Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 104 of 378
Found at i:28686916 original size:50 final size:50
Alignment explanation
Indices: 28686856--28686950 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
28686846 CTAACTCAGG
*
28686856 ATTTAAGTAAATCACA-CTATGAATGTCACAAGTGAACTAATTCAAAAAAA
1 ATTTAAGTAAATCACAGC-ATGAATATCACAAGTGAACTAATTCAAAAAAA
* *
28686906 ATTTAGGTAAATCACAGCATGAATATCACAAGTGAATTAATTCAA
1 ATTTAAGTAAATCACAGCATGAATATCACAAGTGAACTAATTCAA
28686951 TCAATGAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (50 bp):
ATTTAAGTAAATCACAGCATGAATATCACAAGTGAACTAATTCAAAAAAA
Found at i:28689295 original size:18 final size:18
Alignment explanation
Indices: 28689246--28689283 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28689236 ATTAACACTT
28689246 TATTCTATCACCTTAAAC
1 TATTCTATCACCTTAAAC
28689264 TATTCTATCACCTTAAAC
1 TATTCTATCACCTTAAAC
28689282 TA
1 TA
28689284 GTTTACAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTCTATCACCTTAAAC
Found at i:28690778 original size:28 final size:28
Alignment explanation
Indices: 28690745--28690803 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
28690735 AAGGTTGTGG
* ** *
28690745 GCATTGGCAATTGGAGTGCAATTTGCAA
1 GCATTGGCAATTAGAGCACAATTTGAAA
*
28690773 GCATTGGCGATTAGAGCACAATTTGAAA
1 GCATTGGCAATTAGAGCACAATTTGAAA
28690801 GCA
1 GCA
28690804 ACTATTAGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (28 bp):
GCATTGGCAATTAGAGCACAATTTGAAA
Found at i:28692565 original size:42 final size:42
Alignment explanation
Indices: 28692503--28692604 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
28692493 TGAAATGGGT
*
28692503 CTACTCACACGAGCTGTGGATCAGAATGTAAGCTACACGATG
1 CTACTCACACGAGCTATGGATCAGAATGTAAGCTACACGATG
*
28692545 CTACTCACATGAGCTATGGATCAGAATGTAAGCTACACGATG
1 CTACTCACACGAGCTATGGATCAGAATGTAAGCTACACGATG
28692587 CTACTCACACGAGCTATG
1 CTACTCACACGAGCTATG
28692605 AAGTATTCAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CTACTCACACGAGCTATGGATCAGAATGTAAGCTACACGATG
Found at i:28697230 original size:41 final size:40
Alignment explanation
Indices: 28697173--28697311 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
28697163 CGAATGATAT
* *
28697173 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTCACTATAA
* * * *
28697214 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCACTATAA
* * *
28697253 TTCGGGCTAATTCCCGAAGGCAATTGTGCGAA-TCACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTCACTATAA
*
28697294 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
28697312 ACAATCGAGC
Statistics
Matches: 80, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.03
40 50 0.62
41 28 0.35
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCACTATAA
Found at i:28697324 original size:80 final size:81
Alignment explanation
Indices: 28697174--28697325 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 81
28697164 GAATGATATC
** * * * * *
28697174 CGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAACCGGGTTAAGTCCCGAAGGCATTCG
1 CGGGCTAAGTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAATCG
*
28697239 TGCGAGTTACTAAATT
66 AGCGAGTTACTAAATT
* *
28697255 CGGGCTAATTCCCGAAGGCAATTGTGCGAA-TCACTATAACCGGGCTATGTCCCGAAGACAATCG
1 CGGGCTAAGTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAATCG
28697319 AGCGAGT
66 AGCGAGT
28697326 CGCTATATCC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
80 35 0.57
81 26 0.43
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (81 bp):
CGGGCTAAGTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAATCG
AGCGAGTTACTAAATT
Found at i:28697332 original size:40 final size:40
Alignment explanation
Indices: 28697173--28697337 Score: 136
Period size: 40 Copynumber: 4.1 Consensus size: 40
28697163 CGAATGATAT
* ** * * *
28697173 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAA
1 CCGGGCTATGTCCCGAAGGCAATCGTGC-GAGTCACTATAA
* * * *
28697214 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-AA
1 CCGGGCTATGTCCCGAAGGCAATCGTGCGAGTCACTATAA
* * *
28697253 TTCGGGCTAAT-TCCCGAAGGCAATTGTGCGAATCACTATAA
1 -CCGGGCT-ATGTCCCGAAGGCAATCGTGCGAGTCACTATAA
* * * *
28697294 CCGGGCTATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTATGTCCCGAAGGCAATCGTGCGAGTCACTATAA
28697334 CCGG
1 CCGG
28697338 TTAAATTCCG
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.04
40 69 0.68
41 28 0.28
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTATGTCCCGAAGGCAATCGTGCGAGTCACTATAA
Found at i:28697345 original size:80 final size:81
Alignment explanation
Indices: 28697176--28697351 Score: 187
Period size: 80 Copynumber: 2.2 Consensus size: 81
28697166 ATGATATCCG
* ** * * * * * *
28697176 GGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAACCGGGTTAAGTCCCGAAGGCATTCGTG
1 GGCTAATTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAATCGAG
* *
28697241 CGAGTTACTAAATTCG
66 CGAGTCACTAAATTCC
*
28697257 GGCTAATTCCCGAAGGCAATTGTGCGAA-TCACTATAACCGGGCTATGTCCCGAAGACAATCGAG
1 GGCTAATTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAATCGAG
* *
28697321 CGAGTCGCTATA-TCC
66 CGAGTCACTAAATTCC
*
28697336 GGTTAAATT-CCGAAGG
1 GGCT-AATTCCCGAAGG
28697352 TACGTGATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
79 12 0.15
80 43 0.54
81 24 0.30
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (81 bp):
GGCTAATTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAATCGAG
CGAGTCACTAAATTCC
Found at i:28705282 original size:40 final size:40
Alignment explanation
Indices: 28705171--28705311 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
28705161 TTCGAATGAT
* *
28705171 ATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATA
1 ATTCGGGCTAAGTCCCGAAGGC-ATTGTGC-GAGTGACTATA
* * *
28705213 A-CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-A
1 ATTCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTGACTATA
* * *
28705252 ATTCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATA
1 ATTCGGGCTAAGTCCCGAAGGC-ATTGTGCGAGTGACTATA
* *
28705293 A-CCGGGCTATGTCCCGAAG
1 ATTCGGGCTAAGTCCCGAAG
28705312 ACAATCGAGC
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
39 2 0.02
40 52 0.63
41 27 0.33
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATTCGGGCTAAGTCCCGAAGGCATTGTGCGAGTGACTATA
Found at i:28705325 original size:80 final size:81
Alignment explanation
Indices: 28705171--28705325 Score: 213
Period size: 80 Copynumber: 1.9 Consensus size: 81
28705161 TTCGAATGAT
** * * * * *
28705171 ATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAACCGGGTTAAGTCCCGAAGGCAT
1 ATTCGGGCTAAGTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAA
*
28705236 TCGTGCGAGTTACTAA
66 TCGAGCGAGTTACTAA
* *
28705252 ATTCGGGCTAATTCCCGAAGGCAATTGTGCGAA-TCACTATAACCGGGCTATGTCCCGAAGACAA
1 ATTCGGGCTAAGTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAA
28705316 TCGAGCGAGT
66 TCGAGCGAGT
28705326 CGCTATATCC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
80 35 0.55
81 29 0.45
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (81 bp):
ATTCGGGCTAAGTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAA
TCGAGCGAGTTACTAA
Found at i:28705332 original size:40 final size:40
Alignment explanation
Indices: 28705174--28705337 Score: 134
Period size: 40 Copynumber: 4.1 Consensus size: 40
28705164 GAATGATATT
* ** * * *
28705174 CGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAAC
1 CGGGCTATGTCCCGAAGGCAATCGTGC-GAGTCACTATAAC
* * * * *
28705215 CGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-AATT
1 CGGGCTATGTCCCGAAGGCAATCGTGCGAGTCACTATAA-C
* *
28705255 CGGGCTAAT-TCCCGAAGGCAATTGTGCGAATCACTATAAC
1 CGGGCT-ATGTCCCGAAGGCAATCGTGCGAGTCACTATAAC
* * * *
28705295 CGGGCTATGTCCCGAAGACAATCGAGCGAGTCGCTATATC
1 CGGGCTATGTCCCGAAGGCAATCGTGCGAGTCACTATAAC
28705335 CGG
1 CGG
28705338 TTAAATTCCG
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.04
40 69 0.69
41 27 0.27
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CGGGCTATGTCCCGAAGGCAATCGTGCGAGTCACTATAAC
Found at i:28705345 original size:80 final size:81
Alignment explanation
Indices: 28705171--28705351 Score: 188
Period size: 80 Copynumber: 2.3 Consensus size: 81
28705161 TTCGAATGAT
* * ** * * * * *
28705171 ATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAACCGGGTTAAGTCCCGAAGGCAT
1 ATTCCGGCTAATTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAA
* *
28705236 TCGTGCGAGTTACTAA
66 TCGAGCGAGTCACTAA
* *
28705252 ATTCGGGCTAATTCCCGAAGGCAATTGTGCGAA-TCACTATAACCGGGCTATGTCCCGAAGACAA
1 ATTCCGGCTAATTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAA
* *
28705316 TCGAGCGAGTCGCTAT
66 TCGAGCGAGTCACTAA
*
28705332 A-TCCGGTTAAATT-CCGAAGG
1 ATTCCGGCT-AATTCCCGAAGG
28705352 TACGTGATTC
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
79 12 0.14
80 43 0.51
81 29 0.35
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (81 bp):
ATTCCGGCTAATTCCCGAAGGCAATTGTGCGAAGTCACTATAACCGGGCTAAGTCCCGAAGACAA
TCGAGCGAGTCACTAA
Found at i:28713899 original size:13 final size:13
Alignment explanation
Indices: 28713881--28713905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28713871 GAAAATAGTA
28713881 AAATATTAAAAAT
1 AAATATTAAAAAT
28713894 AAATATTAAAAA
1 AAATATTAAAAA
28713906 AATACTAGGG
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATTAAAAAT
Found at i:28714195 original size:18 final size:19
Alignment explanation
Indices: 28714161--28714198 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28714151 CAAAAAATTC
28714161 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
28714180 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
28714198 A
1 A
28714199 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:28714242 original size:12 final size:11
Alignment explanation
Indices: 28714214--28714240 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28714204 AAAAAATTAT
28714214 AAAAATTTCTA
1 AAAAATTTCTA
28714225 AAAAATTTCTA
1 AAAAATTTCTA
28714236 AAAAA
1 AAAAA
28714241 ATATATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAATTTCTA
Found at i:28717508 original size:45 final size:45
Alignment explanation
Indices: 28717444--28717535 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
28717434 TCTGTTTGCC
28717444 AAATGCTCGCTTTTTTTAAATACAATTTAAGAGCACATAATACTT
1 AAATGCTCGCTTTTTTTAAATACAATTTAAGAGCACATAATACTT
28717489 AAATGCTCGCTTTTTTTAAATACAATTTAAGAGCACATAATACTT
1 AAATGCTCGCTTTTTTTAAATACAATTTAAGAGCACATAATACTT
28717534 AA
1 AA
28717536 CTTCGCTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (45 bp):
AAATGCTCGCTTTTTTTAAATACAATTTAAGAGCACATAATACTT
Found at i:28719438 original size:22 final size:20
Alignment explanation
Indices: 28719391--28719438 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 20
28719381 TATAAATATT
28719391 AAATTTACATAAAATTATAA
1 AAATTTACATAAAATTATAA
28719411 AGAATTTAC-TAAAAGATTATTAA
1 A-AATTTACAT-AAA-ATTA-TAA
28719434 AAATT
1 AAATT
28719439 ATAAAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 8 0.33
23 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATTTACATAAAATTATAA
Found at i:28723097 original size:16 final size:16
Alignment explanation
Indices: 28723076--28723107 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28723066 CAAAATTATT
28723076 GGCATATTATTGGTAA
1 GGCATATTATTGGTAA
*
28723092 GGCATATTGTTGGTAA
1 GGCATATTATTGGTAA
28723108 AGATGCTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (16 bp):
GGCATATTATTGGTAA
Found at i:28724781 original size:72 final size:72
Alignment explanation
Indices: 28724696--28724838 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
28724686 AATGATTCAT
* * *
28724696 TTATAATTTTTTAAAACCTATTACGATTATCACGCATCAAGTTTTTGACGCCGTTGCCGGGGAAC
1 TTATAAATTTTTAAAACCTATTACGAATATCACGCATCAAGTTTTTGACGCCGTTGCCGAGGAAC
28724761 TAGGATA
66 TAGGATA
28724768 TTATAAATTTTTAAAACCTATTACGAATATCACGCATCAAGTTTTTGACGCCGTTGCCGAGGAAC
1 TTATAAATTTTTAAAACCTATTACGAATATCACGCATCAAGTTTTTGACGCCGTTGCCGAGGAAC
28724833 TAGGAT
66 TAGGAT
28724839 GTTAGGAACA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (72 bp):
TTATAAATTTTTAAAACCTATTACGAATATCACGCATCAAGTTTTTGACGCCGTTGCCGAGGAAC
TAGGATA
Found at i:28731759 original size:3 final size:3
Alignment explanation
Indices: 28731751--28731804 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
28731741 TTTGATCTTA
28731751 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28731799 AAT AAT
1 AAT AAT
28731805 TCATTACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28735367 original size:24 final size:24
Alignment explanation
Indices: 28735340--28735385 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
28735330 CTTTTAATTA
*
28735340 TATTCATTTTCCGACTTTGGTAAT
1 TATTCATTTTCCCACTTTGGTAAT
** *
28735364 TATTTTTTTTCCCATTTTGGTA
1 TATTCATTTTCCCACTTTGGTA
28735386 CCTAAAGTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (24 bp):
TATTCATTTTCCCACTTTGGTAAT
Found at i:28735534 original size:21 final size:21
Alignment explanation
Indices: 28735509--28735560 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
28735499 AATTATAAAA
28735509 ATACATAAAATAG-AATGAAAT
1 ATACATAAAATAGTAA-GAAAT
*
28735530 ATACA-AAAAT-GTAAGAAGT
1 ATACATAAAATAGTAAGAAAT
*
28735549 ATATATAAAATA
1 ATACATAAAATA
28735561 TCTACATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 9 0.35
20 12 0.46
21 5 0.19
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.25
Consensus pattern (21 bp):
ATACATAAAATAGTAAGAAAT
Found at i:28738352 original size:14 final size:14
Alignment explanation
Indices: 28738333--28738360 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28738323 ACATGCGCTA
28738333 CCACACGCACCCTT
1 CCACACGCACCCTT
28738347 CCACACGCACCCTT
1 CCACACGCACCCTT
28738361 TTTCAATATA
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:0.21, C:0.57, G:0.07, T:0.14
Consensus pattern (14 bp):
CCACACGCACCCTT
Found at i:28739733 original size:22 final size:22
Alignment explanation
Indices: 28739708--28739751 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28739698 AATTATTAAC
* *
28739708 ATAATGAATTTTGCTTAATTTT
1 ATAATAAATTTTGATTAATTTT
28739730 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTGATTAATTTT
28739752 GATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
ATAATAAATTTTGATTAATTTT
Found at i:28745269 original size:46 final size:46
Alignment explanation
Indices: 28745219--28745393 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28745209 TGGTTGAGCA
28745219 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28745265 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28745310 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28745358 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28745394 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 17 0.15
46 48 0.44
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28745375 original size:93 final size:92
Alignment explanation
Indices: 28745216--28745386 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
28745206 GGATGGTTGA
* *
28745216 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28745281 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
*
28745309 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28745374 TGAGTCGAGTTCG
66 TGAGTCGAGTTCG
28745387 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 8 0.11
93 67 0.89
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:28753289 original size:46 final size:46
Alignment explanation
Indices: 28753239--28753414 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28753229 TGGTTGAGCA
28753239 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28753285 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28753330 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28753378 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28753415 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28753395 original size:93 final size:93
Alignment explanation
Indices: 28753236--28753407 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28753226 GGATGGTTGA
* *
28753236 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28753301 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28753329 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28753394 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
28753408 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28760370 original size:46 final size:46
Alignment explanation
Indices: 28760320--28760495 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28760310 TGGTTGAGCA
28760320 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28760366 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
**
28760411 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28760459 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28760496 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28760476 original size:93 final size:93
Alignment explanation
Indices: 28760317--28760488 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28760307 GGATGGTTGA
***
28760317 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
28760382 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28760410 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
28760475 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
28760489 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28765139 original size:16 final size:15
Alignment explanation
Indices: 28765099--28765140 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
28765089 AGATGATAAT
28765099 TATTAATTTATAATTA
1 TATTAA-TTATAATTA
28765115 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
28765131 TATTAATTAT
1 TATTAATTAT
28765141 TATCAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 14 0.61
17 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:28768708 original size:10 final size:10
Alignment explanation
Indices: 28768690--28768741 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
28768680 ATTATTAACA
*
28768690 TAATGAATTT
1 TAATTAATTT
28768700 TAATTAATTTT
1 TAATTAA-TTT
*
28768711 ATAATAAATTT
1 -TAATTAATTT
*
28768722 TGATTAATTT
1 TAATTAATTT
28768732 TAATT-ATTT
1 TAATTAATTT
28768741 T
1 T
28768742 CGACAGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.14
10 18 0.51
11 6 0.17
12 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (10 bp):
TAATTAATTT
Found at i:28768714 original size:22 final size:22
Alignment explanation
Indices: 28768689--28768733 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28768679 AATTATTAAC
*
28768689 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATTAATTTT
*
28768711 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
28768733 A
1 A
28768734 ATTATTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:28770139 original size:32 final size:32
Alignment explanation
Indices: 28770098--28770162 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
28770088 TAGGTAAGTA
* *
28770098 TGTTCATAAGTTAGAAATTTACCGAGTTGCCG
1 TGTTCATAAGTTAGAAAATTACCGAGTTCCCG
28770130 TGTTCATAAGTTAGAAAATTACCGAGTTCCCG
1 TGTTCATAAGTTAGAAAATTACCGAGTTCCCG
28770162 T
1 T
28770163 AAATTTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (32 bp):
TGTTCATAAGTTAGAAAATTACCGAGTTCCCG
Found at i:28772014 original size:15 final size:16
Alignment explanation
Indices: 28771981--28772035 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
28771971 TATATTTAGA
* *
28771981 TTATATATTATGAATTT
1 TTATATATTTTTAA-TT
28771998 TTATATATTTTT-ATT
1 TTATATATTTTTAATT
* *
28772013 TTAAAT-TTTTTAATA
1 TTATATATTTTTAATT
28772028 TTATATAT
1 TTATATAT
28772036 ATTTGATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.16
15 14 0.45
16 2 0.06
17 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATATATTTTTAATT
Found at i:28775170 original size:16 final size:15
Alignment explanation
Indices: 28775157--28775200 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28775147 AAGAAAATTG
*
28775157 GAAGGATGGAAAATC
1 GAAGGATGGAAAATA
*
28775172 GAAGGGTGGAAAACTA
1 GAAGGATGGAAAA-TA
*
28775188 GATGGATGGAAAA
1 GAAGGATGGAAAA
28775201 CATAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.14
Consensus pattern (15 bp):
GAAGGATGGAAAATA
Found at i:28775201 original size:16 final size:16
Alignment explanation
Indices: 28775157--28775201 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
28775147 AAGAAAATTG
*
28775157 GAAGGATGGAAAA-TC
1 GAAGGATGGAAAACTA
*
28775172 GAAGGGTGGAAAACTA
1 GAAGGATGGAAAACTA
*
28775188 GATGGATGGAAAAC
1 GAAGGATGGAAAAC
28775202 ATAATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.44, C:0.07, G:0.36, T:0.13
Consensus pattern (16 bp):
GAAGGATGGAAAACTA
Found at i:28780866 original size:2 final size:2
Alignment explanation
Indices: 28780859--28780883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28780849 AGTATGTACG
28780859 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28780884 GAATAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28781134 original size:31 final size:30
Alignment explanation
Indices: 28781099--28781174 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
28781089 AATAATAGGT
28781099 ATAATAATAAATATAATGATATACGAA-AATA
1 ATAATAATAAATATAATG-TATAC-AAGAATA
*
28781130 ATAATATATATAAAAT-ATGTATACAAGAATA
1 ATAATA-ATA-AATATAATGTATACAAGAATA
*
28781161 ATAA-AATATATATA
1 ATAATAATAAATATA
28781175 CTAATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
28 3 0.08
29 3 0.08
30 3 0.08
31 19 0.50
32 6 0.16
33 4 0.11
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (30 bp):
ATAATAATAAATATAATGTATACAAGAATA
Found at i:28781359 original size:20 final size:21
Alignment explanation
Indices: 28781313--28781365 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
28781303 ATGTACATGG
28781313 AATAATATATAAAAATATAAC
1 AATAATATATAAAAATATAAC
*
28781334 TAATAATAT-TGAAAATATATAC
1 -AATAATATATAAAAATATA-AC
28781356 -ATAATATATA
1 AATAATATATA
28781366 TATATAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 10 0.37
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATATATAAAAATATAAC
Found at i:28781377 original size:15 final size:15
Alignment explanation
Indices: 28781365--28781394 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
28781355 CATAATATAT
28781365 ATATATAACATATACG
1 ATATAT-ACATATACG
28781381 ATATATACATATAC
1 ATATATACATATAC
28781395 ATTAGAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (15 bp):
ATATATACATATACG
Found at i:28781528 original size:2 final size:2
Alignment explanation
Indices: 28781523--28781565 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28781513 CACAACATAA
28781523 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
28781565 A
1 A
28781566 AAATGTAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28781910 original size:16 final size:16
Alignment explanation
Indices: 28781889--28781919 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28781879 ATAAGTATAC
28781889 ATATATATGTACTAAA
1 ATATATATGTACTAAA
28781905 ATATATATGTACTAA
1 ATATATATGTACTAA
28781920 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
ATATATATGTACTAAA
Found at i:28782023 original size:13 final size:14
Alignment explanation
Indices: 28781986--28782026 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
28781976 ATATATATAC
28781986 ATAAATAATAAT-A
1 ATAAATAATAATGA
28781999 AT-AATAAGTAATGA
1 ATAAATAA-TAATGA
28782013 ATAAAT-ATAATGA
1 ATAAATAATAATGA
28782026 A
1 A
28782027 AATAGTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.20
13 13 0.52
14 4 0.16
15 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
ATAAATAATAATGA
Found at i:28784002 original size:18 final size:18
Alignment explanation
Indices: 28783979--28784021 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28783969 TATTAAATAT
*
28783979 TATTATTATTATT-TCTAA
1 TATTATTAATATTATC-AA
28783997 TATTATTAATATTATCAA
1 TATTATTAATATTATCAA
28784015 TATTATT
1 TATTATT
28784022 TTTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTAATATTATCAA
Found at i:28784180 original size:23 final size:22
Alignment explanation
Indices: 28784154--28784197 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
28784144 TTAATATTAG
*
28784154 TATATATTTTTTATATATGTATA
1 TATATACTTTTTATATA-GTATA
28784177 TATATACTTTTTATATAGTAT
1 TATATACTTTTTATATAGTAT
28784198 TATCGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (22 bp):
TATATACTTTTTATATAGTATA
Found at i:28784220 original size:12 final size:12
Alignment explanation
Indices: 28784130--28784237 Score: 59
Period size: 12 Copynumber: 9.3 Consensus size: 12
28784120 AGTATTATAA
*
28784130 TATTATATTCAT
1 TATTATATTTAT
*
28784142 TATTA-ATATTAG
1 TATTATAT-TTAT
*
28784154 TA-TATATTTTT
1 TATTATATTTAT
*
28784165 TA-TATATGTA-
1 TATTATATTTAT
28784175 TATATATACTTT-T
1 TAT-TATA-TTTAT
*
28784188 TA-TATA-GTAT
1 TATTATATTTAT
** *
28784198 TATCGTTTTTAT
1 TATTATATTTAT
28784210 TATTATATTTAT
1 TATTATATTTAT
*
28784222 TATTATACTTAT
1 TATTATATTTAT
28784234 TATT
1 TATT
28784238 TTTACCATTA
Statistics
Matches: 71, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
9 1 0.01
10 5 0.07
11 19 0.27
12 42 0.59
13 4 0.06
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:28784247 original size:21 final size:21
Alignment explanation
Indices: 28784209--28784248 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28784199 ATCGTTTTTA
**
28784209 TTATTATATTTATTATTATAC
1 TTATTATATTTACCATTATAC
*
28784230 TTATTATTTTTACCATTAT
1 TTATTATATTTACCATTAT
28784249 TATTTTTTAT
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:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATATTTACCATTATAC
Found at i:28784257 original size:16 final size:16
Alignment explanation
Indices: 28784230--28784267 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28784220 ATTATTATAC
28784230 TTATTA-TTTTTACCA
1 TTATTATTTTTTACCA
*
28784245 TTATTATTTTTTATCA
1 TTATTATTTTTTACCA
28784261 TTATTAT
1 TTATTAT
28784268 ATGTATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATTTTTTACCA
Found at i:28784608 original size:18 final size:17
Alignment explanation
Indices: 28784587--28784629 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
28784577 ATTATATGGG
28784587 TATATATA-TATATACTTT
1 TATATATAGTAT-TA-TTT
28784605 TATATATAGTATTATTT
1 TATATATAGTATTATTT
28784622 TCATATAT
1 T-ATATAT
28784630 CGTTATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
TATATATAGTATTATTT
Found at i:28784846 original size:25 final size:25
Alignment explanation
Indices: 28784821--28784868 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28784811 TCTAATGTTA
28784821 TATTATAT--ATATGTTTTTCATAT
1 TATTATATACATATGTTTTTCATAT
* *
28784844 TATTATGTACATATGTTTTTTATAT
1 TATTATATACATATGTTTTTCATAT
28784869 CACATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (25 bp):
TATTATATACATATGTTTTTCATAT
Found at i:28785088 original size:21 final size:23
Alignment explanation
Indices: 28785064--28785116 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
28785054 TCTAATTACC
*
28785064 TATTTTTATATTA-TATTA-TAT
1 TATTTTTATACTACTATTAGTAT
28785085 TATTAGTTT-TACTACTATTAGTAT
1 TATT--TTTATACTACTATTAGTAT
28785109 TATTTTTA
1 TATTTTTA
28785117 GTTTCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 8 0.31
24 7 0.27
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (23 bp):
TATTTTTATACTACTATTAGTAT
Found at i:28787334 original size:14 final size:14
Alignment explanation
Indices: 28787315--28787349 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28787305 GAAACTGAAT
*
28787315 TTGAAAAATAGAAA
1 TTGAAAAACAGAAA
*
28787329 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
28787343 TTGAAAA
1 TTGAAAA
28787350 TACTGAGCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:28787388 original size:100 final size:100
Alignment explanation
Indices: 28787120--28787683 Score: 435
Period size: 88 Copynumber: 6.0 Consensus size: 100
28787110 AATTCTTTTA
* * * * * *
28787120 AAAAATAGACA-TT-AAAAGCAGAAATTGAAAATATCTCAGCATGTGAGCC-AATGCTCAACTCA
1 AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGC--GTG-CCCTGAGGCTCAACTCA
* * *
28787182 CTTCTCGCAATATGAGTTGGTTTTTGAAAAATATAAATTG
63 CCTCTCGCAATATGAGTTGATTTTTG--AAACATAAATTG
* *
28787222 --AAA-AGAAA---AAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCT
1 AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCT
*
28787281 CTCGCAATATGAGTTGATTTTTTTGAAAC-TGAATTTG
66 CTCGCAATATGAGTTGA--TTTTTGAAACAT-AAATTG
* *
28787318 AAAAATAGAAA-TTGAAAAGCAGAAATTGAAAATA-CTGAGCGTGCCCTGAGGCTCAACTCACCT
1 AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCT
*
28787381 CTTGCAATATGAGTTGATTTTTGAAACATAAATTG
66 CTCGCAATATGAGTTGATTTTTGAAACATAAATTG
* *
28787416 AAAAATAGAAA--T------------TTGAAAATACCTTAGCGTGTGACCTGAGGCTCAACTCAC
1 AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCAC
28787467 CTCTCGCAATATGAGTTGATTTTTGAAACATAAATTG
64 CTCTCGCAATATGAGTTGATTTTTGAAACATAAATTG
*
28787504 AAAAATAGAAA--T------------TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCAC
1 AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCAC
28787555 CTCTCGCAATATGAGTTGATTTTTGAAACATAAATTG
64 CTCTCGCAATATGAGTTGATTTTTGAAACATAAATTG
*
28787592 AAAAATAGAAA--T------------TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCAC
1 AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCAC
* *
28787643 CTCTAGCAATATGAGTTGATTTTTGAAACATGAATTG
64 CTCTCGCAATATGAGTTGATTTTTGAAACATAAATTG
28787680 AAAA
1 AAAA
28787684 TACCTTAACG
Statistics
Matches: 426, Mismatches: 22, Indels: 42
0.87 0.04 0.09
Matches are distributed among these distances:
85 9 0.02
86 5 0.01
88 233 0.55
95 3 0.01
96 40 0.09
97 1 0.00
98 60 0.14
99 10 0.02
100 46 0.11
101 19 0.04
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (100 bp):
AAAAATAGAAATTTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTTGAAACATAAATTG
Found at i:28787466 original size:88 final size:88
Alignment explanation
Indices: 28787326--28787683 Score: 616
Period size: 88 Copynumber: 4.1 Consensus size: 88
28787316 TGAAAAATAG
** * * *
28787326 AAATTGAAAAGCAGAAA-TTGAAAATA-CTGAGC--GTGCCCTGAGGCTCAACTCACCTCTTGCA
1 AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
28787387 ATATGAGTTGATTTTTGAAACAT
66 ATATGAGTTGATTTTTGAAACAT
*
28787410 AAATTGAAAAATAGAAATTTGAAAATACCTTAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
1 AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
28787475 ATATGAGTTGATTTTTGAAACAT
66 ATATGAGTTGATTTTTGAAACAT
28787498 AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
1 AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
28787563 ATATGAGTTGATTTTTGAAACAT
66 ATATGAGTTGATTTTTGAAACAT
*
28787586 AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTAGCA
1 AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
28787651 ATATGAGTTGATTTTTGAAACAT
66 ATATGAGTTGATTTTTGAAACAT
*
28787674 GAATTGAAAA
1 AAATTGAAAA
28787684 TACCTTAACG
Statistics
Matches: 262, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
84 15 0.06
85 9 0.03
86 5 0.02
88 233 0.89
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (88 bp):
AAATTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTGAAACAT
Found at i:28787757 original size:73 final size:74
Alignment explanation
Indices: 28787589--28787758 Score: 236
Period size: 73 Copynumber: 2.3 Consensus size: 74
28787579 GAAACATAAA
* *
28787589 TTGAAAAATAGAAATTTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTAGCAATA
1 TTGAAAAATAGAAA--TGAAAATACCTCAACGTGTGACCTGAGGCTCAACTCACCCCTAGCAATA
28787654 TGAGTTGATTT
64 TGAGTTGATTT
* * * * *
28787665 TTGAAACAT-GAATTGAAAATACCTTAACGTGTGACCTGAGGCTCAACTTACCCCTCGCAATATG
1 TTGAAAAATAGAAATGAAAATACCTCAACGTGTGACCTGAGGCTCAACTCACCCCTAGCAATATG
28787729 AGTTGATTT
66 AGTTGATTT
*
28787738 TT-AAAAATAGAAATAAAAATA
1 TTGAAAAATAGAAATGAAAATA
28787759 TCAGAATATC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 5 0.06
73 67 0.81
75 3 0.04
76 8 0.10
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (74 bp):
TTGAAAAATAGAAATGAAAATACCTCAACGTGTGACCTGAGGCTCAACTCACCCCTAGCAATATG
AGTTGATTT
Found at i:28799897 original size:11 final size:11
Alignment explanation
Indices: 28799881--28799911 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
28799871 GTAATGTTAA
28799881 AATATATACAT
1 AATATATACAT
28799892 AATATATACAT
1 AATATATACAT
28799903 ATATATATA
1 A-ATATATA
28799912 AAATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATATACAT
Found at i:28800047 original size:31 final size:30
Alignment explanation
Indices: 28800012--28800087 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
28800002 AATAATAGGT
28800012 ATAATAATAAATATAATGATATACGAA-AATA
1 ATAATAATAAATATAATG-TATAC-AAGAATA
*
28800043 ATAATATATATAAAAT-ATGTATACAAGAATA
1 ATAATA-ATA-AATATAATGTATACAAGAATA
*
28800074 ATAA-AATATATATA
1 ATAATAATAAATATA
28800088 CTAATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
28 3 0.08
29 3 0.08
30 3 0.08
31 19 0.50
32 6 0.16
33 4 0.11
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (30 bp):
ATAATAATAAATATAATGTATACAAGAATA
Found at i:28800252 original size:22 final size:24
Alignment explanation
Indices: 28800174--28800289 Score: 89
Period size: 24 Copynumber: 4.9 Consensus size: 24
28800164 ACATATACAT
* * *
28800174 ATAATAATGTTTAAGAATATATAC
1 ATAATAATATATAAAAATATATAC
* ** *
28800198 ATAA-GATGATATGGAAATATGTAC
1 ATAATAAT-ATATAAAAATATATAC
28800222 ATGGAATAATATATAAAAATATA-AC
1 AT--AATAATATATAAAAATATATAC
*
28800247 -TAATAATAT-TGAAAATATATAC
1 ATAATAATATATAAAAATATATAC
28800269 ATAAT-ATATATAAAACATATA
1 ATAATAATATATAAAA-ATATA
28800290 CGATATATAC
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
21 9 0.13
22 14 0.20
23 10 0.14
24 22 0.31
25 2 0.03
26 12 0.17
27 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (24 bp):
ATAATAATATATAAAAATATATAC
Found at i:28800272 original size:20 final size:21
Alignment explanation
Indices: 28800226--28800283 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
28800216 ATGTACATGG
28800226 AATAATATATAAAAATATAAC
1 AATAATATATAAAAATATAAC
*
28800247 TAATAATAT-TGAAAATATATAC
1 -AATAATATATAAAAATATA-AC
28800269 -ATAATATATATAAAA
1 AATAATATATA-AAAA
28800284 CATATACGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 7 0.23
21 10 0.32
22 14 0.45
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAATATATAAAAATATAAC
Found at i:28800290 original size:22 final size:21
Alignment explanation
Indices: 28800230--28800304 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 21
28800220 ACATGGAATA
28800230 ATATATAAAAATATA-ACTAAT
1 ATATATAAAAATATACA-TAAT
28800251 A-ATATTGAAAATATATACATAAT
1 ATATA-T-AAAA-ATATACATAAT
28800274 ATATATAAAACATATACGATATAT
1 ATATATAAAA-ATATAC-ATA-AT
*
28800298 ACATATA
1 ATATATA
28800305 CATTAGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.07
21 2 0.04
22 14 0.31
23 14 0.31
24 12 0.27
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
ATATATAAAAATATACATAAT
Found at i:28800441 original size:2 final size:2
Alignment explanation
Indices: 28800436--28800472 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28800426 CAACATAAAA
28800436 AT 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 AT A
28800473 AAATGTAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28800742 original size:2 final size:2
Alignment explanation
Indices: 28800735--28800764 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28800725 ATAGAATAAA
28800735 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
28800765 CACATGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28805112 original size:46 final size:45
Alignment explanation
Indices: 28805061--28805151 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 45
28805051 ATAAAGTTAG
28805061 GACATATTAGATGGCTGAA-CTAATTAGAACACATTAATTAACTTAA
1 GACATATTA-ATGGCTGAATCTAATTAGAACACATTAATT-ACTTAA
*
28805107 GACATATTAATTGCTGAATCTAATTAGAACACATTAATTACTTAA
1 GACATATTAATGGCTGAATCTAATTAGAACACATTAATTACTTAA
28805152 ACTAAAGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
45 14 0.33
46 29 0.67
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (45 bp):
GACATATTAATGGCTGAATCTAATTAGAACACATTAATTACTTAA
Found at i:28810963 original size:48 final size:48
Alignment explanation
Indices: 28810891--28811020 Score: 197
Period size: 48 Copynumber: 2.7 Consensus size: 48
28810881 ACAATGCCTC
* * * * *
28810891 ATGCAGATGCCAAGTCCCAAACATGGTCTTACACTGGCTTACATAACG
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACA
*
28810939 ATGCCGATGCCATGTCTCAGACATGGTCTTACACTGGCTCACATAACA
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACA
*
28810987 ATGCCGATGCCATGTCCCAGATATGGTCTTACAC
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACAC
28811021 GGTTCCACAT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (48 bp):
ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACA
Found at i:28814444 original size:18 final size:18
Alignment explanation
Indices: 28814414--28814506 Score: 68
Period size: 18 Copynumber: 5.2 Consensus size: 18
28814404 TTTTGCTTTA
*
28814414 TTTTTCTCACTTTTTCCT
1 TTTTTCTCTCTTTTTCCT
* * *
28814432 TTTTTTTTTCTTTTTCAT
1 TTTTTCTCTCTTTTTCCT
* *
28814450 TCTTTCTCTCTTGTT-C-
1 TTTTTCTCTCTTTTTCCT
28814466 TTTTTCAT-TCTTTTTCTCT
1 TTTTTC-TCTCTTTTTC-CT
28814485 TGTTCTT-TCTCTTTTTCCT
1 T-TT-TTCTCTCTTTTTCCT
28814504 TTT
1 TTT
28814507 CTACAGATTG
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
16 11 0.19
17 1 0.02
18 28 0.49
19 5 0.09
20 10 0.18
21 2 0.04
ACGTcount: A:0.03, C:0.23, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTCTCTCTTTTTCCT
Found at i:28814466 original size:24 final size:24
Alignment explanation
Indices: 28814439--28814492 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
28814429 CCTTTTTTTT
28814439 TTCTTTTTCATTCTTTCTCTCTTG
1 TTCTTTTTCATTCTTTCTCTCTTG
*
28814463 TTCTTTTTCATTCTTTTTCTCTTG
1 TTCTTTTTCATTCTTTCTCTCTTG
28814487 TTCTTT
1 TTCTTT
28814493 CTCTTTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (24 bp):
TTCTTTTTCATTCTTTCTCTCTTG
Found at i:28816636 original size:9 final size:10
Alignment explanation
Indices: 28816607--28816634 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28816597 CTTTTTCATG
28816607 AATTTTTTTA
1 AATTTTTTTA
28816617 AATTTTTTTA
1 AATTTTTTTA
28816627 AATTTTTT
1 AATTTTTT
28816635 AATTTCAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:28817894 original size:46 final size:45
Alignment explanation
Indices: 28817840--28817929 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 45
28817830 TAAACTTAGG
** *
28817840 ACATATTAAATGGTTGAA-CTAATTAGAACACATTAATTAACTTAAT
1 ACATATT-AATGACTGAATCTAATTAGAACACATTAAAT-ACTTAAT
* *
28817886 ACATATTAATTACTGAATTTAATTAGAACACATTAAATACTTAA
1 ACATATTAATGACTGAATCTAATTAGAACACATTAAATACTTAA
28817930 AAAAGTAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 13 0.34
46 25 0.66
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (45 bp):
ACATATTAATGACTGAATCTAATTAGAACACATTAAATACTTAAT
Found at i:28819080 original size:22 final size:22
Alignment explanation
Indices: 28819055--28819100 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28819045 AAAGAATGAG
28819055 TAATCTCCACACCAAATGTTCA
1 TAATCTCCACACCAAATGTTCA
*
28819077 TAATCTCCATACCAAATGTTCA
1 TAATCTCCACACCAAATGTTCA
28819099 TA
1 TA
28819101 CAACCAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.30
Consensus pattern (22 bp):
TAATCTCCACACCAAATGTTCA
Found at i:28820062 original size:24 final size:24
Alignment explanation
Indices: 28820010--28820062 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
28820000 TATAAACTTG
*
28820010 AATAACAACATCAATTAACTAATT
1 AATATCAACATCAATTAACTAATT
28820034 AATATCAACATCAATTAACTAATT
1 AATATCAACATCAATTAACTAATT
28820058 AATAT
1 AATAT
28820063 ATTTATTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (24 bp):
AATATCAACATCAATTAACTAATT
Found at i:28824018 original size:46 final size:46
Alignment explanation
Indices: 28823968--28824143 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
28823958 TGGTTGAGCA
28823968 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
28824014 TCCGAACTTGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
28824059 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
28824107 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28824144 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.06
46 59 0.54
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28824124 original size:93 final size:93
Alignment explanation
Indices: 28823965--28824135 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28823955 GGATGGTTGA
* *
28823965 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCCAACTCGTTGAGT
28824030 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
28824058 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCCAA-CTCGTTGAG
28824122 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
28824136 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 4 0.05
93 71 0.95
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:28828761 original size:2 final size:2
Alignment explanation
Indices: 28828754--28828781 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28828744 TTAAAATGTA
28828754 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
28828782 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28831014 original size:407 final size:405
Alignment explanation
Indices: 28830354--28831572 Score: 1598
Period size: 407 Copynumber: 3.0 Consensus size: 405
28830344 TCCAGTGGGC
* * * * *
28830354 ATTGTGTCACTACTTGTGGCAAAATTAGATGGGACAACATGTGTTGTTTCCCCAAAATACAATCT
1 ATTGTGTCACTACTTGTGGCAAAATTAGATAGGTCACCATGTGTTGTTTCCCAAAAACACAATCT
* * * * *
28830419 CTACAAGGTCTAGTCACAACACTTTTGGGTTTCGAAAGTCTTCTAATTGCATCGTATTGATCAAG
66 CTACAAGGTTTGGTCACAACACTTTTGAGTTTTGAAAGTCTTCTAATTGCATCATATTGATCAAG
* * * * ** * * *
28830484 TCTTTGTAAGTATCGATAGTCCACATCGCCTGTCTTTTGAGGTAACACCTCTAGATCTTTTATAG
131 TCTTTGTAAGTTTCGATAATTCACATCACCAAT-TTTTGATGTCACACCTCTAGATCTTGTATAG
* * **
28830549 TAATTTTATTGCAAATAACTTCATTAAAAACTTTGTAACAATTTTC-AATTTATTTTGCTCCTCT
195 TAGTTTTATTGCAAATAACTTCATTAAAAACTTTGTAGCAATTTTCAAAAAT-TTTTGCTCCTCT
* *
28830613 TATTATAA-ATTTTTTTTCATTAATTACATCACAGTTATTTTTGTTAAATCTCATATTAAGCCTT
259 TATTATAACAATTTTTTTCATTAATTACATCACA-CTATTTTTGTTAAATCTCATATTAAGCCTT
* *
28830677 TGGTCACATAGTTGACTTATGCTTATTACGTTAGTTTTCAAACCCTATACAAGTAAATACATTAT
323 TGGTCACATAGTTGACTTATGCTTATTACGTTAGTTTTCAATCCCTATACAAGT-AATACATTTT
28830742 CAAGGTCAAGAAAATCTTTA
387 CAAGGTCAAGAAAA-CTTTA
* *
28830762 ATTGTGTCACAACTAGTGGCAAAATTAGATAGGTCACCATGTGTTGTTTCCCAAAAACACAATCT
1 ATTGTGTCACTACTTGTGGCAAAATTAGATAGGTCACCATGTGTTGTTTCCCAAAAACACAATCT
* * * ** * *
28830827 CCATAAGGTTTGGTCACAATACTTTTGAGTTTTGAAAGTCTTCTAATTATAT-TTATTGATGAAG
66 CTACAAGGTTTGGTCACAACACTTTTGAGTTTTGAAAGTCTTCTAATTGCATCATATTGATCAAG
*
28830891 TCTTTGTAAGTTTCGATAATTCACATCACCAATTTGTTGATGTCACACCTTTAGATCTTGTATAG
131 TCTTTGTAAGTTTCGATAATTCACATCACCAATTT-TTGATGTCACACCTCTAGATCTTGTATAG
* * *
28830956 TAGCTTTGTTACAAATAACTTCATTAAAAACTTTGTAGCAATTTTCAAAAATTTTTGCTCCTCTT
195 TAGTTTTATTGCAAATAACTTCATTAAAAACTTTGTAGCAATTTTCAAAAATTTTTGCTCCTCTT
* * * * *
28831021 ATTATAACAATTCTTTTGATTAATTACATCTCCACTAATTTTGTTAAATATCATATTAAGCCTTT
260 ATTATAACAATTTTTTTCATTAATTACATC-ACACTATTTTTGTTAAATCTCATATTAAGCCTTT
* * * * *
28831086 AGTCATATAGTTGACTTATGCTTATTAAGTTAGTTTTCAATCCCTATATAAGTAATATATTTTCA
324 GGTCACATAGTTGACTTATGCTTATTACGTTAGTTTTCAATCCCTATACAAGTAATACATTTTCA
28831151 AGGTCAAGAAAACATTTA
389 AGGTCAAGAAAAC-TTTA
* *
28831169 ATTGTGTCACTACTTGTGGCAAAATTAGATTGGTCACCATGTGTTGTCT-CCACAAAACACAATC
1 ATTGTGTCACTACTTGTGGCAAAATTAGATAGGTCACCATGTGTTGTTTCCCA-AAAACACAATC
*
28831233 TCTACAAAGTTTGGTCACAACACTTTTGAGTTTTGAAAGTCTTCTAATTGCATCATATTGATCAA
65 TCTACAAGGTTTGGTCACAACACTTTTGAGTTTTGAAAGTCTTCTAATTGCATCATATTGATCAA
* * * * ** *
28831298 ------GTAAGTTTCAATAATTCACACCACCAAACTTTCGATGTCACAAATCTAGATCTTGCATA
130 GTCTTTGTAAGTTTCGATAATTCACATCACC-AATTTTTGATGTCACACCTCTAGATCTTGTATA
* * * *
28831357 GTAGTTTTATTGCAAATAACTTCATTAAAAACTTTGTAGTAATTGTCAAAAGTTTTTGCTCCTTT
194 GTAGTTTTATTGCAAATAACTTCATTAAAAACTTTGTAGCAATTTTCAAAAATTTTTGCTCCTCT
*
28831422 TATTATAACAATTTTTTTCATTAATTACATCACAACTATTTTTGTTAAATCAT-ATATTAAGTCT
259 TATTATAACAATTTTTTTCATTAATTACATCAC-ACTATTTTTGTTAAATC-TCATATTAAGCCT
* * *
28831486 TTGGCCACAT-GCTTGACTTATGCTTATTACGTTAGTTTTCAATCCTTGTACAAGTAATACATTT
322 TTGGTCACATAG-TTGACTTATGCTTATTACGTTAGTTTTCAATCCCTATACAAGTAATACATTT
* *
28831550 TCGAGTTCAAGAAAAACTTTA
386 TCAAGGTCAAG-AAAACTTTA
28831571 AT
1 AT
28831573 AAAGTGTACA
Statistics
Matches: 707, Mismatches: 92, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
401 2 0.00
402 227 0.32
403 10 0.01
406 6 0.01
407 252 0.36
408 208 0.29
409 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (405 bp):
ATTGTGTCACTACTTGTGGCAAAATTAGATAGGTCACCATGTGTTGTTTCCCAAAAACACAATCT
CTACAAGGTTTGGTCACAACACTTTTGAGTTTTGAAAGTCTTCTAATTGCATCATATTGATCAAG
TCTTTGTAAGTTTCGATAATTCACATCACCAATTTTTGATGTCACACCTCTAGATCTTGTATAGT
AGTTTTATTGCAAATAACTTCATTAAAAACTTTGTAGCAATTTTCAAAAATTTTTGCTCCTCTTA
TTATAACAATTTTTTTCATTAATTACATCACACTATTTTTGTTAAATCTCATATTAAGCCTTTGG
TCACATAGTTGACTTATGCTTATTACGTTAGTTTTCAATCCCTATACAAGTAATACATTTTCAAG
GTCAAGAAAACTTTA
Found at i:28834669 original size:39 final size:39
Alignment explanation
Indices: 28834610--28834881 Score: 454
Period size: 39 Copynumber: 7.0 Consensus size: 39
28834600 AAGACACTGA
*
28834610 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* * *
28834649 AAATATATCCAGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* *
28834688 AAATATATCCGGGCCAAAGTCGCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
** *
28834727 AAATGTATCCGAACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
28834766 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
*
28834805 AAATGTATCCGGGCCAAAGTCCCGTAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
28834844 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTG
1 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTG
28834882 ATAATATAAT
Statistics
Matches: 218, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 218 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.22
Consensus pattern (39 bp):
AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:28839859 original size:24 final size:23
Alignment explanation
Indices: 28839830--28839920 Score: 67
Period size: 24 Copynumber: 3.7 Consensus size: 23
28839820 ATATAGTATT
*
28839830 TAAAAATATATACATAAGATGGTA
1 TAAAAATATATACATAAAAT-GTA
* *
28839854 TAAAAACATGTACATGAAAATGTA
1 TAAAAATATATACAT-AAAATGTA
* * *
28839878 TAAGAA-ATATACATAATTAGTAATA
1 TAAAAATATATACATAA--AAT-GTA
28839903 TTAAAAATATATACATAA
1 -TAAAAATATATACATAA
28839921 CATACATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
22 2 0.04
23 7 0.13
24 23 0.43
25 6 0.11
26 5 0.09
27 10 0.19
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
TAAAAATATATACATAAAATGTA
Found at i:28840018 original size:16 final size:17
Alignment explanation
Indices: 28839987--28840021 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28839977 AACTACTTTG
28839987 TACACTACACAAATATA
1 TACACTACACAAATATA
*
28840004 TACAC-ACACACATATA
1 TACACTACACAAATATA
28840020 TA
1 TA
28840022 TACATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (17 bp):
TACACTACACAAATATA
Found at i:28840020 original size:18 final size:19
Alignment explanation
Indices: 28839988--28840025 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28839978 ACTACTTTGT
28839988 ACACTACACAAATATATAC
1 ACACTACACAAATATATAC
*
28840007 ACAC-ACACATATATATAC
1 ACACTACACAAATATATAC
28840025 A
1 A
28840026 TATATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (19 bp):
ACACTACACAAATATATAC
Found at i:28840052 original size:21 final size:22
Alignment explanation
Indices: 28840027--28840138 Score: 108
Period size: 21 Copynumber: 5.2 Consensus size: 22
28840017 ATATATACAT
* *
28840027 ATATA-AATAATAGTATTAGAA
1 ATATACAATAATAATATTAAAA
*
28840048 ATATACAAT-ATAATATTATAA
1 ATATACAATAATAATATTAAAA
* *
28840069 ATATACATATAATAGTATAAAAA
1 ATATACA-ATAATAATATTAAAA
*
28840092 ATATATAACTAATAATATT-AAA
1 ATATACAA-TAATAATATTAAAA
*
28840114 ATATATAATAAT-ATA-TAAAA
1 ATATACAATAATAATATTAAAA
28840134 ATATA
1 ATATA
28840139 ATATTGAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
19 1 0.01
20 11 0.14
21 26 0.33
22 17 0.22
23 23 0.29
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (22 bp):
ATATACAATAATAATATTAAAA
Found at i:28840081 original size:44 final size:45
Alignment explanation
Indices: 28840015--28840138 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 45
28840005 ACACACACAC
* *
28840015 ATATATATACATATATAAATAATAGTATTAGAAATATACAA-T-ATA
1 ATAT-TATAAATATAT-AATAATAGTATTAAAAATATACAACTAATA
* * *
28840060 ATATTATAAATATACATATAATAGTATAAAAAATATATAACTAATA
1 ATATTATAAATATATA-ATAATAGTATTAAAAATATACAACTAATA
28840106 ATATTA-AAATATATAATAATA-TA-TAAAAATATA
1 ATATTATAAATATATAATAATAGTATTAAAAATATA
28840139 ATATTGAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
42 9 0.13
43 3 0.04
44 35 0.51
45 13 0.19
46 9 0.13
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (45 bp):
ATATTATAAATATATAATAATAGTATTAAAAATATACAACTAATA
Found at i:28840122 original size:18 final size:18
Alignment explanation
Indices: 28840075--28840141 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
28840065 ATAAATATAC
* *
28840075 ATATAATAGTATAAAAAA
1 ATATAATAATATATAAAA
28840093 TATATAACTAATAATATTAAAA
1 -ATATAA-TAAT-ATA-TAAAA
28840115 TATATAATAATATATAAAA
1 -ATATAATAATATATAAAA
28840134 ATATAATA
1 ATATAATA
28840142 TTGAAAACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 6 0.14
21 7 0.16
22 11 0.26
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
ATATAATAATATATAAAA
Found at i:28840123 original size:15 final size:15
Alignment explanation
Indices: 28840103--28840159 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
28840093 TATATAACTA
*
28840103 ATAATATTAAAATAT
1 ATAATATTAAAAAAT
28840118 ATAATAATATATAAAAAT
1 ATAAT-AT-TA-AAAAAT
*
28840136 ATAATATTGAAAACAT
1 ATAATATT-AAAAAAT
28840152 ATATATAT
1 ATA-ATAT
28840160 ATATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 5 0.14
16 11 0.31
17 9 0.26
18 10 0.29
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAATATTAAAAAAT
Found at i:28840137 original size:8 final size:9
Alignment explanation
Indices: 28840084--28840189 Score: 56
Period size: 9 Copynumber: 10.8 Consensus size: 9
28840074 CATATAATAG
*
28840084 TATAAAAAA
1 TATATAAAA
28840093 TATATAACTAA
1 TATATAA--AA
28840104 TAATATTAAAA
1 T-ATA-TAAAA
28840115 TATATAATAA
1 TATATAA-AA
28840125 TATATAAAA
1 TATATAAAA
*
28840134 -ATATAATA
1 TATATAAAA
28840142 T-TGA-AAACA
1 TAT-ATAAA-A
28840151 TATATATATATA
1 TATATA-A-A-A
*
28840163 TATATAACA
1 TATATAAAA
28840172 TATATGAAGAA
1 TATAT-AA-AA
28840183 TATATAA
1 TATATAA
28840190 TATAATATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
8 10 0.13
9 21 0.27
10 18 0.23
11 14 0.18
12 11 0.14
13 3 0.04
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
TATATAAAA
Found at i:28840250 original size:3 final size:3
Alignment explanation
Indices: 28840242--28840544 Score: 57
Period size: 3 Copynumber: 100.7 Consensus size: 3
28840232 AAATAACGAC
* * *
28840242 TAA TAA TAA TAA TAA TAT TAA AAA TAA TAA TGA -AA TATA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * *
28840286 -AA CAA -ATA TAA T-A TAA TAG TAA TAT TAA -AA TAA -AG TAA TTAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* * * *
28840328 -AA TAG TAG TAC T-A TATA TAA AAA TATA TACA TACA TATA TAA T-A
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TA-A TA-A TA-A TAA TAA
* *
28840372 TACA TACA CTAA TAT TAA TAA TAA TAA TAA -AA CTGGA -AA TAA TAA
1 TA-A TA-A -TAA TAA TAA TAA TAA TAA TAA TAA -T-AA TAA TAA TAA
* * * * * **
28840417 TAA TTAG TAA TTA TAA TACG TTA GAA -AA TAA TTAA T-A TGT TAA TAA
1 TAA -TAA TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* * * * *
28840463 AAA TAA TAG TAA TGAA -AA TAA TAC TAA CAG TAA TAA TAA -AGA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * *
28840508 TAA TAGA -AA TAA -AA TAA TAG TAA TGA TAT TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28840545 TGTAAAAAAA
Statistics
Matches: 217, Mismatches: 51, Indels: 64
0.65 0.15 0.19
Matches are distributed among these distances:
2 29 0.13
3 146 0.67
4 39 0.18
5 3 0.01
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28842828 original size:29 final size:30
Alignment explanation
Indices: 28842765--28842839 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
28842755 AGATTTCAAT
28842765 TTAATTA-A-AAA-ATAATTTTTTATAAAA
1 TTAATTATATAAATATAATTTTTTATAAAA
* * *
28842792 TTAATTATATTATTATAATTTTTT-TTAAA
1 TTAATTATATAAATATAATTTTTTATAAAA
**
28842821 TTTTTTATATAAATATAAT
1 TTAATTATATAAATATAAT
28842840 ATAAATCCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 7 0.18
28 1 0.03
29 20 0.53
30 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTAATTATATAAATATAATTTTTTATAAAA
Found at i:28845839 original size:13 final size:13
Alignment explanation
Indices: 28845821--28845846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28845811 AAATTTTTTC
28845821 CTTATAAAAATTT
1 CTTATAAAAATTT
28845834 CTTATAAAAATTT
1 CTTATAAAAATTT
28845847 TGTAAAATTT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
CTTATAAAAATTT
Found at i:28854497 original size:2 final size:2
Alignment explanation
Indices: 28854490--28854516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28854480 AAATAAATAA
28854490 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 A
28854517 CTTAAATAGC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28854649 original size:36 final size:36
Alignment explanation
Indices: 28854579--28854649 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
28854569 ATAATAAAAT
** * *
28854579 TAACAATAAAATAATAATTATACAATATTTAAATAA
1 TAACAATAAAATAATAACAATACAATAGTGAAATAA
* *
28854615 TAACAATAAAATAATACCAATATAATAGTGAAATA
1 TAACAATAAAATAATAACAATACAATAGTGAAATA
28854650 GTAGCAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (36 bp):
TAACAATAAAATAATAACAATACAATAGTGAAATAA
Found at i:28855841 original size:16 final size:16
Alignment explanation
Indices: 28855820--28855857 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28855810 TTTGGTTCGC
*
28855820 TGTAATGGAATAGAGT
1 TGTAATGAAATAGAGT
*
28855836 TGTAATGAAATAGGGT
1 TGTAATGAAATAGAGT
28855852 TGTAAT
1 TGTAAT
28855858 CAGTAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (16 bp):
TGTAATGAAATAGAGT
Found at i:28856090 original size:23 final size:22
Alignment explanation
Indices: 28856043--28856155 Score: 88
Period size: 23 Copynumber: 5.0 Consensus size: 22
28856033 AAGATTACTA
*
28856043 TTAA-AAATAATTTAATA-AAA
1 TTAATAAATAATTTAATATAAT
* *
28856063 ATAATAAATAATTTAATCATATT
1 TTAATAAATAATTTAAT-ATAAT
* *
28856086 TTAATATTATTATTTAATATAAT
1 TTAATA-AATAATTTAATATAAT
* *
28856109 TTAATAAAAAATAATATATATAAT
1 TTAATAAATAAT-TTA-ATATAAT
*
28856133 TTAAT-AATATTTTTAATATAAT
1 TTAATAAATA-ATTTAATATAAT
28856155 T
1 T
28856156 ATTTTTATAT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
20 3 0.04
21 12 0.17
22 12 0.17
23 23 0.32
24 22 0.31
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATAAATAATTTAATATAAT
Found at i:28856133 original size:58 final size:56
Alignment explanation
Indices: 28856049--28856159 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 56
28856039 ACTATTAAAA
* *
28856049 ATAATTTAATAAAAATAATAAATAATTTAATCATA-TTTTAATATTATTATTTAAT
1 ATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAATATAATTATTTAAT
28856104 ATAATTTAATAAAAAATAATATATATAATTTAATAATATTTTTAATATAATTATTT
1 ATAATTTAAT-AAAAATAATA-A-ATAATTTAATAATATTTTTAATATAATTATTT
28856160 TTATATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
55 10 0.20
56 10 0.20
57 1 0.02
58 13 0.26
59 16 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (56 bp):
ATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAATATAATTATTTAAT
Found at i:28856149 original size:17 final size:17
Alignment explanation
Indices: 28856118--28856176 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
28856108 TTTAATAAAA
* *
28856118 AATAATATATATAATTT
1 AATAATATTTTTAATTT
*
28856135 AATAATATTTTTAATAT
1 AATAATATTTTTAATTT
*
28856152 AAT--TATTTTTATATTA
1 AATAATATTTTTA-ATTT
*
28856168 AATTATATT
1 AATAATATT
28856177 AAAATATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 8 0.24
16 5 0.15
17 17 0.50
18 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATAATATTTTTAATTT
Found at i:28859161 original size:22 final size:22
Alignment explanation
Indices: 28859136--28859180 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28859126 AGCGTTTTGG
**
28859136 ACAAGAATCTGGTTTATATACA
1 ACAAGAATCACGTTTATATACA
28859158 ACAAGAATCACGTTTATATACA
1 ACAAGAATCACGTTTATATACA
28859180 A
1 A
28859181 TATTAAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (22 bp):
ACAAGAATCACGTTTATATACA
Found at i:28866755 original size:47 final size:46
Alignment explanation
Indices: 28866599--28866960 Score: 264
Period size: 47 Copynumber: 7.7 Consensus size: 46
28866589 GGATATATTA
* * *
28866599 CCGATGCCATGTCCCTGACATGGTCTTACACTGGC--TCTCATATACGCGTG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTC-TGTA--AG-G
* * *
28866649 CTGATGCATGTCCCAGACATGTCTTACACTAGCACAAT-TCT-T-A-G
1 CCGATGCATGTCCCAGACATGTCTTACACT-G-GCTATCTCTGTAAGG
* *
28866693 CCGATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTGTCAAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGT-AAGG
* *
28866740 CCGATGCATGTCCCAGATATGTTTTACACTGGCACTCATCTCTGT---G
1 CCGATGCATGTCCCAGACATGTCTTACACTGG--CT-ATCTCTGTAAGG
* *
28866786 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-AGTATGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATC-TCTGTAAGG
* * ** * *
28866834 CTGATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTG-GATG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTATC-TCTGTAAGG
* *
28866880 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAATATGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTC-T-GTAAGG
*
28866928 CCGAAGCATGTCCCAGACATGTCTTACACTGGC
1 CCGATGCATGTCCCAGACATGTCTTACACTGGC
28866961 ACTCAAATCA
Statistics
Matches: 256, Mismatches: 32, Indels: 52
0.75 0.09 0.15
Matches are distributed among these distances:
42 3 0.01
43 4 0.02
44 29 0.11
45 7 0.03
46 48 0.19
47 85 0.33
48 45 0.18
49 17 0.07
50 15 0.06
51 2 0.01
52 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (46 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGTAAGG
Found at i:28866846 original size:94 final size:94
Alignment explanation
Indices: 28866599--28866965 Score: 435
Period size: 94 Copynumber: 3.9 Consensus size: 94
28866589 GGATATATTA
* * * *
28866599 CCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTCATA-TACGCGTGCTGATGCATGTCCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTA--TG-GCCGATGCATGTCCC
*
28866663 AGACATGTCTTACACTAGCAC-AAT-TCT-TAG
63 AGACATGTCTTACACTAGCACTCATCTCTGT-G
* * * *
28866693 CCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATC-TCTGTCAAGGCCGATGCATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-AGT-ATGGCCGATGCATGTCCCA
* * *
28866755 GATATGTTTTACACTGGCACTCATCTCTGTG
64 GACATGTCTTACACTAGCACTCATCTCTGTG
*
28866786 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCCGATGCATGTCCCAGA
* * *
28866851 CATGTCTTACACTAGCCCTCGTCT-GGATG
66 CATGTCTTACACTAGCACTCATCTCTG-TG
* * *
28866880 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCCGAAGCATGTCCCAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCCGATGCATGTCCCAGA
*
28866945 CATGTCTTACACTGGCACTCA
66 CATGTCTTACACTAGCACTCA
28866966 AATCACCCAA
Statistics
Matches: 234, Mismatches: 29, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
91 33 0.14
92 19 0.08
93 23 0.10
94 139 0.59
95 19 0.08
96 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (94 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCCGATGCATGTCCCAGA
CATGTCTTACACTAGCACTCATCTCTGTG
Found at i:28866858 original size:141 final size:138
Alignment explanation
Indices: 28866599--28866962 Score: 414
Period size: 141 Copynumber: 2.6 Consensus size: 138
28866589 GGATATATTA
* * *
28866599 CCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTCATATACGCGTGCTGATGCATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT-C-TGTGCCGATGCATGTCCCA
* * * * * *
28866664 GACATGTCTTACACTAGCACAATTCTTAGCCGATGCGTGTCCCAGACACGTCTTACACTGGCTAT
64 GACATGTCTTACACTGGCACAAGTCATAGCCGATGCATGTCCCAGACACGTCTTACACTAGCCAT
28866729 C-TCTGTCAAGG
129 CGTCTG--AAGG
* * * *
28866740 CCGATG-CATGTCCCAGATAT-GTTTTACACTGGCACTCATCTCTGTGCCGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCTGTGCCGATG-CATGTCCCAG
* * *
28866803 ACATGGTCTTACACTGGCTATCATAGT-ATGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
65 ACAT-GTCTTACACTGGC-A-CA-AGTCATAGCCGATGCATGTCCCAGACACGTCTTACACTAGC
* * *
28866867 CCTCGTCTGGATG
126 CATCGTCTGAAGG
* *
28866880 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATG-GCCGAAGCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCTGTGCCGATGCATGTCCCAG
28866944 ACATGTCTTACACTGGCAC
65 ACATGTCTTACACTGGCAC
28866963 TCAAATCACC
Statistics
Matches: 189, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
137 8 0.04
138 16 0.08
139 31 0.16
140 34 0.18
141 68 0.36
142 29 0.15
143 3 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (138 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCTGTGCCGATGCATGTCCCAGA
CATGTCTTACACTGGCACAAGTCATAGCCGATGCATGTCCCAGACACGTCTTACACTAGCCATCG
TCTGAAGG
Found at i:28867341 original size:30 final size:30
Alignment explanation
Indices: 28867300--28867357 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
28867290 AAATTTGCAT
* *
28867300 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTACCCCTAGA
28867330 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
28867358 TTTTCGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGA
Found at i:28868610 original size:15 final size:16
Alignment explanation
Indices: 28868582--28868616 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
28868572 AATGATCAGT
28868582 AAAAAATTACTAAAAC
1 AAAAAATTACTAAAAC
*
28868598 AAAAAATT-GTAAAAC
1 AAAAAATTACTAAAAC
28868613 AAAA
1 AAAA
28868617 TTAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAAATTACTAAAAC
Found at i:28882190 original size:16 final size:17
Alignment explanation
Indices: 28882164--28882208 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
28882154 GTTTAACTGG
* *
28882164 TTTAGTTATTTGTTTAT
1 TTTAGTTATTTATGTAT
28882181 TTTA-TTATTTATGTAT
1 TTTAGTTATTTATGTAT
28882197 TTTAGTTATTTA
1 TTTAGTTATTTA
28882209 GATTATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (17 bp):
TTTAGTTATTTATGTAT
Found at i:28886656 original size:46 final size:45
Alignment explanation
Indices: 28886606--28886778 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
28886596 TGGTTGAGCA
*
28886606 TCCGAACTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA-G
* * *
28886652 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A-G
* * *
28886697 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAC
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAG
* *
28886744 ACCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
28886779 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 8 0.08
46 55 0.52
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAG
Found at i:28886762 original size:93 final size:93
Alignment explanation
Indices: 28886603--28886773 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
28886593 GGATGGTTGA
** *
28886603 GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCAAATCACCCAACTCGTTGAGT
28886668 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
28886696 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAA-CACCCAAGCTCGTTGAG
1 GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCAAATCACCCAA-CTCGTTGAG
28886760 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
28886774 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 4 0.06
93 67 0.94
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCAAATCACCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28887040 original size:19 final size:20
Alignment explanation
Indices: 28887003--28887040 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28886993 ATAAGGTGGT
28887003 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28887023 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28887041 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28888390 original size:13 final size:13
Alignment explanation
Indices: 28888372--28888396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28888362 TTGAATAAAA
28888372 GGTAAAAGTGTAG
1 GGTAAAAGTGTAG
28888385 GGTAAAAGTGTA
1 GGTAAAAGTGTA
28888397 AAATGTTGAT
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:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (13 bp):
GGTAAAAGTGTAG
Found at i:28895322 original size:18 final size:19
Alignment explanation
Indices: 28895284--28895322 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28895274 GTGACACCTG
* *
28895284 TTTCCCAAATTTTCATGTT
1 TTTCCAAAATTTTCATATT
28895303 TTTCCAAAATTTTC-TATT
1 TTTCCAAAATTTTCATATT
28895321 TT
1 TT
28895323 ATTTCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTCCAAAATTTTCATATT
Found at i:28904881 original size:40 final size:40
Alignment explanation
Indices: 28904824--28905049 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
28904814 CTAACGGGGT
* * *
28904824 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGC
* *
28904864 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTTCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGC
*
28904904 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGC
* * * *
28904944 TAAGTCTCGAAGGCACTTGTGCGAGTG-GTTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGC
* *
28904984 TAAGTCCCGAAGGCATTTGTGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGC
* * *
28905024 TAAGACCCGATGGC-CTTGTGCGAGTG
1 TAAGTCCCGAAGGCATTTGTGCGAGTG
28905050 GTTATATCCG
Statistics
Matches: 164, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
39 13 0.08
40 151 0.92
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGC
Found at i:28922520 original size:28 final size:28
Alignment explanation
Indices: 28922487--28922544 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
28922477 ACCACCTCAA
28922487 GAAAAATTTTGATGATTTCTCCTTATTG
1 GAAAAATTTTGATGATTTCTCCTTATTG
28922515 GAAAAATTTTGATGATTTCTCCTTATTG
1 GAAAAATTTTGATGATTTCTCCTTATTG
28922543 GA
1 GA
28922545 TTATAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (28 bp):
GAAAAATTTTGATGATTTCTCCTTATTG
Found at i:28925851 original size:26 final size:26
Alignment explanation
Indices: 28925782--28925851 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
28925772 TCATCCCAAT
*
28925782 TTTACCCTTGGTAAAATAATGACAAC
1 TTTACCCTTGGTAAAATTATGACAAC
*
28925808 TTTACCCCTGGTAAAATTATGACAAC
1 TTTACCCTTGGTAAAATTATGACAAC
*
28925834 TTTACCCTTGATAAAATT
1 TTTACCCTTGGTAAAATT
28925852 TTTGAGACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (26 bp):
TTTACCCTTGGTAAAATTATGACAAC
Found at i:28926025 original size:6 final size:6
Alignment explanation
Indices: 28926000--28926056 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
28925990 TCTAAATGAA
* *
28926000 TTCATT TCTCATT TTTATT TTCATT TTCATT TTCA-T TTCTTTT TTCATT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTC-ATT TTCATT
*
28926049 TTAATT TT
1 TTCATT TT
28926057 TAGAAAACCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 4 0.09
6 29 0.67
7 10 0.23
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (6 bp):
TTCATT
Found at i:28933005 original size:5 final size:5
Alignment explanation
Indices: 28932995--28933031 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
28932985 AATAATCAGA
*
28932995 AAAAT AAAAT AAAAT AAAAAT AAAAG AAAAT AAAAT A
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT A
28933032 GACTCAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:28933015 original size:16 final size:16
Alignment explanation
Indices: 28932994--28933029 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28932984 AAATAATCAG
*
28932994 AAAAATAAAATAAAAT
1 AAAAATAAAAGAAAAT
28933010 AAAAATAAAAGAAAAT
1 AAAAATAAAAGAAAAT
28933026 AAAA
1 AAAA
28933030 TAGACTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAATAAAAGAAAAT
Found at i:28934793 original size:16 final size:16
Alignment explanation
Indices: 28934772--28934814 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
28934762 TTAAAAAATG
**
28934772 AATAAATAACTAAAGA
1 AATAAATAAAGAAAGA
28934788 AATAAATAAAGAAAGA
1 AATAAATAAAGAAAGA
*
28934804 AGTAAATAAAG
1 AATAAATAAAG
28934815 CAAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.16
Consensus pattern (16 bp):
AATAAATAAAGAAAGA
Found at i:28934826 original size:3 final size:3
Alignment explanation
Indices: 28934818--28934900 Score: 107
Period size: 3 Copynumber: 27.7 Consensus size: 3
28934808 AATAAAGCAA
28934818 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
28934866 AAG ATT AAT AAT AA- AAA AGAT AAT GAA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT -AAT AAT AAT AA
28934901 AGGAAATGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
2 4 0.06
3 63 0.89
4 4 0.06
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28939786 original size:30 final size:29
Alignment explanation
Indices: 28939735--28939791 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
28939725 CACGGGCTGC
* *
28939735 CACATGGGTGTGTGGCTAGCCCGTGTGGCT
1 CACACGGGCGTGTGGCTAGCCCG-GTGGCT
28939765 CACACGGGCGTGT-GCTCAGCCCGGTGG
1 CACACGGGCGTGTGGCT-AGCCCGGTGG
28939792 AAATGGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.11, C:0.28, G:0.40, T:0.21
Consensus pattern (29 bp):
CACACGGGCGTGTGGCTAGCCCGGTGGCT
Found at i:28940799 original size:2 final size:2
Alignment explanation
Indices: 28940792--28940825 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28940782 CCTAAGCTTG
28940792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28940826 TATGTCGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28941834 original size:22 final size:22
Alignment explanation
Indices: 28941780--28941823 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28941770 GTCCCTTGAT
28941780 GACAATGATATTGCGATATCCA
1 GACAATGATATTGCGATATCCA
28941802 GACAATGATATTGCGATATCCA
1 GACAATGATATTGCGATATCCA
28941824 ACTCTGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (22 bp):
GACAATGATATTGCGATATCCA
Found at i:28941977 original size:18 final size:19
Alignment explanation
Indices: 28941941--28941978 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
28941931 ATTTTACATA
28941941 TAAACATAATAATTATATT
1 TAAACATAATAATTATATT
* *
28941960 TAAA-ATAATTATTTTATT
1 TAAACATAATAATTATATT
28941978 T
1 T
28941979 TATAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAACATAATAATTATATT
Found at i:28942410 original size:21 final size:21
Alignment explanation
Indices: 28942384--28942439 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
28942374 AACAGCGGTG
*
28942384 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
28942405 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
28942426 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
28942440 AACAGCGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:28943096 original size:14 final size:14
Alignment explanation
Indices: 28943077--28943105 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28943067 CCGATACCAA
28943077 ACAGCTTCAATCTC
1 ACAGCTTCAATCTC
28943091 ACAGCTTCAATCTC
1 ACAGCTTCAATCTC
28943105 A
1 A
28943106 GAATCAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.07, T:0.28
Consensus pattern (14 bp):
ACAGCTTCAATCTC
Found at i:28945695 original size:35 final size:35
Alignment explanation
Indices: 28945651--28945723 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
28945641 TTCAATAATG
28945651 TTTTTAGAATCAGAATTGTGATCAAACCATTGATT
1 TTTTTAGAATCAGAATTGTGATCAAACCATTGATT
*
28945686 TTTTTAGAATCAGAATTGTGATCAAACCATTGGTT
1 TTTTTAGAATCAGAATTGTGATCAAACCATTGATT
28945721 TTT
1 TTT
28945724 AGTTCGACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (35 bp):
TTTTTAGAATCAGAATTGTGATCAAACCATTGATT
Done.