGTTTCACTATCAAAGGCAATAATATTATTTGAATG
* * *
22070 CAATTGTTATATTTTTCGTTATTTTTTTGAATGTGCAGGTAGGTATGAGAAGATAGATCGTAAAT
455 CAATTATTATATTTTTCGTTATTTTTTTGAAGGTGCAGGTAGGTAAGAGAAGATAGATCGTAAAT
* * * * *
22135 TCAATGTTTTGGCCCATTACAATGGACAAATTCACTGTATCAAAGAAACCAATTTGAATGATAGT
520 TCAATGTTGTGACCCATTACAATGGACAAACTCACTATATCAAAGAAACCAATTTGAATGACAGT
* *
22200 AAATAAAAGTGAAGGGACTAAATCCACACAAATCAATAAATACAAGGACTATTCTCAAAATTTAA
585 AAATAAAAATGAAGGGACCAAATCCACACAAATCAATAAATACAAGGACTATTCTCAAAATTTAA
*
22265 CAAAAAATAATATTTGTTTCACTCGAATCTGACACGCGGCGATCTTAATATAATATAATAATAAT
650 CAAAAAATAATATTTATTTCACTCGAATCTGACACGCGGCGATCTTAATATAATATAATAATAAT
* * * * * *
22330 TCTTTTATTTTGAATCTATCATGTTATGCGTCTGTTTCAAGATATATAAAAAAAGTTATTTCTAA
715 TCATATATTTTGAAACTACCATCTTATGCGGCTGTTTCAAGATATATAAAAAAAGTTATTTCTAA
22395 AAGTGCCCCTTCATG
780 AAGTGCCCCTTCATG
*
22410 GTTTCAAATGAAT-AAAAATATATTTTTTCTAAAATAGCTCGG-TTA-GGGGTGGTCAAACCCTT
1 GTTTCAAATGAATAAAAAATATATTTTTTCTAAAATAG-TCGGATTACAGGGTGGTCAAACCCTT
* * * * *
22472 ACCTAGCTTTCAATTGAAACATCCATTGGGCAAAAAATTTTCAAATTTTGAA-CTTTTTTATCCT
65 ACCTAGCTGTCAATTGAAACATCAATTGCGCAAAAAA-ATTCAAATTTT-AATATTTTTTAT-CT
* * * * *
22536 -ATCTACTCCCTTC-TTTCATCAAACCCCTGTCCCCAACAATAGCACGTCACATGACATTTTAAT
127 GATCTACTCCCTTCAGTCCATCAAA-CCCAGTCCCCAACAACAGCACGTCACATGACACTTTAAT
* * * *
22599 GAA-T-TTTTT-T-TGAAATTGACATGTCAGGAGGC-GATTACAAATTTCGAGAGTTCTAAAATT
191 AAATTCTTTTTGTCTGAAATTGAC-TCTCAGGAGACAG-TTACAAACTTCGAGA-TTCTAAAATT
* * * * *
22659 GAAAATATAATTATGAAAATA-CCGAATGT-AATCTATGTGACTGTCACCTCCATTTTTCCCACA
253 GAAAATAAAATTACGAAAATATCC-AATGTAAATCTATATGACTGTCACCTCCATCTCTCCCACA
*
22722 AAAATATTCTCACAATTTCTTCTCTATTTAAACCACTCTCCGTTTTGTTAAAGTAAGTTTGCTTT
317 AAAATATTCTCACAATTTCTTCTCTATTTAAACCACTCTCCATTTTGTTAAAGTAAGTTTGCTTT
* * * ** *
22787 TCTTAGTTTTTTTTTTAAT-TATTTTCTTAATTTAGTTAAGTTTCACTATCAATGGGGATAATGT
382 TCTTAG-CTTTTTTTAAATATATTTT-TTAATTTAGTTAAGTTTCACTATCAAAGGCAATAATAT
** * * * * * * **
22851 TATTTGTTTGCAATTATTATATTTTTTTGTTTTTTTTTTTAAGGTGCGGGTTGTTAAGCTAAGAT
445 TATTTGAATGCAATTATTATA-TTTTTCGTTATTTTTTTGAAGGTGCAGGTAGGTAAGAGAAGAT
** * *
22916 -GAATCGTAAATTTGATGTTGTGACCCATTACAATGGACAAACTCATTATATCAAAGACACCAAT
509 AG-ATCGTAAATTCAATGTTGTGACCCATTACAATGGACAAACTCACTATATCAAAGAAACCAAT
* ** *
22980 TTGAATGCAACCAGTAAATAAAAAT-AGAGGGACCAAATCTATGCAAATCAATAAGTACAAGGAC
573 TTGAATG--A-CAGTAAATAAAAATGA-AGGGACCAAATCCACACAAATCAATAAATACAAGGAC
* ** ** * * * * * * *
23044 TATTCTTAGTATTTAACCTAAGATAATATTTATTTCACTTGACTCTGACACGTGGTGTTCTTGAT
634 TATTCTCAAAATTTAACAAAAAATAATATTTATTTCACTCGAATCTGACACGCGGCGATCTTAAT
* * * *
23109 -T--T-TAAAAATAATAT-ATATATTTTTAAGACTGCCATCTTATGTGGC-GTTTTCAAGATATA
699 ATAATATAATAATAAT-TCATATATTTTGAA-ACTACCATCTTATGCGGCTG-TTTCAAGATATA
23168 AAATAATTTT
Statistics
Matches: 640, Mismatches: 98, Indels: 43
0.82 0.13 0.06
Matches are distributed among these distances:
789 11 0.02
790 126 0.20
791 118 0.18
792 177 0.28
793 91 0.14
794 9 0.01
795 108 0.17
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (794 bp):
GTTTCAAATGAATAAAAAATATATTTTTTCTAAAATAGTCGGATTACAGGGTGGTCAAACCCTTA
CCTAGCTGTCAATTGAAACATCAATTGCGCAAAAAAATTCAAATTTTAATATTTTTTATCTGATC
TACTCCCTTCAGTCCATCAAACCCAGTCCCCAACAACAGCACGTCACATGACACTTTAATAAATT
CTTTTTGTCTGAAATTGACTCTCAGGAGACAGTTACAAACTTCGAGATTCTAAAATTGAAAATAA
AATTACGAAAATATCCAATGTAAATCTATATGACTGTCACCTCCATCTCTCCCACAAAAATATTC
TCACAATTTCTTCTCTATTTAAACCACTCTCCATTTTGTTAAAGTAAGTTTGCTTTTCTTAGCTT
TTTTTAAATATATTTTTTAATTTAGTTAAGTTTCACTATCAAAGGCAATAATATTATTTGAATGC
AATTATTATATTTTTCGTTATTTTTTTGAAGGTGCAGGTAGGTAAGAGAAGATAGATCGTAAATT
CAATGTTGTGACCCATTACAATGGACAAACTCACTATATCAAAGAAACCAATTTGAATGACAGTA
AATAAAAATGAAGGGACCAAATCCACACAAATCAATAAATACAAGGACTATTCTCAAAATTTAAC
AAAAAATAATATTTATTTCACTCGAATCTGACACGCGGCGATCTTAATATAATATAATAATAATT
CATATATTTTGAAACTACCATCTTATGCGGCTGTTTCAAGATATATAAAAAAAGTTATTTCTAAA
AGTGCCCCTTCATG
Found at i:29588 original size:88 final size:88
Alignment explanation
Indices: 29419--29774 Score: 333
Period size: 88 Copynumber: 4.1 Consensus size: 88
29409 AGTCAAAACT
* * * * *
29419 GTAATTTTTGGATG-TCGGGGGCAAAATGGTAATTTTTGGATACTTGAAGG-T-AAAATGGTAAT
1 GTAATTTTTGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAAT-GTAAT
** * *
29481 TTTTGGATGTTTGAGGGTAAAATA
65 TTTTGGACATTCGAGGGTAAAATG
* *
29505 ATAATTTTTGGATGTTCAGGGGTAAAATGGTACTTTTTGGAAAGTTCAAGGTTAAAAATGTAATT
1 GTAATTTTTGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAATGTAATT
*
29570 TTTAGACATTCGAGGGTAAAATG
66 TTTGGACATTCGAGGGTAAAATG
* * * * *** *
29593 GTAATTTATGGATGTTTAGGGGTAAAATGGCAATTTTTGGAAAATTTGGGGTCAAAAATGTAATT
1 GTAATTTTTGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAATGTAATT
29658 TTTGGACA-TCTG-GTGGTAAAATG
66 TTTGGACATTC-GAG-GGTAAAATG
* ** *
29681 GTAA-TTTTGGATGTT--TGGGTAAAATGGTAATTTTT-G-AAGTTCAAGGGCAAAAA-G-GATT
1 GTAATTTTTGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAATGTAATT
* *
29739 TTTGGAAAGTTCGAGGTTAAAAAT-
66 TTTGGACA-TTCGAGGGT-AAAATG
*
29763 GTGATTTTTGGA
1 GTAATTTTTGGA
29775 CATCCGATGG
Statistics
Matches: 225, Mismatches: 35, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
81 10 0.04
82 7 0.03
83 27 0.12
84 1 0.00
85 18 0.08
86 13 0.06
87 43 0.19
88 101 0.45
89 5 0.02
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (88 bp):
GTAATTTTTGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAATGTAATT
TTTGGACATTCGAGGGTAAAATG
Found at i:29748 original size:28 final size:30
Alignment explanation
Indices: 29701--29774 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 30
29691 ATGTTTGGGT
*
29701 AAAATGGTAATTTTT-G-AAGTTCAAGGGCA
1 AAAAT-GTGATTTTTGGAAAGTTCAAGGGCA
* **
29730 AAAA-G-GATTTTTGGAAAGTTCGAGGTTA
1 AAAATGTGATTTTTGGAAAGTTCAAGGGCA
29758 AAAATGTGATTTTTGGA
1 AAAATGTGATTTTTGGA
29775 CATCCGATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.16
27 2 0.05
28 14 0.38
29 5 0.14
30 10 0.27
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATGTGATTTTTGGAAAGTTCAAGGGCA
Found at i:29762 original size:111 final size:114
Alignment explanation
Indices: 29559--29829 Score: 325
Period size: 111 Copynumber: 2.4 Consensus size: 114
29549 TTCAAGGTTA
* ** * * * * * *
29559 AAAAT-GTAATTTTTAGACATTCGAGGGTAAAATGGTAATTTATGGATGTTTAGGGGTAAAATGG
1 AAAATGGTAATTTTTGGATGTTCG-GGGTAAAATGGTAATTT-TTGAAGTTCAAGGGCAAAAAGG
* * * *
29623 CAATTTTTGGAAAATTTGGGGTCAAAAATGTAATTTTTGGACATCTGGTGGT
64 -AATTTTTGGAAAATTCGAGGTCAAAAATGTAATTTTTGGACATCCGATGGT
*
29675 AAAATGGTAA-TTTTGGATGTT-TGGGTAAAATGGTAATTTTTGAAGTTCAAGGGCAAAAAGG-A
1 AAAATGGTAATTTTTGGATGTTCGGGGTAAAATGGTAATTTTTGAAGTTCAAGGGCAAAAAGGAA
* * *
29737 TTTTTGGAAAGTTCGAGGTTAAAAATGTGATTTTTGGACATCCGATGGT
66 TTTTTGGAAAATTCGAGGTCAAAAATGTAATTTTTGGACATCCGATGGT
*
29786 AAAATTGTAATTTTTGGATGTTCGGGGTAAAATGGTAATTTTTG
1 AAAATGGTAATTTTTGGATGTTCGGGGTAAAATGGTAATTTTTG
29830 GAAAGTTCGG
Statistics
Matches: 133, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
111 52 0.39
112 11 0.08
113 36 0.27
114 17 0.13
116 13 0.10
117 4 0.03
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (114 bp):
AAAATGGTAATTTTTGGATGTTCGGGGTAAAATGGTAATTTTTGAAGTTCAAGGGCAAAAAGGAA
TTTTTGGAAAATTCGAGGTCAAAAATGTAATTTTTGGACATCCGATGGT
Found at i:29771 original size:30 final size:30
Alignment explanation
Indices: 29441--29951 Score: 210
Period size: 29 Copynumber: 17.6 Consensus size: 30
29431 TGTCGGGGGC
* * *
29441 AAAATGGTAATTTTTGGATACTT-GAAGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTA
* *
29470 AAAATGGTAATTTTTGG-ATGTTTGAGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTA
* *
29499 AAAATAATAATTTTTGG-ATGTTC-AGGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGA-GGGTA
* * *
29528 AAAATGGTACTTTTTGGAAAGTTCAAGGTTA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTA
* *
29559 AAAATGTAATTTTTAGACA-TTCGAGGGT-
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
* * *
29587 AAAATGGTAATTTATGG-ATGTT-TAGGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGA-GGGTA
* * *
29616 AAAATGGCAATTTTTGGAAAATTTG-GGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGT-A
*
29647 AAAATGTAATTTTTGGACA--TCTG-GTGGT-
1 AAAATGTAATTTTTGGAAAGTTC-GAG-GGTA
* *
29675 AAAATGGTAA-TTTTGG-ATGTT--TGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTA
* *
29701 AAAATGGTAATTTTT-G-AAGTTCAAGGGCA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTA
* *
29730 AAAA-G-GATTTTTGGAAAGTTCGAGGTTA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
* * * *
29758 AAAATGTGATTTTTGGACA-TCCGATGGTA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
* *
29787 AAATTGTAATTTTTGG-ATGTTCG-GGGT-
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
**
29814 AAAATGGTAATTTTTGGAAAGTTCG-GTATCA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGT-A
* * **
29845 AAAATTTGA-TTTTGGAAAAGTTCGAGATTA
1 AAAATGTAATTTTTGG-AAAGTTCGAGGGTA
** * * *
29875 AAACGGTAA-TTTTAG-AAGTTTAGGGGGTA
1 AAAATGTAATTTTTGGAAAG-TTCGAGGGTA
*
29904 AAAATGTAATTTTT-GAGAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGA-AAGTTCGAGGGTA
**
29934 AAAATGTTTTTTTTGGAA
1 AAAATGTAATTTTTGGAA
29952 TGTTTGGGGT
Statistics
Matches: 371, Mismatches: 73, Indels: 75
0.71 0.14 0.14
Matches are distributed among these distances:
26 24 0.06
27 11 0.03
28 55 0.15
29 165 0.44
30 93 0.25
31 23 0.06
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGAGGGTA
Found at i:29814 original size:28 final size:28
Alignment explanation
Indices: 29419--29831 Score: 263
Period size: 29 Copynumber: 14.4 Consensus size: 28
29409 AGTCAAAACT
*
29419 GTAATTTTTGGATG-TCGGGGGCAAAATG
1 GTAATTTTTGGATGTTC-GGGGTAAAATG
* *
29447 GTAATTTTTGGATACTT-GAAGGTAAAATG
1 GTAATTTTTGGAT-GTTCG-GGGTAAAATG
* *
29476 GTAATTTTTGGATGTTTGAGGGTAAAATA
1 GTAATTTTTGGATGTTCG-GGGTAAAATG
*
29505 ATAATTTTTGGATGTTCAGGGGTAAAATG
1 GTAATTTTTGGATGTTC-GGGGTAAAATG
* * * *
29534 GTACTTTTTGGAAAGTTCAAGGTTAAAAAT-
1 GTAATTTTTGG-ATGTTC-GGGGT-AAAATG
* **
29564 GTAATTTTTAGACATTCGAGGGTAAAATG
1 GTAATTTTTGGATGTTCG-GGGTAAAATG
* *
29593 GTAATTTATGGATGTTTAGGGGTAAAATG
1 GTAATTTTTGGATG-TTCGGGGTAAAATG
* ** *
29622 GCAATTTTTGGAAAATTTGGGGTCAAAAAT-
1 GTAATTTTTGG-ATGTTCGGGGT--AAAATG
**
29652 GTAATTTTTGGA-CATCTGGTGGTAAAATG
1 GTAATTTTTGGATGTTC-GG-GGTAAAATG
*
29681 GTAA-TTTTGGATGTT-TGGGTAAAATG
1 GTAATTTTTGGATGTTCGGGGTAAAATG
* * * *
29707 GTAATTTTT-GAAGTTCAAGGGCAAAAAG
1 GTAATTTTTGGATGTTC-GGGGTAAAATG
* *
29735 G--ATTTTTGGAAAGTTCGAGGTTAAAAAT-
1 GTAATTTTTGG-ATGTTCG-GGGT-AAAATG
* ** * * *
29763 GTGATTTTTGGACATCCGATGGTAAAATT
1 GTAATTTTTGGATGTTCG-GGGTAAAATG
29792 GTAATTTTTGGATGTTCGGGGTAAAATG
1 GTAATTTTTGGATGTTCGGGGTAAAATG
29820 GTAATTTTTGGA
1 GTAATTTTTGGA
29832 AAGTTCGGTA
Statistics
Matches: 302, Mismatches: 56, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
26 24 0.08
27 6 0.02
28 77 0.25
29 140 0.46
30 45 0.15
31 10 0.03
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (28 bp):
GTAATTTTTGGATGTTCGGGGTAAAATG
Found at i:31608 original size:17 final size:17
Alignment explanation
Indices: 31588--31678 Score: 83
Period size: 17 Copynumber: 5.4 Consensus size: 17
31578 AATTTTTAAT
31588 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
31605 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * * **
31622 TGAACTTAAATTCAACG
1 TAAATTTAAATTTAAAA
* * *
31639 TAATTTTAAATTTATAC
1 TAAATTTAAATTTAAAA
* *
31656 TAAATTCAAACTTAAAA
1 TAAATTTAAATTTAAAA
31673 TAAATT
1 TAAATT
31679 AAAAATGGGT
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:32403 original size:209 final size:209
Alignment explanation
Indices: 32043--32963 Score: 1170
Period size: 209 Copynumber: 4.4 Consensus size: 209
32033 TAAGAAAACA
* * * * * * *
32043 GATTTGGTTCACTTCTTTGCATCTCGTTAGGAAGATGACCACTTTATTGCTTCGACCTACTTCTC
1 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTC
* * * * *
32108 TGTATCTCATTAGGAAGCTGAGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGAATTGA
66 AGTATCTCATAAAGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGA
32173 TATACTTCTCTATATCTCATCAGGAAGATGA-TCGCCTCACTTGTTTTAATCCACTTCTCTGTAT
131 TATACTTCTCTATATCTCATCAGGAAGATGACT-GCCTCACTTGTTTTAATCCACTTCTCTGTAT
32237 CTCATCAGGAAGACG
195 CTCATCAGGAAGACG
*
32252 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACTTGCTTCTC
1 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTC
* * * * *
32317 AGTATCTCATCAAGAAGATAGGGTTCGAAGTTTCGCTCACATTGAGTTTTGTTTCATTGATTTGG
66 AGTATCTCATAAAGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGA
* * * ** ***
32382 TATACTTCTCTGTGTCTCATCAAGAAGATGACTGCCTCACTTGTTACAATTTGCTTCTCTGTATC
131 TATACTTCTCTATATCTCATCAGGAAGATGACTGCCTCACTTGTTTTAATCCACTTCTCTGTATC
*
32447 TCATCAGAAAGACG
196 TCATCAGGAAGACG
* * * * *
32461 AATTTGGTCCACTTCTCTGTATCTTATCAGGAAGACGACCATTTTACTGCTTCGACCTGCTTCTT
1 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTC
* * *
32526 AGTACCTCATTAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGA
66 AGTATCTCATAAAGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGA
* * *
32591 TATACTTCTCTATATCTCATCAGGAAGATGAACAT--CTCACTCGTTTTAATTCGCTTCTCTGTA
131 TATACTTCTCTATATCTCATCAGGAAGATG-AC-TGCCTCACTTGTTTTAATCCACTTCTCTGTA
32654 TCTCATCAGGAAGAC-
194 TCTCATCAGGAAGACG
* * *
32669 GATTTTGGTCCACTTATCTATATCTCATCAGGAAG-CTGACCATTTTATTGCTTCGACCTGCTTC
1 GA-TTTGGTTCACTTCTCTGTATCTCATCAGGAAGAC-GACCATTTTATTGCTTCGACCTGCTTC
* * * *
32733 TCAATATCTTATAAAGTAGCTGGGGTTCGATGTTTCGCTCACATTGAGCTTTGTTTCATTGATTT
64 TCAGTATCTCATAAAGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTT
* * * * ** * *
32798 GGTCTACTTCTCAATATCTCTTCAGGAAGATGACTGCCT-TGTTGTTTTGATCCACTTTTCTGTA
129 GATATACTTCTCTATATCTCATCAGGAAGATGACTGCCTCACTTGTTTTAATCCACTTCTCTGTA
32862 TCTCATCAGGAAGACG
194 TCTCATCAGGAAGACG
* * * * *** ***
32878 AATCTGGTTTACTTCTCTGTATCTCATTAGGAAGGTAACTGCTTTATTGCTTCGACCTGCTTCTC
1 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTC
* *
32943 AGTATCTTATAAAGAATCTGG
66 AGTATCTCATAAAGAAGCTGG
32964 TTTAATGTCG
Statistics
Matches: 617, Mismatches: 86, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
207 1 0.00
208 106 0.17
209 506 0.82
210 3 0.00
211 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (209 bp):
GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTGCTTCTC
AGTATCTCATAAAGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGA
TATACTTCTCTATATCTCATCAGGAAGATGACTGCCTCACTTGTTTTAATCCACTTCTCTGTATC
TCATCAGGAAGACG
Found at i:33282 original size:49 final size:50
Alignment explanation
Indices: 33154--33536 Score: 253
Period size: 49 Copynumber: 7.8 Consensus size: 50
33144 TTATTTTTTA
* * ** *
33154 AGGTACCGGGTTCGCCGTTGTGGCCTCAAATTTTCCCGTCACATCTTC-T
1 AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
* * * * * ** * *
33203 AAAGAACCGGGTTTGCTGTTGCAACCTCAACCCTTCCCTTCAAATCTTCAT
1 -AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
* *
33254 -GGTACCCGGTTCCCCGTTGCGGCCTCAACCTTT-CCTATCACAT-TTCAT
1 AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCT-TCACATCTTCAT
** * * * * *
33302 -GGTACCAAATTTGTCGTTGCGGCCTTAATCTTTCCCATCACAT-TTC-T
1 AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
* * * *
33349 GAGGTACCAGGTTCGCCGTAGCGACATCAACCTTTCCCTTCAAATCTTCAT
1 -AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
** * * * * *
33400 -GGTACTGGGTTTGTCGTTGCGACCTCAACCTTTCCCGTCACATCTTCTT
1 AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
* * * * * * *
33449 AGGTAAC-GAGTTCACCGTTACGGCCTTAACCTTTCCCATCACTTCTTCTT
1 AGGTACCAG-GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
* * * * *
33499 AGGTACCGGGTTTGCCATTGCAGCCTCAACCCTTCCCT
1 AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
33537 GTCAAACCTG
Statistics
Matches: 253, Mismatches: 70, Indels: 20
0.74 0.20 0.06
Matches are distributed among these distances:
47 1 0.00
48 42 0.17
49 104 0.41
50 103 0.41
51 3 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (50 bp):
AGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT
Found at i:33441 original size:146 final size:149
Alignment explanation
Indices: 33229--33542 Score: 357
Period size: 146 Copynumber: 2.1 Consensus size: 149
33219 TGTTGCAACC
* *
33229 TCAACCCTTCCCTTCAAATCTTCATGGTACCCGGTTCCCCGTTGCGGCCTCAACCTTTCCTATCA
1 TCAACCCTTCCCTTCAAATCTTCATGGTACCCGGTTCCCCGTTGCGACCTCAACCTTTCCCATCA
* *** * *
33294 CAT-TTCAT-GGTACCAAATTTGTCGTTGCGGCCTTAATCTTTCCCATCACAT-TTCTGAGGTAC
66 CATCTTCATAGGTAACAAATTCACCGTTACGGCCTTAACCTTTCCCATCACATCTTCTGAGGTAC
33356 CAGGTTCGCCGTAGCGACA
131 CAGGTTCGCCGTAGCGACA
* ** *** *
33375 TCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTGTCGTTGCGACCTCAACCTTTCCCGTCA
1 TCAACCCTTCCCTTCAAATCTTCATGGTACCCGGTTCCCCGTTGCGACCTCAACCTTTCCCATCA
* * * * *
33440 CATCTTCTTAGGTAACGAGTTCACCGTTACGGCCTTAACCTTTCCCATCACTTCTTCTTAGGTAC
66 CATCTTCATAGGTAACAAATTCACCGTTACGGCCTTAACCTTTCCCATCACATCTTCTGAGGTAC
* * * * *
33505 CGGGTTTGCCATTGC-AGCC
131 CAGGTTCGCCGTAGCGA-CA
33524 TCAACCCTTCCCTGTCAAA
1 TCAACCCTTCCCT-TCAAA
33543 CCTGTAGAAT
Statistics
Matches: 137, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
146 59 0.43
147 4 0.03
148 35 0.26
149 34 0.25
150 5 0.04
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (149 bp):
TCAACCCTTCCCTTCAAATCTTCATGGTACCCGGTTCCCCGTTGCGACCTCAACCTTTCCCATCA
CATCTTCATAGGTAACAAATTCACCGTTACGGCCTTAACCTTTCCCATCACATCTTCTGAGGTAC
CAGGTTCGCCGTAGCGACA
Found at i:33535 original size:50 final size:50
Alignment explanation
Indices: 33154--33535 Score: 288
Period size: 50 Copynumber: 7.7 Consensus size: 50
33144 TTATTTTTTA
* ** * *
33154 AGGTACCGGGTTCGCCGTTGTGGCCTCAAATTTTCCCGTCACATCTTCTA
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
* * * * ** * * * *
33204 AAGAACCGGGTTTGCTGTTGCAACCTCAACCCTTCCCTTCAAATCTTCAT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
* * * *
33254 -GGTACCCGGTTCCCCGTTGCGGCCTCAACCTTTCCTATCACAT-TTCAT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
*** * * * * *
33302 -GGTACCAAATTTGTCGTTGCGGCCTTAATCTTTCCCATCACAT-TTCTG
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
* * * * * * *
33350 AGGTACCAGGTTCGCCGTAGCGACATCAACCTTTCCCTTCAAATCTTCAT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
* * * * *
33400 -GGTACTGGGTTTGTCGTTGCGACCTCAACCTTTCCCGTCACATCTTCTT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
* * * * * *
33449 AGGTAACGAGTTCACCGTTACGGCCTTAACCTTTCCCATCACTTCTTCTT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
* * * *
33499 AGGTACCGGGTTTGCCATTGCAGCCTCAACCCTTCCC
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
33536 TGTCAAACCT
Statistics
Matches: 250, Mismatches: 79, Indels: 6
0.75 0.24 0.02
Matches are distributed among these distances:
48 42 0.17
49 103 0.41
50 105 0.42
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (50 bp):
AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
Found at i:34496 original size:23 final size:23
Alignment explanation
Indices: 34469--34524 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
34459 TTGGTTCTTG
34469 TTTTTCTTCTTTTTTT-ATTTATT
1 TTTTTCTTCTTTTTTTCATTTA-T
*
34492 ATTTTTTTCTCTTTTTTTCATTTA-
1 -TTTTTCT-TCTTTTTTTCATTTAT
34516 TTTTTCTTC
1 TTTTTCTTC
34525 ATCGAATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
23 6 0.21
24 6 0.21
25 9 0.32
26 5 0.18
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTCTTCTTTTTTTCATTTAT
Found at i:39733 original size:29 final size:29
Alignment explanation
Indices: 39701--39769 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
39691 TGTCGGGGGT
* * *
39701 TAAAACGGTAAAATTTGGACACTCGAGGG
1 TAAAATGGTAAAATTTAGACACTCAAGGG
**
39730 TAAAATGGTAATTTTTAGACACTCAAGGG
1 TAAAATGGTAAAATTTAGACACTCAAGGG
39759 TAAAATGGTAA
1 TAAAATGGTAA
39770 TTTTTGGATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (29 bp):
TAAAATGGTAAAATTTAGACACTCAAGGG
Found at i:39770 original size:29 final size:29
Alignment explanation
Indices: 39718--39774 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
39708 GTAAAATTTG
*
39718 GACACTCGAGGGTAAAATGGTAATTTTTA
1 GACACTCAAGGGTAAAATGGTAATTTTTA
39747 GACACTCAAGGGTAAAATGGTAATTTTT
1 GACACTCAAGGGTAAAATGGTAATTTTT
39775 GGATGTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.32
Consensus pattern (29 bp):
GACACTCAAGGGTAAAATGGTAATTTTTA
Found at i:39873 original size:30 final size:27
Alignment explanation
Indices: 39726--39934 Score: 148
Period size: 29 Copynumber: 7.1 Consensus size: 27
39716 TGGACACTCG
* * **
39726 AGGGTAAAATGGTAATTTTTAGACACTCA
1 AGGGTAAAAT-GTAATTTTTGGA-AGTTT
*
39755 AGGGTAAAATGGTAATTTTTGGATGTTT
1 AGGGTAAAAT-GTAATTTTTGGAAGTTT
* * *
39783 GGGGGTAAAATAGTAATTTTTGGATGTTC
1 -AGGGTAAAAT-GTAATTTTTGGAAGTTT
* *
39812 AGGGGTAAAATGATACTTTTTGGAAATTTT
1 A-GGGTAAAATG-TAATTTTTGG-AAGTTT
39842 AGGGTCAAAAATGTAATTTTTGAGAAGTTT
1 AGGGT--AAAATGTAATTTTTG-GAAGTTT
*
39872 AGGGGTTAAAATGTAATTTTTGGAAAGTTC
1 A-GGG-TAAAATGTAATTTTTGG-AAGTTT
* * *
39902 AAGGTCAAAATTTAATTTTTGGAGAGTTC
1 AGGGT-AAAATGTAATTTTTGGA-AGTTT
39931 AGGG
1 AGGG
39935 ACCTTTTGGG
Statistics
Matches: 149, Mismatches: 19, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.03
29 95 0.64
30 39 0.26
31 10 0.07
32 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (27 bp):
AGGGTAAAATGTAATTTTTGGAAGTTT
Found at i:39892 original size:60 final size:57
Alignment explanation
Indices: 39726--39934 Score: 190
Period size: 58 Copynumber: 3.6 Consensus size: 57
39716 TGGACACTCG
* * * ** *
39726 AGGGT-AAAATGGTAATTTTTAGACA-CTCAAGGGTAAAATGGTAATTTTTGGATGTTTG
1 AGGGTCAAAAT-GTAATTTTTGGA-AGTTCAGGGGTAAAAT-GTAATTTTTGGAAATTTC
* * * *
39784 GGGGT-AAAATAGTAATTTTTGGATGTTCAGGGGTAAAATGATACTTTTTGGAAATTTT
1 AGGGTCAAAAT-GTAATTTTTGGAAGTTCAGGGGTAAAATG-TAATTTTTGGAAATTTC
* *
39842 AGGGTCAAAAATGTAATTTTTGAGAAGTTTAGGGGTTAAAATGTAATTTTTGGAAAGTTC
1 AGGGTC-AAAATGTAATTTTTG-GAAGTTCAGGGG-TAAAATGTAATTTTTGGAAATTTC
* *
39902 AAGGTCAAAATTTAATTTTTGGAGAGTTCAGGG
1 AGGGTCAAAATGTAATTTTTGGA-AGTTCAGGG
39935 ACCTTTTGGG
Statistics
Matches: 125, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.01
58 51 0.41
59 32 0.26
60 34 0.27
61 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (57 bp):
AGGGTCAAAATGTAATTTTTGGAAGTTCAGGGGTAAAATGTAATTTTTGGAAATTTC
Found at i:39912 original size:29 final size:30
Alignment explanation
Indices: 39756--39934 Score: 149
Period size: 29 Copynumber: 6.1 Consensus size: 30
39746 AGACACTCAA
* **
39756 GGGT-AAAATGGTAATTTTTGG-ATGTTTGG
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTCAG
*
39785 GGGT-AAAATAGTAATTTTTGG-ATGTTCAG
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTCAG
* * *
39814 GGGT-AAAATGATACTTTTTGGAAATTTTA-
1 GGGTCAAAATG-TAATTTTTGGAAAGTTCAG
*
39843 GGGTCAAAAATGTAATTTTT-GAGAAGTTTAG
1 GGGTC-AAAATGTAATTTTTGGA-AAGTTCAG
*
39874 GGGTTAAAATGTAATTTTTGGAAAGTTCA-
1 GGGTCAAAATGTAATTTTTGGAAAGTTCAG
* * *
39903 AGGTCAAAATTTAATTTTTGGAGAGTTCAG
1 GGGTCAAAATGTAATTTTTGGAAAGTTCAG
39933 GG
1 GG
39935 ACCTTTTGGG
Statistics
Matches: 126, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.01
29 75 0.60
30 38 0.30
31 12 0.10
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTCAG
Found at i:40997 original size:30 final size:28
Alignment explanation
Indices: 40962--41047 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 28
40952 ATTAATTAAC
40962 AAATAATTAATGGCTATATTAATGTATAAT
1 AAATAA-TAATGG-TATATTAATGTATAAT
40992 AAATAATAAGTGAGTATATTAATAGTAT-AT
1 AAATAATAA-TG-GTATATTAAT-GTATAAT
*
41022 -AAT-A-AGTGAGTATATTAATGTATAAT
1 AAATAATAATG-GTATATTAATGTATAAT
41048 GAATCTAACT
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
25 4 0.08
26 15 0.29
27 1 0.02
28 1 0.02
29 6 0.12
30 19 0.37
31 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (28 bp):
AAATAATAATGGTATATTAATGTATAAT
Found at i:41023 original size:26 final size:25
Alignment explanation
Indices: 40994--41045 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 25
40984 TGTATAATAA
40994 ATAATAAGTGAGTATATTAATAGTAT
1 ATAATAAGTGAGTATATTAAT-GTAT
41020 ATAATAAGTGAGTATATTAATGTAT
1 ATAATAAGTGAGTATATTAATGTAT
41045 A
1 A
41046 ATGAATCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (25 bp):
ATAATAAGTGAGTATATTAATGTAT
Found at i:41035 original size:15 final size:15
Alignment explanation
Indices: 40994--41036 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
40984 TGTATAATAA
40994 ATAATAAGTGAGTAT
1 ATAATAAGTGAGTAT
41009 AT--TAA-T-AGTAT
1 ATAATAAGTGAGTAT
41020 ATAATAAGTGAGTAT
1 ATAATAAGTGAGTAT
41035 AT
1 AT
41037 TAATGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 7 0.29
12 1 0.04
13 6 0.25
14 1 0.04
15 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (15 bp):
ATAATAAGTGAGTAT
Found at i:41557 original size:17 final size:17
Alignment explanation
Indices: 41537--41625 Score: 70
Period size: 17 Copynumber: 5.2 Consensus size: 17
41527 TTTTAATTTT
*
41537 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
* * *
41554 AATTCAATTTTAAAATG
1 AATTTAAATTTAAAATA
* * *
41571 AACTTAAATTCAACATA
1 AATTTAAATTTAAAATA
* * *
41588 AATTTAATTTTATACTA
1 AATTTAAATTTAAAATA
* *
41605 AATTAAAACTTAAAATA
1 AATTTAAATTTAAAATA
41622 AATT
1 AATT
41626 AAAAATGGGT
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Done.