Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 142 of 167
Found at i:47350576 original size:324 final size:324
Alignment explanation
Indices: 47349987--47350633 Score: 1258
Period size: 324 Copynumber: 2.0 Consensus size: 324
47349977 TCTGACTTTG
47349987 AAAAATCATAAAAAATTTAAGAAAAACAATTAGGGGCTTAAATTTATATGTCTATAATCCTTAAT
1 AAAAATCATAAAAAATTTAAGAAAAACAATTAGGGGCTTAAATTTATATGTCTATAATCCTTAAT
47350052 GAGTCTATTTTTAAGAGAAATAAACGAGAACATCATTTGAATTCTGTATGAAGAGATAATTAATT
66 GAGTCTATTTTTAAGAGAAATAAACGAGAACATCATTTGAATTCTGTATGAAGAGATAATTAATT
47350117 TTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAGAACAGGGGTGACTTTAAAGAATAAACTGTAC
131 TTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAGAACAGGGGTGACTTTAAAGAATAAACTGTAC
47350182 TGATTGGCTAAACCAAAACTTACAAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCATGT
196 TGATTGGCTAAACCAAAACTTACAAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCATGT
* *
47350247 AAAATTATCAGATACTAATTTGGAGTTCTTTAGCTCAAGATAAAAATAGTTTAGTGACTATGAA
261 AAAATTATCAGATACTAATTTGGAGTTCTGTAGCTCAAGATAAAAATAATTTAGTGACTATGAA
47350311 AAAAATCATAAAAAATTTAAGAAAAACAATTAGGGGCTTAAATTTATATGTCTATAATCCTTAAT
1 AAAAATCATAAAAAATTTAAGAAAAACAATTAGGGGCTTAAATTTATATGTCTATAATCCTTAAT
47350376 GAGTCTATTTTTAAGAGAAATAAACGAGAACATCATTTGAATTCTGTATGAAGAGATAATTAATT
66 GAGTCTATTTTTAAGAGAAATAAACGAGAACATCATTTGAATTCTGTATGAAGAGATAATTAATT
47350441 TTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAGAACAGGGGTGACTTTAAAGAATAAACTGTAC
131 TTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAGAACAGGGGTGACTTTAAAGAATAAACTGTAC
*
47350506 TGATTGGCTAAACCAAAACTTATAAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCATGT
196 TGATTGGCTAAACCAAAACTTACAAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCATGT
*
47350571 AAAATTATCATATACTAATTTGGAGTTCTGTAGCTCAAGATAAAAATAATTTAGTGACTATGA
261 AAAATTATCAGATACTAATTTGGAGTTCTGTAGCTCAAGATAAAAATAATTTAGTGACTATGA
47350634 CTCAAGTAGA
Statistics
Matches: 319, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
324 319 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (324 bp):
AAAAATCATAAAAAATTTAAGAAAAACAATTAGGGGCTTAAATTTATATGTCTATAATCCTTAAT
GAGTCTATTTTTAAGAGAAATAAACGAGAACATCATTTGAATTCTGTATGAAGAGATAATTAATT
TTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAGAACAGGGGTGACTTTAAAGAATAAACTGTAC
TGATTGGCTAAACCAAAACTTACAAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCATGT
AAAATTATCAGATACTAATTTGGAGTTCTGTAGCTCAAGATAAAAATAATTTAGTGACTATGAA
Found at i:47350920 original size:284 final size:284
Alignment explanation
Indices: 47350410--47350979 Score: 1086
Period size: 284 Copynumber: 2.0 Consensus size: 284
47350400 CGAGAACATC
47350410 ATTTGAATTCTGTATGAAGAGATAATTAATTTTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAG
1 ATTTGAATTCTGTATGAAGAGATAATTAATTTTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAG
* *
47350475 AACAGGGGTGACTTTAAAGAATAAACTGTACTGATTGGCTAAACCAAAACTTATAAAAATTTTAT
66 AACAGGGGTGACTTTAAAGAATAAACTGTACTAATTGGCAAAACCAAAACTTATAAAAATTTTAT
*
47350540 GGTAAGAAGATATGTGAGTCTAGTTTCATGTAAAATTATCATATACTAATTTGGAGTTCTGTAGC
131 GGTAAGAAGATATGTGAGTCTAGTTTCATGTAAAATTATCAGATACTAATTTGGAGTTCTGTAGC
47350605 TCAAGATAAAAATAATTTAGTGACTATGACTCAAGTAGACAGCTTTGAATGAACTATAAATAATA
196 TCAAGATAAAAATAATTTAGTGACTATGACTCAAGTAGACAGCTTTGAATGAACTATAAATAATA
*
47350670 GTTGAATTATAGAGAATGTTGCAT
261 GTTGAATTATAAAGAATGTTGCAT
*
47350694 ATTTGAATTCTGTATGAAGAGATAATTAATTTTTAGTGAAGAAGGGTTAGAACTGTCAACAGCAG
1 ATTTGAATTCTGTATGAAGAGATAATTAATTTTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAG
47350759 AACAGGGGTGACTTTAAAGAATAAACTGTACTAATTGGCAAAACCAAAACTTATAAAAATTTTAT
66 AACAGGGGTGACTTTAAAGAATAAACTGTACTAATTGGCAAAACCAAAACTTATAAAAATTTTAT
*
47350824 GGTAAGAATATATGTGAGTCTAGTTTCATGTAAAATTATCAGATACTAATTTGGAGTTCTGTAGC
131 GGTAAGAAGATATGTGAGTCTAGTTTCATGTAAAATTATCAGATACTAATTTGGAGTTCTGTAGC
47350889 TCAAGATAAAAATAATTTAGTGACTATGACTCAAGTAGACAGCTTTGAATGAACTATAAATAATA
196 TCAAGATAAAAATAATTTAGTGACTATGACTCAAGTAGACAGCTTTGAATGAACTATAAATAATA
47350954 GTTGAATTATAAAGAATGTTGCAT
261 GTTGAATTATAAAGAATGTTGCAT
47350978 AT
1 AT
47350980 GAACATGAAA
Statistics
Matches: 280, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
284 280 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.32
Consensus pattern (284 bp):
ATTTGAATTCTGTATGAAGAGATAATTAATTTTTAGTGAAGAAGAGTTAGAACTGTCAACAGCAG
AACAGGGGTGACTTTAAAGAATAAACTGTACTAATTGGCAAAACCAAAACTTATAAAAATTTTAT
GGTAAGAAGATATGTGAGTCTAGTTTCATGTAAAATTATCAGATACTAATTTGGAGTTCTGTAGC
TCAAGATAAAAATAATTTAGTGACTATGACTCAAGTAGACAGCTTTGAATGAACTATAAATAATA
GTTGAATTATAAAGAATGTTGCAT
Found at i:47353216 original size:46 final size:46
Alignment explanation
Indices: 47353041--47353216 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
47353031 TGTAACCCGC
* * * *
47353041 CCATAAGCGAGCTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
47353087 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
47353137 -C-TCA-CGAATTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
47353180 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
47353217 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:47353235 original size:46 final size:46
Alignment explanation
Indices: 47353090--47353228 Score: 135
Period size: 47 Copynumber: 3.0 Consensus size: 46
47353080 TTCGCATCCA
47353090 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * * *
47353138 TCA-CGAATTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
47353183 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
47353229 CTAGTGACAT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 27 0.37
47 29 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:47357748 original size:40 final size:40
Alignment explanation
Indices: 47357702--47357781 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
47357692 ACCACTGGCA
47357702 CTCAGGTTTAACAAATCTCGAGTTCCCTACACTGGCTGCC
1 CTCAGGTTTAACAAATCTCGAGTTCCCTACACTGGCTGCC
*
47357742 CTCAGGTTTAACAAATCTCGAGTTCCCTACGCTGGCTGCC
1 CTCAGGTTTAACAAATCTCGAGTTCCCTACACTGGCTGCC
47357782 GAAGTAGTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.28
Consensus pattern (40 bp):
CTCAGGTTTAACAAATCTCGAGTTCCCTACACTGGCTGCC
Found at i:47360305 original size:47 final size:47
Alignment explanation
Indices: 47360241--47360405 Score: 223
Period size: 47 Copynumber: 3.5 Consensus size: 47
47360231 ATAAGTGAAC
47360241 TCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAAT
1 TCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAAT
* * * *
47360288 TCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGTGAAC
1 TCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-CGAAT
47360334 TCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAAT
1 TCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAAT
47360381 TCGGACTCAACTCAACGAGTTCGGA
1 TCGGACTCAACTCAACGAGTTCGGA
47360406 CATTCGCATC
Statistics
Matches: 101, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 28 0.28
47 53 0.52
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (47 bp):
TCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAAT
Found at i:47360319 original size:93 final size:93
Alignment explanation
Indices: 47360195--47360454 Score: 493
Period size: 93 Copynumber: 2.8 Consensus size: 93
47360185 ATAAGCGAGC
* * *
47360195 TCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
1 TCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
47360260 TTCGGATGCCTAGTTACATCTCACGAAT
66 TTCGGATGCCTAGTTACATCTCACGAAT
47360288 TCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
1 TCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
47360353 TTCGGATGCCTAGTTACATCTCACGAAT
66 TTCGGATGCCTAGTTACATCTCACGAAT
47360381 TCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
1 TCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
47360446 TTCGGATGC
66 TTCGGATGC
47360455 TCAACCATCC
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 164 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
TCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
TTCGGATGCCTAGTTACATCTCACGAAT
Found at i:47360451 original size:46 final size:46
Alignment explanation
Indices: 47360183--47360451 Score: 275
Period size: 46 Copynumber: 5.8 Consensus size: 46
47360173 TGTAACCCGC
* * * *
47360183 CCATAAGCGAGCTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
47360229 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
47360279 -C-TCA-CGAATTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
47360322 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
47360372 -C-TCA-CGAATTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
47360415 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
47360452 TGCTCAACCA
Statistics
Matches: 184, Mismatches: 21, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
42 4 0.02
43 8 0.04
44 4 0.02
45 4 0.02
46 89 0.48
47 56 0.30
48 4 0.02
49 4 0.02
50 7 0.04
51 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:47360470 original size:46 final size:45
Alignment explanation
Indices: 47360234--47360463 Score: 179
Period size: 47 Copynumber: 5.0 Consensus size: 45
47360224 CGCATCCATA
47360234 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * * *
47360282 A-CGAATTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
47360327 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * * *
47360375 A-CGAATTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
47360420 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATC
47360464 CTAGTGACAT
Statistics
Matches: 144, Mismatches: 20, Indels: 38
0.71 0.10 0.19
Matches are distributed among these distances:
43 1 0.01
44 12 0.08
45 4 0.03
46 56 0.39
47 58 0.40
48 3 0.02
49 8 0.06
50 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTC
Found at i:47363585 original size:15 final size:16
Alignment explanation
Indices: 47363567--47363596 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47363557 AAGCAGGGGA
47363567 AGGAAAG-AAAGAAAG
1 AGGAAAGAAAAGAAAG
47363582 AGGAAAGAAAAGAAA
1 AGGAAAGAAAAGAAA
47363597 AAGGGAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AGGAAAGAAAAGAAAG
Found at i:47365074 original size:21 final size:21
Alignment explanation
Indices: 47365048--47365133 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
47365038 GGCTTTATCG
* *
47365048 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
47365069 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
47365090 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
* * * *
47365111 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
47365132 AT
1 AT
47365134 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTCATGTGTCGT
Found at i:47366078 original size:25 final size:25
Alignment explanation
Indices: 47366038--47366133 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
47366028 CCAAATAATA
* *
47366038 CGCCATAAAGGATTTCCAGAGAATT
1 CGCCACAAAGGCTTTCCAGAGAATT
* * *
47366063 CGCAACAAAGGCTTTCTAGAGAATA
1 CGCCACAAAGGCTTTCCAGAGAATT
* * *
47366088 CGCCGCAAAGGCTTTTCAGAGGATT
1 CGCCACAAAGGCTTTCCAGAGAATT
* *
47366113 TGCCACAAAGGCTTTCTAGAG
1 CGCCACAAAGGCTTTCCAGAG
47366134 TGGTGAAACA
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (25 bp):
CGCCACAAAGGCTTTCCAGAGAATT
Found at i:47366091 original size:50 final size:50
Alignment explanation
Indices: 47366034--47366133 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
47366024 TTTCCCAAAT
*
47366034 AATACGCCATAAAGGATTTCCAGAGAATTCGCAACAAAGGCTTTCTAGAG
1 AATACGCCACAAAGGATTTCCAGAGAATTCGCAACAAAGGCTTTCTAGAG
* * * * * *
47366084 AATACGCCGCAAAGGCTTTTCAGAGGATTTGCCACAAAGGCTTTCTAGAG
1 AATACGCCACAAAGGATTTCCAGAGAATTCGCAACAAAGGCTTTCTAGAG
47366134 TGGTGAAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (50 bp):
AATACGCCACAAAGGATTTCCAGAGAATTCGCAACAAAGGCTTTCTAGAG
Found at i:47375843 original size:111 final size:109
Alignment explanation
Indices: 47375731--47375938 Score: 321
Period size: 111 Copynumber: 1.9 Consensus size: 109
47375721 TAACTTCCAT
* *
47375731 TCATTCAAAAATTAGGATTTCTATCATAT-ATA-TATATATAAAAGAACTATAAATTATAGAATT
1 TCATTCAAAAATTAGGATTTCTATAATATCATAGTATATATAAAACAACTATAAATTATAGAATT
*
47375794 GTTGGATTTAAATATTTTCATTCATCCAACAATTCATCAATTCA
66 GTTGGATTTAAATATTTTCATTAATCCAACAATTCATCAATTCA
* ** *
47375838 TCATTCAAAAATTAGGATTTCTATAATATGCGTAGGTATATATATGACAACTATAAATTATAGAC
1 TCATTCAAAAATTAGGATTTCTATAATAT-CATA-GTATATATAAAACAACTATAAATTATAGAA
47375903 TTGTTGGATTTAAATATTTTCATTAATCCAACAATT
64 TTGTTGGATTTAAATATTTTCATTAATCCAACAATT
47375939 GATGAAATTC
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 28 0.31
109 2 0.02
111 60 0.67
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (109 bp):
TCATTCAAAAATTAGGATTTCTATAATATCATAGTATATATAAAACAACTATAAATTATAGAATT
GTTGGATTTAAATATTTTCATTAATCCAACAATTCATCAATTCA
Found at i:47379017 original size:14 final size:16
Alignment explanation
Indices: 47378994--47379034 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
47378984 TATTTCTTAT
*
47378994 TATAAAATATAA-A-A
1 TATAACATATAATATA
47379008 TATAACATATAATATA
1 TATAACATATAATATA
47379024 TATAACATATA
1 TATAACATATA
47379035 TATTATCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 12 0.50
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
TATAACATATAATATA
Found at i:47379323 original size:10 final size:10
Alignment explanation
Indices: 47379310--47379418 Score: 52
Period size: 10 Copynumber: 11.3 Consensus size: 10
47379300 ATCATAAAAG
47379310 AATATTTAAA
1 AATATTTAAA
*
47379320 AATATAT-AA
1 AATATTTAAA
*
47379329 AA-ATTGAAA
1 AATATTTAAA
*
47379338 AAAATATTAAA
1 AATAT-TTAAA
47379349 AATA-TT-AA
1 AATATTTAAA
*
47379357 AA-ATGTAAA
1 AATATTTAAA
47379366 ATATATTTAAA
1 A-ATATTTAAA
*
47379377 AAT-TGTAAA
1 AATATTTAAA
* *
47379386 AAAAATTAAA
1 AATATTTAAA
*
47379396 TAT-TGTTAAA
1 AATAT-TTAAA
* *
47379406 AATCTTTTAA
1 AATATTTAAA
47379416 AAT
1 AAT
47379419 TGTAAAAAAG
Statistics
Matches: 73, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
7 1 0.01
8 7 0.10
9 20 0.27
10 30 0.41
11 15 0.21
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.35
Consensus pattern (10 bp):
AATATTTAAA
Found at i:47379358 original size:18 final size:19
Alignment explanation
Indices: 47379310--47379453 Score: 68
Period size: 20 Copynumber: 7.5 Consensus size: 19
47379300 ATCATAAAAG
47379310 AATATTTAAAAATATATAAA
1 AATATTTAAAAATAT-TAAA
**
47379330 AAT-TGAAAAAAATATTAAA
1 AATAT-TTAAAAATATTAAA
*
47379349 AATA-TTAAAAAT-GTAAA
1 AATATTTAAAAATATTAAA
47379366 ATATATTTAAAAAT-TGTAAA
1 A-ATATTTAAAAATAT-TAAA
* * * *
47379386 AAAAATTAAATATTGTTAAA
1 AATATTTAAA-AATATTAAA
* *
47379406 AATCTTTTAAAAT-TGTAAA
1 AATATTTAAAAATAT-TAAA
*
47379425 AA-AGTTATTAAAAATA-AAAA
1 AATA--T-TTAAAAATATTAAA
47379445 AATATTTAA
1 AATATTTAA
47379454 TTTTTTAAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
17 5 0.05
18 14 0.15
19 32 0.34
20 34 0.36
21 9 0.10
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (19 bp):
AATATTTAAAAATATTAAA
Found at i:47379358 original size:28 final size:29
Alignment explanation
Indices: 47379305--47379387 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
47379295 AAAAGATCAT
*
47379305 AAAAGAATATTTAAAAATATATAAAAATTG
1 AAAAAAATATTTAAAAATATATAAAAA-TG
47379335 AAAAAAATA-TTAAAAATAT-TAAAAATG
1 AAAAAAATATTTAAAAATATATAAAAATG
* * *
47379362 TAAAATATATTTAAAAAT-TGTAAAAA
1 AAAAAAATATTTAAAAATATATAAAAA
47379388 AAATTAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 10 0.21
28 20 0.42
29 10 0.21
30 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAAAAATATTTAAAAATATATAAAAATG
Found at i:47379387 original size:9 final size:10
Alignment explanation
Indices: 47379310--47379387 Score: 60
Period size: 10 Copynumber: 8.2 Consensus size: 10
47379300 ATCATAAAAG
*
47379310 AATATTTAAA
1 AATATGTAAA
*
47379320 AATATATAAA
1 AATATGTAAA
*
47379330 AAT-TGAAAAA
1 AATATG-TAAA
47379340 AATAT-TAAA
1 AATATGTAAA
47379349 AATAT-T-AA
1 AATATGTAAA
47379357 AA-ATGTAAA
1 AATATGTAAA
*
47379366 ATATATTTAAA
1 A-ATATGTAAA
47379377 AAT-TGTAAA
1 AATATGTAAA
47379386 AA
1 AA
47379388 AAATTAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 20 0.36
10 21 0.38
11 8 0.14
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (10 bp):
AATATGTAAA
Found at i:47379427 original size:20 final size:19
Alignment explanation
Indices: 47379353--47379483 Score: 68
Period size: 20 Copynumber: 6.7 Consensus size: 19
47379343 ATTAAAAATA
* *
47379353 TTAAAAATGTAAAATATATT
1 TTAAAATTGTAAAAAAT-TT
* **
47379373 TAAAAATTGTAAAAAA-AA
1 TTAAAATTGTAAAAAATTT
*
47379391 TTAAATATTGTTAAAAATCTT
1 TTAAA-ATTGTAAAAAAT-TT
*
47379412 TTAAAATTGTAAAAAAGTTA
1 TTAAAATTGTAAAAAA-TTT
* * *
47379432 TTAAAAAT-AAAAAAATAT
1 TTAAAATTGTAAAAAATTT
** *
47379450 TTAATTTTTTAAAAAAATTAT
1 TTAAAATTGT-AAAAAATT-T
*
47379471 TAAAAATTGTAAA
1 TTAAAATTGTAAA
47379484 TATTTAACAA
Statistics
Matches: 80, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
18 10 0.12
19 16 0.20
20 41 0.51
21 13 0.16
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (19 bp):
TTAAAATTGTAAAAAATTT
Found at i:47379776 original size:20 final size:19
Alignment explanation
Indices: 47379689--47379895 Score: 100
Period size: 20 Copynumber: 10.6 Consensus size: 19
47379679 CCACCAATTC
*
47379689 ACAATTTTTTAATCATTATTT
1 ACAA-TTTTTAATAATT-TTT
*
47379710 ACAAATTTTAATAATTATTT
1 ACAATTTTTAATAATT-TTT
* * *
47379730 GCATTTTTTAAT-ATTTTCC
1 ACAATTTTTAATAATTTT-T
* *
47379749 CCAATTTTTTATAATTTTT
1 ACAATTTTTAATAATTTTT
* *
47379768 ACAAGTTTTAAATAAGGTTTT
1 ACAA-TTTTTAATAA-TTTTT
*
47379789 ATAATTTTTAATAATTTTTTT
1 ACAATTTTTAATAA--TTTTT
*
47379810 ACAA-TATTAA-AATATTTT
1 ACAATTTTTAATAAT-TTTT
* * *
47379828 AAAAAATATTTAATAATTATT
1 --ACAATTTTTAATAATTTTT
** *
47379849 ACAATAATTAAT-TTTTTT
1 ACAATTTTTAATAATTTTT
*
47379867 ACAATTTTTAA-ATTTTTT
1 ACAATTTTTAATAATTTTT
**
47379885 TTAATTTTTAA
1 ACAATTTTTAA
47379896 CATTTTTTAA
Statistics
Matches: 143, Mismatches: 32, Indels: 25
0.71 0.16 0.12
Matches are distributed among these distances:
17 1 0.01
18 34 0.24
19 27 0.19
20 53 0.37
21 25 0.17
22 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (19 bp):
ACAATTTTTAATAATTTTT
Found at i:47379870 original size:18 final size:19
Alignment explanation
Indices: 47379801--47379885 Score: 57
Period size: 18 Copynumber: 4.5 Consensus size: 19
47379791 AATTTTTAAT
47379801 AATTTTTTTACAAT-ATTA
1 AATTTTTTTACAATAATTA
* * * * *
47379819 AAATATTTTAAAAAATATTT
1 AATTTTTTTACAATA-ATTA
* *
47379839 AATAATTATTACAATAATT-
1 AAT-TTTTTTACAATAATTA
**
47379858 AATTTTTTTACAATTTTTA
1 AATTTTTTTACAATAATTA
47379877 AATTTTTTT
1 AATTTTTTT
47379886 TAATTTTTAA
Statistics
Matches: 48, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
18 21 0.44
19 12 0.25
20 8 0.17
21 7 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTTTTTACAATAATTA
Found at i:47379882 original size:19 final size:19
Alignment explanation
Indices: 47379858--47379942 Score: 93
Period size: 19 Copynumber: 4.5 Consensus size: 19
47379848 TACAATAATT
47379858 AATTTTTTTACAATTTTTA
1 AATTTTTTTACAATTTTTA
*
47379877 AATTTTTTT-TAATTTTTA
1 AATTTTTTTACAATTTTTA
* * *
47379895 ACATTTTTTAATAA-TTTAA
1 A-ATTTTTTTACAATTTTTA
*
47379914 ATATTTTTTTACGATTTTTA
1 A-ATTTTTTTACAATTTTTA
47379934 AATTTTTTT
1 AATTTTTTT
47379943 TATAAATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
18 9 0.16
19 38 0.69
20 8 0.15
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (19 bp):
AATTTTTTTACAATTTTTA
Found at i:47379902 original size:20 final size:19
Alignment explanation
Indices: 47379858--47379953 Score: 81
Period size: 18 Copynumber: 5.0 Consensus size: 19
47379848 TACAATAATT
**
47379858 AATTTTTTTACAATTTTTA
1 AATTTTTTTTTAATTTTTA
47379877 AA-TTTTTTTTAATTTTTA
1 AATTTTTTTTTAATTTTTA
**
47379895 ACATTTTTTAATAA--TTTA
1 A-ATTTTTTTTTAATTTTTA
*
47379913 AATATTTTTTTACGATTTTTA
1 AATTTTTTTTTA--ATTTTTA
*
47379934 AATTTTTTTTATAAATTTTA
1 AATTTTTTTT-TAATTTTTA
47379954 CAATATTTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.13
18 20 0.33
19 4 0.07
20 14 0.23
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
AATTTTTTTTTAATTTTTA
Found at i:47383989 original size:16 final size:16
Alignment explanation
Indices: 47383968--47384022 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
47383958 GTTTGGTTCA
*
47383968 TTGTAATAGAATAGGG
1 TTGTAATAGAATAGAG
*
47383984 TTGTAATTGAATAGAG
1 TTGTAATAGAATAGAG
*
47384000 TTGTAATGGAATAGAG
1 TTGTAATAGAATAGAG
*
47384016 CTGTAAT
1 TTGTAAT
47384023 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (16 bp):
TTGTAATAGAATAGAG
Found at i:47384089 original size:44 final size:46
Alignment explanation
Indices: 47384008--47384096 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
47383998 AGTTGTAATG
*
47384008 GAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGGAATT
1 GAATAGAGCTGTAATCAGTAATTCAATTGTTTAGTTGAATGGAATT
*
47384054 GAATAGAGCTGTAAT-AG-AATTC-TTGTGTTTAGTTGAATGGAAT
1 GAATAGAGCTGTAATCAGTAATTCAAT-TGTTTAGTTGAATGGAAT
47384097 AGATGTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 22 0.55
45 2 0.05
46 15 0.38
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (46 bp):
GAATAGAGCTGTAATCAGTAATTCAATTGTTTAGTTGAATGGAATT
Found at i:47384280 original size:12 final size:11
Alignment explanation
Indices: 47384253--47384327 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 11
47384243 TATTAAATAC
47384253 AATTTAATAA-
1 AATTTAATAAT
47384263 AA--TAATATAT
1 AATTTAATA-AT
47384273 AATTTAATAAT
1 AATTTAATAAT
*
47384284 ATTCTTAAT-AT
1 AAT-TTAATAAT
47384295 AATTATTAATAAT
1 AA-T-TTAATAAT
47384308 -ATTTAATAAT
1 AATTTAATAAT
47384318 AATTTTAATA
1 AA-TTTAATA
47384328 TAAAATTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
8 5 0.09
9 1 0.02
10 12 0.23
11 9 0.17
12 24 0.45
13 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:47384297 original size:22 final size:21
Alignment explanation
Indices: 47384269--47384327 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
47384259 ATAAAATAAT
47384269 ATATAA-TTTAATAATATTCTTA
1 ATATAATTTTAATAATA-T-TTA
47384291 ATATAATTATTAATAATATTTA
1 ATATAATT-TTAATAATATTTA
47384313 ATAATAATTTTAATA
1 AT-ATAATTTTAATA
47384328 TAAAATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.50
23 8 0.24
24 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATAATTTTAATAATATTTA
Found at i:47384749 original size:27 final size:27
Alignment explanation
Indices: 47384675--47384763 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 27
47384665 ATAACAAAAT
47384675 AAAAACTCATAG-TCTTT-TGTTATTC
1 AAAAACTCATAGTTCTTTATGTTATTC
*
47384700 AAAAAC-CATAGTCCTTAATTTTATGTTATTC
1 AAAAACTCATAG---TT--CTTTATGTTATTC
47384731 AAAAACTCATAGTTCTTTATGTTATTC
1 AAAAACTCATAGTTCTTTATGTTATTC
47384758 AAAAAC
1 AAAAAC
47384764 ATGAAGAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
24 5 0.09
25 6 0.11
27 18 0.33
28 1 0.02
29 2 0.04
30 3 0.06
31 14 0.26
32 5 0.09
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (27 bp):
AAAAACTCATAGTTCTTTATGTTATTC
Found at i:47386553 original size:53 final size:53
Alignment explanation
Indices: 47386472--47386622 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
47386462 CTTACACGGT
* *
47386472 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
47386527 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
47386580 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
47386623 GCGCACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:47393723 original size:28 final size:28
Alignment explanation
Indices: 47393691--47393749 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
47393681 TACTACAGAA
47393691 ATTCAACCAAAATTATTATATTTAAAAG
1 ATTCAACCAAAATTATTATATTTAAAAG
47393719 ATTCAACCAAAATTATTATATTTAAAAG
1 ATTCAACCAAAATTATTATATTTAAAAG
47393747 ATT
1 ATT
47393750 TATCAATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (28 bp):
ATTCAACCAAAATTATTATATTTAAAAG
Found at i:47394784 original size:19 final size:19
Alignment explanation
Indices: 47394762--47394799 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47394752 ATTAATAAAA
47394762 AAAACTAATAGCCCACATT
1 AAAACTAATAGCCCACATT
*
47394781 AAAACTAATAGCTCACATT
1 AAAACTAATAGCCCACATT
47394800 CTAGTCCAGC
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:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAACTAATAGCCCACATT
Found at i:47399189 original size:27 final size:26
Alignment explanation
Indices: 47399148--47399204 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
47399138 ACGAGGACAT
*
47399148 AAAATATGTTTTTTA-AGTGCAACCACGA
1 AAAATATGTTATTTATAG-GC-ACCA-GA
47399176 AAAATAT-TTATTTATAGGCACCAGA
1 AAAATATGTTATTTATAGGCACCAGA
47399201 AAAA
1 AAAA
47399205 AGCACCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
26 4 0.15
27 8 0.30
28 9 0.33
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (26 bp):
AAAATATGTTATTTATAGGCACCAGA
Found at i:47402101 original size:20 final size:19
Alignment explanation
Indices: 47402063--47402101 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
47402053 GGTGAACACC
*
47402063 AGAACACTCGATACAAAGA
1 AGAACACCCGATACAAAGA
*
47402082 AGAACACCCAGATTCAAAGA
1 AGAACACCC-GATACAAAGA
47402102 TGCCCAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.10
Consensus pattern (19 bp):
AGAACACCCGATACAAAGA
Found at i:47415258 original size:18 final size:18
Alignment explanation
Indices: 47415235--47415272 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
47415225 GATGATAATT
47415235 TAGCCAATTCATCTGACA
1 TAGCCAATTCATCTGACA
47415253 TAGCCAATTCATCTGACA
1 TAGCCAATTCATCTGACA
47415271 TA
1 TA
47415273 CTTCTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (18 bp):
TAGCCAATTCATCTGACA
Found at i:47446403 original size:46 final size:46
Alignment explanation
Indices: 47446280--47446404 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
47446270 TGTAACCCGC
* * *
47446280 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
47446326 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
47446372 CCATAAGGGAACTCAGACTCAACTCAACGAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTT
47446405 TGGATGCTCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:47446873 original size:30 final size:31
Alignment explanation
Indices: 47446830--47446887 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
47446820 TTAACTCAAA
47446830 TTTTGGCAAATTTACAATTTTACCCCTAAAC
1 TTTTGGCAAATTTACAATTTTACCCCTAAAC
* * *
47446861 TTTT-GCATATTTACATTTTTGCCCCTA
1 TTTTGGCAAATTTACAATTTTACCCCTA
47446888 GGCTCGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (31 bp):
TTTTGGCAAATTTACAATTTTACCCCTAAAC
Found at i:47453907 original size:5 final size:5
Alignment explanation
Indices: 47453899--47453924 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
47453889 GAGATGGAAT
47453899 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
47453925 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:47453924 original size:26 final size:26
Alignment explanation
Indices: 47453873--47453924 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
47453863 TGAAATTTTC
* * *
47453873 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
47453899 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
47453925 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:47454102 original size:10 final size:10
Alignment explanation
Indices: 47454082--47454115 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
47454072 AACATCAACC
47454082 CAAATAAACAA
1 CAAA-AAACAA
47454093 CAAAAAACAA
1 CAAAAAACAA
*
47454103 CAAAAAAAAA
1 CAAAAAACAA
47454113 CAA
1 CAA
47454116 GATTATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (10 bp):
CAAAAAACAA
Found at i:47454431 original size:213 final size:213
Alignment explanation
Indices: 47454172--47454572 Score: 601
Period size: 217 Copynumber: 1.9 Consensus size: 213
47454162 GTGGAAGTAA
* *
47454172 ACAACGACATTATAATAAAAAAAACATAAGAAAAAGTCCAAAATACAAAAGAAACTTACACCACT
1 ACAACAACATTATAATAAAAAAAACATAAGAAAAAGTCCAAAATACAAAAGAAACCTACACCACT
* * *
47454237 CCAAACAAAAAAAAAACACAACAAAAGTTCAATTAACCAACGACAGT-AA-CAAACCAAACCAAA
66 CCAAA-AAAAAAAAAACACAACAAAAGCTCAATTAACCAACAACAATAAACCAAACCAAACCAAA
*
47454300 CTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAAGTTTCTTCATGAGTCCA
130 CTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAACTTTCTTCATGAGTCCA
47454365 AATAAACAACAAAAACAAT
195 AATAAACAACAAAAACAAT
* * *
47454384 ACAACAACATTGTAATTAAAAAAAACATAAGCAAAAA-TTCAAAATACAATAGAAACCTACACCA
1 ACAACAACATTATAA-TAAAAAAAACATAAG-AAAAAGTCCAAAATACAAAAGAAACCTACACCA
* * *
47454448 GTCCAAAAAAAAAAGAACACAACAAAAGCTCAATTATCCAACAACAATAACAAACCAAACCAAAC
64 CTCCAAAAAAAAAAAAACACAACAAAAGCTCAATTAACCAACAACAAT---AAACCAAACCAAAC
* *
47454513 CAAACTAATAACAATAACACATCAGTTCAAAAACCATTATAGAATAGTTTAACTTTCTTC
126 CAAACTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAACTTTCTTC
47454573 TTGTGCTTCA
Statistics
Matches: 168, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
212 49 0.29
213 45 0.27
214 5 0.03
216 2 0.01
217 67 0.40
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (213 bp):
ACAACAACATTATAATAAAAAAAACATAAGAAAAAGTCCAAAATACAAAAGAAACCTACACCACT
CCAAAAAAAAAAAAACACAACAAAAGCTCAATTAACCAACAACAATAAACCAAACCAAACCAAAC
TAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAACTTTCTTCATGAGTCCAA
ATAAACAACAAAAACAAT
Found at i:47455661 original size:30 final size:30
Alignment explanation
Indices: 47455626--47455692 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
47455616 GTTAAATTAA
*
47455626 AAATTAATTAATATAATAGTATAATAGCAT
1 AAATTAATTAATATAATAGTACAATAGCAT
47455656 AAATTAATTAATATAATAGTACAATAGCAT
1 AAATTAATTAATATAATAGTACAATAGCAT
47455686 AAATTAA
1 AAATTAA
47455693 AAATAGATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (30 bp):
AAATTAATTAATATAATAGTACAATAGCAT
Found at i:47455933 original size:19 final size:19
Alignment explanation
Indices: 47455909--47455948 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
47455899 CGATACATTT
*
47455909 TTTTTAGTTTAAATTTATA
1 TTTTTAGTATAAATTTATA
*
47455928 TTTTTAGTATAAATTTTTA
1 TTTTTAGTATAAATTTATA
47455947 TT
1 TT
47455949 CAAAGTTGCT
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:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTAGTATAAATTTATA
Found at i:47457794 original size:9 final size:9
Alignment explanation
Indices: 47457782--47457814 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
47457772 TCGAGTTGAT
*
47457782 TCGATTAAT
1 TCGATTAAC
47457791 TCGATTAAC
1 TCGATTAAC
47457800 TCGATTAAC
1 TCGATTAAC
47457809 TCGATT
1 TCGATT
47457815 CGAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (9 bp):
TCGATTAAC
Found at i:47459105 original size:11 final size:11
Alignment explanation
Indices: 47459089--47459143 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
47459079 TTCCATTTTC
*
47459089 TTTATAATTAT
1 TTTATATTTAT
47459100 TTTATATTTTAT
1 TTTATA-TTTAT
*
47459112 TTATCTATTTAT
1 TT-TATATTTAT
47459124 TTTAT-TTTAT
1 TTTATATTTAT
47459134 TATTAT-TTTA
1 T-TTATATTTA
47459144 GTCTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 6 0.16
11 16 0.42
12 13 0.34
13 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTTAT
Found at i:47459123 original size:30 final size:31
Alignment explanation
Indices: 47459089--47459162 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
47459079 TTCCATTTTC
*
47459089 TTTATAATTATTTTA-TATTTTATTTA-TCTA
1 TTTATAATTATTTTATTATTAT-TTTAGTCTA
*
47459119 TTTAT-TTTATTTTATTATTATTTTAGTCTA
1 TTTATAATTATTTTATTATTATTTTAGTCTA
* *
47459149 TTTTTAATTCTTTT
1 TTTATAATTATTTT
47459163 GATTCTTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 12 0.33
30 18 0.50
31 6 0.17
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (31 bp):
TTTATAATTATTTTATTATTATTTTAGTCTA
Found at i:47459126 original size:17 final size:16
Alignment explanation
Indices: 47459104--47459143 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
47459094 AATTATTTTA
47459104 TATTTTA-TTTATCTATT
1 TATTTTATTTTAT-TA-T
47459121 TATTTTATTTTATTAT
1 TATTTTATTTTATTAT
47459137 TATTTTA
1 TATTTTA
47459144 GTCTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 9 0.41
18 5 0.23
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTATTTTATTAT
Found at i:47460859 original size:6 final size:6
Alignment explanation
Indices: 47460844--47460923 Score: 97
Period size: 6 Copynumber: 13.3 Consensus size: 6
47460834 ATTGAGTCTA
* * * * *
47460844 TTTATC TTTATG TTTATG TTTATT TTTATT TTTATT TTCATT TTTATC
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
47460892 TTTATC TTTATT TTTATT TTTATG TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
47460924 GTCTTTATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:47460871 original size:18 final size:18
Alignment explanation
Indices: 47460844--47460923 Score: 108
Period size: 18 Copynumber: 4.4 Consensus size: 18
47460834 ATTGAGTCTA
* *
47460844 TTTATCTTTATGTTTATG
1 TTTATTTTTATTTTTATG
47460862 TTTATTTTTATTTTTAT-
1 TTTATTTTTATTTTTATG
* *
47460879 TTTCATTTTTATCTTTATC
1 TTT-ATTTTTATTTTTATG
47460898 TTTATTTTTATTTTTATG
1 TTTATTTTTATTTTTATG
47460916 TTTATTTT
1 TTTATTTT
47460924 GTCTTTATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
17 3 0.05
18 49 0.89
19 3 0.05
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTTTTATTTTTATG
Found at i:47461879 original size:5 final size:5
Alignment explanation
Indices: 47461871--47461902 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
47461861 TATTATTAAA
47461871 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
47461903 GATATATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:47464321 original size:19 final size:20
Alignment explanation
Indices: 47464276--47464322 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
47464266 GTAGAAATTA
*
47464276 TTATTCTCAGAAAATAGAAT
1 TTATTCTAAGAAAATAGAAT
47464296 TTATTCTAAGAAAATA-AAT
1 TTATTCTAAGAAAATAGAAT
*
47464315 TTCTTCTA
1 TTATTCTA
47464323 CTTTTTGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (20 bp):
TTATTCTAAGAAAATAGAAT
Found at i:47468873 original size:57 final size:58
Alignment explanation
Indices: 47468801--47468926 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 58
47468791 CCAAGTCATT
* * * * *
47468801 TTCATTTTTCTTTTTCTTTTTGGTGCAAACCACATTCATTTCCAAAT-TATT-CCATTTC
1 TTCA-TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGT-TTGCCATTTC
* *
47468859 TTCATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTGTCATTTC
1 TTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTGCCATTTC
*
47468917 TCCATTTTCA
1 TTCATTTTCA
47468927 CTATTTCTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 38 0.66
58 20 0.34
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (58 bp):
TTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTGCCATTTC
Found at i:47472262 original size:15 final size:15
Alignment explanation
Indices: 47472235--47472273 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
47472225 ATGTATTCAT
*
47472235 CCCCGCCCCGCCCTG
1 CCCCGCCCTGCCCTG
*
47472250 CCCTGCCCTGCCCTG
1 CCCCGCCCTGCCCTG
*
47472265 CCCCACCCT
1 CCCCGCCCT
47472274 ACCCCACCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.03, C:0.69, G:0.15, T:0.13
Consensus pattern (15 bp):
CCCCGCCCTGCCCTG
Found at i:47477615 original size:12 final size:12
Alignment explanation
Indices: 47477598--47477622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47477588 TTTAAAAACC
47477598 AAATTTAAACTA
1 AAATTTAAACTA
47477610 AAATTTAAACTA
1 AAATTTAAACTA
47477622 A
1 A
47477623 TTACAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTTAAACTA
Found at i:47480770 original size:50 final size:51
Alignment explanation
Indices: 47480654--47480786 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 51
47480644 CCATGACAGC
* * *
47480654 GGTATATGGCGTAAAACCATAGATGAAAGAGGTTATGCCAATCTGGTATAA
1 GGTATATGGCGTAAGACCATAGACGAAAGAGGTTATGACAATCTGGTATAA
* * * * *
47480705 GGTATATGGCATAAGACTATAGACGAACGAGG-TATGACAGTCTGGTTTAA
1 GGTATATGGCGTAAGACCATAGACGAAAGAGGTTATGACAATCTGGTATAA
* *
47480755 GGTATATGGCGTAAGATCATAGATGAAAGAGG
1 GGTATATGGCGTAAGACCATAGACGAAAGAGG
47480787 CTATTTGTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 42 0.61
51 27 0.39
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.25
Consensus pattern (51 bp):
GGTATATGGCGTAAGACCATAGACGAAAGAGGTTATGACAATCTGGTATAA
Found at i:47483963 original size:28 final size:27
Alignment explanation
Indices: 47483911--47483964 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
47483901 GACGAGACAA
** *
47483911 TAAACAAGGGTAAGTTTGTTGGGATAG
1 TAAACAAGGGTAAGTCCGTTAGGATAG
47483938 TAAACATAGGGTAAGTCCGTTAGGATA
1 TAAACA-AGGGTAAGTCCGTTAGGATA
47483965 AGGGAAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (27 bp):
TAAACAAGGGTAAGTCCGTTAGGATAG
Found at i:47487144 original size:25 final size:24
Alignment explanation
Indices: 47487116--47487168 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
47487106 CACAAACGCA
47487116 GCTCTTTATAAGCGTCCTGATATAG
1 GCTCTTTATAAGCGTCCTGATAT-G
* * *
47487141 GCTCTTTTTGAGCTTCCTGATATG
1 GCTCTTTATAAGCGTCCTGATATG
47487165 GCTC
1 GCTC
47487169 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (24 bp):
GCTCTTTATAAGCGTCCTGATATG
Found at i:47487179 original size:23 final size:25
Alignment explanation
Indices: 47487130--47487187 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
47487120 TTTATAAGCG
** *
47487130 TCCTGATATAGGCTCTTTTTGAGCT
1 TCCTGATATAGGCTCTGCTTGAACT
47487155 TCCTGATAT-GGCTC-GCTTGAACT
1 TCCTGATATAGGCTCTGCTTGAACT
*
47487178 TCCTGTTATA
1 TCCTGATATA
47487188 TGGTTATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 14 0.50
24 5 0.18
25 9 0.32
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.41
Consensus pattern (25 bp):
TCCTGATATAGGCTCTGCTTGAACT
Found at i:47489365 original size:43 final size:43
Alignment explanation
Indices: 47489318--47489422 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 43
47489308 GTCCAGGAAG
* *
47489318 GGTCTTACACGAAATC-GAATAACGATGCCAATGTTCC-AGACAT
1 GGTCTTACACGAAATCACAAT-ACAATGCCAATG-TCCTAGACAT
*
47489361 GGTCTTACACGTAATCACAATACAATGCCAATGTCCTAGACAT
1 GGTCTTACACGAAATCACAATACAATGCCAATGTCCTAGACAT
* *
47489404 GGTCTTACATGTAATCACA
1 GGTCTTACACGAAATCACA
47489423 TCTCGGTAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 3 0.05
43 50 0.89
44 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCACAATACAATGCCAATGTCCTAGACAT
Found at i:47493892 original size:27 final size:27
Alignment explanation
Indices: 47493862--47493916 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
47493852 TAAGTTCTGG
47493862 TAAGTTTTCTTCTCAGGAAATGATGAC
1 TAAGTTTTCTTCTCAGGAAATGATGAC
47493889 TAAGTTTTCTTCTCAGGAAATGATGAC
1 TAAGTTTTCTTCTCAGGAAATGATGAC
47493916 T
1 T
47493917 TCTTCCTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (27 bp):
TAAGTTTTCTTCTCAGGAAATGATGAC
Found at i:47495482 original size:24 final size:24
Alignment explanation
Indices: 47495450--47495501 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
47495440 AGCAAAACAA
47495450 ACATTTAAGGCATTCATCGGGACT
1 ACATTTAAGGCATTCATCGGGACT
*
47495474 ACATTTAAGGCATTCATCGGGAGT
1 ACATTTAAGGCATTCATCGGGACT
47495498 ACAT
1 ACAT
47495502 GACAAAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
ACATTTAAGGCATTCATCGGGACT
Found at i:47502173 original size:21 final size:20
Alignment explanation
Indices: 47502147--47502195 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
47502137 ACCTAGGATG
*
47502147 TGAATTTAATTTAATTGATT
1 TGAATTTAATTAAATTGATT
47502167 ATGAATTGT-ATTAAATTGATT
1 -TGAATT-TAATTAAATTGATT
*
47502188 TAAATTTA
1 TGAATTTA
47502196 CTTGTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 17 0.71
22 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
TGAATTTAATTAAATTGATT
Found at i:47502770 original size:24 final size:25
Alignment explanation
Indices: 47502740--47502796 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
47502730 CAGAGTTACC
*
47502740 TATTAAGCTCACATGAGCTTTCTGA
1 TATTAAGCACACATGAGCTTTCTGA
** *
47502765 T-TTAAGCACTTATGAGCTTTCTGT
1 TATTAAGCACACATGAGCTTTCTGA
47502789 TATTAAGC
1 TATTAAGC
47502797 CCGGATAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (25 bp):
TATTAAGCACACATGAGCTTTCTGA
Found at i:47505460 original size:23 final size:24
Alignment explanation
Indices: 47505408--47505460 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
47505398 ACACAAACGC
* *
47505408 AGCTCTATGTGAGCGTTCTGATAT
1 AGCTCTATATGAGCGTTCTGACAT
47505432 AGGCTCT-TATGAGC-TTCTTGACAT
1 A-GCTCTATATGAGCGTTC-TGACAT
47505456 AGCTC
1 AGCTC
47505461 GCTTGAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 13 0.52
25 5 0.20
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (24 bp):
AGCTCTATATGAGCGTTCTGACAT
Found at i:47510583 original size:7 final size:8
Alignment explanation
Indices: 47510566--47510590 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47510556 TAGGGTTTTG
47510566 TTTTAATT
1 TTTTAATT
47510574 TTTTAATT
1 TTTTAATT
47510582 TTTTAATT
1 TTTTAATT
47510590 T
1 T
47510591 GAGTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:47513256 original size:45 final size:43
Alignment explanation
Indices: 47513191--47513320 Score: 140
Period size: 43 Copynumber: 3.0 Consensus size: 43
47513181 ACATAGGATC
* *
47513191 CAATATGT-GTTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CAATATGTGGTTCCGTGTAAGACCACATCTGGGACGTTGGCAT
47513233 CGATATATGTGGTTCCGTGTAAGACC-CTATCTGGGACAG-TGGCAT
1 C-A-ATATGTGGTTCCGTGTAAGACCAC-ATCTGGGAC-GTTGGCAT
* * ** *
47513278 CAATATGAGATAGCATGTAAGACCACATCTGGGACGTTGGCAT
1 CAATATGTGGTTCCGTGTAAGACCACATCTGGGACGTTGGCAT
47513321 TGTTCGATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.03
43 33 0.45
44 9 0.12
45 29 0.39
46 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
CAATATGTGGTTCCGTGTAAGACCACATCTGGGACGTTGGCAT
Found at i:47515249 original size:17 final size:16
Alignment explanation
Indices: 47515225--47515269 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
47515215 TTTTTGACAG
47515225 TTTCTTTTTTTCTGCC
1 TTTCTTTTTTTCTGCC
*
47515241 TTTCGTTTTTCTCTGCC
1 TTTC-TTTTTTTCTGCC
*
47515258 GTTCTTTTTTTC
1 TTTCTTTTTTTC
47515270 CTTCACTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (16 bp):
TTTCTTTTTTTCTGCC
Found at i:47528261 original size:22 final size:23
Alignment explanation
Indices: 47528235--47528279 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
47528225 ACCTGATCAG
47528235 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
47528257 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
47528280 TCAGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:47528516 original size:28 final size:28
Alignment explanation
Indices: 47528484--47528567 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
47528474 AACACACCAG
* *
47528484 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
47528512 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
47528540 TATAATCCATCCAAAATACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
47528568 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:47528539 original size:23 final size:23
Alignment explanation
Indices: 47528470--47528540 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
47528460 AAATGTCCAA
*
47528470 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
47528493 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
47528521 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
47528541 ATAATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:47543616 original size:96 final size:96
Alignment explanation
Indices: 47543451--47543796 Score: 433
Period size: 96 Copynumber: 3.6 Consensus size: 96
47543441 TTGGAGTCTG
* * * * * * ** *
47543451 GGGCTAACTCTAGTATTTGGTGTCTTTCTTGAATCGGGTACATTCTGTATCTTCCCAATGTTTGA
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAATGTTTGA
*
47543516 GTTATCACCATTTGGTAGATTTTGAAACCTT
66 GTTATCACCATTTGGTAGATTTTGGAACCTT
* * * *
47543547 GGGCTAACTCTAGTATTTAACGTCTTTCTTGAGTCAGTTGCATCCCATGTCTTCTCAATGTTTGC
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAATGTTTGA
* *
47543612 GTTATCAACATTTGGTACATTTTGGAACCTT
66 GTTATCACCATTTGGTAGATTTTGGAACCTT
* ** * * * *
47543643 GGGCTAACTCTAGTATTTGATGTCTTTATTGAGAGAGTTGCATCCCTTAAT-TTCTCATTATTGG
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCAT-ATCTTCTCAATGTTTG
*
47543707 AGTTATCACCATTAGGTAGATTTTGGAACCTT
65 AGTTATCACCATTTGGTAGATTTTGGAACCTT
* * *
47543739 GGGCTAACTCTAGTATTTGATTTCTTTCTTGGGTCGGTTGCATCCCATATCTTCTCAA
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAA
47543797 ATTTTGGTAG
Statistics
Matches: 210, Mismatches: 38, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
95 2 0.01
96 207 0.99
97 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (96 bp):
GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAATGTTTGA
GTTATCACCATTTGGTAGATTTTGGAACCTT
Found at i:47543872 original size:78 final size:78
Alignment explanation
Indices: 47543721--47543873 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 78
47543711 ATCACCATTA
*
47543721 GGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATTTCTTTCTTGGGTCGGTTGCATCCCA
1 GGTAGATTTTGGAACCTTGGGCTAACTC-A-TATTTGATGTCTTTCTTGGG-CGGTTGCATCCCA
47543786 TATCTTCTCAAATTTT
63 TATCTTCTCAAATTTT
* *
47543802 GGTAGATTTTGGAACCTTGGGCTAACTC-TATTTGATGTCTTTGTTGAGG-GAGTTGCATCCCTT
1 GGTAGATTTTGGAACCTTGGGCTAACTCATATTTGATGTCTTTCTTG-GGCG-GTTGCATCCCAT
*
47543865 TTCTTCTCA
64 ATCTTCTCA
47543874 TTGTTGGAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
77 1 0.02
78 35 0.53
79 2 0.03
81 28 0.42
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (78 bp):
GGTAGATTTTGGAACCTTGGGCTAACTCATATTTGATGTCTTTCTTGGGCGGTTGCATCCCATAT
CTTCTCAAATTTT
Found at i:47544036 original size:81 final size:81
Alignment explanation
Indices: 47543895--47544050 Score: 192
Period size: 81 Copynumber: 1.9 Consensus size: 81
47543885 ACCACCATTA
* * * *
47543895 GGTAGATTTTGAAACCTTGGGCTAACTCTAGTATTTGATGTTGTTCTTGAGTCGGTTGCATTCCA
1 GGTAGATTTTGAAACCTTGGGCTAACACTAGTATTTGATGTTGTTCTTGAGTAGGCTGCATCCCA
47543960 TATCTTCTCAATATTT
66 TATCTTCTCAATATTT
* *
47543976 GGTAGATTTTCG-AACCTTGGGCTAGCACTAGTATTTGATGTCT-TTGTTGAG-AGAGCTGCATC
1 GGTAGATTTT-GAAACCTTGGGCTAACACTAGTATTTGATGT-TGTTCTTGAGTAG-GCTGCATC
* *
47544038 CCTTTTCTTCTCA
63 CCATATCTTCTCA
47544051 TTGTTGGAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
80 1 0.02
81 61 0.95
82 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTAGATTTTGAAACCTTGGGCTAACACTAGTATTTGATGTTGTTCTTGAGTAGGCTGCATCCCA
TATCTTCTCAATATTT
Found at i:47544089 original size:177 final size:177
Alignment explanation
Indices: 47543622--47544199 Score: 880
Period size: 177 Copynumber: 3.3 Consensus size: 177
47543612 GTTATCAACA
* * *
47543622 TTTGGTACATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTATTGAGAGAGTTGCATC
1 TTTGGTAGATTTTGGAACCTTGGGCTAACACTAGTATTTGATGTCTTTGTTGAGAGAGTTGCATC
* * * *
47543687 CCTTAAT-TTCTCATTATTGGAGTTATCACCATTAGGTAGATTTTGGAACCTTGGGCTAACTCTA
66 CCTT-TTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTA
*
47543751 GTATTTGATTTCTTTCTTGGGTCGGTTGCATCCCATATCTTCTCAAAT
130 GTATTTGATTTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
* *
47543799 TTTGGTAGATTTTGGAACCTTGGGCT-A-ACT-CTATTTGATGTCTTTGTTGAGGGAGTTGCATC
1 TTTGGTAGATTTTGGAACCTTGGGCTAACACTAGTATTTGATGTCTTTGTTGAGAGAGTTGCATC
47543861 CCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTAG
66 CCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTAG
* *
47543926 TATTTGATGTT-GTTCTTGAGTCGGTTGCATTCCATATCTTCTC-AAT
131 TATTTGAT-TTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
* * *
47543972 ATTTGGTAGATTTTCGAACCTTGGGCTAGCACTAGTATTTGATGTCTTTGTTGAGAGAGCTGCAT
1 -TTTGGTAGATTTTGGAACCTTGGGCTAACACTAGTATTTGATGTCTTTGTTGAGAGAGTTGCAT
47544037 CCCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTA
65 CCCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTA
* * * **
47544102 GTATTTGATTTCTTTCTTGTGTCAGCTGCATCCCGCATCTTCTCAAAT
130 GTATTTGATTTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
* * *
47544150 TTTGGTAGATTTTGGAACCTCGGGCTAACTCTAGTATTTGATATCTTTGT
1 TTTGGTAGATTTTGGAACCTTGGGCTAACACTAGTATTTGATGTCTTTGT
47544200 CGAGTCAGTT
Statistics
Matches: 364, Mismatches: 29, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
173 4 0.01
174 150 0.41
175 4 0.01
176 6 0.02
177 197 0.54
178 3 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (177 bp):
TTTGGTAGATTTTGGAACCTTGGGCTAACACTAGTATTTGATGTCTTTGTTGAGAGAGTTGCATC
CCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTAG
TATTTGATTTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
Found at i:47544284 original size:69 final size:69
Alignment explanation
Indices: 47544171--47544307 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
47544161 TTGGAACCTC
* *
47544171 GGGCTAACTCTAGTATTTGATATCTTTGTCGAGTCAGTTTCATTCCGTATCTTCACAATCTTTGA
1 GGGCTAACTCTAGTATTTGATATCTTTCTCGAGTCAGTTGCATTCCGTATCTTCACAATCTTTGA
47544236 GTTA
66 GTTA
* * * * *
47544240 GGGCTAGCTCTAGTATTTGATTTCTTTC-CTGAGTCAGTTGCATTCCTTATCTTCTCAATGTTTG
1 GGGCTAACTCTAGTATTTGATATCTTTCTC-GAGTCAGTTGCATTCCGTATCTTCACAATCTTTG
47544304 AGTT
65 AGTT
47544308 CCCAACATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (69 bp):
GGGCTAACTCTAGTATTTGATATCTTTCTCGAGTCAGTTGCATTCCGTATCTTCACAATCTTTGA
GTTA
Found at i:47544376 original size:96 final size:96
Alignment explanation
Indices: 47544240--47544442 Score: 264
Period size: 96 Copynumber: 2.1 Consensus size: 96
47544230 CTTTGAGTTA
* * * *
47544240 GGGCTAGCTCTAGTATTTGATTTCTTTCCTGAGTCAGTTGCATTCCTTATCTTCTCAATGTTTGA
1 GGGCTAACTCTAGTATTTAATTTCTTTCCTGAGTCAGTTGCATTCCATATCTTCTCAATGTTCGA
*
47544305 GTTCCCAACATTTAGTAGATTTTGAAACCTT
66 GTTACCAACATTTAGTAGATTTTGAAACCTT
* * **
47544336 GGGCTAACTCTAGTATTTAATGTT-TTTCTTGATTTTGTTGCATTCCATATCTTCTCAATGTTCG
1 GGGCTAACTCTAGTATTTAAT-TTCTTTCCTGAGTCAGTTGCATTCCATATCTTCTCAATGTTCG
* * * *
47544400 ATTTACCACCGTTTGGTAGATTTTGAAACCTT
65 AGTTACCAACATTTAGTAGATTTTGAAACCTT
*
47544432 GGACTAACTCT
1 GGGCTAACTCT
47544443 TCGCTGTATT
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 90 0.98
97 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.43
Consensus pattern (96 bp):
GGGCTAACTCTAGTATTTAATTTCTTTCCTGAGTCAGTTGCATTCCATATCTTCTCAATGTTCGA
GTTACCAACATTTAGTAGATTTTGAAACCTT
Found at i:47545589 original size:11 final size:11
Alignment explanation
Indices: 47545544--47545597 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
47545534 ATTATACATA
47545544 AATTTTAATTT
1 AATTTTAATTT
*
47545555 AATATATAATATT
1 AAT-TTTAAT-TT
47545568 ATATATTTAATTT
1 A-AT-TTTAATTT
*
47545581 AATTTTAATTC
1 AATTTTAATTT
47545592 AATTTT
1 AATTTT
47545598 CACAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 16 0.43
12 7 0.19
13 6 0.16
14 8 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
AATTTTAATTT
Found at i:47555514 original size:43 final size:41
Alignment explanation
Indices: 47555477--47555683 Score: 252
Period size: 42 Copynumber: 5.0 Consensus size: 41
47555467 TTTTTTATAA
* * **
47555477 AAGCGCTGCTAAAGAACATGATCTATAGCGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TT
*
47555519 AAGCGCCGCTAAAGAACATTATCTTTAGCGGCGTTTTTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTT
* * *
47555561 AAGCGTCGCTAAAGAATATTATCTTTAGCGGCGATTTTTTTGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTT-T
*
47555604 AACCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
* * * * *
47555645 AAGTGCCGTTAAAAAACATAATCTTTAGTGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
47555684 CTATAAACGC
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
41 34 0.23
42 75 0.52
43 36 0.25
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
Found at i:47559806 original size:30 final size:30
Alignment explanation
Indices: 47559770--47559827 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
47559760 GTATGTATAA
47559770 ATAATTATATATATGTTAATATTGGATAGC
1 ATAATTATATATATGTTAATATTGGATAGC
*
47559800 ATAATTATATATATGTTAATATTTGATA
1 ATAATTATATATATGTTAATATTGGATA
47559828 TTAGTGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
ATAATTATATATATGTTAATATTGGATAGC
Found at i:47560264 original size:16 final size:17
Alignment explanation
Indices: 47560243--47560280 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
47560233 ATATTTCTAA
47560243 AAAATAAA-ATAATTTT
1 AAAATAAACATAATTTT
47560259 AAAATAAACATAATTTT
1 AAAATAAACATAATTTT
47560276 AAAAT
1 AAAAT
47560281 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATAAACATAATTTT
Found at i:47567934 original size:3 final size:3
Alignment explanation
Indices: 47567926--47567959 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
47567916 ACAAAGATAT
47567926 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47567960 AATATAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47569758 original size:18 final size:18
Alignment explanation
Indices: 47569724--47570019 Score: 186
Period size: 18 Copynumber: 16.1 Consensus size: 18
47569714 TCATTAACAA
* *
47569724 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAATTAT
* *
47569741 TCAGTGACAATCACTTAT
1 TCAGTAACAATCAATTAT
*
47569759 TCCGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* * *
47569777 TCAATAATAA-CTAGTTAT
1 TCAGTAACAATC-AATTAT
*
47569795 TCAGTATCGATCAATTAATCGGTTAT
1 TCAGTA---A-CAATCAA----TTAT
* *
47569821 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
*
47569839 TTAGTAA-AATCAGA-TAT
1 TCAGTAACAATCA-ATTAT
* *
47569856 TCAGTAGCAATTAAGTTAT
1 TCAGTAACAATCAA-TTAT
* *
47569875 TCAGTAACAGTCATTTAT
1 TCAGTAACAATCAATTAT
* * *
47569893 TTAGTGACAATCAGTTAT
1 TCAGTAACAATCAATTAT
**
47569911 TCAGTAATGATCAATTAT
1 TCAGTAACAATCAATTAT
* * *
47569929 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTAT
* *
47569947 TCAGTAACAGTCTATTAT
1 TCAGTAACAATCAATTAT
* *
47569965 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
*
47569983 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* *
47570001 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTAT
47570019 T
1 T
47570020 TTATACCTTT
Statistics
Matches: 213, Mismatches: 51, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
17 18 0.08
18 163 0.77
19 13 0.06
21 1 0.00
22 8 0.04
23 1 0.00
26 9 0.04
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TCAGTAACAATCAATTAT
Found at i:47569952 original size:72 final size:72
Alignment explanation
Indices: 47569817--47570019 Score: 232
Period size: 72 Copynumber: 2.8 Consensus size: 72
47569807 AATTAATCGG
* * ** *
47569817 TTATCCAGTAACAGTCAATTATTTAGTAA-AATCAGA-TATTCAGTAGCAATTAAGTTATTCAGT
1 TTATCCAGTAACAATCAATTATTCAGTAACAATCA-ATTATTCAGTAATAA-TCAGTTATTCAGT
47569880 AACAGTC-A
64 AACAGTCTA
** * * ** *
47569888 TTTATTTAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTA
1 -TTATCCAGTAACAATCAATTATTCAGTAACAATCAATTATTCAGTAATAATCAGTTATTCAGTA
47569953 ACAGTCTA
65 ACAGTCTA
* *
47569961 TTATCCAGTAACAGTCAATTATTCGGTAACAATCAATTATTCAGTAATAATCAGTTATT
1 TTATCCAGTAACAATCAATTATTCAGTAACAATCAATTATTCAGTAATAATCAGTTATT
47570020 TTATACCTTT
Statistics
Matches: 108, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
72 93 0.86
73 15 0.14
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (72 bp):
TTATCCAGTAACAATCAATTATTCAGTAACAATCAATTATTCAGTAATAATCAGTTATTCAGTAA
CAGTCTA
Found at i:47570276 original size:45 final size:45
Alignment explanation
Indices: 47570192--47570291 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
47570182 GAATAGTAAT
**
47570192 AGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCGATAAC
1 AGTAACAGTAACAATATTCAACACACAAAGTGCCAAATCGATAAC
* * * * *
47570237 GGTAATAGTAACAGTATTCGACACACAAAGTGCCAAATCGGTAAC
1 AGTAACAGTAACAATATTCAACACACAAAGTGCCAAATCGATAAC
47570282 AGTAACAGTA
1 AGTAACAGTA
47570292 GTCGGCACAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (45 bp):
AGTAACAGTAACAATATTCAACACACAAAGTGCCAAATCGATAAC
Found at i:47570279 original size:39 final size:38
Alignment explanation
Indices: 47570236--47570325 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 38
47570226 GAATCGATAA
*
47570236 CGGTAATAGTAACAGTATTCGACACACAAAGTGCCAAAT
1 CGGTAATAGTAACAGTAGTCGACACA-AAAGTGCCAAAT
* * * **
47570275 CGGTAACAGTAACAGTAGTCGGCACATAAGTGCCTGAT
1 CGGTAATAGTAACAGTAGTCGACACAAAAGTGCCAAAT
*
47570313 CAGTAAT-GTAACA
1 CGGTAATAGTAACA
47570326 CCCCAAACCC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 6 0.14
38 14 0.33
39 23 0.53
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (38 bp):
CGGTAATAGTAACAGTAGTCGACACAAAAGTGCCAAAT
Found at i:47571423 original size:25 final size:27
Alignment explanation
Indices: 47571386--47571438 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
47571376 TCAAACACGC
47571386 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
47571412 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
47571438 A
1 A
47571439 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:47571874 original size:51 final size:51
Alignment explanation
Indices: 47571813--47571915 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
47571803 AACGAGATCC
47571813 ACACACGAACCGCCTACAATTGGATTACTAACACGATAATCTAACTATTCA
1 ACACACGAACCGCCTACAATTGGATTACTAACACGATAATCTAACTATTCA
47571864 ACACACGAACCGCCTACAATTGGATTACTAACACGATAATCTAACTATTCA
1 ACACACGAACCGCCTACAATTGGATTACTAACACGATAATCTAACTATTCA
47571915 A
1 A
47571916 ATACAAACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (51 bp):
ACACACGAACCGCCTACAATTGGATTACTAACACGATAATCTAACTATTCA
Found at i:47573008 original size:32 final size:32
Alignment explanation
Indices: 47572971--47573035 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
47572961 AATGCTTACC
*
47572971 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATACTA
47573003 ATGCCCATCATCCATTAACTATTAAAATACTA
1 ATGCCCATCATCCATTAACTATTAAAATACTA
47573035 A
1 A
47573036 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATACTA
Found at i:47573344 original size:17 final size:18
Alignment explanation
Indices: 47573318--47573351 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
47573308 TTTCTTTTTC
47573318 ATTTCTTTTATTTCATTT
1 ATTTCTTTTATTTCATTT
47573336 ATTTC-TTTATTTCATT
1 ATTTCTTTTATTTCATT
47573352 ATTAAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTCTTTTATTTCATTT
Found at i:47573346 original size:8 final size:9
Alignment explanation
Indices: 47573318--47573351 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
47573308 TTTCTTTTTC
*
47573318 ATTTCTTTT
1 ATTTCATTT
47573327 ATTTCATTT
1 ATTTCATTT
47573336 ATTTC-TTT
1 ATTTCATTT
47573344 ATTTCATT
1 ATTTCATT
47573352 ATTAAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTCATTT
Found at i:47574991 original size:16 final size:15
Alignment explanation
Indices: 47574970--47575013 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
47574960 CATAAAGCTG
47574970 TTTCAACCCCTCCACT
1 TTTCAACCCCTCCA-T
* *
47574986 TTTCAAACCTTCCAT
1 TTTCAACCCCTCCAT
47575001 TTTCAAGCCCCTC
1 TTTCAA-CCCCTC
47575014 ATCCTACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.20, C:0.43, G:0.02, T:0.34
Consensus pattern (15 bp):
TTTCAACCCCTCCAT
Found at i:47575508 original size:14 final size:15
Alignment explanation
Indices: 47575481--47575509 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47575471 GAAACACTGG
47575481 CTTTGTCTTTTATTC
1 CTTTGTCTTTTATTC
47575496 CTTTGTC-TTTATTC
1 CTTTGTCTTTTATTC
47575510 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (15 bp):
CTTTGTCTTTTATTC
Found at i:47576876 original size:29 final size:30
Alignment explanation
Indices: 47576831--47576898 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
47576821 TGGCCCAAGA
*
47576831 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAATTTGAAGGACTAATAGT
*
47576861 GTAAATATGAAAATTTGAAGGACTAATAGT
1 GTAAATATCAAAATTTGAAGGACTAATAGT
*
47576891 GAAAATAT
1 GTAAATAT
47576899 TTTAAGGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATCAAAATTTGAAGGACTAATAGT
Found at i:47579490 original size:19 final size:19
Alignment explanation
Indices: 47579445--47579491 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
47579435 TAAATATTAA
*
47579445 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
47579464 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
47579483 AATAAAAAT
1 AATAAAAAT
47579492 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:47583899 original size:24 final size:24
Alignment explanation
Indices: 47583867--47583917 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
47583857 GTGAGTTTTA
47583867 AATTCTGACCTAAATTAATCTGCC
1 AATTCTGACCTAAATTAATCTGCC
47583891 AATTCTGACCTAAATTAATCTGCC
1 AATTCTGACCTAAATTAATCTGCC
47583915 AAT
1 AAT
47583918 GTTTTTCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (24 bp):
AATTCTGACCTAAATTAATCTGCC
Found at i:47584933 original size:12 final size:12
Alignment explanation
Indices: 47584916--47584943 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
47584906 TTGGTTATTG
47584916 CTGTAGCAGCTT
1 CTGTAGCAGCTT
47584928 CTGTAGCAGCTT
1 CTGTAGCAGCTT
47584940 CTGT
1 CTGT
47584944 TTTTTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (12 bp):
CTGTAGCAGCTT
Found at i:47589773 original size:45 final size:45
Alignment explanation
Indices: 47589724--47589987 Score: 163
Period size: 46 Copynumber: 5.8 Consensus size: 45
47589714 ACCAGAAATA
* *
47589724 AGTAAGACCATAGCTGAAAGACACTATGGCATCATGATTTAGACG
1 AGTAAGACCATAGCTGAAAGACACTATGGCATCATGATTCAAACG
* * *
47589769 AGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAAATG
1 AGTAAGACCATAGCTGAAAGACACTATGGCATCATGATTCAAACG
* * * * * * ** *
47589814 TGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGCAAATG
1 AGTAAGACCATAGCTGAAAGACACTATGGCATCATGA-TTCAAACG
* * * * * * *
47589860 AATAAGACCATGGTTGAAAGATACCATGGCAAT-ATGACAGT-AAATG
1 AGTAAGACCATAGCTGAAAGACACTATGGC-ATCATG--ATTCAAACG
* ** * * * * *** *
47589906 AATAAGACCACGGTTGAAAGATACCATGGCAACATGACAGAAAATG
1 AGTAAGACCATAGCTGAAAGACACTATGGCATCATGA-TTCAAACG
* *
47589952 AGTAAGACCATAGTTGAAACACACTATGGCATCATG
1 AGTAAGACCATAGCTGAAAGACACTATGGCATCATG
47589988 TCGAAGATAA
Statistics
Matches: 181, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
44 1 0.01
45 70 0.39
46 108 0.60
47 1 0.01
48 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGACACTATGGCATCATGATTCAAACG
Found at i:47589869 original size:46 final size:46
Alignment explanation
Indices: 47589816--47590005 Score: 256
Period size: 46 Copynumber: 4.2 Consensus size: 46
47589806 TTCAAATGTG
*
47589816 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGCAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* *
47589862 TAAGACCATGGTTGAAAGATACCATGGCAATATGACAGTAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* *
47589908 TAAGACCACGGTTGAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* * * * * * * *
47589954 TAAGACCATAGTTGAAACACACTATGGCATCATGTC-GAAGATAAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
47589999 TAAGACC
1 TAAGACC
47590006 GTGGATGGGA
Statistics
Matches: 128, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 13 0.10
46 115 0.90
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
Found at i:47594791 original size:30 final size:30
Alignment explanation
Indices: 47594757--47594817 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
47594747 TCCTTAACTC
47594757 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
47594787 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
47594817 A
1 A
47594818 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:47598216 original size:13 final size:13
Alignment explanation
Indices: 47598198--47598226 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47598188 ATTAAAGAAA
47598198 ATATTATTATATT
1 ATATTATTATATT
47598211 ATATTATTATATT
1 ATATTATTATATT
47598224 ATA
1 ATA
47598227 ATAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:47600081 original size:30 final size:32
Alignment explanation
Indices: 47600021--47600084 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
47600011 CACTTATTTT
47600021 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
47600054 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
47600085 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:47600345 original size:41 final size:41
Alignment explanation
Indices: 47600299--47600454 Score: 217
Period size: 41 Copynumber: 3.8 Consensus size: 41
47600289 ACCGGCTCTT
* *
47600299 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGACATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
47600340 AGCCTGCTAAACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
47600381 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
47600422 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
47600455 TAACGATAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 95 0.91
42 2 0.02
43 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:47602008 original size:13 final size:13
Alignment explanation
Indices: 47601990--47602014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47601980 CCATCGAATG
47601990 CACACAAAATAAA
1 CACACAAAATAAA
47602003 CACACAAAATAA
1 CACACAAAATAA
47602015 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:47602255 original size:21 final size:21
Alignment explanation
Indices: 47602213--47602262 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
47602203 GATTATTTGA
*
47602213 ATTGAATTGAATATTGATTAT
1 ATTGAATTGAATATTGAATAT
*
47602234 ATTGAATTG-ATTTATGAATAT
1 ATTGAATTGAATAT-TGAATAT
47602255 ATGTGAAT
1 AT-TGAAT
47602263 GTTTGAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (21 bp):
ATTGAATTGAATATTGAATAT
Found at i:47602289 original size:30 final size:28
Alignment explanation
Indices: 47602208--47602289 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 28
47602198 GAGATGATTA
*
47602208 TTTGAATTGAATTGAATATTGAT-T-AT
1 TTTGAATTGAAATGAATATTGATGTGAT
* *
47602234 ATTGAATTGATTTATGAATA-T-ATGTGAAT
1 TTTGAATTGA--AATGAATATTGATGTG-AT
47602263 GTTTGAATTGAAATGAATATTGATGTG
1 -TTTGAATTGAAATGAATATTGATGTG
47602290 GAAATTGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
26 11 0.26
27 2 0.05
28 13 0.30
29 3 0.07
30 14 0.33
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (28 bp):
TTTGAATTGAAATGAATATTGATGTGAT
Found at i:47602437 original size:20 final size:21
Alignment explanation
Indices: 47602385--47602439 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 21
47602375 AAAGCGAATG
47602385 GAATTATATTGAATTGAAAATAT
1 GAATTA-ATTG-ATTGAAAATAT
47602408 -ATAGTTAATTGATT-AAAATAT
1 GA-A-TTAATTGATTGAAAATAT
47602429 GAATTAATTGA
1 GAATTAATTGA
47602440 AAACTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 8 0.28
21 8 0.28
22 5 0.17
23 5 0.17
24 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
GAATTAATTGATTGAAAATAT
Found at i:47602661 original size:44 final size:45
Alignment explanation
Indices: 47602570--47602673 Score: 147
Period size: 44 Copynumber: 2.3 Consensus size: 45
47602560 CGATTACTGT
* * *
47602570 TACTGTTACCGTTACTATTACCGATTCTGCACTTTGTGTGTCAAA
1 TACTGTTACTGTTACCATTACCGATTCAGCACTTTGTGTGTCAAA
* **
47602615 TACTGTTACTGTTACCATTATC-ATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACCATTACCGATTCAGCACTTTGTGTGTCAAA
47602659 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
47602674 TGTTACTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 34 0.64
45 19 0.36
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACCATTACCGATTCAGCACTTTGTGTGTCAAA
Found at i:47602670 original size:6 final size:6
Alignment explanation
Indices: 47602659--47602683 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47602649 GTGTGTTGAA
47602659 TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT T
47602684 CCGGATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:47604221 original size:91 final size:89
Alignment explanation
Indices: 47604103--47604270 Score: 255
Period size: 89 Copynumber: 1.9 Consensus size: 89
47604093 GAGTTGATTT
* * **
47604103 TTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTTAACTCACCTCTTGCAATAT
1 TTGAAAAGCAGAAATTGAAAACACCTCAGCGTGT--CCCGAGGCTAAACTCACCTCTCACAATAT
47604168 GAGTTGATTCTTTTGAAATGTAGAAA
64 GAGTTGATTCTTTTGAAATGTAGAAA
* *
47604194 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTAAACTCACCTCTCACAATGTGA
1 TTGAAAAGCAGAAATTGAAAACACCTCAGCGTGTCCCGAGGCTAAACTCACCTCTCACAATATGA
*
47604259 GTTGATTTTTTT
66 GTTGATTCTTTT
47604271 TTTATAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
89 38 0.54
91 32 0.46
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (89 bp):
TTGAAAAGCAGAAATTGAAAACACCTCAGCGTGTCCCGAGGCTAAACTCACCTCTCACAATATGA
GTTGATTCTTTTGAAATGTAGAAA
Found at i:47604489 original size:75 final size:75
Alignment explanation
Indices: 47604369--47604976 Score: 930
Period size: 75 Copynumber: 8.2 Consensus size: 75
47604359 AAATTGAAGA
* * * * *
47604369 ACAAAAATGGAAAACACCTCAAC--GTCTTGAGGTTTAACTCACCTCTCGCAATATGAGCTGATT
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604432 TTTTTGAAAG
66 TTTTTGAAAG
* * *
47604442 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604505 TTTTTGACAA-
66 TTTTTGA-AAG
* ** *
47604515 ACAAAAATTGAAATTACCTC-A-GCATCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTAATT
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604578 TTTTTGAAAG
66 TTTTTGAAAG
47604588 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604653 TTTTTGAAAG
66 TTTTTGAAAG
47604663 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604728 TTTTTGAAAG
66 TTTTTGAAAG
47604738 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604803 TTTTTGAAAG
66 TTTTTGAAAG
* *
47604813 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
47604876 TTTTTGACAA-
66 TTTTTGA-AAG
* * * * * *
47604886 ACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATT
1 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
*
47604951 TTTTTGAAAA
66 TTTTTGAAAG
*
47604961 ACAGAAATTGAAAATA
1 ACAAAAATTGAAAATA
47604977 GAAATGGAAA
Statistics
Matches: 498, Mismatches: 25, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
71 35 0.07
72 3 0.01
73 137 0.28
74 7 0.01
75 316 0.63
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (75 bp):
ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTAATT
TTTTTGAAAG
Found at i:47605030 original size:86 final size:87
Alignment explanation
Indices: 47604901--47605060 Score: 232
Period size: 86 Copynumber: 1.8 Consensus size: 87
47604891 AATTGAAATT
*
47604901 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGA
1 ACCTCAGCG-GTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTTTTGAAAAACAGA
*
47604966 AATTGAAAATAGAAATGGAAAAC
65 AATTAAAAATAGAAATGGAAAAC
* * * * * *
47604989 ACCTCAGC-GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGGTTTTTTTGAAACACATAA
1 ACCTCAGCGGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTTTTGAAAAACAGAA
47605053 ATTAAAAA
66 ATTAAAAA
47605061 AAAGAAATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
86 56 0.88
88 8 0.12
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (87 bp):
ACCTCAGCGGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTTTTGAAAAACAGAA
ATTAAAAATAGAAATGGAAAAC
Found at i:47605442 original size:75 final size:74
Alignment explanation
Indices: 47605071--47605460 Score: 412
Period size: 75 Copynumber: 5.2 Consensus size: 74
47605061 AAAGAAATTA
* ** * * *
47605071 AAAACAGAATTTGAAAGGACCTCGACGTGTGGCCTGAGACTCAACTCACCTCTCGCAATATGAAT
1 AAAACAGAAATTGAAAATACCTCAACGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
47605136 TGATTCTTTTG
64 TGATTTTTTTG
* ** *
47605147 AAAAGCAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AAAA-CAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
47605212 GATTTTTTGATA
65 GATTTTTT--TG
* * * * * *
47605224 AAAATAGAATTTGAAAATATCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
47605289 A--TTTTTG
66 ATTTTTTTG
* * ** * * *
47605296 ACAAACAAAAATTGAAATTACCTC-A-GCATCTTGAGGTTCAACTCACCTCTCGCAATATGAGCT
1 A-AAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
47605359 GATTTTTTTG
65 GATTTTTTTG
* *
47605369 AAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAA-ACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
47605434 GATTTTTTTTG
65 GA-TTTTTTTG
* *
47605445 -AAACATAAATTAAAAA
1 AAAACAGAAATTGAAAA
47605461 AACGAAAATT
Statistics
Matches: 261, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
71 33 0.13
72 4 0.02
73 42 0.16
74 17 0.07
75 73 0.28
76 66 0.25
77 26 0.10
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (74 bp):
AAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTTG
Found at i:47605666 original size:14 final size:13
Alignment explanation
Indices: 47605630--47605674 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
47605620 TTGATTTTTG
47605630 AAAAACAGAAATT
1 AAAAACAGAAATT
**
47605643 AAAAGTAGAAATT
1 AAAAACAGAAATT
47605656 GAAAAACAGAAATT
1 -AAAAACAGAAATT
47605670 AAAAA
1 AAAAA
47605675 TACCTCGGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.69, C:0.04, G:0.11, T:0.16
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:47605689 original size:100 final size:101
Alignment explanation
Indices: 47605458--47605746 Score: 388
Period size: 100 Copynumber: 2.9 Consensus size: 101
47605448 CATAAATTAA
* * * *
47605458 AAAAAC-GAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTTACCTCTCGCAATATGAGA
1 AAAAACAG-AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
47605522 TGA--TTTGAAAAGCAGAATTTGTAAGGCAAAAATTG
65 TGATTTTTGAAAAGCAGAAATTGAAAAGCAAAAATTG
* *
47605557 AAAAATAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAAAATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * *
47605622 GATTTTTGAAAAACAGAAATT-AAAAGTAGAAATTG
66 GATTTTTGAAAAGCAGAAATTGAAAAGCAAAAATTG
* * * *
47605657 AAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
47605722 GATTTTTGAAAAGCATAAATTGAAA
66 GATTTTTGAAAAGCAGAAATTGAAA
47605747 TTACCTCAGC
Statistics
Matches: 166, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
99 59 0.36
100 89 0.54
101 18 0.11
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (101 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAGCAGAAATTGAAAAGCAAAAATTG
Found at i:47605752 original size:73 final size:74
Alignment explanation
Indices: 47605654--47605821 Score: 257
Period size: 73 Copynumber: 2.3 Consensus size: 74
47605644 AAAGTAGAAA
* * * * *
47605654 TTGAAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
47605719 GTTGA-TTT
66 GTTGATTTT
* * *
47605727 TTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
47605792 GTTGATTTT
66 GTTGATTTT
47605801 TTGAAAAGCATAAATTGAAAA
1 TTGAAAAGCATAAATTGAAAA
47605822 AACGGAAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
73 62 0.73
74 23 0.27
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (74 bp):
TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTT
Found at i:47625259 original size:28 final size:28
Alignment explanation
Indices: 47625228--47625287 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
47625218 AAATTTAAAA
*
47625228 AAAAAATTAATTAGACCTAAAAATTTTT
1 AAAAAATTAATTAAACCTAAAAATTTTT
* * * *
47625256 AAAATATTTATTAAATCTTAAAATTTTT
1 AAAAAATTAATTAAACCTAAAAATTTTT
47625284 AAAA
1 AAAA
47625288 TTTTTAATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (28 bp):
AAAAAATTAATTAAACCTAAAAATTTTT
Found at i:47625265 original size:9 final size:9
Alignment explanation
Indices: 47625247--47625294 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
47625237 ATTAGACCTA
47625247 AAAATTTTT
1 AAAATTTTT
47625256 AAAATATTTAT
1 AAAAT-TTT-T
* *
47625267 TAAA-TCTT
1 AAAATTTTT
47625275 AAAATTTTT
1 AAAATTTTT
47625284 AAAATTTTT
1 AAAATTTTT
47625293 AA
1 AA
47625295 TGTTAAGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
8 4 0.12
9 21 0.66
10 3 0.09
11 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
AAAATTTTT
Found at i:47626384 original size:18 final size:18
Alignment explanation
Indices: 47626357--47626427 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
47626347 ATGTCAGTCA
*
47626357 ATAAATAATTTAAAAATT
1 ATAAAAAATTTAAAAATT
47626375 ATAAAAAATTT--AAATT
1 ATAAAAAATTTAAAAATT
*
47626391 TTAAAATAATTATAAAAAGTT
1 ATAAAA-AATT-TAAAAA-TT
47626412 CAT-AAAAATTTAAAAA
1 -ATAAAAAATTTAAAAA
47626428 ATAATAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.23
17 4 0.09
18 11 0.25
19 6 0.14
20 7 0.16
21 5 0.11
22 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
ATAAAAAATTTAAAAATT
Found at i:47626395 original size:16 final size:18
Alignment explanation
Indices: 47626359--47626406 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
47626349 GTCAGTCAAT
*
47626359 AAATAATTTAAAAATTATA
1 AAATAA-TTATAAATTATA
*
47626378 AAA-AATT-TAAATTTTA
1 AAATAATTATAAATTATA
47626394 AAATAATTATAAA
1 AAATAATTATAAA
47626407 AAGTTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 6 0.24
19 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATTATAAATTATA
Found at i:47628465 original size:30 final size:30
Alignment explanation
Indices: 47628375--47628473 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
47628365 TAGGTACAAG
47628375 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
47628405 AGGTAGTAGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
47628435 TGGTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
47628465 TGGTGGTGG
1 TGGTGGTGG
47628474 CAAAGGCTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.18, C:0.06, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Done.