Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 8 of 97
Found at i:3825792 original size:13 final size:13
Alignment explanation
Indices: 3825744--3825791 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
3825734 TTATAGGGAC
3825744 ATTTTAAAAAATA
1 ATTTTAAAAAATA
3825757 ATCTTTAAAGATAATA
1 AT-TTTAAA-A-AATA
*
3825773 TATTTTTAAAAATA
1 -ATTTTAAAAAATA
3825787 ATTTT
1 ATTTT
3825792 TTTTATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 7 0.23
14 10 0.33
15 2 0.07
16 9 0.30
17 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
ATTTTAAAAAATA
Found at i:3825935 original size:46 final size:45
Alignment explanation
Indices: 3825870--3826032 Score: 184
Period size: 45 Copynumber: 3.6 Consensus size: 45
3825860 GTTACATGCC
* * * *
3825870 ATGTATAAAAACATATGACAAGTCATGGTTAACGTATTACACTTAT
1 ATGTACAAAAATATGTGACAAGTCATGGTTAACATATTACACTT-T
* * * * **
3825916 ATATACAAAAATCTGTGACAAGCCATGGTTAGCATATTACACGCT
1 ATGTACAAAAATATGTGACAAGTCATGGTTAACATATTACACTTT
* * *
3825961 ATGTACAAAAATATGTGACAAATCATGGTTAACTTATTACA-TGTC
1 ATGTACAAAAATATGTGACAAGTCATGGTTAACATATTACACT-TT
3826006 ATGTACAAAAATATGTGACAAGTCATG
1 ATGTACAAAAATATGTGACAAGTCATG
3826033 TATAAAAACC
Statistics
Matches: 96, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
45 62 0.65
46 34 0.35
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (45 bp):
ATGTACAAAAATATGTGACAAGTCATGGTTAACATATTACACTTT
Found at i:3825987 original size:91 final size:90
Alignment explanation
Indices: 3825861--3826032 Score: 220
Period size: 91 Copynumber: 1.9 Consensus size: 90
3825851 CACTATTATG
* * * *
3825861 TTACATGCCATGTATAAAAACATATGACAAGTCATGGTTAACGTATTACACT-TATATATACAAA
1 TTACACGCCATGTACAAAAACATATGACAAATCATGGTTAACGTATTACA-TGT-CATATACAAA
*
3825925 AATCTGTGACAAGCCATGGTTAGCATA
64 AATATGTGACAAGCCATGGTTAGCATA
* * * * *
3825952 TTACACGCTATGTACAAAAATATGTGACAAATCATGGTTAACTTATTACATGTCATGTACAAAAA
1 TTACACGCCATGTACAAAAACATATGACAAATCATGGTTAACGTATTACATGTCATATACAAAAA
*
3826017 TATGTGACAAGTCATG
66 TATGTGACAAGCCATG
3826033 TATAAAAACC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
90 25 0.36
91 44 0.64
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (90 bp):
TTACACGCCATGTACAAAAACATATGACAAATCATGGTTAACGTATTACATGTCATATACAAAAA
TATGTGACAAGCCATGGTTAGCATA
Found at i:3826039 original size:24 final size:24
Alignment explanation
Indices: 3825961--3826051 Score: 73
Period size: 24 Copynumber: 3.9 Consensus size: 24
3825951 ATTACACGCT
*
3825961 ATGTACAAAAATATGTGACAAATC
1 ATGTACAAAAATATGTGACAAGTC
* ** *
3825985 ATGGT--TAACTTAT-T-ACATGTC
1 AT-GTACAAAAATATGTGACAAGTC
3826006 ATGTACAAAAATATGTGACAAGTC
1 ATGTACAAAAATATGTGACAAGTC
* **
3826030 ATGTATAAAAACCTGTGACAAG
1 ATGTACAAAAATATGTGACAAG
3826052 CTATGGTTAG
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
20 2 0.04
21 7 0.14
22 6 0.12
23 6 0.12
24 27 0.54
25 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (24 bp):
ATGTACAAAAATATGTGACAAGTC
Found at i:3826094 original size:45 final size:45
Alignment explanation
Indices: 3826030--3826139 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 45
3826020 GTGACAAGTC
* **
3826030 ATGTATAAAAACCTGTGACAAGCTATGGTTAGTTTGTTACACACT
1 ATGTACAAAAACCTGTGACAAGCTATGGTTAGCATGTTACACACT
*
3826075 ATGTACAAAAACCTGTGACAAGCTATGGTTAGCATGTTACACGCT
1 ATGTACAAAAACCTGTGACAAGCTATGGTTAGCATGTTACACACT
**
3826120 ATGTACAAAAATATGTGACA
1 ATGTACAAAAACCTGTGACA
3826140 CGGCATATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (45 bp):
ATGTACAAAAACCTGTGACAAGCTATGGTTAGCATGTTACACACT
Found at i:3826124 original size:114 final size:114
Alignment explanation
Indices: 3825916--3826213 Score: 366
Period size: 114 Copynumber: 2.6 Consensus size: 114
3825906 TTACACTTAT
* *
3825916 ATATACAAAAATCTGTGACAAGCCATGGTTAGCATATTACACGCTATGTACAAAAATATGTGACA
1 ATATACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGCTATGTACAAAAATATGTGACA
* * * *
3825981 A-ATCATGGTTAACTTATTACATGTCATGTACAAAAATATGTGACAAGTC
66 AGCT-ATGGTTAACATATTACACGTCATGTACAAAAATATGTGACAAGGC
* * * ** * **
3826030 ATGTATAAAAACCTGTGACAAGCTATGGTTAGTTTGTTACACACTATGTACAAAAACCTGTGACA
1 ATATACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGCTATGTACAAAAATATGTGACA
* * *
3826095 AGCTATGGTTAGCATGTTACACG-CTATGTACAAAAATATGTGACACGGC
66 AGCTATGGTTAACATATTACACGTC-ATGTACAAAAATATGTGACAAGGC
* * * * *
3826144 ATATACAAAAACCTGTGACAAACCATGATTAGCGTGTTACATGCTATGTACAAAAATATGTGATA
1 ATATACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGCTATGTACAAAAATATGTGACA
3826209 AGCTA
66 AGCTA
3826214 AGTACAAAAA
Statistics
Matches: 153, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
113 1 0.01
114 151 0.99
115 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (114 bp):
ATATACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGCTATGTACAAAAATATGTGACA
AGCTATGGTTAACATATTACACGTCATGTACAAAAATATGTGACAAGGC
Found at i:3826275 original size:69 final size:69
Alignment explanation
Indices: 3826077--3826279 Score: 243
Period size: 69 Copynumber: 2.9 Consensus size: 69
3826067 TACACACTAT
* * *
3826077 GTACAAAAACCTGTGACAAGCTATGGTTAGCATGTTACACGCTATGTACAAAAATATGTGACACG
1 GTACAAAAACCTGTGACAAGCTATGATTAGCATGTTACACGCTATGTACAAAAATATGTGATA-A
3826142 GCATA
65 GCATA
* * * *
3826147 -TACAAAAACCTGTGACAAACCATGATTAGCGTGTTACATGCTATGTACAAAAATATGTGATAAG
1 GTACAAAAACCTGTGACAAGCTATGATTAGCATGTTACACGCTATGTACAAAAATATGTGATAAG
3826211 C-TAA
66 CAT-A
* ***
3826215 GTACAAAAACCTGTGACAAGTTATGATTAATTTGTTACACG-TCATGTACAAAAACT-TGTGATA
1 GTACAAAAACCTGTGACAAGCTATGATTAGCATGTTACACGCT-ATGTACAAAAA-TATGTGATA
3826278 AG
64 AG
3826280 TCATGATTAG
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
67 1 0.01
68 4 0.03
69 109 0.95
70 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (69 bp):
GTACAAAAACCTGTGACAAGCTATGATTAGCATGTTACACGCTATGTACAAAAATATGTGATAAG
CATA
Found at i:3826313 original size:45 final size:45
Alignment explanation
Indices: 3826215--3826306 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
3826205 GATAAGCTAA
* *
3826215 GTACAAAAACCTGTGACAAGTTATGATTAATTTGTTACACGTCAT
1 GTACAAAAACCTGTGACAAGTCATGATTAAGTTGTTACACGTCAT
* * * *
3826260 GTACAAAAACTTGTGATAAGTCATGATTAGGTTGTTACATGTCAT
1 GTACAAAAACCTGTGACAAGTCATGATTAAGTTGTTACACGTCAT
3826305 GT
1 GT
3826307 TGAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (45 bp):
GTACAAAAACCTGTGACAAGTCATGATTAAGTTGTTACACGTCAT
Found at i:3826366 original size:26 final size:26
Alignment explanation
Indices: 3826324--3826468 Score: 107
Period size: 29 Copynumber: 5.3 Consensus size: 26
3826314 AAATACTGCC
*
3826324 GTTACACACCATG-TAAAAAAATA-T
1 GTTACACGCCATGTTAAAAAAATATT
*
3826348 GTTACACGTCATGGTT-AAAAAATATT
1 GTTACACGCCAT-GTTAAAAAAATATT
3826374 GTTACACGCCATGTTGAAAAAAAAATATTGTT
1 GTTACACGCCATGTT---AAAAAAATA---TT
*
3826406 GTTACACGTCATGTTGAAAAAATATTATT
1 GTTACACGCCATGTT-AAAAAA-A-TATT
* * * *
3826435 GTTACACGACATATTTAAAAATATTTT
1 GTTACACGCCAT-GTTAAAAAAATATT
3826462 GTTACAC
1 GTTACAC
3826469 TTTAATACCT
Statistics
Matches: 99, Mismatches: 9, Indels: 23
0.76 0.07 0.18
Matches are distributed among these distances:
24 10 0.10
25 12 0.12
26 13 0.13
27 10 0.10
28 1 0.01
29 26 0.26
30 8 0.08
31 1 0.01
32 18 0.18
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (26 bp):
GTTACACGCCATGTTAAAAAAATATT
Found at i:3826413 original size:32 final size:32
Alignment explanation
Indices: 3826372--3826437 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
3826362 TTAAAAAATA
3826372 TTGTTACACGCCATGTTGAAAAAAAAATATTG
1 TTGTTACACGCCATGTTGAAAAAAAAATATTG
* * *
3826404 TTGTTACACGTCATGTTGAAAAAATATTATTG
1 TTGTTACACGCCATGTTGAAAAAAAAATATTG
3826436 TT
1 TT
3826438 ACACGACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (32 bp):
TTGTTACACGCCATGTTGAAAAAAAAATATTG
Found at i:3826425 original size:29 final size:27
Alignment explanation
Indices: 3826347--3826468 Score: 122
Period size: 29 Copynumber: 4.3 Consensus size: 27
3826337 TAAAAAAATA
3826347 TGTTACACGTCATGGTTAAAAAATA--T
1 TGTTACACGTCAT-GTTAAAAAATATTT
*
3826373 TGTTACACGCCATGTTGAAAAAAAAATATTGT
1 TGTTACACGTCATGTT----AAAAAATATT-T
3826405 TGTTACACGTCATGTTGAAAAAATATTAT
1 TGTTACACGTCATGTT-AAAAAATATT-T
* * *
3826434 TGTTACACGACATATTTAAAAATATTT
1 TGTTACACGTCATGTTAAAAAATATTT
3826461 TGTTACAC
1 TGTTACAC
3826469 TTTAATACCT
Statistics
Matches: 82, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
25 3 0.04
26 12 0.15
27 9 0.11
28 9 0.11
29 33 0.40
32 16 0.20
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (27 bp):
TGTTACACGTCATGTTAAAAAATATTT
Found at i:3826455 original size:58 final size:54
Alignment explanation
Indices: 3826347--3826468 Score: 131
Period size: 61 Copynumber: 2.1 Consensus size: 54
3826337 TAAAAAAATA
* *
3826347 TGTTACACGTCATGGTTAAAAAATATTGTTACACGCCATGTTGAAAAAAAAATATTGT
1 TGTTACACGTCATGGTTAAAAAATATTGTTACACGACATATT---AAAAAAATATT-T
*
3826405 TGTTACACGTCAT-GTTGAAAAAATATTATTGTTACACGACATATT-TAAAAATATTT
1 TGTTACACGTCATGGTT--AAAAA-A-TATTGTTACACGACATATTAAAAAAATATTT
3826461 TGTTACAC
1 TGTTACAC
3826469 TTTAATACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
56 9 0.16
57 12 0.21
58 13 0.23
59 5 0.09
60 1 0.02
61 17 0.30
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (54 bp):
TGTTACACGTCATGGTTAAAAAATATTGTTACACGACATATTAAAAAAATATTT
Found at i:3859251 original size:62 final size:62
Alignment explanation
Indices: 3859154--3859278 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
3859144 AGCTTTCTTT
* *
3859154 GCCAAAACCAGAAGCGAAAATAGACATGTATAGCATGGTAAACAAAAAACCCCTTAAAAGTG
1 GCCAAAACCAGAAGAGAAAATAGACATGTACAGCATGGTAAACAAAAAACCCCTTAAAAGTG
3859216 GCCAAAACCAGAAGAGAAAATAGACATGTACAGCATGGTAAACAAAAAACCCCTTAAAAGTG
1 GCCAAAACCAGAAGAGAAAATAGACATGTACAGCATGGTAAACAAAAAACCCCTTAAAAGTG
3859278 G
1 G
3859279 AAATATCCAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (62 bp):
GCCAAAACCAGAAGAGAAAATAGACATGTACAGCATGGTAAACAAAAAACCCCTTAAAAGTG
Found at i:3860481 original size:2 final size:2
Alignment explanation
Indices: 3860474--3860508 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3860464 TGCTAACCAA
3860474 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3860509 AGACTTGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3884560 original size:18 final size:19
Alignment explanation
Indices: 3884523--3884561 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3884513 AAATATTTAT
* *
3884523 TTTTAATAAATTAGTTAAA
1 TTTTAATAAAATAATTAAA
3884542 TTTTAA-AAAATAATTAAA
1 TTTTAATAAAATAATTAAA
3884560 TT
1 TT
3884562 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TTTTAATAAAATAATTAAA
Found at i:3885978 original size:141 final size:143
Alignment explanation
Indices: 3885703--3885986 Score: 407
Period size: 141 Copynumber: 2.0 Consensus size: 143
3885693 TGCAATAATG
**
3885703 TAAGAGTTTATTTGAATTTTTTAAATAATTTAGAGGCTTTTCAAAACATTATACCTTTGAAATAA
1 TAAGAGTTTATTTGAAAATTTTAAATAATTTAGAGGCTTTTCAAAACATTATACCTTTGAAATAA
*
3885768 TATATATAAAATTTGAATGACTTTAAATTACTAAAATCACATGAAAGTTTTTGAAAATATACTTG
66 TATATATAAAATTTGAATGACTTTAAATTACTAAAATCACATGAAAGTTTTTGAAAATATACTTA
*
3885833 AAATAGTATTTAA
131 AAATAATATTTAA
* * *
3885846 TAAGAGTTTATTT-ACAAATTTTAAATAGTTTAGA-TCTTTTTCAAAACATTATACTTTTGAAAT
1 TAAGAGTTTATTTGA-AAATTTTAAATAATTTAGAGGC-TTTTCAAAACATTATACCTTTGAAAT
* * * *
3885909 -AT-TATCTAAAATTTTAATGACTTTAAATTAAC-AAAATCACATGAAATTTTTTGAAAATGTAC
64 AATATATATAAAATTTGAATGACTTTAAATT-ACTAAAATCACATGAAAGTTTTTGAAAATATAC
3885971 TTAAAATAATATTTAA
128 TTAAAATAATATTTAA
3885987 AAGGTTAAAG
Statistics
Matches: 127, Mismatches: 11, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
141 67 0.53
142 6 0.05
143 54 0.43
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (143 bp):
TAAGAGTTTATTTGAAAATTTTAAATAATTTAGAGGCTTTTCAAAACATTATACCTTTGAAATAA
TATATATAAAATTTGAATGACTTTAAATTACTAAAATCACATGAAAGTTTTTGAAAATATACTTA
AAATAATATTTAA
Found at i:3892282 original size:74 final size:73
Alignment explanation
Indices: 3892199--3892355 Score: 210
Period size: 74 Copynumber: 2.1 Consensus size: 73
3892189 TTCGCCAGTG
* * * *
3892199 AACTAGGGTTTCAAGGATATTA-AGTTTTCTGGGTTATGATAATGTACCTCATTTCACACTTGTA
1 AACTAGGGTTTCAAGGATACTACA-ATTT-TGAGTTATGATAATGTACCTCATTTCACACTTATA
3892263 ATCAGTCAAA
64 ATCAGTCAAA
* *
3892273 AACTAGGGTTTTAAGGATACTACCAATTTTGAGTTATGATAATTTACCTCATTTCACACTTATAA
1 AACTAGGGTTTCAAGGATACTA-CAATTTTGAGTTATGATAATGTACCTCATTTCACACTTATAA
3892338 TCAGTCAAA
65 TCAGTCAAA
*
3892347 ATC-AGGGTT
1 AACTAGGGTT
3892356 GAAAAAATGC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
73 6 0.08
74 64 0.86
75 3 0.04
76 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (73 bp):
AACTAGGGTTTCAAGGATACTACAATTTTGAGTTATGATAATGTACCTCATTTCACACTTATAAT
CAGTCAAA
Found at i:3921351 original size:30 final size:30
Alignment explanation
Indices: 3921303--3921416 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 30
3921293 CTGTAATCTG
** *
3921303 TGTGACTGCAATTTATGCAACTGCAGCTCC
1 TGTGACTGCAGCTCATGCAACTGCAGCTCC
* ** *
3921333 TTTGACTGCAGCTCATGCATTTACAGCTCAC
1 TGTGACTGCAGCTCATGCAACTGCAGCTC-C
* * * * * *
3921364 -GTAACAGCAGGTCCTGCAACTGCACCTCA
1 TGTGACTGCAGCTCATGCAACTGCAGCTCC
*
3921393 TGTGACTGCAGTTCATGCAACTGC
1 TGTGACTGCAGCTCATGCAACTGC
3921417 TGCCCATCTA
Statistics
Matches: 61, Mismatches: 21, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
30 60 0.98
31 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (30 bp):
TGTGACTGCAGCTCATGCAACTGCAGCTCC
Found at i:3921434 original size:45 final size:45
Alignment explanation
Indices: 3921384--3921471 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
3921374 GTCCTGCAAC
3921384 TGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCTAAT
1 TGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCTAAT
3921429 TGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCTA
1 TGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCTA
3921472 GCTGCAGTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (45 bp):
TGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCTAAT
Found at i:3921497 original size:45 final size:45
Alignment explanation
Indices: 3921381--3921499 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 45
3921371 CAGGTCCTGC
* *
3921381 AACTGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCT
1 AACTGCACCTCATGTAAATGCAGTTCATGCAACTGCTGCCCATCT
* * *
3921426 AATTGCACCTCATGTGACTGCAGTTCATGCAACTGCTGCCCATCT
1 AACTGCACCTCATGTAAATGCAGTTCATGCAACTGCTGCCCATCT
* ** *
3921471 AGCTGCAGTTCATGTAAATGCGGTTCATG
1 AACTGCACCTCATGTAAATGCAGTTCATG
3921500 TAAATGCAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (45 bp):
AACTGCACCTCATGTAAATGCAGTTCATGCAACTGCTGCCCATCT
Found at i:3921498 original size:15 final size:15
Alignment explanation
Indices: 3921474--3921575 Score: 107
Period size: 15 Copynumber: 6.8 Consensus size: 15
3921464 CCCATCTAGC
3921474 TGCAGTTCATGTAAA
1 TGCAGTTCATGTAAA
*
3921489 TGCGGTTCATGTAAA
1 TGCAGTTCATGTAAA
3921504 TGCAGTTCATGTAAA
1 TGCAGTTCATGTAAA
* * ***
3921519 TGCAGCTCTTGTGCC
1 TGCAGTTCATGTAAA
*
3921534 TGTAGTTCATGTAAA
1 TGCAGTTCATGTAAA
*
3921549 TGCTA-TTCATGTAAC
1 TGC-AGTTCATGTAAA
*
3921564 TGCAATTCATGT
1 TGCAGTTCATGT
3921576 TTAAGCTGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
14 1 0.01
15 68 0.97
16 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (15 bp):
TGCAGTTCATGTAAA
Found at i:3921508 original size:30 final size:30
Alignment explanation
Indices: 3921381--3921575 Score: 122
Period size: 30 Copynumber: 6.5 Consensus size: 30
3921371 CAGGTCCTGC
** * * *
3921381 AACTGCACCTCATGTGACTGCAGTTCATGC
1 AACTGCAGTTCATGTAAATGCAGTTCATGT
* ** * * **
3921411 AACTGCTGCCCATCTAATTGCACCTCATGT
1 AACTGCAGTTCATGTAAATGCAGTTCATGT
* * * * ** *
3921441 GACTGCAGTTCATGCAACTGCTGCCCATCT
1 AACTGCAGTTCATGTAAATGCAGTTCATGT
* *
3921471 AGCTGCAGTTCATGTAAATGCGGTTCATGT
1 AACTGCAGTTCATGTAAATGCAGTTCATGT
* * *
3921501 AAATGCAGTTCATGTAAATGCAGCTCTTGT
1 AACTGCAGTTCATGTAAATGCAGTTCATGT
** *
3921531 GCCTGTAGTTCATGTAAATGCTA-TTCATGT
1 AACTGCAGTTCATGTAAATGC-AGTTCATGT
*
3921561 AACTGCAATTCATGT
1 AACTGCAGTTCATGT
3921576 TTAAGCTGCT
Statistics
Matches: 121, Mismatches: 43, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
30 120 0.99
31 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (30 bp):
AACTGCAGTTCATGTAAATGCAGTTCATGT
Found at i:3934554 original size:2 final size:2
Alignment explanation
Indices: 3934547--3934575 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3934537 ATAAGCACAA
3934547 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 A
3934576 ATTTGGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3935516 original size:27 final size:27
Alignment explanation
Indices: 3935486--3935551 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
3935476 GTTATACACA
* *
3935486 ATGTTGAAAATTTATATATTATATTTC
1 ATGTTGAAAATTTAGATATTATATGTC
* * *
3935513 ATGTTAAAAATTTAGCTGTTATATGTC
1 ATGTTGAAAATTTAGATATTATATGTC
3935540 ATGTTGAAAATT
1 ATGTTGAAAATT
3935552 CAGTATCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (27 bp):
ATGTTGAAAATTTAGATATTATATGTC
Found at i:3937211 original size:2 final size:2
Alignment explanation
Indices: 3937204--3937238 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3937194 CAACCATGCC
3937204 AT AT 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 AT AT A
3937239 GTAGAAGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3937273 original size:2 final size:2
Alignment explanation
Indices: 3937266--3937298 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3937256 GAAGACGAGN
3937266 AT 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 AT A
3937299 ATGTAGAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3938226 original size:21 final size:22
Alignment explanation
Indices: 3938201--3938246 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3938191 AGTTTAAAAT
*
3938201 TTAATTAATAAAAA-ATAATAA
1 TTAATTAATAAAAATAAAATAA
*
3938222 TTAATTATTAAAAATAAAATAA
1 TTAATTAATAAAAATAAAATAA
3938244 TTA
1 TTA
3938247 TTTCCTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAATTAATAAAAATAAAATAA
Found at i:3938246 original size:18 final size:20
Alignment explanation
Indices: 3938201--3938248 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3938191 AGTTTAAAAT
*
3938201 TTAATTAATAAAAAATAATAA
1 TTAATT-ATTAAAAATAATAA
3938222 TTAATTATTAAAAATAA-AA
1 TTAATTATTAAAAATAATAA
3938241 -TAATTATT
1 TTAATTATT
3938249 TCCTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.31
19 2 0.08
20 10 0.38
21 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATTATTAAAAATAATAA
Found at i:3946458 original size:41 final size:41
Alignment explanation
Indices: 3946413--3946497 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
3946403 TTGACACAGG
** * *
3946413 TAAGATAGGAAATTTTTGTATATTAACCATGTCGACACGAT
1 TAAGATACAAAATTTTCGTATATCAACCATGTCGACACGAT
*
3946454 TAAGATACAAAATTTTCGTATATCAACCGTGTCGACACGAT
1 TAAGATACAAAATTTTCGTATATCAACCATGTCGACACGAT
3946495 TAA
1 TAA
3946498 AACATGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (41 bp):
TAAGATACAAAATTTTCGTATATCAACCATGTCGACACGAT
Found at i:3960210 original size:9 final size:9
Alignment explanation
Indices: 3960198--3960242 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3960188 ATTTAAAAAA
3960198 TTTTAAATT
1 TTTTAAATT
3960207 TTTTAAATT
1 TTTTAAATT
3960216 TTATT--A-T
1 TT-TTAAATT
3960223 TTTTAAATT
1 TTTTAAATT
*
3960232 TTTTATATT
1 TTTTAAATT
3960241 TT
1 TT
3960243 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
6 2 0.06
7 3 0.10
8 2 0.06
9 22 0.71
10 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTAAATT
Found at i:3960214 original size:16 final size:16
Alignment explanation
Indices: 3960195--3960233 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3960185 ATTATTTAAA
3960195 AAATTTTAA-ATTTTTT
1 AAATTTTAATA-TTTTT
*
3960211 AAATTTTATTATTTTT
1 AAATTTTAATATTTTT
3960227 AAATTTT
1 AAATTTT
3960234 TTATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AAATTTTAATATTTTT
Found at i:3960226 original size:25 final size:25
Alignment explanation
Indices: 3960198--3960245 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3960188 ATTTAAAAAA
3960198 TTTTAAATTTTTTAAATTTTATTAT
1 TTTTAAATTTTTTAAATTTTATTAT
*
3960223 TTTTAAATTTTTTATATTTTATT
1 TTTTAAATTTTTTAAATTTTATT
3960246 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTAAATTTTTTAAATTTTATTAT
Found at i:3960242 original size:16 final size:16
Alignment explanation
Indices: 3960206--3960243 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3960196 AATTTTAAAT
3960206 TTTTTAAATTTTATTA
1 TTTTTAAATTTTATTA
3960222 TTTTTAAATTTT-TTA
1 TTTTTAAATTTTATTA
3960237 TATTTTA
1 T-TTTTA
3960244 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAAATTTTATTA
Found at i:3960409 original size:22 final size:21
Alignment explanation
Indices: 3960381--3960431 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
3960371 TTGAGATAAA
*
3960381 AATAATAATTAA-TATTTTAATT
1 AATAATAATTAATTA-ATT-ATT
3960403 AATAATAATTAATTAATTATT
1 AATAATAATTAATTAATTATT
3960424 AATAATAA
1 AATAATAA
3960432 CAGTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.41
22 14 0.52
23 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATAATTAATTAATTATT
Found at i:3960424 original size:11 final size:11
Alignment explanation
Indices: 3960381--3960429 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
3960371 TTGAGATAAA
3960381 AATAA-TAATT
1 AATAATTAATT
*
3960391 AATATTTTAATT
1 AATA-ATTAATT
3960403 AATAA-TAATT
1 AATAATTAATT
3960413 AATTAATT-ATT
1 AA-TAATTAATT
3960424 AATAAT
1 AATAAT
3960430 AACAGTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 15 0.45
11 8 0.24
12 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATAATTAATT
Found at i:3993871 original size:58 final size:58
Alignment explanation
Indices: 3993807--3993923 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
3993797 ACAAATATTA
*
3993807 ACATATTCAATATTTTAATATTTTAAAAGACTGAAAATAAAACCCAAATCTAAGAGCC
1 ACATATTCAAAATTTTAATATTTTAAAAGACTGAAAATAAAACCCAAATCTAAGAGCC
*
3993865 ACATATTCAAAATTTTAATATTTTAAAAGATTGAAAATAAAACCCAAATCTAAGAGCC
1 ACATATTCAAAATTTTAATATTTTAAAAGACTGAAAATAAAACCCAAATCTAAGAGCC
3993923 A
1 A
3993924 ATTACTTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.29
Consensus pattern (58 bp):
ACATATTCAAAATTTTAATATTTTAAAAGACTGAAAATAAAACCCAAATCTAAGAGCC
Found at i:3994281 original size:65 final size:65
Alignment explanation
Indices: 3994212--3994408 Score: 349
Period size: 65 Copynumber: 3.0 Consensus size: 65
3994202 AAACACACAT
3994212 AGAATTTGACATTATTGAAATATCTCATTTCAAGTTTATCTCAGATGATTTAAACAAGAGAAAAA
1 AGAATTTGACATTATTGAAATATCTCATTTCAAGTTTATCTCAGATGATTTAAACAAGAGAAAAA
*
3994277 AGAATTTGACATTATTGAAATATCTCATTTCAAGTTTATCTAAGATGATTTAAACAAGAGAAAAA
1 AGAATTTGACATTATTGAAATATCTCATTTCAAGTTTATCTCAGATGATTTAAACAAGAGAAAAA
* * * *
3994342 AGAATTTGACATTATTGAAATATCTTATTTCAAATATATCTCAGATGATATAAACAAGAGAAAAA
1 AGAATTTGACATTATTGAAATATCTCATTTCAAGTTTATCTCAGATGATTTAAACAAGAGAAAAA
3994407 AG
1 AG
3994409 TTAAAAAAAA
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 126 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (65 bp):
AGAATTTGACATTATTGAAATATCTCATTTCAAGTTTATCTCAGATGATTTAAACAAGAGAAAAA
Found at i:3994805 original size:53 final size:53
Alignment explanation
Indices: 3994745--3994848 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
3994735 GGCAGAGTGT
*
3994745 TTTGTTTGAACTTGAAGTCTAATGGGATTGGCTTGTGATTGGATTTTTGGGTA
1 TTTGTTTGAACTTGAAGTCTAATGGGATTGGCTTATGATTGGATTTTTGGGTA
** * * *
3994798 TTTGTTTGGGCTTGAGGTCTAATGGGATTGGCTTATGGTTGGGTTTTTGGG
1 TTTGTTTGAACTTGAAGTCTAATGGGATTGGCTTATGATTGGATTTTTGGG
3994849 AGTAAGATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.14, C:0.06, G:0.35, T:0.45
Consensus pattern (53 bp):
TTTGTTTGAACTTGAAGTCTAATGGGATTGGCTTATGATTGGATTTTTGGGTA
Found at i:3995822 original size:18 final size:17
Alignment explanation
Indices: 3995799--3995838 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
3995789 CACCTATTTC
3995799 AAAAAA-TAAGAAATAAA
1 AAAAAAGTAA-AAATAAA
3995816 TAAAAAAGTAAAAATAAA
1 -AAAAAAGTAAAAATAAA
3995834 AAAAA
1 AAAAA
3995839 TGATGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAAAGTAAAAATAAA
Found at i:3997390 original size:16 final size:16
Alignment explanation
Indices: 3997369--3997399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3997359 AATCAATCAA
*
3997369 TGAAATAAAGGAAAAG
1 TGAAATAAAAGAAAAG
3997385 TGAAATAAAAGAAAA
1 TGAAATAAAAGAAAA
3997400 AGACCAAATA
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:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (16 bp):
TGAAATAAAAGAAAAG
Found at i:3997576 original size:8 final size:8
Alignment explanation
Indices: 3997563--3997587 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3997553 AGGGTCTCGA
3997563 TTCGAAAT
1 TTCGAAAT
3997571 TTCGAAAT
1 TTCGAAAT
3997579 TTCGAAAT
1 TTCGAAAT
3997587 T
1 T
3997588 CTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (8 bp):
TTCGAAAT
Found at i:3997601 original size:1 final size:1
Alignment explanation
Indices: 3997595--3997634 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
3997585 ATTCTAATTA
*
3997595 TTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3997635 AAGTAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:3997618 original size:21 final size:21
Alignment explanation
Indices: 3997592--3997634 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3997582 GAAATTCTAA
3997592 TTATTTTTTTTTTTTTTTTTT
1 TTATTTTTTTTTTTTTTTTTT
3997613 TTATTTTTTTTTTTTTTTTTT
1 TTATTTTTTTTTTTTTTTTTT
3997634 T
1 T
3997635 AAGTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (21 bp):
TTATTTTTTTTTTTTTTTTTT
Found at i:3997621 original size:20 final size:20
Alignment explanation
Indices: 3997596--3997635 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3997586 TTCTAATTAT
3997596 TTTTTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTTTTTA
3997616 TTTTTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTTTTTA
3997636 AGTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTTTA
Found at i:4001870 original size:39 final size:39
Alignment explanation
Indices: 4001827--4001902 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
4001817 ATCAATCATC
4001827 TAAAATTTATGAACATAAACAACAAGAAAAAGTTAAGCA
1 TAAAATTTATGAACATAAACAACAAGAAAAAGTTAAGCA
*
4001866 TAAAATTTATGAACATAAACAACAGGAAAAAGTTAAG
1 TAAAATTTATGAACATAAACAACAAGAAAAAGTTAAG
4001903 AAAAAATAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (39 bp):
TAAAATTTATGAACATAAACAACAAGAAAAAGTTAAGCA
Found at i:4002179 original size:21 final size:20
Alignment explanation
Indices: 4002155--4002193 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4002145 ATATTAAAAA
4002155 TTATGAATAAAAAAAAGTTTT
1 TTAT-AATAAAAAAAAGTTTT
* *
4002176 TTATATTTAAAAAAAGTT
1 TTATAATAAAAAAAAGTT
4002194 ACAAAGAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
TTATAATAAAAAAAAGTTTT
Found at i:4002546 original size:92 final size:92
Alignment explanation
Indices: 4002442--4002631 Score: 240
Period size: 92 Copynumber: 2.1 Consensus size: 92
4002432 TATCTCATAT
* * * * * *
4002442 TATTTTATTTTTCAATGTTAAATGCAATTAATGTAAACG-GGTGCATATCAACTAGTTAAAGAT-
1 TATTTTATTTTTCAATATTAAATGCAATTAATG-AAAAGTGATGCAGATCAACTAATTAAAAATA
* * *
4002505 GGAGTTTTGAGAGAGATTGAGTTACTATA
65 GAAG-TTTAAGAGAGATTGAGTTACTACA
* *
4002534 TATTTTATTTTTCAATATTAAATGTAATTAATGAAAAGTGATGTAGATCAACTAATTAAAAATAG
1 TATTTTATTTTTCAATATTAAATGCAATTAATGAAAAGTGATGCAGATCAACTAATTAAAAATAG
*
4002599 AAGTTTAAGAGAGATTGAGTTATTACA
66 AAGTTTAAGAGAGATTGAGTTACTACA
4002626 TATTTT
1 TATTTT
4002632 GCAGTAAGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
91 4 0.05
92 77 0.92
93 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.39
Consensus pattern (92 bp):
TATTTTATTTTTCAATATTAAATGCAATTAATGAAAAGTGATGCAGATCAACTAATTAAAAATAG
AAGTTTAAGAGAGATTGAGTTACTACA
Found at i:4002828 original size:18 final size:18
Alignment explanation
Indices: 4002805--4002840 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4002795 TGTATATATC
4002805 AATATATATAA-ATAATTA
1 AATATA-ATAATATAATTA
4002823 AATATAATAATATAATTA
1 AATATAATAATATAATTA
4002841 TTATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATAATAATATAATTA
Found at i:4006408 original size:20 final size:20
Alignment explanation
Indices: 4006383--4006430 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4006373 TGTAATTGTT
*
4006383 ATATCAAACAATAAAGAGAA
1 ATATCAAACAATAAAAAGAA
4006403 ATATCAAACAATAAAAAGAA
1 ATATCAAACAATAAAAAGAA
*
4006423 ATTTCAAA
1 ATATCAAA
4006431 ACCCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (20 bp):
ATATCAAACAATAAAAAGAA
Found at i:4009886 original size:29 final size:31
Alignment explanation
Indices: 4009848--4009906 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
4009838 TTCCTTCTTT
* *
4009848 TTTCTGTTTCTCTC-TTCGTTCTT-TCTTCC
1 TTTCTCTTTCTCTCTTTCATTCTTCTCTTCC
4009877 TTTCTCTTTCTCTCTTTCATTCTTCTCTTC
1 TTTCTCTTTCTCTCTTTCATTCTTCTCTTC
4009907 GGTTGTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.50
30 8 0.31
31 5 0.19
ACGTcount: A:0.02, C:0.32, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTCTCTTTCTCTCTTTCATTCTTCTCTTCC
Found at i:4010811 original size:96 final size:96
Alignment explanation
Indices: 4010633--4010811 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
4010623 TGCGGGATTG
* * ** * * *
4010633 TTGGTGTTCATTCTTTGCTTGATTCATGATTTTTGTTGTTTGGGTTTTTACTTTCTTGCATTCTT
1 TTGGTGTTCATTCTTTGCTTAATTCATGATTTTCGTCCTTTGGGTCTTTACGTTCTTGCATGCTT
*
4010698 TACTGGGTATCATAATAGTGTAACTGGTTTA
66 TACTGGGTATCACAATAGTGTAACTGGTTTA
* * *
4010729 TTGGTTTTCATTCTTTGCTTAATTCTTGATTTTCGTCCTTTGGGTCTTTACGTTCTTGTATGCTT
1 TTGGTGTTCATTCTTTGCTTAATTCATGATTTTCGTCCTTTGGGTCTTTACGTTCTTGCATGCTT
* *
4010794 TATTGGGTATGACAATAG
66 TACTGGGTATCACAATAG
4010812 AGTAGTCAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.15, C:0.13, G:0.20, T:0.53
Consensus pattern (96 bp):
TTGGTGTTCATTCTTTGCTTAATTCATGATTTTCGTCCTTTGGGTCTTTACGTTCTTGCATGCTT
TACTGGGTATCACAATAGTGTAACTGGTTTA
Found at i:4010937 original size:47 final size:46
Alignment explanation
Indices: 4010860--4010952 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 46
4010850 TGATACCTAC
4010860 GTCTTAATTAATTTTTTTTTCCTTTAGATTTGCAAACAACTATTCA
1 GTCTTAATTAATTTTTTTTTCCTTTAGATTTGCAAACAACTATTCA
4010906 GTCTTAATTAATTTTTTTTTTCCTTTAGATTTGCAAACAACTATTCA
1 GTCTTAATTAA-TTTTTTTTTCCTTTAGATTTGCAAACAACTATTCA
4010953 ATCAGATCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 11 0.24
47 35 0.76
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (46 bp):
GTCTTAATTAATTTTTTTTTCCTTTAGATTTGCAAACAACTATTCA
Found at i:4024257 original size:14 final size:14
Alignment explanation
Indices: 4024226--4024282 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
4024216 AAAAAAAAAT
* *
4024226 ATTATAAAAACTTG
1 ATTATAAAAATTTA
4024240 ATTATAAAAATTTA
1 ATTATAAAAATTTA
*
4024254 ATTA-AAAATTTTA
1 ATTATAAAAATTTA
* *
4024267 TATTTTAAAAAATTA
1 -ATTATAAAAATTTA
4024282 A
1 A
4024283 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 8 0.23
14 20 0.57
15 7 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
ATTATAAAAATTTA
Found at i:4024322 original size:13 final size:14
Alignment explanation
Indices: 4024306--4024337 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4024296 TAATAAAAAA
4024306 ATTTTA-TTTAAAT
1 ATTTTATTTTAAAT
4024319 ATTTTATTTTAAAT
1 ATTTTATTTTAAAT
4024333 -TTTTA
1 ATTTTA
4024338 AATTTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTATTTTAAAT
Found at i:4025543 original size:17 final size:19
Alignment explanation
Indices: 4025521--4025555 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
4025511 ATTTGATCAA
4025521 CTGATT-TTTT-TTTTCTG
1 CTGATTATTTTGTTTTCTG
4025538 CTGATTATTTTGTTTTCT
1 CTGATTATTTTGTTTTCT
4025556 TTTGGTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.69
Consensus pattern (19 bp):
CTGATTATTTTGTTTTCTG
Found at i:4029488 original size:2 final size:2
Alignment explanation
Indices: 4029481--4029527 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4029471 TCTTCTACTC
4029481 CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4029522 CT CT CT
1 CT CT CT
4029528 TAGTTTGCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4074235 original size:8 final size:8
Alignment explanation
Indices: 4074222--4074246 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4074212 GGCACTGAAT
4074222 AATTGTAG
1 AATTGTAG
4074230 AATTGTAG
1 AATTGTAG
4074238 AATTGTAG
1 AATTGTAG
4074246 A
1 A
4074247 TGTAGATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (8 bp):
AATTGTAG
Found at i:4078916 original size:28 final size:28
Alignment explanation
Indices: 4078876--4078939 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
4078866 ATAAGTAATG
4078876 ACCAACCCACAAACACACTTACAGAGAA
1 ACCAACCCACAAACACACTTACAGAGAA
**
4078904 ACCAACCCACAAACACACTTGTAGAGAA
1 ACCAACCCACAAACACACTTACAGAGAA
4078932 ACCAACCC
1 ACCAACCC
4078940 TGTTTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.47, C:0.38, G:0.08, T:0.08
Consensus pattern (28 bp):
ACCAACCCACAAACACACTTACAGAGAA
Found at i:4092589 original size:42 final size:43
Alignment explanation
Indices: 4092501--4092598 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
4092491 AATATTTTTT
* * * *
4092501 TAATTAATA-TTTTATATTAAATATAGTAACTGAAAAATCATT
1 TAATTAATATTTTTACATTAAATATAATAACTAAAAAATCATG
*
4092543 TAATTAATATTTTTACATT-AATATAATAATTAACAAAAT-ATG
1 TAATTAATATTTTTACATTAAATATAATAACTAA-AAAATCATG
4092585 TAATT-AT-TTTTTAC
1 TAATTAATATTTTTAC
4092599 TATATTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 7 0.14
41 2 0.04
42 27 0.55
43 13 0.27
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (43 bp):
TAATTAATATTTTTACATTAAATATAATAACTAAAAAATCATG
Found at i:4093499 original size:17 final size:17
Alignment explanation
Indices: 4093479--4093511 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4093469 AAAAAATGTG
*
4093479 AATTTAGTTTTTATATA
1 AATTTAATTTTTATATA
4093496 AATTTAATTTTTATAT
1 AATTTAATTTTTATAT
4093512 TTTTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTAATTTTTATATA
Found at i:4096182 original size:6 final size:6
Alignment explanation
Indices: 4096166--4096197 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
4096156 GTTGGCCGCT
4096166 TCCTATC TCCTTC TCCTTC TCCTTC TCCTTC T
1 TCCT-TC TCCTTC TCCTTC TCCTTC TCCTTC T
4096198 TGTTACTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCTTC
Found at i:4107062 original size:15 final size:14
Alignment explanation
Indices: 4107044--4107103 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
4107034 AATAAAAAAA
4107044 ATATTTTAATTTTTT
1 ATATTTT-ATTTTTT
** *
4107059 ATATTTTTATTAATA
1 ATA-TTTTATTTTTT
4107074 ATATTTTATTTTTT
1 ATATTTTATTTTTT
*
4107088 -TGATTTTATTATTT
1 AT-ATTTTATTTTTT
4107102 AT
1 AT
4107104 TTTAAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
13 1 0.03
14 19 0.54
15 11 0.31
16 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
ATATTTTATTTTTT
Found at i:4110906 original size:51 final size:51
Alignment explanation
Indices: 4110851--4110948 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
4110841 AAAAAATATG
*
4110851 TATGTCTACTTTCTCAGTTCCTCGTATGTATGTCCCGATTCCAAAGGCATC
1 TATGTCTACTTTCTCAGTTCCTCGTACGTATGTCCCGATTCCAAAGGCATC
4110902 TATGTCTACTTTCTCAGTTCCTCGTACGTATGTCCCGATTCCAAAGG
1 TATGTCTACTTTCTCAGTTCCTCGTACGTATGTCCCGATTCCAAAGG
4110949 TCTATGAACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (51 bp):
TATGTCTACTTTCTCAGTTCCTCGTACGTATGTCCCGATTCCAAAGGCATC
Found at i:4112854 original size:2 final size:2
Alignment explanation
Indices: 4112847--4112878 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4112837 AAATAACTAT
*
4112847 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4112879 AAACTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4114299 original size:15 final size:15
Alignment explanation
Indices: 4114278--4114309 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
4114268 TATATAACTA
4114278 TTATTTTTATT-TAT
1 TTATTTTTATTCTAT
4114292 TTATTTTTATTCTAT
1 TTATTTTTATTCTAT
4114307 TTA
1 TTA
4114310 CTCATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
TTATTTTTATTCTAT
Found at i:4119284 original size:24 final size:24
Alignment explanation
Indices: 4119191--4119280 Score: 63
Period size: 24 Copynumber: 3.8 Consensus size: 24
4119181 ACATGTGACT
*
4119191 AAACACGTGACAGATTACATGATA
1 AAACATGTGACAGATTACATGATA
* * * * * *
4119215 GAACATGAGATAGAATACATAACA
1 AAACATGTGACAGATTACATGATA
* * * * *
4119239 AAATATGTGGCAAAGTACGTGATA
1 AAACATGTGACAGATTACATGATA
*
4119263 AAACATGTGATAGATTAC
1 AAACATGTGACAGATTAC
4119281 GTGACACACA
Statistics
Matches: 44, Mismatches: 22, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (24 bp):
AAACATGTGACAGATTACATGATA
Found at i:4119443 original size:2 final size:2
Alignment explanation
Indices: 4119436--4119511 Score: 111
Period size: 2 Copynumber: 38.5 Consensus size: 2
4119426 TACAGAGGTG
4119436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
**
4119477 NG AT 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 AT AT A
4119512 ATCTAACTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
1 2 0.03
2 64 0.96
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4122594 original size:13 final size:13
Alignment explanation
Indices: 4122576--4122601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4122566 CATCCATATC
4122576 GGACTTCTAAGCT
1 GGACTTCTAAGCT
4122589 GGACTTCTAAGCT
1 GGACTTCTAAGCT
4122602 ATCTCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
GGACTTCTAAGCT
Found at i:4124896 original size:17 final size:15
Alignment explanation
Indices: 4124858--4124887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4124848 TATAAAATGA
*
4124858 GAAATTTTATATTTT
1 GAAATTGTATATTTT
4124873 GAAATTGTATATTTT
1 GAAATTGTATATTTT
4124888 ATGAAATTGA
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:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
GAAATTGTATATTTT
Found at i:4127112 original size:12 final size:12
Alignment explanation
Indices: 4127092--4127133 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
4127082 TGTAGACATC
4127092 TAAA-AAAAATAA
1 TAAATAAAAA-AA
4127104 TAAATAAAAAAA
1 TAAATAAAAAAA
*
4127116 TTAATTAAAAAAA
1 -TAAATAAAAAAA
4127129 TAAAT
1 TAAAT
4127134 TGTAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAAAAAA
Found at i:4127113 original size:16 final size:16
Alignment explanation
Indices: 4127092--4127152 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
4127082 TGTAGACATC
4127092 TAAAAAAAATAATAAA
1 TAAAAAAAATAATAAA
*
4127108 TAAAAAAATTAATTAAA
1 TAAAAAAAATAA-TAAA
* **
4127125 -AAAATAAATTGT-AA
1 TAAAAAAAATAATAAA
4127139 TAAAATAAAATAAT
1 TAAAA-AAAATAAT
4127153 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
14 2 0.06
15 5 0.15
16 23 0.68
17 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAAAAAAATAATAAA
Found at i:4127162 original size:19 final size:20
Alignment explanation
Indices: 4127125--4127162 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
4127115 ATTAATTAAA
*
4127125 AAAATAAATTGTAATAAAAT
1 AAAATAAATTGTAAAAAAAT
*
4127145 AAAAT-AATTTTAAAAAAA
1 AAAATAAATTGTAAAAAAA
4127163 AGGGAGAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATAAATTGTAAAAAAAT
Found at i:4128286 original size:3 final size:3
Alignment explanation
Indices: 4128273--4128341 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
4128263 GAGGCTTGCA
* *
4128273 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AATT CAT GAT ACA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AAT
*
4128318 -AT AAA AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
4128342 TAAATGGAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.09
3 48 0.86
4 3 0.05
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4130892 original size:30 final size:30
Alignment explanation
Indices: 4130856--4130927 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
4130846 TTGTGTCATT
*
4130856 TTTTATTATTTAATTATTATTTTC-ATTTTA
1 TTTTATTATTTAATCA-TATTTTCTATTTTA
* *
4130886 TTTTATTTTTTTATCATATTTTCTATTTTA
1 TTTTATTATTTAATCATATTTTCTATTTTA
4130916 TTTCTAATTATT
1 TTT-T-ATTATT
4130928 ATTTTTTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 7 0.20
30 22 0.63
31 1 0.03
32 5 0.14
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (30 bp):
TTTTATTATTTAATCATATTTTCTATTTTA
Found at i:4130930 original size:18 final size:17
Alignment explanation
Indices: 4130864--4130932 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 17
4130854 TTTTTTATTA
4130864 TTTAATTATTATTTTCAT
1 TTTAATTATTATTTT-AT
4130882 TTT-ATT-TTATTTT-T
1 TTTAATTATTATTTTAT
*
4130896 TTATCATATTTTCTATTTTAT
1 TT-T-A-ATTAT-TATTTTAT
4130917 TTCTAATTATTATTTT
1 TT-TAATTATTATTTT
4130933 TTCCATACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
14 3 0.07
15 1 0.02
16 7 0.17
17 3 0.07
18 12 0.29
19 5 0.12
20 7 0.17
21 4 0.10
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATTATTATTTTAT
Found at i:4133161 original size:9 final size:9
Alignment explanation
Indices: 4133147--4133200 Score: 72
Period size: 9 Copynumber: 5.8 Consensus size: 9
4133137 TACCTCTCTT
4133147 TTTTTTTTA
1 TTTTTTTTA
4133156 TTTTTTTTA
1 TTTTTTTTA
4133165 TTTTTTTTA
1 TTTTTTTTA
*
4133174 TTTTTTGTCA
1 TTTTTT-TTA
*
4133184 TTTTTATTCA
1 TTTTT-TTTA
4133194 TTTTTTT
1 TTTTTTT
4133201 GTTTATGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
9 26 0.62
10 15 0.36
11 1 0.02
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:4133161 original size:10 final size:10
Alignment explanation
Indices: 4133146--4133200 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
4133136 GTACCTCTCT
4133146 TTTTTTTTTA
1 TTTTTTTTTA
4133156 -TTTTTTTTA
1 TTTTTTTTTA
4133165 -TTTTTTTTA
1 TTTTTTTTTA
* *
4133174 TTTTTTGTCA
1 TTTTTTTTTA
* *
4133184 TTTTTATTCA
1 TTTTTTTTTA
4133194 TTTTTTT
1 TTTTTTT
4133201 GTTTATGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
9 18 0.46
10 21 0.54
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:4133197 original size:25 final size:26
Alignment explanation
Indices: 4133159--4133225 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 26
4133149 TTTTTTATTT
** *
4133159 TTTTTATTTTTTTTATTT-TTTGTCA
1 TTTTTATTAATTTTATTTGTTTATCA
* *
4133184 TTTTTATTCATTTT-TTTGTTTATGA
1 TTTTTATTAATTTTATTTGTTTATCA
*
4133209 TTTTTTTTAATTTTATT
1 TTTTTATTAATTTTATT
4133226 ATAATTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 3 0.09
25 29 0.85
26 2 0.06
ACGTcount: A:0.15, C:0.03, G:0.04, T:0.78
Consensus pattern (26 bp):
TTTTTATTAATTTTATTTGTTTATCA
Found at i:4140480 original size:14 final size:14
Alignment explanation
Indices: 4140463--4140522 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
4140453 ATTATAATTA
4140463 TTATTTTATTTTTT
1 TTATTTTATTTTTT
*
4140477 TTATTTTA-TTATT
1 TTATTTTATTTTTT
* * * *
4140490 ATCTTTTAATTTTC
1 TTATTTTATTTTTT
*
4140504 ATATTTTATATTTTT
1 TTATTTTAT-TTTTT
4140519 TTAT
1 TTAT
4140523 ATTTTTATCT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
13 10 0.29
14 18 0.51
15 7 0.20
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTTATTTTTT
Found at i:4140516 original size:34 final size:31
Alignment explanation
Indices: 4140450--4140529 Score: 81
Period size: 34 Copynumber: 2.5 Consensus size: 31
4140440 AATTATATTA
* * *
4140450 TTTATTATAATTATT-ATTTTATTTTTTTTAT
1 TTTATTAT-ATTTTTAATTTTATATTTTATAT
4140481 TTTATTATTATCTTTTAATTTTCATATTTTATAT
1 TTTATTA-TAT-TTTTAATTTT-ATATTTTATAT
*
4140515 TTTTTTATATTTTTA
1 TTTATTATATTTTTA
4140530 TCTTAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 9 0.22
32 9 0.22
33 8 0.20
34 15 0.37
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTATTATATTTTTAATTTTATATTTTATAT
Found at i:4140585 original size:3 final size:3
Alignment explanation
Indices: 4140572--4140615 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
4140562 TGCATCATAA
*
4140572 ATT ACT ATT ATT ATT ATTT ATT -TT ATTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT ATT A-TT ATT ATT ATT ATT ATT A
4140616 AATATAAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4140589 original size:9 final size:10
Alignment explanation
Indices: 4140579--4140615 Score: 60
Period size: 9 Copynumber: 3.9 Consensus size: 10
4140569 TAAATTACTA
4140579 TTATTATTAT
1 TTATTATTAT
4140589 TTATT-TTAT
1 TTATTATTAT
4140598 TTATTATTA-
1 TTATTATTAT
4140607 TTATTATTA
1 TTATTATTA
4140616 AATATAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTATTAT
Found at i:4141469 original size:14 final size:15
Alignment explanation
Indices: 4141450--4141492 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4141440 AGCCATCCCC
4141450 ATTTTTTT-TTTATA
1 ATTTTTTTATTTATA
*
4141464 ATTTTTTTATTTATT
1 ATTTTTTTATTTATA
* *
4141479 GTTATTTTATTTAT
1 ATTTTTTTATTTAT
4141493 TTATTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (15 bp):
ATTTTTTTATTTATA
Found at i:4141508 original size:23 final size:23
Alignment explanation
Indices: 4141464--4141508 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4141454 TTTTTTTATA
* *
4141464 ATTTTTTTATTTATTGTTATTTT
1 ATTTATTTATTTATTGTAATTTT
4141487 ATTTATTTATTTAATT-TAATTT
1 ATTTATTTATTT-ATTGTAATTT
4141509 AACTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTATTTATTTATTGTAATTTT
Found at i:4157544 original size:268 final size:266
Alignment explanation
Indices: 4157068--4157588 Score: 900
Period size: 268 Copynumber: 2.0 Consensus size: 266
4157058 CATTTTTATT
4157068 TGATTTATTATTAATTATAAACTTATGTTATATAAAAATCTTTTTTATATTTTCAAAAATTTATT
1 TGATTTATTATTAATTATAAACTTATGTTATATAAAAATCTTTTTTATATTTTCAAAAATTTATT
**
4157133 TTAAATAGATAAAAAATAAAATTAATTTTTTTTATTTTGAGTAAAGAAATTAGTGATTAATAAAA
66 TTAAATAGATAAAAAATAAAATTAATTTTTTTTATTTTGAACAAAGAAATTAGTGATTAATAAAA
*
4157198 GTTATTTATTAAATACCTTTATGATAATTATAATTAAAATTAAAGTTTATATAAATTGTTTTGCC
131 GTTATTTATTAAATACCTTTATGATAATTATAATTAAAATTAAAGTTTATATAAATTATTTTGCC
* * * *
4157263 AAACAATTTATTTATAAAACAGAGCTTATAAAAAGTAAATTTACCAAACAACTTTAANCATCTTT
196 AAACAATTTATTTATAAAACAAAACTTATAAAAAGTAAATTTACCAAAAAAATTTAA-CATCTTT
4157328 TTTTTAA
260 TTTTTAA
*
4157335 TGATTTATTATTAATTATAAACTTTATGTTATATAAAAATCTTTTTTATATTTTTAAAAATTTAT
1 TGATTTATTATTAATTATAAAC-TTATGTTATATAAAAATCTTTTTTATATTTTCAAAAATTTAT
*
4157400 TTTAAATAGATAAAAAATAAAGTTAA-TTTTTTTATTTTGAACAAAGAAATTAGTGATTAATAAA
65 TTTAAATAGATAAAAAATAAAATTAATTTTTTTTATTTTGAACAAAGAAATTAGTGATTAAT-AA
*
4157464 AAGTTATTTATTAAATACCTTTATGATAATTTTAATTAAAATTAAAGTTTATATAAATTATTTTG
129 AAGTTATTTATTAAATACCTTTATGATAATTATAATTAAAATTAAAGTTTATATAAATTATTTTG
* *
4157529 CCAAACAATTTATTTATAAAATAAAACTTATAAAAAGTAAATTTATCAAAAAAATTTAAC
194 CCAAACAATTTATTTATAAAACAAAACTTATAAAAAGTAAATTTACCAAAAAAATTTAAC
4157589 TTAATTGTAA
Statistics
Matches: 240, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
267 56 0.23
268 184 0.77
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (266 bp):
TGATTTATTATTAATTATAAACTTATGTTATATAAAAATCTTTTTTATATTTTCAAAAATTTATT
TTAAATAGATAAAAAATAAAATTAATTTTTTTTATTTTGAACAAAGAAATTAGTGATTAATAAAA
GTTATTTATTAAATACCTTTATGATAATTATAATTAAAATTAAAGTTTATATAAATTATTTTGCC
AAACAATTTATTTATAAAACAAAACTTATAAAAAGTAAATTTACCAAAAAAATTTAACATCTTTT
TTTTAA
Found at i:4169760 original size:2 final size:2
Alignment explanation
Indices: 4169753--4169802 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
4169743 AAACAAATAC
*
4169753 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4169794 AT AT AT AT A
1 AT AT AT AT A
4169803 AAACAAGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4171094 original size:3 final size:3
Alignment explanation
Indices: 4171086--4171120 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4171076 GTGAAGTTGA
*
4171086 ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4171121 AAGTAAGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4179026 original size:35 final size:35
Alignment explanation
Indices: 4178979--4179048 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
4178969 TTTAAGACTT
* *
4178979 AGTTTACTCTCGTGCAAAAGGAAATTATACAACTA
1 AGTTTACCCTCGTGCAAAAGAAAATTATACAACTA
* *
4179014 AGTTTACCCTCGTGCAGAAGAAAATTATACGACTA
1 AGTTTACCCTCGTGCAAAAGAAAATTATACAACTA
4179049 GCTTTAGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (35 bp):
AGTTTACCCTCGTGCAAAAGAAAATTATACAACTA
Found at i:4184961 original size:967 final size:967
Alignment explanation
Indices: 4183087--4185023 Score: 3705
Period size: 967 Copynumber: 2.0 Consensus size: 967
4183077 GATGCCAGTC
*
4183087 AATCTCACGCGCAACGCGATTGCGTCGATCAACACTGGCGATGTGAACTCGAAGCCGTTGGTTCA
1 AATCTCACGCGCAACGCGATTGCGTCGATCAACACTGGCGATGTGAACTCCAAGCCGTTGGTTCA
4183152 GGTGGTGGATATCAAGCTGATTGGCAATTCTCAGGAGAGATACCGGTTTCTACTATCCGATTCCG
66 GGTGGTGGATATCAAGCTGATTGGCAATTCTCAGGAGAGATACCGGTTTCTACTATCCGATTCCG
4183217 AGTCCTCTCAGCACGCGATGCTCGCCACTCAGCTCAATGAACAAGTCAGGACCGGACGAGTCAAG
131 AGTCCTCTCAGCACGCGATGCTCGCCACTCAGCTCAATGAACAAGTCAGGACCGGACGAGTCAAG
*
4183282 AAAGGATCTATCATCCAGTTGATCGACTATGTTTGCAGCACTGTTCAGAATCGTAGGTGCGATTG
196 AAAGGATCTATCATCCAGTTGATCGACTACGTTTGCAGCACTGTTCAGAATCGTAGGTGCGATTG
* *
4183347 ACTGCTTTTCTACTTAAAACTAATGAATTAATTTGAATGTTGATATACGAATTTTTTTCGGACAG
261 ACTGCTTTTCTACTTAAAACTAATGAATTAATTTGAATGTTGATATACGAATTTTTTTCGAAAAG
4183412 TAAGTATTGATATACGATTATGTAGTTTCAAAATTCAGTTTGGGAAGACTTGAGATTCAAATTTG
326 TAAGTATTGATATACGATTATGTAGTTTCAAAATTCAGTTTGGGAAGACTTGAGATTCAAATTTG
*
4183477 ATCCTTTTATTTTTTAAAATACAAGAGCAAAGTTCGCCCTTTTTTTTTTTGGGTTGAAGATTTGA
391 ATCCTTTTATTTTTTAAAATACAAGAGCAAAGTTCGCCCTTTTTTTTTTTAGGTTGAAGATTTGA
4183542 GAAATTCAAATTCATTTTTATTAAGCGTTCAAGTTGATTGGTGCCTTGAATACAAAGTTGAAGGA
456 GAAATTCAAATTCATTTTTATTAAGCGTTCAAGTTGATTGGTGCCTTGAATACAAAGTTGAAGGA
4183607 ACTTTTAAGTAGATGAATTATCGTTAATCCTATCCACTCCTAATGAACTTAAATAAAAGGTAAGG
521 ACTTTTAAGTAGATGAATTATCGTTAATCCTATCCACTCCTAATGAACTTAAATAAAAGGTAAGG
*
4183672 CTAGGACCATTGTCGAGTAGATTATTCATATTCAAGTTATCAATTAAAGTAAGGAGGAAAGGAAA
586 CTAGGACCATTGTCGAGTAGATTATTCATATTCAAGATATCAATTAAAGTAAGGAGGAAAGGAAA
4183737 TCATATTATTCATTCTCCACAGTGTATAATTTGAAATCAAATATGTTACATAGCCTTCAGAAACA
651 TCATATTATTCATTCTCCACAGTGTATAATTTGAAATCAAATATGTTACATAGCCTTCAGAAACA
*
4183802 TGTTTTGAAAATAATTACGTTTCATGCCTTATAAGTCACTACATGTTCGTGGAAGTTCTATTGCT
716 TGTTTTGAAAATAATTACATTTCATGCCTTATAAGTCACTACATGTTCGTGGAAGTTCTATTGCT
4183867 TTCAGCTCGTTTGATTGAGAGTTGGTGACATGTTCATTTAAGAAGTCTTGGATAAATTTTTTTGT
781 TTCAGCTCGTTTGATTGAGAGTTGGTGACATGTTCATTTAAGAAGTCTTGGATAAATTTTTTTGT
*
4183932 TGTTCTCTCTGTGCAGGATTATTGTCGTGCTGAATATGGAGACTATAATTCCAGAGTATGAAATA
846 TGTTCTCTCTGTGCAGGATTATTGTCGTGCTAAATATGGAGACTATAATTCCAGAGTATGAAATA
4183997 ATTGGGAATCCAAAACTTCTTACGGATTCTGATTCAACAACTAACAAGTCATTGCCT
911 ATTGGGAATCCAAAACTTCTTACGGATTCTGATTCAACAACTAACAAGTCATTGCCT
*
4184054 AATCTCACGCGCAACGCGATTGCGTCGATCAACGCTGGCGATGTGAACTCCAAGCCGTTGGTTCA
1 AATCTCACGCGCAACGCGATTGCGTCGATCAACACTGGCGATGTGAACTCCAAGCCGTTGGTTCA
4184119 GGTGGTGGATATCAAGCTGATTGGCAATTCTCAGGAGAGATACCGGTTTCTACTATCCGATTCCG
66 GGTGGTGGATATCAAGCTGATTGGCAATTCTCAGGAGAGATACCGGTTTCTACTATCCGATTCCG
4184184 AGTCCTCTCAGCACGCGATGCTCGCCACTCAGCTCAATGAACAAGTCAGGACCGGACGAGTCAAG
131 AGTCCTCTCAGCACGCGATGCTCGCCACTCAGCTCAATGAACAAGTCAGGACCGGACGAGTCAAG
4184249 AAAGGATCTATCATCCAGTTGATCGACTACGTTTGCAGCACTGTTCAGAATCGTAGGTGCGATTG
196 AAAGGATCTATCATCCAGTTGATCGACTACGTTTGCAGCACTGTTCAGAATCGTAGGTGCGATTG
4184314 ACTGCTTTTCTACTTAAAACTAATGAATTAATTTGAATGTTGATATACGAATTTTTTT-GAAAAG
261 ACTGCTTTTCTACTTAAAACTAATGAATTAATTTGAATGTTGATATACGAATTTTTTTCGAAAAG
* *
4184378 TAAGTATTGATATACGATTTTGTAGTTTCAAAATTCAGTTTGGGAAGACTTGAGATTCAGATTTG
326 TAAGTATTGATATACGATTATGTAGTTTCAAAATTCAGTTTGGGAAGACTTGAGATTCAAATTTG
****
4184443 ATCCTTTTATTTTTTAAAATACAAGAGCAAAGTTCTTTTTTTTTTTTTTTTAGGTTGAAGATTTG
391 ATCCTTTTATTTTTTAAAATACAAGAGCAAAGTTC-GCCCTTTTTTTTTTTAGGTTGAAGATTTG
4184508 AGAAATTCAAATTCATTTTTATTAAGCGTTCAAGTTGATTGGTGCCTTGAATACAAAGTTGAAGG
455 AGAAATTCAAATTCATTTTTATTAAGCGTTCAAGTTGATTGGTGCCTTGAATACAAAGTTGAAGG
*
4184573 AACTTTTAAGTAGATGAATTATCGTTAATCCTATCCACTGCTAATGAACTTAAATAAAAGGTAAG
520 AACTTTTAAGTAGATGAATTATCGTTAATCCTATCCACTCCTAATGAACTTAAATAAAAGGTAAG
4184638 GCTAGGACCATTGTCGAGTAGATTATTCATATTCAAGATATCAATTAAAGTAAGGAGGAAAGGAA
585 GCTAGGACCATTGTCGAGTAGATTATTCATATTCAAGATATCAATTAAAGTAAGGAGGAAAGGAA
4184703 ATCATATTATTCATTCTCCACAGTGTATAATTTGAAATCAAATATGTTACATAGCCTTCAGAAAC
650 ATCATATTATTCATTCTCCACAGTGTATAATTTGAAATCAAATATGTTACATAGCCTTCAGAAAC
4184768 ATGTTTTGAAAATAATTACATTTCATGCCTTATAAGTCACTACATGTTCGTGGAAGTTCTATTGC
715 ATGTTTTGAAAATAATTACATTTCATGCCTTATAAGTCACTACATGTTCGTGGAAGTTCTATTGC
4184833 TTTCAGCTCGTTTGATTGAGAGTTGGTGACATGTTCATTTAAGAAGTCTTGGATAAATTTTTTTG
780 TTTCAGCTCGTTTGATTGAGAGTTGGTGACATGTTCATTTAAGAAGTCTTGGATAAATTTTTTTG
4184898 TTGTTCTCTCTGTGCAGGATTATTGTCGTGCTAAATATGGAGACTATAATTCCAGAGTATGAAAT
845 TTGTTCTCTCTGTGCAGGATTATTGTCGTGCTAAATATGGAGACTATAATTCCAGAGTATGAAAT
*
4184963 AATTGGGAATTCAAAACTTCTTACGGATTCTGATTCAACAACTAACAAGTCATTGCCT
910 AATTGGGAATCCAAAACTTCTTACGGATTCTGATTCAACAACTAACAAGTCATTGCCT
4185021 AAT
1 AAT
4185024 AGCAATTCGC
Statistics
Matches: 952, Mismatches: 17, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
966 102 0.11
967 850 0.89
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (967 bp):
AATCTCACGCGCAACGCGATTGCGTCGATCAACACTGGCGATGTGAACTCCAAGCCGTTGGTTCA
GGTGGTGGATATCAAGCTGATTGGCAATTCTCAGGAGAGATACCGGTTTCTACTATCCGATTCCG
AGTCCTCTCAGCACGCGATGCTCGCCACTCAGCTCAATGAACAAGTCAGGACCGGACGAGTCAAG
AAAGGATCTATCATCCAGTTGATCGACTACGTTTGCAGCACTGTTCAGAATCGTAGGTGCGATTG
ACTGCTTTTCTACTTAAAACTAATGAATTAATTTGAATGTTGATATACGAATTTTTTTCGAAAAG
TAAGTATTGATATACGATTATGTAGTTTCAAAATTCAGTTTGGGAAGACTTGAGATTCAAATTTG
ATCCTTTTATTTTTTAAAATACAAGAGCAAAGTTCGCCCTTTTTTTTTTTAGGTTGAAGATTTGA
GAAATTCAAATTCATTTTTATTAAGCGTTCAAGTTGATTGGTGCCTTGAATACAAAGTTGAAGGA
ACTTTTAAGTAGATGAATTATCGTTAATCCTATCCACTCCTAATGAACTTAAATAAAAGGTAAGG
CTAGGACCATTGTCGAGTAGATTATTCATATTCAAGATATCAATTAAAGTAAGGAGGAAAGGAAA
TCATATTATTCATTCTCCACAGTGTATAATTTGAAATCAAATATGTTACATAGCCTTCAGAAACA
TGTTTTGAAAATAATTACATTTCATGCCTTATAAGTCACTACATGTTCGTGGAAGTTCTATTGCT
TTCAGCTCGTTTGATTGAGAGTTGGTGACATGTTCATTTAAGAAGTCTTGGATAAATTTTTTTGT
TGTTCTCTCTGTGCAGGATTATTGTCGTGCTAAATATGGAGACTATAATTCCAGAGTATGAAATA
ATTGGGAATCCAAAACTTCTTACGGATTCTGATTCAACAACTAACAAGTCATTGCCT
Found at i:4196164 original size:22 final size:22
Alignment explanation
Indices: 4196139--4196226 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
4196129 TAACTTTTCG
* *
4196139 ATTTTTGGGCATTACGTGACTA
1 ATTTTTAGACATTACGTGACTA
* *
4196161 ATTTTTAGACATTGCGTTACTA
1 ATTTTTAGACATTACGTGACTA
* *
4196183 ATTTTTAGATATTGCGTGACTA
1 ATTTTTAGACATTACGTGACTA
*
4196205 ATTTTTA-AGTATTACGTGACTA
1 ATTTTTAGA-CATTACGTGACTA
4196227 GTTAATATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 1 0.02
22 57 0.98
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.44
Consensus pattern (22 bp):
ATTTTTAGACATTACGTGACTA
Found at i:4196299 original size:23 final size:23
Alignment explanation
Indices: 4196273--4196331 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
4196263 GTGTGACTGC
* *
4196273 TTAGTAAAGTATTATATGACTAA
1 TTAGTAAAGCATTACATGACTAA
* * *
4196296 TTAGTAAGGCATTACGTGACTAG
1 TTAGTAAAGCATTACATGACTAA
*
4196319 TTAGTAAGGCATT
1 TTAGTAAAGCATT
4196332 GTCTAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (23 bp):
TTAGTAAAGCATTACATGACTAA
Found at i:4196382 original size:22 final size:22
Alignment explanation
Indices: 4196331--4196383 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
4196321 AGTAAGGCAT
*
4196331 TGTCTAAAAATCAGTCACGCAA
1 TGTCTAAAAATCAGTCACACAA
* * *
4196353 TG-CTTAAAATTTAGTCACATAA
1 TGTC-TAAAAATCAGTCACACAA
4196375 TGTCTAAAA
1 TGTCTAAAA
4196384 CCAGTTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (22 bp):
TGTCTAAAAATCAGTCACACAA
Found at i:4196463 original size:22 final size:22
Alignment explanation
Indices: 4196432--4196484 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4196422 TCAATCTCAT
* * * *
4196432 AATACTTAAAAATCAGTGATAC
1 AATACCTAAAAACCAATAATAC
*
4196454 AATGCCTAAAAACCAATAATAC
1 AATACCTAAAAACCAATAATAC
4196476 AATACCTAA
1 AATACCTAA
4196485 TAACTGATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.23
Consensus pattern (22 bp):
AATACCTAAAAACCAATAATAC
Found at i:4210533 original size:2 final size:2
Alignment explanation
Indices: 4210520--4210569 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
4210510 TCGGCTTTGA
*
4210520 AT AT AC 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
4210562 AT AT AT AT
1 AT AT AT AT
4210570 TTTTTTAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4221346 original size:2 final size:2
Alignment explanation
Indices: 4221339--4221365 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4221329 CTAAGGATGA
4221339 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4221366 AACAATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4227284 original size:23 final size:23
Alignment explanation
Indices: 4227231--4227292 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
4227221 ATAATCTAGA
* *
4227231 ATTTAATTAAAATATTAATAATT
1 ATTTAATTTAAATATTAACAATT
* * *
4227254 A-ATCATTTAAATATTAACATTT
1 ATTTAATTTAAATATTAACAATT
4227276 ATTTAATTTAAATATTA
1 ATTTAATTTAAATATTA
4227293 TTATGATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTTAAATATTAACAATT
Found at i:4227332 original size:112 final size:116
Alignment explanation
Indices: 4227191--4227407 Score: 309
Period size: 112 Copynumber: 1.9 Consensus size: 116
4227181 TTATGTGATA
*
4227191 TTTTATTTTTATTAGATTTTTTAAATATTAATAATCT-AGAATTTAATTAAAATATTAATAATTA
1 TTTTATTTTTATTAGATTTTTAAAATATTAATAAT-TGAGAATTTAATTAAAATATTAATAATTA
*
4227255 ATCATTTAAATATTAACATTTATTTA-A-TTT-AAATATTATTATGATTAAT
65 ATAATTTAAATATTAACATTTATTTATATTTTAAAATATTATTATGATTAAT
** * * *
4227304 TTTTA-TTTTATTTTATTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGA
1 TTTTATTTTTATTAGATTTTTAAAATATTAATAATTGAGAATTTAATTAAAATATTAATAATTAA
* *
4227368 TAATTTCAATATTAATATTTATTTATATTTTAAAATATTA
66 TAATTTAAATATTAACATTTATTTATATTTTAAAATATTA
4227408 ATATTTTATT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
111 1 0.01
112 73 0.80
113 6 0.07
114 3 0.03
115 8 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (116 bp):
TTTTATTTTTATTAGATTTTTAAAATATTAATAATTGAGAATTTAATTAAAATATTAATAATTAA
TAATTTAAATATTAACATTTATTTATATTTTAAAATATTATTATGATTAAT
Found at i:4227354 original size:27 final size:27
Alignment explanation
Indices: 4227321--4227373 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
4227311 TTATTTTATT
4227321 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
4227348 TTTAAAATATTAATAATTGATAATTT
1 TTTAAAATATTAATAATTGATAATTT
4227374 CAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:4227358 original size:139 final size:129
Alignment explanation
Indices: 4227234--4227515 Score: 324
Period size: 130 Copynumber: 2.1 Consensus size: 129
4227224 ATCTAGAATT
*
4227234 TAATTAAAATATTAATA-ATTAATCA-TTT-AAATATTAACA-TTTATTTAATTTAAATATTATT
1 TAATTAAAATATTAATATATTAAT-ATTTTAAAATATTAACATTTTATTTAATTTAAATATTATG
*
4227295 ATGATTAATTTTTATTTTATTTTATTTTTAAAATATTAATAATTGA-TAATTTATTTAAAATATT
65 ATGA-TAA-----A--TTATTTTATTTTTAAAA-ATTAATAATTAATTAATTTATTTAAAATATT
4227359 AATAATTGA
121 AATAATTGA
** * *
4227368 TAATTTCAATATTAATATTTATTTATATTTTAAAATATTAATATTTTATTTAATTTAAATATTAT
1 TAATTAAAATATTAATA--TATTAATATTTTAAAATATTAACATTTTATTTAATTTAAATATTAT
* * *
4227433 GATGATCAATTATTTTATTTTTGAAAATTAATAATTAATTAA-TTATTTAAAATATTAATAATAG
64 GATGATAAATTATTTTATTTTTAAAAATTAATAATTAATTAATTTATTTAAAATATTAATAATTG
4227497 A
129 A
*
4227498 TAATTTAAATATTAATAT
1 TAATTAAAATATTAATAT
4227516 TTTATTTAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 20
0.81 0.06 0.12
Matches are distributed among these distances:
128 1 0.01
130 49 0.37
131 19 0.15
133 1 0.01
134 15 0.11
136 1 0.01
137 8 0.06
138 12 0.09
139 25 0.19
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (129 bp):
TAATTAAAATATTAATATATTAATATTTTAAAATATTAACATTTTATTTAATTTAAATATTATGA
TGATAAATTATTTTATTTTTAAAAATTAATAATTAATTAATTTATTTAAAATATTAATAATTGA
Found at i:4227494 original size:27 final size:27
Alignment explanation
Indices: 4227321--4227494 Score: 95
Period size: 27 Copynumber: 6.6 Consensus size: 27
4227311 TTATTTTATT
*
4227321 TTTAAAATATTAATAATTGA-TAATTTA
1 TTTAAAATATTAATAATTAATTAA-TTA
*
4227348 TTTAAAATATTAATAATTGA-T-A--A
1 TTTAAAATATTAATAATTAATTAATTA
* * *
4227371 TTT-CAATATTAAT-ATTTATTTA-TA
1 TTTAAAATATTAATAATTAATTAATTA
*
4227395 TTTTAAAATATTAAT-ATT--TTATTTAA
1 -TTTAAAATATTAATAATTAATTAATT-A
* * *
4227421 TTT-AAATATTATGATGATCAATTATTTTA
1 TTTAAAATATTA--ATAATTAATTA-ATTA
*
4227450 TTTTTGAAA-ATTAATAATTAATTAATTA
1 --TTTAAAATATTAATAATTAATTAATTA
4227478 TTTAAAATATTAATAAT
1 TTTAAAATATTAATAAT
4227495 AGATAATTTA
Statistics
Matches: 120, Mismatches: 10, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.03
22 10 0.08
23 5 0.04
24 11 0.09
25 7 0.06
26 22 0.18
27 32 0.27
28 3 0.03
29 13 0.11
30 3 0.03
31 7 0.06
32 3 0.03
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (27 bp):
TTTAAAATATTAATAATTAATTAATTA
Found at i:4229520 original size:3 final size:3
Alignment explanation
Indices: 4229512--4229536 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4229502 CATGTTGGTT
4229512 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
4229537 AGTTGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:4235919 original size:31 final size:33
Alignment explanation
Indices: 4235884--4235950 Score: 77
Period size: 35 Copynumber: 2.1 Consensus size: 33
4235874 CAATGTTTTA
4235884 AAAAAATAA-AAAT-ATT-TTTATAAATTAATAT
1 AAAAAATAATAAATGATTATTTATAAATTAA-AT
* *
4235915 AAAAATTAATAAATGATTAATTTATCAATTAAAT
1 AAAAAATAATAAATGATT-ATTTATAAATTAAAT
4235949 AA
1 AA
4235951 TATCTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
31 8 0.27
32 4 0.13
33 3 0.10
34 4 0.13
35 11 0.37
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
AAAAAATAATAAATGATTATTTATAAATTAAAT
Found at i:4254166 original size:36 final size:36
Alignment explanation
Indices: 4254119--4254196 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
4254109 CTCATCCACC
4254119 AAGATTCTATTCATTCTCCTTATCACAATAAGAGTG
1 AAGATTCTATTCATTCTCCTTATCACAATAAGAGTG
4254155 AAGATTCTATTCATTCTCCTTATCACAATAAGAGTG
1 AAGATTCTATTCATTCTCCTTATCACAATAAGAGTG
4254191 AAGATT
1 AAGATT
4254197 TCACAACCCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (36 bp):
AAGATTCTATTCATTCTCCTTATCACAATAAGAGTG
Found at i:4255158 original size:47 final size:47
Alignment explanation
Indices: 4255086--4255229 Score: 207
Period size: 47 Copynumber: 3.1 Consensus size: 47
4255076 GCTTTAAGCA
* * *
4255086 TGGTACTGCAAGCGGTTTTTTTATGCTATATAGTTGGGTCCTGTTTC
1 TGGTACTGCAAGCGGTTTTTGTATGCTGTATAGTTGGGTCATGTTTC
* * * *
4255133 TGGTACAGCAGGCGGGTTTTGTATGCTGTATGGTTGGGTCATGTTTC
1 TGGTACTGCAAGCGGTTTTTGTATGCTGTATAGTTGGGTCATGTTTC
* *
4255180 TGGTGCTGCAAGCGGTTTTTGTATGCTGTGTAGTTGGGTCATGTTTC
1 TGGTACTGCAAGCGGTTTTTGTATGCTGTATAGTTGGGTCATGTTTC
4255227 TGG
1 TGG
4255230 ACTTTTAGTA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 84 1.00
ACGTcount: A:0.12, C:0.13, G:0.33, T:0.42
Consensus pattern (47 bp):
TGGTACTGCAAGCGGTTTTTGTATGCTGTATAGTTGGGTCATGTTTC
Found at i:4264127 original size:20 final size:19
Alignment explanation
Indices: 4264099--4264137 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4264089 TTAAGATATA
*
4264099 TATTAAAAATATATTTAAAT
1 TATTAAAAAAAT-TTTAAAT
*
4264119 TATTTAAAAAATTTTAAAT
1 TATTAAAAAAATTTTAAAT
4264138 CAATGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTAAAAAAATTTTAAAT
Found at i:4265552 original size:6 final size:6
Alignment explanation
Indices: 4265541--4265573 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4265531 AACCCAATGA
*
4265541 TTTTCT TTTTCT TTTTCT TTATC- TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
4265574 GGAGTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:4289817 original size:2 final size:2
Alignment explanation
Indices: 4289810--4289929 Score: 186
Period size: 2 Copynumber: 60.0 Consensus size: 2
4289800 TACTTATCTA
4289810 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
** *
4289852 AT AT NN NT 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
* * *
4289894 AT AT AT AT AT AT AT AT AT AT AT TT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4289930 GTAAACTGTG
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 109 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4300144 original size:40 final size:41
Alignment explanation
Indices: 4300098--4300182 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
4300088 AAAAAAAAAA
*
4300098 TAGAGTTTAAA-TCTCCAAATATAT-ATAAAAAATTCACCCT
1 TAGAGTTTAAATTC-CCAAATATATAAAAAAAAATTCACCCT
* * *
4300138 TAGAGTTTGAATTCCCAATTATATAAAAAAAAATTCACGCT
1 TAGAGTTTAAATTCCCAAATATATAAAAAAAAATTCACCCT
4300179 TAGA
1 TAGA
4300183 AATACTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
40 19 0.49
41 20 0.51
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (41 bp):
TAGAGTTTAAATTCCCAAATATATAAAAAAAAATTCACCCT
Found at i:4300181 original size:41 final size:40
Alignment explanation
Indices: 4300098--4300182 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
4300088 AAAAAAAAAA
*
4300098 TAGAGTTTAAATCTCCAAATATATATAAAAAATTCACCCT
1 TAGAGTTTAAATCTCCAAATATATAAAAAAAATTCACCCT
* * *
4300138 TAGAGTTTGAAT-TCCCAATTATATAAAAAAAAATTCACGCT
1 TAGAGTTTAAATCT-CCAAATATAT-AAAAAAAATTCACCCT
4300179 TAGA
1 TAGA
4300183 AATACTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 1 0.03
40 20 0.51
41 18 0.46
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (40 bp):
TAGAGTTTAAATCTCCAAATATATAAAAAAAATTCACCCT
Found at i:4300661 original size:27 final size:25
Alignment explanation
Indices: 4300603--4300669 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 25
4300593 TATAAGAATC
*
4300603 TATTTAATTCAAAATAAAAATATAAA
1 TATTTAATT-AAAATAAAAAAATAAA
* *
4300629 GATTTAATTAAATGTAATAAAAATAAA
1 TATTTAATTAAA-ATAA-AAAAATAAA
*
4300656 TATTTATTTAAAAT
1 TATTTAATTAAAAT
4300670 TTTCATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 3 0.09
26 12 0.36
27 18 0.55
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (25 bp):
TATTTAATTAAAATAAAAAAATAAA
Found at i:4302679 original size:15 final size:16
Alignment explanation
Indices: 4302649--4302682 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4302639 TAATTTTAAT
4302649 AATATTGAATAATTTA
1 AATATTGAATAATTTA
*
4302665 AATATT-AATATTTTA
1 AATATTGAATAATTTA
4302680 AAT
1 AAT
4302683 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATTGAATAATTTA
Found at i:4316743 original size:21 final size:21
Alignment explanation
Indices: 4316717--4316757 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4316707 ATTGGAAGAA
*
4316717 TGGAAAATGCTTTTC-TTTTCT
1 TGGAAAAAG-TTTTCATTTTCT
4316738 TGGAAAAAGTTTTCATTTTC
1 TGGAAAAAGTTTTCATTTTC
4316758 CAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (21 bp):
TGGAAAAAGTTTTCATTTTCT
Found at i:4317373 original size:21 final size:21
Alignment explanation
Indices: 4317334--4317373 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4317324 AAAAGAAACC
* *
4317334 AAAGAGGGAAAAATAAAAAAA
1 AAAGAGGAAAAAAGAAAAAAA
*
4317355 AAAGAGGAAAAAAGGAAAA
1 AAAGAGGAAAAAAGAAAAA
4317374 GGAAATGATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (21 bp):
AAAGAGGAAAAAAGAAAAAAA
Found at i:4320400 original size:3 final size:3
Alignment explanation
Indices: 4320387--4320429 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
4320377 ATGTAAAAGA
*
4320387 AAG AA- AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
4320430 AGACTCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4324059 original size:22 final size:23
Alignment explanation
Indices: 4324024--4324067 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4324014 TAAAAAAATT
4324024 AAAATATTATTTAT-TAATTTTA
1 AAAATATTATTTATATAATTTTA
4324046 AAAATTATTA-TTATATAATTTT
1 AAAA-TATTATTTATATAATTTT
4324068 TTGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATATTATTTATATAATTTTA
Found at i:4328940 original size:18 final size:18
Alignment explanation
Indices: 4328917--4328967 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
4328907 CTACACTATG
4328917 AATTACTAAAGAATGTTT
1 AATTACTAAAGAATGTTT
4328935 AATTACT----AATGTTT
1 AATTACTAAAGAATGTTT
4328949 AATTACTAAAGAATGTTT
1 AATTACTAAAGAATGTTT
4328967 A
1 A
4328968 GCCTCTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.48
18 15 0.52
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (18 bp):
AATTACTAAAGAATGTTT
Found at i:4328947 original size:14 final size:14
Alignment explanation
Indices: 4328928--4328957 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4328918 ATTACTAAAG
4328928 AATGTTTAATTACT
1 AATGTTTAATTACT
4328942 AATGTTTAATTACT
1 AATGTTTAATTACT
4328956 AA
1 AA
4328958 AGAATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
AATGTTTAATTACT
Found at i:4330840 original size:2 final size:2
Alignment explanation
Indices: 4330835--4330866 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4330825 CAAAGACTTG
4330835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4330867 AAGTTGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4338198 original size:2 final size:2
Alignment explanation
Indices: 4338191--4338217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4338181 TTAACTACCA
4338191 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4338218 TTTTATGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4344938 original size:30 final size:30
Alignment explanation
Indices: 4344896--4344978 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
4344886 GTGAAAAAAA
* * *
4344896 TGTTGAATTATTTATTATGTAATGTTTGTT
1 TGTTGGATTATTTACTATGTAATGTCTGTT
* **
4344926 TGCTT-GATTATTTACCACATAATGTCTGTT
1 TG-TTGGATTATTTACTATGTAATGTCTGTT
4344956 TGTTGGATTATTTACTATGTAAT
1 TGTTGGATTATTTACTATGTAAT
4344979 TAGCATAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.90
31 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (30 bp):
TGTTGGATTATTTACTATGTAATGTCTGTT
Done.