Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 191 of 230
Found at i:57569060 original size:14 final size:14
Alignment explanation
Indices: 57569038--57569076 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
57569028 CCTAAATCTT
* *
57569038 AAACTCTAAACCAT
1 AAACCCTAAACCAA
*
57569052 ATACCCTAAACCAA
1 AAACCCTAAACCAA
57569066 AAACCCTAAAC
1 AAACCCTAAAC
57569077 TATAGTGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAACCAA
Found at i:57569356 original size:41 final size:41
Alignment explanation
Indices: 57569272--57569419 Score: 185
Period size: 41 Copynumber: 3.6 Consensus size: 41
57569262 CATTAGCGGT
** * *
57569272 GCTTTCT-AGAAAACGCCGCTAAA-AATAGAGCATTCACAGC
1 GCTTTCTCA-AAAACGCCGCTAAAGCCTTGAGCATTCGCAGC
*
57569312 GCTTTCTCAAAAACGTCGCTAAAGCCTTGAGCATTCGCAGC
1 GCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTCGCAGC
* *
57569353 GCTTTCTCAAAAACGCCGCTAAAACCTTGAGCATTAGC-GAC
1 GCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTCGCAG-C
*
57569394 GCTTTCTTAAAAACGCCGCTAAAGCC
1 GCTTTCTCAAAAACGCCGCTAAAGCC
57569420 CCGAAAGCTC
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
40 21 0.22
41 74 0.78
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (41 bp):
GCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTCGCAGC
Found at i:57569559 original size:32 final size:32
Alignment explanation
Indices: 57569513--57569573 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
57569503 GCGTTTTCCA
* *
57569513 TAAAGCGCCGCTAATGCTCGATCTTTAGCCGC
1 TAAAACGCCGCTAATGCTCGACCTTTAGCCGC
57569545 TAAAACGCCGCTAATGCTCGACCTTTAGC
1 TAAAACGCCGCTAATGCTCGACCTTTAGC
57569574 GGCATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (32 bp):
TAAAACGCCGCTAATGCTCGACCTTTAGCCGC
Found at i:57570635 original size:84 final size:83
Alignment explanation
Indices: 57570446--57570710 Score: 290
Period size: 83 Copynumber: 3.2 Consensus size: 83
57570436 TAATTTAATT
* * *
57570446 AAATCAAAATAAAAT-TTGTTAAACGACAGGAATAAATCTCGAAATAGA-ATTATTTGA-TT-AC
1 AAATC-AAATAAAATATTGTTAAACG-CAGGAATAAATCTCGAAACAGATTTTATTTAATTTAAC
* * * *
57570507 GTCTTTATTTGGAAACAATACA
64 -TC-TAATTTAGAAACAAAATA
* * *
57570529 ATATCGAATAAAATATTGTTAAACGGCAGGAATAAAT-TCCGAAACAGATTTTATTTAATTTAAT
1 AAATCAAATAAAATATTGTTAAAC-GCAGGAATAAATCT-CGAAACAGATTTTATTTAATTTAAC
57570593 TCTAATTTAGAAACAAAATA
64 TCTAATTTAGAAACAAAATA
* *
57570613 AAATCAAATCAAATATTGTTAAAC-AAGAGAATAAATCTCGAAACAGATTTTATTTAATTTAACT
1 AAATCAAATAAAATATTGTTAAACGCAG-GAATAAATCTCGAAACAGATTTTATTTAATTTAACT
* *
57570677 CCAATTTAGAAATAAAATA
65 CTAATTTAGAAACAAAATA
*
57570696 AAATAAAATAAAATA
1 AAATCAAATAAAATA
57570711 AAATAAAATC
Statistics
Matches: 155, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
82 11 0.07
83 95 0.61
84 44 0.28
85 4 0.03
86 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (83 bp):
AAATCAAATAAAATATTGTTAAACGCAGGAATAAATCTCGAAACAGATTTTATTTAATTTAACTC
TAATTTAGAAACAAAATA
Found at i:57570696 original size:5 final size:5
Alignment explanation
Indices: 57570686--57570719 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
57570676 TCCAATTTAG
57570686 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
57570720 CTTGTTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:57570839 original size:86 final size:88
Alignment explanation
Indices: 57570736--57571034 Score: 245
Period size: 86 Copynumber: 3.4 Consensus size: 88
57570726 AAACAGTTGG
** *
57570736 AATAAATCTTGAAACAGATTTTA-TTTAATTTAATTTCTCGTTTTTGGCAACAAAATCAAAATGT
1 AATAAATCCCGAAACAGATTTTAGTTTAATTTAATTTCTCGTTTTTGGAAACAAAATCAAAAT-T
*
57570800 -AAT-AAATCCGTTGAACGGTGGA
65 AAATAAAATCCGTTGAACGGCGGA
* * *
57570822 AATAAATCCCGAAACAGATTTTATTTTAATTTTAA-TACTCGTTTTTTGGAAATAAAATCAAAAT
1 AATAAATCCCGAAACAGATTTTAGTTTAA-TTTAATTTCTCG-TTTTTGGAAACAAAATCAAAAT
** *
57570886 TAGAATAAAATTTGTTGAACGGCGGG
64 TA-AATAAAATCCGTTGAACGGCGGA
* * * * * * * * **
57570912 AGTAAATCCCAAAATAGATTTTAGTTAAATTTAATTTCCCG--TTCGGAAATAAAATAAAAATGG
1 AATAAATCCCGAAACAGATTTTAGTTTAATTTAATTTCTCGTTTTTGGAAACAAAATCAAAATTA
* * *
57570975 AATAAAATCCATTAAACAGC-GA
66 AATAAAATCCGTTGAACGGCGGA
* ** *
57570997 GAATAAATCCTGAAATGGATTTTA-TTTACTTTTAATTT
1 -AATAAATCCCGAAACAGATTTTAGTTTA-ATTTAATTT
57571035 GAAAACAAAA
Statistics
Matches: 172, Mismatches: 32, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
85 4 0.02
86 63 0.37
87 29 0.17
88 25 0.15
89 8 0.05
90 43 0.25
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (88 bp):
AATAAATCCCGAAACAGATTTTAGTTTAATTTAATTTCTCGTTTTTGGAAACAAAATCAAAATTA
AATAAAATCCGTTGAACGGCGGA
Found at i:57571092 original size:73 final size:73
Alignment explanation
Indices: 57570968--57571105 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 73
57570958 AAATAAAATA
* * ***
57570968 AAAATGGAATAAAATCCATTAAACAGCGAGAATAAATCCTGAAATGGATTTTATTTACTTTTAAT
1 AAAATCGAATAAAATCCATTAAACAGCGAGAATAAATCCCGAAACAAATTTTATTTACTTTTAAT
57571033 TTGAAAAC
66 TTGAAAAC
* * *
57571041 AAAATCGAATAAAATCTATTAAAC-GACGGGAATAAATCCCGAAACAAATTTTATTTAGTTTTAA
1 AAAATCGAATAAAATCCATTAAACAG-CGAGAATAAATCCCGAAACAAATTTTATTTACTTTTAA
57571105 T
65 T
57571106 ATTCTTTTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 1 0.02
73 55 0.98
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (73 bp):
AAAATCGAATAAAATCCATTAAACAGCGAGAATAAATCCCGAAACAAATTTTATTTACTTTTAAT
TTGAAAAC
Found at i:57574145 original size:21 final size:21
Alignment explanation
Indices: 57574119--57574171 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
57574109 AGCGGTGGCG
* *
57574119 GTGAGATTAGTTACTGTAGTA
1 GTGAGATTAGATACTGTAGCA
*
57574140 GTGAGATTAGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
57574161 GTGAGATTAGA
1 GTGAGATTAGA
57574172 AACAATGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:57575762 original size:45 final size:45
Alignment explanation
Indices: 57575698--57575790 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
57575688 TCATAGTTTA
57575698 ACAGAAATAAATAGTCACCCTGATACTAGTGTATATATATATATT
1 ACAGAAATAAATAGTCACCCTGATACTAGTGTATATATATATATT
57575743 ACAGAAATAAATAGTCACCCTGATACTAGTGTATATATATATATT
1 ACAGAAATAAATAGTCACCCTGATACTAGTGTATATATATATATT
57575788 ACA
1 ACA
57575791 AACTTCAGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (45 bp):
ACAGAAATAAATAGTCACCCTGATACTAGTGTATATATATATATT
Found at i:57583582 original size:20 final size:21
Alignment explanation
Indices: 57583559--57583599 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57583549 TAAATTTCTC
*
57583559 CAAAATATTT-TCTAAGTATT
1 CAAAATATTTATCAAAGTATT
*
57583579 CAAAGTATTTATCAAAGTATT
1 CAAAATATTTATCAAAGTATT
57583600 TGGAGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
CAAAATATTTATCAAAGTATT
Found at i:57592221 original size:106 final size:105
Alignment explanation
Indices: 57592093--57592317 Score: 281
Period size: 106 Copynumber: 2.1 Consensus size: 105
57592083 AGTTTATTTC
* * * * *
57592093 TTAAGAATGTATTGGTCCTTTTGACGCGAAGAGGGATGACAAACCAAGCACCCTACCCCAGTTAT
1 TTAACAATGTTTTGGTCCTTTTGACACGAAGAGGGATGACAAACCAAGCACCCCACCCCAGTTAC
* * *
57592158 TTAGCCCAACACACTCCTATTTTTTTTTATTATTATTTTGG
66 TTAGCCCAACACACTCCTAATTTTTTTTATT-TAATTCTGG
* * * * *
57592199 TTAATAATGTTTTGG-CCATTTTGACACGAAGTGGGATGACAACCCAAGCACCCCATCCCGGTTA
1 TTAACAATGTTTTGGTCC-TTTTGACACGAAGAGGGATGACAAACCAAGCACCCCACCCCAGTTA
* *
57592263 CTTAGCCCAACACACTCTTAATTTTTTTTGTTTAATTCTGG
65 CTTAGCCCAACACACTCCTAATTTTTTTTATTTAATTCTGG
*
57592304 TTAACAAAGTTTTG
1 TTAACAATGTTTTG
57592318 TGTAACACGT
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
105 21 0.21
106 81 0.79
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (105 bp):
TTAACAATGTTTTGGTCCTTTTGACACGAAGAGGGATGACAAACCAAGCACCCCACCCCAGTTAC
TTAGCCCAACACACTCCTAATTTTTTTTATTTAATTCTGG
Found at i:57593094 original size:14 final size:14
Alignment explanation
Indices: 57593075--57593129 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
57593065 AACATGCAAG
57593075 AAAATA-AAGAAAAT
1 AAAATATAA-AAAAT
*
57593089 AAAATATAAAATAT
1 AAAATATAAAAAAT
57593103 AAAATATATAACAGAAT
1 AAAATATA-AA-A-AAT
57593120 AAAA-ATAAAA
1 AAAATATAAAA
57593130 TAAAATTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 19 0.54
15 6 0.17
16 4 0.11
17 6 0.17
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (14 bp):
AAAATATAAAAAAT
Found at i:57593264 original size:25 final size:25
Alignment explanation
Indices: 57593236--57593287 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
57593226 TATGGGCTTG
57593236 AAAATTCTCCTATTTTACCACATCC
1 AAAATTCTCCTATTTTACCACATCC
57593261 AAAATTCTCCTATTTTACCACATCC
1 AAAATTCTCCTATTTTACCACATCC
57593286 AA
1 AA
57593288 CATAAGGTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAATTCTCCTATTTTACCACATCC
Found at i:57598138 original size:13 final size:13
Alignment explanation
Indices: 57598120--57598180 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
57598110 CTAGTTTAGC
57598120 AATGCTTTTAAAA
1 AATGCTTTTAAAA
57598133 AATGCTTTTAAAA
1 AATGCTTTTAAAA
* *
57598146 AATACTTTTGAAA
1 AATGCTTTTAAAA
* * **
57598159 AGTGCTGTGGAAA
1 AATGCTTTTAAAA
57598172 AATGCTTTT
1 AATGCTTTT
57598181 GAGAAGTACT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AATGCTTTTAAAA
Found at i:57598192 original size:13 final size:13
Alignment explanation
Indices: 57598137--57598200 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
57598127 TTAAAAAATG
* *
57598137 CTTTTAAAAAATA
1 CTTTTGAAAAGTA
*
57598150 CTTTTGAAAAGTG
1 CTTTTGAAAAGTA
* * * *
57598163 CTGTGGAAAAATG
1 CTTTTGAAAAGTA
*
57598176 CTTTTGAGAAGTA
1 CTTTTGAAAAGTA
57598189 CTTTTGAAAAGT
1 CTTTTGAAAAGT
57598201 TTGGTTTAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:57598197 original size:26 final size:26
Alignment explanation
Indices: 57598137--57598198 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
57598127 TTAAAAAATG
* *
57598137 CTTTTAAAAAATACTTTTGAAAAGTG
1 CTTTTGAAAAATACTTTTGAAAAGTA
* * * *
57598163 CTGTGGAAAAATGCTTTTGAGAAGTA
1 CTTTTGAAAAATACTTTTGAAAAGTA
57598189 CTTTTGAAAA
1 CTTTTGAAAA
57598199 GTTTGGTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAATACTTTTGAAAAGTA
Found at i:57599827 original size:30 final size:31
Alignment explanation
Indices: 57599793--57599854 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
57599783 TCTGGTTTCA
*
57599793 TGCATGTAACGTAGG-TTTTGCATGCATTCT
1 TGCATGCAACGTAGGTTTTTGCATGCATTCT
* *
57599823 TGCATGCAACGTGGGTTTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGCATTCT
57599854 T
1 T
57599855 AAACTTTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (31 bp):
TGCATGCAACGTAGGTTTTTGCATGCATTCT
Found at i:57604368 original size:30 final size:31
Alignment explanation
Indices: 57604334--57604395 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
57604324 TTTGGTTTCA
*
57604334 TGCATGTAACGTAGG-TTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGGATTCT
*
57604364 TGCATGCAACGTGGGTTTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGGATTCT
57604395 T
1 T
57604396 AAACTTTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (31 bp):
TGCATGCAACGTAGGTTTTTGCATGGATTCT
Found at i:57615672 original size:36 final size:36
Alignment explanation
Indices: 57615624--57615695 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
57615614 GAGTGAGACA
57615624 TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
1 TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
* * *
57615660 TTGAATGTGATGGGATAGGTGTAGTGGAGGTAGGTG
1 TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
57615696 GCGTATTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.47, T:0.28
Consensus pattern (36 bp):
TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
Found at i:57621077 original size:6 final size:6
Alignment explanation
Indices: 57621066--57621094 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
57621056 TAATAATTAC
57621066 ATATTT ATATTT ATATTT ATATTT ATATT
1 ATATTT ATATTT ATATTT ATATTT ATATT
57621095 AAATCACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:57621275 original size:40 final size:39
Alignment explanation
Indices: 57621196--57621284 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 39
57621186 AAAATTTATA
* * *
57621196 TTTAATACAATAAAATATTTATTATATTTATTTGTGTTTT
1 TTTAATATAATAAAACATTTATTATATTTATTGGTG-TTT
57621236 TTTAATATAATAAAACATTTATTATATTTA-TGGTAGTTT
1 TTTAATATAATAAAACATTTATTATATTTATTGGT-GTTT
57621275 TTTAATATAA
1 TTTAATATAA
57621285 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 16 0.36
40 29 0.64
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (39 bp):
TTTAATATAATAAAACATTTATTATATTTATTGGTGTTT
Found at i:57628337 original size:19 final size:19
Alignment explanation
Indices: 57628309--57628372 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
57628299 AATTTTAGAG
*
57628309 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
57628328 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
57628347 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
57628368 GATAT
1 GATAT
57628373 ATACAATCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 22 0.55
21 18 0.45
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:57628391 original size:19 final size:21
Alignment explanation
Indices: 57628310--57628385 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
57628300 ATTTTAGAGG
57628310 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
* *
57628329 ATATGCAATTTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
57628350 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
57628371 ATATACAATCTTAGA
1 ATATACAATCTTAGA
57628386 ATATATGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.33
21 34 0.67
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:57628609 original size:19 final size:21
Alignment explanation
Indices: 57628585--57628623 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
57628575 GTTTTCTTTT
*
57628585 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
57628604 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
57628624 TTAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:57628853 original size:3 final size:3
Alignment explanation
Indices: 57628845--57628881 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
57628835 ATTAATTTTG
57628845 TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
57628882 ACCTACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:57629245 original size:51 final size:50
Alignment explanation
Indices: 57629142--57629256 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 50
57629132 ATTTTCCACG
* **
57629142 TTTTATATTATAATTATATATTTCATTTTTTTTGTAAATGCATGAATATA
1 TTTTATATTATAATTATATATTTCATTGTTTTCATAAATGCATGAATATA
* * *
57629192 TTTTATATGTATATATT-TATATTTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATAT-TATA-ATTATATA-TTTCATTGTTTTCATAAATGCATGAATATA
57629243 TTTTATATATATAA
1 TTTTATAT-TATAA
57629257 GTTTTATAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
50 9 0.16
51 24 0.44
52 22 0.40
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (50 bp):
TTTTATATTATAATTATATATTTCATTGTTTTCATAAATGCATGAATATA
Found at i:57633241 original size:15 final size:15
Alignment explanation
Indices: 57633213--57633254 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
57633203 CAAATTTTTC
57633213 AAAAA-AAA-AAAAG
1 AAAAAGAAAGAAAAG
*
57633226 AGAAAGAAAGAAAAG
1 AAAAAGAAAGAAAAG
57633241 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
57633255 ATGAGAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.16
14 3 0.12
15 18 0.72
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:57633248 original size:19 final size:20
Alignment explanation
Indices: 57633216--57633253 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
57633206 ATTTTTCAAA
57633216 AAAAAAAAAGAGAAAGAAAG
1 AAAAAAAAAGAGAAAGAAAG
*
57633236 AAAAGAAAA-AGAAAGAAA
1 AAAAAAAAAGAGAAAGAAA
57633254 AATGAGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAGAAAG
Found at i:57634792 original size:131 final size:132
Alignment explanation
Indices: 57634475--57635054 Score: 872
Period size: 131 Copynumber: 4.5 Consensus size: 132
57634465 CGGTGAAACG
* *
57634475 CCAAGCCTTGTCTCCTTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG-
1 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * * * *
57634539 AGTAGTGGAACAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGCGGGAAGTAGATTTAAGC
66 AGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
57634604 CA
131 CA
*
57634606 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGT
1 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
*
57634671 AGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGC
66 AGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
57634736 CA
131 CA
* * * *
57634738 CCAAGCCTTATCTCCTTCAGCAACAGCGGAGTA-GTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * * *
57634802 AGTAGTGAAGCAGATCAAATACGGTAAATCTTATCTTTCGAAGATAATGGGAAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
57634867 CA
131 CA
* * *
57634869 CAAAGCCTTGTCTCCCTAAGCAGCAGC-G-G-A-G-T-AAG-TTGTAGATCCTATCTCCCTAAGC
1 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
*
57634927 AGTAGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
57634992 CA
131 CA
* * * *
57634994 CCAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAAATCTTATCTCCCT
1 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
57635055 GAAGTTGCAG
Statistics
Matches: 405, Mismatches: 36, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
125 108 0.27
126 4 0.01
127 2 0.00
128 3 0.01
129 2 0.00
130 2 0.00
131 179 0.44
132 105 0.26
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (132 bp):
CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
AGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
CA
Found at i:57635094 original size:44 final size:43
Alignment explanation
Indices: 57635041--57635416 Score: 232
Period size: 44 Copynumber: 8.7 Consensus size: 43
57635031 GAAGATGGCA
*
57635041 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-AT
* * * *
57635085 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAT
* * * *** *
57635128 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAT
* * * ** *
57635169 AGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTCAGCAGCA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAACCAT
* * * *
57635212 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATAGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-ACCAT
* *
57635257 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-AT
* * * * *
57635301 AATCCTATCTCCCTGAAATTGCAGTGGAGCGGATCAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAT
** * ** * *** *
57635344 GGGTCTTTTCTATCTGAAGTTGCAG-AGAGCAGA-TCGCATC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAT
*
57635385 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
57635417 GCTAAGTAAA
Statistics
Matches: 259, Mismatches: 58, Indels: 33
0.74 0.17 0.09
Matches are distributed among these distances:
40 42 0.16
41 15 0.06
42 9 0.03
43 49 0.19
44 111 0.43
45 30 0.12
46 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAT
Found at i:57635272 original size:45 final size:43
Alignment explanation
Indices: 57635038--57635500 Score: 198
Period size: 44 Copynumber: 10.7 Consensus size: 43
57635028 GTTGAAGATG
* * *
57635038 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAA-AA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCA
* * * * * *
57635080 CCGATAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAA-AA
1 GC-A-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCA
* ** * * *
57635124 CCTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCA
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCA
* * * * *
57635166 TCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTCAGCA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCA
* * *
57635209 GCAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATA
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAG-CA
* *
57635254 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA-AGCA
* * * * * *
57635298 G-ATAATCCTATCTCCCTGAAATTGCAGTGGAGCGGATCAAAACC
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGCA
***** * ** * *
57635342 TTGGGTCTTTTCTATCTGAAGTTGCAG-AGAGCAGA-T-CGCA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCA
* * * * *
57635382 TCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-CA
* * * **
57635426 ACAAGTCTCATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAATAA
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCA
* * * *
57635470 ACAAATCCTGTCTCCCT-AAGTTGTAGTGGAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
57635501 TGGATTAGAG
Statistics
Matches: 322, Mismatches: 73, Indels: 51
0.72 0.16 0.11
Matches are distributed among these distances:
40 44 0.14
41 13 0.04
42 9 0.03
43 60 0.19
44 156 0.48
45 37 0.11
46 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCA
Found at i:57635329 original size:216 final size:217
Alignment explanation
Indices: 57635030--57635510 Score: 718
Period size: 216 Copynumber: 2.2 Consensus size: 217
57635020 CGGAGTAGGT
* * * *
57635030 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCGATAATCCTATCT
1 TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCT
* * * *
57635095 CCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
66 CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTATCTGAAGTTGCAGAGAGCAG
* * * * *
57635160 ATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTCAG-CAGCAAGTCTTATCCTC
131 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTCATCCTC
*
57635224 CTGAAGTTGCAGTGAGGTAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
57635246 TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCT
1 TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCT
* *
57635311 CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGGTCTTTTCTATCTGAAGTTGCAGAGAGCAG
66 CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTATCTGAAGTTGCAGAGAGCAG
*
57635376 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAACAAGTCTCATCCTC
131 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTCATCCTC
57635441 CTGAAGTTGCAGTGAGGCAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
* * * * **
57635463 T-AA-ATAAACAAATCCTGTCTCCCT-AAGTTGTAGTGGAGTGGATTAGAG
1 TGAAGAT-AGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAG
57635511 TGATGGATTT
Statistics
Matches: 240, Mismatches: 23, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
215 23 0.10
216 181 0.75
217 36 0.15
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (217 bp):
TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCT
CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTATCTGAAGTTGCAGAGAGCAG
ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTCATCCTC
CTGAAGTTGCAGTGAGGCAGAC
Found at i:57635907 original size:21 final size:21
Alignment explanation
Indices: 57635811--57635896 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
57635801 ATTTTCGAGG
*
57635811 ATATACAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
57635830 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
57635851 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
57635872 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
57635893 ATAT
1 ATAT
57635897 ACATTATTAG
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 18 0.28
21 46 0.72
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:57636363 original size:3 final size:3
Alignment explanation
Indices: 57636342--57636388 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
57636332 GTTTTTAGTC
57636342 TAT T-T TAT TAAT T-T TAT TAT TAT TA- TAT TAT GTAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
57636386 TAT
1 TAT
57636389 ACCTACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.15
3 27 0.69
4 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57640155 original size:41 final size:41
Alignment explanation
Indices: 57640110--57640192 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
57640100 CAATTTGATT
* *
57640110 CTAATATCTAATCAGGTTTGCTACACAATTCAAAATCCATC
1 CTAATATCTAATCAGCTTTCCTACACAATTCAAAATCCATC
* *
57640151 CTAATATCTTATCAGCTTTCCTACACAATTCGAAATCCATC
1 CTAATATCTAATCAGCTTTCCTACACAATTCAAAATCCATC
57640192 C
1 C
57640193 AAACTCTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (41 bp):
CTAATATCTAATCAGCTTTCCTACACAATTCAAAATCCATC
Found at i:57650767 original size:7 final size:7
Alignment explanation
Indices: 57650747--57650785 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
57650737 CCAGAATCTC
57650747 GAACCTT
1 GAACCTT
57650754 GAA-CTT
1 GAACCTT
57650760 GAACCTT
1 GAACCTT
57650767 GAACCTT
1 GAACCTT
* *
57650774 AAACTTT
1 GAACCTT
57650781 GAACC
1 GAACC
57650786 CCAAATCCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (7 bp):
GAACCTT
Found at i:57650872 original size:14 final size:14
Alignment explanation
Indices: 57650853--57650891 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
57650843 AAGTTTTGGG
57650853 TTCAAGGTTCAATA
1 TTCAAGGTTCAATA
*
57650867 TTCAAGATTCAATA
1 TTCAAGGTTCAATA
57650881 TTCAA-GTTCAA
1 TTCAAGGTTCAA
57650892 GGTTTAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (14 bp):
TTCAAGGTTCAATA
Found at i:57651216 original size:23 final size:23
Alignment explanation
Indices: 57651190--57651235 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
57651180 TTGTCTTTAA
*
57651190 ATTTTAATGATGTGGTAAAATTT
1 ATTTTAATGACGTGGTAAAATTT
*
57651213 ATTTTGATGACGTGGTAAAATTT
1 ATTTTAATGACGTGGTAAAATTT
57651236 TATTGGTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (23 bp):
ATTTTAATGACGTGGTAAAATTT
Found at i:57655292 original size:3 final size:3
Alignment explanation
Indices: 57655284--57655315 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
57655274 TACGTAATTC
57655284 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
57655316 TCAAGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:57663995 original size:27 final size:29
Alignment explanation
Indices: 57663965--57664018 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
57663955 CATCTCAAAG
* *
57663965 CACATCACATTGG-T-ATAAGAAATAAAA
1 CACATCACAATGGATAATAAAAAATAAAA
57663992 CACATCACAATGGATAATAAAAAATAA
1 CACATCACAATGGATAATAAAAAATAA
57664019 GATAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 1 0.04
29 10 0.43
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (29 bp):
CACATCACAATGGATAATAAAAAATAAAA
Found at i:57669084 original size:16 final size:16
Alignment explanation
Indices: 57669052--57669098 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
57669042 GTTATGTATG
*
57669052 AATTTTAA-TAATTTA
1 AATTTTAATTAATATA
57669067 AATTTTAATTAATATA
1 AATTTTAATTAATATA
* *
57669083 AAATGTAATTCAATAT
1 AATTTTAATT-AATAT
57669099 TTCTCAGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
AATTTTAATTAATATA
Found at i:57670120 original size:27 final size:26
Alignment explanation
Indices: 57670083--57670137 Score: 101
Period size: 27 Copynumber: 2.1 Consensus size: 26
57670073 TATTAAAACA
57670083 TTAATACTGGATGGAACCACTGGCTG
1 TTAATACTGGATGGAACCACTGGCTG
57670109 TTAAGTACTGGATGGAACCACTGGCTG
1 TTAA-TACTGGATGGAACCACTGGCTG
57670136 TT
1 TT
57670138 CTGGGCGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (26 bp):
TTAATACTGGATGGAACCACTGGCTG
Found at i:57672281 original size:40 final size:41
Alignment explanation
Indices: 57672192--57672284 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
57672182 ACGAGATTTG
* * * *
57672192 CACTTCGGTG-CCTCTGTATACACTTTTGTGTCCCTGTTCG
1 CACTTCGGTGCCCTCTGTATACACATTTGGGCCCCTGTTCA
* *
57672232 CACTACGGTGCCCT-TGTTTACACATTTGGGCCCCTG-TCTA
1 CACTTCGGTGCCCTCTGTATACACATTTGGGCCCCTGTTC-A
57672272 CACTTCGGTGCCC
1 CACTTCGGTGCCC
57672285 CTATTATGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.05
40 39 0.89
41 3 0.07
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.34
Consensus pattern (41 bp):
CACTTCGGTGCCCTCTGTATACACATTTGGGCCCCTGTTCA
Found at i:57672284 original size:20 final size:19
Alignment explanation
Indices: 57672192--57672286 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
57672182 ACGAGATTTG
*
57672192 CACTTCGGTGCCTCTGTATA
1 CACTTCGGTGCCCCTGT-TA
** * *
57672212 CACTTTTGTGTCCCTGTTCG
1 CACTTCGGTGCCCCTGTT-A
* *
57672232 CACTACGGTGCCCTTGTTTA
1 CACTTCGGTGCCCCTG-TTA
*
57672252 CACATTTGG-GCCCCTGTCTA
1 CAC-TTCGGTGCCCCTGT-TA
57672272 CACTTCGGTGCCCCT
1 CACTTCGGTGCCCCT
57672287 ATTATGCATC
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
19 6 0.11
20 44 0.80
21 5 0.09
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.35
Consensus pattern (19 bp):
CACTTCGGTGCCCCTGTTA
Found at i:57675050 original size:57 final size:56
Alignment explanation
Indices: 57674955--57675150 Score: 182
Period size: 57 Copynumber: 3.4 Consensus size: 56
57674945 AGACATTCAC
* * *
57674955 TTAACTAAGATAGCCACAAATGCATCTTTTTAATAGAGATAGCCATAAAGGTTTCCTT
1 TTAACAAAGATAGCCACAAAGGC-TCTTTTTAACAGAGATAGCCATAAAGG-TTCCTT
* * *
57675013 TTAACAAAGATAGCTACAAAGGCTCTTTTTAACAGAGATAGCCACAAAGGCTCC-T
1 TTAACAAAGATAGCCACAAAGGCTCTTTTTAACAGAGATAGCCATAAAGGTTCCTT
* * * * *
57675068 TTAACATAGATTGGCCACAAAGGATTTCTTTTAACATAGATCA-CCATAAAGGCTTCCTT
1 TTAACAAAGA-TAGCCACAAAGGCTCT-TTTTAACAGAGAT-AGCCATAAAGG-TTCCTT
* * *
57675127 ATAATAAAGATCA-CTACAAAGGCT
1 TTAACAAAGAT-AGCCACAAAGGCT
57675151 TTCGTTTTAA
Statistics
Matches: 112, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
55 10 0.09
56 15 0.13
57 45 0.40
58 34 0.30
59 8 0.07
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (56 bp):
TTAACAAAGATAGCCACAAAGGCTCTTTTTAACAGAGATAGCCATAAAGGTTCCTT
Found at i:57675051 original size:28 final size:28
Alignment explanation
Indices: 57674962--57675121 Score: 135
Period size: 29 Copynumber: 5.6 Consensus size: 28
57674952 CACTTAACTA
* *
57674962 AGATAGCCACAAATGCATCTTTTTAATAG
1 AGATAGCCACAAAGGC-TCTTTTTAACAG
* * * *
57674991 AGATAGCCATAAAGGTTTCCTTTTAACAA
1 AGATAGCCACAAAGG-CTCTTTTTAACAG
*
57675020 AGATAGCTACAAAGGCTCTTTTTAACAG
1 AGATAGCCACAAAGGCTCTTTTTAACAG
* *
57675048 AGATAGCCACAAAGGCTC-CTTTAACAT
1 AGATAGCCACAAAGGCTCTTTTTAACAG
* * * *
57675075 AGATTGGCCACAAAGGATTTCTTTTAACAT
1 AGA-TAGCCACAAAGGCTCT-TTTTAACAG
*
57675105 AGATCA-CCATAAAGGCT
1 AGAT-AGCCACAAAGGCT
57675122 TCCTTATAAT
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
27 10 0.10
28 39 0.37
29 45 0.43
30 11 0.10
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (28 bp):
AGATAGCCACAAAGGCTCTTTTTAACAG
Found at i:57679610 original size:31 final size:32
Alignment explanation
Indices: 57679551--57679615 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
57679541 GGCAAATTAC
*
57679551 AAGAGTAATTGAGTCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57679583 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57679614 AA
1 AA
57679616 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:57682767 original size:14 final size:14
Alignment explanation
Indices: 57682748--57682799 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
57682738 GGTAGGCAAA
57682748 TTTTTTTTTTGCGC
1 TTTTTTTTTTGCGC
57682762 TTTTTTTTTTGCTTTTTGC
1 TTTTTTTTTTGC-----GC
57682781 TTTTTTTTTTGCGC
1 TTTTTTTTTTGCGC
57682795 TTTTT
1 TTTTT
57682800 ACTCTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 19 0.58
19 14 0.42
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTTGCGC
Found at i:57682779 original size:21 final size:20
Alignment explanation
Indices: 57682753--57682857 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 20
57682743 GCAAATTTTT
57682753 TTTTTGCGCTTTTTTTTTTGC
1 TTTTT-CGCTTTTTTTTTTGC
57682774 TTTTT-GCTTTTTTTTTTGCGC
1 TTTTTCGCTTTTTTTTTT--GC
* **
57682795 TTTTTACTCTTTTTTTTGCGC
1 TTTTT-CGCTTTTTTTTTTGC
* *
57682816 TTTTTTGCTTTTTTTTACTG-
1 TTTTTCGCTTTTTTTT-TTGC
*
57682836 TTTTT-GC-TGTTTTTTTGC
1 TTTTTCGCTTTTTTTTTTGC
57682854 TTTT
1 TTTT
57682858 ATTTAAAGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.03
18 10 0.14
19 14 0.20
20 14 0.20
21 20 0.29
23 9 0.13
ACGTcount: A:0.02, C:0.13, G:0.12, T:0.72
Consensus pattern (20 bp):
TTTTTCGCTTTTTTTTTTGC
Found at i:57682782 original size:19 final size:19
Alignment explanation
Indices: 57682760--57682857 Score: 92
Period size: 19 Copynumber: 4.9 Consensus size: 19
57682750 TTTTTTTTGC
57682760 GCTTTTTTTTTTGCTTTTT
1 GCTTTTTTTTTTGCTTTTT
57682779 GCTTTTTTTTTTGCGCTTTTT
1 GCTTTTTTTTTT--GCTTTTT
* *
57682800 ACTCTTTTTTTTGCGCTTTTTT
1 GCT-TTTTTTTT-TGC-TTTTT
*
57682822 GCTTTTTTTTACTG-TTTTT
1 GCTTTTTTTT-TTGCTTTTT
*
57682841 GC-TGTTTTTTTGCTTTT
1 GCTTTTTTTTTTGCTTTT
57682858 ATTTAAAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
17 2 0.03
18 10 0.15
19 19 0.29
21 19 0.29
22 15 0.23
ACGTcount: A:0.02, C:0.13, G:0.12, T:0.72
Consensus pattern (19 bp):
GCTTTTTTTTTTGCTTTTT
Found at i:57682811 original size:33 final size:32
Alignment explanation
Indices: 57682748--57682813 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
57682738 GGTAGGCAAA
*
57682748 TTTTTTTTTTGCGCTTTTTTTTTTGCTTTTTGC
1 TTTTTTTTTTGCGCTTTTTTCTTT-CTTTTTGC
57682781 TTTTTTTTTTGCGCTTTTTACTCTTT-TTTTTGC
1 TTTTTTTTTTGCGCTTTTT--TCTTTCTTTTTGC
57682814 GCTTTTTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 26 0.87
35 4 0.13
ACGTcount: A:0.02, C:0.14, G:0.11, T:0.74
Consensus pattern (32 bp):
TTTTTTTTTTGCGCTTTTTTCTTTCTTTTTGC
Found at i:57682820 original size:33 final size:32
Alignment explanation
Indices: 57682750--57682821 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
57682740 TAGGCAAATT
* **
57682750 TTTTTTTTGCGCTTTTTTTTTTGCTTTTTGCTT
1 TTTTTTTTGCGCTTTTTTCTTT-CTTTTTGCGC
57682783 TTTTTTTTGCGCTTTTTACTCTTT-TTTTTGCGC
1 TTTTTTTTGCGCTTTTT--TCTTTCTTTTTGCGC
57682816 TTTTTT
1 TTTTTT
57682822 GCTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 30 0.88
35 4 0.12
ACGTcount: A:0.01, C:0.14, G:0.11, T:0.74
Consensus pattern (32 bp):
TTTTTTTTGCGCTTTTTTCTTTCTTTTTGCGC
Found at i:57682840 original size:30 final size:30
Alignment explanation
Indices: 57682807--57682862 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
57682797 TTTACTCTTT
*
57682807 TTTTTGC-GCTTTTTTGCTTTTTTTTACTG
1 TTTTTGCTGCTTTTTTGCTTTTATTTACTG
*
57682836 TTTTTGCTGTTTTTTTGCTTTTATTTA
1 TTTTTGCTGCTTTTTTGCTTTTATTTA
57682863 AAGAATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.05, C:0.11, G:0.12, T:0.71
Consensus pattern (30 bp):
TTTTTGCTGCTTTTTTGCTTTTATTTACTG
Found at i:57683454 original size:31 final size:32
Alignment explanation
Indices: 57683395--57683459 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
57683385 GGCAAATTAC
57683395 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57683427 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57683458 AA
1 AA
57683460 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:57702912 original size:17 final size:17
Alignment explanation
Indices: 57702890--57702928 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
57702880 TAGAATTGGG
*
57702890 TTGAAAAAATTATTTAA
1 TTGAAAAAATTAATTAA
57702907 TTG-AAAAATTAATTAA
1 TTGAAAAAATTAATTAA
57702923 TT-AAAA
1 TTGAAAA
57702929 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TTGAAAAAATTAATTAA
Found at i:57702930 original size:14 final size:15
Alignment explanation
Indices: 57702894--57702934 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
57702884 ATTGGGTTGA
*
57702894 AAAAATTATTTAATT
1 AAAAATTAATTAATT
57702909 GAAAAATTAATTAATT
1 -AAAAATTAATTAATT
57702925 -AAAATTAATT
1 AAAAATTAATT
57702935 TAATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AAAAATTAATTAATT
Found at i:57723317 original size:24 final size:24
Alignment explanation
Indices: 57723269--57723315 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
57723259 ACTGGTCACA
* *
57723269 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTAAGGAGGAATATTTG
57723293 GAGAGATTTAAGGAGAGAATATT
1 GAGAGATTTAAGGAG-GAATATT
57723316 GGGGATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (24 bp):
GAGAGATTTAAGGAGGAATATTTG
Found at i:57723532 original size:55 final size:55
Alignment explanation
Indices: 57723441--57723554 Score: 174
Period size: 55 Copynumber: 2.1 Consensus size: 55
57723431 CATATTGCCT
* ** *
57723441 GGGAATCAAGGGTGCGATGATCATCGTTTTGTGGAATAATAGTGTTCGGATCGAA
1 GGGAATCAAGGGTGCGATGATCATCGATTTACGGAATAAGAGTGTTCGGATCGAA
* *
57723496 GGGAATCAATGGTGCGATGATCATTGATTTACGGAATAAGAGTGTTCGGATCGAA
1 GGGAATCAAGGGTGCGATGATCATCGATTTACGGAATAAGAGTGTTCGGATCGAA
57723551 GGGA
1 GGGA
57723555 GTCTGCAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (55 bp):
GGGAATCAAGGGTGCGATGATCATCGATTTACGGAATAAGAGTGTTCGGATCGAA
Found at i:57724037 original size:27 final size:27
Alignment explanation
Indices: 57723986--57724177 Score: 160
Period size: 27 Copynumber: 7.1 Consensus size: 27
57723976 TCGATATCTA
** * * *
57723986 GACCGAAATACCCTTAAAGGTTAAAAA
1 GACCGAAATACCCTCGATGGGTAAAAT
*
57724013 GACCGAAATAACCTCGATGGGTAAAAT
1 GACCGAAATACCCTCGATGGGTAAAAT
**
57724040 GATTGAAATACCCTCGATGGGTAAAAT
1 GACCGAAATACCCTCGATGGGTAAAAT
* *
57724067 GATCGAAATACCCTCGACGGGTAAAAT
1 GACCGAAATACCCTCGATGGGTAAAAT
* *
57724094 GACTGAAATGCTCC-C-ATAGGGTAAAAT
1 GACCGAAATAC-CCTCGAT-GGGTAAAAT
* *
57724121 GATCGAAATACCCCCG-TAGGGTAAAAT
1 GACCGAAATACCCTCGAT-GGGTAAAAT
* *
57724148 GACTGTAATACCC-CTG-TAGGGTAAAAT
1 GACCGAAATACCCTC-GAT-GGGTAAAAT
57724175 GAC
1 GAC
57724178 TGTAATGCCC
Statistics
Matches: 139, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.03
27 133 0.96
28 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (27 bp):
GACCGAAATACCCTCGATGGGTAAAAT
Found at i:57724065 original size:54 final size:53
Alignment explanation
Indices: 57724007--57724176 Score: 200
Period size: 54 Copynumber: 3.2 Consensus size: 53
57723997 CCTTAAAGGT
* * * *
57724007 TAAAAAGACCGAAATAACCTCGATGGGTAAAATGATTGAAATACCCTCGAT-GGG
1 TAAAATGATCGAAATACCCTCGATGGGTAAAATGACTGAAATACCC-C-ATAGGG
* *
57724061 TAAAATGATCGAAATACCCTCGACGGGTAAAATGACTGAAATGCTCCCATAGGG
1 TAAAATGATCGAAATACCCTCGATGGGTAAAATGACTGAAATAC-CCCATAGGG
* * *
57724115 TAAAATGATCGAAATACCCCCG-TAGGGTAAAATGACTGTAATACCCCTGTAGGG
1 TAAAATGATCGAAATACCCTCGAT-GGGTAAAATGACTGAAATACCCC-ATAGGG
57724169 TAAAATGA
1 TAAAATGA
57724177 CTGTAATGCC
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
53 5 0.05
54 94 0.93
55 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (53 bp):
TAAAATGATCGAAATACCCTCGATGGGTAAAATGACTGAAATACCCCATAGGG
Found at i:57724178 original size:27 final size:27
Alignment explanation
Indices: 57724031--57724337 Score: 217
Period size: 27 Copynumber: 11.5 Consensus size: 27
57724021 TAACCTCGAT
* *
57724031 GGGTAAAATGATTGAAATA-CCCTCG-A
1 GGGTAAAATGACTGTAATACCCCT-GTA
*
57724057 TGGGTAAAATGA-TCGAAATA-CCCTCG-A
1 -GGGTAAAATGACT-GTAATACCCCT-GTA
* * *
57724084 CGGGTAAAATGACTGAAATGCTCCC-ATA
1 -GGGTAAAATGACTGTAATAC-CCCTGTA
* *
57724112 GGGTAAAATGA-TCGAAATACCCCCGTA
1 GGGTAAAATGACT-GTAATACCCCTGTA
57724139 GGGTAAAATGACTGTAATACCCCTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
* * *
57724166 GGGTAAAATGACTGTAATGCCCGTATA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
57724193 GGGTAAAATGAGC-GTAAT-CCCCTATA
1 GGGTAAAATGA-CTGTAATACCCCTGTA
* * * ** *
57724219 AGGTAAATTGACCGTAACGCCCTTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
57724246 GGGTAAAATGA-TCGTCATACCCCTGTA
1 GGGTAAAATGACT-GTAATACCCCTGTA
* * * *
57724273 GGATAAAATGACCGTAATGCCCCTCTA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
57724300 GGGTAAAATGACCGTAATA-CCCTGGT-
1 GGGTAAAATGACTGTAATACCCCT-GTA
57724326 GGGT-AAATGACT
1 GGGTAAAATGACT
57724338 ATTTTTGCCT
Statistics
Matches: 234, Mismatches: 32, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
25 8 0.03
26 33 0.14
27 186 0.79
28 4 0.02
29 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGTAAAATGACTGTAATACCCCTGTA
Found at i:57724416 original size:24 final size:24
Alignment explanation
Indices: 57724381--57724439 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
57724371 TATGTGGTTA
*
57724381 AATGACTAATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
*
57724405 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
57724429 AATGACTGATT
1 AATGACTGATT
57724440 CTGAGCATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:57724711 original size:64 final size:64
Alignment explanation
Indices: 57724607--57724893 Score: 312
Period size: 64 Copynumber: 4.5 Consensus size: 64
57724597 TTTACTACGA
* * *
57724607 TGCTACTGATGGCTTTGTGCTGATCATAGTACCGTTACTGATGGCTTTGTATCGATCATAGT-AC
1 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATA-TCAC
* *
57724671 TGTTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATTA-
1 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCAC
* * * * * * * * *
57724734 TCGTTACCGATGG-TTGTGTACTGAT-ATTTTACTGTTACTGATGGCTATGTGCCGATTATATCA
1 T-GCTACTGATGGCTT-TGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCA
57724797 C
64 C
* * * * * *
57724798 TGCCACTAATGGCTTTATGCCGATCATGTTACCGTTACTGATGGCTGTGTGTCGATTATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCAC
* * *
57724862 TGCTATTGATGGCTTTGTGCCAATCACATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
57724894 TATACTTATG
Statistics
Matches: 186, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
63 49 0.26
64 137 0.74
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCAC
Found at i:57724741 original size:38 final size:33
Alignment explanation
Indices: 57724610--57724880 Score: 224
Period size: 32 Copynumber: 8.5 Consensus size: 33
57724600 ACTACGATGC
57724610 TACTGATGGCTTTGTG-CTGATCATAG-TACCGT
1 TACTGATGGCTTTGTGTC-GATCATAGTTACCGT
* *
57724642 TACTGATGGCTTTGTATCGATCATAG-TACTGT
1 TACTGATGGCTTTGTGTCGATCATAGTTACCGT
*
57724674 TACTGATGGCTTTGTGCCGATCATA-TTACCGT
1 TACTGATGGCTTTGTGTCGATCATAGTTACCGT
*
57724706 TACTGATGGCTTTGTGTCGATCATA-TTATCGT
1 TACTGATGGCTTTGTGTCGATCATAGTTACCGT
* * *
57724738 TACCGATGG--TTGTGTACTGAT-AT-TTTACTGT
1 TACTGATGGCTTTGTGT-C-GATCATAGTTACCGT
* * * * * *
57724769 TACTGATGGCTATGTGCCGATTATA-TCACTGC
1 TACTGATGGCTTTGTGTCGATCATAGTTACCGT
* * * *
57724801 CACTAATGGCTTTATGCCGATCAT-GTTACCGT
1 TACTGATGGCTTTGTGTCGATCATAGTTACCGT
* * * * *
57724833 TACTGATGGCTGTGTGTCGATTATA-TCACTGC
1 TACTGATGGCTTTGTGTCGATCATAGTTACCGT
*
57724865 TATTGATGGCTTTGTG
1 TACTGATGGCTTTGTG
57724881 CCAATCACAT
Statistics
Matches: 194, Mismatches: 34, Indels: 22
0.78 0.14 0.09
Matches are distributed among these distances:
30 6 0.03
31 19 0.10
32 164 0.85
33 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (33 bp):
TACTGATGGCTTTGTGTCGATCATAGTTACCGT
Found at i:57737520 original size:28 final size:28
Alignment explanation
Indices: 57737478--57737559 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
57737468 AACAGTCTGG
*
57737478 GCCTTAGCCTGATACAGTAATAGTATGA
1 GCCTTAGCCTAATACAGTAATAGTATGA
* * * *
57737506 GCCTTAGCCCAATACAGTAACAGTGTGG
1 GCCTTAGCCTAATACAGTAATAGTATGA
57737534 GCCTTAGCCTAATACAGTAACTAGTA
1 GCCTTAGCCTAATACAGTAA-TAGTA
57737560 CAGTGAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 42 0.93
29 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (28 bp):
GCCTTAGCCTAATACAGTAATAGTATGA
Found at i:57737714 original size:26 final size:26
Alignment explanation
Indices: 57737685--57737760 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
57737675 TATAAGCAAT
*
57737685 AGTATCGCAGCAAAGCTGCCAGTAAC
1 AGTATCGCAGCAAAGTTGCCAGTAAC
*
57737711 AGTATAGC-GACAAAGTTGCCAGTAAC
1 AGTATCGCAG-CAAAGTTGCCAGTAAC
* *
57737737 AGTATCGTAGTAAAGTTGCCAGTA
1 AGTATCGCAGCAAAGTTGCCAGTA
57737761 CTAGTATACT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 41 0.95
27 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (26 bp):
AGTATCGCAGCAAAGTTGCCAGTAAC
Found at i:57737988 original size:27 final size:27
Alignment explanation
Indices: 57737958--57738261 Score: 233
Period size: 27 Copynumber: 11.4 Consensus size: 27
57737948 GGCATTTTGG
*
57737958 TCATTTTACCCTACTGGGGTATTTC-A
1 TCATTTTACCCTTCTGGGGTATTTCGA
**
57737984 GTCATTTTA-CCTTACAAGGGTATTTCGA
1 -TCATTTTACCCTT-CTGGGGTATTTCGA
*
57738012 TCATTTCACCCTTC-GAGGGTA-TTCTGA
1 TCATTTTACCCTTCTG-GGGTATTTC-GA
* * *
57738039 TCATTTCACCCTTCGGGGGTATTCCGA
1 TCATTTTACCCTTCTGGGGTATTTCGA
57738066 TCATTTTACCCTTC-GGGGTATTTCGA
1 TCATTTTACCCTTCTGGGGTATTTCGA
** * *
57738092 TCATTTTACCCTTCAAGAGTATTTCGG
1 TCATTTTACCCTTCTGGGGTATTTCGA
* **
57738119 TCATTTTATCCTTC-AAGGTATTTC-A
1 TCATTTTACCCTTCTGGGGTATTTCGA
*
57738144 GTCATTTTACCTTTC-GGAGGTATTTC-A
1 -TCATTTTACCCTTCTGG-GGTATTTCGA
** *
57738171 GTCATTTTACAATT-TGGGGGTATTTTAGA
1 -TCATTTTACCCTTCT-GGGGTA-TTTCGA
*
57738200 -CATTTTACCC-TATGAGGGTATTTCGA
1 TCATTTTACCCTTCTG-GGGTATTTCGA
*
57738226 TCATTTTACCC-TAT--GGTATTTCGA
1 TCATTTTACCCTTCTGGGGTATTTCGA
57738250 TCATTTTACCCT
1 TCATTTTACCCT
57738262 ATGAGGGTAT
Statistics
Matches: 234, Mismatches: 25, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
24 21 0.09
26 58 0.25
27 141 0.60
28 13 0.06
29 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCTGGGGTATTTCGA
Found at i:57738023 original size:54 final size:54
Alignment explanation
Indices: 57737958--57738273 Score: 271
Period size: 54 Copynumber: 5.9 Consensus size: 54
57737948 GGCATTTTGG
* *
57737958 TCATTTTACCCTACTGGGGTATTTCAG-TCATTTTACCTTACAAGGGTATTTCGA
1 TCATTTTACCCTTC-GGGGTATTTCAGATCATTTTACCTTACGAGGGTATTTCGA
* * * * *
57738012 TCATTTCACCCTTCGAGGGTA-TTCTGATCATTTCACCCTT-CGGGGGTATTCCGA
1 TCATTTTACCCTTCG-GGGTATTTCAGATCATTTTA-CCTTACGAGGGTATTTCGA
* * *
57738066 TCATTTTACCCTTCGGGGTATTTC-GATCATTTTACCCTT-CAAGAGTATTTCGG
1 TCATTTTACCCTTCGGGGTATTTCAGATCATTTTA-CCTTACGAGGGTATTTCGA
* ** *
57738119 TCATTTTATCCTTCAAGGTATTTCAG-TCATTTTACCTTTCG-GAGGTATTTC-A
1 TCATTTTACCCTTCGGGGTATTTCAGATCATTTTACCTTACGAG-GGTATTTCGA
** * * * *
57738171 GTCATTTTACAATTTGGGGGTATTTTAGA-CATTTTACCCTATGAGGGTATTTCGA
1 -TCATTTTAC-CCTTCGGGGTATTTCAGATCATTTTACCTTACGAGGGTATTTCGA
* *
57738226 TCATTTTACCCTAT---GGTATTTC-GATCATTTTACCCTATGAGGGTATTT
1 TCATTTTACCCT-TCGGGGTATTTCAGATCATTTTACCTTACGAGGGTATTT
57738274 TGGTCATCAC
Statistics
Matches: 215, Mismatches: 33, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
50 2 0.01
51 30 0.14
52 5 0.02
53 79 0.37
54 93 0.43
55 6 0.03
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (54 bp):
TCATTTTACCCTTCGGGGTATTTCAGATCATTTTACCTTACGAGGGTATTTCGA
Found at i:57738114 original size:107 final size:106
Alignment explanation
Indices: 57737957--57738261 Score: 295
Period size: 107 Copynumber: 2.9 Consensus size: 106
57737947 GGGCATTTTG
* *
57737957 GTCATTTTACCCTACTGGGGTATTTC-AGTCATTTTA-CCTTACAAGGGTATTTCGATCATTTCA
1 GTCATTTTACCCTTC-GGGGTATTTCGA-TCATTTTACCCTT-CAAGGGTATTTCGATCATTTTA
* * *
57738020 CCCTTCGAGGGTA-TTCTGATCATTTCACCCTTCGGGGGTATTCC-
63 CCCTTC-AAGGTATTTCAG-TCATTTCACCCTTCGGAGGTATTCCA
* * *
57738064 GATCATTTTACCCTTCGGGGTATTTCGATCATTTTACCCTTCAAGAGTATTTCGGTCATTTTATC
1 G-TCATTTTACCCTTCGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACC
* * *
57738129 CTTCAAGGTATTTCAGTCATTTTACCTTTCGGAGGTATTTCA
65 CTTCAAGGTATTTCAGTCATTTCACCCTTCGGAGGTATTCCA
** * * *
57738171 GTCATTTTACAATTTGGGGGTATTTTAGA-CATTTTACCCTAT-GAGGGTATTTCGATCATTTTA
1 GTCATTTTAC-CCTTCGGGGTA-TTTCGATCATTTTACCCT-TCAAGGGTATTTCGATCATTTTA
* *
57738234 CCC-T-ATGGTATTTC-GATCATTTTACCCT
63 CCCTTCAAGGTATTTCAG-TCATTTCACCCT
57738262 ATGAGGGTAT
Statistics
Matches: 168, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
104 1 0.01
105 20 0.12
106 36 0.21
107 87 0.52
108 24 0.14
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (106 bp):
GTCATTTTACCCTTCGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCC
TTCAAGGTATTTCAGTCATTTCACCCTTCGGAGGTATTCCA
Found at i:57738280 original size:27 final size:26
Alignment explanation
Indices: 57737934--57738280 Score: 231
Period size: 27 Copynumber: 13.1 Consensus size: 26
57737924 TATAACAGTT
* * * *
57737934 ATTTCACCCTTTAGGGCATTTTGGTC
1 ATTTTACCCTTGAGGGTATTTCGGTC
*
57737960 ATTTTACCCTACTG-GGGTATTTCAGTC
1 ATTTTACCCT--TGAGGGTATTTCGGTC
* *
57737987 ATTTTA-CCTTACAAGGGTATTTCGATC
1 ATTTTACCCTT--GAGGGTATTTCGGTC
* *
57738014 ATTTCACCCTTCGAGGGTA-TTCTGATC
1 ATTTTACCCTT-GAGGGTATTTC-GGTC
* * * *
57738041 ATTTCACCCTTCGGGGGTATTCCGATC
1 ATTTTACCCTT-GAGGGTATTTCGGTC
*
57738068 ATTTTACCCTTCG-GGGTATTTCGATC
1 ATTTTACCCTT-GAGGGTATTTCGGTC
* *
57738094 ATTTTACCCTTCAAGAGTATTTCGGTC
1 ATTTTACCCTT-GAGGGTATTTCGGTC
* * * *
57738121 ATTTTATCCTTCAAGGTATTTCAGTC
1 ATTTTACCCTTGAGGGTATTTCGGTC
* *
57738147 ATTTTACCTTTCG-GAGGTATTTCAGTC
1 ATTTTACCCTT-GAG-GGTATTTCGGTC
** * ** *
57738174 ATTTTACAATTTGGGGGTATTTTAGAC
1 ATTTTAC-CCTTGAGGGTATTTCGGTC
*
57738201 ATTTTACCCTATGAGGGTATTTCGATC
1 ATTTTACCCT-TGAGGGTATTTCGGTC
* *
57738228 ATTTTACCC-T-ATGGTATTTCGATC
1 ATTTTACCCTTGAGGGTATTTCGGTC
*
57738252 ATTTTACCCTATGAGGGTATTTTGGTC
1 ATTTTACCCT-TGAGGGTATTTCGGTC
57738279 AT
1 AT
57738281 CACAGTGTAA
Statistics
Matches: 264, Mismatches: 40, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
24 23 0.09
25 1 0.00
26 61 0.23
27 168 0.64
28 11 0.04
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (26 bp):
ATTTTACCCTTGAGGGTATTTCGGTC
Found at i:57741777 original size:3 final size:3
Alignment explanation
Indices: 57741769--57741813 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
57741759 TTTTAGAGTA
57741769 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57741814 ACATTTAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:57742986 original size:49 final size:49
Alignment explanation
Indices: 57742906--57743096 Score: 167
Period size: 49 Copynumber: 3.9 Consensus size: 49
57742896 TCCTAGCACT
* * * *
57742906 CACGCCAA-CTGGTTAGTAACTAAGATACCCTACCAGTGGCTCATCATA
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTCATCATA
*
57742954 CACGCCAATCTGGTTAGCAACTAACATGCCCTACCAGTGGC-CTATCATA
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTC-ATCATA
* * * * * * *
57743003 TACTCCCACCTAGTTAGCAACTAGCATGCCTTACCAGTGGTCTAGCA-CATG
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGG-CT--CATCATA
* * * *
57743054 TAC-CC-TTCTAGTTTGCAACTAGCATGCCCTACCAGTGGCTCAT
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTCAT
57743097 GATAATCGGA
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
46 2 0.02
48 11 0.09
49 97 0.80
50 3 0.02
51 6 0.05
52 1 0.01
53 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (49 bp):
CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTCATCATA
Found at i:57747739 original size:20 final size:20
Alignment explanation
Indices: 57747706--57747745 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
57747696 GGTCTCGATA
* *
57747706 CTAAGGGAAGGTATCAATAC
1 CTAAGAGAAAGTATCAATAC
*
57747726 CTAAGAGAAAGTATCGATAC
1 CTAAGAGAAAGTATCAATAC
57747746 TTCAAGCATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
CTAAGAGAAAGTATCAATAC
Found at i:57759056 original size:22 final size:22
Alignment explanation
Indices: 57759025--57759083 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
57759015 AAAATTAAGC
*
57759025 TAAAAGTAAAAAT-AAAATGCAA
1 TAAAAATAAAAATAAAAATG-AA
57759047 TAAAAATAAAAATAAAAATGAA
1 TAAAAATAAAAATAAAAATGAA
57759069 TAAATTAATAAAAAT
1 TAAA--AATAAAAAT
57759084 TGAGTGTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 18 0.55
23 6 0.18
24 9 0.27
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (22 bp):
TAAAAATAAAAATAAAAATGAA
Found at i:57765758 original size:51 final size:51
Alignment explanation
Indices: 57765682--57765794 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
57765672 AAGACCATAA
* *
57765682 ATGAAAGATGTTATAGTAGTCTAGTATGTGGTACGTAGCGTAAGGTCATGG
1 ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
57765733 ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
1 ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
57765784 ATGAAAGATGT
1 ATGAAAGATGT
57765795 CATGGCAGCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (51 bp):
ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
Found at i:57766026 original size:33 final size:33
Alignment explanation
Indices: 57765988--57766075 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 33
57765978 CCTCCGGGAT
57765988 AGTAAACACGAAACAGAGTAAGCCCATCAGGAC
1 AGTAAACACGAAACAGAGTAAGCCCATCAGGAC
* * * * * ** *
57766021 AGTAAACATGGAATAGAGTAAGTCCGTTGGGAT
1 AGTAAACACGAAACAGAGTAAGCCCATCAGGAC
* *
57766054 AGTAAATACAAAACAGAGTAAG
1 AGTAAACACGAAACAGAGTAAG
57766076 TCTATTGGGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (33 bp):
AGTAAACACGAAACAGAGTAAGCCCATCAGGAC
Found at i:57769435 original size:20 final size:19
Alignment explanation
Indices: 57769395--57769431 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
57769385 AAAGTAGTGG
57769395 AAATTTATTTTCTTAGAAT
1 AAATTTATTTTCTTAGAAT
57769414 AAATTTGATTTT-TTAGAA
1 AAATTT-ATTTTCTTAGAA
57769432 ATAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (19 bp):
AAATTTATTTTCTTAGAAT
Found at i:57777199 original size:20 final size:20
Alignment explanation
Indices: 57777174--57777211 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57777164 TATTCTCTCT
57777174 TTTTTTGTGAAAAAAAAAAG
1 TTTTTTGTGAAAAAAAAAAG
57777194 TTTTTTGTGAAAAAAAAA
1 TTTTTTGTGAAAAAAAAA
57777212 GAAACATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTTTTGTGAAAAAAAAAAG
Found at i:57801556 original size:7 final size:7
Alignment explanation
Indices: 57801538--57801587 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
57801528 TTTCTTAAGC
57801538 GATGTGG
1 GATGTGG
* *
57801545 AATGTGT
1 GATGTGG
57801552 GATGTGG
1 GATGTGG
57801559 GATGTGG
1 GATGTGG
57801566 GATGTGG
1 GATGTGG
*
57801573 GATATGG
1 GATGTGG
*
57801580 GATATGG
1 GATGTGG
57801587 G
1 G
57801588 TATATATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (7 bp):
GATGTGG
Found at i:57802085 original size:58 final size:58
Alignment explanation
Indices: 57801988--57802159 Score: 276
Period size: 57 Copynumber: 3.0 Consensus size: 58
57801978 CAAAATCTTA
57801988 ATATTTATATATAAAATATTATGTGTTACTATA-AGTGTAAGTTTGTCTTTCTTTTTTT
1 ATATTTATATATAAAATATTATGTGTTACTATATA-TGTAAGTTTGTCTTTCTTTTTTT
* *
57802046 ATATCTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTT-TTTTTAT
1 ATATTTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTTCTTTTTTT
* * *
57802103 ATATTTATATATAAAATATTCTGTGTTACTATATGTGCAAGTTTGTCTTTCTTTTTT
1 ATATTTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTTCTTTTTT
57802160 ATTGGACTTT
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
57 52 0.50
58 52 0.50
59 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (58 bp):
ATATTTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTTCTTTTTTT
Found at i:57805860 original size:43 final size:44
Alignment explanation
Indices: 57805812--57805901 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 44
57805802 GCAGGTCAAA
* *
57805812 TAATATTAAAATAACCTACACTAATTA-AGTTTAAGTGAGAAGC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAC
* * *
57805855 TAATATTAAAATAGCCTACACTCATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAC
57805899 TAA
1 TAA
57805902 AAATAGAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 24 0.59
44 17 0.41
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAC
Found at i:57805928 original size:25 final size:25
Alignment explanation
Indices: 57805881--57805930 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
57805871 TACACTCATC
* *
57805881 AGAGTTTAAGTGGGAAACTAAAAAT
1 AGAGTTTAACTGGGAAACGAAAAAT
57805906 AGAGTTTAACTGGGAGAA-GAAAAAT
1 AGAGTTTAACTGGGA-AACGAAAAAT
57805931 CGAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (25 bp):
AGAGTTTAACTGGGAAACGAAAAAT
Found at i:57806137 original size:13 final size:12
Alignment explanation
Indices: 57806108--57806137 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
57806098 TAAAAGAGTT
57806108 ATTAATTAAAAA
1 ATTAATTAAAAA
57806120 ATTAATTAAAAA
1 ATTAATTAAAAA
57806132 ACTTAA
1 A-TTAA
57806138 AAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAATTAAAAA
Found at i:57810881 original size:26 final size:26
Alignment explanation
Indices: 57810842--57810896 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
57810832 TGCATAGTTC
* *
57810842 AAGATAGTCTCGTGGTGGGCTTTGGA
1 AAGATAGGCCCGTGGTGGGCTTTGGA
*
57810868 AAGATAGGCCCGTGGTGTGCTTTGGA
1 AAGATAGGCCCGTGGTGGGCTTTGGA
57810894 AAG
1 AAG
57810897 GATGGCGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.13, G:0.38, T:0.27
Consensus pattern (26 bp):
AAGATAGGCCCGTGGTGGGCTTTGGA
Found at i:57813214 original size:43 final size:43
Alignment explanation
Indices: 57813114--57813214 Score: 98
Period size: 43 Copynumber: 2.3 Consensus size: 43
57813104 TACATGTAAC
*** *
57813114 CTCATATCGATGCCAATAGCCCAGTTATAGTCTTACACGAAAT
1 CTCATATCGATGCCAATAGCCCAAACATAGTCTCACACGAAAT
* * * *
57813157 -TACATATTGCTGCCAAT-GTCCCAAACATGGTCTCACACGAAGT
1 CT-CATATCGATGCCAATAG-CCCAAACATAGTCTCACACGAAAT
57813200 CTCATATCGATGCCA
1 CTCATATCGATGCCA
57813215 TATCTCAGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.04
43 42 0.93
44 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (43 bp):
CTCATATCGATGCCAATAGCCCAAACATAGTCTCACACGAAAT
Found at i:57822808 original size:31 final size:32
Alignment explanation
Indices: 57822754--57822814 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
57822744 TCAAATCTCT
*
57822754 TATATCATAATCCATTGATCCAAATACATTTCA
1 TATATCATAATACATTGATCCAAATA-ATTTCA
57822787 TATATCA-AATACATT-ATCCAAATAATTT
1 TATATCATAATACATTGATCCAAATAATTT
57822815 TTCTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 9 0.33
32 7 0.26
33 7 0.26
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.38
Consensus pattern (32 bp):
TATATCATAATACATTGATCCAAATAATTTCA
Found at i:57825925 original size:58 final size:57
Alignment explanation
Indices: 57825804--57825951 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 57
57825794 TTGGCACTTT
* *
57825804 ATTTTTTCTAATTTGGTATCTAAATTTTTTTGGCTCAATTTGGTACTTGAATTTAAC
1 ATTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCAATTTGGTACTTGAACTTAAC
* *
57825861 ACTTTTTT-TAAATTTGGTATCTAAACTTTTTTGGGTCATATTTGGTACTTGAACTTGAC
1 A-TTTTTTCT-AATTTGGTATCTAAACTTTTTTGGCTCA-ATTTGGTACTTGAACTTAAC
* *
57825920 -TTTTTTCCTAATTTGGTACCTAAGCATTTTTT
1 ATTTTTT-CTAATTTGGTATCTAAAC-TTTTTT
57825952 TTAGGTTTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
57 8 0.10
58 46 0.58
59 25 0.32
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.52
Consensus pattern (57 bp):
ATTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCAATTTGGTACTTGAACTTAAC
Found at i:57826095 original size:25 final size:25
Alignment explanation
Indices: 57826067--57826114 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
57826057 AAAGGAAATT
57826067 TATG-TTAAAAAATTAGATATTAAGC
1 TATGCTTAAAAAATTA-ATATTAAGC
**
57826092 TATGCTTAATGAATTAATATTAA
1 TATGCTTAAAAAATTAATATTAA
57826115 AGAAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (25 bp):
TATGCTTAAAAAATTAATATTAAGC
Found at i:57826863 original size:136 final size:136
Alignment explanation
Indices: 57826608--57826984 Score: 479
Period size: 136 Copynumber: 2.8 Consensus size: 136
57826598 TGCATTTAAT
* * ** * * * *
57826608 TGTGCGTTGTGTACCCACAGCAAAAGCATATTCCAACTGCGTCCATTTTACCGTGCAAGCACAAC
1 TGTGCGCTGTGTATCCACAAAAAAAACAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
* *
57826673 CCTCTGACAACTTTTATCTGTGAGTATGTTGTGATTCCACTGCAATTGTCAGATTTTATCTGCAT
66 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCACTGCAATTGTAAGATTTTATCTGCAT
*
57826738 TATATG
131 TATATA
* *
57826744 TGTGCGCTGTGTATCCACAAAAAAAATAGATTCCAACTGCGTCCATTTTACTGTGTGAGCACAAC
1 TGTGCGCTGTGTATCCACAAAAAAAACAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
* * * *
57826809 CCTCTGACAGCTTTTTTCTGCGAGTATGTTGTGTTTCCA-TGGCTATTAG-AAGATTTTATCTGC
66 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCACT-GCAATT-GTAAGATTTTATCTGC
57826872 ATTATATA
129 ATTATATA
** * * * * *
57826880 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAAATGCGTCCATTTTATTGTACGAGCAGAAC
1 TGTGCGCTGTGTATCCACAAAAAAAACAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
* * *
57826945 CCTCTAACAACTTTTATCTGCGAGCATGTTGTGCTTCCAC
66 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCAC
57826985 GGCCAGTGGC
Statistics
Matches: 207, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
135 1 0.00
136 205 0.99
137 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (136 bp):
TGTGCGCTGTGTATCCACAAAAAAAACAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCACTGCAATTGTAAGATTTTATCTGCAT
TATATA
Found at i:57827394 original size:39 final size:39
Alignment explanation
Indices: 57827350--57827426 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
57827340 TGCGAAACTA
*
57827350 TTTGTCATTGTACTGAATTGATTGACATGTGAAATTGTG
1 TTTGTCATTGTACTGAATTGATTAACATGTGAAATTGTG
57827389 TTTGTCATTGTACTGAATTGATTAACATGTGAAATTGT
1 TTTGTCATTGTACTGAATTGATTAACATGTGAAATTGT
57827427 TTGCTATTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (39 bp):
TTTGTCATTGTACTGAATTGATTAACATGTGAAATTGTG
Found at i:57828580 original size:3 final size:3
Alignment explanation
Indices: 57828572--57828615 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
57828562 ATATAATTCA
57828572 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
57828616 AAGAAACCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:57838097 original size:29 final size:29
Alignment explanation
Indices: 57838062--57838118 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
57838052 CCATTTAATT
*
57838062 TTATTTCTCTTAATTTATTTTGCAATCAC
1 TTATTTCGCTTAATTTATTTTGCAATCAC
57838091 TTATTTCGCTTAATTTATTTTGCAATCA
1 TTATTTCGCTTAATTTATTTTGCAATCA
57838119 TGTTTTTACT
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:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (29 bp):
TTATTTCGCTTAATTTATTTTGCAATCAC
Found at i:57844357 original size:14 final size:15
Alignment explanation
Indices: 57844335--57844363 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57844325 ATTTATCTAT
57844335 TTAATTTTATTTTGC
1 TTAATTTTATTTTGC
57844350 TTAA-TTTATTTTGC
1 TTAATTTTATTTTGC
57844364 AATCACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
TTAATTTTATTTTGC
Found at i:57845329 original size:26 final size:26
Alignment explanation
Indices: 57845300--57845349 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
57845290 TGTATTTTTA
*
57845300 ATTTCA-TAATAATATAAAAATATAAT
1 ATTTCATTAAAAAT-TAAAAATATAAT
*
57845326 ATTTTATTAAAAATTAAAAATATA
1 ATTTCATTAAAAATTAAAAATATA
57845350 TAGAATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTTCATTAAAAATTAAAAATATAAT
Found at i:57849573 original size:24 final size:24
Alignment explanation
Indices: 57849546--57849597 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
57849536 AATCACAATC
* *
57849546 AAATACATTATGCTAATAAATGCT
1 AAATACATTATACTAATAAATACT
* *
57849570 AAATATATTATACTCATAAATACT
1 AAATACATTATACTAATAAATACT
57849594 AAAT
1 AAAT
57849598 CTCCTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATACATTATACTAATAAATACT
Found at i:57850645 original size:26 final size:27
Alignment explanation
Indices: 57850595--57850645 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
57850585 AAATATTAGA
* *
57850595 AACAATTAAACACGAACAAAATAGAAT
1 AACAAATAAACACAAACAAAATAGAAT
*
57850622 AACAAATAAACA-AAACAAGATAGA
1 AACAAATAAACACAAACAAAATAGA
57850646 TGGAAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.67, C:0.14, G:0.08, T:0.12
Consensus pattern (27 bp):
AACAAATAAACACAAACAAAATAGAAT
Found at i:57855302 original size:15 final size:14
Alignment explanation
Indices: 57855272--57855311 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
57855262 TAAAAAGAAG
*
57855272 TAATTAAA-ATAAA
1 TAATTAAATAAAAA
57855285 TAATTAAGATAAAAA
1 TAATTAA-ATAAAAA
57855300 TAATTAAATAAA
1 TAATTAAATAAA
57855312 TCAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 7 0.29
14 6 0.25
15 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
TAATTAAATAAAAA
Found at i:57855798 original size:19 final size:19
Alignment explanation
Indices: 57855774--57855815 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
57855764 CAAAATTCAA
57855774 AATAAATACATAATAAA-AT
1 AATAAA-ACATAATAAATAT
*
57855793 AATAAAATATAATAAATAT
1 AATAAAACATAATAAATAT
57855812 AATA
1 AATA
57855816 TTGGGCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAAACATAATAAATAT
Found at i:57855811 original size:9 final size:9
Alignment explanation
Indices: 57855783--57855815 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
57855773 AAATAAATAC
57855783 ATAATAAA-
1 ATAATAAAT
57855791 ATAATAAAAT
1 ATAAT-AAAT
57855801 ATAATAAAT
1 ATAATAAAT
57855810 ATAATA
1 ATAATA
57855816 TTGGGCTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAATAAAT
Found at i:57858385 original size:99 final size:99
Alignment explanation
Indices: 57858276--57858473 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
57858266 AAAACTACGT
* *
57858276 TCGAGGTGTTCCTGATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCACATAATGCAGAT
1 TCGAGGTGTTCCTAATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
57858341 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
66 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
57858375 TCGAGGTGTTCCTAATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
1 TCGAGGTGTTCCTAATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
57858440 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
66 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
57858474 CTAGAATGTT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (99 bp):
TCGAGGTGTTCCTAATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
CTAATATGAAAATTTTTGGCACAAAATTCAACCA
Found at i:57858536 original size:78 final size:78
Alignment explanation
Indices: 57858407--57858550 Score: 209
Period size: 78 Copynumber: 1.8 Consensus size: 78
57858397 AAATCACAAA
* * *
57858407 ATTTAAACTAGAGTTTCCTCAAATAATGCAGATCTAATATGAAAATTTTTGGCACAAAATTCAAC
1 ATTTAAACTAGAGTTTCCTCAAATAACGCAGAACTAATATGAAAAGTTTTGGCACAAAATTCAAC
57858472 CACTAGAATGTTT
66 CACTAGAATGTTT
* * * *
57858485 ATTTAAATTGGAGTTTCCTCAAATAACGTAGAACTAATCT-AGAAAGTTTTGGCACAAAATTCAA
1 ATTTAAACTAGAGTTTCCTCAAATAACGCAGAACTAATATGA-AAAGTTTTGGCACAAAATTCAA
57858549 CC
65 CC
57858551 CACAATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 1 0.02
78 57 0.98
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (78 bp):
ATTTAAACTAGAGTTTCCTCAAATAACGCAGAACTAATATGAAAAGTTTTGGCACAAAATTCAAC
CACTAGAATGTTT
Found at i:57859961 original size:17 final size:18
Alignment explanation
Indices: 57859924--57859961 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
57859914 ATTTTTTAAA
*
57859924 AATCAATATTTAGTTTTAT
1 AATCAATATTTAG-CTTAT
57859943 AATCAATATTTA-CTTAT
1 AATCAATATTTAGCTTAT
57859960 AA
1 AA
57859962 AAATTAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
AATCAATATTTAGCTTAT
Found at i:57860203 original size:13 final size:13
Alignment explanation
Indices: 57860185--57860209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57860175 TTTTCTTTGT
57860185 TTTTTATTTTATC
1 TTTTTATTTTATC
57860198 TTTTTATTTTAT
1 TTTTTATTTTAT
57860210 AACACATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTATC
Found at i:57861992 original size:14 final size:14
Alignment explanation
Indices: 57861969--57862037 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
57861959 TGTATGAGTA
57861969 TCTGTATCTGTATT
1 TCTGTATCTGTATT
* *
57861983 TCTGTGTCTGTATA
1 TCTGTATCTGTATT
* ** *
57861997 TCCGTATCCCTATA
1 TCTGTATCTGTATT
* *
57862011 TCTTTATTTGTATT
1 TCTGTATCTGTATT
*
57862025 TCTATATCTGTAT
1 TCTGTATCTGTAT
57862038 ACGGGGTGAC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (14 bp):
TCTGTATCTGTATT
Found at i:57867329 original size:25 final size:26
Alignment explanation
Indices: 57867301--57867353 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
57867291 CACTTTTGAG
57867301 TTAATAAAA-TTCT-TTGAGTTTTCTT
1 TTAA-AAAATTTCTCTTGAGTTTTCTT
*
57867326 TTAAAAAATTTCTCTTGAGTTTTTTT
1 TTAAAAAATTTCTCTTGAGTTTTCTT
57867352 TT
1 TT
57867354 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 8 0.32
26 13 0.52
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (26 bp):
TTAAAAAATTTCTCTTGAGTTTTCTT
Found at i:57867359 original size:25 final size:25
Alignment explanation
Indices: 57867301--57867361 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
57867291 CACTTTTGAG
*
57867301 TTAATAAAATTCTTTGAGTTTTCTT
1 TTAATAAATTTCTTTGAGTTTTCTT
*
57867326 TTAAAAAATTTCTCTTGAGTTTT-TT
1 TTAATAAATTTCT-TTGAGTTTTCTT
**
57867351 TTTTTAAATTT
1 TTAATAAATTT
57867362 AACAATCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (25 bp):
TTAATAAATTTCTTTGAGTTTTCTT
Found at i:57868375 original size:20 final size:21
Alignment explanation
Indices: 57868350--57868389 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57868340 TGTCTTTATC
*
57868350 AATTTT-TATATAAATTTTAA
1 AATTTTCTAAATAAATTTTAA
*
57868370 AATTTTCTAAATAAGTTTTA
1 AATTTTCTAAATAAATTTTA
57868390 CTAATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTTTCTAAATAAATTTTAA
Found at i:57868478 original size:24 final size:24
Alignment explanation
Indices: 57868433--57868478 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
57868423 TCATTAACTG
*
57868433 TTAGGTACAAAAATAGTGCAAAGT
1 TTAGGTACAAAAATAGTACAAAGT
*
57868457 TTAGGTACCAAAATGAG-ACAAA
1 TTAGGTACAAAAAT-AGTACAAA
57868479 AATATAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (24 bp):
TTAGGTACAAAAATAGTACAAAGT
Found at i:57872672 original size:13 final size:13
Alignment explanation
Indices: 57872654--57872679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57872644 AGGTGTAGGC
57872654 CCACATGGGCATG
1 CCACATGGGCATG
57872667 CCACATGGGCATG
1 CCACATGGGCATG
57872680 TGGGTTTTGG
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:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
CCACATGGGCATG
Found at i:57874937 original size:24 final size:24
Alignment explanation
Indices: 57874908--57874955 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
57874898 CGAGGAGGTT
*
57874908 AAGCGCGTGGAGCACTAAAATAGA
1 AAGCGCGTGGAGAACTAAAATAGA
*
57874932 AAGCGCGTGGAGAACTAGAATAGA
1 AAGCGCGTGGAGAACTAAAATAGA
57874956 GACCGAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.31, T:0.12
Consensus pattern (24 bp):
AAGCGCGTGGAGAACTAAAATAGA
Found at i:57875554 original size:21 final size:22
Alignment explanation
Indices: 57875499--57875555 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
57875489 TATTAGGTTA
*
57875499 ATTGAATTGGTATGTTTATATATG
1 ATTGAA-T-GTATGTTTAAATATG
* *
57875523 ATTGAA-ATATGTTTAAATCT-
1 ATTGAATGTATGTTTAAATATG
57875543 ATTGAATGTATGT
1 ATTGAATGTATGT
57875556 ACAAATAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
24 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (22 bp):
ATTGAATGTATGTTTAAATATG
Found at i:57875787 original size:54 final size:54
Alignment explanation
Indices: 57875718--57875862 Score: 175
Period size: 54 Copynumber: 2.7 Consensus size: 54
57875708 GTATACTTAT
* * * * * *
57875718 CACACGGTCTGCGACACGACCGTGTGTATCAAGTTAGT-GAGTCACATGGTCTGG
1 CACACGGTCTACGACACGACCGTGTGTATCAAGTCAGTAAACT-ACATGATATGG
* * *
57875772 CACACAGTCTACGACACAACTGTGTGTATCAAGTCAGTAAACTACATGATATGG
1 CACACGGTCTACGACACGACCGTGTGTATCAAGTCAGTAAACTACATGATATGG
* *
57875826 CACATGGTCTACGACACGGCCGTGTGTATCAAGTCAG
1 CACACGGTCTACGACACGACCGTGTGTATCAAGTCAG
57875863 AGAGTTACAC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 74 0.97
55 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (54 bp):
CACACGGTCTACGACACGACCGTGTGTATCAAGTCAGTAAACTACATGATATGG
Found at i:57875893 original size:42 final size:42
Alignment explanation
Indices: 57875834--57875916 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
57875824 GGCACATGGT
*
57875834 CTACGACACGGCCGTGTGTATC-AAGTCAGAGAGTTACACGGC
1 CTACGACAAGGCCGTGTG-ATCTAAGTCAGAGAGTTACACGGC
* *
57875876 CTACGACAAGGTCGTGTGATCTAAGTCAGTGAGTTACACGG
1 CTACGACAAGGCCGTGTGATCTAAGTCAGAGAGTTACACGG
57875917 TTTAAGACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (42 bp):
CTACGACAAGGCCGTGTGATCTAAGTCAGAGAGTTACACGGC
Found at i:57876701 original size:358 final size:358
Alignment explanation
Indices: 57876038--57876749 Score: 1158
Period size: 358 Copynumber: 2.0 Consensus size: 358
57876028 TTTCAATTTT
* * *
57876038 TCCTTAGATTTTTTGAATTATTTCAAACTAGTCTCGTTTTGATCCCGAAATATTTTTAGGGCCTC
1 TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTAAGGGCCTC
* * *
57876103 GAAAATTTAATTTAAGGCCTAAATGTTTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAAT
66 GAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAAT
**
57876168 ATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCTGTAA
131 ATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATAA
* * *
57876233 CCCTAGACCGGCGACGGAAACGGGTTAGGGGTGTTATATTAGGTCGACCTTTTTTAGCCACTGCT
196 CCCTAGACCGGCAACGGAAACGGGTTAGGGGTGTTACATTAGGTCGACCTCTTTTAGCCACTGCT
* *
57876298 AGAACTATTATTGATATGGGTACTGGTGAACTTGTGCTTGTGTAGGTGATGAAAAGATTACTCTT
261 AGAACTATTATTGATATAGGTACTGGTGAACTTGTGCTTGTGTAGGTGATAAAAAGATTACTCTT
57876363 CAAGCACATGATTTTGTGAGAGTCCCTAGAGAA
326 CAAGCACATGATTTTGTGAGAGTCCCTAGAGAA
* *
57876396 TCCTTAGATTTTCTGAATTATTTCAAATTAGTCCCGTTTTGATCTC-AAACTATTTTAAGGGCCT
1 TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAA-TATTTTAAGGGCCT
57876460 CGAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAA
65 CGAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAA
* * * *
57876525 TGTTGAATAGCATTATTAAATTGTTTAGATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATA
130 TATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATA
** *
57876590 ACCCTAGACTTGCAACGGAAACTGGTTAGGGGTGTTACATTAGGTCGACC-CTTTTAGCCACTGC
195 ACCCTAGACCGGCAACGGAAACGGGTTAGGGGTGTTACATTAGGTCGACCTCTTTTAGCCACTGC
* * *
57876654 TAGAATTGTTATTGATATAGGTACTGGTGAACTTGTGCTTCGTGTAGGTGATAAAAATATTACTC
260 TAGAACTATTATTGATATAGGTACTGGTGAACTTGTGCTT-GTGTAGGTGATAAAAAGATTACTC
*
57876719 TTCAAGCACGTGATTTTGTGAGAGTCCCTAG
324 TTCAAGCACATGATTTTGTGAGAGTCCCTAG
57876750 TCAGTGAGAT
Statistics
Matches: 326, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
357 53 0.16
358 273 0.84
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (358 bp):
TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTAAGGGCCTC
GAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAAT
ATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATAA
CCCTAGACCGGCAACGGAAACGGGTTAGGGGTGTTACATTAGGTCGACCTCTTTTAGCCACTGCT
AGAACTATTATTGATATAGGTACTGGTGAACTTGTGCTTGTGTAGGTGATAAAAAGATTACTCTT
CAAGCACATGATTTTGTGAGAGTCCCTAGAGAA
Found at i:57877926 original size:23 final size:23
Alignment explanation
Indices: 57877877--57877926 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
57877867 CCATGTCTTT
57877877 TTTTTTCCTTTTTAAATCTATT-
1 TTTTTTCCTTTTTAAATCTATTC
* * *
57877899 TTTTTTTCTTTTCTTAATTTATTC
1 TTTTTTCCTTTT-TAAATCTATTC
57877923 TTTT
1 TTTT
57877927 ATTTCATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 8 0.35
24 4 0.17
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTAAATCTATTC
Found at i:57877975 original size:17 final size:15
Alignment explanation
Indices: 57877953--57877994 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 15
57877943 AATCATATTG
57877953 ATTTTATTTAGTTTTAT
1 ATTTTATTTA--TTTAT
57877970 ATTTTATTTATTTAT
1 ATTTTATTTATTTAT
57877985 ATTTCTATTT
1 ATTT-TATTT
57877995 CTATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 5 0.21
17 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
ATTTTATTTATTTAT
Found at i:57877979 original size:21 final size:22
Alignment explanation
Indices: 57877955--57878009 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
57877945 TCATATTGAT
57877955 TTTATTTAGTTTTATATTT-TA
1 TTTATTTAGTTTTATATTTCTA
*
57877976 TTTATTTA-TATTTCTATTTCTA
1 TTTATTTAGT-TTTATATTTCTA
*
57877998 TTT-TTTTGTTTT
1 TTTATTTAGTTTT
57878010 TGTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTATTTAGTTTTATATTTCTA
Found at i:57878015 original size:5 final size:6
Alignment explanation
Indices: 57878000--57878084 Score: 80
Period size: 6 Copynumber: 13.7 Consensus size: 6
57877990 TATTTCTATT
* * * *
57878000 TTTTTG TTTTTG TTTTTA TTTTTA TTTATG TTTTTCTG TTTTTC TTCTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG -TTTT-TG TTTTTG TT-TTTG
* * *
57878051 TTTTTG TTTTTG CTTTTG TTTTTA TTTTTA TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
57878085 ATTATGCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
6 53 0.79
7 12 0.18
8 2 0.03
ACGTcount: A:0.06, C:0.05, G:0.09, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:57887683 original size:14 final size:14
Alignment explanation
Indices: 57887664--57887700 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
57887654 GTTTTTGGGT
*
57887664 TTTAGGATTTAGTG
1 TTTAGGATTTAGGG
*
57887678 TTTAGGGTTTAGGG
1 TTTAGGATTTAGGG
57887692 TTTAGGATT
1 TTTAGGATT
57887701 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:57889416 original size:9 final size:9
Alignment explanation
Indices: 57889402--57889434 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
57889392 TTAAGAAATA
57889402 TAAAATATC
1 TAAAATATC
57889411 TAAAAT-TC
1 TAAAATATC
57889419 TTAAAATATC
1 -TAAAATATC
57889429 TAAAAT
1 TAAAAT
57889435 TCGGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAATATC
Done.