Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 129 of 325
Found at i:38913565 original size:46 final size:46
Alignment explanation
Indices: 38913487--38913663 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
38913477 CCACCACATT
*
38913487 ATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAG
1 ATGAG-GCCAGTGTAAGACCATGTCTGGGACATGGCATTGGC-TTGAG
* * *
38913535 ACGAGGGCAGTGTAAGA-CATGTCTGGGACAT-GCATCT-GCTACGAG
1 ATGAGGCCAGTGTAAGACCATGTCTGGGACATGGCAT-TGGCT-TGAG
* * *
38913580 ATGATAGTCAGTGTAAGACCATGTCTGGGACATGGCA-TGACTTGAG
1 ATGA-GGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCTTGAG
*
38913626 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
1 ATGAG-GCCAGTGTAAGACCATGTCTGGGACATGGCAT
38913664 CGGCACCTTA
Statistics
Matches: 109, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
44 1 0.01
45 12 0.11
46 63 0.58
47 26 0.24
48 7 0.06
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.23
Consensus pattern (46 bp):
ATGAGGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCTTGAG
Found at i:38916532 original size:2 final size:2
Alignment explanation
Indices: 38916525--38916551 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38916515 CAATCACATT
38916525 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38916552 TCTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38918372 original size:40 final size:40
Alignment explanation
Indices: 38918293--38918460 Score: 232
Period size: 40 Copynumber: 4.2 Consensus size: 40
38918283 CGGATGATAA
* * * *
38918293 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
38918333 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
38918373 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
38918413 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
38918453 CC-GGCTAA
1 CCGGGCTAA
38918461 ATCCCGAGGA
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
39 8 0.07
40 102 0.91
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:38920101 original size:39 final size:39
Alignment explanation
Indices: 38919923--38920118 Score: 211
Period size: 39 Copynumber: 5.0 Consensus size: 39
38919913 ACTTGAAACC
** **
38919923 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * * *
38919962 AATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * *
38920001 ATTTCCAGCACGTAGCCTGCGGACTTTAAGTCCGGTTAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
38920040 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
38920079 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
38920118 A
1 A
38920119 CATCACTGAA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
38 17 0.13
39 117 0.87
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
Found at i:38921949 original size:40 final size:40
Alignment explanation
Indices: 38921775--38921947 Score: 228
Period size: 40 Copynumber: 4.4 Consensus size: 40
38921765 AAACCAAGTA
* * *
38921775 CCTTCAGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
38921814 CCTT-GGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
38921853 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38921893 CCTTCGGGACTTAGCTCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
38921933 CCTTCGGGACTTAGC
1 CCTTCGGGACTTAGC
38921948 TCAGTTATCA
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
38 8 0.07
39 30 0.25
40 82 0.68
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38930041 original size:26 final size:26
Alignment explanation
Indices: 38929983--38930043 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
38929973 TATTTTCTCG
38929983 AAATTTTACCAGGATCAAAATCGTGA
1 AAATTTTACCAGGATCAAAATCGTGA
* * * *
38930009 AATTTTTACCAGG-TGTAAAATTGTTA
1 AAATTTTACCAGGAT-CAAAATCGTGA
38930035 AAATTTTAC
1 AAATTTTAC
38930044 TCCGGCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (26 bp):
AAATTTTACCAGGATCAAAATCGTGA
Found at i:38933236 original size:23 final size:23
Alignment explanation
Indices: 38933187--38933236 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
38933177 ATGCACATTT
*
38933187 TTTTATATGTTTTAGTTTTTTAC
1 TTTTATATGTTTTAGTTGTTTAC
38933210 TTTTATATTGTTTT-GTATGTTTA-
1 TTTTATA-TGTTTTAGT-TGTTTAC
38933233 TTTT
1 TTTT
38933237 CATTTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (23 bp):
TTTTATATGTTTTAGTTGTTTAC
Found at i:38935722 original size:40 final size:40
Alignment explanation
Indices: 38935678--38935786 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
38935668 TTCACAATTT
* *
38935678 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAATCACCA
* * *
38935718 GCACAATTGCCTTCGGGTCTTAACCCGGATGTAATTACCA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAATCACCA
* * *
38935758 GCATAAAT-TCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
38935787 ATCATTCAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
39 18 0.31
40 41 0.69
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAATCACCA
Found at i:38942988 original size:17 final size:18
Alignment explanation
Indices: 38942946--38942994 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
38942936 AGTTGAAAAG
38942946 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
38942965 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
38942982 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
38942995 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:38943884 original size:40 final size:40
Alignment explanation
Indices: 38943818--38943984 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
38943808 AAATTGAATG
* * *
38943818 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
38943857 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
38943897 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
38943937 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
38943977 ATATCCGG
1 ATATCCGG
38943985 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:38947258 original size:40 final size:40
Alignment explanation
Indices: 38947213--38947378 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
38947203 CGGAATATAA
38947213 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
38947253 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
38947293 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * *
38947333 CCGGATATAATTTCCAGCA-TAATGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38947371 CCGGATAT
1 CCGGATAT
38947379 CATTCAATTT
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
38 13 0.12
39 11 0.10
40 81 0.77
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38950021 original size:39 final size:39
Alignment explanation
Indices: 38949949--38950110 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
38949939 TATGGTAACC
* *
38949949 CGCACAAATGCCTTCGGGGCTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTC-GGGCTTAGCCCGGATATCACAACT
*
38949989 CGCACAATTGCCTTCGAGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
38950028 CACACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
38950067 CGCACAATTGCCTTCGGGCTTAGCCC-GATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
38950105 CGCACA
1 CGCACA
38950111 TTCATACACA
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
38 17 0.15
39 84 0.73
40 14 0.12
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:38952261 original size:30 final size:30
Alignment explanation
Indices: 38952217--38952275 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
38952207 CTTTAATACG
*
38952217 ACTTTGGCAAAATTACATTTTTGCCCCTAA
1 ACTTTGGCAAAATTACACTTTTGCCCCTAA
* *
38952247 ACTTTTGCATAATTACACTTTTGCCCCTA
1 ACTTTGGCAAAATTACACTTTTGCCCCTA
38952276 GGCTCGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.39
Consensus pattern (30 bp):
ACTTTGGCAAAATTACACTTTTGCCCCTAA
Found at i:38953944 original size:11 final size:12
Alignment explanation
Indices: 38953928--38953976 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
38953918 CACCACCCAA
38953928 CAACCACCATAT
1 CAACCACCATAT
*
38953940 C-ACCA-CATACAA
1 CAACCACCAT--AT
38953952 CAACCACCAT-T
1 CAACCACCATAT
38953963 CAACCACCATAT
1 CAACCACCATAT
38953975 CA
1 CA
38953977 CAACTGTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
10 3 0.10
11 14 0.47
12 6 0.20
13 4 0.13
14 3 0.10
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (12 bp):
CAACCACCATAT
Found at i:38954083 original size:67 final size:69
Alignment explanation
Indices: 38953956--38954083 Score: 172
Period size: 67 Copynumber: 1.9 Consensus size: 69
38953946 ATACAACAAC
* * * *
38953956 CACCATTCAACCACCATATCACAACTGTACTCACTACTCTTGTGCCAAAACCTAACAACCACCAT
1 CACCATTCAACCACCACATCACAACTATACTCACTACTCTTGTGCCAAAACCCAAAAACCACCAT
38954021 ATAT
66 ATAT
**
38954025 CACCATTCAA-CACCACATCACAA-TCATAC-CACTACTCTTGTGCCACCACCCAAAAACCA
1 CACCATTCAACCACCACATCACAACT-ATACTCACTACTCTTGTGCCAAAACCCAAAAACCA
38954084 ATTTCTTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 27 0.52
68 15 0.29
69 10 0.19
ACGTcount: A:0.37, C:0.39, G:0.04, T:0.20
Consensus pattern (69 bp):
CACCATTCAACCACCACATCACAACTATACTCACTACTCTTGTGCCAAAACCCAAAAACCACCAT
ATAT
Found at i:38960214 original size:41 final size:41
Alignment explanation
Indices: 38960169--38960286 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
38960159 TGAAAGATAA
38960169 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
38960210 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
38960240 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
38960281 ATGTAG
1 ATGTAG
38960287 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:38960225 original size:71 final size:71
Alignment explanation
Indices: 38960137--38960300 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
38960127 GAGATGTATC
38960137 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
38960202 AGGACA
66 AGGACA
38960208 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
38960273 AGGACA
66 AGGACA
38960279 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
38960301 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:38967777 original size:41 final size:41
Alignment explanation
Indices: 38967732--38967849 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
38967722 TGAAAGATAA
38967732 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
38967773 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
38967803 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
38967844 ATGTAG
1 ATGTAG
38967850 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:38967788 original size:71 final size:71
Alignment explanation
Indices: 38967700--38967863 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
38967690 GAGATGTATC
38967700 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
38967765 AGGACA
66 AGGACA
38967771 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
38967836 AGGACA
66 AGGACA
38967842 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
38967864 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:38975276 original size:10 final size:9
Alignment explanation
Indices: 38975260--38975284 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38975250 GTAAAAATGA
38975260 ATTTTTTTT
1 ATTTTTTTT
38975269 ATTTTTTTT
1 ATTTTTTTT
38975278 ATTTTTT
1 ATTTTTT
38975285 GGTGAATTAT
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:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:38977796 original size:3 final size:3
Alignment explanation
Indices: 38977788--38977816 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38977778 GTCAAAGTTA
38977788 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38977817 AGATGAATCT
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):
TAT
Found at i:38978156 original size:8 final size:8
Alignment explanation
Indices: 38978143--38978195 Score: 79
Period size: 8 Copynumber: 6.6 Consensus size: 8
38978133 TAGTCTAGTT
*
38978143 AGAGTAAA
1 AGAGCAAA
*
38978151 AGAGTAAA
1 AGAGCAAA
38978159 AGAGCAAA
1 AGAGCAAA
38978167 AGAGCAAA
1 AGAGCAAA
38978175 AGAGCAAA
1 AGAGCAAA
38978183 AGAGCAAA
1 AGAGCAAA
*
38978191 GGAGC
1 AGAGC
38978196 TTAAGCTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.04
Consensus pattern (8 bp):
AGAGCAAA
Found at i:38980722 original size:8 final size:8
Alignment explanation
Indices: 38980709--38980735 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38980699 ACTATTTTAA
38980709 AAATTATT
1 AAATTATT
38980717 AAATTATT
1 AAATTATT
38980725 AAATTATT
1 AAATTATT
38980733 AAA
1 AAA
38980736 ATTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTATT
Found at i:38980742 original size:8 final size:9
Alignment explanation
Indices: 38980708--38980744 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
38980698 AACTATTTTA
38980708 AAAATTATT
1 AAAATTATT
38980717 -AAATTATT
1 AAAATTATT
38980725 -AAATTATT
1 AAAATTATT
38980733 AAAATT-TT
1 AAAATTATT
38980741 AAAA
1 AAAA
38980745 ATATATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAATTATT
Found at i:38980763 original size:36 final size:34
Alignment explanation
Indices: 38980691--38980780 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 34
38980681 TTCAAAAAAT
38980691 ATTATAAAACTATTTTAAAAATTATTAAATTATTAA
1 ATTATAAAA--ATTTTAAAAATTATTAAATTATTAA
* * * *
38980727 ATTATTAAAATTTTAAAAATATATATTATTTTTTAA
1 ATTATAAAAATTTTAAAAAT-TAT-TAAATTATTAA
38980763 ATTATAAAAATATTTAAA
1 ATTATAAAAAT-TTTAAA
38980781 TGTTTATGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 11 0.24
35 3 0.07
36 26 0.57
37 6 0.13
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (34 bp):
ATTATAAAAATTTTAAAAATTATTAAATTATTAA
Found at i:38981100 original size:26 final size:26
Alignment explanation
Indices: 38981071--38981132 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
38981061 TCACCTCATT
* *
38981071 TATT-TATTAATAATTTTTTAATTTAA
1 TATTCTATAAATAATTTTATAATTT-A
*
38981097 TATTCTATAAATTATTTTATAATTTA
1 TATTCTATAAATAATTTTATAATTTA
38981123 TATTC-ATAAA
1 TATTCTATAAA
38981133 CATAGTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.16
26 10 0.31
27 17 0.53
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTCTATAAATAATTTTATAATTTA
Found at i:38981141 original size:27 final size:27
Alignment explanation
Indices: 38981083--38981146 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
38981073 TTTATTAATA
* *
38981083 ATTTTTTAATTTAATATTCTATAAATT
1 ATTTTATAATTTAATATTCTATAAAAT
38981110 ATTTTATAATTT-ATATTC-ATAAACAT
1 ATTTTATAATTTAATATTCTATAAA-AT
*
38981136 AGTTT-TAATTT
1 ATTTTATAATTT
38981147 TGTGACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.33
26 11 0.33
27 11 0.33
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTTTATAATTTAATATTCTATAAAAT
Found at i:38981144 original size:25 final size:26
Alignment explanation
Indices: 38981086--38981146 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
38981076 ATTAATAATT
* *
38981086 TTTTAATTTAATATTCTATAAATTAT
1 TTTTAATTTAATATTCTATAAAATAG
38981112 TTTATAATTT-ATATTC-ATAAACATAG
1 TTT-TAATTTAATATTCTATAAA-ATAG
38981138 TTTTAATTT
1 TTTTAATTT
38981147 TGTGACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 11 0.35
26 14 0.45
27 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTAATTTAATATTCTATAAAATAG
Found at i:38986035 original size:43 final size:43
Alignment explanation
Indices: 38985886--38986040 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 43
38985876 ATATCGTATA
* *
38985886 ATGCCAACATCCCAGACATGGTCTTACATGCT-ATC-CAATATCC
1 ATGCCAACATCCCAGACATGGTCTTACACG-TAATCAC-ATATCG
* * *
38985929 ATGCC-ACTATCCCAGACAGGGTCTTACAC-AAATCAAATA-CG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACGTAATCACATATCG
** * ** *
38985970 ATATCGATGTCCTAGACATGGTCTTACACGTAATCACATATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
*
38986013 ATGCCAACGTCCCAGACATGGTCTTACA
1 ATGCCAACATCCCAGACATGGTCTTACA
38986041 TGAGAACACA
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
41 22 0.25
42 17 0.19
43 49 0.56
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCAACATCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:38990043 original size:15 final size:15
Alignment explanation
Indices: 38990011--38990039 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38990001 ATTTACTGTG
38990011 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
38990026 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
38990040 ATTTCCGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:38990649 original size:30 final size:28
Alignment explanation
Indices: 38990607--38990667 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
38990597 GAATTTGAGT
*
38990607 AATTAGGGCTAAATTGTAAAAATAAAT-A
1 AATTAGGGCTAAAATGT-AAAATAAATGA
*
38990635 AATTAAGGGACTAAAATGTGAAATAAATGA
1 AATT-AGGG-CTAAAATGTAAAATAAATGA
38990665 AAT
1 AAT
38990668 GTATGGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.14
29 12 0.43
30 12 0.43
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.26
Consensus pattern (28 bp):
AATTAGGGCTAAAATGTAAAATAAATGA
Found at i:38991192 original size:41 final size:42
Alignment explanation
Indices: 38991147--38991262 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 42
38991137 GATATGTGCG
* *
38991147 TTCATGTAAGACCACGTCTGGGACATTGGCAT-CATATTTGA
1 TTCATGTAAGACCACGTCTGGGACATTGGCATCCAGATATGA
* * * *
38991188 TTCATGTAAAACC-CTATCTAGGACAGTGGCATCCAGATATGA
1 TTCATGTAAGACCAC-GTCTGGGACATTGGCATCCAGATATGA
* *
38991230 TTACATGTAAGACCACGCCTGGGACGTTGGCAT
1 TT-CATGTAAGACCACGTCTGGGACATTGGCAT
38991263 TGTAAAATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
40 1 0.02
41 26 0.44
42 9 0.15
43 22 0.37
44 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (42 bp):
TTCATGTAAGACCACGTCTGGGACATTGGCATCCAGATATGA
Found at i:38992509 original size:2 final size:2
Alignment explanation
Indices: 38992502--38992530 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38992492 AAGTTTCGGC
38992502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38992531 GTGCATAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38993286 original size:25 final size:25
Alignment explanation
Indices: 38993234--38993286 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
38993224 GGGTGTTACA
* **
38993234 AGCTGTATAACAGGAAGCTTATCCG
1 AGCTGTATAACAGGAAGCTCATAAG
38993259 AGCTGTATAAC-GAGAAGCTCATAAG
1 AGCTGTATAACAG-GAAGCTCATAAG
38993284 AGC
1 AGC
38993287 CATAATCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (25 bp):
AGCTGTATAACAGGAAGCTCATAAG
Found at i:38993459 original size:26 final size:25
Alignment explanation
Indices: 38993387--38993477 Score: 60
Period size: 26 Copynumber: 3.6 Consensus size: 25
38993377 AACGAGCCAT
**
38993387 ATCGGGAAGCTC-TGAGGAGCCATTA
1 ATCGGGAAGCTCATGAAAAGCC-TTA
* * * *
38993412 ACCAGGAAGGTCA-CAAAGAGCCTTTA
1 ATCGGGAAGCTCATGAAA-AGCC-TTA
*
38993438 ATCGGGAAGCTCATGAAAAGCCATA
1 ATCGGGAAGCTCATGAAAAGCCTTA
*
38993463 TATCGGGACGCTCAT
1 -ATCGGGAAGCTCAT
38993478 AAGAGCTGTG
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
25 12 0.24
26 34 0.69
27 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAAAAGCCTTA
Found at i:38993929 original size:10 final size:10
Alignment explanation
Indices: 38993914--38993958 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
38993904 TATATGAGTA
*
38993914 AATTTAACTC
1 AATTTAATTC
*
38993924 AATTTAATAC
1 AATTTAATTC
38993934 AATTTATATTC
1 AATTTA-ATTC
*
38993945 AATTCAATTC
1 AATTTAATTC
38993955 AATT
1 AATT
38993959 CACATATTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTTAATTC
Found at i:38993948 original size:21 final size:20
Alignment explanation
Indices: 38993914--38993958 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
38993904 TATATGAGTA
*
38993914 AATTTAACTCAATTTAATAC
1 AATTTAACTCAATTCAATAC
* *
38993934 AATTTATATTCAATTCAATTC
1 AATTTA-ACTCAATTCAATAC
38993955 AATT
1 AATT
38993959 CACATATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAACTCAATTCAATAC
Found at i:39000266 original size:23 final size:23
Alignment explanation
Indices: 39000239--39000285 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39000229 AAATAGGATG
39000239 AATGGTAAGTTAAGTGCCATGTT
1 AATGGTAAGTTAAGTGCCATGTT
39000262 AATGGTAAGTTAAGTGCCATGTT
1 AATGGTAAGTTAAGTGCCATGTT
39000285 A
1 A
39000286 TATGAACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.34
Consensus pattern (23 bp):
AATGGTAAGTTAAGTGCCATGTT
Found at i:39000414 original size:2 final size:2
Alignment explanation
Indices: 39000407--39000433 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39000397 CCTATGTCGG
39000407 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39000434 GGTAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39000865 original size:15 final size:13
Alignment explanation
Indices: 39000832--39000864 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
39000822 GACACACGGG
39000832 CGTGTGTCTAGAC
1 CGTGTGTCTAGAC
39000845 CGTGTGTCTAGAC
1 CGTGTGTCTAGAC
*
39000858 AGTGTGT
1 CGTGTGT
39000865 GACACATGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (13 bp):
CGTGTGTCTAGAC
Found at i:39004038 original size:5 final size:5
Alignment explanation
Indices: 39004028--39004066 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
39004018 GCCTAATATG
* *
39004028 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
39004067 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:39004459 original size:24 final size:25
Alignment explanation
Indices: 39004407--39004453 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39004397 TAGCCCTCTT
*
39004407 GAGCTTCCCGTTATATAGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
39004432 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
39004454 CGGAGCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:39004584 original size:26 final size:26
Alignment explanation
Indices: 39004526--39004584 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
39004516 GTCCCAATAT
39004526 ATGGCTCTTCGTAAGCTTCCCGATTA
1 ATGGCTCTTCGTAAGCTTCCCGATTA
** * * **
39004552 AAAGCTCTTTGTGAGCTTCTTGATTA
1 ATGGCTCTTCGTAAGCTTCCCGATTA
39004578 ATGGCTC
1 ATGGCTC
39004585 CTTATAGCTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATGGCTCTTCGTAAGCTTCCCGATTA
Found at i:39004622 original size:23 final size:23
Alignment explanation
Indices: 39004578--39004624 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
39004568 TTCTTGATTA
* *
39004578 ATGGCTCCTTATAGCTTTCTGAT
1 ATGGCTCCTTATAACTTCCTGAT
39004601 ATGGCTCGCTTA-AACTTCCTGAT
1 ATGGCTC-CTTATAACTTCCTGAT
39004624 A
1 A
39004625 ATAAGCTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (23 bp):
ATGGCTCCTTATAACTTCCTGAT
Found at i:39007245 original size:40 final size:39
Alignment explanation
Indices: 39007194--39007338 Score: 141
Period size: 40 Copynumber: 3.6 Consensus size: 39
39007184 GCGACTCGCT
* ** *
39007194 CAAAAGCCTTCGGGACATAGCCCGGTTATAATAGCTTGCA
1 CAAATGCCTTCGGGACATAGCCCGGTT-TGGTAACTTGCA
* * * *
39007234 TAAATGCCTTCGGGAC-TAATCCCGGATTTGGGAACTCGCA
1 CAAATGCCTTCGGGACAT-AGCCCGG-TTTGGTAACTTGCA
*
39007274 CAAATGCCTTCGGGA-ATTAACCCGGTTTTGGTAACTTGCA
1 CAAATGCCTTCGGGACA-TAGCCCGG-TTTGGTAACTTGCA
*
39007314 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACATAGCCCGG
39007339 ATACCATTCA
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 81 0.95
41 3 0.04
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACATAGCCCGGTTTGGTAACTTGCA
Found at i:39007299 original size:80 final size:80
Alignment explanation
Indices: 39007187--39007340 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 80
39007177 GAATATAGCG
* * * *
39007187 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATAGCTTGCATAAATGCCTTCGGGACTA
1 ACTCGCACAAAAGCCTTCGGGACATAACCCGGTTATAATAACTTGCACAAATGCCTTCGGGACTA
*
39007252 ATCCCGGATTTGGGA
66 AGCCCGGATTTGGGA
* * **
39007267 ACTCGCACAAATGCCTTCGGGA-ATTAACCCGGTTTTGGTAACTTGCACAAATGCCTTCGGGACT
1 ACTCGCACAAAAGCCTTCGGGACA-TAACCCGGTTATAATAACTTGCACAAATGCCTTCGGGACT
*
39007331 TAGCCCGGAT
65 AAGCCCGGAT
39007341 ACCATTCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.02
80 62 0.98
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACAAAAGCCTTCGGGACATAACCCGGTTATAATAACTTGCACAAATGCCTTCGGGACTA
AGCCCGGATTTGGGA
Found at i:39011065 original size:93 final size:93
Alignment explanation
Indices: 39010953--39011124 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
39010943 GCCCATAAGT
* *
39010953 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39011018 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
39011046 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39011111 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
39011125 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39011120 original size:46 final size:46
Alignment explanation
Indices: 39010945--39011120 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
39010935 TGTAACCCGC
* * *
39010945 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
39010991 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
39011041 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
39011084 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39011121 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:39013542 original size:29 final size:29
Alignment explanation
Indices: 39013503--39013590 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
39013493 CAAAGATAAC
*
39013503 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
39013532 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
39013561 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
39013591 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:39013561 original size:15 final size:15
Alignment explanation
Indices: 39013503--39013581 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
39013493 CAAAGATAAC
*
39013503 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
39013517 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
39013532 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
39013546 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
39013561 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
39013576 AAGAAA
1 AAGAAA
39013582 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:39013590 original size:15 final size:15
Alignment explanation
Indices: 39013514--39013590 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
39013504 AGAAAACCGA
39013514 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
39013529 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
39013543 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
39013557 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
39013573 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
39013588 ATA
1 ATA
39013591 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:39016652 original size:93 final size:93
Alignment explanation
Indices: 39016540--39016711 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
39016530 GCCCATAAGT
* *
39016540 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39016605 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
39016633 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39016698 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
39016712 CAAATATCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39016707 original size:46 final size:46
Alignment explanation
Indices: 39016532--39016707 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
39016522 TGTAACCCGC
* * *
39016532 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
39016578 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
39016628 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
39016671 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39016708 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:39020246 original size:40 final size:40
Alignment explanation
Indices: 39020187--39020328 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
39020177 AAATTGAATG
* * *
39020187 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
39020227 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
39020267 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
39020307 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
39020329 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:39020329 original size:40 final size:39
Alignment explanation
Indices: 39020226--39020354 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
39020216 TGCTGGAAAT
* * *
39020226 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
39020266 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
39020306 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
39020346 TATATCCGG
1 TATATCCGG
39020355 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:39028242 original size:40 final size:40
Alignment explanation
Indices: 39028176--39028342 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39028166 AAATTGAATG
* * *
39028176 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
39028215 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
39028255 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
39028295 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
39028335 ATATCCGG
1 ATATCCGG
39028343 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39034537 original size:55 final size:56
Alignment explanation
Indices: 39034464--39034591 Score: 179
Period size: 55 Copynumber: 2.3 Consensus size: 56
39034454 ATCATGATAC
* *
39034464 ATGAATGTATGTAAGACCATTAGCTTAAGATCCATGGA-AAGATC-AATATGACTGA
1 ATGAATGTATGTAAGACCATGAGCTTAAGACCCAT-GATAAGATCTAATATGACTGA
* * * *
39034519 ATGAATGTATGTATGACCATGAGGTTAAGACCCATGATAAGATCTGATATGATTGA
1 ATGAATGTATGTAAGACCATGAGCTTAAGACCCATGATAAGATCTAATATGACTGA
39034575 ATGAATGTATGTAAGAC
1 ATGAATGTATGTAAGAC
39034592 TATATGGTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
54 2 0.03
55 37 0.58
56 25 0.39
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (56 bp):
ATGAATGTATGTAAGACCATGAGCTTAAGACCCATGATAAGATCTAATATGACTGA
Found at i:39034601 original size:56 final size:55
Alignment explanation
Indices: 39034464--39034607 Score: 177
Period size: 56 Copynumber: 2.6 Consensus size: 55
39034454 ATCATGATAC
* *
39034464 ATGAATGTATGTAAGACCAT-TAGCTTAAGATCCATGGAAAGATCAATATGACTGA
1 ATGAATGTATGTAAGACCATAT-GGTTAAGACCCATGGAAAGATCAATATGACTGA
* * *
39034519 ATGAATGTATGTATGACCATGA-GGTTAAGACCCAT-GATAAGATCTGATATGATTGA
1 ATGAATGTATGTAAGACCAT-ATGGTTAAGACCCATGGA-AAGATC-AATATGACTGA
*
39034575 ATGAATGTATGTAAGACTATATGGTTAAGACCC
1 ATGAATGTATGTAAGACCATATGGTTAAGACCC
39034608 GTGGCATTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
54 2 0.03
55 37 0.48
56 38 0.49
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (55 bp):
ATGAATGTATGTAAGACCATATGGTTAAGACCCATGGAAAGATCAATATGACTGA
Found at i:39036275 original size:19 final size:19
Alignment explanation
Indices: 39036251--39036288 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39036241 TATAGAAAGG
*
39036251 ATTTAGCTCGGATGGGTAA
1 ATTTAGCCCGGATGGGTAA
39036270 ATTTAGCCCGGATGGGTAA
1 ATTTAGCCCGGATGGGTAA
39036289 TCTTGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (19 bp):
ATTTAGCCCGGATGGGTAA
Found at i:39050581 original size:26 final size:26
Alignment explanation
Indices: 39050551--39050600 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
39050541 CTCATAATAG
* *
39050551 TTTTAAATGGGAAGTTCACAAAGAAC
1 TTTTAAATAGGAAGCTCACAAAGAAC
* *
39050577 TTTTAATTAGGAAGCTCACGAAGA
1 TTTTAAATAGGAAGCTCACAAAGA
39050601 GCCTATCAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (26 bp):
TTTTAAATAGGAAGCTCACAAAGAAC
Found at i:39055412 original size:22 final size:23
Alignment explanation
Indices: 39055343--39055526 Score: 279
Period size: 23 Copynumber: 8.1 Consensus size: 23
39055333 CCTAGCCTCT
*
39055343 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39055366 TTTTATAACT-GGGCAT-AG-CC
1 TTTAATAACTGGGGCATAAGCCC
39055386 TTTAATAACTGGGGCAT-AGCCC
1 TTTAATAACTGGGGCATAAGCCC
39055408 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
39055431 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39055454 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
39055478 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
39055502 TTTAATAACT-GGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
39055524 TTT
1 TTT
39055527 TGCACTTCCT
Statistics
Matches: 152, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
20 11 0.07
21 10 0.07
22 39 0.26
23 46 0.30
24 46 0.30
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:39055467 original size:24 final size:24
Alignment explanation
Indices: 39055322--39055527 Score: 281
Period size: 24 Copynumber: 9.0 Consensus size: 24
39055312 TGCTTATCAT
*
39055322 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
39055347 ATAACTGGGGCAAAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
39055370 ATAACT-GGGCAT-AG-CC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39055390 ATAACTGGGGCAT-AGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39055412 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
39055435 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
39055459 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
39055483 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39055506 ATAACT-GGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
39055528 GCACTTCCTC
Statistics
Matches: 169, Mismatches: 5, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
19 3 0.02
20 8 0.05
21 10 0.06
22 36 0.21
23 46 0.27
24 54 0.32
25 12 0.07
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:39055599 original size:9 final size:9
Alignment explanation
Indices: 39055585--39055641 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
39055575 ATCTCATGTG
39055585 CATATCATA
1 CATATCATA
*
39055594 CATATCATGTG
1 CATATCA--TA
39055605 CATATCATA
1 CATATCATA
* *
39055614 CATGTCATGTG
1 CATATCA--TA
39055625 CATATCATA
1 CATATCATA
39055634 CATATCAT
1 CATATCAT
39055642 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:39055601 original size:20 final size:20
Alignment explanation
Indices: 39055573--39055643 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
39055563 GCATTTATGA
*
39055573 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
39055593 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
39055613 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
39055633 ACATATCATGT
1 ACATATCATGT
39055644 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:39055608 original size:11 final size:11
Alignment explanation
Indices: 39055578--39055632 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
39055568 TATGAACATC
39055578 TCATGTGCATA
1 TCATGTGCATA
*
39055589 TCA--TACATA
1 TCATGTGCATA
39055598 TCATGTGCATA
1 TCATGTGCATA
* *
39055609 TCA--TACATG
1 TCATGTGCATA
39055618 TCATGTGCATA
1 TCATGTGCATA
39055629 TCAT
1 TCAT
39055633 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:39063544 original size:23 final size:24
Alignment explanation
Indices: 39063475--39063685 Score: 326
Period size: 23 Copynumber: 9.0 Consensus size: 24
39063465 GCTTTATCAT
*
39063475 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
39063500 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39063524 ATAACTGGGGCAT-AGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39063546 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
39063569 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
39063593 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
39063617 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39063640 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
39063663 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
39063686 GCACTTCCTC
Statistics
Matches: 177, Mismatches: 5, Indels: 9
0.93 0.03 0.05
Matches are distributed among these distances:
22 17 0.10
23 78 0.44
24 70 0.40
25 12 0.07
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:39063658 original size:94 final size:93
Alignment explanation
Indices: 39063475--39063686 Score: 354
Period size: 94 Copynumber: 2.3 Consensus size: 93
39063465 GCTTTATCAT
* *
39063475 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAG
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAG
39063539 CCCTTTAATAACTGGGGCATAAGCCCTTTA
64 CCCTTTAATAACTGGGGCATAAGCCCTTTA
* *
39063569 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCAT-AGC
39063634 CCTTTAATAACTGGGGCATAAGCCCTTTA
65 CCTTTAATAACTGGGGCATAAGCCCTTTA
39063663 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
39063687 CACTTCCTCC
Statistics
Matches: 112, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
93 44 0.39
94 68 0.61
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (93 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAGCC
CTTTAATAACTGGGGCATAAGCCCTTTA
Found at i:39063757 original size:9 final size:9
Alignment explanation
Indices: 39063743--39063799 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
39063733 ATCTCATGTG
39063743 CATATCATA
1 CATATCATA
*
39063752 CATATCATGTG
1 CATATCA--TA
39063763 CATATCATA
1 CATATCATA
* *
39063772 CATGTCATGTG
1 CATATCA--TA
39063783 CATATCATA
1 CATATCATA
39063792 CATATCAT
1 CATATCAT
39063800 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:39063759 original size:20 final size:20
Alignment explanation
Indices: 39063731--39063801 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
39063721 GCATTTATGA
*
39063731 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
39063751 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
39063771 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
39063791 ACATATCATGT
1 ACATATCATGT
39063802 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:39063766 original size:11 final size:11
Alignment explanation
Indices: 39063736--39063790 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
39063726 TATGAACATC
39063736 TCATGTGCATA
1 TCATGTGCATA
*
39063747 TCA--TACATA
1 TCATGTGCATA
39063756 TCATGTGCATA
1 TCATGTGCATA
* *
39063767 TCA--TACATG
1 TCATGTGCATA
39063776 TCATGTGCATA
1 TCATGTGCATA
39063787 TCAT
1 TCAT
39063791 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:39067240 original size:29 final size:29
Alignment explanation
Indices: 39067207--39067338 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
39067197 GTGACGAGAT
39067207 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
39067236 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * ***
39067265 TGGCATTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
39067294 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
39067323 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
39067339 AAATCGAGTA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:39070005 original size:3 final size:3
Alignment explanation
Indices: 39069997--39070042 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
39069987 TTAACTTTTA
39069997 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39070043 AATGTGGCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39070760 original size:20 final size:20
Alignment explanation
Indices: 39070729--39070795 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
39070719 TTTATAAAAT
39070729 TTTAT-ATATTTTTTCTATA
1 TTTATAATATTTTTTCTATA
** *
39070748 TTTATAAT-TTTTTTAGGATT
1 TTTATAATATTTTTT-CTATA
39070768 TTTATAATATTTTTTCTA-A
1 TTTATAATATTTTTTCTATA
*
39070787 TTTTTAATA
1 TTTATAATA
39070796 AAAATTAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 19 0.50
20 13 0.34
21 6 0.16
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTATAATATTTTTTCTATA
Found at i:39070825 original size:28 final size:28
Alignment explanation
Indices: 39070780--39070847 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
39070770 TATAATATTT
*
39070780 TTTCTAAT-TTTTAATAAAAATTAAAT-A
1 TTTCTTATATTTTAAT-AAAATTAAATAA
* *
39070807 TTTCTTATATTTTATTAAAATTTAATAA
1 TTTCTTATATTTTAATAAAATTAAATAA
39070835 TTT-TTATAATTTT
1 TTTCTTAT-ATTTT
39070848 TATTGGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTCTTATATTTTAATAAAATTAAATAA
Found at i:39076051 original size:22 final size:23
Alignment explanation
Indices: 39076004--39076051 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39075994 ATTTAATTTC
*
39076004 AAAAAATTAAGTGATTAAAACAA
1 AAAAAATTAAGTGACTAAAACAA
*
39076027 AAAAAATT-AGATGACTAAAATAA
1 AAAAAATTAAG-TGACTAAAACAA
39076050 AA
1 AA
39076052 CAAACTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (23 bp):
AAAAAATTAAGTGACTAAAACAA
Found at i:39077442 original size:21 final size:21
Alignment explanation
Indices: 39077416--39077457 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39077406 TTAACGGGAC
* *
39077416 AGCTAACGTGGCCAGTTAATT
1 AGCTAACATGACCAGTTAATT
*
39077437 AGCTAATATGACCAGTTAATT
1 AGCTAACATGACCAGTTAATT
39077458 TGCCATGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (21 bp):
AGCTAACATGACCAGTTAATT
Found at i:39077550 original size:29 final size:31
Alignment explanation
Indices: 39077517--39077578 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
39077507 TATTTTTTTG
* *
39077517 TTTTTTAATAAATGGCTCAATAT-TTT-TAC
1 TTTTTGAATAAATGGCCCAATATGTTTGTAC
**
39077546 TTTTTGCGTAAATGGCCCAATATGTTTGTAC
1 TTTTTGAATAAATGGCCCAATATGTTTGTAC
39077577 TT
1 TT
39077579 CTTCTTCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.70
30 3 0.11
31 5 0.19
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (31 bp):
TTTTTGAATAAATGGCCCAATATGTTTGTAC
Found at i:39078215 original size:9 final size:9
Alignment explanation
Indices: 39078203--39078228 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39078193 TCTTCTTTTC
39078203 TTTTTCTTA
1 TTTTTCTTA
39078212 TTTTTCTTA
1 TTTTTCTTA
39078221 TTTTTCTT
1 TTTTTCTT
39078229 TTATTGCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:39082022 original size:63 final size:63
Alignment explanation
Indices: 39081923--39082048 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
39081913 ATCATGTGGA
39081923 GCCATATGTCCCTCTGCCCATAGGAAATAATGCTTCAACATCATGGTACCCTAACTTGAGAGC
1 GCCATATGTCCCTCTGCCCATAGGAAATAATGCTTCAACATCATGGTACCCTAACTTGAGAGC
39081986 GCCATATGTCCCTCTGCCCATAGGAAATAATGCTTCAACATCATGGTACCCTAACTTGAGAGC
1 GCCATATGTCCCTCTGCCCATAGGAAATAATGCTTCAACATCATGGTACCCTAACTTGAGAGC
39082049 TACCAATCAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (63 bp):
GCCATATGTCCCTCTGCCCATAGGAAATAATGCTTCAACATCATGGTACCCTAACTTGAGAGC
Found at i:39123439 original size:65 final size:65
Alignment explanation
Indices: 39123335--39123462 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
39123325 CCCCTAGGGT
* * *
39123335 TAAGGTTGACCTGAATTCATGTTTGACTGTTACTATTTACTGCACGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTAAATGCATGTTTGACTGCTACTATTTACTGCACGCCATGTTATTATTATCTGA
*
39123400 TAAGGTTGACCTAAATGCATGTTTGACTGCTACTATTTACTGCATGCCATGTTATTATTATCT
1 TAAGGTTGACCTAAATGCATGTTTGACTGCTACTATTTACTGCACGCCATGTTATTATTATCT
39123463 AATGCATGGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (65 bp):
TAAGGTTGACCTAAATGCATGTTTGACTGCTACTATTTACTGCACGCCATGTTATTATTATCTGA
Found at i:39123809 original size:34 final size:32
Alignment explanation
Indices: 39123715--39123809 Score: 86
Period size: 34 Copynumber: 2.9 Consensus size: 32
39123705 TATGGGCCAT
* **
39123715 ACTGTTATCTGAAAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAAAA-GGGCTTAGGCCCAGTCC
*
39123748 ACTG-TATTTTGAAAAGGGCTTCA-GCCCAGTACCC
1 ACTGTTA-TCTGAAAAGGGCTT-AGGCCCAGT--CC
*
39123782 ACTGTTATCTGAATAGGGCTTAGGCCCA
1 ACTGTTATCTGAAAAGGGCTTAGGCCCA
39123810 ATGGGCTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
32 14 0.28
33 13 0.26
34 21 0.42
35 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (32 bp):
ACTGTTATCTGAAAAGGGCTTAGGCCCAGTCC
Found at i:39127593 original size:65 final size:65
Alignment explanation
Indices: 39127489--39127616 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 65
39127479 CCTCTAGGGT
*
39127489 TAAGGTTGACCTGAATGCATGTTTGACTGTTGCTATTTACTGCACACCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACACCATGTTATTATTATCTGA
**
39127554 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCT
1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACACCATGTTATTATTATCT
39127617 AATGCATGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (65 bp):
TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACACCATGTTATTATTATCTGA
Found at i:39137673 original size:22 final size:22
Alignment explanation
Indices: 39137643--39137687 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39137633 TAAAAGGACC
39137643 TTTTCGCAAAAGATGTAAAATA
1 TTTTCGCAAAAGATGTAAAATA
* *
39137665 TTTTTGCAAAAGGTGTAAAATA
1 TTTTCGCAAAAGATGTAAAATA
39137687 T
1 T
39137688 GTGGTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (22 bp):
TTTTCGCAAAAGATGTAAAATA
Found at i:39148214 original size:17 final size:17
Alignment explanation
Indices: 39148188--39148227 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39148178 TAATTTCGAA
*
39148188 AAAGGACTAAATCGCAT
1 AAAGGGCTAAATCGCAT
39148205 AAAGGGCTAAATCGCAT
1 AAAGGGCTAAATCGCAT
39148222 AAAGGG
1 AAAGGG
39148228 AAAAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (17 bp):
AAAGGGCTAAATCGCAT
Found at i:39149525 original size:48 final size:48
Alignment explanation
Indices: 39149420--39149585 Score: 187
Period size: 48 Copynumber: 3.5 Consensus size: 48
39149410 TACGTGTGCT
* * * *
39149420 AGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATAT-TGA-GAG-C
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-ACAAGCC
* * *
39149465 ACGTGTAAGACATGTCTGGCACATGCATCGGTCTCGAGATATACCAGCC
1 A-GTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
*
39149514 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
* * *
39149562 ACTGTAAGACTTGCCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
39149586 GCGTCAGCTT
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
45 1 0.01
46 29 0.28
47 4 0.04
48 67 0.65
49 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
Found at i:39149662 original size:49 final size:49
Alignment explanation
Indices: 39149605--39149775 Score: 152
Period size: 49 Copynumber: 3.5 Consensus size: 49
39149595 TGTTGTGTGT
*
39149605 CAGTGTAAGACCTATCTAGGACATGGCATCGACAC-CGATAGAT-GAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGAC-CTCGATAGATGGA-AGC
* * * * * * **
39149654 CAGTGTAAGACTTGTTTGGGACAAGGCATCGGCCTCGATATATGGAATT
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGACCTCGATAGATGGAAGC
* * * **
39149703 TAGTGTAAGACCTGTCTAGGACATGGCATCGACTTTGAT-G-TGCTAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGACCTCGATAGATGGAAGC
*
39149750 CAGTGTAAGACCATGTCTGGGACATG
1 CAGTGTAAGACC-TGTCTAGGACATG
39149776 ACGTCGGCAT
Statistics
Matches: 95, Mismatches: 24, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
47 14 0.15
48 13 0.14
49 66 0.69
50 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTAGGACATGGCATCGACCTCGATAGATGGAAGC
Found at i:39155503 original size:15 final size:15
Alignment explanation
Indices: 39155459--39155495 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
39155449 ATAAAGATCT
39155459 ATGATG-AGTATATG
1 ATGATGTAGTATATG
39155473 ATGATGTAGTATATG
1 ATGATGTAGTATATG
39155488 ATGATGTA
1 ATGATGTA
39155496 CGATATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (15 bp):
ATGATGTAGTATATG
Found at i:39157037 original size:71 final size:71
Alignment explanation
Indices: 39156953--39157116 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
39156943 CGATTTGTCT
39156953 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
39157018 CTTTCA
66 CTTTCA
39157024 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
39157089 CTTTCA
66 CTTTCA
39157095 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
39157117 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:39157154 original size:71 final size:70
Alignment explanation
Indices: 39156953--39157150 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
39156943 CGATTTGTCT
* * * *
39156953 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
39157018 CTTTCA
65 CTTTCA
* * * *
39157024 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
39157089 CTTTCA
65 CTTTCA
* *
39157095 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
39157151 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:39163332 original size:71 final size:71
Alignment explanation
Indices: 39163248--39163411 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
39163238 CGATTTGTCT
39163248 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
39163313 CTTTCA
66 CTTTCA
39163319 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
39163384 CTTTCA
66 CTTTCA
39163390 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
39163412 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:39163449 original size:71 final size:70
Alignment explanation
Indices: 39163248--39163445 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
39163238 CGATTTGTCT
* * * *
39163248 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
39163313 CTTTCA
65 CTTTCA
* * * *
39163319 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
39163384 CTTTCA
65 CTTTCA
* *
39163390 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
39163446 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:39167561 original size:39 final size:39
Alignment explanation
Indices: 39167512--39167731 Score: 307
Period size: 39 Copynumber: 5.6 Consensus size: 39
39167502 AATGTTCGAG
39167512 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
39167551 TGATACCCGGGCTAAGCCC-AAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
39167589 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
39167628 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
39167667 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
39167707 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
39167732 TGTTTTGAAC
Statistics
Matches: 163, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
38 36 0.22
39 87 0.53
40 40 0.25
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.22
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:39167607 original size:77 final size:78
Alignment explanation
Indices: 39167512--39167731 Score: 325
Period size: 77 Copynumber: 2.8 Consensus size: 78
39167502 AATGTTCGAG
39167512 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATACCCGGGCTAAGCCC-AAGGCA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATACCCGGGCTAAGCCCGAAGGCA
39167576 ATTGTGCGAGCTA
66 ATTGTGCGAGCTA
*
39167589 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTATGATACCCGGGCTAAGCCCGAAGGCA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATACCCGGGCTAAGCCCGAAGGCA
* *
39167654 ATTGTGCGAGTTG
66 ATTGTGCGAGCTA
* * * ** * *
39167667 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATGATACCCGGGCTAAG-CCCGAAGG
39167732 TGTTTTGAAC
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
77 57 0.44
78 32 0.25
79 32 0.25
80 8 0.06
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.22
Consensus pattern (78 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATACCCGGGCTAAGCCCGAAGGCA
ATTGTGCGAGCTA
Found at i:39177760 original size:71 final size:70
Alignment explanation
Indices: 39177622--39177761 Score: 174
Period size: 71 Copynumber: 2.0 Consensus size: 70
39177612 ATGGATGTGT
* * * ** * *
39177622 ATGATTATTGATTATGTGTGTATGAGTATTTGAATTCCACCCGGGCTAAGTCCCGAAGGCGAATA
1 ATGATTATTGATTATGTGTGCATGAGAAATTGAATGACACCCGGGCTAAGCCCCGAAGACGAATA
39177687 TGCTA
66 TGCTA
* *
39177692 ATGATTATTGATGTATGTGTGCATGAGAAATTGAATGATATCCGGGCTAAGCCCCGAAGAC-AAT
1 ATGATTATTGAT-TATGTGTGCATGAGAAATTGAATGACACCCGGGCTAAGCCCCGAAGACGAA-
39177756 TATGCT
64 TATGCT
39177762 GAAATTATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
70 14 0.24
71 45 0.76
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (70 bp):
ATGATTATTGATTATGTGTGCATGAGAAATTGAATGACACCCGGGCTAAGCCCCGAAGACGAATA
TGCTA
Found at i:39177829 original size:39 final size:39
Alignment explanation
Indices: 39177729--39177875 Score: 158
Period size: 39 Copynumber: 3.8 Consensus size: 39
39177719 AAATTGAATG
* * * * *
39177729 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TACT
* *
39177768 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTACT
**
39177807 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTTGT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTACT
*
39177845 -TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
39177876 AAATCGTGAT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
37 27 0.29
38 9 0.10
39 56 0.60
40 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTACT
Found at i:39185898 original size:40 final size:40
Alignment explanation
Indices: 39185796--39185979 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
39185786 AAATTGAATG
* * * * *
39185796 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
39185836 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
39185876 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
39185916 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
39185956 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
39185980 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:39198390 original size:40 final size:39
Alignment explanation
Indices: 39198346--39198499 Score: 191
Period size: 39 Copynumber: 3.9 Consensus size: 39
39198336 ATTCAAAACA
* * ** * *
39198346 CCTTCGGGACGTAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
39198386 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
39198426 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
39198465 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
39198500 TTCATTCACA
Statistics
Matches: 100, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 60 0.60
40 40 0.40
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:39198457 original size:39 final size:39
Alignment explanation
Indices: 39198376--39198499 Score: 194
Period size: 39 Copynumber: 3.2 Consensus size: 39
39198366 TATGGTAACC
* *
39198376 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
39198416 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39198455 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
39198494 CGCACA
1 CGCACA
39198500 TTCATTCACA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 60 0.78
40 17 0.22
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39209747 original size:43 final size:42
Alignment explanation
Indices: 39209599--39209762 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 42
39209589 TATGTGTTAT
*
39209599 CGTGTAACACCATGTCTGGGACGTTGGCATCGCT-TTGTGATTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCG-TATT-TGA-TTA
* * ** *
39209643 CGTGTAAGACCATGTTTGGGACATTGGCATCGTATACGATTT
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATTA
*
39209685 CGTGTAAGATGC-TGTCTGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGA-CCATGTCTGGGAC-GTTGGCATCG-TATTTGATTA
* *
39209728 CATGTAAGACCATGTCTGGGACGTTGGCATTGTAT
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGTAT
39209763 GAGCTTATGT
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 33 0.33
43 36 0.36
44 30 0.30
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATTA
Found at i:39220658 original size:38 final size:39
Alignment explanation
Indices: 39220486--39220725 Score: 303
Period size: 40 Copynumber: 6.2 Consensus size: 39
39220476 CGGATGATAA
* * *
39220486 CGAAGGCATTTGTGCTAGTGACTA-ATTCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-CCGGGCTAAGTCC
* * *
39220525 CGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACT-ATACCGGGCTAAGTCC
39220565 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-CCGGGCTAAGTCC
39220605 CGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCC
39220644 C-AAGGCATTTGTGCGAGTTACTATAACCGGGCT-AGT-C
1 CGAAGGCATTTGTGCGAGTTACTAT-ACCGGGCTAAGTCC
* * *
39220681 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATA-CCGGGCTAAGTCC
39220720 CGAAGG
1 CGAAGG
39220726 TACTTGGTTT
Statistics
Matches: 184, Mismatches: 8, Indels: 18
0.88 0.04 0.09
Matches are distributed among these distances:
37 8 0.04
38 49 0.27
39 54 0.29
40 73 0.40
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CGAAGGCATTTGTGCGAGTTACTATACCGGGCTAAGTCC
Found at i:39223696 original size:9 final size:9
Alignment explanation
Indices: 39223682--39223706 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39223672 GCTTTTACCG
39223682 TTTGATGAA
1 TTTGATGAA
39223691 TTTGATGAA
1 TTTGATGAA
39223700 TTTGATG
1 TTTGATG
39223707 TTATCCTCGG
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (9 bp):
TTTGATGAA
Found at i:39228573 original size:40 final size:40
Alignment explanation
Indices: 39228490--39228731 Score: 289
Period size: 40 Copynumber: 6.2 Consensus size: 40
39228480 CGGATGATAA
* * *
39228490 CGAAGGCATTTGTGCTAGTGACTA-ATTC-GGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
39228528 CGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
39228568 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
39228608 TGAAGGCATTTGTGAGAGTTACTATAACCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* *
39228648 CGAAGGCATTTGTGCGAGTTACTATAACTGGGCT-AGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * * *
39228687 CGAAGACATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
39228726 CGAAGG
1 CGAAGG
39228732 TACTTGTTTG
Statistics
Matches: 181, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
38 30 0.17
39 37 0.20
40 113 0.62
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:39245419 original size:27 final size:27
Alignment explanation
Indices: 39245352--39245458 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 27
39245342 GTTAAGACCC
* * *
39245352 TCAAGTTGTAAAATTACTAAAATACCC
1 TCAATTTGTAAAATTACTGAAATACCA
* * * *
39245379 CCGAGTTATAAAATTACTGAAATACC-
1 TCAATTTGTAAAATTACTGAAATACCA
* *
39245405 TCTAATTTGTGAAATTACCGAAATACCA
1 TC-AATTTGTAAAATTACTGAAATACCA
*
39245433 TCAGTTTGTAAAATTACTGAAATACC
1 TCAATTTGTAAAATTACTGAAATACC
39245459 CTTATAGTGT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
26 1 0.02
27 62 0.95
28 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (27 bp):
TCAATTTGTAAAATTACTGAAATACCA
Found at i:39245540 original size:27 final size:27
Alignment explanation
Indices: 39245467--39245530 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
39245457 CCCTTATAGT
39245467 GTAAAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
39245494 GTAAAATGATCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
39245521 GTAAAATGAC
1 GTAAAATGAC
39245531 GATTATGCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCCTGTAGG
Found at i:39245724 original size:26 final size:27
Alignment explanation
Indices: 39245667--39245717 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
39245657 TGGAGGAAGT
*
39245667 ACTG-TACTGGTGACTATGTCACATTC
1 ACTGTTACTGGTGACTATGCCACATTC
*
39245693 ACTGTTACTGGTGGCT-TGCCACATT
1 ACTGTTACTGGTGACTATGCCACATT
39245718 TATTGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
ACTGTTACTGGTGACTATGCCACATTC
Found at i:39248957 original size:41 final size:41
Alignment explanation
Indices: 39248883--39249225 Score: 526
Period size: 41 Copynumber: 8.4 Consensus size: 41
39248873 CGTTTTACCA
** *
39248883 AAAACGCCGCT-AAAAGCAGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
* *
39248923 AAAACCCCGCTAAAAATAAGAGCATTAACGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
*
39248964 AAAACGCCGCTAAAAATAAGAGCATTAGTGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
39249005 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
* ** *
39249046 AAAACGCTGCTAAAAATCGGAGCATTAGCGGCGCTTTTAGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
* ** * * *
39249087 AAAGCGCCGCTAAAAATCGGAGCATTAGGGGCACTTTTAGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
39249128 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
*
39249169 AAAACGCCGCTAAAAATAAGAGCATTAGTGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
39249210 AAAACGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
39249226 GTTTAGGGTT
Statistics
Matches: 278, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
40 10 0.04
41 268 0.96
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
Found at i:39249323 original size:21 final size:22
Alignment explanation
Indices: 39249299--39249342 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
39249289 GGTTTATGTA
*
39249299 TTATGGTTTAAGGGTT-GGGGT
1 TTATGATTTAAGGGTTAGGGGT
39249320 TTATGATTTAAGGGTTAGGGGT
1 TTATGATTTAAGGGTTAGGGGT
39249342 T
1 T
39249343 AGGGGTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (22 bp):
TTATGATTTAAGGGTTAGGGGT
Found at i:39249341 original size:7 final size:7
Alignment explanation
Indices: 39249331--39249364 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
39249321 TATGATTTAA
39249331 GGGTTAG
1 GGGTTAG
39249338 GGGTTAG
1 GGGTTAG
39249345 GGGTTAG
1 GGGTTAG
39249352 GGGTTAG
1 GGGTTAG
39249359 GGGTTA
1 GGGTTA
39249365 ATACTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.29
Consensus pattern (7 bp):
GGGTTAG
Found at i:39249603 original size:21 final size:21
Alignment explanation
Indices: 39249577--39249620 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39249567 TTATGGTTAG
* *
39249577 GGGATATAGTTTAGGGTTTAA
1 GGGATATACTTTAGGGATTAA
39249598 GGGATATACTTTAGGGATTAA
1 GGGATATACTTTAGGGATTAA
39249619 GG
1 GG
39249621 TTATAGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (21 bp):
GGGATATACTTTAGGGATTAA
Found at i:39249955 original size:14 final size:14
Alignment explanation
Indices: 39249936--39249978 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39249926 CCCCGATTTC
39249936 CCCCAACTTCTTCT
1 CCCCAACTTCTTCT
*
39249950 CCCCAA-AT-TTC-
1 CCCCAACTTCTTCT
39249961 CCCCAACTTCTTCT
1 CCCCAACTTCTTCT
39249975 CCCC
1 CCCC
39249979 CAAAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 4 0.17
14 10 0.42
ACGTcount: A:0.16, C:0.53, G:0.00, T:0.30
Consensus pattern (14 bp):
CCCCAACTTCTTCT
Found at i:39249959 original size:25 final size:25
Alignment explanation
Indices: 39249931--39249978 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
39249921 AATTTCCCCG
39249931 ATTTCCCCCAACTTCTTCTCCCCAA
1 ATTTCCCCCAACTTCTTCTCCCCAA
39249956 ATTTCCCCCAACTTCTTCTCCCC
1 ATTTCCCCCAACTTCTTCTCCCC
39249979 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (25 bp):
ATTTCCCCCAACTTCTTCTCCCCAA
Found at i:39249979 original size:15 final size:15
Alignment explanation
Indices: 39249934--39249981 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
39249924 TTCCCCGATT
39249934 TCCCCCAACTTCTTC
1 TCCCCCAACTTCTTC
*
39249949 T-CCCCAA---ATT-
1 TCCCCCAACTTCTTC
39249959 TCCCCCAACTTCTTC
1 TCCCCCAACTTCTTC
39249974 TCCCCCAA
1 TCCCCCAA
39249982 AATTTTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 1 0.04
11 8 0.31
14 8 0.31
15 9 0.35
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.29
Consensus pattern (15 bp):
TCCCCCAACTTCTTC
Found at i:39253214 original size:183 final size:183
Alignment explanation
Indices: 39252906--39253457 Score: 1014
Period size: 183 Copynumber: 3.0 Consensus size: 183
39252896 GATATAGTTC
* * * * *
39252906 CATGTGTCTATATTAGTGAATTAATGTTGTATATGTTTCAGTTACTGCTTCCTGCTCCTCCAGCA
1 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
39252971 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
* *
39253036 GTTTTCATATTTGCTTAAACTGAAATATATCTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
39253089 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
1 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
39253154 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
* *
39253219 GTTTTTATATTTGATTGAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
39253272 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
1 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
39253337 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
*
39253402 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTACTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
39253455 CAT
1 CAT
39253458 CTGTTCTAGG
Statistics
Matches: 357, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 357 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (183 bp):
CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
Found at i:39253678 original size:15 final size:15
Alignment explanation
Indices: 39253658--39253686 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39253648 AGAGTAGACC
39253658 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
39253673 AGGTACGTTTTATT
1 AGGTACGTTTTATT
39253687 TCAAAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:39254437 original size:274 final size:274
Alignment explanation
Indices: 39253948--39254499 Score: 1077
Period size: 274 Copynumber: 2.0 Consensus size: 274
39253938 CCAACCTTAT
39253948 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
39254013 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
39254078 AAAGACTTGAAAATAGTTCTATCGAGCTCATTTACTATTGAATATTTATTTCCAATTTACTTATA
131 AAAGACTTGAAAATAGTTCTATCGAGCTCATTTACTATTGAATATTTATTTCCAATTTACTTATA
*
39254143 AAAATTAAACTACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTATATTAATAAC
196 AAAATTAAACTACGATTCTTTTTTTATATTATTATATGCAAATTACTATTTTTTATATTAATAAC
39254208 GTTTGATTTTAATA
261 GTTTGATTTTAATA
39254222 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
*
39254287 GCAAGATATAATGGATCCTCCCTAGGTGTAACAATGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
39254352 AAAGACTTGAAAATAGTTCTATCGAGCTCATTTACTATTGAATATTTATTTCCAATTTACTTATA
131 AAAGACTTGAAAATAGTTCTATCGAGCTCATTTACTATTGAATATTTATTTCCAATTTACTTATA
*
39254417 AAAATTAAACTACGATTCTTTTTTTATATTATTATATGCAAATTACTATTTTTTATATTAATAAT
196 AAAATTAAACTACGATTCTTTTTTTATATTATTATATGCAAATTACTATTTTTTATATTAATAAC
39254482 GTTTGATTTTAATA
261 GTTTGATTTTAATA
39254496 TTTA
1 TTTA
39254500 CGATTCTTTT
Statistics
Matches: 275, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
274 275 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (274 bp):
TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
AAAGACTTGAAAATAGTTCTATCGAGCTCATTTACTATTGAATATTTATTTCCAATTTACTTATA
AAAATTAAACTACGATTCTTTTTTTATATTATTATATGCAAATTACTATTTTTTATATTAATAAC
GTTTGATTTTAATA
Found at i:39254664 original size:15 final size:15
Alignment explanation
Indices: 39254646--39254675 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39254636 ATAATTTTTA
39254646 TAAATATTATTTAAT
1 TAAATATTATTTAAT
39254661 TAAATATTATTTAAT
1 TAAATATTATTTAAT
39254676 CCCGCTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATATTATTTAAT
Found at i:39254820 original size:9 final size:9
Alignment explanation
Indices: 39254781--39255172 Score: 125
Period size: 9 Copynumber: 42.4 Consensus size: 9
39254771 ATTTGATATC
*
39254781 ATAATTTAT
1 ATAACTTAT
*
39254790 ATAACTTAC
1 ATAACTTAT
* * *
39254799 AAAACGTAC
1 ATAACTTAT
39254808 ATAACTTAT
1 ATAACTTAT
*
39254817 ATAACTTAG
1 ATAACTTAT
*
39254826 ATAA-ATAT
1 ATAACTTAT
*
39254834 ATAACTTAC
1 ATAACTTAT
*
39254843 ATAACTTAC
1 ATAACTTAT
39254852 ATAATACTTAAAT
1 AT-A-ACTT--AT
**
39254865 ATATTTTATAT
1 ATA-ACT-TAT
* *
39254876 CATAATTTAC
1 -ATAACTTAT
*
39254886 ATAACTTAC
1 ATAACTTAT
39254895 ATAACTTAT
1 ATAACTTAT
*
39254904 ATAACTTAG
1 ATAACTTAT
*
39254913 ATAA-ATAT
1 ATAACTTAT
* *
39254921 ATAATTTAC
1 ATAACTTAT
*
39254930 ATAA-ATAT
1 ATAACTTAT
* *
39254938 ATATCATAT
1 ATAACTTAT
*
39254947 CATAACTTAC
1 -ATAACTTAT
*
39254957 ATAACTTAC
1 ATAACTTAT
*
39254966 ATAAATATAT
1 ATAACT-TAT
* *
39254976 TTGA--TAT
1 ATAACTTAT
*
39254983 CATAATTTAT
1 -ATAACTTAT
*
39254993 ATAACTTAC
1 ATAACTTAT
* * *
39255002 AAAACGTAC
1 ATAACTTAT
39255011 ATAACTTAT
1 ATAACTTAT
*
39255020 ATAACTTAG
1 ATAACTTAT
*
39255029 ATAA-ATAT
1 ATAACTTAT
*
39255037 ATAACTTAC
1 ATAACTTAT
*
39255046 ATAACTTAC
1 ATAACTTAT
39255055 ATAATACTTAAAT
1 AT-A-ACTT--AT
**
39255068 ATATTTTATAT
1 ATA-ACT-TAT
* *
39255079 CATAATTTAC
1 -ATAACTTAT
*
39255089 ATAACTTAC
1 ATAACTTAT
39255098 ATAACTTAT
1 ATAACTTAT
*
39255107 ATAACTTAG
1 ATAACTTAT
*
39255116 ATAA-ATAT
1 ATAACTTAT
* *
39255124 ATAATTTAC
1 ATAACTTAT
*
39255133 ATAA-ATAT
1 ATAACTTAT
* *
39255141 ATATCATAT
1 ATAACTTAT
*
39255150 CATAACTTAC
1 -ATAACTTAT
*
39255160 ATAACTTAC
1 ATAACTTAT
39255169 ATAA
1 ATAA
39255173 TACTTAAATA
Statistics
Matches: 293, Mismatches: 66, Indels: 48
0.72 0.16 0.12
Matches are distributed among these distances:
7 3 0.01
8 36 0.12
9 193 0.66
10 25 0.09
11 16 0.05
12 12 0.04
13 8 0.03
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAACTTAT
Found at i:39254951 original size:96 final size:96
Alignment explanation
Indices: 39254753--39255154 Score: 396
Period size: 96 Copynumber: 4.1 Consensus size: 96
39254743 ATAAAAAACT
* * *
39254753 TACATAATACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAACTTATA
1 TACATAATACTTAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
* * * *
39254818 TAACTTAGATAAATATATAACTTACATAACT
66 TAACATAGATAAATACATAACATACATAACA
* * * *
39254849 TACATAATACTTAAATATATTTTATATCATAATTTACATAACTTACATAACTTATATAACTTAGA
1 TACATAATACTTAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
* * *
39254914 TAA-ATATATAATTTACATAAATATATATCATATCATAACT
66 TAACATAGAT-A---A-AT--ACATA-A-CATA-CATAACA
* *
39254954 TACATAACTTACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAACTTA
1 TACATAA--TACTTAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTA
* * * * *
39255019 TATAACTTAGATAAATATATAACTTACATAACT
64 GATAACATAGATAAATACATAACATACATAACA
* * * *
39255052 TACATAATACTTAAATATATTTTATATCATAATTTACATAACTTACATAACTTATATAACTTAGA
1 TACATAATACTTAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
* * * *
39255117 TAA-ATATATAATTTACATAA-ATATATATCA
66 TAACATAGATAA-ATACATAACATACATAACA
39255147 TATCATAA
1 TA-CATAA
39255155 CTTACATAAC
Statistics
Matches: 256, Mismatches: 35, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
95 18 0.07
96 127 0.50
98 14 0.05
99 4 0.02
100 3 0.01
101 5 0.02
102 5 0.02
103 3 0.01
104 4 0.02
105 14 0.05
107 55 0.21
108 4 0.02
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (96 bp):
TACATAATACTTAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
TAACATAGATAAATACATAACATACATAACA
Found at i:39255025 original size:116 final size:113
Alignment explanation
Indices: 39254830--39255049 Score: 309
Period size: 116 Copynumber: 1.9 Consensus size: 113
39254820 ACTTAGATAA
* * * * *
39254830 ATATATAACTTACATAACTTACATAATACTTAAATATATTTTATATCATAATTTACATAACTTAC
1 ATATATAACTTACATAACTTACATAATAATTAAATATATATTATATCATAACTTACAAAACGTAC
*
39254895 ATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATATC
66 ATAACTTATATAACTTAGATAAATATATAACTTACATAAATATATATC
**
39254943 ATATCATAACTTACATAACTTACATAAATATATTTGATATCATAATT-TAT-ATAACTTACAAAA
1 ATAT-ATAACTTACATAACTTACAT-AATA-ATTAAATAT-AT-ATTATATCATAACTTACAAAA
39255006 CGTACATAACTTATATAACTTAGATAAATATATAACTTACATAA
61 CGTACATAACTTATATAACTTAGATAAATATATAACTTACATAA
39255050 CTTACATAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
113 4 0.04
114 20 0.21
115 4 0.04
116 59 0.63
117 5 0.05
118 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (113 bp):
ATATATAACTTACATAACTTACATAATAATTAAATATATATTATATCATAACTTACAAAACGTAC
ATAACTTATATAACTTAGATAAATATATAACTTACATAAATATATATC
Found at i:39255100 original size:203 final size:203
Alignment explanation
Indices: 39254749--39255172 Score: 834
Period size: 203 Copynumber: 2.1 Consensus size: 203
39254739 TGAAATAAAA
39254749 AACTTACATAA--TACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAA
1 AACTTACATAACTTACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAA
39254812 CTTATATAACTTAGATAAATATATAACTTACATAACTTACATAATACTTAAATATATTTTATATC
66 CTTATATAACTTAGATAAATATATAACTTACATAACTTACATAATACTTAAATATATTTTATATC
39254877 ATAATTTACATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATAT
131 ATAATTTACATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATAT
39254942 CATATCAT
196 CATATCAT
39254950 AACTTACATAACTTACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAA
1 AACTTACATAACTTACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAA
39255015 CTTATATAACTTAGATAAATATATAACTTACATAACTTACATAATACTTAAATATATTTTATATC
66 CTTATATAACTTAGATAAATATATAACTTACATAACTTACATAATACTTAAATATATTTTATATC
39255080 ATAATTTACATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATAT
131 ATAATTTACATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATAT
39255145 CATATCAT
196 CATATCAT
39255153 AACTTACATAACTTACATAA
1 AACTTACATAACTTACATAA
39255173 TACTTAAATA
Statistics
Matches: 221, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
201 11 0.05
203 210 0.95
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.38
Consensus pattern (203 bp):
AACTTACATAACTTACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAA
CTTATATAACTTAGATAAATATATAACTTACATAACTTACATAATACTTAAATATATTTTATATC
ATAATTTACATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATAT
CATATCAT
Done.