Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 71 of 129
Found at i:13519738 original size:173 final size:173
Alignment explanation
Indices: 13519490--13519959 Score: 739
Period size: 173 Copynumber: 2.7 Consensus size: 173
13519480 TTATGCGAAT
13519490 CAAACATACCTATAATCTTCAATGCTTCCATTGAAATCTTAAGCCTTCCAATTTTAAAATATTTA
1 CAAACATACCTATAATCTTCAATGCTTCCATTGAAATCTTAAGCCTTCCAATTTTAAAATATTTA
*
13519555 AATTTTATGAGCTTTTCAACTAAATCTTGTAATCTTAAATTTTTCAATGATGAAACCTTTAACCT
66 AATTTTATGAGCTTTTCAACTAAATCTTGTAATCTTAAATTTTTCAATGATGAAATCTTTAACCT
*
13519620 ATAAAATATTAATTTCATTTCTTCTCTATTTTTTTCCACAAAC
131 ATAAAATATTAATTTCATTTCTTCTCTATTCTTTTCCACAAAC
13519663 CAAACATACCTATAATCTTCAATGCTTCCATTGAAATCTTAAGCCTTCCAATTTTAAAATATTTA
1 CAAACATACCTATAATCTTCAATGCTTCCATTGAAATCTTAAGCCTTCCAATTTTAAAATATTTA
*
13519728 AATTTTATGAGCTTTTCAACTAAATCTTGTAATCTTAAAATTTTCAATGATGAAATCTTTAACCT
66 AATTTTATGAGCTTTTCAACTAAATCTTGTAATCTTAAATTTTTCAATGATGAAATCTTTAACCT
13519793 ATAAAATATTAATTTCATTTCTTCTCTATTCTTTTCCACAAAC
131 ATAAAATATTAATTTCATTTCTTCTCTATTCTTTTCCACAAAC
* * * * * ** *
13519836 CAAACATGCCAATAAT-TTGAAATGTTTTCATTGAAATCTTAAGTTTTTCAATTTTAAAATATTT
1 CAAACATACCTATAATCTT-CAATGCTTCCATTGAAATCTTAAGCCTTCCAATTTTAAAATATTT
* * * * * ** *
13519900 -AATCTT-TGAGTTTTTCAACTAAACCTAGTAATTTTAGGTCTTTCAATGATGAAATCTTTA
65 AAATTTTATGAGCTTTTCAACTAAATCTTGTAATCTTAAATTTTTCAATGATGAAATCTTTA
13519960 GCTTTACAAT
Statistics
Matches: 276, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
171 46 0.17
172 7 0.03
173 223 0.81
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (173 bp):
CAAACATACCTATAATCTTCAATGCTTCCATTGAAATCTTAAGCCTTCCAATTTTAAAATATTTA
AATTTTATGAGCTTTTCAACTAAATCTTGTAATCTTAAATTTTTCAATGATGAAATCTTTAACCT
ATAAAATATTAATTTCATTTCTTCTCTATTCTTTTCCACAAAC
Found at i:13529046 original size:22 final size:22
Alignment explanation
Indices: 13529016--13529103 Score: 149
Period size: 22 Copynumber: 4.0 Consensus size: 22
13529006 TATAGAAATG
*
13529016 TGACACAATATGTGGTTTACAA
1 TGACACAATATATGGTTTACAA
* *
13529038 TGACGCAATATGTGGTTTACAA
1 TGACACAATATATGGTTTACAA
13529060 TGACACAATATATGGTTTACAA
1 TGACACAATATATGGTTTACAA
13529082 TGACACAATATATGGTTTACAA
1 TGACACAATATATGGTTTACAA
13529104 GTTCATAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (22 bp):
TGACACAATATATGGTTTACAA
Found at i:13530449 original size:20 final size:20
Alignment explanation
Indices: 13530405--13530474 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 20
13530395 GTTTCAAGGC
* *
13530405 TTTAAGGTTCCATTTAGGG-
1 TTTAAGGTTTCATCTAGGGT
*
13530424 TTTAAGGCTTCATCTAGGGT
1 TTTAAGGTTTCATCTAGGGT
*
13530444 TTTAA-GTTTCACCTAGGGT
1 TTTAAGGTTTCATCTAGGGT
13530463 TTTAAGGTTTCA
1 TTTAAGGTTTCA
13530475 CCTATAGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 33 0.75
20 11 0.25
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (20 bp):
TTTAAGGTTTCATCTAGGGT
Found at i:13530485 original size:19 final size:17
Alignment explanation
Indices: 13530444--13530525 Score: 56
Period size: 19 Copynumber: 4.4 Consensus size: 17
13530434 CATCTAGGGT
*
13530444 TTTAAGTTTCACCTAGGG
1 TTTAAGTTTCACCTA-AG
13530462 TTTTAAGGTTTCACCTATAG
1 -TTTAA-GTTTCACCTA-AG
* *
13530482 TTTAGGGTCTCACCTAAGG
1 TTTA-AGTTTCACCTAA-G
*
13530501 TTTCAAGTTTCACCTCAAA
1 TTT-AAGTTTCACCT-AAG
13530520 TTTAAG
1 TTTAAG
13530526 ATTTTGTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.08
19 33 0.65
20 14 0.27
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (17 bp):
TTTAAGTTTCACCTAAG
Found at i:13530561 original size:26 final size:26
Alignment explanation
Indices: 13530532--13530588 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
13530522 TAAGATTTTG
* *
13530532 TTTTATGGTTATACTTTAGGGTTTCA
1 TTTTAGGGTTATACATTAGGGTTTCA
* *
13530558 TTTTAGGGTTTTACATTAGGTTTTCA
1 TTTTAGGGTTATACATTAGGGTTTCA
*
13530584 ATTTA
1 TTTTA
13530589 AGATTTCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.18, T:0.54
Consensus pattern (26 bp):
TTTTAGGGTTATACATTAGGGTTTCA
Found at i:13530766 original size:3 final size:3
Alignment explanation
Indices: 13530758--13530806 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
13530748 CATTAAAAAT
*
13530758 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TCTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA
13530805 TT
1 TT
13530807 TAATAATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.88
4 5 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13531016 original size:15 final size:16
Alignment explanation
Indices: 13530996--13531035 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
13530986 CATTAAAAAT
13530996 AAATTAAAACATAT-A
1 AAATTAAAACATATGA
*
13531011 AAATTAAATCATATGA
1 AAATTAAAACATATGA
13531027 AAATTAAAA
1 AAATTAAAA
13531036 TAAACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
AAATTAAAACATATGA
Found at i:13532209 original size:23 final size:23
Alignment explanation
Indices: 13532166--13532214 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13532156 CCATTTTCTA
*
13532166 TTGCTATTGCTTGCCTCTTTTTT
1 TTGCTATTGCTTGCCTATTTTTT
*
13532189 TTGCTATTGCTT-TCTAATTTTTT
1 TTGCTATTGCTTGCCT-ATTTTTT
13532212 TTG
1 TTG
13532215 TGCTCTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.08, C:0.16, G:0.12, T:0.63
Consensus pattern (23 bp):
TTGCTATTGCTTGCCTATTTTTT
Found at i:13532302 original size:15 final size:16
Alignment explanation
Indices: 13532282--13532312 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13532272 CCCAAATGCC
13532282 TTTTTTTAT-TTTTTA
1 TTTTTTTATGTTTTTA
13532297 TTTTTTTATGTTTTTA
1 TTTTTTTATGTTTTTA
13532313 GTTTCTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTTTTTATGTTTTTA
Found at i:13533172 original size:31 final size:31
Alignment explanation
Indices: 13533137--13533231 Score: 127
Period size: 35 Copynumber: 2.9 Consensus size: 31
13533127 GATTGAACTG
*
13533137 TAAGTCGAATGAGGTGATCGAGACTAAACCA
1 TAAGTTGAATGAGGTGATCGAGACTAAACCA
13533168 TAAGTTAAATGAATGAGGTGATCGAGACTAAACCA
1 TAAG-T---TGAATGAGGTGATCGAGACTAAACCA
* *
13533203 TAAGTTAAATGAGGTGATCGAGATTAAAC
1 TAAGTTGAATGAGGTGATCGAGACTAAAC
13533232 TGCAAGTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
31 26 0.46
32 1 0.02
34 1 0.02
35 29 0.51
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (31 bp):
TAAGTTGAATGAGGTGATCGAGACTAAACCA
Found at i:13533187 original size:35 final size:35
Alignment explanation
Indices: 13533143--13533214 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
13533133 ACTGTAAGTC
13533143 GAATGAGGTGATCGAGACTAAACCATAAGTTAAAT
1 GAATGAGGTGATCGAGACTAAACCATAAGTTAAAT
13533178 GAATGAGGTGATCGAGACTAAACCATAAGTTAAAT
1 GAATGAGGTGATCGAGACTAAACCATAAGTTAAAT
13533213 GA
1 GA
13533215 GGTGATCGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (35 bp):
GAATGAGGTGATCGAGACTAAACCATAAGTTAAAT
Found at i:13533239 original size:31 final size:31
Alignment explanation
Indices: 13533080--13533251 Score: 128
Period size: 31 Copynumber: 5.4 Consensus size: 31
13533070 GTGATAAAAA
* * * * *
13533080 AAATAAGGATGATTGAGATTGAACTGCAAGTC
1 AAATGAGG-TGATCGAGATTAAACTGTAAGTT
* * * * *
13533112 AAATGAAGTAATCAAGATTGAACTGTAAGTC
1 AAATGAGGTGATCGAGATTAAACTGTAAGTT
* * **
13533143 GAATGAGGTGATCGAGACTAAACCATAAGTT
1 AAATGAGGTGATCGAGATTAAACTGTAAGTT
* **
13533174 AAATGAATGAGGTGATCGAGACTAAACCATAAGTT
1 --A--AATGAGGTGATCGAGATTAAACTGTAAGTT
*
13533209 AAATGAGGTGATCGAGATTAAACTGCAAGTT
1 AAATGAGGTGATCGAGATTAAACTGTAAGTT
*
13533240 AAGTGAGGTGAT
1 AAATGAGGTGAT
13533252 AGATAATTTG
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
31 78 0.68
32 6 0.05
33 1 0.01
35 30 0.26
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (31 bp):
AAATGAGGTGATCGAGATTAAACTGTAAGTT
Found at i:13533404 original size:32 final size:33
Alignment explanation
Indices: 13533346--13533587 Score: 181
Period size: 32 Copynumber: 7.5 Consensus size: 33
13533336 AGGTAAACTG
** * *
13533346 GGCTTAAATTTTTGTAAGG-GCTAACTAAATTA
1 GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
* * * *
13533378 TGCTTAAA-TTTCATTAGGAGTCAACTAAATAA
1 GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
* * * **
13533410 GGCTTAAAGTTTCATT-GGTGTCAGCTAAGCTA
1 GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
13533442 GGCTTAAATTTTCATTA-GTGCCAACTAAATTA
1 GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
* * **
13533474 GACTTAAATTTTCATTGGGTGCCAACTAGGTTA
1 GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
* ** *
13533507 GGCTTAAATTTTCATT-GGTGCTAGTTAAACT-
1 GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
* * * * *
13533538 GGACTTAAATTTTCATTGGGTACTAGCTAAATTT
1 GG-CTTAAATTTTCATTAGGTGCCAACTAAATTA
* *
13533572 GACTTAAAGTTTCATT
1 GGCTTAAATTTTCATT
13533588 GATGCCAGCT
Statistics
Matches: 169, Mismatches: 34, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
31 9 0.05
32 99 0.59
33 60 0.36
34 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (33 bp):
GGCTTAAATTTTCATTAGGTGCCAACTAAATTA
Found at i:13533517 original size:65 final size:65
Alignment explanation
Indices: 13533379--13533558 Score: 202
Period size: 65 Copynumber: 2.8 Consensus size: 65
13533369 ACTAAATTAT
* * * * * * *
13533379 GCTTAAA-TTTCATTAGGAGTCAACTAAATAAGGCTTAAAGTTTCATT-GGTGTCAGCTAAGCTA
1 GCTTAAATTTTCATTA-GTGCCAACTAAATTAGACTTAAATTTTCATTGGGTGCCAACTAAGCTA
13533442 G
65 G
* *
13533443 GCTTAAATTTTCATTAGTGCCAACTAAATTAGACTTAAATTTTCATTGGGTGCCAACTAGGTTAG
1 GCTTAAATTTTCATTAGTGCCAACTAAATTAGACTTAAATTTTCATTGGGTGCCAACTAAGCTAG
* * ** * *
13533508 GCTTAAATTTTCATTGGTGCTAGTTAAACTGGACTTAAATTTTCATTGGGT
1 GCTTAAATTTTCATTAGTGCCAACTAAATTAGACTTAAATTTTCATTGGGT
13533559 ACTAGCTAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
64 33 0.33
65 66 0.67
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (65 bp):
GCTTAAATTTTCATTAGTGCCAACTAAATTAGACTTAAATTTTCATTGGGTGCCAACTAAGCTAG
Found at i:13533578 original size:65 final size:65
Alignment explanation
Indices: 13533368--13533615 Score: 191
Period size: 65 Copynumber: 3.8 Consensus size: 65
13533358 TGTAAGGGCT
* * * * *
13533368 AACTAAATTATG-CTTAAA-TTTCATTAGGAGTCAACTAAA-TAAGGCTTAAAGTTTCATTGGTG
1 AACTAAATTA-GACTTAAATTTTCATT-GGTGCCAGCTAAACT-AGACTTAAATTTTCATTGG-G
13533430 T--C
62 TACC
* ** * * * * *
13533432 AGCTAAGCTAGGCTTAAATTTTCATTAGTGCCAACTAAATTAGACTTAAATTTTCATTGGGTGCC
1 AACTAAATTAGACTTAAATTTTCATTGGTGCCAGCTAAACTAGACTTAAATTTTCATTGGGTACC
** * * * * *
13533497 AACTAGGTTAGGCTTAAATTTTCATTGGTGCTAGTTAAACTGGACTTAAATTTTCATTGGGTACT
1 AACTAAATTAGACTTAAATTTTCATTGGTGCCAGCTAAACTAGACTTAAATTTTCATTGGGTACC
* * * * * *
13533562 AGCTAAATTTGACTTAAAGTTTCATTGATGCCAGCTAGACTTGACTTAAATTTT
1 AACTAAATTAGACTTAAATTTTCATTGGTGCCAGCTAAACTAGACTTAAATTTT
13533616 TAGAAGTTTC
Statistics
Matches: 149, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
63 3 0.02
64 40 0.27
65 106 0.71
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (65 bp):
AACTAAATTAGACTTAAATTTTCATTGGTGCCAGCTAAACTAGACTTAAATTTTCATTGGGTACC
Found at i:13533594 original size:97 final size:99
Alignment explanation
Indices: 13533370--13533674 Score: 297
Period size: 97 Copynumber: 3.1 Consensus size: 99
13533360 TAAGGGCTAA
* * * *
13533370 CTAAATTATG-CTTAAA-TTTCATTAGGA-GTCAACTA-AATAAGGCTTAAAGTTTCATTGGTGT
1 CTAAATTA-GACTTAAAGTTTCATT-GGATGCCAACTAGACTTAGGCTTAAATTTTCATTGGTGT
* * * *
13533431 CAGCTAAGCTAGG-CTTAAATTTTCATT-AGTGCCAA
64 CAGCTAAACT-GGACTTAAATTTTCATTGAGTACTAG
* * *
13533466 CTAAATTAGACTTAAATTTTCATTGGGTGCCAACTAG-GTTAGGCTTAAATTTTCATTGGTG-CT
1 CTAAATTAGACTTAAAGTTTCATTGGATGCCAACTAGACTTAGGCTTAAATTTTCATTGGTGTC-
* *
13533529 AGTTAAACTGGACTTAAATTTTCATTGGGTACTAG
65 AGCTAAACTGGACTTAAATTTTCATTGAGTACTAG
* * * * *** *
13533564 CTAAATTTGACTTAAAGTTTCATT-GATGCCAGCTAGACTT-GACTTAAATTTTTAGAAGTTTCA
1 CTAAATTAGACTTAAAGTTTCATTGGATGCCAACTAGACTTAGGCTTAAATTTTCATTGGTGTCA
13533627 GCTAAACTGGACTTAAATTTTCATTGAGTACTAG
66 GCTAAACTGGACTTAAATTTTCATTGAGTACTAG
**
13533661 AAAAATTAGACTTA
1 CTAAATTAGACTTA
13533675 GATTTTCACA
Statistics
Matches: 173, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
95 1 0.01
96 19 0.11
97 124 0.72
98 29 0.17
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (99 bp):
CTAAATTAGACTTAAAGTTTCATTGGATGCCAACTAGACTTAGGCTTAAATTTTCATTGGTGTCA
GCTAAACTGGACTTAAATTTTCATTGAGTACTAG
Found at i:13533606 original size:32 final size:31
Alignment explanation
Indices: 13533412--13533652 Score: 167
Period size: 32 Copynumber: 7.5 Consensus size: 31
13533402 CTAAATAAGG
* * * *
13533412 CTTAAAGTTTCATTGGTGTCAGCTAAGCTAGG
1 CTTAAATTTTCATTGGTGCCAGCTAA-CTTGA
* * *
13533444 CTTAAATTTTCATTAGTGCCAACTAAATTAGA
1 CTTAAATTTTCATTGGTGCCAGCTAACTT-GA
* ** *
13533476 CTTAAATTTTCATTGGGTGCCAACTAGGTTAGG
1 CTTAAATTTTCATT-GGTGCCAGCTAACTT-GA
* * *
13533509 CTTAAATTTTCATTGGTGCTAGTTAAACTGGA
1 CTTAAATTTTCATTGGTGCCAGCT-AACTTGA
* * *
13533541 CTTAAATTTTCATTGGGTACTAGCTAAATTTGA
1 CTTAAATTTTCATT-GGTGCCAGCT-AACTTGA
* *
13533574 CTTAAAGTTTCATTGATGCCAGCTAGACTTGA
1 CTTAAATTTTCATTGGTGCCAGCTA-ACTTGA
* *** ** *
13533606 CTTAAATTTTTAGAAGTTTCAGCTAAACTGGA
1 CTTAAATTTTCATTGGTGCCAGCT-AACTTGA
13533638 CTTAAATTTTCATTG
1 CTTAAATTTTCATTG
13533653 AGTACTAGAA
Statistics
Matches: 163, Mismatches: 40, Indels: 12
0.76 0.19 0.06
Matches are distributed among these distances:
31 2 0.01
32 103 0.63
33 58 0.36
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (31 bp):
CTTAAATTTTCATTGGTGCCAGCTAACTTGA
Found at i:13534716 original size:146 final size:146
Alignment explanation
Indices: 13534522--13534813 Score: 462
Period size: 146 Copynumber: 2.0 Consensus size: 146
13534512 TAGCAACCTC
* * * * *
13534522 TCAATCCCATAAATTCAAGATGATACCTCACCTCTTGATTACAAAATAGCTTAATAGAAATGTAA
1 TCAATCCCACAAATTCAAGAGGATACCTCACATCTTGATTACAAAATAGCTTAATAAAAATGCAA
*
13534587 ACTT-AAAC-ACATCTCAAAGGTTAAGTGTTTGCCTAATAATGCACAAAGAAATATGATGAATGA
66 A-TTAAAACAAC-TCTCAAAGGCTAAGTGTTTGCCTAATAATGCACAAAGAAATATGATGAATGA
13534650 AGAACACAATATTGCTTG
129 AGAACACAATATTGCTTG
* *
13534668 TCAATCCCACAAATTCAAGAGGATACCTCACATTTTGATTACAAAATAGCTTAGTAAAAATGCAA
1 TCAATCCCACAAATTCAAGAGGATACCTCACATCTTGATTACAAAATAGCTTAATAAAAATGCAA
*
13534733 ATTAAAACAACTCTCAAAGGCTAAGTGTTTGCCTAATAATGTACAAAGAAATATGATGAATGAAG
66 ATTAAAACAACTCTCAAAGGCTAAGTGTTTGCCTAATAATGCACAAAGAAATATGATGAATGAAG
*
13534798 AACACAATATTTCTTG
131 AACACAATATTGCTTG
13534814 GATACAACAA
Statistics
Matches: 134, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
145 2 0.01
146 130 0.97
147 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (146 bp):
TCAATCCCACAAATTCAAGAGGATACCTCACATCTTGATTACAAAATAGCTTAATAAAAATGCAA
ATTAAAACAACTCTCAAAGGCTAAGTGTTTGCCTAATAATGCACAAAGAAATATGATGAATGAAG
AACACAATATTGCTTG
Found at i:13535131 original size:73 final size:74
Alignment explanation
Indices: 13535045--13535204 Score: 200
Period size: 74 Copynumber: 2.2 Consensus size: 74
13535035 CTAGGAAGAT
** * ** *
13535045 TCGATTGGTTCAAGTTTTGGTGCC-ATTTACACATTTGAAAATCA-TGACCCGATCGATCCCTT-
1 TCGATTGGTTCAAGTTTTGGAACCAATTCACACATTACAAAAACACT-ACCCGATCGATCCCTTC
13535107 TCTTGAGGAGA
65 T-TTGAGGAGA
* *
13535118 TCGATTGGTTCAAGTTTTGGAACCAATTCACACCTTACAAAAACACTACCTGATCGATCCCTTCT
1 TCGATTGGTTCAAGTTTTGGAACCAATTCACACATTACAAAAACACTACCCGATCGATCCCTTCT
*
13535183 TTGAGGGGA
66 TTGAGGAGA
13535192 TCGATTGGTTCAA
1 TCGATTGGTTCAA
13535205 AGGGGTGATC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
73 22 0.29
74 51 0.68
75 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (74 bp):
TCGATTGGTTCAAGTTTTGGAACCAATTCACACATTACAAAAACACTACCCGATCGATCCCTTCT
TTGAGGAGA
Found at i:13536811 original size:16 final size:16
Alignment explanation
Indices: 13536790--13536825 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13536780 CATACAAGCT
* *
13536790 GATACCAATTGTTATA
1 GATACCAATTATTAAA
13536806 GATACCAATTATTAAA
1 GATACCAATTATTAAA
13536822 GATA
1 GATA
13536826 TGTTATCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (16 bp):
GATACCAATTATTAAA
Found at i:13543409 original size:21 final size:21
Alignment explanation
Indices: 13543385--13543450 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
13543375 TTGTTTCTTT
13543385 TTTTTTTCTTCATTCTTTCAC
1 TTTTTTTCTTCATTCTTTCAC
** *
13543406 TTTTTTTTCTTTTTTC-CTCACC
1 -TTTTTTTCTTCATTCTTTCA-C
*
13543428 TTTTTTTTTTCATTCTTTCAC
1 TTTTTTTCTTCATTCTTTCAC
13543449 TT
1 TT
13543451 CTTCTTTTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTTCTTCATTCTTTCAC
Found at i:13543409 original size:22 final size:22
Alignment explanation
Indices: 13543384--13543469 Score: 88
Period size: 22 Copynumber: 3.9 Consensus size: 22
13543374 TTTGTTTCTT
13543384 TTTTTTTTCTTCATTCTTTCAC
1 TTTTTTTTCTTCATTCTTTCAC
** *
13543406 TTTTTTTTCTTTTTTC-CTCACC
1 TTTTTTTTCTTCATTCTTTCA-C
13543428 TTTTTTTT-TTCATTCTTTCAC
1 TTTTTTTTCTTCATTCTTTCAC
13543449 TTCTTCTTTTCCTTC-TTCTTT
1 TT-TT-TTTT-CTTCATTCTTT
13543470 AAGTGGATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 11 0.21
22 28 0.54
23 4 0.08
24 6 0.12
25 3 0.06
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTTTTCTTCATTCTTTCAC
Found at i:13543413 original size:24 final size:22
Alignment explanation
Indices: 13543381--13543469 Score: 67
Period size: 24 Copynumber: 3.9 Consensus size: 22
13543371 CTCTTTGTTT
13543381 CTTTTTTTTTTCTTCATTCTTTCA
1 CTTTTTTTTTT-TTC-TTCTTTCA
*
13543405 CTTTTTTTTCTTTT-TTC-CTCA
1 CTTTTTTTT-TTTTCTTCTTTCA
*
13543426 C-CTTTTTTTTTTCATTCTTTCA
1 CTTTTTTTTTTTTC-TTCTTTCA
**
13543448 CTTCTTCTTTTCCTTCTTCTTT
1 CTT-TT-TTTTTTTTCTTCTTT
13543470 AAGTGGATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
19 4 0.08
20 6 0.12
21 7 0.13
22 7 0.13
24 19 0.37
25 9 0.17
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.70
Consensus pattern (22 bp):
CTTTTTTTTTTTTCTTCTTTCA
Found at i:13543954 original size:8 final size:8
Alignment explanation
Indices: 13543920--13543987 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
13543910 CATAACCATT
13543920 TTTTTATC
1 TTTTTATC
13543928 TTTTT-T-
1 TTTTTATC
**
13543934 TTTTTGCC
1 TTTTTATC
13543942 TTTTTTATC
1 -TTTTTATC
13543951 TTTTTATC
1 TTTTTATC
*
13543959 TTTTTTTC
1 TTTTTATC
*
13543967 TTCTT-TC
1 TTTTTATC
13543974 TTTTTTAT-
1 -TTTTTATC
13543982 TTTTTA
1 TTTTTA
13543988 ACATGCTCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.10
7 9 0.18
8 28 0.57
9 7 0.14
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTATC
Found at i:13543958 original size:31 final size:31
Alignment explanation
Indices: 13543919--13543987 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
13543909 TCATAACCAT
13543919 TTTTTTATCTTTTTTT-TT-TTGCCTTTTTTA
1 TTTTTTATCTTTTTTTCTTCTT-CCTTTTTTA
*
13543949 TCTTTTTATCTTTTTTTCTTCTTTCTTTTTTA
1 T-TTTTTATCTTTTTTTCTTCTTCCTTTTTTA
13543981 TTTTTTA
1 TTTTTTA
13543988 ACATGCTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 1 0.03
31 21 0.60
32 11 0.31
33 2 0.06
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.80
Consensus pattern (31 bp):
TTTTTTATCTTTTTTTCTTCTTCCTTTTTTA
Found at i:13550386 original size:23 final size:23
Alignment explanation
Indices: 13550360--13550403 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
13550350 TTAAGTGCAA
13550360 TTATCTATATTTTATT-TTATTCT
1 TTATCTA-ATTTTATTATTATTCT
*
13550383 TTATTTAATTTTATTATTATT
1 TTATCTAATTTTATTATTATT
13550404 AGATTAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATCTAATTTTATTATTATTCT
Found at i:13555275 original size:20 final size:19
Alignment explanation
Indices: 13555246--13555305 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
13555236 AAAAGATGTC
*
13555246 AAAATGAAAAAGAAAAAAA
1 AAAAAGAAAAAGAAAAAAA
* *
13555265 CAAAAGTAAAAGTAAAAAAA
1 AAAAAGAAAAAG-AAAAAAA
13555285 AAAAAGAAAAAGAAAGAAAA
1 AAAAAGAAAAAGAAA-AAAA
13555305 A
1 A
13555306 TGAAGACTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.35
20 22 0.65
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAAA
Found at i:13555311 original size:10 final size:10
Alignment explanation
Indices: 13555251--13555305 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
13555241 ATGTCAAAAT
13555251 GAAAAAGAAA
1 GAAAAAGAAA
13555261 -AAAACA-AAA
1 GAAAA-AGAAA
*
13555270 GTAAAAGTAAA
1 GAAAAAG-AAA
*
13555281 -AAAAAAAAA
1 GAAAAAGAAA
13555290 GAAAAAGAAA
1 GAAAAAGAAA
13555300 GAAAAA
1 GAAAAA
13555306 TGAAGACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
9 11 0.31
10 22 0.61
11 3 0.08
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.04
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:13556342 original size:24 final size:23
Alignment explanation
Indices: 13556310--13556369 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
13556300 AATTCTGAAA
13556310 TTTTGGATGTGAAACCTTGAAATT
1 TTTTGGATGTGAAACCTTG-AATT
* *
13556334 TTTTGGATGAGAAACTTTGAATT
1 TTTTGGATGTGAAACCTTGAATT
*
13556357 TTTT-GTTGTGAAA
1 TTTTGGATGTGAAA
13556370 TATTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.22
23 8 0.25
24 17 0.53
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (23 bp):
TTTTGGATGTGAAACCTTGAATT
Found at i:13556356 original size:23 final size:24
Alignment explanation
Indices: 13556310--13556361 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
13556300 AATTCTGAAA
*
13556310 TTTTGGATGTGAAACCTTGAAATT
1 TTTTGGATGAGAAACCTTGAAATT
*
13556334 TTTTGGATGAGAAACTTTG-AATT
1 TTTTGGATGAGAAACCTTGAAATT
13556357 TTTTG
1 TTTTG
13556362 TTGTGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (24 bp):
TTTTGGATGAGAAACCTTGAAATT
Found at i:13557157 original size:65 final size:65
Alignment explanation
Indices: 13557088--13557268 Score: 166
Period size: 66 Copynumber: 2.8 Consensus size: 65
13557078 TTGATCTTGG
* * * *
13557088 TCACTCATTTTTATCTCAACTTGGTCTAAATCATTTTATTTTTTTGACTTGCTG-TTCGATCCGA
1 TCACTCATTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCG-TGATTCGATACGA
13557152 A
65 A
* * *** * * * **
13557153 TCACTTATTTTCAATCTCAACTCAATCCAGATCATGTCATTTTTTTGACTCGTGATTTGATACTT
1 TCACTCATTTT-TATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCGTGATTCGATACGA
*
13557218 G
65 A
* * * *
13557219 TCATTCATTTTTATCTCAGCTTGGTCCAGATCATTTTAATTTTTTAACTC
1 TCACTCATTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTC
13557269 ATTGCTCAAT
Statistics
Matches: 88, Mismatches: 26, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
65 42 0.48
66 46 0.52
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (65 bp):
TCACTCATTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCGTGATTCGATACGAA
Found at i:13557261 original size:66 final size:65
Alignment explanation
Indices: 13557035--13557268 Score: 173
Period size: 65 Copynumber: 3.7 Consensus size: 65
13557025 GGTTAGCTAT
* * * * *
13557035 TTTTTATCTCAACTTAGTCCA-A--A--TTATTTTTTTTACTTGC-AATTTGATCTTGGTCACTC
1 TTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCGCTGATTTGATCTT-GTCATTC
13557094 A
65 A
* * * * *
13557095 TTTTTATCTCAACTTGGTCTAAATCATTTTATTTTTTTGACTTGCTG-TTCGATC-CGAATCACT
1 TTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCGCTGATTTGATCTTG--TCA-T
13557158 T-A
63 TCA
* *** * *
13557160 TTTTCAATCTCAACTCAATCCAGATCATGTCATTTTTTTGACTCG-TGATTTGATACTTGTCATT
1 TTTT-TATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCGCTGATTTGAT-CTTGTCATT
13557224 CA
64 CA
* * *
13557226 TTTTTATCTCAGCTTGGTCCAGATCATTTTAATTTTTTAACTC
1 TTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTC
13557269 ATTGCTCAAT
Statistics
Matches: 133, Mismatches: 27, Indels: 23
0.73 0.15 0.13
Matches are distributed among these distances:
60 19 0.14
61 1 0.01
63 2 0.02
65 64 0.48
66 45 0.34
67 1 0.01
68 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (65 bp):
TTTTTATCTCAACTTGGTCCAGATCATTTTATTTTTTTGACTCGCTGATTTGATCTTGTCATTCA
Found at i:13559389 original size:3 final size:3
Alignment explanation
Indices: 13559381--13559439 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
13559371 CATTAAAATT
13559381 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13559429 TTA TTA TTA TT
1 TTA TTA TTA TT
13559440 TGTGAGAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13559518 original size:22 final size:22
Alignment explanation
Indices: 13559493--13559534 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13559483 TGTATATTTA
* *
13559493 TATTTATATCTCTAGAATTAAG
1 TATTTATATCCCTAAAATTAAG
*
13559515 TATTTGTATCCCTAAAATTA
1 TATTTATATCCCTAAAATTA
13559535 GGATAAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (22 bp):
TATTTATATCCCTAAAATTAAG
Found at i:13563465 original size:22 final size:22
Alignment explanation
Indices: 13563439--13563480 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13563429 TGTATATTTA
* *
13563439 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
13563461 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
13563481 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:13563655 original size:3 final size:3
Alignment explanation
Indices: 13563647--13563714 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
13563637 GTTTTTCCAC
13563647 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13563695 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
13563715 CTTTGTTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13563851 original size:3 final size:3
Alignment explanation
Indices: 13563845--13563899 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
13563835 TTAGAAGAAT
*
13563845 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13563893 TT- TTA TT
1 TTA TTA TT
13563900 TTCATTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13563965 original size:15 final size:16
Alignment explanation
Indices: 13563945--13563984 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
13563935 CATCAAAAAT
13563945 AAATTAAAACATAT-A
1 AAATTAAAACATATGA
*
13563960 AAATTAAATCATATGA
1 AAATTAAAACATATGA
13563976 AAATTAAAA
1 AAATTAAAA
13563985 TAAACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
AAATTAAAACATATGA
Found at i:13564015 original size:35 final size:34
Alignment explanation
Indices: 13563950--13564034 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 34
13563940 AAAATAAATT
* * *
13563950 AAAACATATAAAATTAAATCATATGAAAATTAAA
1 AAAACATATAAATTTAAACCATAAGAAAATTAAA
13563984 ATAAACATATAAATTTAAACCATAA-AGAAATTAAA
1 A-AAACATATAAATTTAAACCATAAGA-AAATTAAA
*
13564019 AATACATA-AAATTTAA
1 AAAACATATAAATTTAA
13564035 TCTGTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
33 8 0.18
34 8 0.18
35 29 0.64
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAACATATAAATTTAAACCATAAGAAAATTAAA
Found at i:13565266 original size:15 final size:15
Alignment explanation
Indices: 13565246--13565275 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13565236 GCTTAAATGC
*
13565246 TTTTTTTATTTTTTA
1 TTTTTTTATGTTTTA
13565261 TTTTTTTATGTTTTA
1 TTTTTTTATGTTTTA
13565276 AATTTTCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTTATGTTTTA
Found at i:13565728 original size:22 final size:22
Alignment explanation
Indices: 13565702--13565743 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13565692 TGTATATTTA
* *
13565702 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
13565724 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
13565744 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:13565919 original size:3 final size:3
Alignment explanation
Indices: 13565911--13565946 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
13565901 GTTTTTTCAC
13565911 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13565947 TAATAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13566075 original size:3 final size:3
Alignment explanation
Indices: 13566067--13566112 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
13566057 TTAAAAGAAT
*
13566067 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13566113 TTCATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13566178 original size:15 final size:16
Alignment explanation
Indices: 13566158--13566197 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
13566148 CATCAAAAAT
13566158 AAATTAAAACATAT-A
1 AAATTAAAACATATGA
*
13566173 AAATTAAATCATATGA
1 AAATTAAAACATATGA
13566189 AAATTAAAA
1 AAATTAAAA
13566198 TAAACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
AAATTAAAACATATGA
Found at i:13566228 original size:35 final size:34
Alignment explanation
Indices: 13566163--13566247 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 34
13566153 AAAATAAATT
* * *
13566163 AAAACATATAAAATTAAATCATATGAAAATTAAA
1 AAAACATATAAATTTAAACCATAAGAAAATTAAA
13566197 ATAAACATATAAATTTAAACCATAA-AGAAATTAAA
1 A-AAACATATAAATTTAAACCATAAGA-AAATTAAA
*
13566232 AATACATA-AAATTTAA
1 AAAACATATAAATTTAA
13566248 TCTGTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
33 8 0.18
34 8 0.18
35 29 0.64
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAACATATAAATTTAAACCATAAGAAAATTAAA
Found at i:13567944 original size:22 final size:22
Alignment explanation
Indices: 13567914--13567955 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13567904 TGTATATTTA
* *
13567914 TATTCGTATCTCTAGAATTAAG
1 TATTCGTATCCCTAAAATTAAG
*
13567936 TATTTGTATCCCTAAAATTA
1 TATTCGTATCCCTAAAATTA
13567956 GGATAGACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATTCGTATCCCTAAAATTAAG
Found at i:13568286 original size:3 final size:3
Alignment explanation
Indices: 13568278--13568314 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
13568268 TTAGAAGCAT
13568278 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13568315 TTCATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:13568380 original size:15 final size:16
Alignment explanation
Indices: 13568360--13568399 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
13568350 CATCAAAAAT
13568360 AAATTAAAACATAT-A
1 AAATTAAAACATATGA
*
13568375 AAATTAAATCATATGA
1 AAATTAAAACATATGA
13568391 AAATTAAAA
1 AAATTAAAA
13568400 TAAACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
AAATTAAAACATATGA
Found at i:13568430 original size:35 final size:34
Alignment explanation
Indices: 13568365--13568449 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 34
13568355 AAAATAAATT
* * *
13568365 AAAACATATAAAATTAAATCATATGAAAATTAAA
1 AAAACATATAAATTTAAACCATAAGAAAATTAAA
13568399 ATAAACATATAAATTTAAACCATAA-AGAAATTAAA
1 A-AAACATATAAATTTAAACCATAAGA-AAATTAAA
*
13568434 AATACATA-AAATTTAA
1 AAAACATATAAATTTAA
13568450 TTTATAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
33 8 0.18
34 8 0.18
35 29 0.64
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAACATATAAATTTAAACCATAAGAAAATTAAA
Found at i:13570796 original size:20 final size:19
Alignment explanation
Indices: 13570753--13570818 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 19
13570743 TACTACGTTT
*
13570753 GAAAGAGAAAAATAAAAAAGA
1 GAAAGAGAAAAA-AAAGAA-A
13570774 GAAAGAGAAAGAAAAAGAAA
1 GAAAGAGAAA-AAAAAGAAA
*
13570794 GAAA-ACAAAACAAAAAGAAA
1 GAAAGA-GAAA-AAAAAGAAA
13570814 -AAAGA
1 GAAAGA
13570819 TTACTCTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.10
20 18 0.46
21 15 0.38
22 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (19 bp):
GAAAGAGAAAAAAAAGAAA
Found at i:13571955 original size:39 final size:39
Alignment explanation
Indices: 13571907--13572108 Score: 172
Period size: 39 Copynumber: 5.2 Consensus size: 39
13571897 AGTTGTGCAT
* * *
13571907 CTCTATTGTTGAGGAGTTTTTATTTTTAAAGTTATGTGC
1 CTCTATTGTTGAAGAGCTTTTATTTTTAAAGTTATATGC
* * **
13571946 CTCTGTTGTTGAAGAGCTCTTATTTTTAAAGTGGTATGC
1 CTCTATTGTTGAAGAGCTTTTATTTTTAAAGTTATATGC
* * * * *
13571985 CTCTGTTGTT-AAAACGCCTTTATTTTTAAAATTGTATGC
1 CTCTATTGTTGAAGA-GCTTTTATTTTTAAAGTTATATGC
* * * ** * *
13572024 CTTTATTATTGAAAAGCCCTTATTGTTAAAGTTTTATGC
1 CTCTATTGTTGAAGAGCTTTTATTTTTAAAGTTATATGC
* * * *
13572063 CTCTATAGTTGAGGAGTTTTTATTTTTAAAGTTATGTGC
1 CTCTATTGTTGAAGAGCTTTTATTTTTAAAGTTATATGC
*
13572102 CTTTATT
1 CTCTATT
13572109 TTCAACGAGC
Statistics
Matches: 129, Mismatches: 32, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
38 3 0.02
39 122 0.95
40 4 0.03
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.48
Consensus pattern (39 bp):
CTCTATTGTTGAAGAGCTTTTATTTTTAAAGTTATATGC
Found at i:13572085 original size:78 final size:78
Alignment explanation
Indices: 13571907--13572108 Score: 235
Period size: 78 Copynumber: 2.6 Consensus size: 78
13571897 AGTTGTGCAT
* * * * * *
13571907 CTCTATTGTTGAGGAGTTTTTATTTTTAAAGTTATGTGCCTCTGTTGTTGAAGAGCTCTTATTTT
1 CTCTATTGTTGAGGAGTTTTTATTTTTAAAGTTATGTGCCTTTATTATTGAAAAGCCCTTATTGT
13571972 TAAAGTGGTATGC
66 TAAAGTGGTATGC
* ** ** * * *
13571985 CTCTGTTGTT-AAAACGCCTTTATTTTTAAAATTGTATGCCTTTATTATTGAAAAGCCCTTATTG
1 CTCTATTGTTGAGGA-GTTTTTATTTTTAAAGTTATGTGCCTTTATTATTGAAAAGCCCTTATTG
**
13572049 TTAAAGTTTTATGC
65 TTAAAGTGGTATGC
*
13572063 CTCTATAGTTGAGGAGTTTTTATTTTTAAAGTTATGTGCCTTTATT
1 CTCTATTGTTGAGGAGTTTTTATTTTTAAAGTTATGTGCCTTTATT
13572109 TTCAACGAGC
Statistics
Matches: 97, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
77 2 0.02
78 93 0.96
79 2 0.02
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.48
Consensus pattern (78 bp):
CTCTATTGTTGAGGAGTTTTTATTTTTAAAGTTATGTGCCTTTATTATTGAAAAGCCCTTATTGT
TAAAGTGGTATGC
Found at i:13573505 original size:29 final size:28
Alignment explanation
Indices: 13573459--13573540 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
13573449 CCAAGTTGAC
13573459 ATTTTTAGTATTTT-TTTAGTTTTTTTATT
1 ATTTTTA-T-TTTTATTTAGTTTTTTTATT
* *
13573488 ATTTGTTCTTTTTATTTA-TTTTATTTGTT
1 ATTT-TTATTTTTATTTAGTTTT-TTTATT
*
13573517 CTTTTTATTATTTATTT-GTTTTTT
1 ATTTTTATT-TTTATTTAGTTTTTT
13573541 AAATATTCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
28 14 0.32
29 28 0.64
30 2 0.05
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (28 bp):
ATTTTTATTTTTATTTAGTTTTTTTATT
Found at i:13573509 original size:25 final size:24
Alignment explanation
Indices: 13573471--13573529 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 24
13573461 TTTTAGTATT
13573471 TTTTTAGTTT-TTTTATTATTTGTTC
1 TTTTTA-TTTATTTT-TTATTTGTTC
13573496 TTTTTATTTA--TTTTATTTGTTC
1 TTTTTATTTATTTTTTATTTGTTC
13573518 TTTTTA-TTATTT
1 TTTTTATTTATTT
13573530 ATTTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 3 0.10
22 16 0.52
23 3 0.10
24 3 0.10
25 6 0.19
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (24 bp):
TTTTTATTTATTTTTTATTTGTTC
Found at i:13573514 original size:22 final size:20
Alignment explanation
Indices: 13573478--13573540 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 20
13573468 ATTTTTTTAG
13573478 TTTTT-TTA-TTATTTGTTC
1 TTTTTATTATTTATTTGTTC
13573496 TTTTTATTTATTTTATTTGTTC
1 TTTTTA-TTA-TTTATTTGTTC
13573518 TTTTTATTATTTATTTGTT-
1 TTTTTATTATTTATTTGTTC
13573537 TTTT
1 TTTT
13573541 AAATATTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.12
19 4 0.10
20 13 0.32
21 3 0.07
22 16 0.39
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTATTATTTATTTGTTC
Found at i:13573530 original size:25 final size:22
Alignment explanation
Indices: 13573486--13573540 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
13573476 AGTTTTTTTA
13573486 TTATTTGTTCTTTTTATTTATT
1 TTATTTGTTCTTTTTATTTATT
13573508 TTATTTGTTCTTTTTA-TTA-T
1 TTATTTGTTCTTTTTATTTATT
13573528 TTATTTGTT-TTTT
1 TTATTTGTTCTTTT
13573541 AAATATTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.12
20 10 0.30
21 3 0.09
22 16 0.48
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (22 bp):
TTATTTGTTCTTTTTATTTATT
Found at i:13578274 original size:25 final size:25
Alignment explanation
Indices: 13578246--13578293 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
13578236 AGTGAAAACC
13578246 AAGTTCTTGTAAGAGAATGAACAAG
1 AAGTTCTTGTAAGAGAATGAACAAG
13578271 AAGTTCTTGTAAGAGAATGAACA
1 AAGTTCTTGTAAGAGAATGAACA
13578294 TACTCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (25 bp):
AAGTTCTTGTAAGAGAATGAACAAG
Found at i:13581013 original size:23 final size:22
Alignment explanation
Indices: 13580983--13581025 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13580973 ATATATTAAA
* *
13580983 TTTTAAATAATTATTATAATTT
1 TTTTAAATAATAACTATAATTT
13581005 TTTTGAAATAATAACTATAAT
1 TTTT-AAATAATAACTATAAT
13581026 ATCTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAATAATAACTATAATTT
Found at i:13581600 original size:124 final size:123
Alignment explanation
Indices: 13581437--13581679 Score: 310
Period size: 124 Copynumber: 2.0 Consensus size: 123
13581427 GCTATTAAAA
* *
13581437 AAAATTTTTAGAGATTATTCAATGCGTTTTTGACGAAAAATACCTTGAGTAATCACGTCATAAAA
1 AAAATTTTTAGAGATTATTCAATGCGTTTTTAACGAAAAACACCTTGAGTAATCACGTCATAAAA
* *
13581502 ATTTATGAA-AGGATTATTGAAAGCATTTTTTATCATAAACGCTTTTAATAACCCTATT
66 ATTTATGAAGA-GATTATTGAAAGCATTTTTTATCAGAAACGCTTTCAATAACCCTATT
* * ** * *
13581560 AAAATGTTTTTGAGATTATTCAA-GATGTTTTTAATTAAAAACGCCTTGAGTAATCATGTCATAA
1 AAAAT-TTTTAGAGATTATTCAATG-CGTTTTTAACGAAAAACACCTTGAGTAATCACGTCATAA
* * ** *
13581624 AATTTTATGAAGAGATTATTGAATGTGTTTTTTGTCAGAAACGCTTTCAATAACCC
64 AAATTTATGAAGAGATTATTGAAAGCATTTTTTATCAGAAACGCTTTCAATAACCC
13581680 CATTTTTTGG
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
123 6 0.06
124 95 0.93
125 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (123 bp):
AAAATTTTTAGAGATTATTCAATGCGTTTTTAACGAAAAACACCTTGAGTAATCACGTCATAAAA
ATTTATGAAGAGATTATTGAAAGCATTTTTTATCAGAAACGCTTTCAATAACCCTATT
Found at i:13584571 original size:20 final size:20
Alignment explanation
Indices: 13584542--13584588 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
13584532 TAATTTCGCA
* *
13584542 TAATAAATAGTTAGAACATC
1 TAATATATAGTTAAAACATC
13584562 TAATATATAGTTAAAACATC
1 TAATATATAGTTAAAACATC
13584582 TAATATA
1 TAATATA
13584589 AATTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (20 bp):
TAATATATAGTTAAAACATC
Found at i:13585471 original size:20 final size:20
Alignment explanation
Indices: 13585442--13585487 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
13585432 TAAAGTTTGG
* *
13585442 TTTTCCATTAAATGTTTAGA
1 TTTTCAATTAAATGTTCAGA
*
13585462 TTTTCAATTAAGTGTTCAGA
1 TTTTCAATTAAATGTTCAGA
*
13585482 CTTTCA
1 TTTTCA
13585488 TGATTAGCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTTCAATTAAATGTTCAGA
Found at i:13603099 original size:36 final size:36
Alignment explanation
Indices: 13603043--13603174 Score: 160
Period size: 36 Copynumber: 3.7 Consensus size: 36
13603033 GGAGAGGAAA
13603043 TGGTATGAAAAAATTT-TATTTGATTAATGATCTTGG
1 TGGTATG-AAAAATTTCTATTTGATTAATGATCTTGG
** * *
13603079 TGGTATGAAAGCTTTCTATTTGATTGATGATCTTAG
1 TGGTATGAAAAATTTCTATTTGATTAATGATCTTGG
* * *
13603115 TGGTATGAAAAATTTTTATTTGATTAATGATCATGA
1 TGGTATGAAAAATTTCTATTTGATTAATGATCTTGG
*
13603151 TGGTAT-ACAAAATTTCTACTTGAT
1 TGGTATGA-AAAATTTCTATTTGAT
13603175 GATATTGACA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 7 0.09
36 74 0.91
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (36 bp):
TGGTATGAAAAATTTCTATTTGATTAATGATCTTGG
Found at i:13609122 original size:25 final size:24
Alignment explanation
Indices: 13609080--13609136 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
13609070 TATTGACATA
13609080 ATTATTAATTATTAAAAATCATTT
1 ATTATTAATTATTAAAAATCATTT
*
13609104 ATTATTACATTAATT-AAAATGATTT
1 ATTATTA-ATT-ATTAAAAATCATTT
13609129 ATTATTAA
1 ATTATTAA
13609137 AATAATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.27
25 19 0.63
26 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTATTAATTATTAAAAATCATTT
Found at i:13609137 original size:16 final size:16
Alignment explanation
Indices: 13609114--13609154 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13609104 ATTATTACAT
* *
13609114 TAATTAAAATGATTTA
1 TAATTAAAATAATTGA
*
13609130 TTATTAAAATAATTGA
1 TAATTAAAATAATTGA
13609146 TAATTAAAA
1 TAATTAAAA
13609155 AATAATTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TAATTAAAATAATTGA
Found at i:13609142 original size:25 final size:25
Alignment explanation
Indices: 13609094--13609143 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13609084 TTAATTATTA
* *
13609094 AAAATCATTTATTATTACATTAATT
1 AAAATCATTTATTATTAAAATAATT
*
13609119 AAAATGATTTATTATTAAAATAATT
1 AAAATCATTTATTATTAAAATAATT
13609144 GATAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAATCATTTATTATTAAAATAATT
Found at i:13609170 original size:18 final size:19
Alignment explanation
Indices: 13609134--13609189 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
13609124 GATTTATTAT
*
13609134 TAAAATAATTGATA-ATTAA
1 TAAAATAATT-ATATTTTAA
13609153 -AAAATAATTATATTTTAA
1 TAAAATAATTATATTTTAA
*
13609171 TAATAATATTTA-ATTTTAA
1 TAA-AATAATTATATTTTAA
13609190 CAATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 13 0.41
19 9 0.28
20 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TAAAATAATTATATTTTAA
Found at i:13612738 original size:17 final size:16
Alignment explanation
Indices: 13612637--13612761 Score: 53
Period size: 17 Copynumber: 7.7 Consensus size: 16
13612627 GGGTTTTGAA
13612637 TTTTAGGGTTTCAAGGG
1 TTTTAGGGTTTCAA-GG
*
13612654 TTTTA-GGTTTTATA-G
1 TTTTAGGGTTTCA-AGG
* *
13612669 TTTTAAGGTTTCAAAAG
1 TTTTAGGGTTTC-AAGG
** *
13612686 TTTT-GGAACTT-AGGG
1 TTTTAGG-GTTTCAAGG
* *
13612701 TTTTGAAGGTTTGAA-G
1 TTTT-AGGGTTTCAAGG
13612717 TTTTAGGGTTTCACAGG
1 TTTTAGGGTTTCA-AGG
** *
13612734 TTTTAGATTTTTAAGG
1 TTTTAGGGTTTCAAGG
13612750 TTTATAGGGTTT
1 TTT-TAGGGTTT
13612762 AGAGGGTTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 22
0.66 0.15 0.18
Matches are distributed among these distances:
15 19 0.24
16 27 0.34
17 33 0.42
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.47
Consensus pattern (16 bp):
TTTTAGGGTTTCAAGG
Found at i:13612829 original size:25 final size:25
Alignment explanation
Indices: 13612775--13612862 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 25
13612765 GGGTTTTATG
* *
13612775 GTTTTGAATTTTTAAGGTTTTGATGA
1 GTTTTGAATTTTTAAGG-TTTCAAGA
* *
13612801 -TTTTGGATTTTTAAGGTCTCAAGA
1 GTTTTGAATTTTTAAGGTTTCAAGA
* *
13612825 GTTTT-AATTTTTAGGGTTTCAAGG
1 GTTTTGAATTTTTAAGGTTTCAAGA
*
13612849 GTTTTAGATTTTTT
1 GTTTT-GAATTTTT
13612863 TTTTTTGAGA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 25 0.50
25 19 0.38
26 6 0.12
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (25 bp):
GTTTTGAATTTTTAAGGTTTCAAGA
Found at i:13613301 original size:15 final size:16
Alignment explanation
Indices: 13613281--13613320 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
13613271 CAAGATTTTC
*
13613281 AAAATTATTTTTTA-A
1 AAAATTATTTTGTATA
13613296 AAAATTATTTTGTATA
1 AAAATTATTTTGTATA
*
13613312 AATATTATT
1 AAAATTATT
13613321 CTATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AAAATTATTTTGTATA
Found at i:13616424 original size:22 final size:22
Alignment explanation
Indices: 13616380--13616458 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
13616370 GGGTGTCAAT
* *
13616380 TAATCTGGGCTTGAGGTATCAGC
1 TAATCTAGGCTTG-GGTACCAGC
13616403 TAATCTAGGCTTGGGTACCAGC
1 TAATCTAGGCTTGGGTACCAGC
* * *
13616425 TACTC-AGGGCTTGGGTGCCAAC
1 TAATCTA-GGCTTGGGTACCAGC
*
13616447 TAAACTAGGCTT
1 TAATCTAGGCTT
13616459 AAACTTGAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.02
22 33 0.70
23 13 0.28
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (22 bp):
TAATCTAGGCTTGGGTACCAGC
Found at i:13616595 original size:29 final size:29
Alignment explanation
Indices: 13616551--13616627 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
13616541 TTAAGTGCAA
* * **
13616551 GCTAAACTAGGTTTAAAATTTGTATG-CT
1 GCTAAACTGGGCTTAAAATCCGTATGCCT
* *
13616579 AGCTAAATTGGGCTT-AAATCCGTGTGCCT
1 -GCTAAACTGGGCTTAAAATCCGTATGCCT
13616608 GCTAAACTGGGCTTAAAATC
1 GCTAAACTGGGCTTAAAATC
13616628 TAACTGCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (29 bp):
GCTAAACTGGGCTTAAAATCCGTATGCCT
Found at i:13625924 original size:27 final size:27
Alignment explanation
Indices: 13625891--13625960 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
13625881 TTTGGTTCAG
*
13625891 ATTTTTAGGGTTTTGAGGGTTTTAAAA
1 ATTTTTAGGGTTTTGAGGGTTTAAAAA
* **
13625918 ATTTTTAAGGTTTCAAGGGTTTAAAAA
1 ATTTTTAGGGTTTTGAGGGTTTAAAAA
*
13625945 AATTTTAGGGTTTTGA
1 ATTTTTAGGGTTTTGA
13625961 ATTTTAAAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (27 bp):
ATTTTTAGGGTTTTGAGGGTTTAAAAA
Found at i:13625965 original size:15 final size:15
Alignment explanation
Indices: 13625945--13626091 Score: 76
Period size: 15 Copynumber: 9.9 Consensus size: 15
13625935 GGTTTAAAAA
13625945 AATTTTAGGGTTTTG
1 AATTTTAGGGTTTTG
** *
13625960 AATTTTAAAGTTTCG
1 AATTTTAGGGTTTTG
*
13625975 AAGGTTTCA-GGTTTTAG
1 AA--TTTTAGGGTTTT-G
*
13625992 AGTTTTAGGGTTTTG
1 AATTTTAGGGTTTTG
* *
13626007 AATTATAAGGTTTTG
1 AATTTTAGGGTTTTG
13626022 AA----A--GTTTTG
1 AATTTTAGGGTTTTG
* * *
13626031 GACTTTAGGGTTTCG
1 AATTTTAGGGTTTTG
13626046 AAGGTTTT-GAGGTTTTG
1 AA--TTTTAG-GGTTTTG
*
13626063 AAATTTTGGGGTTTTG
1 -AATTTTAGGGTTTTG
13626079 AATTTTAGGGTTT
1 AATTTTAGGGTTT
13626092 CGAAGGTTTT
Statistics
Matches: 100, Mismatches: 17, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
9 7 0.07
11 1 0.01
13 1 0.01
15 51 0.51
16 22 0.22
17 16 0.16
18 2 0.02
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (15 bp):
AATTTTAGGGTTTTG
Found at i:13626082 original size:72 final size:71
Alignment explanation
Indices: 13625969--13626104 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 71
13625959 GAATTTTAAA
* *
13625969 GTTTCGAAGGTTTCAGGTTTTAGAGTTTTAGGGTTTTGAATTATAAGGTTTTGAAAGTTTTGGAC
1 GTTTCGAAGGTTTCAGGTTTTAGAATTTTAGGGTTTTGAATTATAAGGTTTCGAAAGTTTTGGAC
13626034 TTTAGG
66 TTTAGG
* * * * *
13626040 GTTTCGAAGGTTTTGAGGTTTT-GAAATTTTGGGGTTTTGAATTTTAGGGTTTCGAAGGTTTTGG
1 GTTTCGAAGG-TTTCAGGTTTTAG-AATTTTAGGGTTTTGAATTATAAGGTTTCGAAAGTTTTGG
13626104 A
64 A
13626105 TTGTTAAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
71 11 0.20
72 45 0.80
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.46
Consensus pattern (71 bp):
GTTTCGAAGGTTTCAGGTTTTAGAATTTTAGGGTTTTGAATTATAAGGTTTCGAAAGTTTTGGAC
TTTAGG
Found at i:13626130 original size:17 final size:17
Alignment explanation
Indices: 13626108--13626163 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
13626098 TTTTGGATTG
13626108 TTAAAGTTTCAAAGGTT
1 TTAAAGTTTCAAAGGTT
13626125 TTAAAGGTTTC-AAGGTT
1 TTAAA-GTTTCAAAGGTT
** *
13626142 TTAGGCGTTTCAAGGGTT
1 TTA-AAGTTTCAAAGGTT
13626160 TTAA
1 TTAA
13626164 TGGTTTTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (17 bp):
TTAAAGTTTCAAAGGTT
Found at i:13626168 original size:9 final size:9
Alignment explanation
Indices: 13626121--13626219 Score: 50
Period size: 9 Copynumber: 11.7 Consensus size: 9
13626111 AAGTTTCAAA
*
13626121 GGTTTTAAA
1 GGTTTTAAG
*
13626130 GGTTTCAA-
1 GGTTTTAAG
13626138 GGTTTT-AG
1 GGTTTTAAG
*
13626146 GCGTTTCAAG
1 G-GTTTTAAG
*
13626156 GGTTTTAAT
1 GGTTTTAAG
13626165 GGTTTT--G
1 GGTTTTAAG
* *
13626172 GATTTTTAG
1 GGTTTTAAG
*
13626181 GG-TTCAAG
1 GGTTTTAAG
13626189 GGTTTT--G
1 GGTTTTAAG
* *
13626196 GATTTTTAG
1 GGTTTTAAG
*
13626205 GGTTTCAAG
1 GGTTTTAAG
13626214 GGTTTT
1 GGTTTT
13626220 GGACTTTTAG
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
7 12 0.18
8 12 0.18
9 39 0.59
10 3 0.05
ACGTcount: A:0.18, C:0.05, G:0.30, T:0.46
Consensus pattern (9 bp):
GGTTTTAAG
Found at i:13626194 original size:24 final size:25
Alignment explanation
Indices: 13626154--13626243 Score: 121
Period size: 24 Copynumber: 3.7 Consensus size: 25
13626144 AGGCGTTTCA
* *
13626154 AGGGTTTTAATGGTTTTGGATTTTT
1 AGGGTTTCAAGGGTTTTGGATTTTT
13626179 AGGG-TTCAAGGGTTTTGGATTTTT
1 AGGGTTTCAAGGGTTTTGGATTTTT
*
13626203 AGGGTTTCAAGGGTTTTGGACTTTT
1 AGGGTTTCAAGGGTTTTGGATTTTT
**
13626228 A-GGTTTTGAGGGTTTT
1 AGGGTTTCAAGGGTTTT
13626244 CATAGTTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
24 35 0.59
25 24 0.41
ACGTcount: A:0.16, C:0.03, G:0.32, T:0.49
Consensus pattern (25 bp):
AGGGTTTCAAGGGTTTTGGATTTTT
Found at i:13633545 original size:18 final size:17
Alignment explanation
Indices: 13633524--13633566 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
13633514 AAAATGAAAT
*
13633524 AAATAAAATCGAAAGTAA
1 AAATAAAATC-AAAATAA
13633542 AAATAAAATCAAAATAA
1 AAATAAAATCAAAATAA
13633559 ATAATAAA
1 A-AATAAA
13633567 TAAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (17 bp):
AAATAAAATCAAAATAA
Found at i:13633567 original size:11 final size:11
Alignment explanation
Indices: 13633553--13633577 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13633543 AATAAAATCA
13633553 AAATAAATAAT
1 AAATAAATAAT
13633564 AAATAAATAAT
1 AAATAAATAAT
13633575 AAA
1 AAA
13633578 ATCAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:13634316 original size:3 final size:3
Alignment explanation
Indices: 13634310--13634371 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
13634300 AATAATAATA
* *
13634310 ATG ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
* *
13634358 ATA ATG ATA ATG AT
1 ATG ATG ATG ATG AT
13634372 AATAATAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:13634401 original size:21 final size:19
Alignment explanation
Indices: 13634383--13634425 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
13634373 ATAATAGTGC
13634383 TAATATAATATACTATAGTA
1 TAATA-AATATACTATAGTA
*
13634403 TAATAAATATAGTAT--TA
1 TAATAAATATACTATAGTA
13634420 TAATAA
1 TAATAA
13634426 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (19 bp):
TAATAAATATACTATAGTA
Found at i:13634491 original size:3 final size:3
Alignment explanation
Indices: 13634419--13634472 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
13634409 ATATAGTATT
13634419 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13634467 ATA ATA
1 ATA ATA
13634473 CTATCATACT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13634562 original size:13 final size:13
Alignment explanation
Indices: 13634387--13634588 Score: 63
Period size: 15 Copynumber: 14.5 Consensus size: 13
13634377 TAGTGCTAAT
13634387 ATAATATACTATA
1 ATAATATACTATA
*
13634400 GTATAATA-AATATA
1 --ATAATATACTATA
* *
13634414 GTATTATA--ATA
1 ATAATATACTATA
*
13634425 ATAATAATAATAATA
1 ATAAT-ATACT-ATA
*
13634440 ATAATAATAATAATA
1 ATAAT-ATACT-ATA
*
13634455 ATAATAATAATAATA
1 ATAAT-ATACT-ATA
13634470 ATACTATCATACTATA
1 ATA--AT-ATACTATA
* *
13634486 ATAATATGCAAT-
1 ATAATATACTATA
* * *
13634498 GTAATGTACTGTA
1 ATAATATACTATA
13634511 CTATACACTATACTATA
1 --ATA-A-TATACTATA
*
13634528 ATAATACTAATATA
1 ATAATA-TACTATA
13634542 A-AACTATACTATA
1 ATAA-TATACTATA
*
13634555 ATATTATACTATA
1 ATAATATACTATA
* *
13634568 ACACATTATCCTATA
1 ATA-A-TATACTATA
13634583 ATAATA
1 ATAATA
13634589 ATAAATAATA
Statistics
Matches: 146, Mismatches: 24, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
11 6 0.04
12 14 0.10
13 30 0.21
14 19 0.13
15 57 0.39
16 7 0.05
17 13 0.09
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (13 bp):
ATAATATACTATA
Found at i:13660184 original size:21 final size:21
Alignment explanation
Indices: 13660160--13660200 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13660150 ACCAGGCCCT
*
13660160 GGTGCAGGCAAACCAAGCCTA
1 GGTGAAGGCAAACCAAGCCTA
* *
13660181 GGTGAAGGCACACCAGGCCT
1 GGTGAAGGCAAACCAAGCCT
13660201 CGGTAAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.10
Consensus pattern (21 bp):
GGTGAAGGCAAACCAAGCCTA
Found at i:13663071 original size:21 final size:21
Alignment explanation
Indices: 13663047--13663089 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13663037 TAGATCATAT
13663047 ACTCTACAATGTACTCTAACA
1 ACTCTACAATGTACTCTAACA
*
13663068 ACTCTACAATTTACTCTAACA
1 ACTCTACAATGTACTCTAACA
13663089 A
1 A
13663090 TGGATTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.30
Consensus pattern (21 bp):
ACTCTACAATGTACTCTAACA
Found at i:13668914 original size:145 final size:145
Alignment explanation
Indices: 13668651--13668994 Score: 553
Period size: 145 Copynumber: 2.4 Consensus size: 145
13668641 TTTAATATTA
* * *
13668651 ATTAATTTATGCGGCTTATTAATTTTATGCCCAAGAAAAGTAATGAACTAAATTTCGTCAAACAT
1 ATTAATTTATGCGGCTTATTAACTTTGTCCCCAAGAAAAGTAATGAACTAAATTTCGTCAAACAT
* *
13668716 TCATAGTAGTCAAACGAGCAACATGGATGGATCACGTAGAAACATGTACACTTGCTGCCCACGAA
66 TCATAGTAGTCAAACAAGAAACATGGATGGATCACGTAGAAACATGTACACTTGCTGCCCACGAA
*
13668781 ACAACATGGAGAAGC
131 ACAACACGGAGAAGC
* **
13668796 ATTAATTTATGCGGCTTATTAACTTTGTCCCCAAGAAAAGTAATGAACTAAATTTCTTGGAACAT
1 ATTAATTTATGCGGCTTATTAACTTTGTCCCCAAGAAAAGTAATGAACTAAATTTCGTCAAACAT
* *
13668861 TCATAGTAGTCAAACAAGAAACATGGATGGATCACGTAGAAACATGTAGACTTGTTGCCCACGAA
66 TCATAGTAGTCAAACAAGAAACATGGATGGATCACGTAGAAACATGTACACTTGCTGCCCACGAA
13668926 ACAACACGGAGAAGC
131 ACAACACGGAGAAGC
* * * *
13668941 ATTAATTTACGCGGCTTATTCACTTTGTCCCCAAGAAAATTACTGAACTAAATT
1 ATTAATTTATGCGGCTTATTAACTTTGTCCCCAAGAAAAGTAATGAACTAAATT
13668995 GCATGCAGCT
Statistics
Matches: 184, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
145 184 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (145 bp):
ATTAATTTATGCGGCTTATTAACTTTGTCCCCAAGAAAAGTAATGAACTAAATTTCGTCAAACAT
TCATAGTAGTCAAACAAGAAACATGGATGGATCACGTAGAAACATGTACACTTGCTGCCCACGAA
ACAACACGGAGAAGC
Found at i:13669638 original size:14 final size:14
Alignment explanation
Indices: 13669619--13669650 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13669609 CAAAAAAAAA
13669619 AATTTATAAGTAAT
1 AATTTATAAGTAAT
*
13669633 AATTTATAAGTGAT
1 AATTTATAAGTAAT
13669647 AATT
1 AATT
13669651 CCGAATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (14 bp):
AATTTATAAGTAAT
Found at i:13673089 original size:9 final size:9
Alignment explanation
Indices: 13673075--13673101 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13673065 ATATTTTAAA
13673075 ATAATTTTT
1 ATAATTTTT
13673084 ATAATTTTT
1 ATAATTTTT
13673093 ATAATTTTT
1 ATAATTTTT
13673102 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:13677078 original size:10 final size:10
Alignment explanation
Indices: 13677058--13677092 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
13677048 CTTCTAAAAC
13677058 CTTTT-CTTT
1 CTTTTACTTT
13677067 CTTTTACTTT
1 CTTTTACTTT
*
13677077 CTTTTTCTTT
1 CTTTTACTTT
13677087 CTTTTA
1 CTTTTA
13677093 TTAATGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (10 bp):
CTTTTACTTT
Found at i:13678774 original size:2 final size:2
Alignment explanation
Indices: 13678724--13678754 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13678714 ACTCAAATTG
13678724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13678755 CACACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13683842 original size:18 final size:17
Alignment explanation
Indices: 13683788--13683843 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
13683778 TAAGTTTAGA
13683788 TTTA-GTTTAGGGTTT-G
1 TTTAGGTTTA-GGTTTGG
*
13683804 TTTAGGATTTGAGGATTGG
1 TTTAGG-TTT-AGGTTTGG
13683823 TTTAAGGTTTAGGTTTGG
1 TTT-AGGTTTAGGTTTGG
13683841 TTT
1 TTT
13683844 GGGCTTGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 4 0.12
17 1 0.03
18 17 0.52
19 8 0.24
20 3 0.09
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (17 bp):
TTTAGGTTTAGGTTTGG
Found at i:13687483 original size:134 final size:134
Alignment explanation
Indices: 13687236--13687503 Score: 367
Period size: 134 Copynumber: 2.0 Consensus size: 134
13687226 ATATATGCAC
* *
13687236 TGATTACCATGTTTTTCTTAAGTGACAATCTCATCAAACTTTAATTATCACAAATTAGATAACTT
1 TGATTACCATGTTTTCCTTAAGTGACAATCTCATCAAACTTTAAATATCACAAATTAGATAACTT
* * * * * *
13687301 TTAAGTCCACAAAAGGAAATCTTGTTTTTATAAATTGAATGTTCCATTACAAAAAACCATAGAAA
66 TTAAGTCCACAAAAGGAAATCTCGTGTTTATAAACTGAATATTCCATTACAAAAAACCACAAAAA
13687366 CTTT
131 CTTT
* * *
13687370 TGATTACCATGTTTTCCTTAAGTGATAATCTCATCAAACTTTAAATATTACAAATTAGAT-GCAT
1 TGATTACCATGTTTTCCTTAAGTGACAATCTCATCAAACTTTAAATATCACAAATTAGATAAC-T
* * * * * *
13687434 TTTGAGTCCACAAATGGATATCTCGTGTTTATAAACTGAATATTTCATTATAGAAAACCACAAAA
65 TTTAAGTCCACAAAAGGAAATCTCGTGTTTATAAACTGAATATTCCATTACAAAAAACCACAAAA
13687499 ACTTT
130 ACTTT
13687504 ATGTTGCTCC
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
133 1 0.01
134 115 0.99
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (134 bp):
TGATTACCATGTTTTCCTTAAGTGACAATCTCATCAAACTTTAAATATCACAAATTAGATAACTT
TTAAGTCCACAAAAGGAAATCTCGTGTTTATAAACTGAATATTCCATTACAAAAAACCACAAAAA
CTTT
Found at i:13688189 original size:6 final size:6
Alignment explanation
Indices: 13688172--13688219 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
13688162 GTTTTATTGG
* * *
13688172 ATTTGA ATTTTGA ATTTGA ATTTGA ATTTTTA GTTTTA ATTTGA ATTT
1 ATTTGA A-TTTGA ATTTGA ATTTGA A-TTTGA ATTTGA ATTTGA ATTT
13688220 TGATTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 26 0.72
7 10 0.28
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.58
Consensus pattern (6 bp):
ATTTGA
Found at i:13688196 original size:19 final size:19
Alignment explanation
Indices: 13688172--13688231 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
13688162 GTTTTATTGG
*
13688172 ATTTGAATTTTGAATTTGA
1 ATTTGAATTTTGAATTTCA
* * *
13688191 ATTTGAATTTTTAGTTTTA
1 ATTTGAATTTTGAATTTCA
13688210 ATTTGAATTTTG-ATTTCA
1 ATTTGAATTTTGAATTTCA
13688228 ATTT
1 ATTT
13688232 TATTTTAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
18 8 0.23
19 27 0.77
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (19 bp):
ATTTGAATTTTGAATTTCA
Found at i:13688225 original size:12 final size:12
Alignment explanation
Indices: 13688171--13688236 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
13688161 AGTTTTATTG
13688171 GATTTGAATTTT
1 GATTTGAATTTT
13688183 GAATTTGAA-TTT
1 G-ATTTGAATTTT
* *
13688195 GAATTTTTAGTTTT
1 G-A-TTTGAATTTT
*
13688209 AATTTGAATTTT
1 GATTTGAATTTT
*
13688221 GATTTCAATTTT
1 GATTTGAATTTT
13688233 -ATTT
1 GATTT
13688237 TAGTTTTTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 4 0.09
12 25 0.57
13 12 0.27
14 3 0.07
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (12 bp):
GATTTGAATTTT
Found at i:13690076 original size:6 final size:6
Alignment explanation
Indices: 13690066--13690106 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
13690056 TCTTAGTTTT
* *
13690066 AATTTG GATTTG AATTTG AATTTG AATTTA AATTTG AATTT
1 AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG AATTT
13690107 TTAGTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
AATTTG
Found at i:13690120 original size:12 final size:11
Alignment explanation
Indices: 13690105--13690160 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 11
13690095 AAATTTGAAT
*
13690105 TTTTAGTTTTAA
1 TTTTAATTTT-A
13690117 TTTTAATTTTGA
1 TTTTAATTTT-A
13690129 TTTTAATTTTA
1 TTTTAATTTTA
*
13690140 TTTTAGTTTT-
1 TTTTAATTTTA
13690150 TGTTTAATTTT
1 T-TTTAATTTT
13690161 GAGTCAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
10 1 0.03
11 18 0.46
12 20 0.51
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:13690132 original size:18 final size:18
Alignment explanation
Indices: 13690062--13690143 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
13690052 TTAATCTTAG
* *
13690062 TTTTAATTTGGATTTGAA
1 TTTTAATTTTGATTTTAA
* *
13690080 TTTGAA-TTTGAATTTAAA
1 TTTTAATTTTG-ATTTTAA
* *
13690098 TTTGAATTTTTAGTTTTAA
1 TTTTAATTTTGA-TTTTAA
13690117 TTTTAATTTTGATTTTAA
1 TTTTAATTTTGATTTTAA
13690135 TTTT-ATTTT
1 TTTTAATTTT
13690144 AGTTTTTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.15
18 28 0.52
19 18 0.33
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTAATTTTGATTTTAA
Found at i:13690150 original size:18 final size:18
Alignment explanation
Indices: 13690105--13690149 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
13690095 AAATTTGAAT
13690105 TTTTAGTTTTAATTTTAA
1 TTTTAGTTTTAATTTTAA
13690123 TTTT-GATTTTAATTTT-A
1 TTTTAG-TTTTAATTTTAA
13690140 TTTTAGTTTT
1 TTTTAGTTTT
13690150 TGTTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (18 bp):
TTTTAGTTTTAATTTTAA
Found at i:13691255 original size:8 final size:7
Alignment explanation
Indices: 13691243--13691297 Score: 76
Period size: 7 Copynumber: 7.9 Consensus size: 7
13691233 NNNNNNNNNA
13691243 AAAAAAC
1 AAAAAAC
13691250 AAAAAAC
1 AAAAAAC
13691257 AAAAAAC
1 AAAAAAC
*
13691264 AAAAAAT
1 AAAAAAC
13691271 AAAAAA-
1 AAAAAAC
*
13691277 ACAAAAC
1 AAAAAAC
13691284 AAAAAAAC
1 -AAAAAAC
13691292 AAAAAA
1 AAAAAA
13691298 TAACAATGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 5 0.12
7 32 0.74
8 6 0.14
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAAAAC
Found at i:13691288 original size:28 final size:29
Alignment explanation
Indices: 13691244--13691300 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
13691234 NNNNNNNNAA
13691244 AAAAACAAAAAACAAAAAACAAAAAATAA
1 AAAAACAAAAAACAAAAAACAAAAAATAA
*
13691273 AAAAACAAAACA-AAAAAACAAAAAATAA
1 AAAAACAAAAAACAAAAAACAAAAAATAA
13691301 CAATGTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.04
Consensus pattern (29 bp):
AAAAACAAAAAACAAAAAACAAAAAATAA
Found at i:13692117 original size:26 final size:27
Alignment explanation
Indices: 13692079--13692135 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
13692069 CTGTAGGGAT
* *
13692079 CGAAAATAATTTTTTAGAAATTTTTGG
1 CGAAAATAATTTTCTAAAAATTTTTGG
13692106 CGAAAA-AATTTTCTAAAAATTTTTGG
1 CGAAAATAATTTTCTAAAAATTTTTGG
13692132 -GAAA
1 CGAAA
13692136 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 18 0.64
27 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (27 bp):
CGAAAATAATTTTCTAAAAATTTTTGG
Found at i:13692734 original size:41 final size:40
Alignment explanation
Indices: 13692657--13692736 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
13692647 GCTCCAGGTT
* *
13692657 TTTTTTTCTTTTTTTTTATTTTCATTTATTTGTTTATTTG
1 TTTTTTTCTTTTTTTTTATTTTCATTGATTAGTTTATTTG
13692697 TTTTTTTCTATTTTTTTTA-TTT-ATTAGATTAGATTTATTT
1 TTTTTTTCT-TTTTTTTTATTTTCATT-GATTAG-TTTATTT
13692737 AATATTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 3 0.09
40 16 0.46
41 16 0.46
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.76
Consensus pattern (40 bp):
TTTTTTTCTTTTTTTTTATTTTCATTGATTAGTTTATTTG
Found at i:13692784 original size:21 final size:23
Alignment explanation
Indices: 13692739--13692789 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
13692729 ATTTATTTAA
13692739 TATTTTTATCTTTATCTTATTTT
1 TATTTTTATCTTTATCTTATTTT
* *
13692762 TATTTTTGT-TTTA-CTTTTTTT
1 TATTTTTATCTTTATCTTATTTT
13692783 TATTTTT
1 TATTTTT
13692790 TTTCTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.54
22 4 0.15
23 8 0.31
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (23 bp):
TATTTTTATCTTTATCTTATTTT
Found at i:13692792 original size:30 final size:31
Alignment explanation
Indices: 13692742--13692819 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
13692732 TATTTAATAT
*
13692742 TTTTATCTTTATCTTATTTTTATT-TTTGTTTTAC
1 TTTTAT-TTTAT-TT-TTTTTATTCTTT-ATTTAC
*
13692776 TTTT-TTTTATTTTTTTTCTTCTTTATTTAC
1 TTTTATTTTATTTTTTTTATTCTTTATTTAC
*
13692806 TTTTATTTTGTTTT
1 TTTTATTTTATTTT
13692820 ATATTCTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 16 0.41
31 13 0.33
32 5 0.13
33 1 0.03
34 4 0.10
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.78
Consensus pattern (31 bp):
TTTTATTTTATTTTTTTTATTCTTTATTTAC
Found at i:13692799 original size:21 final size:21
Alignment explanation
Indices: 13692739--13692799 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
13692729 ATTTATTTAA
* *
13692739 TATTTTTATCTTTATCTTATTTT
1 TATTTTTGT-TTT-TCTTTTTTT
*
13692762 TATTTTTGTTTTACTTTTTTT
1 TATTTTTGTTTTTCTTTTTTT
13692783 TATTTTT-TTTCTTCTTT
1 TATTTTTGTTT-TTCTTT
13692800 ATTTACTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.09
21 19 0.58
22 3 0.09
23 8 0.24
ACGTcount: A:0.11, C:0.08, G:0.02, T:0.79
Consensus pattern (21 bp):
TATTTTTGTTTTTCTTTTTTT
Found at i:13692809 original size:21 final size:20
Alignment explanation
Indices: 13692742--13692814 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
13692732 TATTTAATAT
*
13692742 TTTTATCTTTATCTTATTTTTA
1 TTTTAT-TTTA-CTTTTTTTTA
*
13692764 TTTTTGTTTTACTTTTTTTTA
1 -TTTTATTTTACTTTTTTTTA
13692785 TTTT-TTTT-CTTCTTTATTTA
1 TTTTATTTTACTT-TTT-TTTA
13692805 CTTTTATTTT
1 -TTTTATTTT
13692815 GTTTTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.07
19 7 0.16
20 8 0.18
21 13 0.30
22 8 0.18
23 5 0.11
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTTATTTTACTTTTTTTTA
Found at i:13692821 original size:10 final size:9
Alignment explanation
Indices: 13692656--13692792 Score: 51
Period size: 10 Copynumber: 13.9 Consensus size: 9
13692646 CGCTCCAGGT
*
13692656 TTTTTTTTCT
1 TTTTTTTT-A
13692666 TTTTTTTTA
1 TTTTTTTTA
*
13692675 TTTTCATTTA
1 TTTT-TTTTA
*
13692685 TTTGTTTATTTG
1 -TT-TTT-TTTA
13692697 TTTTTTTCTA
1 TTTTTTT-TA
13692707 TTTTTTTTA
1 TTTTTTTTA
*
13692716 TTTATTAGATTA
1 TTT-TT--TTTA
* *
13692728 GATTTATTTA
1 -TTTTTTTTA
* *
13692738 ATATTTTTA
1 TTTTTTTTA
*
13692747 TCTTTATCTTA
1 T-TTT-TTTTA
*
13692758 TTTTTATT-
1 TTTTTTTTA
*
13692766 TTTGTTTTA
1 TTTTTTTTA
13692775 CTTTTTTTTA
1 -TTTTTTTTA
13692785 TTTTTTTT
1 TTTTTTTT
13692793 CTTCTTTATT
Statistics
Matches: 96, Mismatches: 18, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
8 6 0.06
9 29 0.30
10 41 0.43
11 9 0.09
12 9 0.09
13 2 0.02
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:13692920 original size:58 final size:57
Alignment explanation
Indices: 13692841--13693168 Score: 521
Period size: 57 Copynumber: 5.7 Consensus size: 57
13692831 ATAAAAATCA
* * *
13692841 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAGAAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
*
13692898 AAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
1 AAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
* *
13692956 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
* * * *
13693013 AAAAAATATTTTTGGGAAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAATTTCA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
* *
13693070 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
*
13693127 AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCC
1 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
13693169 CTACACAAGA
Statistics
Matches: 248, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
57 156 0.63
58 92 0.37
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
Found at i:13693058 original size:114 final size:114
Alignment explanation
Indices: 13692829--13693168 Score: 560
Period size: 115 Copynumber: 3.0 Consensus size: 114
13692819 TATATTCTTT
** *
13692829 AAATAAAAATCAAAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCTTTAGAAATAAA
1 AAATAAATTTCAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
*
13692893 TTTCCAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAA
65 TTTCCAAAAAATA-TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAA
13692944 AAATAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
1 AAATAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
* *
13693009 TTCCAAAAAATATTTTTGGGAAAAAGTTGAAAATATCAATTTTTCTTAA
66 TTCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAA
13693058 AAATAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AAAGTAAA
1 AAATAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA-TAAA
13693122 TTTCCAAAAAAATATTTTT-GGAGAAAAGTTGAAAGTATCAATTTTCC
65 TTTCC-AAAAAATATTTTTGGGA-AAAAGTTGAAAGTATCAATTTTCC
13693169 CTACACAAGA
Statistics
Matches: 213, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
113 3 0.01
114 102 0.48
115 107 0.50
116 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (114 bp):
AAATAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
TTCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:13693860 original size:32 final size:32
Alignment explanation
Indices: 13693819--13693882 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
13693809 ATATTAAGAG
13693819 AATGATTAATCCTCCTTT-CAATCTTATCCTTT
1 AATGATTAATCCT-CTTTACAATCTTATCCTTT
*
13693851 AATGATTAATCCTCTTTACAATCTTATTCTTT
1 AATGATTAATCCTCTTTACAATCTTATCCTTT
13693883 TTTTAGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.48
Consensus pattern (32 bp):
AATGATTAATCCTCTTTACAATCTTATCCTTT
Found at i:13694899 original size:3 final size:3
Alignment explanation
Indices: 13694891--13694931 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
13694881 ACATGTACAA
* *
13694891 AAT AAT AAT AAT AAT AAT ATT CA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13694932 TCAACACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:13694919 original size:20 final size:21
Alignment explanation
Indices: 13694894--13694935 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
13694884 TGTACAAAAT
13694894 AATAATAATAATAAT-ATTCA
1 AATAATAATAATAATAATTCA
13694914 AATAATAATAATAATAATTCA
1 AATAATAATAATAATAATTCA
13694935 A
1 A
13694936 CACAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAATAATAATAATTCA
Found at i:13695116 original size:28 final size:28
Alignment explanation
Indices: 13695047--13695117 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
13695037 TTAAATTAAA
13695047 ATAACATATTTAATATGATATTTGAAATTT
1 ATAA-ATATTTAATATGATATTTGAAA-TT
* * *
13695077 AAAAATTTTTAATGTGATATTT-AAATT
1 ATAAATATTTAATATGATATTTGAAATT
13695104 ATAAATATATTAAT
1 ATAAATAT-TTAAT
13695118 TAATACGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 8 0.23
28 8 0.23
29 16 0.46
30 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (28 bp):
ATAAATATTTAATATGATATTTGAAATT
Found at i:13695804 original size:24 final size:24
Alignment explanation
Indices: 13695752--13695805 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
13695742 TATCATTTAG
*
13695752 GAAAAATAAAAAAAATATAAAGTA
1 GAAAAATAAAAAAAATATAAAGGA
*
13695776 TAAAAATATAAGAAAAA-A-AAAGGA
1 GAAAAATA-AA-AAAAATATAAAGGA
13695800 GAAAAA
1 GAAAAA
13695806 GGCGTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (24 bp):
GAAAAATAAAAAAAATATAAAGGA
Found at i:13706555 original size:19 final size:19
Alignment explanation
Indices: 13706533--13706601 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
13706523 TTGGAAAATA
*
13706533 GTTTATGGTTTGACTTAGG
1 GTTTAGGGTTTGACTTAGG
*
13706552 GTTTAGGGTTTGACCTAGG
1 GTTTAGGGTTTGACTTAGG
*
13706571 GTTT-GGGTTTGACTTAAG
1 GTTTAGGGTTTGACTTAGG
*
13706589 GTTTAAGGTTTGA
1 GTTTAGGGTTTGA
13706602 ATAAGACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
18 16 0.36
19 28 0.64
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.43
Consensus pattern (19 bp):
GTTTAGGGTTTGACTTAGG
Found at i:13709487 original size:3 final size:3
Alignment explanation
Indices: 13709481--13709520 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
13709471 TTTGTAAAAA
* *
13709481 ATT ATT ATT ATT ATT ATT ATT ATT ATCA ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
13709521 TTAAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13710094 original size:129 final size:126
Alignment explanation
Indices: 13709842--13710299 Score: 463
Period size: 129 Copynumber: 3.7 Consensus size: 126
13709832 TTTATTATAG
* * * * * *
13709842 TAATTTAATATGTATTTAAGTTTAGA-TA-ATT--AATCTACTATGTAATTTAAT-AGTAGTATT
1 TAATTTAATATGTAGTTAATTTTATATTATATTAAAATTTAATATGTAATTTAATAAGGA-TATT
* * * ** * * *
13709902 AAAGTAATTTTC--ATAAAATATCATATGTCAAATTTCCATGAAGTGATTGTAAAGGTATTTTAA
65 ATAGTAATTTTCAAACAAAATATCACATGTCAAATTTTTATAAAG-CAATG-AAA-GTATTTTAA
*
13709965 TAATTTAATATGTAGTTAATTTTATATTATATTAAAATTTAATATGTAATTTAATATGGATATTA
1 TAATTTAATATGTAGTTAATTTTATATTATATTAAAATTTAATATGTAATTTAATAAGGATATTA
*
13710030 TAGTAAATTTCAAACAAAATATCACATGTCAAATTTTTATAAAGCAATGGCAAAGCTATTTTAA
66 TAGTAATTTTCAAACAAAATATCACATGTCAAATTTTTATAAAGCAAT-G-AAAG-TATTTTAA
* * * * * *
13710094 T-ATTTCAATATGTAGTTAATTTTGTATTATGTTAAAATTTCATACGTAATTTAATAAGGGTCTT
1 TAATTT-AATATGTAGTTAATTTTATATTATATTAAAATTTAATATGTAATTTAATAAGGATATT
* * * *
13710158 A-AGATAATTTTCAAATAAAATACCACATATTAAATTTTTATAAAGCAAT---AGTATTTTAA
65 ATAG-TAATTTTCAAACAAAATATCACATGTCAAATTTTTATAAAGCAATGAAAGTATTTTAA
** * * *
13710217 TAATTTAATACATAGCTAATTTTATATTATGTTAAAATTTAATAAGTAATTTAATAAGGATATTA
1 TAATTTAATATGTAGTTAATTTTATATTATATTAAAATTTAATATGTAATTTAATAAGGATATTA
*
13710282 TAGTAATTTTGAAACAAA
66 TAGTAATTTTCAAACAAA
13710300 GTCAACTTCT
Statistics
Matches: 283, Mismatches: 39, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
123 96 0.34
124 10 0.04
125 3 0.01
127 32 0.11
128 11 0.04
129 131 0.46
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (126 bp):
TAATTTAATATGTAGTTAATTTTATATTATATTAAAATTTAATATGTAATTTAATAAGGATATTA
TAGTAATTTTCAAACAAAATATCACATGTCAAATTTTTATAAAGCAATGAAAGTATTTTAA
Found at i:13710857 original size:2 final size:2
Alignment explanation
Indices: 13710850--13710895 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13710840 CTCGTATGAA
13710850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13710892 AT AT
1 AT AT
13710896 GAGGCAAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13711106 original size:4 final size:4
Alignment explanation
Indices: 13711097--13711132 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
13711087 GATTTCTCTT
13711097 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC-A TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
13711133 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Done.