Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 185 of 214
Found at i:54333833 original size:13 final size:13
Alignment explanation
Indices: 54333815--54333872 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
54333805 TTTTTTATTA
*
54333815 AATTATATTTAAT
1 AATTATATTTTAT
54333828 AATTATTATTTTA-
1 AATTA-TATTTTAT
54333841 AATTATATTTTAT
1 AATTATATTTTAT
*
54333854 ACTATTATATATTAT
1 A--ATTATATTTTAT
54333869 AATT
1 AATT
54333873 TTAGTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.18
13 14 0.36
14 6 0.15
15 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATATTTTAT
Found at i:54333921 original size:60 final size:58
Alignment explanation
Indices: 54333736--54333927 Score: 162
Period size: 60 Copynumber: 3.2 Consensus size: 58
54333726 TATTTTATAG
* *
54333736 TATTATATATTATGATTTTAGTAAATTCATATAAGAATATT-TTAATATTA-AGA-AT-TT
1 TATTATA-ATTATAATTTTAGTAAATTCATATAAGAATTTTATTAA-ATTATA-ATATATT
* * * * * *
54333793 TATTA-AATTATATTTTTTATTAAATT-ATATTTAATAATTATTATTTTAAATTATATTTTATAC
1 TATTATAATTATA-ATTTTAGTAAATTCATA--TAAGAATT-TTA--TTAAATTATAATATAT-T
54333856 TATTATATATTATAATTTTAGTAAATTCATATAAGAATTTTATTAAATTATAATATATT
1 TATTATA-ATTATAATTTTAGTAAATTCATATAAGAATTTTATTAAATTATAATATATT
54333915 TAATTATAATTAT
1 T-ATTATAATTAT
54333928 GTTTAAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
55 8 0.08
56 12 0.11
57 11 0.10
58 2 0.02
59 6 0.06
60 24 0.23
61 6 0.06
62 4 0.04
63 12 0.11
64 12 0.11
65 9 0.08
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (58 bp):
TATTATAATTATAATTTTAGTAAATTCATATAAGAATTTTATTAAATTATAATATATT
Found at i:54334164 original size:45 final size:44
Alignment explanation
Indices: 54334078--54334168 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
54334068 ACCTCTATTC
* *
54334078 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
*** *
54334122 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCATTA
54334167 CA
1 CA
54334169 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
Found at i:54334168 original size:16 final size:16
Alignment explanation
Indices: 54334147--54334216 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
54334137 TTGATTTGCT
54334147 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
54334163 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
54334179 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
54334195 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
54334211 AATACA
1 ATTACA
54334217 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.31, C:0.36, G:0.01, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:54341731 original size:56 final size:56
Alignment explanation
Indices: 54341645--54341776 Score: 228
Period size: 56 Copynumber: 2.4 Consensus size: 56
54341635 GGAGCAAGGC
* *
54341645 AAATTAAAGATACAAGGTAGTGAATCTGATATCTCAGCTCATTTTCAGAGAAAACA
1 AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
* *
54341701 AAATTAAAGATATAAGTTAGTGAATCTGATATCTCAGCTCATTTTTACAGAAAACA
1 AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
54341757 AAATTAAAGATATAAGGTAG
1 AAATTAAAGATATAAGGTAG
54341777 CTCTCTTGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (56 bp):
AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
Found at i:54349662 original size:23 final size:23
Alignment explanation
Indices: 54349572--54349663 Score: 89
Period size: 23 Copynumber: 3.9 Consensus size: 23
54349562 GAGCCATGAT
*
54349572 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-TACGAGCTG--AAA
54349598 CGGTAAGCTC-TATCGAGCTGAAA
1 CGGTAAGCTCATA-CGAGCTGAAA
* *
54349621 CGGTAAGGTCCGTA-GAGCTGAAA
1 CGGTAAGCT-CATACGAGCTGAAA
*
54349644 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACGAGCTG
54349664 TGGTGAGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.05
23 33 0.58
24 2 0.04
25 9 0.16
26 10 0.18
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAA
Found at i:54349951 original size:29 final size:29
Alignment explanation
Indices: 54349918--54349973 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
54349908 TATAATGTAT
54349918 ATAGTATTTGTAACATTTCATTTGCATAA
1 ATAGTATTTGTAACATTTCATTTGCATAA
54349947 ATAGTATTTGTAACATTTCATTTGCAT
1 ATAGTATTTGTAACATTTCATTTGCAT
54349974 TCATGTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (29 bp):
ATAGTATTTGTAACATTTCATTTGCATAA
Found at i:54356541 original size:41 final size:41
Alignment explanation
Indices: 54356507--54356620 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
54356497 ACCGGCAATT
* *
54356507 AGCCTGCTAGACTTAAAGTCCGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
* *
54356548 AGCCTGCTAGACATAAAGTCTGAAATATTTTACTGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
* *
54356589 AACCTGCTAGACATAAAGTCTGAATTATTTCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCA
54356621 TTGGCAATAG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
Found at i:54358812 original size:19 final size:19
Alignment explanation
Indices: 54358767--54358806 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
54358757 AGTTCATGTT
* *
54358767 TTCATTTCACATTTTCATA
1 TTCAATTCACATTTTCAAA
54358786 TTCAATTCACATTTTCAAA
1 TTCAATTCACATTTTCAAA
54358805 TT
1 TT
54358807 ATATTCCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCAATTCACATTTTCAAA
Found at i:54359068 original size:44 final size:44
Alignment explanation
Indices: 54359000--54359158 Score: 186
Period size: 44 Copynumber: 3.7 Consensus size: 44
54358990 AGCAGTAACA
* * * *
54359000 GTAATAGTATTCAACACACAAAGTGTCGACTCTGTAATAGTACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTACG
*
54359044 GTAACAGTATTCGACACACAAAGTGCCGAAT-TGGTAACAGTAACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATCT-GTAATAGT-ACG
* * *
54359089 GTAACCGTATTCGAAACACAAAGTGCCGAATC-G--ATA--ACA
1 GTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTACG
54359128 GTAACAGTATTCGACACACAAAGTGCCGAAT
1 GTAACAGTATTCGACACACAAAGTGCCGAAT
54359159 TAGTAACAGT
Statistics
Matches: 101, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
39 31 0.31
42 2 0.02
43 1 0.01
44 35 0.35
45 32 0.32
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (44 bp):
GTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTACG
Found at i:54359087 original size:39 final size:39
Alignment explanation
Indices: 54358994--54359175 Score: 175
Period size: 39 Copynumber: 4.4 Consensus size: 39
54358984 AACGGTAGCA
* * * *
54358994 GTAACAGTAATAGTATTCAACACACAAAGTGTCGACTCTG
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-TG
* *
54359034 TAATAGTACGGTAACAGTATTCGACACACAAAGTGCCGAATTG
1 --GTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
* *
54359077 GTAACAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAATCG
1 GTAACAGTAAC----A--GTATTCGACACACAAAGTGCCGAATTG
* *
54359122 ATAACAGTAACAGTATTCGACACACAAAGTGCCGAATTA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
54359161 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
54359176 GTCGGCTTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
39 45 0.38
41 3 0.03
42 2 0.02
43 3 0.03
44 29 0.25
45 35 0.30
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
Found at i:54359172 original size:45 final size:44
Alignment explanation
Indices: 54358992--54359175 Score: 209
Period size: 45 Copynumber: 4.2 Consensus size: 44
54358982 GTAACGGTAG
* * * *
54358992 CAGTAACAGTAATAGTATTCAACACACAAAGTGTCGACTCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-TGTAA
* *
54359037 TAGT-ACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT-GTAA
* * * *
54359081 CAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAATCG---
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTGTAA
54359122 -A-TAACAGTAACAGTATTCGACACACAAAGTGCCGAATTAGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT-GTAA
54359165 CAGTAACAGTA
1 CAGTAACAGTA
54359176 GTCGGCTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
39 33 0.28
40 2 0.02
43 1 0.01
44 38 0.32
45 43 0.37
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (44 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTGTAA
Found at i:54362840 original size:5 final size:5
Alignment explanation
Indices: 54362830--54362856 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
54362820 ACTACACGAT
54362830 GAAAA GAAAA GAAAA GAAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GA
54362857 TTATATATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:54367903 original size:22 final size:22
Alignment explanation
Indices: 54367878--54367941 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
54367868 TCTCCGATTA
54367878 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
54367900 TTAGCACATTTGTGCTCTATGT
1 TTAGCACATTAGTGCTCTCTGT
* *
54367922 ATAGCACTTTAGTGCTCTCT
1 TTAGCACATTAGTGCTCTCT
54367942 ATTCAATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:54379549 original size:11 final size:11
Alignment explanation
Indices: 54379485--54379558 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
54379475 CTAAATAATA
*
54379485 AAAATATTTTT
1 AAAATATATTT
*
54379496 AAAATTTAATTAT
1 AAAATAT-ATT-T
*
54379509 AAAA-ATATAT
1 AAAATATATTT
**
54379519 AAAATATCAACT
1 AAAATAT-ATTT
54379531 AAATATATATTT
1 AAA-ATATATTT
54379543 AAAATATATTT
1 AAAATATATTT
54379554 AAAAT
1 AAAAT
54379559 TTTTAATTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
10 5 0.10
11 23 0.46
12 13 0.26
13 9 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATATATTT
Found at i:54379907 original size:36 final size:36
Alignment explanation
Indices: 54379860--54379932 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
54379850 TTTTTATGGA
54379860 TAAACTATAAAAACGGTCATCCAGCTATGCCATTCG
1 TAAACTATAAAAACGGTCATCCAGCTATGCCATTCG
*
54379896 TAAACTATAAAAACGGTCATCCAGCTATGCCTTTCG
1 TAAACTATAAAAACGGTCATCCAGCTATGCCATTCG
54379932 T
1 T
54379933 TCTATTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (36 bp):
TAAACTATAAAAACGGTCATCCAGCTATGCCATTCG
Found at i:54381279 original size:61 final size:61
Alignment explanation
Indices: 54381152--54381278 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
54381142 TATATTTAAA
*** *
54381152 ATTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGGGCAAAATTTATTGAT
1 ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
* ** *
54381213 ATTTTTAGAATTAGAACTAAAACAATAAATTTTGTAAACATTGAGGGTTAAATTTGTTGA-
1 ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
54381273 ATTTTT
1 ATTTTT
54381279 TTTATATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 6 0.10
61 52 0.90
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (61 bp):
ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
Found at i:54383263 original size:19 final size:19
Alignment explanation
Indices: 54383233--54383290 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
54383223 ATTAAAAAAA
54383233 TATAAA-ATTTTGAATTTT
1 TATAAATATTTTGAATTTT
54383251 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
* *
54383270 AAAAAATTATTTTGAATTTT
1 TATAAA-TATTTTGAATTTT
54383290 T
1 T
54383291 TTTTGTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 6 0.17
19 16 0.46
20 13 0.37
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:54383482 original size:24 final size:23
Alignment explanation
Indices: 54383437--54383480 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54383427 AATTCGAATT
*
54383437 ACTTATTTTGATTGACTCAAATA
1 ACTTAATTTGATTGACTCAAATA
54383460 ACTTAATTTGATT-AGCTCAAA
1 ACTTAATTTGATTGA-CTCAAA
54383481 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
ACTTAATTTGATTGACTCAAATA
Found at i:54384456 original size:7 final size:6
Alignment explanation
Indices: 54384437--54384472 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
54384427 TGCAGTGAAT
*
54384437 ATAAATA ATAAAA ATAAAA ATAAAA ATAAAA GTAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
54384473 GGTATAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:54385237 original size:35 final size:35
Alignment explanation
Indices: 54385191--54385260 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
54385181 ACTACTGTTG
54385191 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
1 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
54385226 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
1 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
54385261 TGGGAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
Found at i:54388565 original size:47 final size:47
Alignment explanation
Indices: 54388514--54388610 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
54388504 CATCAACCTT
54388514 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
1 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
54388561 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
1 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
54388608 ATT
1 ATT
54388611 CCTCTGCCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (47 bp):
ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
Found at i:54395595 original size:17 final size:17
Alignment explanation
Indices: 54395568--54395601 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
54395558 CGATTCAAAG
54395568 TAAATAAATTATTAAAAA
1 TAAATAAATTA-TAAAAA
54395586 TAAA-AAATTATAAAAA
1 TAAATAAATTATAAAAA
54395602 CCAAATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAAATTATAAAAA
Found at i:54400776 original size:16 final size:16
Alignment explanation
Indices: 54400728--54400776 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
54400718 TCAAGAATAC
54400728 TTATATTTAGAACAA-
1 TTATATTTAGAACAAT
* * *
54400743 CTATTATTTGGAAAAAT
1 TTA-TATTTAGAACAAT
54400760 TTATATTTAGAACAAT
1 TTATATTTAGAACAAT
54400776 T
1 T
54400777 GTGTTTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
TTATATTTAGAACAAT
Found at i:54403308 original size:4 final size:4
Alignment explanation
Indices: 54403301--54403354 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
54403291 CATAACATTA
54403301 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
54403349 TATG TA
1 TATG TA
54403355 AAGGTGTCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:54403504 original size:17 final size:17
Alignment explanation
Indices: 54403482--54403514 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54403472 GCCCATCTCC
54403482 GAAGCTTGGCAAATATG
1 GAAGCTTGGCAAATATG
54403499 GAAGCTTGGCAAATAT
1 GAAGCTTGGCAAATAT
54403515 AATCTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (17 bp):
GAAGCTTGGCAAATATG
Found at i:54413112 original size:18 final size:19
Alignment explanation
Indices: 54413076--54413113 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
54413066 ATAAAAACAA
*
54413076 AAATTGAATATTGCAAAAT
1 AAATTGAATAATGCAAAAT
54413095 AAATTGAATAAT-CAAAAT
1 AAATTGAATAATGCAAAAT
54413113 A
1 A
54413114 GTCTCACATA
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:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
AAATTGAATAATGCAAAAT
Found at i:54419455 original size:2 final size:2
Alignment explanation
Indices: 54419448--54419485 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
54419438 ACCTTTATAA
* *
54419448 GT GT GT GT GT GT GT GT CT GT GT GT GT GT GT TT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
54419486 ATAATTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.45, T:0.53
Consensus pattern (2 bp):
GT
Found at i:54425038 original size:3 final size:3
Alignment explanation
Indices: 54425030--54425057 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54425020 CTTTACCATC
54425030 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54425058 TTGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54427536 original size:16 final size:17
Alignment explanation
Indices: 54427510--54427546 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
54427500 GTTTTTTCCG
*
54427510 GGAGAAGTGGGAAAGGA
1 GGAGAAGTGGGAAAGCA
54427527 GGAG-AGTGGGAAAGCA
1 GGAGAAGTGGGAAAGCA
54427543 GGAG
1 GGAG
54427547 TTGAAGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.38, C:0.03, G:0.54, T:0.05
Consensus pattern (17 bp):
GGAGAAGTGGGAAAGCA
Found at i:54432661 original size:24 final size:24
Alignment explanation
Indices: 54432634--54432685 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54432624 TTTCTAGAAG
* **
54432634 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
54432658 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
54432682 ATTT
1 ATTT
54432686 GACTTTGATT
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:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:54441704 original size:3 final size:3
Alignment explanation
Indices: 54441696--54441733 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54441686 ATCACGTGTT
54441696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54441734 TGGATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54441815 original size:73 final size:73
Alignment explanation
Indices: 54441734--54441892 Score: 309
Period size: 73 Copynumber: 2.2 Consensus size: 73
54441724 TATTATTATT
*
54441734 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
54441799 ATTTTAAG
66 ATTTTAAG
54441807 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
54441872 ATTTTAAG
66 ATTTTAAG
54441880 TGGATGTAATGAT
1 TGGATGTAATGAT
54441893 TCCAACTAAG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 85 1.00
ACGTcount: A:0.27, C:0.05, G:0.26, T:0.42
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:54446128 original size:3 final size:3
Alignment explanation
Indices: 54446120--54446151 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54446110 ATCACGTGTT
54446120 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54446152 TGGATGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54446271 original size:73 final size:73
Alignment explanation
Indices: 54446152--54446310 Score: 309
Period size: 73 Copynumber: 2.2 Consensus size: 73
54446142 TATTATTATT
*
54446152 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
54446217 ATTTTAAG
66 ATTTTAAG
54446225 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
54446290 ATTTTAAG
66 ATTTTAAG
54446298 TGGATGTAATGAT
1 TGGATGTAATGAT
54446311 TCCAACTAAG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 85 1.00
ACGTcount: A:0.27, C:0.05, G:0.26, T:0.42
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:54451732 original size:9 final size:9
Alignment explanation
Indices: 54451718--54451742 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54451708 TTGACATGAC
54451718 TTTGTCATT
1 TTTGTCATT
54451727 TTTGTCATT
1 TTTGTCATT
54451736 TTTGTCA
1 TTTGTCA
54451743 CATTTGCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (9 bp):
TTTGTCATT
Found at i:54454759 original size:33 final size:33
Alignment explanation
Indices: 54454716--54454783 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
54454706 CAAAGTTACC
* *
54454716 TTCACGAGCAACGACATCATCTTAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
54454749 TTCACAAGCAACGACATCATCTCAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
54454782 TT
1 TT
54454784 GCTAAAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (33 bp):
TTCACAAGCAACGACATCATCTCAGTGGAAACA
Found at i:54460130 original size:12 final size:12
Alignment explanation
Indices: 54460113--54460173 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
54460103 AGGCAACCCA
54460113 ATTTTTATTTTT
1 ATTTTTATTTTT
54460125 ATTTTTA--TTT
1 ATTTTTATTTTT
54460135 ATTTTT-TTCTTT
1 ATTTTTATT-TTT
*
54460147 A-CTTTATTTATT
1 ATTTTTATTT-TT
54460159 A-TTTTA-TTTT
1 ATTTTTATTTTT
54460169 ATTTT
1 ATTTT
54460174 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 12 0.29
11 9 0.22
12 20 0.49
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:54460147 original size:22 final size:20
Alignment explanation
Indices: 54460113--54460181 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 20
54460103 AGGCAACCCA
54460113 ATTTTTATTTTTATTTTTATTT
1 ATTTTT-TTTTTA-TTTTATTT
*
54460135 ATTTTTTTCTTTACTTTATTT
1 ATTTTTTT-TTTATTTTATTT
*
54460156 ATTATTTTATTTTATTTTACTT
1 ATT-TTTT-TTTTATTTTATTT
54460178 ATTT
1 ATTT
54460182 GGATATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 13 0.32
22 27 0.66
23 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTTTATTTTATTT
Found at i:54460152 original size:17 final size:15
Alignment explanation
Indices: 54460116--54460173 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 15
54460106 CAACCCAATT
54460116 TTTATTTTTATTTTTA
1 TTTATTTTT-TTTTTA
54460132 TTTATTTTTTTCTTTA
1 TTTATTTTTTT-TTTA
*
54460148 CTTTATTTATTATTTTA
1 -TTTATTT-TTTTTTTA
54460165 TTTTATTTT
1 -TTTATTTT
54460174 ACTTATTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 2 0.05
16 14 0.38
17 18 0.49
18 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTTTTTA
Found at i:54461220 original size:20 final size:20
Alignment explanation
Indices: 54461195--54461233 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54461185 CCTAAAGCAT
*
54461195 AAAAAAATGAGAAAAAAAAC
1 AAAAAAAAGAGAAAAAAAAC
*
54461215 AAAAAAAAGATAAAAAAAA
1 AAAAAAAAGAGAAAAAAAA
54461234 ATAATTTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGAGAAAAAAAAC
Found at i:54461237 original size:10 final size:10
Alignment explanation
Indices: 54461195--54461237 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
54461185 CCTAAAGCAT
54461195 AAAAAAATGAGA
1 AAAAAAAT-A-A
*
54461207 AAAAAAACAA
1 AAAAAAATAA
54461217 AAAAAAGATAA
1 AAAAAA-ATAA
54461228 AAAAAAATAA
1 AAAAAAATAA
54461238 TTTGGGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 11 0.39
11 10 0.36
12 7 0.25
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:54463792 original size:10 final size:10
Alignment explanation
Indices: 54463777--54463801 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54463767 ATAATCAATA
54463777 TTTTTTTATT
1 TTTTTTTATT
54463787 TTTTTTTATT
1 TTTTTTTATT
54463797 TTTTT
1 TTTTT
54463802 GAACAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:54465356 original size:23 final size:21
Alignment explanation
Indices: 54465336--54465402 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 21
54465326 TCCATTTACC
54465336 TTTTTTATATATATTATTTTA
1 TTTTTTATATATATTATTTTA
*
54465357 TTTTATTATGTACTATTATTTTAA
1 TTTT-TTATATA-TATTATTTT-A
54465381 TTCTTTT-TATCATA-TATTTTA
1 TT-TTTTATAT-ATATTATTTTA
54465402 T
1 T
54465403 CTAGTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 6 0.15
22 12 0.31
23 13 0.33
24 6 0.15
25 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (21 bp):
TTTTTTATATATATTATTTTA
Found at i:54465622 original size:25 final size:23
Alignment explanation
Indices: 54465584--54465642 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
54465574 TAATAAACTA
* *
54465584 TTTTTAT-TCTACATACATATCT
1 TTTTTATATATACATACATATAT
*
54465606 TTGATTTATATATACATACTTATAT
1 TT--TTTATATATACATACATATAT
54465631 TTTTTATATATA
1 TTTTTATATATA
54465643 TTTTATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.06
23 10 0.32
24 5 0.16
25 14 0.45
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTTATATATACATACATATAT
Found at i:54465648 original size:20 final size:20
Alignment explanation
Indices: 54465614--54465663 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
54465604 CTTTGATTTA
* *
54465614 TATATACATA-CTTATATTT
1 TATATACATATTTTATAATT
* *
54465633 TTTATATATATTTTATAATT
1 TATATACATATTTTATAATT
54465653 TATATACATAT
1 TATATACATAT
54465664 ACATATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATACATATTTTATAATT
Found at i:54474704 original size:24 final size:24
Alignment explanation
Indices: 54474666--54474917 Score: 123
Period size: 24 Copynumber: 10.8 Consensus size: 24
54474656 TGAATTGGAT
* *
54474666 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
54474691 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
** *
54474715 AATTT-AAA-AATTTTGT-TGAT-
1 AATTTAAAATAATAATATATGATA
* * **
54474735 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
54474760 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
* *
54474784 AATTT-AAA-AATATTA-AGGATA
1 AATTTAAAATAATAATATATGATA
* *
54474805 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
54474829 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
54474852 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
54474875 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* *
54474899 AATCTAAAATAATGATATA
1 AATTTAAAATAATAATATA
54474918 AAATACACTT
Statistics
Matches: 168, Mismatches: 43, Indels: 33
0.69 0.18 0.14
Matches are distributed among these distances:
20 4 0.02
21 11 0.07
22 20 0.12
23 49 0.29
24 71 0.42
25 13 0.08
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:54476598 original size:15 final size:15
Alignment explanation
Indices: 54476578--54476630 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
54476568 ACCGTTGAAA
*
54476578 CCCTAAATCTCAAAC
1 CCCTAAATCTCTAAC
54476593 CCCTAAA-CATCTAAC
1 CCCTAAATC-TCTAAC
*
54476608 CCCTAAACCTCTAAC
1 CCCTAAATCTCTAAC
54476623 CCCTAAAT
1 CCCTAAAT
54476631 TAACCTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 1 0.03
15 32 0.94
16 1 0.03
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCTAAC
Found at i:54477202 original size:41 final size:41
Alignment explanation
Indices: 54477157--54477557 Score: 287
Period size: 41 Copynumber: 9.8 Consensus size: 41
54477147 AGGCAGGAGA
* *
54477157 ATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATCCAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* * *
54477198 ATTAGCAGCGCTTAAATAAAACCGCCACTAAAGATCCAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* ** * *
54477239 ATTAGCGGCGCTGAAATAAAGTCGCCGCTAAAGA-CCTGAGCT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAG-T
* * * * * *
54477281 TTTA-CGGCGTTCATATAATAACACCACTAAAGATCTAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* * * * *
54477321 ATTAGCGTCGCTAAAATAAAATCGCCGCTAAAGA-CCTGAGCT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAG-T
* * * *
54477363 -TTTGCGGCGTTCATATAAAAACGCCACTAAAGAT-TAGAG-
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCA-AGT
* * *
54477402 ATTTAGCGGCGCTCAGATAAAAATGCCACTAAAGAT-CAGAGA
1 A-TTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCA-AGT
** * * *** *
54477444 ATTAGCCACGCCCAGATAAAAACGCCACTAAAGATAGGAGA
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* ** *
54477485 ATTAGCGGCGCT-AAGATAAAAACGCCACTATAGATCCGTGC
1 ATTAGCGGCGCTCAA-ATAAAAACGCCACTAAAGATCCAAGT
* * *
54477526 ATTAGTGGCGCACAAATAAAAACGCCGCTAAA
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAA
54477558 TGTTTAAAAA
Statistics
Matches: 280, Mismatches: 66, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
40 8 0.03
41 263 0.94
42 9 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
Found at i:54484272 original size:7 final size:6
Alignment explanation
Indices: 54484252--54484302 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
54484242 GTTTCCCTGC
* * * *
54484252 AAAATA AAAATA AAAATT AAAATA AATAATA AGAA-A AAATTA AAATTA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
54484300 AAA
1 AAA
54484303 TGTGTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
5 3 0.08
6 30 0.79
7 5 0.13
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:54505110 original size:18 final size:19
Alignment explanation
Indices: 54505065--54505110 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
54505055 TGTAATTAGA
*
54505065 AAAATGAATAAAAACTATT
1 AAAATAAATAAAAACTATT
*
54505084 ATAAA-AAAT-AAAACTTTT
1 A-AAATAAATAAAAACTATT
54505102 AAAATAAAT
1 AAAATAAAT
54505111 TCAAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 4 0.17
20 3 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAATAAAAACTATT
Found at i:54519630 original size:20 final size:21
Alignment explanation
Indices: 54519605--54519644 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
54519595 CCACACTTCC
54519605 AATTGTATGTACTT-ATCTTT
1 AATTGTATGTACTTAATCTTT
*
54519625 AATTGTATGTGCTTAATCTT
1 AATTGTATGTACTTAATCTT
54519645 GTTTATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (21 bp):
AATTGTATGTACTTAATCTTT
Found at i:54523903 original size:60 final size:60
Alignment explanation
Indices: 54523828--54523949 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
54523818 ACAAACTCTA
54523828 CTAACAGTGAACCAAATACACTAAATCTATTTAATGTATAGATTAAACTTGAGTTTCAAT
1 CTAACAGTGAACCAAATACACTAAATCTATTTAATGTATAGATTAAACTTGAGTTTCAAT
54523888 CTAACAGTGAACCAAATACACTAAATCTATTTAATGTATAGATTAAACTTGAGTTTCAAT
1 CTAACAGTGAACCAAATACACTAAATCTATTTAATGTATAGATTAAACTTGAGTTTCAAT
54523948 CT
1 CT
54523950 GTAAAGCTCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (60 bp):
CTAACAGTGAACCAAATACACTAAATCTATTTAATGTATAGATTAAACTTGAGTTTCAAT
Found at i:54524614 original size:3 final size:3
Alignment explanation
Indices: 54524606--54524631 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54524596 TTCATCCTCA
54524606 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
54524632 ATCATGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:54535234 original size:21 final size:20
Alignment explanation
Indices: 54535210--54535276 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
54535200 TTACTTTCCT
*
54535210 TTTAGCTCTCTCGAGCTTTTG
1 TTTAGCTCTAT-GAGCTTTTG
* *
54535231 TTTAACACATATGAG-TTTTCG
1 TTTAGCTC-TATGAGCTTTT-G
*
54535252 TTTAGCTCTTTTGAGCTTTTG
1 TTTAGCTC-TATGAGCTTTTG
54535273 TTTA
1 TTTA
54535277 ACCCTTATGG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 4 0.11
21 26 0.72
22 6 0.17
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTAGCTCTATGAGCTTTTG
Found at i:54535301 original size:42 final size:42
Alignment explanation
Indices: 54535210--54535358 Score: 140
Period size: 42 Copynumber: 3.5 Consensus size: 42
54535200 TTACTTTCCT
* * * *
54535210 TTTAGCTCTCTCGAGCTTTTGTTTAACACATATGAGTTT-TCG
1 TTTAGCTCTCACGAGCTTCTGTTTAACACTTATGGGTTTCT-G
*** * *
54535252 TTTAGCTCTTTTGAGCTTTTGTTTAACCCTTATGGGTTTCTG
1 TTTAGCTCTCACGAGCTTCTGTTTAACACTTATGGGTTTCTG
* * * *
54535294 TTCAGCTCTTACAAGCTTCTGTTCAACTA-TTATGGGTTTCTG
1 TTTAGCTCTCACGAGCTTCTGTTTAAC-ACTTATGGGTTTCTG
*
54535336 TTTAGCTCTCATGAGCTTCTGTT
1 TTTAGCTCTCACGAGCTTCTGTT
54535359 CAGCCTTCGA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
42 88 0.99
43 1 0.01
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTAGCTCTCACGAGCTTCTGTTTAACACTTATGGGTTTCTG
Found at i:54535304 original size:21 final size:21
Alignment explanation
Indices: 54535255--54535362 Score: 81
Period size: 21 Copynumber: 5.1 Consensus size: 21
54535245 GTTTTCGTTT
* * *
54535255 AGCTCTTTTGAGCTTTTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * *
54535276 AACCCTTATGGGTTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
**
54535297 AGCTCTTACAAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * * * *
54535318 AACTATTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
*
54535339 AGCTCTCATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
54535360 AGC
1 AGC
54535363 CTTCGAGCTT
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:54540583 original size:25 final size:26
Alignment explanation
Indices: 54540554--54540609 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
54540544 TGTAAACAAT
* *
54540554 AAGCTCT-TTCAAGCTGAATAACGAG
1 AAGCTCTATGCAAGCTAAATAACGAG
* *
54540579 AAGCT-TATGCGAGCTAAATAACGGG
1 AAGCTCTATGCAAGCTAAATAACGAG
54540604 AAGCTC
1 AAGCTC
54540610 ATGTGAGCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (26 bp):
AAGCTCTATGCAAGCTAAATAACGAG
Found at i:54540617 original size:25 final size:25
Alignment explanation
Indices: 54540565--54540636 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
54540555 AGCTCTTTCA
* *
54540565 AGCTGAATAACGAGAAGCTTATGCG
1 AGCTGAATAACGGGAAGCTCATGCG
* *
54540590 AGCTAAATAACGGGAAGCTCATGTG
1 AGCTGAATAACGGGAAGCTCATGCG
* *
54540615 AGCTGAGTATCGGGAAGCTCAT
1 AGCTGAATAACGGGAAGCTCAT
54540637 AAGAGTTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (25 bp):
AGCTGAATAACGGGAAGCTCATGCG
Found at i:54542386 original size:25 final size:25
Alignment explanation
Indices: 54542353--54542416 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
54542343 ACGAGCTGTA
* *
54542353 AACAGGAAGCTCCTCTAAGCTGAAT
1 AACAGGAAGCTCATCTAAGCTAAAT
* *
54542378 AACAGGAAGCTCATGTGAGCTAAAT
1 AACAGGAAGCTCATCTAAGCTAAAT
*
54542403 AACGGGAAGCTCAT
1 AACAGGAAGCTCAT
54542417 AAGAGCTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (25 bp):
AACAGGAAGCTCATCTAAGCTAAAT
Found at i:54544559 original size:27 final size:27
Alignment explanation
Indices: 54544494--54544565 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
54544484 TAGTGGAGGG
* *
54544494 ACTGCCACAGGTGGCACCAATGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
* * * *
54544521 AGTGGCAGAGGCAGCACCAAAGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
54544548 ACTGCCACAGGCGGCACC
1 ACTGCCACAGGCGGCACC
54544566 CCCCCTTTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.33, G:0.32, T:0.10
Consensus pattern (27 bp):
ACTGCCACAGGCGGCACCAAAGGTGCC
Found at i:54544989 original size:159 final size:157
Alignment explanation
Indices: 54544670--54544994 Score: 485
Period size: 158 Copynumber: 2.1 Consensus size: 157
54544660 TACGAAAAGA
* * *
54544670 AATAAAAAATGAAAATAGTATATTTACTGAAAGTAATAAAATTCGAAAAAAGAAAAATACGAACA
1 AATAAAATACGAAAATAATATATTTACTGAAAGTAATAAAATTCGAAAAAAGAAAAATACGAACA
54544735 AATGGCCAAAATAAGGGTTTTTCAATAAATTTATATAAAAAACATACTAAAATAACACATTTCAA
66 AATGGCCAAAATAAGGGTTTTTCAATAAATTTATATAAAAAACATACTAAAATAACACATTTCAA
54544800 ACATTATGTACTAAAATAATATAAAAT
131 ACATTATGTACTAAAATAATATAAAAT
**
54544827 AATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAA-TCTGAAAATAAGAAAAATACGAA
1 AATAAAATACGAAAATAATATATTTACTGAAAGTAATAAAATTC-GAAAA-AAGAAAAATACGAA
* * * * *
54544891 CAAATGGCCAAAATGAGGGTTTTTTACTAAATTTATATAAAAAA-ATACACTAAATTAATACATT
64 CAAATGGCCAAAATAAGGGTTTTTCAATAAATTTATATAAAAAACAT--ACTAAAATAACACATT
*
54544955 TCAAACTTTATGTTA-TAAAATAATATAAAAT
127 TCAAACATTATG-TACTAAAATAATATAAAAT
54544986 AATAAAATA
1 AATAAAATA
54544995 GTATTAATTT
Statistics
Matches: 152, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
156 2 0.01
157 43 0.28
158 55 0.36
159 50 0.33
160 2 0.01
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (157 bp):
AATAAAATACGAAAATAATATATTTACTGAAAGTAATAAAATTCGAAAAAAGAAAAATACGAACA
AATGGCCAAAATAAGGGTTTTTCAATAAATTTATATAAAAAACATACTAAAATAACACATTTCAA
ACATTATGTACTAAAATAATATAAAAT
Found at i:54545344 original size:159 final size:160
Alignment explanation
Indices: 54545009--54545619 Score: 916
Period size: 160 Copynumber: 3.9 Consensus size: 160
54544999 TAATTTAGTG
* *
54545009 TGTTTGAAATGTATTAATTTAGTGTGTCTTTTTATATAAATTTAGTAAAAAAACCCTCATTTTGG
1 TGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAACCTTCATTTTGG
* *
54545074 TCATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAAATATACTATTTTCGTA
66 CCATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTC-AAAAAATATACTATTTTCGTA
*
54545139 TTTTATTATTTTATATTATTTTATTACATAAA
130 TTTTATTATTTTATATTATTTTAGTACA-AAA
54545171 -GTTTGAAATGTATTAATTTAGTGT-TTTTTTTATATAAATTTAGTAAAAAAACCTTCATTTTGG
1 TGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAACCTTCATTTTGG
* * *
54545234 CCATTTGTTTGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTAT
66 CCATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
54545299 TTTATTATTTTATATTATTTTAGTACAAAA
131 TTTATTATTTTATATTATTTTAGTACAAAA
* * *
54545329 TGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTATTAAAAAATCC-TCATTTTGG
1 TGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAACCTTCATTTTGG
*
54545393 CCATTTGTTCGTATTTTTCTTATTTTCAAATTTTATTACTTTC-AAAAATATACTATTTTCGTAT
66 CCATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
*
54545457 TTTATTATTTTATATTATTTTAGTACATAA
131 TTTATTATTTTATATTATTTTAGTACAAAA
* * * * * *
54545487 TATTTGAAATGTATTATTTTAGTGTGTTTTTTTTTATATAAATATAGT-GAAAAACATTTATTTT
1 TGTTTGAAATGTATTAATTTAGTGTG--TTTTTTTATATAAATTTAGTAAAAAAACCTTCATTTT
* **
54545551 GGCCATTTGTTCGTA--TTT-TT-TTTCCGAATTTTATTACTTTCAGCAAATATACTATTTTCGT
64 GGCCATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGT
*
54545612 TTTTTATT
129 ATTTTATT
54545620 TCTTTTCGTA
Statistics
Matches: 417, Mismatches: 26, Indels: 17
0.91 0.06 0.04
Matches are distributed among these distances:
156 19 0.05
157 26 0.06
158 80 0.19
159 124 0.30
160 144 0.35
161 24 0.06
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (160 bp):
TGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAACCTTCATTTTGG
CCATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
TTTATTATTTTATATTATTTTAGTACAAAA
Found at i:54545683 original size:319 final size:318
Alignment explanation
Indices: 54545009--54545619 Score: 867
Period size: 319 Copynumber: 1.9 Consensus size: 318
54544999 TAATTTAGTG
* * ** *
54545009 TGTTTGAAATGTATTAATTTAGTGTGTCTTTTTATATAAATTTAGTAAAAAAACCCTCATTTTGG
1 TGTTTGAAATGTATTATTTTAATGACTATTTTTATATAAATTTAGTAAAAAAACCCTCATTTTGG
* **
54545074 TCATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAAATATACTATTTTCGTA
66 CCATTTGTTCGTATTTTTCTTATTTTCAAATTTTATTACTTTC-AAAAAATATACTATTTTCGTA
*
54545139 TTTTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTTTTTTTTAT
130 TTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTTTTTTTTAT
* * * * *
54545204 ATAAATTTAGTAAAAAAACCTTCATTTTGGCCATTTGTTTGTATTTTTCTTATTTTCGGATTTTA
195 ATAAATATAGTAAAAAAACATTCATTTTGGCCATTTGTTCGTA-TTTTCTTATTTCCGAATTTTA
* *
54545269 TTACTTTCAAAAAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACAAAA
259 TTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTAAAAAA
* ** * * *
54545329 TGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTA-TTAAAAAATCCTCATTTTGG
1 TGTTTGAAATGTATTATTTTAATGACTATTTTTATATAAATTTAGTAAAAAAACCCTCATTTTGG
54545393 CCATTTGTTCGTATTTTTCTTATTTTCAAATTTTATTACTTTC-AAAAATATACTATTTTCGTAT
66 CCATTTGTTCGTATTTTTCTTATTTTCAAATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
*
54545457 TTTATTATTTTATATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTGTGTTTTTTTT
131 TTTATTATTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTA--GTG-TTTTTTT
* *
54545521 TATATAAATATAGT-GAAAAACATTTATTTTGGCCATTTGTTCGTA-TTT-TT-TTTCCGAATTT
192 TATATAAATATAGTAAAAAAACATTCATTTTGGCCATTTGTTCGTATTTTCTTATTTCCGAATTT
** *
54545582 TATTACTTTCAGCAAATATACTATTTTCGTTTTTTATT
257 TATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
54545620 TCTTTTCGTA
Statistics
Matches: 267, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
315 43 0.16
316 2 0.01
317 71 0.27
318 1 0.00
319 88 0.33
320 62 0.23
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (318 bp):
TGTTTGAAATGTATTATTTTAATGACTATTTTTATATAAATTTAGTAAAAAAACCCTCATTTTGG
CCATTTGTTCGTATTTTTCTTATTTTCAAATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTTTTTTTTATA
TAAATATAGTAAAAAAACATTCATTTTGGCCATTTGTTCGTATTTTCTTATTTCCGAATTTTATT
ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTAAAAAA
Found at i:54546151 original size:43 final size:43
Alignment explanation
Indices: 54546072--54546259 Score: 248
Period size: 43 Copynumber: 4.5 Consensus size: 43
54546062 AAATATATAT
* *
54546072 TTTTTTTAAATTTTAAAATATTTTTTACATAC---TTTTTTAA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTAA
54546112 TTTTTTTTAAATTTTAAAATA-TTTTAAAATACTTTTTTTTTTAA
1 -TTTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTTTTAA
54546156 TTTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTTTTAA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTTTTAA
*
54546199 TTTTTTT-AATTTTAAAATATTTTTAAAGTA--TTTTTTTTAA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTAA
*
54546239 TTTTTTAAAATTTTTAAAATA
1 TTTTTTTAAA-TTTTAAAATA
54546260 AAAATGGGCC
Statistics
Matches: 136, Mismatches: 4, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
40 25 0.18
41 22 0.16
42 22 0.16
43 59 0.43
44 8 0.06
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (43 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTAA
Found at i:54546178 original size:17 final size:17
Alignment explanation
Indices: 54546132--54546181 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
54546122 ATTTTAAAAT
54546132 ATTTTAAAATACTTTTT-
1 ATTTTAAAATA-TTTTTA
* *
54546149 -TTTT-TAATTTTTTTA
1 ATTTTAAAATATTTTTA
54546164 ATTTTAAAATATTTTTA
1 ATTTTAAAATATTTTTA
54546181 A
1 A
54546182 AATACTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.19
15 3 0.12
16 8 0.31
17 10 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAAAATATTTTTA
Found at i:54546221 original size:17 final size:17
Alignment explanation
Indices: 54546176--54546224 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
54546166 TTTAAAATAT
54546176 TTTTAAAATACTTTTT--
1 TTTTAAAATA-TTTTTAA
* *
54546192 TTTT-TAATTTTTTTAA
1 TTTTAAAATATTTTTAA
54546208 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
54546225 AGTATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 5 0.19
15 3 0.12
16 8 0.31
17 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:54572833 original size:15 final size:15
Alignment explanation
Indices: 54572815--54572844 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54572805 ATAAATGCAG
54572815 AAAAATTAAAGTATT
1 AAAAATTAAAGTATT
*
54572830 AAAAATTTAAGTATT
1 AAAAATTAAAGTATT
54572845 CAATTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAAATTAAAGTATT
Found at i:54595570 original size:20 final size:19
Alignment explanation
Indices: 54595545--54595583 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
54595535 GTGCGTCTGC
54595545 TTCTTTCCTTCTTTCTCTTT
1 TTCTTTCCTTCTTT-TCTTT
*
54595565 TTCTTTCTTTCTTTTCTTT
1 TTCTTTCCTTCTTTTCTTT
54595584 CTAATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (19 bp):
TTCTTTCCTTCTTTTCTTT
Found at i:54598190 original size:41 final size:41
Alignment explanation
Indices: 54598133--54598245 Score: 192
Period size: 41 Copynumber: 2.8 Consensus size: 41
54598123 TTTAACGTAT
* *
54598133 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
54598174 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
54598215 TCACCGGCACTTAGCCTGCTAGGTTTATAAC
1 TCACCGGCACTTAGCCTGCTAGGTTTATAAC
54598246 TGCAATGACC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
40 2 0.03
41 67 0.97
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:54598750 original size:5 final size:5
Alignment explanation
Indices: 54598740--54598783 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
54598730 ATAAGTAAGT
*
54598740 TATTA TATTA TATTA TTATAA TATTA TATTA TTATTA TA-TA TAT
1 TATTA TATTA TATTA -TATTA TATTA TATTA -TATTA TATTA TAT
54598784 AAAACAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.12
5 21 0.62
6 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:54598756 original size:8 final size:8
Alignment explanation
Indices: 54598745--54598774 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
54598735 TAAGTTATTA
54598745 TATTATAT
1 TATTATAT
*
54598753 TATTATAA
1 TATTATAT
54598761 TATTATAT
1 TATTATAT
54598769 TATTAT
1 TATTAT
54598775 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:54598763 original size:16 final size:16
Alignment explanation
Indices: 54598739--54598783 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
54598729 AATAAGTAAG
54598739 TTATTATATTATATTA
1 TTATTATATTATATTA
*
54598755 TTATAATATTATATTA
1 TTATTATATTATATTA
54598771 TTATTATA-TATAT
1 TTATTATATTATAT
54598784 AAAACAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATATTATATTA
Found at i:54599533 original size:14 final size:15
Alignment explanation
Indices: 54599505--54599534 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54599495 TACTACAAGG
54599505 TTATTTTATTTTAAA
1 TTATTTTATTTTAAA
54599520 TTATTTTA-TTTAAA
1 TTATTTTATTTTAAA
54599534 T
1 T
54599535 GCCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTATTTTAAA
Found at i:54599908 original size:25 final size:25
Alignment explanation
Indices: 54599880--54600013 Score: 115
Period size: 22 Copynumber: 5.6 Consensus size: 25
54599870 ACTTTAGCGC
*
54599880 GCTCTTTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
* * * *
54599905 GCTCTCTGACTACTAGAACGTTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
*
54599930 GCTCTCTGATT-TTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTTAGT
*
54599954 GCTCTCTG--T-TTAGCACATCT-GT
1 GCTCTCTGATTATTAGCACGT-TAGT
*
54599976 GCTCTCTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
54599998 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
54600014 TGCATACTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
21 1 0.01
22 37 0.41
23 1 0.01
24 18 0.20
25 33 0.37
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:54615010 original size:85 final size:85
Alignment explanation
Indices: 54614865--54615106 Score: 261
Period size: 85 Copynumber: 2.8 Consensus size: 85
54614855 GCAAACGTTT
* *** * * *
54614865 GCGGCGTTTTTTCCTACAAACGCCGCTATAGATTTGGACCTTCAGCGGCGCTTTTTTCACAAACG
1 GCGGCGTTTTTT--TACAAACACCGCTATAGATCAAGACCTTTAGCGACGCTTTTATCACAAACG
*
54614930 CCGTTATAGATCATGACCTTTA
64 CCGCTATAGATCATGACCTTTA
* *
54614952 GCGGCGTTTTTTTACAAACACCGCTATAGATCAAGACCTTTAGCGACACTTTTCTCACAAACGCC
1 GCGGCGTTTTTTTACAAACACCGCTATAGATCAAGACCTTTAGCGACGCTTTTATCACAAACGCC
* *
54615017 GCTATATATCATGATCTTTA
66 GCTATAGATCATGACCTTTA
* * * * * * * *
54615037 ACGACGCTTTTTTCAAAAACACCACTATA-ACTCAAAACCTTTAGCGACGCTTTGATTACAAACG
1 GCGGCG-TTTTTTTACAAACACCGCTATAGA-TCAAGACCTTTAGCGACGCTTTTATCACAAACG
54615101 CCGCTA
64 CCGCTA
54615107 AAAGTACCGT
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
85 67 0.51
86 53 0.40
87 12 0.09
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (85 bp):
GCGGCGTTTTTTTACAAACACCGCTATAGATCAAGACCTTTAGCGACGCTTTTATCACAAACGCC
GCTATAGATCATGACCTTTA
Found at i:54615079 original size:43 final size:43
Alignment explanation
Indices: 54614871--54615106 Score: 208
Period size: 43 Copynumber: 5.5 Consensus size: 43
54614861 GTTTGCGGCG
* *** * *
54614871 TTTTTTCCTACAAACGCCGCTATAGATTTGGACCTTCAGCGGCGC
1 TTTTTT-C-ACAAACACCGCTATAGATCAAGACCTTTAGCGACGC
* * * *
54614916 TTTTTTCACAAACGCCGTTATAGATCATGACCTTTAGCGGCG-
1 TTTTTTCACAAACACCGCTATAGATCAAGACCTTTAGCGACGC
* *
54614958 TTTTTTTACAAACACCGCTATAGATCAAGACCTTTAGCGACAC
1 TTTTTTCACAAACACCGCTATAGATCAAGACCTTTAGCGACGC
* * * * * *
54615001 TTTTCTCACAAACGCCGCTATATATCATGATCTTTAACGACGC
1 TTTTTTCACAAACACCGCTATAGATCAAGACCTTTAGCGACGC
* * *
54615044 TTTTTTCAAAAACACCACTATA-ACTCAAAACCTTTAGCGACGC
1 TTTTTTCACAAACACCGCTATAGA-TCAAGACCTTTAGCGACGC
* *
54615087 TTTGATT-ACAAACGCCGCTA
1 TTT-TTTCACAAACACCGCTA
54615107 AAAGTACCGT
Statistics
Matches: 157, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
42 37 0.24
43 111 0.71
44 3 0.02
45 6 0.04
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (43 bp):
TTTTTTCACAAACACCGCTATAGATCAAGACCTTTAGCGACGC
Found at i:54615098 original size:86 final size:85
Alignment explanation
Indices: 54614921--54615106 Score: 230
Period size: 86 Copynumber: 2.2 Consensus size: 85
54614911 GGCGCTTTTT
* * * * * *
54614921 TCACAAACGCCGTTATAGATCATGACCTTTAGCGGCGTTTTTTTACAAACACCGCTATAGATCAA
1 TCACAAACGCCGCTATAGATCATGACCTTTAACGACGTTTTTTCAAAAACACCACTATAGATCAA
* **
54614986 GACCTTTAGCGACACTTTTC
66 AACCTTTAGCGACACTTTGA
* *
54615006 TCACAAACGCCGCTATATATCATGATCTTTAACGACGCTTTTTTCAAAAACACCACTATA-ACTC
1 TCACAAACGCCGCTATAGATCATGACCTTTAACGACG-TTTTTTCAAAAACACCACTATAGA-TC
*
54615070 AAAACCTTTAGCGACGCTTTGA
64 AAAACCTTTAGCGACACTTTGA
*
54615092 TTACAAACGCCGCTA
1 TCACAAACGCCGCTA
54615107 AAAGTACCGT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 33 0.38
86 53 0.62
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (85 bp):
TCACAAACGCCGCTATAGATCATGACCTTTAACGACGTTTTTTCAAAAACACCACTATAGATCAA
AACCTTTAGCGACACTTTGA
Found at i:54620683 original size:7 final size:7
Alignment explanation
Indices: 54620667--54620697 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
54620657 TCCCAACCCT
*
54620667 TAAACAA
1 TAAACCA
54620674 TAAACCA
1 TAAACCA
54620681 TAAACCA
1 TAAACCA
54620688 TAAACCA
1 TAAACCA
54620695 TAA
1 TAA
54620698 TACTATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCA
Found at i:54620800 original size:16 final size:17
Alignment explanation
Indices: 54620764--54620805 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
54620754 CACTATAATC
54620764 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
54620782 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
54620798 ATTATTTA
1 ATTATTTA
54620806 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:54620971 original size:28 final size:26
Alignment explanation
Indices: 54620935--54620999 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 26
54620925 CCTAAACCCT
54620935 TAACTCTTAACCCTCAACCCCTAACTCCTA
1 TAAC-CTTAACCC-CAACCCCTAA-T-CTA
*
54620965 -AACCTTAAACCCCAACCCTTAATCTA
1 TAACCTT-AACCCCAACCCCTAATCTA
54620991 TAACCTTAA
1 TAACCTTAA
54621000 ACCATAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 5 0.16
27 7 0.22
28 12 0.38
29 8 0.25
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (26 bp):
TAACCTTAACCCCAACCCCTAATCTA
Found at i:54621018 original size:21 final size:21
Alignment explanation
Indices: 54620992--54621058 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
54620982 CTTAATCTAT
*
54620992 AACCTTAAACCATAAACTGTG
1 AACCTTAAACCATAAACTGTA
* * **
54621013 ACCCTTAAACCCTAAACCATA
1 AACCTTAAACCATAAACTGTA
54621034 AACCTTAAACCATAAACTGTA
1 AACCTTAAACCATAAACTGTA
54621055 AACC
1 AACC
54621059 ATAACCCCTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (21 bp):
AACCTTAAACCATAAACTGTA
Found at i:54621030 original size:7 final size:7
Alignment explanation
Indices: 54621013--54621115 Score: 53
Period size: 7 Copynumber: 14.4 Consensus size: 7
54621003 ATAAACTGTG
54621013 ACCCTTAA
1 ACCC-TAA
54621021 ACCCTAA
1 ACCCTAA
*
54621028 ACCATAA
1 ACCCTAA
*
54621035 ACCTTAA
1 ACCCTAA
*
54621042 ACCATAA
1 ACCCTAA
**
54621049 ACTGTAA
1 ACCCTAA
*
54621056 ACCATAA
1 ACCCTAA
*
54621063 CCCCTAA
1 ACCCTAA
54621070 ACCCATAA
1 ACCC-TAA
* *
54621078 TCCATAA
1 ACCCTAA
* *
54621085 AACTTAA
1 ACCCTAA
* *
54621092 ACTCTAT
1 ACCCTAA
* *
54621099 ACCATAT
1 ACCCTAA
54621106 ACCCTAA
1 ACCCTAA
54621113 ACC
1 ACC
54621116 AAAAACCTTA
Statistics
Matches: 71, Mismatches: 23, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
7 62 0.87
8 9 0.13
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (7 bp):
ACCCTAA
Found at i:54621035 original size:14 final size:14
Alignment explanation
Indices: 54621018--54621128 Score: 96
Period size: 14 Copynumber: 7.9 Consensus size: 14
54621008 CTGTGACCCT
54621018 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
54621032 TAAACCTTAAACCA
1 TAAACCCTAAACCA
**
54621046 TAAACTGTAAACCA
1 TAAACCCTAAACCA
*
54621060 TAACCCCTAAACCCA
1 TAAACCCTAAA-CCA
* * * *
54621075 TAATCCATAAAACT
1 TAAACCCTAAACCA
* *
54621089 TAAACTCTATACCA
1 TAAACCCTAAACCA
*
54621103 TATACCCTAAACCA
1 TAAACCCTAAACCA
* *
54621117 AAAACCTTAAAC
1 TAAACCCTAAAC
54621129 TATAGAGATA
Statistics
Matches: 74, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
14 62 0.84
15 12 0.16
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:54621494 original size:41 final size:41
Alignment explanation
Indices: 54621437--54621556 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 41
54621427 AATGTTTTTG
* *
54621437 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGTAT
1 TAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGAGCAT
54621478 TAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCAT
1 TAGCGGCGCTTCTCCAAAAACGCCGCTAAAG-CCCTGAGCAT
*
54621520 TAGCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
1 TAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGA
54621557 AAGGTAAGAA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
41 36 0.48
42 39 0.52
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.18
Consensus pattern (41 bp):
TAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGAGCAT
Found at i:54622420 original size:19 final size:19
Alignment explanation
Indices: 54622396--54622489 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
54622386 AATCATATCT
54622396 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
54622415 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
54622434 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* * *
54622453 TCTAAGATTACAAACCATA
1 TCTAAGATTGCATATCATA
54622472 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
54622490 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54622445 original size:38 final size:38
Alignment explanation
Indices: 54622373--54622489 Score: 180
Period size: 38 Copynumber: 3.0 Consensus size: 38
54622363 AAATTAAATC
54622373 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-AAATCATA---TCTAAGATTGCATATCATA
*
54622415 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACAAATCATATCTAAGATTGCATATCATA
*
54622453 TCTAAGATTACAAACCATATCTAAGATTGCATATCAT
1 TCTAAGATTACAAATCATATCTAAGATTGCATATCAT
54622490 TGAAGATTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
38 54 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (38 bp):
TCTAAGATTACAAATCATATCTAAGATTGCATATCATA
Found at i:54622750 original size:64 final size:64
Alignment explanation
Indices: 54622646--54623050 Score: 659
Period size: 64 Copynumber: 6.3 Consensus size: 64
54622636 ATTGGCCTAT
* * * *
54622646 TACAATATCAATTCGGCAATAGGTATATACCCATACAATTCAATTCAG-CAATATATGTATACAT
1 TACAAT-TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTC-GTCAATATAAGTATATAT
54622710 A
64 A
54622711 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
1 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
*
54622775 TACAATTCAATTCGGCAATAGGTGTATTCCTATACAATTCAATTCGTCAATATAAGTATATATA
1 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
* * * *
54622839 TACAATTCAATTCGGCAATAGTTGTATACTTATACAACTCAATTCATCAATATAAGTATATATA
1 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
* **
54622903 TACAATTCAATTCGGAAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATGCA
1 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
* *
54622967 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATACATA
1 TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
54623031 TACAATTCAATTCGGCAATA
1 TACAATTCAATTCGGCAATA
54623051 TATAGCCATG
Statistics
Matches: 317, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
63 1 0.00
64 310 0.98
65 6 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (64 bp):
TACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATA
Found at i:54623051 original size:32 final size:32
Alignment explanation
Indices: 54622646--54623052 Score: 433
Period size: 32 Copynumber: 12.7 Consensus size: 32
54622636 ATTGGCCTAT
**
54622646 TACAATATCAATTCGGCAATAGGT-A-TATACCCA
1 TACAAT-TCAATTCGGCAATA--TAAGTATACATA
* *
54622679 TACAATTCAATTCAGCAATATATGTATACATA
1 TACAATTCAATTCGGCAATATAAGTATACATA
*** *
54622711 TACAATTCAATTCGGCAATAGGTGTATACCTA
1 TACAATTCAATTCGGCAATATAAGTATACATA
* *
54622743 TACAATTCAATTCGTCAATATAAGTATATATA
1 TACAATTCAATTCGGCAATATAAGTATACATA
*** * *
54622775 TACAATTCAATTCGGCAATAGGTGTATTCCTA
1 TACAATTCAATTCGGCAATATAAGTATACATA
* *
54622807 TACAATTCAATTCGTCAATATAAGTATATATA
1 TACAATTCAATTCGGCAATATAAGTATACATA
* *
54622839 TACAATTCAATTCGGCAATAGT-TGTATACTTA
1 TACAATTCAATTCGGCAATA-TAAGTATACATA
* ** *
54622871 TACAACTCAATTCATCAATATAAGTATATATA
1 TACAATTCAATTCGGCAATATAAGTATACATA
* *** *
54622903 TACAATTCAATTCGGAAATAGGTGTATACCTA
1 TACAATTCAATTCGGCAATATAAGTATACATA
* ***
54622935 TACAATTCAATTCGTCAATATAAGTATATGCA
1 TACAATTCAATTCGGCAATATAAGTATACATA
*** *
54622967 TACAATTCAATTCGGCAATAGGTGTATACCTA
1 TACAATTCAATTCGGCAATATAAGTATACATA
54622999 TACAATTCAATTCGGCAATATAAGTATACATA
1 TACAATTCAATTCGGCAATATAAGTATACATA
54623031 TACAATTCAATTCGGCAATATA
1 TACAATTCAATTCGGCAATATA
54623053 TAGCCATGTA
Statistics
Matches: 304, Mismatches: 66, Indels: 9
0.80 0.17 0.02
Matches are distributed among these distances:
30 1 0.00
31 1 0.00
32 295 0.97
33 7 0.02
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (32 bp):
TACAATTCAATTCGGCAATATAAGTATACATA
Found at i:54625260 original size:54 final size:55
Alignment explanation
Indices: 54625177--54625280 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 55
54625167 TCTTCCACGG
*
54625177 AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATTTTTTCCTTGA
1 AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATCTTTTCCTTGA
* * *
54625232 AGAAACTTTCAG-GATACTCGATCGCCAACTGTAAATTCAATATCTTTTC
1 AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATCTTTTC
54625281 TTTTCAGATC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 33 0.73
55 12 0.27
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (55 bp):
AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATCTTTTCCTTGA
Found at i:54628160 original size:7 final size:7
Alignment explanation
Indices: 54628148--54628197 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
54628138 ACTCCAATTT
54628148 TTTAGGG
1 TTTAGGG
54628155 TTTAGGG
1 TTTAGGG
*
54628162 TTTAAGGT
1 TTT-AGGG
54628170 TTTAGGG
1 TTTAGGG
*
54628177 TTTATGG
1 TTTAGGG
*
54628184 TTTAAGG
1 TTTAGGG
54628191 TTTAGGG
1 TTTAGGG
54628198 ATCCCCCACG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 31 0.84
8 6 0.16
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:54628172 original size:22 final size:22
Alignment explanation
Indices: 54628147--54628197 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
54628137 AACTCCAATT
54628147 TTTTAGGGTTTAGGGTTTAAGG
1 TTTTAGGGTTTAGGGTTTAAGG
*
54628169 TTTTAGGGTTTATGGTTTAAGG
1 TTTTAGGGTTTAGGGTTTAAGG
54628191 -TTTAGGG
1 TTTTAGGG
54628198 ATCCCCCACG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (22 bp):
TTTTAGGGTTTAGGGTTTAAGG
Found at i:54628175 original size:15 final size:15
Alignment explanation
Indices: 54628155--54628186 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54628145 TTTTTTAGGG
54628155 TTTAGGGTTTAAGGT
1 TTTAGGGTTTAAGGT
*
54628170 TTTAGGGTTTATGGT
1 TTTAGGGTTTAAGGT
54628185 TT
1 TT
54628187 AAGGTTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (15 bp):
TTTAGGGTTTAAGGT
Found at i:54630540 original size:39 final size:39
Alignment explanation
Indices: 54630483--54630602 Score: 195
Period size: 39 Copynumber: 3.1 Consensus size: 39
54630473 TCCAATACAC
* *
54630483 CGGCACATAGCCTACTAGGCACTTAGCCCGAATAATCAT
1 CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
* *
54630522 CGGCACAAAGCCTGCTAGGCAATTAGCCCGAATAATCAC
1 CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
*
54630561 CGGCACAAAGCCTGCTAGGCACTTATCCCGAATAATCAT
1 CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
54630600 CGG
1 CGG
54630603 ATTTTTATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (39 bp):
CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
Found at i:54632090 original size:44 final size:44
Alignment explanation
Indices: 54632041--54632126 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
54632031 TATCAACATA
*
54632041 AATTTTCTTTCCATA-AGTATGTTTGGTAGGAAAGATGAAAAAAT
1 AATTTTCTTTCAATAGA-TATGTTTGGTAGGAAAGATGAAAAAAT
54632085 AATTTTCTTTCAATAGATATGTTTGGTAGGAAAGATGAAAAA
1 AATTTTCTTTCAATAGATATGTTTGGTAGGAAAGATGAAAAA
54632127 TAGAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (44 bp):
AATTTTCTTTCAATAGATATGTTTGGTAGGAAAGATGAAAAAAT
Found at i:54633315 original size:20 final size:20
Alignment explanation
Indices: 54633282--54633320 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54633272 AAGACTTCCA
54633282 AACATCTTACAAAATATTTTT
1 AACATCTTACAAAA-ATTTTT
*
54633303 AACA-CTTAGAAAAATTTT
1 AACATCTTACAAAAATTTT
54633321 GGACAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (20 bp):
AACATCTTACAAAAATTTTT
Found at i:54633455 original size:27 final size:27
Alignment explanation
Indices: 54633425--54633480 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
54633415 TTTCAAAAAG
54633425 TATGGATACCTATTGTATTTTTATCGA
1 TATGGATACCTATTGTATTTTTATCGA
*
54633452 TATGGATATCTATTGTATTTTTATCGA
1 TATGGATACCTATTGTATTTTTATCGA
54633479 TA
1 TA
54633481 CCATCTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (27 bp):
TATGGATACCTATTGTATTTTTATCGA
Found at i:54634019 original size:40 final size:38
Alignment explanation
Indices: 54633972--54634046 Score: 114
Period size: 40 Copynumber: 1.9 Consensus size: 38
54633962 ATTTGGATAA
*
54633972 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCACTAAAAAT-AAGCATTACCGGCG-TTTTTGG
*
54634012 AAAACGCCGCTAAAAATAAGCATTACCGGCGTTTT
1 AAAACGCCACTAAAAATAAGCATTACCGGCGTTTT
54634047 CAAAAAAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 4 0.12
39 13 0.39
40 16 0.48
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (38 bp):
AAAACGCCACTAAAAATAAGCATTACCGGCGTTTTTGG
Found at i:54634060 original size:39 final size:40
Alignment explanation
Indices: 54633970--54634053 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
54633960 GCATTTGGAT
* * *
54633970 AAAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTACCGGCGCTTTTC
**
54634010 GGAAAACGCCGCTAAAAAT-AAGCATTACCGGCG-TTTTC
1 AAAAAACGCCGCTAAAAATCAAGCATTACCGGCGCTTTTC
54634048 AAAAAA
1 AAAAAA
54634054 GTGCCGCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
38 8 0.22
39 13 0.35
40 16 0.43
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTACCGGCGCTTTTC
Found at i:54634153 original size:41 final size:41
Alignment explanation
Indices: 54634096--54634216 Score: 224
Period size: 41 Copynumber: 3.0 Consensus size: 41
54634086 TGAGTTTTTG
* *
54634096 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
54634137 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
54634178 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
54634217 CCGCTTTTGA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
Found at i:54634614 original size:14 final size:14
Alignment explanation
Indices: 54634589--54634615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54634579 ATATATACAG
54634589 TTTAGGGTATATGA
1 TTTAGGGTATATGA
54634603 TTTAGGGTATATG
1 TTTAGGGTATATG
54634616 GTTAATTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTAGGGTATATGA
Found at i:54634695 original size:14 final size:15
Alignment explanation
Indices: 54634667--54634699 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
54634657 AAGATTTATA
54634667 GATTATGGAATTAGG
1 GATTATGGAATTAGG
54634682 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
54634696 GATT
1 GATT
54634700 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:54634947 original size:21 final size:22
Alignment explanation
Indices: 54634922--54634971 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
54634912 TAAGATTTAG
*
54634922 GGGTTAGTA-GTTAGGGGTTAA
1 GGGTTAGTATGTTAGAGGTTAA
*
54634943 GGGTTA-AATGTTAGAGGTTAA
1 GGGTTAGTATGTTAGAGGTTAA
*
54634964 GAGTTAGT
1 GGGTTAGT
54634972 GATCTAGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (22 bp):
GGGTTAGTATGTTAGAGGTTAA
Found at i:54639467 original size:43 final size:43
Alignment explanation
Indices: 54639407--54639497 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
54639397 CTTTGAGTTC
* * * *
54639407 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
54639449 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
54639492 ATTACC
1 ATTACC
54639498 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:54639892 original size:42 final size:42
Alignment explanation
Indices: 54639770--54639995 Score: 276
Period size: 43 Copynumber: 5.3 Consensus size: 42
54639760 AAGATATATT
* ** * * *
54639770 TTTAGTGGCGTTTGTGTTAAAAGCGCCGCTAAAGCTCAAT-ATC
1 TTTAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTC-TTGGTC
54639813 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
54639856 TTTAGCGGCGTTTGTGAGG-AAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
54639898 TTTAGTGGCGTTTTTGGGGAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
* *
54639940 TTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
54639983 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
54639996 ATTTATAAAA
Statistics
Matches: 161, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.01
42 75 0.47
43 82 0.51
44 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:54640124 original size:22 final size:21
Alignment explanation
Indices: 54640087--54640131 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
54640077 TTTAGTGGCG
* *
54640087 CTAAAAAACGCTGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
54640108 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
54640130 CT
1 CT
54640132 GTTTTGGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.13
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:54640809 original size:19 final size:19
Alignment explanation
Indices: 54640785--54640823 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54640775 GTGTTTTGTA
54640785 TTTATGT-TGAATACATATT
1 TTTATGTGT-AATACATATT
*
54640804 TTTATGTGTTATACATATT
1 TTTATGTGTAATACATATT
54640823 T
1 T
54640824 GGTTGATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (19 bp):
TTTATGTGTAATACATATT
Found at i:54641683 original size:20 final size:20
Alignment explanation
Indices: 54641653--54641690 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54641643 TATGAATGAC
54641653 ATTTGAATTTGATTATTTGTT
1 ATTTGAATTTGA-TATTTGTT
54641674 ATTT-AATTTGATATTTG
1 ATTTGAATTTGATATTTG
54641691 GATGGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (20 bp):
ATTTGAATTTGATATTTGTT
Found at i:54642514 original size:102 final size:102
Alignment explanation
Indices: 54642326--54642522 Score: 288
Period size: 102 Copynumber: 1.9 Consensus size: 102
54642316 ATTTTTAACT
* * **
54642326 AATTTGCATGAAATAATAGTAATGGAAATATTACCAAAAAAAAATATTAAGTTAGTTTGTTATTG
1 AATTTGCATGAAATAATAGTAATCGAAATATTA-CAAAAAAAAATATAAAACTAGTTTGTTATTG
* *
54642391 GACATTCTAACGTAAGTCAACTGCAAATTAAATTTATA
65 GACATTCTAACATAAGTCAACTACAAATTAAATTTATA
* * *
54642429 AATTTGCATGAAATAATAGTAATCGAAATATTA-AAAAAGAAGTCATAAAACTGGTTTGTTATTG
1 AATTTGCATGAAATAATAGTAATCGAAATATTACAAAAAAAAAT-ATAAAACTAGTTTGTTATTG
54642493 GACATTCTAACATAAGTCAACTACAAATTA
65 GACATTCTAACATAAGTCAACTACAAATTA
54642523 GATATGTAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 8 0.10
102 44 0.52
103 32 0.38
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (102 bp):
AATTTGCATGAAATAATAGTAATCGAAATATTACAAAAAAAAATATAAAACTAGTTTGTTATTGG
ACATTCTAACATAAGTCAACTACAAATTAAATTTATA
Found at i:54645244 original size:21 final size:21
Alignment explanation
Indices: 54645219--54645258 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54645209 GAAAGAGAAG
54645219 AAAATTATTGGATTAGACATA
1 AAAATTATTGGATTAGACATA
54645240 AAAATTATTGGATTAGACA
1 AAAATTATTGGATTAGACA
54645259 CATTTTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (21 bp):
AAAATTATTGGATTAGACATA
Found at i:54645525 original size:18 final size:19
Alignment explanation
Indices: 54645488--54645524 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54645478 TTGGTGGGAA
54645488 TATAAAT-TTTAGAGTTTT
1 TATAAATATTTAGAGTTTT
*
54645506 TATAAATATTTTGAGTTTT
1 TATAAATATTTAGAGTTTT
54645525 AAAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAGTTTT
Found at i:54645530 original size:18 final size:20
Alignment explanation
Indices: 54645493--54645531 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
54645483 GGGAATATAA
*
54645493 ATTTTAGAGTTTTTATAAAT
1 ATTTTAGAGTTTTTAAAAAT
54645513 ATTTT-GAG-TTTTAAAAAT
1 ATTTTAGAGTTTTTAAAAAT
54645531 A
1 A
54645532 ACATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTTTAGAGTTTTTAAAAAT
Found at i:54649655 original size:27 final size:26
Alignment explanation
Indices: 54649610--54649958 Score: 232
Period size: 27 Copynumber: 13.0 Consensus size: 26
54649600 AAAGTCATGA
* *
54649610 ACCGAAATACCTTCGATGGGTAAAATT
1 ACCGAAATACCCT-AATGGGTAAAATT
** *
54649637 ATTGAAATACCCCTAATGGGTATAATT
1 ACCGAAATA-CCCTAATGGGTAAAATT
* * *
54649664 ACTGGAATACCCTTAATAGGTAAAATT
1 ACCGAAATACCC-TAATGGGTAAAATT
* ** *
54649691 ACTGAAATACCCCCGATGGGTATAATT
1 ACCGAAATA-CCCTAATGGGTAAAATT
* * * *
54649718 ATCAAAATGCCCCTAATAGGTAAAATT
1 ACCGAAAT-ACCCTAATGGGTAAAATT
*
54649745 ACCGAAATACCCTCGATGGGTAAAATT
1 ACCGAAATACCCT-AATGGGTAAAATT
* * * * *
54649772 ATCAAAATACCCTCGATAGATAAAATT
1 ACCGAAATACCCT-AATGGGTAAAATT
* * *
54649799 ATCGAAATACCCCCAATAGGTAAAATT
1 ACCGAAATA-CCCTAATGGGTAAAATT
** *
54649826 ATAGAAATACCCTCATAGGGTAAAATT
1 ACCGAAATACCCTAAT-GGGTAAAATT
** *
54649853 ACTAAAATACCCTCGATGGGTAAAATT
1 ACCGAAATACCCT-AATGGGTAAAATT
** * *
54649880 ACAAAAATACCCTCAATAGATAAAATT
1 ACCGAAATACCCT-AATGGGTAAAATT
* *
54649907 ACTGAAATACCCTGATGGGTAAAATT
1 ACCGAAATACCCTAATGGGTAAAATT
*
54649933 ATCGAAATACCCTTATAT-GGTAAAAT
1 ACCGAAATACCC-TA-ATGGGTAAAAT
54649959 GACTGTTATA
Statistics
Matches: 257, Mismatches: 55, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
26 32 0.12
27 212 0.82
28 13 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (26 bp):
ACCGAAATACCCTAATGGGTAAAATT
Found at i:54649697 original size:54 final size:53
Alignment explanation
Indices: 54649628--54649963 Score: 333
Period size: 54 Copynumber: 6.2 Consensus size: 53
54649618 ACCTTCGATG
* * * **
54649628 GGTAAAATTATTGAAATACCCCTAATGGGTATAATTA-CTGGAATACCCTTAATA
1 GGTAAAATTACTGAAATA-CCCTGATGGGTAAAATTATC-AAAATACCCTTAATA
* * * *
54649682 GGTAAAATTACTGAAATACCCCCGATGGGTATAATTATCAAAATGCCCCTAATA
1 GGTAAAATTACTGAAATA-CCCTGATGGGTAAAATTATCAAAATACCCTTAATA
* **
54649736 GGTAAAATTACCGAAATACCCTCGATGGGTAAAATTATCAAAATACCCTCGATA
1 GGTAAAATTACTGAAATACCCT-GATGGGTAAAATTATCAAAATACCCTTAATA
* ** * *
54649790 GATAAAATTA-TCGAAATACCCCCAATAGGTAAAATTAT-AGAAATACCC-TCATA
1 GGTAAAATTACT-GAAATA-CCCTGATGGGTAAAATTATCA-AAATACCCTTAATA
* *
54649843 GGGTAAAATTACTAAAATACCCTCGATGGGTAAAATTA-CAAAAATACCCTCAATA
1 -GGTAAAATTACTGAAATACCCT-GATGGGTAAAATTATC-AAAATACCCTTAATA
* *
54649898 GATAAAATTACTGAAATACCCTGATGGGTAAAATTATCGAAATACCCTT-ATA
1 GGTAAAATTACTGAAATACCCTGATGGGTAAAATTATCAAAATACCCTTAATA
*
54649950 TGGTAAAATGACTG
1 -GGTAAAATTACTG
54649964 TTATATCCCT
Statistics
Matches: 235, Mismatches: 34, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
52 3 0.01
53 44 0.19
54 179 0.76
55 9 0.04
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (53 bp):
GGTAAAATTACTGAAATACCCTGATGGGTAAAATTATCAAAATACCCTTAATA
Found at i:54649754 original size:81 final size:80
Alignment explanation
Indices: 54649612--54649945 Score: 372
Period size: 81 Copynumber: 4.1 Consensus size: 80
54649602 AGTCATGAAC
* ** * * *
54649612 CGAAATACCTTCGATGGGTAAAATTATTGAAATACCCCTAATGGGTATAATTACTGGAATACCCT
1 CGAAATACCCTCGATGGGTAAAATTATCAAAATACCCCTAATAGGTAAAATTACTGAAATACCC-
*
54649677 TAATAGGTAAAATTA-
65 TGATAGGTAAAATTAT
* * * *
54649692 CTGAAATACCCCCGATGGGTATAATTATCAAAATGCCCCTAATAGGTAAAATTACCGAAATACCC
1 C-GAAATACCCTCGATGGGTAAAATTATCAAAATACCCCTAATAGGTAAAATTACTGAAATACCC
*
54649757 TCGATGGGTAAAATTAT
65 T-GATAGGTAAAATTAT
* * * * *
54649774 CAAAATACCCTCGATAGATAAAATTATCGAAATACCCCCAATAGGTAAAATTA-TAGAAATACCC
1 CGAAATACCCTCGATGGGTAAAATTATCAAAATACCCCTAATAGGTAAAATTACT-GAAATACCC
*
54649838 TCATAGGGTAAAATTA-
65 TGATA-GGTAAAATTAT
* *
54649854 CTAAAATACCCTCGATGGGTAAAATTA-CAAAAATA-CCCTCAATAGATAAAATTACTGAAATAC
1 C-GAAATACCCTCGATGGGTAAAATTATC-AAAATACCCCT-AATAGGTAAAATTACTGAAATAC
*
54649917 CCTGATGGGTAAAATTAT
63 CCTGATAGGTAAAATTAT
54649935 CGAAATACCCT
1 CGAAATACCCT
54649946 TATATGGTAA
Statistics
Matches: 213, Mismatches: 31, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
80 28 0.13
81 183 0.86
82 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (80 bp):
CGAAATACCCTCGATGGGTAAAATTATCAAAATACCCCTAATAGGTAAAATTACTGAAATACCCT
GATAGGTAAAATTAT
Found at i:54650137 original size:27 final size:26
Alignment explanation
Indices: 54650100--54650196 Score: 79
Period size: 26 Copynumber: 3.7 Consensus size: 26
54650090 AGGGGAAATG
**
54650100 TACTG-TACTGGTGGCTTTACCACATA
1 TACTGTTACTGGCAGCTTTACCACA-A
**
54650126 TACTGTTACTGGCAGCTTTACTGCAA
1 TACTGTTACTGGCAGCTTTACCACAA
* * * * * *
54650152 TACTGTTACCGACAGCTCTGCTACGA
1 TACTGTTACTGGCAGCTTTACCACAA
*
54650178 TACTGTTACTGGTAGCTTT
1 TACTGTTACTGGCAGCTTT
54650197 GCTGCATTAT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 41 0.73
27 15 0.27
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTACCACAA
Found at i:54650154 original size:26 final size:26
Alignment explanation
Indices: 54650125--54650227 Score: 100
Period size: 26 Copynumber: 4.0 Consensus size: 26
54650115 TTTACCACAT
*
54650125 ATACTGTTACTGGCAGCTTTACTGCA
1 ATACTGTTACTGGCAGCTTTGCTGCA
* * * * *
54650151 ATACTGTTACCGACAGCTCTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTGCA
*
54650177 ATACTGTTACTGGTAGCTTTGCTGCA
1 ATACTGTTACTGGCAGCTTTGCTGCA
* * *
54650203 TTA-TAATTACTGGCAGCTATGCTGC
1 ATACT-GTTACTGGCAGCTTTGCTGC
54650228 GAATTGGTGT
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
25 1 0.02
26 59 0.98
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCA
Found at i:54650220 original size:52 final size:52
Alignment explanation
Indices: 54650125--54650225 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
54650115 TTTACCACAT
* *
54650125 ATACTGTTACTGGCAGCTTTACTGCAATACTGTTACCGACAGCTCTGCTACG
1 ATACTGTTACTGGCAGCTTTACTGCAATACTATTACCGACAGCTATGCTACG
* * * * *
54650177 ATACTGTTACTGGTAGCTTTGCTGCATTA-TAATTACTGGCAGCTATGCT
1 ATACTGTTACTGGCAGCTTTACTGCAATACT-ATTACCGACAGCTATGCT
54650226 GCGAATTGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 1 0.02
52 40 0.98
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (52 bp):
ATACTGTTACTGGCAGCTTTACTGCAATACTATTACCGACAGCTATGCTACG
Found at i:54654448 original size:21 final size:22
Alignment explanation
Indices: 54654424--54654469 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
54654414 GTTGTTAAAA
*
54654424 TTTTTATAATTTGTATTTA-CT
1 TTTTTATAATTTATATTTATCT
*
54654445 TTTTTATACTTTATATTTATCT
1 TTTTTATAATTTATATTTATCT
54654467 TTT
1 TTT
54654470 CTCATTAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTATAATTTATATTTATCT
Found at i:54657425 original size:19 final size:20
Alignment explanation
Indices: 54657390--54657428 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
54657380 AATACATGTG
54657390 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
*
54657410 TAATAATGAA-ATATGTATT
1 TAATAATAAACATATGTATT
54657429 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Done.