Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 227 of 292
Found at i:66156938 original size:13 final size:14
Alignment explanation
Indices: 66156917--66156945 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
66156907 TGAAAAATGG
66156917 ATTAGAAAATATTT
1 ATTAGAAAATATTT
66156931 ATTA-AAAATATTT
1 ATTAGAAAATATTT
66156944 AT
1 AT
66156946 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:66157505 original size:31 final size:32
Alignment explanation
Indices: 66157456--66157519 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
66157446 ATATTAAATA
*
66157456 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
66157487 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
66157519 A
1 A
66157520 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:66158468 original size:15 final size:15
Alignment explanation
Indices: 66158445--66158488 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
66158435 TATCAAATTT
66158445 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* *
66158460 ATTTTGATT-AAATTT
1 ATATTGATTGAAA-TC
66158475 ATATTGATTGAAAT
1 ATATTGATTGAAAT
66158489 ATAATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:66159018 original size:18 final size:19
Alignment explanation
Indices: 66158997--66159070 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
66158987 AATGAAACGA
66158997 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
66159015 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
* * *
66159034 GAAA---ACATA-CA-CTT
1 GAAATTGAGATATGAGATT
66159048 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
66159067 GAAA
1 GAAA
66159071 ACATACACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
14 6 0.14
15 1 0.02
16 4 0.09
17 4 0.09
18 9 0.21
19 15 0.35
20 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:66159051 original size:33 final size:33
Alignment explanation
Indices: 66159013--66159078 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
66159003 GAATTGAGAA
66159013 TTGAAATTGAGATATGAGATTGAAAACATACAC
1 TTGAAATTGAGATATGAGATTGAAAACATACAC
66159046 TTGAAATTGAGATATGAGATTGAAAACATACAC
1 TTGAAATTGAGATATGAGATTGAAAACATACAC
66159079 CAAAAGGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (33 bp):
TTGAAATTGAGATATGAGATTGAAAACATACAC
Found at i:66160301 original size:28 final size:28
Alignment explanation
Indices: 66160258--66160363 Score: 69
Period size: 28 Copynumber: 3.7 Consensus size: 28
66160248 GAAATCAGTG
66160258 TTAA-CTGGG-CATTAGCCCATATCAATA
1 TTAATCTGGGCCA-TAGCCCATATCAATA
*
66160285 TTAATCTGGGCCATAGCCCCT-TACAATGTCAGA
1 TTAATCTGGGCCATAGCCCATAT-CAA--T---A
* *
66160318 GTATAT-TGGGCC-TAGCCCATATCAGTA
1 TTA-ATCTGGGCCATAGCCCATATCAATA
*
66160345 TTAATCTGGGCCGTAGCCC
1 TTAATCTGGGCCATAGCCC
66160364 TACTACAAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 23
0.69 0.06 0.26
Matches are distributed among these distances:
26 2 0.03
27 14 0.23
28 21 0.34
29 2 0.03
30 2 0.03
32 9 0.15
33 10 0.16
34 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (28 bp):
TTAATCTGGGCCATAGCCCATATCAATA
Found at i:66160341 original size:60 final size:59
Alignment explanation
Indices: 66160270--66160399 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 59
66160260 AACTGGGCAT
66160270 TAGCCCATATCAATATTAATCTGGGCCATAGCCCCT-TACAATGTC-AGAGTATATTGGGCC
1 TAGCCCATATCAATATTAATCTGGGCCATAG-CCCTATACAA-GTCGAGA-TATATTGGGCC
* *
66160330 TAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTACTACAAGTCGAGATATATTGGGCC
1 TAGCCCATATCAATATTAATCTGGGCCATAGCCCTA-TACAAGTCGAGATATATTGGGCC
*
66160390 TTGCCCATAT
1 TAGCCCATAT
66160400 TAACACAGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
59 4 0.06
60 52 0.81
61 8 0.12
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (59 bp):
TAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATATATTGGGCC
Found at i:66161680 original size:14 final size:14
Alignment explanation
Indices: 66161655--66161697 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
66161645 GCTATAGGGG
*
66161655 AGAA-AAGAAAAACA
1 AGAAGAAGAAAAA-T
66161669 AGAAGAAGAAAAAT
1 AGAAGAAGAAAAAT
66161683 AGAAGAAGAGAAAAT
1 AGAAGAAGA-AAAAT
66161698 GAAATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (14 bp):
AGAAGAAGAAAAAT
Found at i:66162903 original size:3 final size:3
Alignment explanation
Indices: 66162895--66162953 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
66162885 AAACATACTA
66162895 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
66162942 AAT AAT AAT AAT
1 AAT AAT AAT AAT
66162954 TTTAAAATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:66162970 original size:26 final size:29
Alignment explanation
Indices: 66162897--66162975 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
66162887 ACATACTAAA
**
66162897 TAATAATAATAATAATAATAATAATAATAA
1 TAATAAT-ATAATAATAATAATAATAATTT
66162927 TAATAATATAATAATAATAATAATAATTT
1 TAATAATATAATAATAATAATAATAATTT
*
66162956 TAA-AATATATCTAATAATAA
1 TAATAATATA-ATAATAATAA
66162976 AAATTTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.13
29 32 0.71
30 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
TAATAATATAATAATAATAATAATAATTT
Found at i:66163085 original size:19 final size:18
Alignment explanation
Indices: 66163048--66163091 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
66163038 ATACATGCAG
66163048 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
66163065 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
66163084 TACTAATT
1 TAATAATT
66163092 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:66168656 original size:52 final size:49
Alignment explanation
Indices: 66168476--66168665 Score: 194
Period size: 47 Copynumber: 3.9 Consensus size: 49
66168466 ACATAGTCAT
* ** * *
66168476 ATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-ATCAC
1 ATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* * *
66168524 ATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAGCAC
1 ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* *
66168571 ATATCACA--CCGATGCCATATCCCGGATATGGTCTTATACGGAAGCAC
1 ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* *
66168618 ATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 ATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
66168666 ATCACATTTC
Statistics
Matches: 119, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 8 0.07
49 1 0.01
52 31 0.26
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
Found at i:66175191 original size:15 final size:16
Alignment explanation
Indices: 66175173--66175203 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
66175163 TTTTTTAATA
66175173 TATTTTT-CTTTTCTT
1 TATTTTTCCTTTTCTT
66175188 TATTTTTCCTTTTCTT
1 TATTTTTCCTTTTCTT
66175204 GTAAATAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTTCCTTTTCTT
Found at i:66178569 original size:46 final size:46
Alignment explanation
Indices: 66178514--66178694 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
66178504 TAGGATGGTT
66178514 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
66178560 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
66178606 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
66178653 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66178695 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:66178675 original size:93 final size:93
Alignment explanation
Indices: 66178516--66178686 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
66178506 GGATGGTTGA
* *
66178516 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
66178581 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
66178609 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
66178674 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
66178687 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:66181698 original size:15 final size:15
Alignment explanation
Indices: 66181659--66181737 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
66181649 GTATCTTAGG
*
66181659 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
66181674 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
66181689 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
66181703 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
66181718 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
66181732 TTTCTT
1 TTTCTT
66181738 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:66184158 original size:46 final size:46
Alignment explanation
Indices: 66184103--66184283 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
66184093 TAGGATGGTT
66184103 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
66184149 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
66184195 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
66184242 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66184284 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:66184264 original size:93 final size:93
Alignment explanation
Indices: 66184105--66184275 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
66184095 GGATGGTTGA
* *
66184105 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
66184170 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
66184198 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
66184263 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
66184276 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:66189039 original size:21 final size:21
Alignment explanation
Indices: 66189010--66189097 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 21
66189000 GCCATGTCCC
66189010 TAGTCCACACGGGCGTGTGCCT
1 TAGT-CACACGGGCGTGTGCCT
* *
66189032 TAGTCACACGGTCGTGTACCT
1 TAGTCACACGGGCGTGTGCCT
* *
66189053 CACTTCACACGGGCGTGTGCCT
1 TA-GTCACACGGGCGTGTGCCT
* * *
66189075 CAGTCACATGGTCGTGTGTCCT
1 TAGTCACACGGGCGTGTG-CCT
66189097 T
1 T
66189098 CTTTACACGG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 29 0.54
22 25 0.46
ACGTcount: A:0.15, C:0.31, G:0.27, T:0.27
Consensus pattern (21 bp):
TAGTCACACGGGCGTGTGCCT
Found at i:66194035 original size:30 final size:30
Alignment explanation
Indices: 66193986--66194044 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
66193976 AATTTTTTAT
*
66193986 TTTCCCTCTAAAATTTTAC-TCCCTCCCAC
1 TTTCCCCCTAAAATTTTACTTCCCTCCCAC
*
66194015 TTTCCCCCTAAAACTTTTACTTCCTTCCCA
1 TTTCCCCCTAAAA-TTTTACTTCCCTCCCA
66194045 TCCCACCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 6 0.23
31 8 0.31
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTCCCCCTAAAATTTTACTTCCCTCCCAC
Found at i:66194142 original size:18 final size:18
Alignment explanation
Indices: 66194119--66194178 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
66194109 ACTCTCCTTA
66194119 TTTACTTTCCCTCAAACT
1 TTTACTTTCCCTCAAACT
* *
66194137 TTTAC--TCTCTAAAACTT
1 TTTACTTTCCCTCAAAC-T
*
66194154 TTTATTTTCCC-CTAAACT
1 TTTACTTTCCCTC-AAACT
66194172 TTTACTT
1 TTTACTT
66194179 CTCACTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 12 0.38
19 7 0.22
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTACTTTCCCTCAAACT
Found at i:66199546 original size:46 final size:44
Alignment explanation
Indices: 66199442--66199549 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
66199432 TGTCTTTGAC
** * * *
66199442 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
66199486 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
66199532 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
66199550 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:66201991 original size:131 final size:130
Alignment explanation
Indices: 66201824--66202215 Score: 545
Period size: 131 Copynumber: 3.0 Consensus size: 130
66201814 AAATTTAGAG
* * * *
66201824 AACATGAGTGAAATTCTAAAGGAATACTT-GATTATTTGGAACAAACAGGAGATCGTAACCCAGC
1 AACATGAGTGAAATTCCAAAGGAATA-TTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGC
*
66201888 ACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTGTTGAAGAATTTTTA
65 ACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCATGTTGAAGAATTTTTA
66201953 A
130 A
* * * * *
66201954 AGACATGAATGAAATTCCAAAGGAATGTTCAATTATTTTGAACAAACAGGAAATTGCAACCTAGC
1 A-ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGC
*
66202019 ACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCATTTTGAAGAATTTTTA
65 ACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCATGTTGAAGAATTTTTA
66202084 A
130 A
* * *
66202085 AAGCATGAGTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACAAGAAATCACAACCCAGC
1 AA-CATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGC
* * ** * * * *
66202150 ATGATAGGGCACGATT-CCCGAATTGCCAAACACCGAGTATTGCCTTCATTTTAAAGAATTCTTA
65 ACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCATGTTGAAGAATTTTTA
66202214 A
130 A
66202215 A
1 A
66202216 TGAATAATTA
Statistics
Matches: 233, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
130 48 0.21
131 185 0.79
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (130 bp):
AACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGCA
CGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCATGTTGAAGAATTTTTAA
Found at i:66211689 original size:4 final size:4
Alignment explanation
Indices: 66211680--66211705 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
66211670 AGCTGTTGAT
66211680 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
66211706 GTCAAAACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:66219144 original size:19 final size:20
Alignment explanation
Indices: 66219120--66219163 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
66219110 AATTATAAAA
66219120 AAAAATCAATAAAATTT-AT
1 AAAAATCAATAAAATTTAAT
* * *
66219139 AAAAATTATTAAATTTTAAT
1 AAAAATCAATAAAATTTAAT
66219159 AAAAA
1 AAAAA
66219164 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATCAATAAAATTTAAT
Found at i:66219163 original size:40 final size:41
Alignment explanation
Indices: 66219108--66219187 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
66219098 GTATGGCAAA
* *
66219108 TAAATTATAAAAAAAAATCA-ATAAAATTTA-TAAAAATTAT
1 TAAATTATAAAAAAAAAT-ATAAAAAATATATTAAAAATTAT
* *
66219148 TAAATTTTAATAAAAAATATAAAAAATATATTAAAAATTA
1 TAAATTATAAAAAAAAATATAAAAAATATATTAAAAATTA
66219188 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.03
40 24 0.71
41 9 0.26
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (41 bp):
TAAATTATAAAAAAAAATATAAAAAATATATTAAAAATTAT
Found at i:66219213 original size:21 final size:21
Alignment explanation
Indices: 66219158--66219233 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
66219148 TAAATTTTAA
* *
66219158 TAAAAAATATAAAAAATATAT
1 TAAAAATTATAAAAAAAATAT
*
66219179 TAAAAATTAGAAAAAAAAT-T
1 TAAAAATTATAAAAAAAATAT
* **
66219199 TAAAATTTTATAAAAATCATA-
1 TAAAA-ATTATAAAAAAAATAT
*
66219220 CAAAAATTATAAAA
1 TAAAAATTATAAAA
66219234 TGTATCAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
20 14 0.32
21 30 0.68
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (21 bp):
TAAAAATTATAAAAAAAATAT
Found at i:66219356 original size:11 final size:10
Alignment explanation
Indices: 66219331--66219365 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
66219321 GACATATGGC
*
66219331 AAAAAATGAT
1 AAAAAATTAT
66219341 AAAAAATTAT
1 AAAAAATTAT
66219351 AGAAAAATTAT
1 A-AAAAATTAT
66219362 AAAA
1 AAAA
66219366 TGCTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:66219402 original size:10 final size:10
Alignment explanation
Indices: 66219387--66219553 Score: 76
Period size: 9 Copynumber: 17.6 Consensus size: 10
66219377 GTACAATAAA
66219387 TTTTATATAT
1 TTTTATATAT
66219397 TTTTATGA-A-
1 TTTTAT-ATAT
66219406 TTTTATAT-T
1 TTTTATATAT
66219415 TCTTTATAT-T
1 T-TTTATATAT
66219425 TTTTATA-AT
1 TTTTATATAT
66219434 TTTCT-TATGA-
1 TTT-TATAT-AT
* * *
66219444 CTTTATAAAA
1 TTTTATATAT
*
66219454 TTTTATAGTTTT
1 TTTTATA--TAT
*
66219466 TTTTCTATAT
1 TTTTATATAT
*
66219476 TTCTATATA-
1 TTTTATATAT
*
66219485 TTCTATA-AT
1 TTTTATATAT
*
66219494 TTTT-TACA-
1 TTTTATATAT
66219502 TTTTATATAT
1 TTTTATATAT
66219512 TTTTATAT-T
1 TTTTATATAT
* *
66219521 TTTAATA-AA
1 TTTTATATAT
*
66219530 TTTTAAATA-
1 TTTTATATAT
66219539 TTTTA-ATAT
1 TTTTATATAT
66219548 TTTTAT
1 TTTTAT
66219554 TAAAATTTAA
Statistics
Matches: 121, Mismatches: 16, Indels: 40
0.68 0.09 0.23
Matches are distributed among these distances:
8 11 0.09
9 57 0.47
10 45 0.37
11 2 0.02
12 6 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATATAT
Found at i:66219425 original size:17 final size:18
Alignment explanation
Indices: 66219385--66219582 Score: 77
Period size: 19 Copynumber: 10.4 Consensus size: 18
66219375 TGGTACAATA
66219385 AATTTTATATATTTTTAT
1 AATTTTATATATTTTTAT
66219403 GAATTTTATAT-TTCTTTAT
1 -AATTTTATATATT-TTTAT
*
66219422 -ATTTTTTATAATTTTCTTAT
1 AATTTTATAT-A-TTT-TTAT
* * *
66219442 GACTTTATAAAATTTTATAGTT
1 AATTTTAT-ATATTTT-TA--T
** * *
66219464 TTTTTTCTATATTTCTAT
1 AATTTTATATATTTTTAT
*
66219482 ATATTCTATA-ATTTTT-T
1 A-ATTTTATATATTTTTAT
66219499 ACATTTTATATATTTTTAT
1 A-ATTTTATATATTTTTAT
* * *
66219518 ATTTTTA-ATAAATTTTAA
1 AATTTTATAT-ATTTTTAT
66219536 ATATTTTA-ATATTTTTATT
1 A-ATTTTATATATTTTTA-T
*
66219555 AAAATTTA-ATAATTTTTAT
1 -AATTTTATAT-ATTTTTAT
66219574 AACTTTTAT
1 AA-TTTTAT
66219583 TGTTTATATT
Statistics
Matches: 134, Mismatches: 25, Indels: 39
0.68 0.13 0.20
Matches are distributed among these distances:
17 19 0.14
18 34 0.25
19 43 0.32
20 21 0.16
21 11 0.08
22 6 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTTTATATATTTTTAT
Found at i:66219447 original size:28 final size:29
Alignment explanation
Indices: 66219388--66219459 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
66219378 TACAATAAAT
**
66219388 TTTATATATTTTTATGAATTTTATATTTC
1 TTTATATATTTTTATGAATTTTATATGAC
*
66219417 TTTATAT-TTTTTAT-AATTTTCTTATGAC
1 TTTATATATTTTTATGAATTTT-ATATGAC
* *
66219445 TTTATAAAATTTTAT
1 TTTATATATTTTTAT
66219460 AGTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.17
28 17 0.47
29 13 0.36
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTATATATTTTTATGAATTTTATATGAC
Found at i:66219532 original size:28 final size:28
Alignment explanation
Indices: 66219501--66219574 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
66219491 AATTTTTTAC
*
66219501 ATTTTATATATTTTTATATTTTTAATAAA
1 ATTTAATA-ATTTTTATATTTTTAATAAA
* * *
66219530 TTTTAA-ATATTTTAATATTTTTATTAAA
1 ATTTAATA-ATTTTTATATTTTTAATAAA
66219558 ATTTAATAATTTTTATA
1 ATTTAATAATTTTTATA
66219575 ACTTTTATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTAATAATTTTTATATTTTTAATAAA
Found at i:66219561 original size:20 final size:21
Alignment explanation
Indices: 66219532--66219573 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
66219522 TTAATAAATT
66219532 TTAAATATTTTAAT-ATTTTTA
1 TTAAATA-TTTAATAATTTTTA
66219553 TTAAA-ATTTAATAATTTTTA
1 TTAAATATTTAATAATTTTTA
66219573 T
1 T
66219574 AACTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAATATTTAATAATTTTTA
Found at i:66219581 original size:19 final size:19
Alignment explanation
Indices: 66219489--66219581 Score: 79
Period size: 19 Copynumber: 5.0 Consensus size: 19
66219479 TATATATTCT
*
66219489 ATAATTTTT-TACATTTT-
1 ATAATTTTTATAAATTTTA
*
66219506 ATATATTTTTAT-ATTTTTA
1 ATA-ATTTTTATAAATTTTA
*
66219525 ATAAATTTTA-AATATTTTA
1 ATAATTTTTATAA-ATTTTA
*
66219544 AT-ATTTTTATTAAAATTTA
1 ATAATTTTTA-TAAATTTTA
*
66219563 ATAATTTTTATAACTTTTA
1 ATAATTTTTATAAATTTTA
66219582 TTGTTTATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.05
18 23 0.38
19 25 0.42
20 9 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATAATTTTTATAAATTTTA
Found at i:66220124 original size:15 final size:16
Alignment explanation
Indices: 66220104--66220140 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
66220094 ACGCGACAAT
66220104 AATATTATCATT-CTA
1 AATATTATCATTACTA
*
66220119 AATATTATGATTACTA
1 AATATTATCATTACTA
66220135 AA-ATTA
1 AATATTA
66220141 ATTTTACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (16 bp):
AATATTATCATTACTA
Found at i:66220200 original size:41 final size:41
Alignment explanation
Indices: 66220143--66220220 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
66220133 TAAAATTAAT
66220143 TTTACATGTGACATTTACTTATTGCATAATATAAGACTAAC
1 TTTACATGTGACATTTACTTATTGCATAATATAAGACTAAC
66220184 TTTACATGTGACATTTACTTATTGCATAATATAAGAC
1 TTTACATGTGACATTTACTTATTGCATAATATAAGAC
66220221 GTAATCAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (41 bp):
TTTACATGTGACATTTACTTATTGCATAATATAAGACTAAC
Found at i:66223001 original size:20 final size:21
Alignment explanation
Indices: 66222972--66223023 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
66222962 TGTTATACTT
* * *
66222972 TGATTGATTAA-GTAAAAATA
1 TGATTAATTAAGGAAAAAACA
66222992 TGATTAATTAAGGAAAAAACA
1 TGATTAATTAAGGAAAAAACA
*
66223013 TCATTAATTAA
1 TGATTAATTAA
66223024 ATTAGAGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (21 bp):
TGATTAATTAAGGAAAAAACA
Found at i:66223293 original size:21 final size:21
Alignment explanation
Indices: 66223273--66223311 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
66223263 TTTTCATGGT
66223273 TGAGAATTTGAT-GAAATTGG
1 TGAGAATTTGATAGAAATTGG
*
66223293 TGTGAATTTGATAGAAATT
1 TGAGAATTTGATAGAAATT
66223312 AAGCTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
TGAGAATTTGATAGAAATTGG
Found at i:66228690 original size:26 final size:25
Alignment explanation
Indices: 66228639--66228690 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
66228629 AATTAATTTT
* *
66228639 ATTATTTTTAATTAATTATCATTTA
1 ATTATTTTTAATTAATTACCAATTA
66228664 ATTATTGTTTAA-TAATATACCAATTA
1 ATTATT-TTTAATTAAT-TACCAATTA
66228690 A
1 A
66228691 AACTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTATTTTTAATTAATTACCAATTA
Found at i:66228880 original size:16 final size:16
Alignment explanation
Indices: 66228861--66228899 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
66228851 GTTTTTATGA
66228861 TTTAATATTCA-ATAAT
1 TTTAATATT-ATATAAT
*
66228877 TTTAATATTATTTAAT
1 TTTAATATTATATAAT
66228893 TTTAATA
1 TTTAATA
66228900 ATATCTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATATTATATAAT
Found at i:66233345 original size:14 final size:14
Alignment explanation
Indices: 66233326--66233354 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
66233316 AGGTATGAGA
66233326 TAGTTCCAAAATAT
1 TAGTTCCAAAATAT
66233340 TAGTTCCAAAATAT
1 TAGTTCCAAAATAT
66233354 T
1 T
66233355 CTTGATTTCA
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:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGTTCCAAAATAT
Found at i:66235397 original size:14 final size:14
Alignment explanation
Indices: 66235378--66235408 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66235368 ATTGTGTGAA
*
66235378 AAAATAAATAGAAT
1 AAAATAAATAAAAT
66235392 AAAATAAATAAAAT
1 AAAATAAATAAAAT
66235406 AAA
1 AAA
66235409 GAACACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:66239847 original size:14 final size:14
Alignment explanation
Indices: 66239828--66239858 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66239818 CACTTTGTGA
*
66239828 AAAATAAATAGAAT
1 AAAATAAATAAAAT
66239842 AAAATAAATAAAAT
1 AAAATAAATAAAAT
66239856 AAA
1 AAA
66239859 GAACACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:66242331 original size:24 final size:24
Alignment explanation
Indices: 66242304--66242355 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
66242294 TTTCTAGAAG
*
66242304 ATTTAATAATTATTAGTATAATAT
1 ATTTAACAATTATTAGTATAATAT
* * *
66242328 ATTTAGCATTTATTAGTATAATTT
1 ATTTAACAATTATTAGTATAATAT
66242352 ATTT
1 ATTT
66242356 GACCTACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTTAACAATTATTAGTATAATAT
Found at i:66247660 original size:78 final size:78
Alignment explanation
Indices: 66247571--66247727 Score: 233
Period size: 78 Copynumber: 2.0 Consensus size: 78
66247561 ATTCATGGCT
* * * *
66247571 AATCACATCTTTATAAGTATGAATTATTGTAATTTAGGCAAATGATTACAACTCTCAATAGAAGG
1 AATCACATCTTTATAAGTACGAATCATTCTAATTTAGGCAAATGATTACAACTCTCAATAAAAGG
*
66247636 AGCTAATTAAAGG
66 AGCTAATCAAAGG
* * * *
66247649 AATCACATCTTTATAAGTGCGAATCATTCTAGTTTAGGCAAATGATTACCACTCTCAATAAAATG
1 AATCACATCTTTATAAGTACGAATCATTCTAATTTAGGCAAATGATTACAACTCTCAATAAAAGG
66247714 AGCTAATCAAAGG
66 AGCTAATCAAAGG
66247727 A
1 A
66247728 GAGGATTCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (78 bp):
AATCACATCTTTATAAGTACGAATCATTCTAATTTAGGCAAATGATTACAACTCTCAATAAAAGG
AGCTAATCAAAGG
Found at i:66256181 original size:26 final size:26
Alignment explanation
Indices: 66256152--66256248 Score: 88
Period size: 27 Copynumber: 3.7 Consensus size: 26
66256142 TTAGTTTACC
*
66256152 AAATTACTGAAATACCCCCAGTTGTA
1 AAATTACTCAAATACCCCCAGTTGTA
* *
66256178 AAATTAC-CAAAGTACCCCCGGTTTATA
1 AAATTACTCAAA-TACCCCCAG-TTGTA
* * * *
66256205 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTCAAATA-CCCCCAGTTGTA
*
66256232 AAATTACTGAAATACCC
1 AAATTACTCAAATACCC
66256249 TCGACATATA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
25 3 0.05
26 17 0.30
27 29 0.52
28 7 0.12
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (26 bp):
AAATTACTCAAATACCCCCAGTTGTA
Found at i:66256206 original size:27 final size:26
Alignment explanation
Indices: 66256176--66256403 Score: 123
Period size: 27 Copynumber: 8.4 Consensus size: 26
66256166 CCCCCAGTTG
* *
66256176 TAAAATTACCAAAGTACCCCCGGTTTA
1 TAAAATTACCAAA-TACCCTCGATTTA
* *
66256203 TAAAATTACCCAAATATCCTCGATTTG
1 TAAAATTA-CCAAATACCCTCGATTTA
* **
66256230 TAAAATTACTGAAATACCCTCGACATA
1 TAAAATTAC-CAAATACCCTCGATTTA
* *
66256257 TAAAATTATCAAAGTACCCTCGAATTA
1 TAAAATTACCAAA-TACCCTCGATTTA
* **
66256284 TAAAAATTACTATTTTACCCTCGATTTA
1 T-AAAATTACCA-AATACCCTCGATTTA
* * ** **
66256312 CAGAATTATTATTTTACCCTCGATTTA
1 TAAAATTACCA-AATACCCTCGATTTA
* * ** *
66256339 CAAAATTACTATTTTACCCTCAATTTA
1 TAAAATTACCA-AATACCCTCGATTTA
* * **
66256366 CAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCA-AATACCCTCGATTTA
*
66256393 GAAAATTACCA
1 TAAAATTACCA
66256404 TTTTACCCTA
Statistics
Matches: 167, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.02
27 138 0.83
28 25 0.15
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (26 bp):
TAAAATTACCAAATACCCTCGATTTA
Found at i:66256404 original size:27 final size:27
Alignment explanation
Indices: 66256271--66256412 Score: 196
Period size: 27 Copynumber: 5.2 Consensus size: 27
66256261 ATTATCAAAG
66256271 TACCCTCGAATTATA-AAAATTACTATTT
1 TACCCTCG-ATT-TACAAAATTACTATTT
* *
66256299 TACCCTCGATTTACAGAATTATTATTT
1 TACCCTCGATTTACAAAATTACTATTT
66256326 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * *
66256353 TACCCTCAATTTACAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
66256380 TACCCTCGATTTAGAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
66256407 TACCCT
1 TACCCT
66256413 AGGGTGTTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
26 2 0.02
27 93 0.90
28 8 0.08
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTATTT
Found at i:66256691 original size:27 final size:26
Alignment explanation
Indices: 66256647--66256698 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
66256637 CTCACTGCAA
*
66256647 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
66256674 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
66256699 GCAGCCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:66256943 original size:6 final size:6
Alignment explanation
Indices: 66256912--66257005 Score: 86
Period size: 6 Copynumber: 15.3 Consensus size: 6
66256902 TTGCATTCAC
* * *
66256912 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTTTG ATTCTG ATTCT-
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
66256960 ATCACCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
66257006 AATGTTTCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.07
6 58 0.81
7 6 0.08
8 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:66256957 original size:31 final size:31
Alignment explanation
Indices: 66256912--66256991 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
66256902 TTGCATTCAC
* *
66256912 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
* * *
66256943 ATTTTGATTCTGATTCTATCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
66256974 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTG
66256992 ATTCTAGTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:66256968 original size:25 final size:24
Alignment explanation
Indices: 66256915--66256994 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 24
66256905 CATTCACATT
66256915 CTGATTTTGATTCTG-TTACCTGATA
1 CTGATTTTGATTCTGATT--CTGATA
66256940 CTGATTTTGATTCTGATTCT-ATCA
1 CTGATTTTGATTCTGATTCTGAT-A
* *
66256964 CCTGATTCTGATTCTGATTCTGATT
1 -CTGATTTTGATTCTGATTCTGATA
66256989 CTGATT
1 CTGATT
66256995 CTAGTTCTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.04
24 9 0.18
25 34 0.69
26 4 0.08
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (24 bp):
CTGATTTTGATTCTGATTCTGATA
Found at i:66262658 original size:13 final size:13
Alignment explanation
Indices: 66262640--66262665 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66262630 GTGCAGGGGA
66262640 CACACGGCCATGG
1 CACACGGCCATGG
66262653 CACACGGCCATGG
1 CACACGGCCATGG
66262666 GAGGGAACCG
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:0.38, G:0.31, T:0.08
Consensus pattern (13 bp):
CACACGGCCATGG
Found at i:66273038 original size:19 final size:19
Alignment explanation
Indices: 66273016--66273053 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
66273006 AATAAAAATA
66273016 TAAAAAAATATT-ATTAATT
1 TAAAAAAAT-TTAATTAATT
66273035 TAAAAAAATTTAATTAATT
1 TAAAAAAATTTAATTAATT
66273054 ACTAACGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAAAATTTAATTAATT
Found at i:66277178 original size:21 final size:21
Alignment explanation
Indices: 66277152--66277192 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
66277142 GTGACATGAT
66277152 AAACTCGCAAGAAGAAAATAC
1 AAACTCGCAAGAAGAAAATAC
66277173 AAACTCGCAAGAAGAAAATA
1 AAACTCGCAAGAAGAAAATA
66277193 AAAAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.17, G:0.15, T:0.10
Consensus pattern (21 bp):
AAACTCGCAAGAAGAAAATAC
Found at i:66278653 original size:3 final size:3
Alignment explanation
Indices: 66278645--66278674 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
66278635 AAATAGGCAT
66278645 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
66278675 AGAAGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:66301731 original size:20 final size:20
Alignment explanation
Indices: 66301666--66301730 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
66301656 CTCCCATGTT
*
66301666 TTAATTATATTTTTAAATTA
1 TTAATTATATTATTAAATTA
* * *
66301686 TCAA-TATAATATTAATAATA
1 TTAATTATATTATTAA-ATTA
*
66301706 TT-ATTTTATTATTAAATTA
1 TTAATTATATTATTAAATTA
66301725 TTAATT
1 TTAATT
66301731 TAACTATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 15 0.44
20 19 0.56
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTATATTATTAAATTA
Found at i:66301738 original size:20 final size:19
Alignment explanation
Indices: 66301678--66301742 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
66301668 AATTATATTT
* *
66301678 TTAAATTATCAATATAATA
1 TTAAATTATTAATTTAATA
* * *
66301697 TTAATAATATTATTTTATTA
1 TTAA-ATTATTAATTTAATA
66301717 TTAAATTATTAATTTAACTA
1 TTAAATTATTAATTTAA-TA
66301737 TTAAAT
1 TTAAAT
66301743 GACATGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTATTAATTTAATA
Found at i:66301831 original size:17 final size:17
Alignment explanation
Indices: 66301773--66301833 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
66301763 ATTAAATTGA
66301773 AAATAAAAATTTTAAAG
1 AAATAAAAATTTTAAAG
**
66301790 AAATATACAACTAAATT-AA-
1 AAATA-A-AA--ATTTTAAAG
66301809 AAATAAAAATTTTAAAG
1 AAATAAAAATTTTAAAG
66301826 AAATAAAA
1 AAATAAAA
66301834 TGTTGTCGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 15 0.44
18 2 0.06
19 7 0.21
20 2 0.06
21 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAAAAATTTTAAAG
Found at i:66306625 original size:45 final size:45
Alignment explanation
Indices: 66306561--66306654 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
66306551 TTGGTATTCT
*
66306561 TCTTTAATACGAAGATGATTTGTCAAAGCCTCAAGAGATATTTCC
1 TCTTCAATACGAAGATGATTTGTCAAAGCCTCAAGAGATATTTCC
66306606 TCTTCAATACGAAGATGATTTGTCAAAGCCTCAAGAGATATTTCC
1 TCTTCAATACGAAGATGATTTGTCAAAGCCTCAAGAGATATTTCC
66306651 TCTT
1 TCTT
66306655 TCTTATGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (45 bp):
TCTTCAATACGAAGATGATTTGTCAAAGCCTCAAGAGATATTTCC
Found at i:66308206 original size:24 final size:24
Alignment explanation
Indices: 66308178--66308223 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
66308168 TATCATGATT
*
66308178 TTTTATAAATATTTTAATTATTTA
1 TTTTATAAATATTTAAATTATTTA
*
66308202 TTTTATAATTATTTAAATTATT
1 TTTTATAAATATTTAAATTATT
66308224 GATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTATAAATATTTAAATTATTTA
Found at i:66310879 original size:33 final size:33
Alignment explanation
Indices: 66310832--66310898 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
66310822 CAAAATGTTA
66310832 GGATTTTTCAATGGATGAATATAGTTGAATTAT
1 GGATTTTTCAATGGATGAATATAGTTGAATTAT
*
66310865 GGATTTTTCCATGGATGAATATAGTTGAATTAT
1 GGATTTTTCAATGGATGAATATAGTTGAATTAT
66310898 G
1 G
66310899 AAATTTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.42
Consensus pattern (33 bp):
GGATTTTTCAATGGATGAATATAGTTGAATTAT
Found at i:66311719 original size:26 final size:26
Alignment explanation
Indices: 66311690--66311759 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
66311680 CCTGATATAT
66311690 GGCTCTTCATGAGCTT-CTCAATTAAA
1 GGCTCTTCATGAGCTTCCT-AATTAAA
* *
66311716 GGCTCTTTATGAGCTTCCTAATTAAT
1 GGCTCTTCATGAGCTTCCTAATTAAA
66311742 GGCTCTTCA-GAGCTTCCT
1 GGCTCTTCATGAGCTTCCT
66311760 GATATGGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.22
26 29 0.73
27 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCTAATTAAA
Found at i:66311770 original size:23 final size:23
Alignment explanation
Indices: 66311716--66311792 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 23
66311706 CTCAATTAAA
* *
66311716 GGCTCTTTATGAGCTTCCTAATTAAT
1 GGCTCTTCA-GAGCTTCCTGA-T-AT
66311742 GGCTCTTCAGAGCTTCCTGATAT
1 GGCTCTTCAGAGCTTCCTGATAT
*
66311765 GGCTCTTCGGAGCTTCCTGATAT
1 GGCTCTTCAGAGCTTCCTGATAT
66311788 GGCTC
1 GGCTC
66311793 ACTTGAACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
23 29 0.60
24 1 0.02
25 10 0.21
26 8 0.17
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (23 bp):
GGCTCTTCAGAGCTTCCTGATAT
Found at i:66311803 original size:23 final size:22
Alignment explanation
Indices: 66311740--66311810 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
66311730 TTCCTAATTA
*
66311740 ATGGCTCTTCAGAGCTTCCTGAT
1 ATGGCTCTTC-GAACTTCCTGAT
*
66311763 ATGGCTCTTCGGAGCTTCCTGAT
1 ATGGCTCTTC-GAACTTCCTGAT
*
66311786 ATGGCTCACTT-GAACTTCCCGAT
1 ATGGCT--CTTCGAACTTCCTGAT
66311809 AT
1 AT
66311811 ACGGCTATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 40 0.93
25 3 0.07
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (22 bp):
ATGGCTCTTCGAACTTCCTGAT
Found at i:66311884 original size:73 final size:71
Alignment explanation
Indices: 66311751--66311891 Score: 158
Period size: 73 Copynumber: 2.0 Consensus size: 71
66311741 TGGCTCTTCA
* * * *
66311751 GAGCTTCCTGATATGGCTCTTCGGAGCTTCCTGATATGGCTCACTTGAACTTCCCGATATACGGC
1 GAGCTTCCTGATATGGATCTTCGGAGCTACCCGATATGGCTCACATGAACTTCCCGATATACGGC
66311816 TATCCG
66 TATCCG
* * * * * *
66311822 GAGCTTCTTGATTAATGGATCTTCGGAGCTACCCGTTATTGGCTCGCATGAGCTT-CCTATATAT
1 GAGCTTCCTGA-T-ATGGATCTTCGGAGCTACCCGATA-TGGCTCACATGAACTTCCCGATATAC
66311886 GGCTAT
63 GGCTAT
66311892 TATGAACTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
71 10 0.18
72 1 0.02
73 33 0.58
74 13 0.23
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (71 bp):
GAGCTTCCTGATATGGATCTTCGGAGCTACCCGATATGGCTCACATGAACTTCCCGATATACGGC
TATCCG
Found at i:66311946 original size:25 final size:25
Alignment explanation
Indices: 66311918--66311965 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
66311908 TACAGCCCGG
66311918 ATAAGCTT-CTCATTATATAGCTCAC
1 ATAAGCTTCCT-ATTATATAGCTCAC
*
66311943 ATAAGCTTCCTATTATATTGCTC
1 ATAAGCTTCCTATTATATAGCTC
66311966 GAGAGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (25 bp):
ATAAGCTTCCTATTATATAGCTCAC
Found at i:66317705 original size:17 final size:18
Alignment explanation
Indices: 66317672--66317707 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
66317662 TCGAAACAGG
66317672 TCGGTTAACCGAAAAAAT
1 TCGGTTAACCGAAAAAAT
*
66317690 TCGGTTAACCAAAAAAAT
1 TCGGTTAACCGAAAAAAT
66317708 AATATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (18 bp):
TCGGTTAACCGAAAAAAT
Found at i:66319296 original size:17 final size:18
Alignment explanation
Indices: 66319269--66319303 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
66319259 AATAAATATT
66319269 TTTATTTGCTGTAATTTA
1 TTTATTTGCTGTAATTTA
66319287 TTTA-TTGCTGTAATTTA
1 TTTATTTGCTGTAATTTA
66319304 CAAACTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (18 bp):
TTTATTTGCTGTAATTTA
Found at i:66322020 original size:9 final size:9
Alignment explanation
Indices: 66322008--66322059 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
66321998 GCTTTTTTTT
66322008 GTTAATTCA
1 GTTAATTCA
66322017 GTTAATTCA
1 GTTAATTCA
*
66322026 GTTAAATC-
1 GTTAATTCA
* *
66322034 GTTTAAATCG
1 G-TTAATTCA
*
66322044 GTTAATTCG
1 GTTAATTCA
66322053 GTTAATT
1 GTTAATT
66322060 TTTATACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 1 0.03
9 37 0.95
10 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (9 bp):
GTTAATTCA
Found at i:66322399 original size:21 final size:21
Alignment explanation
Indices: 66322360--66322400 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
66322350 AGCTAATGTC
* * *
66322360 CTTAATTTTCAACAGTAAACT
1 CTTAATTTCCAAAAATAAACT
66322381 CTTAATTTCCAAAAATAAAC
1 CTTAATTTCCAAAAATAAAC
66322401 GAAGGCATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (21 bp):
CTTAATTTCCAAAAATAAACT
Found at i:66326428 original size:10 final size:10
Alignment explanation
Indices: 66326407--66326484 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
66326397 CAACCCAATC
66326407 TTTATTTTTA
1 TTTATTTTTA
66326417 TTT-TTATTTA
1 TTTATT-TTTA
*
66326427 -TTATTTTTC
1 TTTATTTTTA
* *
66326436 TTTCTTTTTT
1 TTTATTTTTA
66326446 TTTATTATTTA
1 TTTATT-TTTA
66326457 -TTA-TTTTA
1 TTTATTTTTA
*
66326465 TTTTATTTTATT
1 -TTTATTTT-TA
66326477 TTTATTTT
1 TTTATTTT
66326485 AGTTAAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
8 4 0.07
9 8 0.15
10 27 0.50
11 14 0.26
12 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:66326454 original size:30 final size:31
Alignment explanation
Indices: 66326404--66326482 Score: 110
Period size: 30 Copynumber: 2.6 Consensus size: 31
66326394 AGGCAACCCA
*
66326404 ATCTTTATTTTTATTT-TTATTTATTATTTT
1 ATCTTTATTTTTTTTTATTATTTATTATTTT
*
66326434 -TCTTTCTTTTTTTTTATTATTTATTATTTT
1 ATCTTTATTTTTTTTTATTATTTATTATTTT
66326464 AT-TTTATTTTATTTTTATT
1 ATCTTTATTTT-TTTTTATT
66326483 TTAGTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.30
30 21 0.49
31 9 0.21
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (31 bp):
ATCTTTATTTTTTTTTATTATTTATTATTTT
Found at i:66326638 original size:42 final size:42
Alignment explanation
Indices: 66326592--66326725 Score: 173
Period size: 42 Copynumber: 3.2 Consensus size: 42
66326582 ATCCATGGTA
*
66326592 CCAAACAGTTCTATTCCAGCCCA-AAGTGCCATATCCCTGCTG
1 CCAAACAGTTCTATTCCAGCCCAGAA-TGCCATATCCCTGCAG
*
66326634 CCAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGCAG
1 CCAAACAGTTCTATTCCAGCCCAGAATGCCATATCCCTGCAG
* * **
66326676 CCAAACAGTCCTATTCCAGCCCTAGAATCCCCA-AAACCTGCAG
1 CCAAACAGTTCTATTCCAGCCC-AGAAT-GCCATATCCCTGCAG
66326719 CCAAACA
1 CCAAACA
66326726 CCCATTTTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
42 58 0.71
43 21 0.26
44 3 0.04
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.20
Consensus pattern (42 bp):
CCAAACAGTTCTATTCCAGCCCAGAATGCCATATCCCTGCAG
Found at i:66327885 original size:21 final size:20
Alignment explanation
Indices: 66327840--66327898 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
66327830 ATAAAATTTA
66327840 AAAAAAATAAAGAAAAAAGG
1 AAAAAAATAAAGAAAAAAGG
*
66327860 AAAAAAATAAAGAAAAATGAGT
1 AAAAAAATAAAGAAAAA--AGG
*
66327882 AAAAAAA-GAAGAAAAAA
1 AAAAAAATAAAGAAAAAA
66327899 AATGAATACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.03
20 17 0.49
21 8 0.23
22 9 0.26
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAAAATAAAGAAAAAAGG
Found at i:66331333 original size:46 final size:46
Alignment explanation
Indices: 66331273--66331500 Score: 305
Period size: 46 Copynumber: 5.0 Consensus size: 46
66331263 TTTGACATGA
* * * * * ** *
66331273 TGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTC-TGCCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** * *
66331319 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCAAATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
66331365 TGCCATGGTATCTTTCAACGATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
66331411 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
66331457 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
66331501 AGAGCACACT
Statistics
Matches: 162, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 4 0.02
46 158 0.98
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:66334709 original size:3 final size:3
Alignment explanation
Indices: 66334701--66334729 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
66334691 AACAAGAATC
66334701 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
66334730 GGGTTGGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:66355672 original size:2 final size:2
Alignment explanation
Indices: 66355667--66355713 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
66355657 ATATATATAT
*
66355667 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
66355709 AG AG A
1 AG AG A
66355714 AACACTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66356811 original size:14 final size:14
Alignment explanation
Indices: 66356792--66356829 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
66356782 TGTTTAACTC
66356792 AAAATGACTTCT-G
1 AAAATGACTTCTAG
*
66356805 AAAAATGATTTCTAG
1 -AAAATGACTTCTAG
66356820 AAAATGACTT
1 AAAATGACTT
66356830 ACGCTGCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (14 bp):
AAAATGACTTCTAG
Found at i:66366456 original size:57 final size:57
Alignment explanation
Indices: 66366368--66366481 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
66366358 AACATGTTAG
66366368 TCTTAACAGTGACAGGCGAACTAAATTCCAAAGTAGCAGGAGAAAGCCACTTGTCCA
1 TCTTAACAGTGACAGGCGAACTAAATTCCAAAGTAGCAGGAGAAAGCCACTTGTCCA
66366425 TCTTAACAGTGACAGGCGAACTAAATTCCAAAGTAGCAGGAGAAAGCCACTTGTCCA
1 TCTTAACAGTGACAGGCGAACTAAATTCCAAAGTAGCAGGAGAAAGCCACTTGTCCA
66366482 ACAAAACCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (57 bp):
TCTTAACAGTGACAGGCGAACTAAATTCCAAAGTAGCAGGAGAAAGCCACTTGTCCA
Found at i:66370045 original size:17 final size:17
Alignment explanation
Indices: 66370023--66370059 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
66370013 TAAGAAGGAA
66370023 TAATTAAAAATTTTAAT
1 TAATTAAAAATTTTAAT
*
66370040 TAATTAAAATTTTTAAT
1 TAATTAAAAATTTTAAT
66370057 TAA
1 TAA
66370060 AAATCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTAAAAATTTTAAT
Found at i:66370403 original size:20 final size:20
Alignment explanation
Indices: 66370380--66370428 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
66370370 CAAATTACTG
66370380 TAAAAATATCAATATTATAT
1 TAAAAATATCAATATTATAT
** *
66370400 TAAACTTATC-ATATTGTAT
1 TAAAAATATCAATATTATAT
66370419 T-AAAATATCA
1 TAAAAATATCA
66370429 GCTTTTATGC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 8 0.35
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAAATATCAATATTATAT
Found at i:66370525 original size:15 final size:15
Alignment explanation
Indices: 66370505--66370536 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
66370495 TTGGATGGCT
66370505 AAATTTGATAAAGGG
1 AAATTTGATAAAGGG
66370520 AAATTTGATAAAGGG
1 AAATTTGATAAAGGG
66370535 AA
1 AA
66370537 CTATGATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (15 bp):
AAATTTGATAAAGGG
Found at i:66370543 original size:15 final size:15
Alignment explanation
Indices: 66370505--66370543 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
66370495 TTGGATGGCT
*
66370505 AAATTTGATAAAGGG
1 AAATATGATAAAGGG
*
66370520 AAATTTGATAAAGGG
1 AAATATGATAAAGGG
*
66370535 AACTATGAT
1 AAATATGAT
66370544 GAGATGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (15 bp):
AAATATGATAAAGGG
Found at i:66387520 original size:12 final size:12
Alignment explanation
Indices: 66387503--66387527 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66387493 CAAATATACC
66387503 ACCAGATTTATT
1 ACCAGATTTATT
66387515 ACCAGATTTATT
1 ACCAGATTTATT
66387527 A
1 A
66387528 AGAATAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ACCAGATTTATT
Found at i:66389503 original size:13 final size:14
Alignment explanation
Indices: 66389480--66389508 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
66389470 CATACCAGAG
66389480 TTATCTATTTATTA
1 TTATCTATTTATTA
66389494 TTAT-TATTTATTA
1 TTATCTATTTATTA
66389507 TT
1 TT
66389509 CTTCTGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATCTATTTATTA
Found at i:66391062 original size:38 final size:38
Alignment explanation
Indices: 66391011--66391085 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
66391001 AGGAATGTAC
66391011 TCATATGTAAATTGCCAAATGGCGATTCTGATTTTTTG
1 TCATATGTAAATTGCCAAATGGCGATTCTGATTTTTTG
66391049 TCATATGTAAATTGCCAAATGGCGATTCTGATTTTTT
1 TCATATGTAAATTGCCAAATGGCGATTCTGATTTTTT
66391086 TGGGGAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (38 bp):
TCATATGTAAATTGCCAAATGGCGATTCTGATTTTTTG
Found at i:66401340 original size:30 final size:29
Alignment explanation
Indices: 66401290--66401347 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
66401280 GCAACCCAAT
66401290 CTTTCTTTTTATTTTTATTTATTATTTTC
1 CTTTCTTTTTATTTTTATTTATTATTTTC
66401319 CTTTCTTTTCT-TTTATTATTTATTATTTT
1 CTTTCTTTT-TATTT-TTATTTATTATTTT
66401348 ATTTTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (29 bp):
CTTTCTTTTTATTTTTATTTATTATTTTC
Found at i:66402631 original size:116 final size:115
Alignment explanation
Indices: 66402341--66402636 Score: 339
Period size: 118 Copynumber: 2.5 Consensus size: 115
66402331 GCTTAGATCG
*
66402341 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGTTTGTG
1 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGTTGTG
* ** *
66402406 TGACGTGACAAGTAAAACTCCGCTAGCCGAGGTTATAAGTATGGCTCAAATCA
66 TGACGTGACAAGTAAAACTCCGCTAACCGAAATAATAAGTATGG--C-AATCA
* *
66402459 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTTGCATCAAAAGGTTGTG
1 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGTTGTG
**** * * *
66402524 TGACGTGTTGGGTAAAACTCCGCTAACCGGAAATAAATAATTTTAGG-AGT-A
66 TGACGTGACAAGTAAAACTCCGCTAACC-GAAAT-AATAAGTAT-GGCAATCA
* * *
66402575 TG-TTGGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGTCATCTCT-CTTCGCGTCAAAAGGTT
1 TGACT-GACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCAT-TCTACTTCGCGTCAAAAGGTT
66402637 TAATATATTC
Statistics
Matches: 154, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
115 1 0.01
116 52 0.34
117 5 0.03
118 85 0.55
119 3 0.02
120 6 0.04
121 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (115 bp):
TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGTTGTG
TGACGTGACAAGTAAAACTCCGCTAACCGAAATAATAAGTATGGCAATCA
Found at i:66402685 original size:15 final size:15
Alignment explanation
Indices: 66402667--66402699 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
66402657 AAATAATAAT
*
66402667 AAATTAAAAAAATCA
1 AAATCAAAAAAATCA
66402682 AAATCAAAAAAATCA
1 AAATCAAAAAAATCA
66402697 AAA
1 AAA
66402700 AAGTAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATCAAAAAAATCA
Found at i:66402850 original size:5 final size:5
Alignment explanation
Indices: 66402842--66402871 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
66402832 TGGAAGACTC
66402842 TATTT TATTT TATTT TATTT TATTT ATATT
1 TATTT TATTT TATTT TATTT TATTT -TATT
66402872 AGGATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:66402897 original size:27 final size:28
Alignment explanation
Indices: 66402867--66402919 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
66402857 TATTTTATTT
66402867 ATATTAGGA-TAATTAATATTAAGATAA
1 ATATTAGGATTAATTAATATTAAGATAA
* *
66402894 ATATTAGGATTATTTAATTTTAAGAT
1 ATATTAGGATTAATTAATATTAAGAT
66402920 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (28 bp):
ATATTAGGATTAATTAATATTAAGATAA
Found at i:66402925 original size:27 final size:26
Alignment explanation
Indices: 66402863--66402925 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
66402853 ATTTTATTTT
66402863 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
** * *
66402890 ATAAATATTAGGATTATTTAATTTTAAG
1 AT-TTTATTAGGA-TAATTAATATTAAG
66402918 ATTTTATT
1 ATTTTATT
66402926 TTAATTATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:66402940 original size:10 final size:10
Alignment explanation
Indices: 66402921--66402952 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
66402911 TTTTAAGATT
66402921 TTAT-TTTAA
1 TTATCTTTAA
66402930 TTATCTTTAA
1 TTATCTTTAA
66402940 TTATCTTTAA
1 TTATCTTTAA
66402950 TTA
1 TTA
66402953 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:66406253 original size:27 final size:27
Alignment explanation
Indices: 66406222--66406481 Score: 295
Period size: 27 Copynumber: 9.6 Consensus size: 27
66406212 TTAGTTTACC
*
66406222 AAATTACCAAAACACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
66406249 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
66406276 AAATCACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** *
66406303 AAATTACTAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
66406330 AAATCACCAAAATACCCCTGATTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * **
66406357 AAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
66406384 AAATTACCAAAATACCACTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
66406411 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
66406438 AAATTACCAAAGTACCCTTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
**
66406465 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
66406482 TCGACCTGTA
Statistics
Matches: 189, Mismatches: 44, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 189 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:66406287 original size:54 final size:54
Alignment explanation
Indices: 66406212--66406482 Score: 346
Period size: 54 Copynumber: 5.0 Consensus size: 54
66406202 TTAGAATACT
** *
66406212 TTAGTTTACCAAATTACCAAAACACCCCTGGTTTGTAAAATTACTAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC
* * * *
66406266 TTGGTTTATAAAATCACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCA
1 TTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC
* * * *
66406320 TTGGTTTATAAAATCACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC
* *
66406374 TTAGTTTACAAAATTACCAAAATACCACTGGTTTGTAAAATTA-TCAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACT-AAAATACCC
* * * * * * *
66406428 CTAGTTTGTAAAATTACCAAAGTACCCTTGATTTGTGAAATTACTGAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC
66406482 T
1 T
66406483 CGACCTGTAA
Statistics
Matches: 188, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
54 187 0.99
55 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
TTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC
Found at i:66406553 original size:27 final size:27
Alignment explanation
Indices: 66406222--66406553 Score: 294
Period size: 27 Copynumber: 12.3 Consensus size: 27
66406212 TTAGTTTACC
* * *
66406222 AAATTACCAAAACACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* * *
66406249 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
66406276 AAATCACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* * * *
66406303 AAATTACTAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
66406330 AAATCACCAAAATACCCCTGATTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
**
66406357 AAATTACCAAAATACCCTT-AGTTTACA
1 AAATTACCAAAATACCCTTGA-TTTGTA
*
66406384 AAATTACCAAAATACCAC-TGGTTTGTA
1 AAATTACCAAAATACC-CTTGATTTGTA
* *
66406411 AAATTATCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
66406438 AAATTACCAAAGTACCCTTGATTTGTG
1 AAATTACCAAAATACCCTTGATTTGTA
** * **
66406465 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
*** * *
66406492 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
66406519 AAATTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
*
66406546 GAATTACC
1 AAATTACC
66406554 GTTTTACCCT
Statistics
Matches: 246, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
26 2 0.01
27 242 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGATTTGTA
Found at i:66406562 original size:81 final size:82
Alignment explanation
Indices: 66406352--66406590 Score: 236
Period size: 81 Copynumber: 2.9 Consensus size: 82
66406342 TACCCCTGAT
* ** * ***
66406352 TTGTAAAATTACCAAAATACCCTT-AGTTTACAAAATTACCAAAATACCACT-GGTTTGTAAAAT
1 TTGTAAAATTACCAAAGTACCCTTGA-TTTATGAAATTACCGAAATACC-CTCGACCTGTAAAAT
* * *
66406415 TATCAAAATACCC-CTAGT
64 TATCGAAATACCCTCGAGC
* *
66406433 TTGTAAAATTACCAAAGTACCCTTGATTTGTGAAATTACTGAAATACCCTCGACCTGTAAAATTA
1 TTGTAAAATTACCAAAGTACCCTTGATTTATGAAATTACCGAAATACCCTCGACCTGTAAAATTA
*
66406498 TTGAAATACCCTCGA-C
66 TCGAAATACCCTCGAGC
*** ** **
66406514 TTGTAAAATTACCAAAGTACCCTTGATTTAT-AGAATTACCGTTTTACCCTCGATTTACAAAATT
1 TTGTAAAATTACCAAAGTACCCTTGATTTATGA-AATTACCGAAATACCCTCGACCTGTAAAATT
66406578 ATCGAAATACCCT
65 ATCGAAATACCCT
66406591 TGTAGGGTAG
Statistics
Matches: 131, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
80 3 0.02
81 125 0.95
82 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (82 bp):
TTGTAAAATTACCAAAGTACCCTTGATTTATGAAATTACCGAAATACCCTCGACCTGTAAAATTA
TCGAAATACCCTCGAGC
Found at i:66406588 original size:27 final size:26
Alignment explanation
Indices: 66406243--66406590 Score: 157
Period size: 27 Copynumber: 12.9 Consensus size: 26
66406233 ACACCCCTGG
* * *
66406243 TTTGTAAAATTACTAAAATACCCTTGG
1 TTTGTAAAATTAC-GAAATACCCTCGA
* * * *
66406270 TTTATAAAATCACCAAAATACCC-CTA
1 TTTGTAAAATTA-CGAAATACCCTCGA
* * * *
66406296 GTTTGTAAAATTACTAAAATACCATTGG
1 -TTTGTAAAATTAC-GAAATACCCTCGA
* * *
66406324 TTTATAAAATCACCAAAATACCC-CTGA
1 TTTGTAAAATTA-CGAAATACCCTC-GA
* *
66406351 TTTGTAAAATTACCAAAATACCCT-TA
1 TTTGTAAAATTA-CGAAATACCCTCGA
** * *
66406377 GTTTACAAAATTACCAAAATACCACT-GG
1 -TTTGTAAAATTA-CGAAATACC-CTCGA
* *
66406405 TTTGTAAAATTATCAAAATACCC-CTA
1 TTTGTAAAATTA-CGAAATACCCTCGA
* *
66406431 GTTTGTAAAATTACCAAAGTACCCTTGA
1 -TTTGTAAAATTACGAAA-TACCCTCGA
*
66406459 TTTGTGAAATTACTGAAATACCCTCGA
1 TTTGTAAAATTAC-GAAATACCCTCGA
** *
66406486 CCTGTAAAATTATTGAAATACCCTCGA
1 TTTGTAAAATTA-CGAAATACCCTCGA
* * *
66406513 CTTGTAAAATTACCAAAGTACCCTTGA
1 TTTGTAAAATTACGAAA-TACCCTCGA
* * ***
66406540 TTTATAGAATTACCGTTTTACCCTCGA
1 TTTGTAAAATTA-CGAAATACCCTCGA
**
66406567 TTTACAAAATTATCGAAATACCCT
1 TTTGTAAAATTA-CGAAATACCCT
66406591 TGTAGGGTAG
Statistics
Matches: 248, Mismatches: 56, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
26 10 0.04
27 229 0.92
28 9 0.04
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (26 bp):
TTTGTAAAATTACGAAATACCCTCGA
Found at i:66406607 original size:27 final size:27
Alignment explanation
Indices: 66406580--66406791 Score: 223
Period size: 27 Copynumber: 7.9 Consensus size: 27
66406570 ACAAAATTAT
*
66406580 CGAAATACCCTTGTAGGGTAGAAATAT
1 CGAAATACCCTTGTAGGGTAGAAATAC
* *
66406607 CGAAATACCCCTGCAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* * *
66406634 CAAAATAACCTTGTAGGGTAGAATTAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
** *
66406661 TAAAATACCC-TGTAGGGTAGAATTAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* *
66406687 CGAAATACTCTTGTAGGATAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* *
66406714 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* * * *
66406741 TGAAATACTCC-TATAAGGTAGAATTAC
1 CGAAATAC-CCTTGTAGGGTAGAAATAC
* *
66406768 CGAGATACCCTTGTGGGGTA-AAAT
1 CGAAATACCCTTGTAGGGTAGAAAT
66406792 TACCATTTTA
Statistics
Matches: 154, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
26 28 0.18
27 124 0.81
28 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (27 bp):
CGAAATACCCTTGTAGGGTAGAAATAC
Found at i:66406640 original size:54 final size:53
Alignment explanation
Indices: 66406582--66406736 Score: 204
Period size: 53 Copynumber: 2.9 Consensus size: 53
66406572 AAAATTATCG
*
66406582 AAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTGCAGGGTAGAAATACCA
1 AAATACCCTTGTAGGGTAGAAATA-CGAAATACCCCTGTAGGGTAGAAATACCA
* * * * *
66406636 AAATAACCTTGTAGGGTAGAATTACTAAAATA-CCCTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAAATAC-GAAATACCCCTGTAGGGTAGAAATACCA
* *
66406689 AAATACTCTTGTAGGATAGAAATACCGAAATACCCCTGTAGGGTAGAA
1 AAATACCCTTGTAGGGTAGAAATA-CGAAATACCCCTGTAGGGTAGAA
66406737 TTACTGAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
53 44 0.51
54 43 0.49
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (53 bp):
AAATACCCTTGTAGGGTAGAAATACGAAATACCCCTGTAGGGTAGAAATACCA
Found at i:66406746 original size:54 final size:54
Alignment explanation
Indices: 66406574--66406795 Score: 250
Period size: 54 Copynumber: 4.1 Consensus size: 54
66406564 CGATTTACAA
* * * *
66406574 AATTATCGAAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTGCAGGGTAG
1 AATTACCGAAATACTCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
* * * **
66406628 AAATACCAAAATAAC-CTTGTAGGGTAGAATTACTAAAATA-CCCTGTAGGGTAG
1 AATTACCGAAAT-ACTCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
*
66406681 AATTACCGAAATACTCTTGTAGGATAGAAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACTCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
* * * * * * * * *
66406735 AATTACTGAAATACTCCTATAAGGTAGAATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACTCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
66406789 AATTACC
1 AATTACC
66406796 ATTTTACCCC
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
52 2 0.01
53 43 0.31
54 93 0.66
55 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (54 bp):
AATTACCGAAATACTCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
Found at i:66406761 original size:107 final size:108
Alignment explanation
Indices: 66406572--66406795 Score: 281
Period size: 107 Copynumber: 2.1 Consensus size: 108
66406562 CTCGATTTAC
* * *
66406572 AAAATTATCGAAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTGCAGGGTAGAAATACCAA
1 AAAATTACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCCTGCAGGGTAGAAATACCAA
* * * *
66406637 AATAACCTTGTAGGGTAGAATTACTAAAATACCC-TGTAGGGT
66 AATAACCCTATAAGGTAGAATTACCAAAATACCCTTGTAGGGT
* * * * **
66406679 AGAATTACCGAAATACTCTTGTAGGATAGAAATACCGAAATACCCCTGTAGGGTAGAATTACTGA
1 AAAATTACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCCTGCAGGGTAGAAATACCAA
* * *
66406744 AAT-ACTCCTATAAGGTAGAATTACCGAGATACCCTTGTGGGGT
66 AATAAC-CCTATAAGGTAGAATTACCAAAATACCCTTGTAGGGT
66406787 AAAATTACC
1 AAAATTACC
66406796 ATTTTACCCC
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 2 0.02
107 81 0.83
108 15 0.15
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (108 bp):
AAAATTACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCCTGCAGGGTAGAAATACCAA
AATAACCCTATAAGGTAGAATTACCAAAATACCCTTGTAGGGT
Found at i:66406806 original size:81 final size:80
Alignment explanation
Indices: 66406582--66406781 Score: 247
Period size: 80 Copynumber: 2.5 Consensus size: 80
66406572 AAAATTATCG
* * * * * * * * * *
66406582 AAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTGCAGGGTAGAAATACCAAAATAACCTTG
1 AAATACCC-TATAAGGTAGAATTACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCCTG
66406647 TAGGGTAGAATTACTA
65 TAGGGTAGAATTACTA
* * *
66406663 AAATACCCTGTAGGGTAGAATTACCGAAATACTCTTGTAGGATAGAAATACCGAAATACCCCTGT
1 AAATACCCTATAAGGTAGAATTACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCCTGT
*
66406728 AGGGTAGAATTACTG
66 AGGGTAGAATTACTA
*
66406743 AAATACTCCTATAAGGTAGAATTACCGAGATACCCTTGT
1 AAATAC-CCTATAAGGTAGAATTACCGAAATACCCTTGT
66406782 GGGGTAAAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
80 68 0.65
81 36 0.35
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (80 bp):
AAATACCCTATAAGGTAGAATTACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCCTGT
AGGGTAGAATTACTA
Found at i:66407131 original size:2 final size:2
Alignment explanation
Indices: 66407124--66407151 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66407114 GCTTCACCAC
66407124 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
66407152 CTGTTCTGGT
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:66407200 original size:27 final size:26
Alignment explanation
Indices: 66407148--66407207 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
66407138 ATATATATAT
*
66407148 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
66407174 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
66407201 ATATCTG
1 ATATCTG
66407208 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:66407335 original size:6 final size:6
Alignment explanation
Indices: 66407326--66407483 Score: 121
Period size: 6 Copynumber: 25.8 Consensus size: 6
66407316 TTGCATTCAC
* *
66407326 ATTCTG ATTCTG ATTCTG -TTACTTG -TTACTG ATTCGG ATTCTG GTTCTG
1 ATTCTG ATTCTG ATTCTG ATT-C-TG ATT-CTG ATTCTG ATTCTG ATTCTG
* *
66407375 ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG A-TCTG -TTACCTA ATTCTG
1 ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * *
66407424 ATTCTG ATTTTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTG ATTCTC
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
*
66407473 ATTTTG ATTCT
1 ATTCTG ATTCT
66407484 AGTTTTGATA
Statistics
Matches: 123, Mismatches: 16, Indels: 26
0.75 0.10 0.16
Matches are distributed among these distances:
5 10 0.08
6 93 0.76
7 16 0.13
8 4 0.03
ACGTcount: A:0.17, C:0.18, G:0.16, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:66407376 original size:37 final size:37
Alignment explanation
Indices: 66407326--66407407 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
66407316 TTGCATTCAC
*
66407326 ATTCTGATTCTGATTCTG-TTACTTGTTA-CTGATTCGG
1 ATTCTGATTCTGATTCTGATT-C-TGTTACCTGATACGG
* *
66407363 ATTCTGGTTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACGG
66407400 ATTCTGAT
1 ATTCTGAT
66407408 CTGTTACCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.13
37 32 0.82
38 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (37 bp):
ATTCTGATTCTGATTCTGATTCTGTTACCTGATACGG
Found at i:66407388 original size:43 final size:41
Alignment explanation
Indices: 66407327--66407429 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 41
66407317 TGCATTCACA
* *
66407327 TTCTGATTCTGATTCTGTTACTTGTTACTGATTCGGATTCTGG
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCGGA-TCT-G
*
66407370 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATCTG
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCGGATCTG
*
66407411 TTACCTAATTCTGATTCTG
1 TT--CTGATTCTGATTCTG
66407430 ATTTTGATTC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
41 3 0.06
42 3 0.06
43 48 0.89
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (41 bp):
TTCTGATTCTGATTCTGTTACCTGATACTGATTCGGATCTG
Found at i:66407400 original size:19 final size:19
Alignment explanation
Indices: 66407335--66407460 Score: 81
Period size: 19 Copynumber: 6.8 Consensus size: 19
66407325 CATTCTGATT
66407335 CTGATTCTG-TTACTTGTTA-
1 CTGATTCTGATT-C-TGTTAC
*
66407354 CTGATTCGGATTCTGGTT--
1 CTGATTCTGATTCT-GTTAC
66407372 CTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGTTAC
* *
66407391 CTGATACTGATTCTG--AT
1 CTGATTCTGATTCTGTTAC
*
66407408 CTG-TTACCTAATTCTGATT--
1 CTGATT--CTGATTCTG-TTAC
* *
66407427 CTGATTTTGATTCTGTCAC
1 CTGATTCTGATTCTGTTAC
66407446 CTGATTCTGATTCTG
1 CTGATTCTGATTCTG
66407461 ATTCTGATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
16 1 0.01
17 8 0.09
18 29 0.34
19 43 0.51
20 4 0.05
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (19 bp):
CTGATTCTGATTCTGTTAC
Found at i:66407453 original size:31 final size:31
Alignment explanation
Indices: 66407391--66407471 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
66407381 ATTCTGTTAC
* *
66407391 CTGATACTGATTCTGA-TCTGTTACCTAATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATT
* *
66407421 CTGATTCTGATTTTGATTCTGTCACCTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATT
66407452 CTGATTCTGATTCTGATTCT
1 CTGATTCTGATTCTGATTCT
66407472 CATTTTGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 14 0.31
31 31 0.69
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.47
Consensus pattern (31 bp):
CTGATTCTGATTCTGATTCTGTCACCTAATT
Found at i:66407481 original size:55 final size:54
Alignment explanation
Indices: 66407363--66407492 Score: 156
Period size: 55 Copynumber: 2.4 Consensus size: 54
66407353 ACTGATTCGG
* * *
66407363 ATTCTGGTTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATCTGTTACCTA
1 ATTCTGATTCTGATTTTGATTCTGTCACCTGATACTGATTCTGATCTGTTA-CTA
* *
66407418 ATTCTGATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTGATTCTGATT-CTC
1 ATTCTGATTCTGATTTTGATTCTGTCACCTGATACTGATTCTGA-TCTG-TTACTA
*
66407473 ATTTTGATTCT-AGTTTTGAT
1 ATTCTGATTCTGA-TTTTGAT
66407493 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 59 0.89
56 4 0.06
57 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (54 bp):
ATTCTGATTCTGATTTTGATTCTGTCACCTGATACTGATTCTGATCTGTTACTA
Found at i:66408852 original size:56 final size:56
Alignment explanation
Indices: 66408785--66408894 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
66408775 GAGTGTGGAC
* * *
66408785 TGTCGTGTTCTCCAAGGAATTTATTTCTGTTGGTTGCTATTCTTGAACGTAAGGTG
1 TGTCATGTTCTCCAAGGAATTTATTGCCGTTGGTTGCTATTCTTGAACGTAAGGTG
* *
66408841 TGTCATGTTCTCCAAGGAATTTATTGCCGTTGGTTGCTATTTTTGAAGGTAAGG
1 TGTCATGTTCTCCAAGGAATTTATTGCCGTTGGTTGCTATTCTTGAACGTAAGG
66408895 AGTTAATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (56 bp):
TGTCATGTTCTCCAAGGAATTTATTGCCGTTGGTTGCTATTCTTGAACGTAAGGTG
Found at i:66411001 original size:26 final size:26
Alignment explanation
Indices: 66410972--66411053 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
66410962 TGATAAAAAT
*
66410972 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
66410998 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
66411024 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
66411050 TGAT
1 TGAT
66411054 CGGCATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:66424239 original size:20 final size:20
Alignment explanation
Indices: 66424214--66424258 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
66424204 TTTAGAAATG
* *
66424214 GGAGCATTACCGGAATTTAC
1 GGAGCATCACCGGAACTTAC
66424234 GGAGCATCACCGGAACTTAC
1 GGAGCATCACCGGAACTTAC
66424254 -GAGCA
1 GGAGCA
66424259 ATACTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (20 bp):
GGAGCATCACCGGAACTTAC
Found at i:66427238 original size:30 final size:30
Alignment explanation
Indices: 66427204--66427264 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66427194 TCCTTAACTC
66427204 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * * *
66427234 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
66427264 A
1 A
66427265 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:66431577 original size:9 final size:8
Alignment explanation
Indices: 66431559--66431601 Score: 61
Period size: 9 Copynumber: 5.2 Consensus size: 8
66431549 TTAATAAATC
66431559 ATTAAAAA
1 ATTAAAAA
66431567 ATTATAAAA
1 ATTA-AAAA
66431576 ATTATAAAA
1 ATTA-AAAA
66431585 ATTAAAAA
1 ATTAAAAA
66431593 A-TAAAAA
1 ATTAAAAA
66431600 AT
1 AT
66431602 AGTCCAATCG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.21
8 9 0.27
9 17 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
ATTAAAAA
Found at i:66438499 original size:41 final size:41
Alignment explanation
Indices: 66438461--66438876 Score: 314
Period size: 41 Copynumber: 10.2 Consensus size: 41
66438451 AGAAATAGAA
*
66438461 GCGTTTTTGTCTAAAACGCCACTAAAAACATATCAATAGCG
1 GCGTTTTTGTCTAAAACGCCACTAAAAACATATAAATAGCG
* * * * *
66438502 GCGGTTTTATCAAAAATGCCACTAAAAACATATCAATAGCG
1 GCGTTTTTGTCTAAAACGCCACTAAAAACATATAAATAGCG
* * *
66438543 GCGGTTTTATCTAAAACGCCACTAAAAAC-TGATCAATAGCG
1 GCGTTTTTGTCTAAAACGCCACTAAAAACAT-ATAAATAGCG
* ** * **
66438584 TCG-TTTTCACGT-AAACGCCACTAAAAACTTGGGAAATAGCG
1 GCGTTTTTGTC-TAAAACGCCACTAAAAACAT-ATAAATAGCG
* ** *
66438625 ACGTTTTTGTCCT-AAACGCCACT-AAAAGTTATCAATAGCG
1 GCGTTTTTGT-CTAAAACGCCACTAAAAACATATAAATAGCG
** * * * *
66438665 GCGTTTTAATCCAAAACGCCACTAAAAAGTAGAGAAATAGCG
1 GCGTTTTTGTCTAAAACGCCACTAAAAA-CATATAAATAGCG
* * * *
66438707 GCGTTTTTGTC-CAAACTCCACTAAAAAGCATAGAAATAGTG
1 GCGTTTTTGTCTAAAACGCCACTAAAAA-CATATAAATAGCG
* * *
66438748 GCGTTTTTGTC-CAAACGCCAGTAAAAACAGGGA-AAATAGCG
1 GCGTTTTTGTCTAAAACGCCACTAAAAACA--TATAAATAGCG
* * * * * * *
66438789 GCGTTTTTATGTAAAACACCACTAAAAATAGAGAAATAGAG
1 GCGTTTTTGTCTAAAACGCCACTAAAAACATATAAATAGCG
*
66438830 GCGTTTTTGT-TAAAACGCCACT-AAAAC-TAATCAATAGCG
1 GCGTTTTTGTCTAAAACGCCACTAAAAACAT-ATAAATAGCG
66438869 GCGTTTTT
1 GCGTTTTT
66438877 AGGACCAAAC
Statistics
Matches: 309, Mismatches: 53, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
39 20 0.06
40 61 0.20
41 180 0.58
42 47 0.15
43 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (41 bp):
GCGTTTTTGTCTAAAACGCCACTAAAAACATATAAATAGCG
Found at i:66438733 original size:123 final size:120
Alignment explanation
Indices: 66438444--66438855 Score: 356
Period size: 123 Copynumber: 3.4 Consensus size: 120
66438434 AACGCCGCAA
** ** * *
66438444 AAAAAT-GAGAAATAGAAGCGTTTTTGTCTAAAACGCCACTAAAAA-CATATCAATAGCGGCGGT
1 AAAAATAGAGAAATAGCGGCGTTTTTG--T-AAACGCCACTAAAAAGCATAGAAATAGCGACGTT
* * *
66438507 TTTATCAAAAATGCCACTAAAAACA--TATCAATAGCGGCGGTTTTATCTAAAACGCCACT
63 TTTGTC-CAAACGCCACT-AAAACAGGTATCAATAGCGGC-GTTTTATCTAAAACGCCACT
** * * * *
66438566 AAAAACT-GATCAATAGCGTCGTTTTCACGTAAACGCCACTAAAAA-CTTGGGAAATAGCGACGT
1 AAAAA-TAGAGAAATAGCGGCGTTTT--TGTAAACGCCACTAAAAAGCAT-AGAAATAGCGACGT
* *
66438629 TTTTGTCCTAAACGCCACT-AAA-AGTTATCAATAGCGGCGTTTTAATCCAAAACGCCACT
62 TTTTGTCC-AAACGCCACTAAAACAGGTATCAATAGCGGCGTTTT-ATCTAAAACGCCACT
* * *
66438688 AAAAAGTAGAGAAATAGCGGCGTTTTTGTCCAAACTCCACTAAAAAGCATAGAAATAGTGGCGTT
1 AAAAA-TAGAGAAATAGCGGCGTTTTTGT--AAACGCCACTAAAAAGCATAGAAATAGCGACGTT
* * * * *
66438753 TTTGTCCAAACGCCAGTAAAAACAGGGA-AAATAGCGGCGTTTTTATGTAAAACACCACT
63 TTTGTCCAAACGCCACT-AAAACAGGTATCAATAGCGGCG-TTTTATCTAAAACGCCACT
*
66438812 AAAAATAGAGAAATAGAGGCGTTTTTGTTAAAACGCCACTAAAA
1 AAAAATAGAGAAATAGCGGCGTTTTTG-T-AAACGCCACTAAAA
66438856 CTAATCAATA
Statistics
Matches: 237, Mismatches: 36, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
120 1 0.00
121 10 0.04
122 64 0.27
123 121 0.51
124 33 0.14
125 8 0.03
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (120 bp):
AAAAATAGAGAAATAGCGGCGTTTTTGTAAACGCCACTAAAAAGCATAGAAATAGCGACGTTTTT
GTCCAAACGCCACTAAAACAGGTATCAATAGCGGCGTTTTATCTAAAACGCCACT
Found at i:66438766 original size:164 final size:162
Alignment explanation
Indices: 66438462--66438816 Score: 373
Period size: 164 Copynumber: 2.2 Consensus size: 162
66438452 GAAATAGAAG
*
66438462 CGTTTTTGTCTAAAACGCCACTAAAAACATATCAATAGCGGCGGTTTTATCAAAAATGCCACTAA
1 CGTTTTTGTCTAAAACGCCACTAAAAACATATCAATAGCGGCGGTTTTATCAAAAACGCCACTAA
* ** *
66438527 AAACATATCAATAGCGGCGGTTTTATCTAAAACGCCACTAAAAACTGATCAATAGCGTCGTTTTC
66 AAACAGAGAAATAGCGGCGGTTTTATCTAAAACGCCACTAAAAACTGA-CAATAGCGGCGTTTT-
*
66438592 ACGTAAACGCCACTAAAAACTTGGG-AAATAGCGA
129 ACGTAAACGCCACTAAAAAC-AGGGAAAATAGCGA
** *
66438626 CGTTTTTGTCCT-AAACGCCACT-AAAAGTTATCAATAGCGGC-GTTTTAATCCAAAACGCCACT
1 CGTTTTTGT-CTAAAACGCCACTAAAAACATATCAATAGCGGCGGTTTT-ATCAAAAACGCCACT
* * * * * *
66438688 AAAAAGTAGAGAAATAGCGGCGTTTTTGTC-CAAACTCCACTAAAAAGCATAGA-AATAGTGGCG
64 AAAAA-CAGAGAAATAGCGGCGGTTTTATCTAAAACGCCACTAAAAA-C-T-GACAATAGCGGCG
* * *
66438751 TTTT-TGTCCAAACGCCAGTAAAAACAGGGAAAATAGCGG
125 TTTTACGT--AAACGCCACTAAAAACAGGGAAAATAGCGA
* * *
66438790 CGTTTTTATGTAAAACACCACTAAAAA
1 CGTTTTTGTCTAAAACGCCACTAAAAA
66438817 TAGAGAAATA
Statistics
Matches: 159, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
162 7 0.04
163 53 0.33
164 90 0.57
165 7 0.04
166 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (162 bp):
CGTTTTTGTCTAAAACGCCACTAAAAACATATCAATAGCGGCGGTTTTATCAAAAACGCCACTAA
AAACAGAGAAATAGCGGCGGTTTTATCTAAAACGCCACTAAAAACTGACAATAGCGGCGTTTTAC
GTAAACGCCACTAAAAACAGGGAAAATAGCGA
Done.