Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 167 of 222
Found at i:53459860 original size:47 final size:46
Alignment explanation
Indices: 53459804--53459968 Score: 181
Period size: 47 Copynumber: 3.5 Consensus size: 46
53459794 ATGTGTTATA
53459804 AATTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCC
1 AATTTAATGTATAATGCTGTCCAATTTTAAGTATATT-ATGCTGTCC
* * * *
53459851 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCT
1 AATTTAATGTATAATGCTGTCCAATTTTAAGTATA-TTATGCTGTCC
** *
53459898 AATTCGATGTATAATGCTGTCC-A-TTTAGAGCATATTATTGCTGTCC
1 AATTTAATGTATAATGCTGTCCAATTTTA-AGTATATTA-TGCTGTCC
* * *
53459944 AATTTGATGAATAAATTCTGTCCAA
1 AATTTAATGTAT-AATGCTGTCCAA
53459969 AACAGGGTTG
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
45 6 0.06
46 22 0.22
47 68 0.69
48 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (46 bp):
AATTTAATGTATAATGCTGTCCAATTTTAAGTATATTATGCTGTCC
Found at i:53474861 original size:12 final size:12
Alignment explanation
Indices: 53474844--53474882 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
53474834 CGACTCGCCC
53474844 ATATTAATTTTT
1 ATATTAATTTTT
*
53474856 ATATTATTTTTT
1 ATATTAATTTTT
*
53474868 ATA-TAATTTTA
1 ATATTAATTTTT
53474879 ATAT
1 ATAT
53474883 ATATAATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:53475043 original size:30 final size:30
Alignment explanation
Indices: 53474999--53475059 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
53474989 ACTTAACAAG
53474999 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
53475029 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
53475059 C
1 C
53475060 TATAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:53480920 original size:17 final size:17
Alignment explanation
Indices: 53480895--53480928 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53480885 GGTTCAACTA
*
53480895 TTTAATTAATTTTTATT
1 TTTAATTAATTATTATT
*
53480912 TTTATTTAATTATTATT
1 TTTAATTAATTATTATT
53480929 GAATAAGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATTAATTATTATT
Found at i:53483493 original size:2 final size:2
Alignment explanation
Indices: 53483486--53483523 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
53483476 GGTATTTGGG
53483486 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
53483524 TTAGTTGGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53485985 original size:21 final size:21
Alignment explanation
Indices: 53485961--53486010 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
53485951 ACACGGTTTG
* *
53485961 GCCACATGGCCACGTTCTTGA
1 GCCACACGACCACGTTCTTGA
*
53485982 GCCACACGACCATGTTCTTGA
1 GCCACACGACCACGTTCTTGA
53486003 GCCACACG
1 GCCACACG
53486011 GGCTAAGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.20
Consensus pattern (21 bp):
GCCACACGACCACGTTCTTGA
Found at i:53500785 original size:12 final size:10
Alignment explanation
Indices: 53500759--53500783 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53500749 TAAAGGAAAC
53500759 TATATTTCAA
1 TATATTTCAA
53500769 TATATTTCAA
1 TATATTTCAA
53500779 TATAT
1 TATAT
53500784 ATATATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATTTCAA
Found at i:53501784 original size:5 final size:5
Alignment explanation
Indices: 53501768--53501819 Score: 68
Period size: 5 Copynumber: 9.8 Consensus size: 5
53501758 TAAAGAAAGA
*
53501768 AAAAT GAAAAT AAAAT AAAAT AAAAT AAAAT AAAAC AAAAT ATAATAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AA-AT
53501816 AAAA
1 AAAA
53501820 ACTCACAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 30 0.71
6 9 0.21
7 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:53506047 original size:43 final size:43
Alignment explanation
Indices: 53505997--53506191 Score: 205
Period size: 43 Copynumber: 4.5 Consensus size: 43
53505987 AGATACTGGT
* * *
53505997 CTAAAGAACATGATCTTTAGTGGTGCTTCCCATAAAAATGCCG
1 CTAAAGAACATGATCTTTAGCGGTGCTTCTCACAAAAATGCCG
* * * **
53506040 TTAAAGAACATGATCTTTAGCGGTACTT-TTACTAAAAGCGCCG
1 CTAAAGAACATGATCTTTAGCGGTGCTTCTCAC-AAAAATGCCG
* *
53506083 CTATAA-AAAATGATCTTTCGCGGTGCTTCTCACAAAAATGCCG
1 CTA-AAGAACATGATCTTTAGCGGTGCTTCTCACAAAAATGCCG
** ***
53506126 CTGTAGAACATGATCTTTAGCAACGCTTCTCACAAAAATGCCG
1 CTAAAGAACATGATCTTTAGCGGTGCTTCTCACAAAAATGCCG
* *
53506169 CTAAAGATCATGTTCTTTAGCGG
1 CTAAAGAACATGATCTTTAGCGG
53506192 CATTTGTAAG
Statistics
Matches: 120, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
42 2 0.02
43 113 0.94
44 5 0.04
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (43 bp):
CTAAAGAACATGATCTTTAGCGGTGCTTCTCACAAAAATGCCG
Found at i:53512953 original size:23 final size:23
Alignment explanation
Indices: 53512927--53512970 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
53512917 AGTCACTAAA
53512927 AAAACTAAAAGAAAT-ATATTAGT
1 AAAA-TAAAAGAAATCATATTAGT
* *
53512950 AAAATAATAGTAATCATATTA
1 AAAATAAAAGAAATCATATTA
53512971 TTTGTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAATAAAAGAAATCATATTAGT
Found at i:53521676 original size:61 final size:59
Alignment explanation
Indices: 53521549--53521677 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 59
53521539 TGCATTGATT
* *
53521549 TTTTTAATATATTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAGAAGTTG
1 TTTTGAATATATTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAGAAGTTC
* * * * *
53521608 TTCTGAATATTTTTGTATAAATTATTTTTATATT-TTGTCCTATTTAATAAAATATAAGTTC
1 TTTTGAATATATTTGTACAAACTATTTTTATATTATT-T-C-ATTTAATAAAATAGAAGTTC
53521669 TTTTGAATA
1 TTTTGAATA
53521678 AGGCAATAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.03
59 30 0.51
60 1 0.02
61 26 0.44
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (59 bp):
TTTTGAATATATTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAGAAGTTC
Found at i:53529810 original size:127 final size:126
Alignment explanation
Indices: 53529542--53530026 Score: 584
Period size: 127 Copynumber: 3.9 Consensus size: 126
53529532 GTTAAGCAGG
53529542 ACCATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTT
1 ACCATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTT
* ** * * *
53529607 TTT-AGTACTTTTGCTGACAATGTGTCCTAG-TTGAAGTGTTTTTTACCTTATTTTTTCAGA
66 TTTCAGTACTTTTGCTGACAGTGCATCCT-GCTTGAAGCGTTTTTTACCCTATTTTTTTAGA
* * * * * * * * *
53529667 ATCATCTT-TCCAAAATTATATTTCCAGAAATTACTTTAGAAAAAGAGCGTCCAGTTAGGAGCTG
1 ACCATCTTCT-CAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTT
53529731 TTTTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTTTACCCTATTTTTTTAGA
65 TTTTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCG-TTTTTTACCCTATTTTTTTAGA
* * * *** * *
53529794 ACCATCTTTTTAAAATTATTTTTTAAGAAACTACTGTAGAAAAAGAATGTCTAGCTGGGAACTTT
1 ACCATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTT
* * * *
53529859 TTTTAGTACTTTTACTGATAGTGCATCCTGCTTGAAGCGTTTTTTA-CC-ATATTTTTAGA
66 TTTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTTACCCTATTTTTTTAGA
* * * * * * *
53529918 ACTATCTTCTTAAAATTATTTTTTCGGAAACTATTGTAGAAAAATAGCATCCAACTGTGAGCTTT
1 ACCATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTT
* *
53529983 TTTCAGTACTTTTGCTGACAGTGCATCCTACTTGAAGCATTTTT
66 TTTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTT
53530027 GAACACAAGT
Statistics
Matches: 304, Mismatches: 51, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
124 102 0.34
125 60 0.20
126 36 0.12
127 105 0.35
128 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (126 bp):
ACCATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTT
TTTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTTACCCTATTTTTTTAGA
Found at i:53529959 original size:124 final size:124
Alignment explanation
Indices: 53529545--53530026 Score: 558
Period size: 124 Copynumber: 3.9 Consensus size: 124
53529535 AAGCAGGACC
53529545 ATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTTTT
1 ATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTTTT
* ** * *
53529610 -AGTACTTTTGCTGACAATGTGTCCTAG-TTGAAGTGTTTTTTACCTTATTTTTTCAGAA-T
66 CAGTACTTTTGCTGACAGTGCATCCT-GCTTGAAGCGTTTTTTACCATA-TTTTT-AGAACT
* * * * * * * *
53529669 CATCTT-TCCAAAATTATATTTCCAGAAATTACTTTAGAAAAAGAGCGTCCAGTTAGGAGCTGTT
1 -ATCTTCT-CAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTT
* *
53529733 TTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTTTACCCTATTTTTTTAGAACC
64 TTCAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCG-TTTTTTA-CC-ATATTTTTAGAACT
* * * *** * *
53529797 ATCTTTTTAAAATTATTTTTTAAGAAACTACTGTAGAAAAAGAATGTCTAGCTGGGAACTTTTTT
1 ATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTTTT
* * *
53529862 TAGTACTTTTACTGATAGTGCATCCTGCTTGAAGCGTTTTTTACCATATTTTTAGAACT
66 CAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTTACCATATTTTTAGAACT
* * * * * *
53529921 ATCTTCTTAAAATTATTTTTTCGGAAACTATTGTAGAAAAATAGCATCCAACTGTGAGCTTTTTT
1 ATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTTTT
* *
53529986 CAGTACTTTTGCTGACAGTGCATCCTACTTGAAGCATTTTT
66 CAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTT
53530027 GAACACAAGT
Statistics
Matches: 299, Mismatches: 50, Indels: 17
0.82 0.14 0.05
Matches are distributed among these distances:
124 102 0.34
125 58 0.19
126 36 0.12
127 94 0.31
128 8 0.03
129 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (124 bp):
ATCTTCTCAAAATTATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTTTT
CAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTTACCATATTTTTAGAACT
Found at i:53535783 original size:18 final size:18
Alignment explanation
Indices: 53535760--53535800 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
53535750 AAAATATATC
53535760 AACTAAAAATCAAATTTA
1 AACTAAAAATCAAATTTA
53535778 AACTAAAAATCAAATTTA
1 AACTAAAAATCAAATTTA
53535796 AACTA
1 AACTA
53535801 TTTATAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (18 bp):
AACTAAAAATCAAATTTA
Found at i:53536871 original size:17 final size:17
Alignment explanation
Indices: 53536849--53536892 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
53536839 TTAAATTATC
53536849 CATTAAATATTTAAATT
1 CATTAAATATTTAAATT
*
53536866 CATTAAATATTTATATT
1 CATTAAATATTTAAATT
* *
53536883 TAGTAAATAT
1 CATTAAATAT
53536893 AAAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (17 bp):
CATTAAATATTTAAATT
Found at i:53548276 original size:3 final size:3
Alignment explanation
Indices: 53548261--53548341 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
53548251 TTTAAGATTT
* * ** * * *
53548261 TTA TTA TTG TTA TTA TTA TTA TTA ATA CCA TCA TCA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
53548309 TTA TTA TTA TTA ATA CCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53548342 AATTGTTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:53557400 original size:6 final size:6
Alignment explanation
Indices: 53557389--53557415 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53557379 AAGTGACTTT
53557389 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
53557416 CTATGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:53557543 original size:18 final size:15
Alignment explanation
Indices: 53557501--53557543 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
53557491 CGTTATGTCT
53557501 GCGACCGCGACAAAC
1 GCGACCGCGACAAAC
53557516 GCGA-CGCGACTGAAAAC
1 GCGACCGCGAC---AAAC
53557533 GCGACCGCGAC
1 GCGACCGCGAC
53557544 CGCAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.25
15 4 0.17
17 8 0.33
18 6 0.25
ACGTcount: A:0.30, C:0.37, G:0.30, T:0.02
Consensus pattern (15 bp):
GCGACCGCGACAAAC
Found at i:53560750 original size:25 final size:24
Alignment explanation
Indices: 53560722--53560784 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
53560712 AATAAAGATA
*
53560722 AAATATTTAAATCCAAATATTTTAC
1 AAATATTAAAAT-CAAATATTTTAC
** *
53560747 AAATTAAAAAAATCAAATATTTTGC
1 AAA-TATTAAAATCAAATATTTTAC
53560772 AAATATTCAAAAT
1 AAATATT-AAAAT
53560785 TTACTCTACC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
24 2 0.07
25 22 0.73
26 6 0.20
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATTAAAATCAAATATTTTAC
Found at i:53565358 original size:7 final size:7
Alignment explanation
Indices: 53565346--53565372 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53565336 ATTTCATATT
53565346 AATTTTA
1 AATTTTA
53565353 AATTTTA
1 AATTTTA
53565360 AATTTTA
1 AATTTTA
53565367 AATTTT
1 AATTTT
53565373 TTTCTATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:53568994 original size:20 final size:19
Alignment explanation
Indices: 53568954--53568997 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
53568944 TTAATTTTTA
* *
53568954 TAAATTTTTAAAAAATTAT
1 TAAAATTTTAAAAAATAAT
53568973 TAAAATTTTAAAAAATAAAT
1 TAAAATTTTAAAAAAT-AAT
53568993 TAAAA
1 TAAAA
53568998 ATTAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTTAAAAAATAAT
Found at i:53569002 original size:19 final size:19
Alignment explanation
Indices: 53568961--53569002 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
53568951 TTATAAATTT
* *
53568961 TTAAAAAATTATTAAAATT
1 TTAAAAAATAATTAAAATA
53568980 TTAAAAAATAAATTAAAA-A
1 TTAAAAAAT-AATTAAAATA
53568999 TTAA
1 TTAA
53569003 TATAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAAATAATTAAAATA
Found at i:53569293 original size:19 final size:20
Alignment explanation
Indices: 53569257--53569294 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53569247 TTTTTTTGAA
**
53569257 ATTTTTAAACTTTAATTAAT
1 ATTTTTAAAAGTTAATTAAT
53569277 ATTTTTAAAAGTT-ATTAA
1 ATTTTTAAAAGTTAATTAA
53569295 AAACATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTTAAAAGTTAATTAAT
Found at i:53569673 original size:8 final size:8
Alignment explanation
Indices: 53569654--53569695 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
53569644 AAGGTTCAAA
53569654 TTCCACTTT
1 TTCCA-TTT
53569663 TTCCATTT
1 TTCCATTT
*
53569671 TTCCCTTT
1 TTCCATTT
53569679 TTCCATTT
1 TTCCATTT
*
53569687 TTCCCTTT
1 TTCCATTT
53569695 T
1 T
53569696 ATTTTTCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 25 0.83
9 5 0.17
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (8 bp):
TTCCATTT
Found at i:53569680 original size:16 final size:16
Alignment explanation
Indices: 53569654--53569695 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
53569644 AAGGTTCAAA
53569654 TTCCACTTTTTCCATTT
1 TTCC-CTTTTTCCATTT
53569671 TTCCCTTTTTCCATTT
1 TTCCCTTTTTCCATTT
53569687 TTCCCTTTT
1 TTCCCTTTT
53569696 ATTTTTCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCCCTTTTTCCATTT
Found at i:53571776 original size:14 final size:14
Alignment explanation
Indices: 53571757--53571784 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53571747 AGAGAACTCT
53571757 ATTATGCAATTAAG
1 ATTATGCAATTAAG
53571771 ATTATGCAATTAAG
1 ATTATGCAATTAAG
53571785 TCCTGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATTATGCAATTAAG
Found at i:53577044 original size:108 final size:108
Alignment explanation
Indices: 53576842--53577058 Score: 373
Period size: 108 Copynumber: 2.0 Consensus size: 108
53576832 ACATTAGTAT
53576842 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
1 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
*
53576907 ACCATCAACAACCAAGGACTAGTTGAGAACTCCAAACCCGACA
66 ACCATCAACAACCAAGGACCAGTTGAGAACTCCAAACCCGACA
*
53576950 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGTCAAGG
1 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
* * *
53577015 ACCATTAACAACCCAA-GACCAGTTTAGAACTCCAAACCTGACA
66 ACCATCAACAA-CCAAGGACCAGTTGAGAACTCCAAACCCGACA
53577058 T
1 T
53577059 AACACCAATA
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
108 99 0.96
109 4 0.04
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.18
Consensus pattern (108 bp):
TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
ACCATCAACAACCAAGGACCAGTTGAGAACTCCAAACCCGACA
Found at i:53588247 original size:11 final size:11
Alignment explanation
Indices: 53588233--53588262 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
53588223 AATAATATCC
53588233 AAATAAATTTA
1 AAATAAATTTA
53588244 AAATAAATTTA
1 AAATAAATTTA
53588255 AAATAAAT
1 AAATAAAT
53588263 ATTAGTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAAATTTA
Found at i:53589777 original size:5 final size:6
Alignment explanation
Indices: 53589760--53589790 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
53589750 ACTGAATTTG
53589760 ATTTATT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTT-TT ATTTTT ATTTTT ATTTTT ATTTTT
53589791 TGGTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:53590359 original size:132 final size:132
Alignment explanation
Indices: 53590200--53590525 Score: 428
Period size: 132 Copynumber: 2.5 Consensus size: 132
53590190 TTTACACTTG
* ** *
53590200 AAGATAAGATTTGCCGT-TTTGAATCTGCTCCGCTACTACTTAGATAGACAAGATCTG-TAAT-T
1 AAGATAAGATTTGTCGTCTTTG-ATCTGCTCCGCTACTACTTAGGGAGATAAGATCTGCT-ATCT
* *
53590262 TCCAACCTATTCCACTGCTGAC-CAGTGG-GACAAGGCTCGGTGACTTAAGTCTGCTTCCCACTA
64 T-CAACCTACTCCACTGCTG-CTCAG-GGAGACAAGGCTCGGTGACTTAAATCTGCTTCCCACTA
53590325 TCCTGAA
126 TCCTGAA
* **
53590332 AAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTGCTATCTTC
1 AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTACTTAGGGAGATAAGATCTGCTATCTTC
*** * * *
53590397 AACCTACTCTGGTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAATCTGCTTCCCACTATCTTG
66 AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTCGGTGACTTAAATCTGCTTCCCACTATCCTG
*
53590462 GA
131 AA
53590464 AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTACTTAGGGAGATAAGATCTGCTATC
1 AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTACTTAGGGAGATAAGATCTGCTATC
53590526 CTTACTGATC
Statistics
Matches: 170, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
131 3 0.02
132 160 0.94
133 7 0.04
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (132 bp):
AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTACTTAGGGAGATAAGATCTGCTATCTTC
AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTCGGTGACTTAAATCTGCTTCCCACTATCCTG
AA
Found at i:53601646 original size:17 final size:17
Alignment explanation
Indices: 53601624--53601661 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
53601614 ACACTTTGGG
53601624 ATTCTAATTAATGCAAT
1 ATTCTAATTAATGCAAT
53601641 ATTCTAATTAATGCAAT
1 ATTCTAATTAATGCAAT
53601658 ATTC
1 ATTC
53601662 AAATCCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (17 bp):
ATTCTAATTAATGCAAT
Found at i:53605958 original size:109 final size:107
Alignment explanation
Indices: 53605722--53605942 Score: 280
Period size: 115 Copynumber: 2.0 Consensus size: 107
53605712 ATACAATAAC
* * *
53605722 TAAAACTATTAAAATTTTACTTTAAATAACATTTATACCTTCTCTCTCTATAGAAATTGAATAAA
1 TAAAAATATTAAAATTTTACTATAAATAACATTTATACCTTCTCTCTATATAGAAATTGAATAAA
* *
53605787 ATTGTTTTTGTCATTTTCAACGGAATTGGTGTCCAGTTAATAA
66 ATTGTTTTTGTCATTTCCAACGGAATTGGTGTCCAATTAAT-A
*
53605830 CTAAAAATATTAAAATTTTACTATAAATAATATTTATACCTTCTCTCTTTATATATATTGAAATT
1 -TAAAAATATTAAAATTTTACTATAAATAACATTTATACCTTCTCTC----TATATA--GAAATT
* ** *
53605895 GAATAAAGTTGTTTTTGTCATTTCCAATTGAATTGGTGTCTAATTAAT
59 GAATAAAATTGTTTTTGTCATTTCCAACGGAATTGGTGTCCAATTAAT
53605943 TCAATTATAG
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
109 43 0.45
113 5 0.05
115 48 0.50
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (107 bp):
TAAAAATATTAAAATTTTACTATAAATAACATTTATACCTTCTCTCTATATAGAAATTGAATAAA
ATTGTTTTTGTCATTTCCAACGGAATTGGTGTCCAATTAATA
Found at i:53609115 original size:31 final size:31
Alignment explanation
Indices: 53609079--53609140 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
53609069 AGATAATTTT
53609079 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
53609110 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
53609141 TAATTTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:53609702 original size:33 final size:32
Alignment explanation
Indices: 53609655--53609727 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 32
53609645 TTGTTCTTTA
* * * *
53609655 AAAAAAAAG-AAAAAAGCGCAAAAAAACCCGC
1 AAAAAAAAGCCAAAAAGCCCAAAAAAAACCAC
53609686 AAAAGAAAAGCCAAAAAGCCCAAAAAAAACCAC
1 AAAA-AAAAGCCAAAAAGCCCAAAAAAAACCAC
53609719 AAAAAAAAG
1 AAAAAAAAG
53609728 TTGCCTACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 4 0.11
32 10 0.28
33 22 0.61
ACGTcount: A:0.70, C:0.19, G:0.11, T:0.00
Consensus pattern (32 bp):
AAAAAAAAGCCAAAAAGCCCAAAAAAAACCAC
Found at i:53609709 original size:21 final size:22
Alignment explanation
Indices: 53609676--53609723 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
53609666 AAAAGCGCAA
*
53609676 AAAAACCCGCAAAAGAAAAGC-C
1 AAAAACCCGCAAAA-AAAACCAC
*
53609698 AAAAAGCC-CAAAAAAAACCAC
1 AAAAACCCGCAAAAAAAACCAC
53609719 AAAAA
1 AAAAA
53609724 AAAGTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.67, C:0.25, G:0.08, T:0.00
Consensus pattern (22 bp):
AAAAACCCGCAAAAAAAACCAC
Found at i:53615310 original size:31 final size:31
Alignment explanation
Indices: 53615274--53615335 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
53615264 AGATAATTTT
53615274 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
53615305 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
53615336 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:53617022 original size:21 final size:21
Alignment explanation
Indices: 53616996--53617035 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53616986 ATACGCCAAC
53616996 AGAAGCTCATAAGAGCTGAAT
1 AGAAGCTCATAAGAGCTGAAT
*
53617017 AGAAGCTCGTAAGAGCTGA
1 AGAAGCTCATAAGAGCTGA
53617036 TCCACCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAT
Found at i:53619682 original size:27 final size:27
Alignment explanation
Indices: 53619644--53619697 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
53619634 CTTGGGTCAC
53619644 ATGGTGCTAGGCCATGTATTAGGCTAT
1 ATGGTGCTAGGCCATGTATTAGGCTAT
53619671 ATGGTGCTAGGCCATGTATTAGGCTAT
1 ATGGTGCTAGGCCATGTATTAGGCTAT
53619698 GTAACTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (27 bp):
ATGGTGCTAGGCCATGTATTAGGCTAT
Found at i:53623571 original size:17 final size:18
Alignment explanation
Indices: 53623541--53623577 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
53623531 GTTTGAAAAA
53623541 AATAAAATATATATAAAT
1 AATAAAATATATATAAAT
53623559 AATAAAA-ATATATAAAT
1 AATAAAATATATATAAAT
53623576 AA
1 AA
53623578 AAGTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATATATATAAAT
Found at i:53634362 original size:55 final size:56
Alignment explanation
Indices: 53634290--53634527 Score: 286
Period size: 55 Copynumber: 4.3 Consensus size: 56
53634280 TGCATGCTTA
* * * *
53634290 ATTATGATATGTGCA-TAATGAAACTAGTAAGCATGATTATATACATGCATACCCT
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * * *
53634345 ATTATGATATGTGCA-TAATAAAACTAGTAAGCATGACTATGTACATGCATGCTCA
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * * *
53634400 ATTTTTATATGTGCACT-ATGAAACTAGTAAGCATCACTATGTACATGAATGCTCT
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * * * * *
53634455 ATTTTGATATGTGCACTTA-GAAACTAATGATCATCACTATGTACATGCATGCCTT
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
53634510 ATTATGATATGTGCACTA
1 ATTATGATATGTGCACTA
53634528 TATACATTTC
Statistics
Matches: 160, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
55 158 0.99
56 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (56 bp):
ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
Found at i:53634556 original size:59 final size:55
Alignment explanation
Indices: 53634290--53634560 Score: 183
Period size: 55 Copynumber: 4.9 Consensus size: 55
53634280 TGCATGCTTA
* * * * * * * * * *
53634290 ATTATGATATGTGCA-TAATGAAACTAGTAAGCATGATTATATACATGCATACCCT
1 ATTATGATATGTGCACTTA-GAAACCAATGAGCATCACTATGTACATGAATGCTCT
* * * * * *
53634345 ATTATGATATGTGCA-TAATA-AAACTAGTAAGCATGACTATGTACATGCATGCTCA
1 ATTATGATATGTGCACT--TAGAAACCAATGAGCATCACTATGTACATGAATGCTCT
* * * * *
53634400 ATTTTTATATGTGCAC-TATGAAACTAGTAAGCATCACTATGTACATGAATGCTCT
1 ATTATGATATGTGCACTTA-GAAACCAATGAGCATCACTATGTACATGAATGCTCT
* * * *
53634455 ATTTTGATATGTGCACTTAGAAACTAATGATCATCACTATGTACATGCATGC-CTT
1 ATTATGATATGTGCACTTAGAAACCAATGAGCATCACTATGTACATGAATGCTC-T
* *
53634510 ATTATGATATGTGCACTATATACATTTCCAATGAGCATCACTATGTACATG
1 ATTATGATATGTGCACT-TAGA-A--ACCAATGAGCATCACTATGTACATG
53634561 GTTGTTACAT
Statistics
Matches: 184, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
53 2 0.01
54 1 0.01
55 152 0.83
56 5 0.03
57 2 0.01
59 22 0.12
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (55 bp):
ATTATGATATGTGCACTTAGAAACCAATGAGCATCACTATGTACATGAATGCTCT
Found at i:53645568 original size:23 final size:24
Alignment explanation
Indices: 53645532--53645623 Score: 100
Period size: 23 Copynumber: 3.9 Consensus size: 24
53645522 GGACTCATCA
53645532 CAGCTCGTAT-GAGCTTACCGTTT
1 CAGCTCGTATAGAGCTTACCGTTT
53645555 CAGCTC-TATAGAGCTTACCGTTT
1 CAGCTCGTATAGAGCTTACCGTTT
* * *
53645578 TAGTTTG-ATAGAGCTTACCGTTTAT
1 CAGCTCGTATAGAGCTTACCG-TT-T
* *
53645603 CAGCTCGAAAAGAGCTTACCG
1 CAGCTCGTATAGAGCTTACCG
53645624 ATCATGGCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.05
23 35 0.61
24 2 0.04
25 5 0.09
26 12 0.21
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (24 bp):
CAGCTCGTATAGAGCTTACCGTTT
Found at i:53645806 original size:20 final size:20
Alignment explanation
Indices: 53645772--53645821 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
53645762 CTATGTAATT
53645772 ATATGGATGAA-TTACCATTG
1 ATATGGAT-AAGTTACCATTG
* **
53645792 ATATGTATAAGTTACGGTTG
1 ATATGGATAAGTTACCATTG
53645812 ATATGGATAA
1 ATATGGATAA
53645822 ATTTTTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (20 bp):
ATATGGATAAGTTACCATTG
Found at i:53646450 original size:51 final size:51
Alignment explanation
Indices: 53646406--53646505 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
53646396 AATTATTTAA
53646406 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAAAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAAAGCAAATTGAGATT
* * * *
53646457 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAAAGCAAATTGAGA
53646506 GGAAATTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.25
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAAAGCAAATTGAGATT
Found at i:53646492 original size:22 final size:22
Alignment explanation
Indices: 53646465--53646519 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
53646455 TTAAATATGG
53646465 ATTTGAGAGAAATTTG-GAAGGAA
1 ATTTGAGAGAAA-TTGAG-AGGAA
53646488 A-TTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
53646510 ATTTGAGAGA
1 ATTTGAGAGA
53646520 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.24
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:53646517 original size:12 final size:12
Alignment explanation
Indices: 53646465--53646518 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
53646455 TTAAATATGG
53646465 ATTTGAGA-GAA
1 ATTTGAGAGGAA
53646476 ATTTG-GAAGGAA
1 ATTTGAG-AGGAA
*
53646488 A-TTGAGAGCAA
1 ATTTGAGAGGAA
53646499 A-TTGAGAGGAA
1 ATTTGAGAGGAA
53646510 ATTTGAGAG
1 ATTTGAGAG
53646519 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 1 0.03
11 24 0.65
12 12 0.32
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:53647368 original size:16 final size:16
Alignment explanation
Indices: 53647344--53647374 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53647334 CAGTTTTTTT
53647344 AAAAAAAAAAGAAAAG
1 AAAAAAAAAAGAAAAG
*
53647360 AAAAGAAAAAGAAAA
1 AAAAAAAAAAGAAAA
53647375 ATGAATGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAG
Found at i:53647598 original size:8 final size:8
Alignment explanation
Indices: 53647554--53647580 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
53647544 TATTTTTTTT
53647554 AAAAATTA
1 AAAAATTA
53647562 AAAAATTA
1 AAAAATTA
53647570 AAAAATTA
1 AAAAATTA
53647578 AAA
1 AAA
53647581 TATATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATTA
Found at i:53647628 original size:18 final size:19
Alignment explanation
Indices: 53647607--53647649 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
53647597 AATATTTTTA
* *
53647607 AAAAAATTA-TAAATCTGT
1 AAAAAATTATTAAATATAT
*
53647625 AAAATATTATTAAATATAT
1 AAAAAATTATTAAATATAT
53647644 AAAAAA
1 AAAAAA
53647650 ATTTAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAATTATTAAATATAT
Found at i:53648041 original size:18 final size:18
Alignment explanation
Indices: 53647990--53648089 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 18
53647980 TATTAATTTT
* *
53647990 TAATATTTTTGAAATTTATT
1 TAAT-TTTTTAAAATTTA-A
*
53648010 TAATATTTTATAAATTTCAA
1 TAATTTTTTA-AAATTT-AA
*
53648030 TAATTTTTTAAAATTTTA
1 TAATTTTTTAAAATTTAA
* ** *
53648048 TAATTTTTAAAAAAATAT
1 TAATTTTTTAAAATTTAA
53648066 TAAATTTTTTAAAA--TAA
1 T-AATTTTTTAAAATTTAA
53648083 TAATTTT
1 TAATTTT
53648090 AAATTTTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
16 6 0.09
17 3 0.05
18 15 0.23
19 21 0.32
20 19 0.29
21 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TAATTTTTTAAAATTTAA
Found at i:53659290 original size:19 final size:21
Alignment explanation
Indices: 53659266--53659311 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
53659256 AAACTGCTAT
53659266 TTTTTTACTATTTT-TT-TTG
1 TTTTTTACTATTTTCTTGTTG
*
53659285 TTTTTTATTATTTTCTTGTTG
1 TTTTTTACTATTTTCTTGTTG
53659306 TTTTTT
1 TTTTTT
53659312 TTCACTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 9 0.38
ACGTcount: A:0.09, C:0.04, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTACTATTTTCTTGTTG
Found at i:53661647 original size:89 final size:90
Alignment explanation
Indices: 53661532--53661705 Score: 228
Period size: 89 Copynumber: 1.9 Consensus size: 90
53661522 TTTTTTTCAT
* * * * *
53661532 TCAATTGAGTACTTAAAATTTTAAAATGTACCAAAAAGA-TCCTTAAACTTTTTTAAAA-AATAC
1 TCAATTGAGTACTTAAAATTTAAAAATGCACCAAAAAGACT-CTCAAAATTTTTCAAAACAA-AC
*
53661595 AATTAAG-CCCTTGTTTTTTTTAACAC
64 AATTAAGTCCCTGGTTTTTTTTAACAC
* * *
53661621 TCAATTGAGTACTTGAACTTTAAAAATGCATCAAAAAGACTCTCAAAATTTTTCAAAACAAACAA
1 TCAATTGAGTACTTAAAATTTAAAAATGCACCAAAAAGACTCTCAAAATTTTTCAAAACAAACAA
53661686 TTAAGTCCCTGGTTTTTTTT
66 TTAAGTCCCTGGTTTTTTTT
53661706 TTCTTTTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
89 57 0.78
90 16 0.22
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (90 bp):
TCAATTGAGTACTTAAAATTTAAAAATGCACCAAAAAGACTCTCAAAATTTTTCAAAACAAACAA
TTAAGTCCCTGGTTTTTTTTAACAC
Found at i:53661919 original size:29 final size:28
Alignment explanation
Indices: 53661885--53661958 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
53661875 AATAAAAATC
53661885 AATAAAAGTTATAAAAATGA-TTAAATTAT
1 AATAAAA-TTATAAAAAT-ATTTAAATTAT
* *
53661914 AATAAAAATATAAAAATATTTAAATTTT
1 AATAAAATTATAAAAATATTTAAATTAT
* *
53661942 ATTAAAAATTAGAAAAA
1 AAT-AAAATTATAAAAA
53661959 AAAATTGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 19 0.50
29 18 0.47
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (28 bp):
AATAAAATTATAAAAATATTTAAATTAT
Found at i:53661936 original size:28 final size:28
Alignment explanation
Indices: 53661885--53661950 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
53661875 AATAAAAATC
*
53661885 AATAAAAGTTATAAAAATGATTAAATTAT
1 AATAAAA-ATATAAAAATGATTAAATTAT
*
53661914 AATAAAAATATAAAAAT-ATTTAAATTTT
1 AATAAAAATATAAAAATGA-TTAAATTAT
*
53661942 ATTAAAAAT
1 AATAAAAAT
53661951 TAGAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 25 0.76
29 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAAAAATATAAAAATGATTAAATTAT
Found at i:53662000 original size:11 final size:11
Alignment explanation
Indices: 53661986--53662019 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
53661976 AAAAAATTGT
*
53661986 AAAATTTTATA
1 AAAATTTTAAA
*
53661997 AAAATCTTAAA
1 AAAATTTTAAA
53662008 AAAATTTTAAA
1 AAAATTTTAAA
53662019 A
1 A
53662020 TGCATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATTTTAAA
Found at i:53662030 original size:30 final size:30
Alignment explanation
Indices: 53661967--53662030 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
53661957 AAAAAATTGT
**
53661967 AAAATCATAAAAAAATTGTAAAATTTTATA
1 AAAATCATAAAAAAATTGTAAAATCATATA
* *
53661997 AAAATCTTAAAAAAATTTTAAAATGCATA-A
1 AAAATCATAAAAAAATTGTAAAAT-CATATA
53662027 AAAA
1 AAAA
53662031 GACCCTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAATCATAAAAAAATTGTAAAATCATATA
Found at i:53662339 original size:20 final size:21
Alignment explanation
Indices: 53662314--53662360 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
53662304 AAATATTTAG
*
53662314 ATATTTTTAT-ATTTTTATTA
1 ATATTTTTATAACTTTTATTA
53662334 ATATTTTTATAACTTTTATTA
1 ATATTTTTATAACTTTTATTA
53662355 AT-TTTT
1 ATATTTT
53662361 ATTTTTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
ATATTTTTATAACTTTTATTA
Found at i:53664520 original size:10 final size:10
Alignment explanation
Indices: 53664505--53664540 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
53664495 GGTAAGTCTG
53664505 AAAAAAATTC
1 AAAAAAATTC
53664515 -AAAAAATTC
1 AAAAAAATTC
*
53664524 AAAAAAAATC
1 AAAAAAATTC
53664534 AAAAAAA
1 AAAAAAA
53664541 ATTCGTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:53664527 original size:8 final size:9
Alignment explanation
Indices: 53664506--53664539 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
53664496 GTAAGTCTGA
53664506 AAAAAATTC
1 AAAAAATTC
53664515 AAAAAATTC
1 AAAAAATTC
*
53664524 AAAAAAAATC
1 -AAAAAATTC
53664534 AAAAAA
1 AAAAAA
53664540 AATTCGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAATTC
Found at i:53668888 original size:19 final size:20
Alignment explanation
Indices: 53668860--53668897 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
53668850 TTTATCAAAA
*
53668860 AAAATGAATTT-ATTTGATT
1 AAAATAAATTTAATTTGATT
53668879 AAAATAAATTTAATTTGAT
1 AAAATAAATTTAATTTGAT
53668898 CCTATAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
AAAATAAATTTAATTTGATT
Found at i:53672272 original size:45 final size:45
Alignment explanation
Indices: 53672214--53672303 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
53672204 AAAGAACTTA
53672214 ACCGTTTCCGGGTTCTTTGTATATTTGAAAGTGACTTCATTAACT
1 ACCGTTTCCGGGTTCTTTGTATATTTGAAAGTGACTTCATTAACT
*
53672259 ACCGTTTCCGGGTTCTTTGTATATTTGAAAGTGACTTTATTAACT
1 ACCGTTTCCGGGTTCTTTGTATATTTGAAAGTGACTTCATTAACT
53672304 GTCTCTTTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (45 bp):
ACCGTTTCCGGGTTCTTTGTATATTTGAAAGTGACTTCATTAACT
Found at i:53676138 original size:7 final size:7
Alignment explanation
Indices: 53676127--53676158 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53676117 TGATTGATTT
*
53676127 TGATGAT
1 TGATGAA
53676134 TGATGAA
1 TGATGAA
53676141 TGATGAA
1 TGATGAA
53676148 TGATGAA
1 TGATGAA
53676155 TGAT
1 TGAT
53676159 TATTACTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (7 bp):
TGATGAA
Found at i:53695911 original size:19 final size:17
Alignment explanation
Indices: 53695873--53695912 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
53695863 CTTTTCATTT
53695873 TTATTTTTTTTATATCA
1 TTATTTTTTTTATATCA
*
53695890 TTATTTTTTCTTACTATTA
1 TTATTTTTT-TTA-TATCA
53695909 TTAT
1 TTAT
53695913 ACCATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 3 0.15
19 8 0.40
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTTTTTATATCA
Found at i:53696266 original size:16 final size:17
Alignment explanation
Indices: 53696235--53696267 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
53696225 TCTATTATTT
*
53696235 TATATACTATATATATG
1 TATATACTAAATATATG
53696252 TATAT-CTAAATATATG
1 TATATACTAAATATATG
53696268 CGAATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (17 bp):
TATATACTAAATATATG
Found at i:53707884 original size:89 final size:89
Alignment explanation
Indices: 53707257--53707872 Score: 1009
Period size: 89 Copynumber: 6.9 Consensus size: 89
53707247 GAGTAGCAGT
* * * * *
53707257 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA-AAAAGCGGATCTTGTCTTCATGTAT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAA-CAGATCTTGTCTTCATGTAT
* *
53707321 TGGCGGGAAGTAGATCAAGGACAAC
65 TGGCGTGAAGTAGATCAAAGACAAC
* *
53707346 AGATTTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAGAACAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
53707411 GGCGTGAAGTAGATCAAAGACAAC
66 GGCGTGAAGTAGATCAAAGACAAC
*
53707435 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAGAACAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
*
53707500 GGCGTGAAGTAGATCAAAGAGAAC
66 GGCGTGAAGTAGATCAAAGACAAC
* *
53707524 AAATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTATCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
53707589 GGCGTGAAGTAGATCAAAGACAAC
66 GGCGTGAAGTAGATCAAAGACAAC
* ** * * *
53707613 AGATCTTGTCTCCCAATACAAGTGGTGGAGTAGATCAAAGAGAATAGATCTTGTCTTCATGTGTT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
*
53707678 GGCGTAAAGTAGATCAAAGACAAC
66 GGCGTGAAGTAGATCAAAGACAAC
*
53707702 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTATCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
*
53707767 GGCGTGAAGTAGATCGAAGACAAC
66 GGCGTGAAGTAGATCAAAGACAAC
*
53707791 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGACCTTGTCTTCATGTATT
1 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
53707856 GGCGTGAAGTAGATCAA
66 GGCGTGAAGTAGATCAA
53707873 GCACAGCAGA
Statistics
Matches: 490, Mismatches: 36, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
89 487 0.99
90 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (89 bp):
AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAACAGATCTTGTCTTCATGTATT
GGCGTGAAGTAGATCAAAGACAAC
Found at i:53709763 original size:16 final size:17
Alignment explanation
Indices: 53709732--53709764 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
53709722 TCTATTATTT
*
53709732 TATATACTATATATATG
1 TATATACTAAATATATG
53709749 TATAT-CTAAATATATG
1 TATATACTAAATATATG
53709765 CGAATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (17 bp):
TATATACTAAATATATG
Found at i:53716035 original size:21 final size:21
Alignment explanation
Indices: 53716006--53716045 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53715996 TGAAATGATT
* *
53716006 CTTTTCAATCCATTGTTTTCA
1 CTTTACAATCAATTGTTTTCA
53716027 CTTTACAATCAATTGTTTT
1 CTTTACAATCAATTGTTTT
53716046 GCTGTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.53
Consensus pattern (21 bp):
CTTTACAATCAATTGTTTTCA
Found at i:53723088 original size:36 final size:37
Alignment explanation
Indices: 53723019--53723088 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
53723009 TAGATTTCTT
* *
53723019 ATATCATTATATTAAATTATTTAAATATTATTTAAAA
1 ATATCATTATAGTAAATTATTTAAATATAATTTAAAA
53723056 ATATCATTATAGTAAA-TATTTAAATATAATTTA
1 ATATCATTATAGTAAATTATTTAAATATAATTTA
53723089 TTATTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 16 0.52
37 15 0.48
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATATCATTATAGTAAATTATTTAAATATAATTTAAAA
Found at i:53725679 original size:6 final size:6
Alignment explanation
Indices: 53725661--53725713 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
53725651 ATAATTTTTG
**
53725661 TATACA TAT--A TATACA TATACA TATACA TATACA T-TTTA TAATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA T-ATACA
53725707 TATACA T
1 TATACA T
53725714 CTTCCTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.10
5 3 0.08
6 29 0.74
7 3 0.08
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (6 bp):
TATACA
Found at i:53725710 original size:24 final size:24
Alignment explanation
Indices: 53725678--53725745 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 24
53725668 ATATATACAT
53725678 ATACATATACATATACATTTTATA
1 ATACATATACATATACATTTTATA
* *
53725702 ATACATATACATCTTCCTATTTTATA
1 ATACATATACAT-ATAC-ATTTTATA
* * *
53725728 ATCCATACATATATACAT
1 ATACATATACATATACAT
53725746 GCATTTTCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 14 0.40
25 4 0.11
26 17 0.49
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (24 bp):
ATACATATACATATACATTTTATA
Found at i:53725884 original size:15 final size:16
Alignment explanation
Indices: 53725864--53725896 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
53725854 TTTCAAAATT
53725864 TACTTATATATAT-CA
1 TACTTATATATATACA
53725879 TACTTATATATATACA
1 TACTTATATATATACA
53725895 TA
1 TA
53725897 TTTTGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (16 bp):
TACTTATATATATACA
Found at i:53727882 original size:109 final size:109
Alignment explanation
Indices: 53727478--53727870 Score: 621
Period size: 109 Copynumber: 3.6 Consensus size: 109
53727468 TGGCTATTTG
* * * *
53727478 GCTATTTGGTTAAACGAG--AAATCGACACCCAGCACATTAGGGCATG-TTCCTCAAATTTCCAA
1 GCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAA
* * *
53727540 ACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGGATATTTG
66 ACGCAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTA
* *
53727584 GCTATTTGGTTGCATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAA
1 GCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAA
53727649 ACGCAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTA
66 ACGCAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTA
* * * *
53727693 GCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTGTCTCGAATTTTCAA
1 GCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAA
*
53727758 ATGCAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTA
66 ACGCAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTA
* *
53727802 GCTATTTGGTTGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAA
1 GCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAA
53727867 ACGC
66 ACGC
53727871 TATATATTGC
Statistics
Matches: 265, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
106 15 0.06
108 26 0.10
109 224 0.85
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (109 bp):
GCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAA
ACGCAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTA
Found at i:53728966 original size:45 final size:45
Alignment explanation
Indices: 53728902--53729238 Score: 399
Period size: 45 Copynumber: 7.5 Consensus size: 45
53728892 TTCGTTGTTT
* *
53728902 TTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
53728947 TTCGATTTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
53728992 TTCGATCTACTTCGCTGCCAATACATGAAGACAAGACCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * *
53729037 TTCGATCTACTTTGCTGCCAGTACAGGAAGACAAGATCTGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
53729082 TTC-AGTCCACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATC
1 TTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * * * * * *
53729127 TTTGATCTACTTCAC-GCTAATACATGAAGATAAGATCTGTTTTC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
** * ** * *
53729171 TTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTACTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * *
53729216 TTCGATCCACTTCACTACCAATA
1 TTCGATCTACTTCGCTGCCAATA
53729239 TAGGTGTAAG
Statistics
Matches: 247, Mismatches: 42, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
44 39 0.16
45 207 0.84
46 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (45 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
Found at i:53729068 original size:135 final size:134
Alignment explanation
Indices: 53728902--53729238 Score: 460
Period size: 135 Copynumber: 2.5 Consensus size: 134
53728892 TTCGTTGTTT
* **
53728902 TTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATTTACTTCACTGCCA
1 TTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTGCCA
*
53728967 ATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGACCTG
66 ATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGACCTG
53729032 CTATC
130 CTATC
* * *
53729037 TTCGATCTACTTTGCTGCCAGTACAGGAAGACAAGATCTGTTATCTTC-AGTCCACTTCGCTGCC
1 TTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGA-TCCACTTCACTGCC
* * * * *
53729101 AATACAGGAAGATAAGATCTGCTATCTTTGATCTACTTCACGCTAATACATGAAGATAAGATCTG
65 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGACCTG
* *
53729166 TTTTC
130 CTATC
** ** * * *
53729171 TTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTACTATCTTCGATCCACTTCACTACCA
1 TTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTGCCA
53729236 ATA
66 ATA
53729239 TAGGTGTAAG
Statistics
Matches: 176, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
134 81 0.46
135 95 0.54
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (134 bp):
TTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTGCCA
ATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGACCTGC
TATC
Found at i:53735344 original size:6 final size:6
Alignment explanation
Indices: 53735335--53735380 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
53735325 GATTCAAAAA
* *
53735335 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAAC AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
53735381 AAGAAAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (6 bp):
AAAATC
Found at i:53735358 original size:18 final size:18
Alignment explanation
Indices: 53735328--53735380 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
53735318 GGGTTCAGAT
53735328 TCAAAAA-AAAATCAAAA
1 TCAAAAACAAAATCAAAA
*
53735345 TCAAAATCAAAATCAAAA
1 TCAAAAACAAAATCAAAA
*
53735363 TCAAAAACAAAAACAAAA
1 TCAAAAACAAAATCAAAA
53735381 AAGAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (18 bp):
TCAAAAACAAAATCAAAA
Found at i:53735381 original size:6 final size:6
Alignment explanation
Indices: 53735329--53735399 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
53735319 GGTTCAGATT
* * * * *
53735329 CAAAAA -AAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
*
53735376 CAAAAA -AGAAAA GAAAAA TCAAAA
1 CAAAAA CA-AAAA CAAAAA -CAAAA
53735400 GTAAAAAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
5 5 0.09
6 48 0.83
7 5 0.09
ACGTcount: A:0.76, C:0.13, G:0.03, T:0.08
Consensus pattern (6 bp):
CAAAAA
Found at i:53735381 original size:12 final size:12
Alignment explanation
Indices: 53735328--53735381 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
53735318 GGGTTCAGAT
53735328 TCAAAAA-AAAA
1 TCAAAAACAAAA
*
53735339 TCAAAATCAAAA
1 TCAAAAACAAAA
*
53735351 TCAAAATCAAAA
1 TCAAAAACAAAA
53735363 TCAAAAACAAAA
1 TCAAAAACAAAA
*
53735375 ACAAAAA
1 TCAAAAA
53735382 AGAAAAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 6 0.15
12 33 0.85
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (12 bp):
TCAAAAACAAAA
Found at i:53737238 original size:87 final size:87
Alignment explanation
Indices: 53737092--53737607 Score: 782
Period size: 87 Copynumber: 5.9 Consensus size: 87
53737082 CAGATAAGTG
* *
53737092 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAAACGAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
53737157 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * *
53737179 AAGATAGCAGATCTTACCTTCTTGCATTAACAGCGAAGCAGATCAAAAACGAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
*
53737244 TCGGTTGCAGTGGAGCTAGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * * *
53737266 AAGATAGCAGATCTTTCCTTCCTGCATTAACAACGAAGTAGATCGAAAATGAAGCCTTACCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
*
53737331 TCAGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
** *
53737353 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGTAAAGCAGATCGAAAACGAAGCCTTGCCTTCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
* * * *
53737418 TCGGTTGCATTAGAGCCGGTTG
66 TCGGTTGCAGTGGAGCTGGTTA
53737440 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
* *
53737505 TCGGATGTAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* ** *
53737527 AAGATAGCAGATCTTACCTTCCTATATTAACAGCAAAGCAGATCGAAAAC-AATGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAA-GCCTTGCCTCC
*
53737591 ATCAGTTGCAGTGGAGC
65 ATCGGTTGCAGTGGAGC
53737608 AGATTGAAGT
Statistics
Matches: 384, Mismatches: 44, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
86 2 0.01
87 382 0.99
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACGAAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCTGGTTA
Found at i:53739135 original size:16 final size:15
Alignment explanation
Indices: 53739110--53739144 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
53739100 TTAATAATAA
*
53739110 TATTATTATTATTAC
1 TATTATTATTAGTAC
53739125 TATTAATTATTAGTAC
1 TATT-ATTATTAGTAC
53739141 TATT
1 TATT
53739145 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTATTATTAGTAC
Found at i:53741617 original size:17 final size:17
Alignment explanation
Indices: 53741595--53741629 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53741585 CATTGGCCTC
53741595 TCTTTTTCTCTT-TTTTT
1 TCTTTTTC-CTTATTTTT
53741612 TCTTTTTCCTTATTTTT
1 TCTTTTTCCTTATTTTT
53741629 T
1 T
53741630 TAAACAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTTTCCTTATTTTT
Found at i:53745527 original size:106 final size:107
Alignment explanation
Indices: 53745335--53745537 Score: 293
Period size: 106 Copynumber: 1.9 Consensus size: 107
53745325 TGAATTAAGA
* * * *
53745335 TTTAAGAGGATATTTGACTATTTGGTCAAACGAAAAAATCGAAGCCCAGCACATTAGCGCACGTT
1 TTTAAGAGGATATTCGACTATTTGGTCAAACGAAAAAATCGAAACCAAACACATTAGCGCACGTT
*
53745400 TCCTCGAATTTCCAAACGCAAAATATTACCTTACTCTGAAAT
66 TCCTCGAATTCCCAAACGCAAAATATTACCTTACTCTGAAAT
* * *
53745442 TTTAA-AGGATATTCGGCTATTTGGTCGAACGAAAAAATCGAAACCAAACACATTAGGGCACGCT
1 TTTAAGAGGATATTCGACTATTTGGTCAAACGAAAAAATCGAAACCAAACACATTAGCGCACG-T
* *
53745506 TT-CTCGAATTCCCAAATGCAAAATATTGCCTT
65 TTCCTCGAATTCCCAAACGCAAAATATTACCTT
53745538 TATTATTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 77 0.91
107 8 0.09
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (107 bp):
TTTAAGAGGATATTCGACTATTTGGTCAAACGAAAAAATCGAAACCAAACACATTAGCGCACGTT
TCCTCGAATTCCCAAACGCAAAATATTACCTTACTCTGAAAT
Found at i:53746052 original size:18 final size:19
Alignment explanation
Indices: 53746001--53746061 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
53745991 CTGATATTTC
*
53746001 TATTAATTTAAAATA-TAGT
1 TATTAAATTAAAATAGTA-T
* *
53746020 TATTAAATGAGAATAGT-T
1 TATTAAATTAAAATAGTAT
*
53746038 TATTAAATTAAAATAGAAT
1 TATTAAATTAAAATAGTAT
53746057 TATTA
1 TATTA
53746062 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.44
19 18 0.53
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TATTAAATTAAAATAGTAT
Found at i:53746596 original size:27 final size:26
Alignment explanation
Indices: 53746558--53746614 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
53746548 TTTTAGTCCT
53746558 TTGGCACATTGGTGCCGCCAATGGCA
1 TTGGCACATTGGTGCCGCCAATGGCA
*
53746584 TTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCGCCAATGGCA
53746611 TTGG
1 TTGG
53746615 GGTGATCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (26 bp):
TTGGCACATTGGTGCCGCCAATGGCA
Found at i:53746709 original size:29 final size:29
Alignment explanation
Indices: 53746648--53746747 Score: 168
Period size: 29 Copynumber: 3.5 Consensus size: 29
53746638 TTTTTTTGAT
53746648 ATATTTTGGTAAAT-AAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
*
53746675 TTTATTTTGGTAAATAAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAAGTTGTA
53746705 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
53746734 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
53746748 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
28 13 0.19
29 53 0.78
30 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:53747229 original size:55 final size:56
Alignment explanation
Indices: 53747170--53747310 Score: 180
Period size: 57 Copynumber: 2.5 Consensus size: 56
53747160 TTGTTATTAA
* *
53747170 ATTTTAATA-AGATTATTATTAAATATAATTTAAT-AATAATAAATAATTTAATCAC
1 ATTTTAATATA-ATTATTATTAAAAATAATTTAATAAATAATAAATAATTTAATAAC
* * *
53747225 ATTTTAATATAATTTTTGTTAAAAATAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAAAATAATTTAAT-AAATAATAAATAATTTAATAAC
*
53747282 ATTCTTAATATAAATATTA-TAAAAATAAT
1 ATT-TTAATATAATTATTATTAAAAATAAT
53747311 ATATAACCTG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 29 0.39
56 1 0.01
57 32 0.43
58 12 0.16
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (56 bp):
ATTTTAATATAATTATTATTAAAAATAATTTAATAAATAATAAATAATTTAATAAC
Found at i:53747624 original size:21 final size:21
Alignment explanation
Indices: 53747597--53747650 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
53747587 TGATTTGTTA
*
53747597 TTTTTGCTACTGTTTTTTCA-
1 TTTTTGCTACTGTTTTCTCAC
*
53747617 TGTTTTGCTATTGTTTTCTCAC
1 T-TTTTGCTACTGTTTTCTCAC
*
53747639 TTTTTGCCACTG
1 TTTTTGCTACTG
53747651 CCTTCCATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (21 bp):
TTTTTGCTACTGTTTTCTCAC
Found at i:53758051 original size:31 final size:31
Alignment explanation
Indices: 53758009--53758116 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
53757999 AAGTTATTAT
*
53758009 TTGGGGCCTGAACTTGGAAACTTTTCCCACA
1 TTGGGGCCTGAACTTGGCAACTTTTCCCACA
*
53758040 TTGGGGTCTGAACTTGGCAA-TTGTTCCCACA
1 TTGGGGCCTGAACTTGGCAACTT-TTCCCACA
* * * *
53758071 TTAGGACCTGCACTTGGCAGCTTTTCCCACA
1 TTGGGGCCTGAACTTGGCAACTTTTCCCACA
*
53758102 TTGGTGCCTGAACTT
1 TTGGGGCCTGAACTT
53758117 CTTTTTGGTC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.03
31 60 0.94
32 2 0.03
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.31
Consensus pattern (31 bp):
TTGGGGCCTGAACTTGGCAACTTTTCCCACA
Found at i:53758268 original size:60 final size:58
Alignment explanation
Indices: 53758192--53758305 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 58
53758182 TTTTCAAGGA
* * *
53758192 CTAACTTGGATAAAAAAAAAGTTGAAGT-CCCAATGTGGGAACATTTTCCAAGTTCAGGGC
1 CTAACTTGGA-CAAAAAAAAGTT-AAGTCCCCAATGTGGGAA-AGTTGCCAAGTTCAGGGC
* * *
53758252 CTAACTTGGACCAAAAAAAGTTCAGTCCCCTATGTGGGAAAGTTGCCAAGTTCA
1 CTAACTTGGACAAAAAAAAGTTAAGTCCCCAATGTGGGAAAGTTGCCAAGTTCA
53758306 AATCCCAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 15 0.32
59 22 0.47
60 10 0.21
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (58 bp):
CTAACTTGGACAAAAAAAAGTTAAGTCCCCAATGTGGGAAAGTTGCCAAGTTCAGGGC
Found at i:53764987 original size:102 final size:100
Alignment explanation
Indices: 53764879--53765116 Score: 257
Period size: 102 Copynumber: 2.3 Consensus size: 100
53764869 ATGTCACTTT
*
53764879 TTCATGTGGAGTCACCAAAATCAGTAAAAAAAAACTC-CCTAATGA-CAACTCTAGATGTGGCGG
1 TTCATGTGGAGTCACCAAAATCAGTAAAAAAAAACTCACCCAAT-ACCAACTCTAGATGTGGCGG
* * **
53764942 CACC-AGTAATTCTTTTTTTTACTTTTTCGGTGTTGCCTC
65 CACCGA-TAA---TTTATTTTACTTTTTCGATAATGCCTC
* ** * * *
53764981 TTCATGTGGAGTCACCCAAATCAGTAAAAAGAAATTTTCACCCAATACCAACTTTAGTTGTGGTG
1 TTCATGTGGAGTCACCAAAATCAGTAAAAA-AAA-ACTCACCCAATACCAACTCTAGATGTGGCG
*
53765046 GCACCGATAATTTATTTTACTTTTTTGATAATGCCTC
64 GCACCGATAATTTATTTTACTTTTTCGATAATGCCTC
* * *
53765083 TTCATGTGGAGGCACTAAAATCTGTAAAAAAAAA
1 TTCATGTGGAGTCACCAAAATCAGTAAAAAAAAA
53765117 TTTTCCTAGT
Statistics
Matches: 114, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
101 3 0.03
102 77 0.68
103 3 0.03
104 3 0.03
105 27 0.24
106 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (100 bp):
TTCATGTGGAGTCACCAAAATCAGTAAAAAAAAACTCACCCAATACCAACTCTAGATGTGGCGGC
ACCGATAATTTATTTTACTTTTTCGATAATGCCTC
Found at i:53765208 original size:105 final size:98
Alignment explanation
Indices: 53765078--53765350 Score: 264
Period size: 102 Copynumber: 2.7 Consensus size: 98
53765068 TTTTGATAAT
* * *
53765078 GCCTCTTCATGTGGAGGCACTAAAATCTGTAAAAAAAAATTTTCCTAGTGTCAACTCCAAATGTG
1 GCCTCTT-ATGT-GAGGCACCAAAATCTGTAAAAAAAAATTTCCCTGGTGTCAACTCCAAATGTG
* **
53765143 GCAACACTGGTACTTGTTATTTTTTG-AATTATTCGGTGCC
64 GCAACACTAGTA---G-T-TTTTTTGAAATT-TTCAATGCC
* *
53765183 GCCTCTATATGTAGAGGCACCAAAATCTGTAAAAAGAAAATTTCCTCTGGTGCCAACTCAAAATG
1 GCCTCT-TATGT-GAGGCACCAAAATCTGTAAAAA-AAAATTTCC-CTGGTGTCAACTCCAAATG
** *
53765248 TGATAGCACTAGTAGTTTTTTTGAAATTTTCAATGCC
62 TGGCAACACTAGTAGTTTTTTTGAAATTTTCAATGCC
* *
53765285 -CCTTCTTTATGTGGGGACACCAAAATCAGT-AAAAAAAATTTCCCTTGGTGTCAACTCCAAATG
1 GCC-TC-TTATGTGAGG-CACCAAAATCTGTAAAAAAAAATTTCCC-TGGTGTCAACTCCAAATG
53765348 TGG
62 TGG
53765351 TGGCAACTGA
Statistics
Matches: 143, Mismatches: 17, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
99 1 0.01
100 27 0.19
101 9 0.06
102 33 0.23
103 6 0.04
104 1 0.01
105 31 0.22
106 9 0.06
107 26 0.18
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (98 bp):
GCCTCTTATGTGAGGCACCAAAATCTGTAAAAAAAAATTTCCCTGGTGTCAACTCCAAATGTGGC
AACACTAGTAGTTTTTTTGAAATTTTCAATGCC
Found at i:53766570 original size:101 final size:99
Alignment explanation
Indices: 53766304--53766573 Score: 382
Period size: 101 Copynumber: 2.7 Consensus size: 99
53766294 GATACCAAGA
53766304 GAAATTTTTTTTTACTGATTTTGGTGCCTCCACATGAAGAGGCGACACCGAAAAATTCAAAAAAA
1 GAAATTTTTTTTTACTGATTTTGGTGCCTCCACATGAAGAGGCGACACCGAAAAATT--AAAAAA
* * * * **
53766369 AATTATAGGTGTCGTCACATTTGGAGTTGGCACTAG
64 ATTTATAGGTGCCGCCACATCTAAAGTTGGCACTAG
* *
53766405 GAAATTTTTTTTTA-TAGATTTTGGTGCCTCCACATGATGAGGCGACACCGAAAAAGTAAAAAAA
1 GAAATTTTTTTTTACT-GATTTTGGTGCCTCCACATGAAGAGGCGACACCGAAAAATTAAAAAAA
53766469 TTTACT-GGTGCCGCCACATCTAAAGTTGGCACTAGG
65 TTTA-TAGGTGCCGCCACATCTAAAGTTGGCACTA-G
* *
53766505 GGAATTTCTTTTTTACTGATTTTGGTGCCTCCACATGAAGAGGCGGCACCGAAAAATTAAAAAAA
1 GAAATTT-TTTTTTACTGATTTTGGTGCCTCCACATGAAGAGGCGACACCGAAAAATTAAAAAAA
53766570 TTTA
65 TTTA
53766574 ACAAAAATTA
Statistics
Matches: 152, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
99 33 0.22
100 9 0.06
101 109 0.72
102 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (99 bp):
GAAATTTTTTTTTACTGATTTTGGTGCCTCCACATGAAGAGGCGACACCGAAAAATTAAAAAAAT
TTATAGGTGCCGCCACATCTAAAGTTGGCACTAG
Found at i:53769050 original size:17 final size:17
Alignment explanation
Indices: 53769028--53769065 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53769018 ATATTATTGC
* *
53769028 ATATATTACATATATAT
1 ATATATAACAAATATAT
53769045 ATATATAACAAATATAT
1 ATATATAACAAATATAT
53769062 -TATA
1 ATATA
53769066 ACCATATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATAACAAATATAT
Found at i:53771549 original size:40 final size:40
Alignment explanation
Indices: 53771494--53771608 Score: 123
Period size: 40 Copynumber: 3.0 Consensus size: 40
53771484 CAACTTTCGT
53771494 CAGTTTATCTGACTAGTGCTAGGCACATAATTATATTTGC
1 CAGTTTATCTGACTAGTGCTAGGCACATAATTATATTTGC
* * * * *
53771534 CAGTTTATCTGACTAGCGTTAGGCAC--AA--ATCTTCGT
1 CAGTTTATCTGACTAGTGCTAGGCACATAATTATATTTGC
* *
53771570 CAGTTTATCTGACTAATGCT-GGCACACTTATTATATTTG
1 CAGTTTATCTGACTAGTGCTAGGCACA-TAATTATATTTG
53771609 TCGGTTTACC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
35 5 0.08
36 22 0.37
38 3 0.05
40 29 0.49
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (40 bp):
CAGTTTATCTGACTAGTGCTAGGCACATAATTATATTTGC
Found at i:53771557 original size:75 final size:76
Alignment explanation
Indices: 53771461--53771632 Score: 224
Period size: 76 Copynumber: 2.3 Consensus size: 76
53771451 ATATTTGTTG
* * *
53771461 GTTTATCCGACTAGCTCTAGGCGCAACT-TTCGTCAGTTTATCTGACTAGTGCTAGGCACA-TAA
1 GTTTATCCGACTAGCTCTAGGCACAAATCTTCGTCAGTTTATCTGACTAATGCT-GGCACACTAA
53771524 TTATATTTGCCA
65 TTATATTTGCCA
* *
53771536 GTTTATCTGACTAGCGT-TAGGCACAAATCTTCGTCAGTTTATCTGACTAATGCTGGCACACTTA
1 GTTTATCCGACTAGC-TCTAGGCACAAATCTTCGTCAGTTTATCTGACTAATGCTGGCACACTAA
* *
53771600 TTATATTTGTCG
65 TTATATTTGCCA
* *
53771612 GTTTACCCGACTAGCACTAGG
1 GTTTATCCGACTAGCTCTAGG
53771633 TGCAAAACTT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
75 29 0.35
76 54 0.65
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (76 bp):
GTTTATCCGACTAGCTCTAGGCACAAATCTTCGTCAGTTTATCTGACTAATGCTGGCACACTAAT
TATATTTGCCA
Found at i:53774862 original size:28 final size:27
Alignment explanation
Indices: 53774823--53775027 Score: 230
Period size: 28 Copynumber: 7.4 Consensus size: 27
53774813 CATGTCATAA
*
53774823 AAAAGGAAGCCTTTGTGGTGATTTATG
1 AAAAGGAAGCCTTTGTGGTGATCTATG
* *
53774850 AAAAGAGAAGCCTTTGTGGCGATCTATA
1 AAAAG-GAAGCCTTTGTGGTGATCTATG
*
53774878 AAAAGGGAAGCCTTTGTGGTGATCTATA
1 AAAA-GGAAGCCTTTGTGGTGATCTATG
* *
53774906 AAAAGGGAAGCCTTTATGGTGATCTATA
1 AAAA-GGAAGCCTTTGTGGTGATCTATG
**
53774934 AAAAGGAAAGCCTTTGTGGCAATCTATG
1 AAAAGG-AAGCCTTTGTGGTGATCTATG
* * *
53774962 AAAATTGAAGCCTTTGTCGCGATCTATG
1 AAAA-GGAAGCCTTTGTGGTGATCTATG
* *
53774990 AAAATGGAAGTCTTTGTGGTAATCTATG
1 AAAA-GGAAGCCTTTGTGGTGATCTATG
*
53775018 AAATGGAAGC
1 AAAAGGAAGC
53775028 TTGCATGGAA
Statistics
Matches: 155, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
27 12 0.08
28 141 0.91
29 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (27 bp):
AAAAGGAAGCCTTTGTGGTGATCTATG
Found at i:53774910 original size:56 final size:56
Alignment explanation
Indices: 53774819--53775020 Score: 260
Period size: 56 Copynumber: 3.6 Consensus size: 56
53774809 TAAACATGTC
* * *
53774819 ATAAAAAAGGAAGCCTTTGTGGTGATTTATGAAAAGAGAAGCCTTTGTGGCGATCT
1 ATAAAAAGGGAAGCCTTTGTGGTAATCTATGAAAAGAGAAGCCTTTGTGGCGATCT
* * * * *
53774875 ATAAAAAGGGAAGCCTTTGTGGTGATCTATAAAAAGGGAAGCCTTTATGGTGATCT
1 ATAAAAAGGGAAGCCTTTGTGGTAATCTATGAAAAGAGAAGCCTTTGTGGCGATCT
* * ** *
53774931 ATAAAAAGGAAAGCCTTTGTGGCAATCTATGAAAATTGAAGCCTTTGTCGCGATCT
1 ATAAAAAGGGAAGCCTTTGTGGTAATCTATGAAAAGAGAAGCCTTTGTGGCGATCT
* * *
53774987 ATGAAAATGGAAGTCTTTGTGGTAATCTATGAAA
1 ATAAAAAGGGAAGCCTTTGTGGTAATCTATGAAA
53775021 TGGAAGCTTG
Statistics
Matches: 126, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 126 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (56 bp):
ATAAAAAGGGAAGCCTTTGTGGTAATCTATGAAAAGAGAAGCCTTTGTGGCGATCT
Found at i:53774960 original size:84 final size:84
Alignment explanation
Indices: 53774819--53775025 Score: 263
Period size: 84 Copynumber: 2.5 Consensus size: 84
53774809 TAAACATGTC
* *
53774819 ATAAAAAAGGAAGCCTTTGTGGTGATTTATGAAAA-GAGAAGCCTTTGTGGCGATCTATAAAAAG
1 ATAAAAAAGGAAGCCTTTGTGGTGATCTATGAAAAGGA-AAGCCTTTGTGGCAATCTATAAAAAG
* *
53774883 GGAAGCCTTTGTGGTGATCT
65 GGAAGCCTTTGTCGCGATCT
* * * * **
53774903 ATAAAAAGGGAAGCCTTTATGGTGATCTATAAAAAGGAAAGCCTTTGTGGCAATCTATGAAAATT
1 ATAAAAAAGGAAGCCTTTGTGGTGATCTATGAAAAGGAAAGCCTTTGTGGCAATCTATAAAAAGG
53774968 GAAGCCTTTGTCGCGATCT
66 GAAGCCTTTGTCGCGATCT
* * * * *
53774987 ATGAAAATGGAAGTCTTTGTGGTAATCTATGAAATGGAA
1 ATAAAAAAGGAAGCCTTTGTGGTGATCTATGAAAAGGAA
53775026 GCTTGCATGG
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
84 103 0.98
85 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (84 bp):
ATAAAAAAGGAAGCCTTTGTGGTGATCTATGAAAAGGAAAGCCTTTGTGGCAATCTATAAAAAGG
GAAGCCTTTGTCGCGATCT
Found at i:53778182 original size:18 final size:18
Alignment explanation
Indices: 53778159--53778199 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
53778149 CACCCTCTCC
53778159 TGTGTTGAGTGGTTCCTA
1 TGTGTTGAGTGGTTCCTA
53778177 TGTGTTGAGTGGTTCCTA
1 TGTGTTGAGTGGTTCCTA
53778195 TGTGT
1 TGTGT
53778200 CATTAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.10, G:0.34, T:0.46
Consensus pattern (18 bp):
TGTGTTGAGTGGTTCCTA
Found at i:53783995 original size:16 final size:18
Alignment explanation
Indices: 53783974--53784019 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
53783964 TTAGCTTGTG
53783974 TTTATATTATAA-A-ATA
1 TTTATATTATAATATATA
53783990 TTTATAAATTATAATATATA
1 TTTAT--ATTATAATATATA
53784010 TTTATTATTA
1 TTTA-TATTA
53784020 GATAGGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.20
18 7 0.28
19 5 0.20
20 7 0.28
21 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATATTATAATATATA
Found at i:53785716 original size:21 final size:21
Alignment explanation
Indices: 53785692--53785734 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53785682 ATTAGTGTTC
* *
53785692 ACTCTTTTGTATAGGTTAATA
1 ACTCTTTTGTATAAGCTAATA
53785713 ACTCTTTTGTATAAGCTAATA
1 ACTCTTTTGTATAAGCTAATA
53785734 A
1 A
53785735 TTGTCGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
ACTCTTTTGTATAAGCTAATA
Found at i:53786692 original size:16 final size:16
Alignment explanation
Indices: 53786671--53786701 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53786661 TTCACTATTA
*
53786671 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
53786687 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
53786702 GCATGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:53792754 original size:57 final size:57
Alignment explanation
Indices: 53792684--53792845 Score: 306
Period size: 57 Copynumber: 2.8 Consensus size: 57
53792674 AGAAATGGGA
* *
53792684 AATCATTTGGAAATGATTATGATTTTCTCCAAAATGAAAATGAAAATGGAGAAATTG
1 AATCATATGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATGGAGAAATTG
53792741 AATCATATGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATGGAGAAATTG
1 AATCATATGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATGGAGAAATTG
53792798 AATCATATGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATG
1 AATCATATGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATG
53792846 AAAATGAAAA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 103 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (57 bp):
AATCATATGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATGGAGAAATTG
Found at i:53792858 original size:13 final size:13
Alignment explanation
Indices: 53792828--53792865 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
53792818 GGTTTTCTCC
53792828 AAAATGAAAATG-
1 AAAATGAAAATGA
53792840 AAAATGAAAATGA
1 AAAATGAAAATGA
53792853 AAAATGAAAATGA
1 AAAATGAAAATGA
53792866 CCTGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:53792878 original size:7 final size:6
Alignment explanation
Indices: 53792828--53792865 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
53792818 GGTTTTCTCC
53792828 AAAATG AAAATG AAAATG AAAATG AAAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG -AAAATG AAAATG A
53792866 CCTGAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:53793124 original size:30 final size:30
Alignment explanation
Indices: 53793088--53793147 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
53793078 AGACTAGGAG
53793088 TTTGTTTTTCTAGTTGAAATAAACTTCTAC
1 TTTGTTTTTCTAGTTGAAATAAACTTCTAC
*
53793118 TTTGTTTTTCTAGTTGTAATAAACTTCTAC
1 TTTGTTTTTCTAGTTGAAATAAACTTCTAC
53793148 AATTCAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTGTTTTTCTAGTTGAAATAAACTTCTAC
Found at i:53794365 original size:24 final size:24
Alignment explanation
Indices: 53794338--53794390 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
53794328 GGCTTTGAGA
53794338 CTAAAATTGAAATTAACCAATGGT
1 CTAAAATTGAAATTAACCAATGGT
*
53794362 CT-AAATTGCAATTAACCAATGGT
1 CTAAAATTGAAATTAACCAATGGT
*
53794385 CCAAAA
1 CTAAAA
53794391 CAACAATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
CTAAAATTGAAATTAACCAATGGT
Found at i:53798782 original size:80 final size:78
Alignment explanation
Indices: 53798698--53798955 Score: 331
Period size: 80 Copynumber: 3.3 Consensus size: 78
53798688 AAAATATATA
*
53798698 AATTGAATTAAAGGTATGGATTTTATATATGTATATGTGAGGTTTTCGAATATATATGTATATAC
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGG--TTCGAATATATATGTATATAC
53798763 ATGTATAAGTTCTTG
64 ATGTATAAGTTCTTG
* * *
53798778 AATTGAATTAAAGTTATGAATTATATATATGTATAAGTGAGGTTCGAATATATATATGTATATAC
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCG-A-ATATATATGTATATAC
*
53798843 ATGTATAAGTTTTTG
64 ATGTATAAGTTCTTG
* * * * *
53798858 AATTGAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTCG-A-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
* * *
53798921 ATACAAGTACTTG
66 GTATAAGTTCTTG
* *
53798934 AGTTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
53798956 GTAAATACTT
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
76 44 0.28
77 1 0.01
78 4 0.03
79 1 0.01
80 107 0.68
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
GTATAAGTTCTTG
Found at i:53799354 original size:31 final size:30
Alignment explanation
Indices: 53799316--53799542 Score: 167
Period size: 31 Copynumber: 7.2 Consensus size: 30
53799306 GATAAGTATA
*
53799316 TATATGCATTTGGTTATATACCTTTGATGTG
1 TATATGCATTCGGTTATATA-CTTTGATGTG
* *
53799347 TATATGCATTCGATT-TAAGTA-TTTGATAGGTA
1 TATATGCATTCGGTTAT-A-TACTTTGAT--GTG
* *
53799379 TATATGCATTCGGTTGTACACATTTGATGTG
1 TATATGCATTCGGTTATATAC-TTTGATGTG
* *
53799410 TATATGCATTCGATTATAAGTA-TTTGATAGGTA
1 TATATGCATTCGGTTAT-A-TACTTTGAT--GTG
*
53799443 TATATGCATTCGGTTGTATACATTTGATGTG
1 TATATGCATTCGGTTATATAC-TTTGATGTG
* *
53799474 TATATGCATTCGGTTATAAGTA-GTTGATAAGTA
1 TATATGCATTCGGTTAT-A-TACTTTGAT--GTG
*
53799507 TATATGCATTCGGTTATAAGTA-TTTGATGAG
1 TATATGCATTCGGTTAT-A-TACTTTGATGTG
53799538 TATAT
1 TATAT
53799543 ACATACATTT
Statistics
Matches: 160, Mismatches: 19, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
30 7 0.04
31 69 0.43
32 22 0.14
33 62 0.39
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (30 bp):
TATATGCATTCGGTTATATACTTTGATGTG
Found at i:53799413 original size:33 final size:33
Alignment explanation
Indices: 53799314--53799543 Score: 216
Period size: 33 Copynumber: 7.2 Consensus size: 33
53799304 TTGATAAGTA
*
53799314 TATATATGCATTTGGTTAT-A-TACCTTTGATGTG
1 TATATATGCATTCGGTTATAAGTA--TTTGATGTG
*
53799347 --TATATGCATTCGATT-TAAGTATTTGATAG-G
1 TATATATGCATTCGGTTATAAGTATTTGAT-GTG
* *
53799377 TATATATGCATTCGGTTGTACA-CATTTGATGTG
1 TATATATGCATTCGGTTATA-AGTATTTGATGTG
*
53799410 --TATATGCATTCGATTATAAGTATTTGATAG-G
1 TATATATGCATTCGGTTATAAGTATTTGAT-GTG
* *
53799441 TATATATGCATTCGGTTGTATA-CATTTGATGTG
1 TATATATGCATTCGGTTATA-AGTATTTGATGTG
* **
53799474 --TATATGCATTCGGTTATAAGTAGTTGATAAG
1 TATATATGCATTCGGTTATAAGTATTTGATGTG
*
53799505 TATATATGCATTCGGTTATAAGTATTTGATGAG
1 TATATATGCATTCGGTTATAAGTATTTGATGTG
53799538 TATATA
1 TATATA
53799544 CATACATTTG
Statistics
Matches: 163, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
30 10 0.06
31 63 0.39
32 19 0.12
33 69 0.42
34 2 0.01
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (33 bp):
TATATATGCATTCGGTTATAAGTATTTGATGTG
Found at i:53799451 original size:64 final size:64
Alignment explanation
Indices: 53799314--53799521 Score: 346
Period size: 64 Copynumber: 3.3 Consensus size: 64
53799304 TTGATAAGTA
* * *
53799314 TATATATGCATTTGGTTATATACCTTTGATGTGTATATGCATTCGATT-TAAGTATTTGATAGG
1 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
*
53799377 TATATATGCATTCGGTTGTACACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
1 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
* * *
53799441 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGGTTATAAGTAGTTGATAAG
1 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
53799505 TATATATGCATTCGGTT
1 TATATATGCATTCGGTT
53799522 ATAAGTATTT
Statistics
Matches: 136, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
63 44 0.32
64 92 0.68
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (64 bp):
TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
Found at i:53799532 original size:64 final size:64
Alignment explanation
Indices: 53799301--53799542 Score: 335
Period size: 64 Copynumber: 3.8 Consensus size: 64
53799291 ATTTATATCT
* * *
53799301 TATTTGATAAGTATATATATGCATTTGGTTATATACCTTTGATGTGTATATGCATTCGATT-TAA
1 TATTTGATAAG--TATATATGCATTCGGTTATACACATTTGATGTGTATATGCATTCGATTATAA
53799365 G
64 G
* *
53799366 TATTTGATAGGTATATATGCATTCGGTTGTACACATTTGATGTGTATATGCATTCGATTATAAG
1 TATTTGATAAGTATATATGCATTCGGTTATACACATTTGATGTGTATATGCATTCGATTATAAG
* * * *
53799430 TATTTGATAGGTATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGGTTATAAG
1 TATTTGATAAGTATATATGCATTCGGTTATACACATTTGATGTGTATATGCATTCGATTATAAG
* * *
53799494 TAGTTGATAAGTATATATGCATTCGGTTATA-AGTATTTGATGAGTATAT
1 TATTTGATAAGTATATATGCATTCGGTTATACA-CATTTGATGTGTATAT
53799543 ACATACATTT
Statistics
Matches: 163, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
63 45 0.28
64 108 0.66
65 10 0.06
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (64 bp):
TATTTGATAAGTATATATGCATTCGGTTATACACATTTGATGTGTATATGCATTCGATTATAAG
Found at i:53803603 original size:32 final size:32
Alignment explanation
Indices: 53803562--53803627 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
53803552 GTAACGCCCA
53803562 AAATTGGTACTGAATTGATTGTTTAATGTCTT
1 AAATTGGTACTGAATTGATTGTTTAATGTCTT
*
53803594 AAATTGGTACTTAATTGATTGTTTAATGTCTT
1 AAATTGGTACTGAATTGATTGTTTAATGTCTT
53803626 AA
1 AA
53803628 TGTCGAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (32 bp):
AAATTGGTACTGAATTGATTGTTTAATGTCTT
Found at i:53804642 original size:16 final size:15
Alignment explanation
Indices: 53804618--53804657 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
53804608 AATGAGTGAA
53804618 ATTAAAGAAAAAACAT
1 ATTAAAGAAAAAA-AT
* *
53804634 ATTATAGAATAAAAT
1 ATTAAAGAAAAAAAT
53804649 ATTAAAGAA
1 ATTAAAGAA
53804658 TGTATATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (15 bp):
ATTAAAGAAAAAAAT
Found at i:53804652 original size:15 final size:16
Alignment explanation
Indices: 53804618--53804658 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
53804608 AATGAGTGAA
*
53804618 ATTAAAGAAAAAACAT
1 ATTAAAGAATAAACAT
*
53804634 ATTATAGAATAAA-AT
1 ATTAAAGAATAAACAT
53804649 ATTAAAGAAT
1 ATTAAAGAAT
53804659 GTATATATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (16 bp):
ATTAAAGAATAAACAT
Found at i:53812115 original size:110 final size:106
Alignment explanation
Indices: 53811888--53812116 Score: 230
Period size: 110 Copynumber: 2.1 Consensus size: 106
53811878 GGAAATTTTT
* * *
53811888 TTAAAAT-AAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTT
1 TTAAAATAAAGGCAATATTTCGCATTTAGAAAATCGAGAAAACGTGCCCTAACGTACTGGGTTTC
** **
53811952 GATTTCTCGTTCGACCAAATGGCCAAATATCCTTTTAGACT
66 GATTTCTCGTTCGACCAAATAACCAAATATCCTTTTAGAAA
* * ** *
53811993 TTCCAAATAATAAAGGCAATATTTCGTATTTAGAAATTCGAGAAGTCGTGCCCTAACTTACTGGG
1 TT---AA-AATAAAGGCAATATTTCGCATTTAGAAAATCGAGAAAACGTGCCCTAACGTACTGGG
*
53812058 TTTCGATTTTTCTTGCGTT-GAACCTAAATAACCGAATATCCTTTTA-AAA
62 TTTCGA--TTTC-T-CGTTCG-ACC-AAATAACCAAATATCCTTTTAGAAA
53812107 TTAAAATAAA
1 TTAAAATAAA
53812117 TGAGGTTTAA
Statistics
Matches: 100, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
105 2 0.02
108 2 0.02
109 3 0.03
110 57 0.57
111 2 0.02
112 4 0.04
113 2 0.02
114 10 0.10
115 18 0.18
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (106 bp):
TTAAAATAAAGGCAATATTTCGCATTTAGAAAATCGAGAAAACGTGCCCTAACGTACTGGGTTTC
GATTTCTCGTTCGACCAAATAACCAAATATCCTTTTAGAAA
Found at i:53823196 original size:13 final size:13
Alignment explanation
Indices: 53823165--53823189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53823155 CTAATTCTAT
53823165 AAAAAAACTTATA
1 AAAAAAACTTATA
53823178 AAAAAAACTTAT
1 AAAAAAACTTAT
53823190 TTAAAAAGCA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAAACTTATA
Found at i:53823549 original size:19 final size:20
Alignment explanation
Indices: 53823514--53823552 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
53823504 TTCCAAAAAT
*
53823514 CTTAGAAAATGTTTTGAACA
1 CTTAGAAAATATTTTGAACA
53823534 CTTAGAAAA-ATTTTGAACA
1 CTTAGAAAATATTTTGAACA
53823553 AAATTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
CTTAGAAAATATTTTGAACA
Found at i:53823595 original size:20 final size:20
Alignment explanation
Indices: 53823570--53823612 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
53823560 AAAACAGTTT
*
53823570 AAACATTTTTAACTCAATTG
1 AAACATTTTTAAATCAATTG
*
53823590 AAACATTTTTAAATCGATTG
1 AAACATTTTTAAATCAATTG
53823610 AAA
1 AAA
53823613 AATTGTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
AAACATTTTTAAATCAATTG
Found at i:53824279 original size:22 final size:23
Alignment explanation
Indices: 53824254--53824297 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
53824244 ATGGTTATGC
53824254 AAATGCA-ATATTTT-AGAAAACG
1 AAATGCAGAT-TTTTCAGAAAACG
53824276 AAATGCAGATTTTTCAGAAAAC
1 AAATGCAGATTTTTCAGAAAAC
53824298 TTCCTACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (23 bp):
AAATGCAGATTTTTCAGAAAACG
Done.