Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 91 of 352
Found at i:28820266 original size:70 final size:70
Alignment explanation
Indices: 28820153--28820297 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
28820143 TTACACTGAC
*
28820153 TCTCACGTTAAGTCGATGCCATGTCCCAGACATGGTCTTATACTAACTCTCATGTTAAGTCGATA
1 TCTCACGTTAAGTCGATGCCATGTCCCAAACATGGTCTTATACTAACTCTCATGTTAAGTCGATA
28820218 CCATG
66 CCATG
*
28820223 TCTCACGTTAAGTCGATGCCATGTCCCAAACATGGTCTTATACTAACTCTCATGTTAAGTCGATG
1 TCTCACGTTAAGTCGATGCCATGTCCCAAACATGGTCTTATACTAACTCTCATGTTAAGTCGATA
28820288 CCATG
66 CCATG
28820293 TCTCA
1 TCTCA
28820298 GACATGGTCT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (70 bp):
TCTCACGTTAAGTCGATGCCATGTCCCAAACATGGTCTTATACTAACTCTCATGTTAAGTCGATA
CCATG
Found at i:28820292 original size:47 final size:47
Alignment explanation
Indices: 28820223--28820453 Score: 177
Period size: 47 Copynumber: 4.9 Consensus size: 47
28820213 CGATACCATG
* *
28820223 TCTCACGTTAAGTCGATGCCATGTCCCAAACATGGTCTTATACTAAC
1 TCTCACGTTAAGTCGATGCCATGTCCCAGACATGGTCTTACACTAAC
* * *
28820270 TCTCATGTTAAGTCGATGCCATGTCTCAGACATGGTCTTACACTGAC
1 TCTCACGTTAAGTCGATGCCATGTCCCAGACATGGTCTTACACTAAC
** * ** *
28820317 TCTCACGTATCTGTGCCGATGCCATGTCCCAGACATGGTTTTTTACTGAC
1 TCTCACGT-TAAGT--CGATGCCATGTCCCAGACATGGTCTTACACTAAC
* * * * * *
28820367 ACATCA--TTTAGCCGATG-TATGTCCTAGACAT-GTCTTACACTAGC
1 TC-TCACGTTAAGTCGATGCCATGTCCCAGACATGGTCTTACACTAAC
* * *
28820411 TCT--CGTCTCAATGCCGATGCCATGTCCCGGACATGGTGTTACA
1 TCTCACGT-T-AA-GTCGATGCCATGTCCCAGACATGGTCTTACA
28820454 TTGGCTCTCA
Statistics
Matches: 144, Mismatches: 29, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
43 2 0.01
44 10 0.07
45 13 0.09
46 12 0.08
47 60 0.42
48 12 0.08
49 1 0.01
50 31 0.22
51 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (47 bp):
TCTCACGTTAAGTCGATGCCATGTCCCAGACATGGTCTTACACTAAC
Found at i:28820319 original size:117 final size:117
Alignment explanation
Indices: 28820106--28820321 Score: 333
Period size: 117 Copynumber: 1.8 Consensus size: 117
28820096 TTACACTAGC
* * *
28820106 TCTCACGCTAAGTCGACGCCATGTCCTAGACAGGGTCTTACACTGACTCTCACGTTAAGTCGATG
1 TCTCACGCTAAGTCGACGCCATGTCCCAAACAGGGTCTTACACTAACTCTCACGTTAAGTCGATG
*
28820171 CCATGTCCCAGACATGGTCTTATACTAACTCTCATGTTAAGTCGATACCATG
66 CCATGTCCCAGACATGGTCTTACACTAACTCTCATGTTAAGTCGATACCATG
* * * * *
28820223 TCTCACGTTAAGTCGATGCCATGTCCCAAACATGGTCTTATACTAACTCTCATGTTAAGTCGATG
1 TCTCACGCTAAGTCGACGCCATGTCCCAAACAGGGTCTTACACTAACTCTCACGTTAAGTCGATG
* *
28820288 CCATGTCTCAGACATGGTCTTACACTGACTCTCA
66 CCATGTCCCAGACATGGTCTTACACTAACTCTCA
28820322 CGTATCTGTG
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 88 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (117 bp):
TCTCACGCTAAGTCGACGCCATGTCCCAAACAGGGTCTTACACTAACTCTCACGTTAAGTCGATG
CCATGTCCCAGACATGGTCTTACACTAACTCTCATGTTAAGTCGATACCATG
Found at i:28823496 original size:20 final size:24
Alignment explanation
Indices: 28823466--28823510 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 24
28823456 TCAATATACT
28823466 AATTCCATTCA-A-AAGG-ACATC
1 AATTCCATTCATAGAAGGAACATC
28823487 AATT-CATTCATAGAAGGAACATC
1 AATTCCATTCATAGAAGGAACATC
28823510 A
1 A
28823511 TATACATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 4 0.19
23 6 0.29
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.24
Consensus pattern (24 bp):
AATTCCATTCATAGAAGGAACATC
Found at i:28824243 original size:47 final size:48
Alignment explanation
Indices: 28824133--28824348 Score: 175
Period size: 47 Copynumber: 4.7 Consensus size: 48
28824123 GTGTATACGT
* * ** *
28824133 GCTGATG-CATGTCCCAGACATGTCTTACACTTGC-ACGAAGCTT-A-
1 GCTGATGCCATGTCCCAGACACGTCTTACACTGGCTACTCATCTTGAC
*
28824177 GCTGATG-CGTGTCCCAGACACGTCTTACACTGGCTAC-CATCATTGA-
1 GCTGATGCCATGTCCCAGACACGTCTTACACTGGCTACTCATC-TTGAC
* * * *
28824223 GGTCGAT-CCATGTCCTAGACACGTCTTACACTAGC-ACTCATCTTTAC
1 GCT-GATGCCATGTCCCAGACACGTCTTACACTGGCTACTCATCTTGAC
* ** **
28824270 GCTGATGCCATGTCCCAGACACAGTCTTACACTGGCTA-TCGTAATGTG
1 GCTGATGCCATGTCCCAGACAC-GTCTTACACTGGCTACTCATCTTGAC
* *
28824318 GCTGAT-ACATGTCCCGGACACGTCTTACACT
1 GCTGATGCCATGTCCCAGACACGTCTTACACT
28824349 AGCCCTTGTC
Statistics
Matches: 141, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 33 0.23
45 4 0.03
46 21 0.15
47 60 0.43
48 22 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
GCTGATGCCATGTCCCAGACACGTCTTACACTGGCTACTCATCTTGAC
Found at i:28824329 original size:94 final size:93
Alignment explanation
Indices: 28824086--28824396 Score: 272
Period size: 94 Copynumber: 3.3 Consensus size: 93
28824076 TTAAGTTGCC
* * * * * *
28824086 GATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCGTGTATACGT-GCTGATGCATGTCCCAG
1 GATGCCATGTCCCAGACACGGTCTTACACTGGCTATC--GTA-ATGTGGCTGATACATGTCCCAG
* * * *
28824150 ACATGTCTTACACTTGCACGAAGC-TTAGCT
63 ACACGTCTTACACTAGCACTAATCTTTAGCT
* * * * * * *
28824180 GATG-CGTGTCCCAGACAC-GTCTTACACTGGCTACCATCAT-TGAGGTCGATCCATGTCCTAGA
1 GATGCCATGTCCCAGACACGGTCTTACACTGGCTATCGTAATGTG-GCT-GATACATGTCCCAGA
*
28824242 CACGTCTTACACTAGCACTCATCTTTACGCT
64 CACGTCTTACACTAGCACTAATCTTTA-GCT
* *
28824273 GATGCCATGTCCCAGACACAGTCTTACACTGGCTATCGTAATGTGGCTGATACATGTCCCGGACA
1 GATGCCATGTCCCAGACACGGTCTTACACTGGCTATCGTAATGTGGCTGATACATGTCCCAGACA
* ** ** *
28824338 CGTCTTACACTAGCCCTTGTCTCAATGCC
66 CGTCTTACACTAGCACTAATCTTTA-GCT
* *
28824367 GATGCCATTTCCCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACACGGTCTTACACT
28824397 AGCTCTCACA
Statistics
Matches: 175, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
88 1 0.01
89 1 0.01
90 3 0.02
91 31 0.18
92 17 0.10
93 19 0.11
94 80 0.46
95 21 0.12
96 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGACACGGTCTTACACTGGCTATCGTAATGTGGCTGATACATGTCCCAGACA
CGTCTTACACTAGCACTAATCTTTAGCT
Found at i:28826415 original size:22 final size:22
Alignment explanation
Indices: 28826377--28826421 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28826367 CAATGGTATT
* *
28826377 CAGACAAGTTGTCAGTAAGTTG
1 CAGACAAGTTCTCAGTAAATTG
28826399 CAGACAAGCTTCT-AGTAAATTG
1 CAGACAAG-TTCTCAGTAAATTG
28826421 C
1 C
28826422 GATATGTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (22 bp):
CAGACAAGTTCTCAGTAAATTG
Found at i:28829054 original size:12 final size:12
Alignment explanation
Indices: 28829024--28829060 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28829014 GTTTTATGAG
28829024 TAAATTTAG-TTT
1 TAAA-TTAGATTT
28829036 T-AATTAGATTT
1 TAAATTAGATTT
28829047 TAAATTAGATTT
1 TAAATTAGATTT
28829059 TA
1 TA
28829061 TTTTCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
12 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TAAATTAGATTT
Found at i:28832194 original size:21 final size:24
Alignment explanation
Indices: 28832169--28832212 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28832159 GGCACGTTAT
*
28832169 TTTTTGTT-TTGT-TTCTTCTTGG
1 TTTTGGTTCTTGTGTTCTTCTTGG
28832191 TTTTGGTTCTTGTGTTCTTCTT
1 TTTTGGTTCTTGTGTTCTTCTT
28832213 TTTACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.00, C:0.11, G:0.18, T:0.70
Consensus pattern (24 bp):
TTTTGGTTCTTGTGTTCTTCTTGG
Found at i:28832763 original size:22 final size:21
Alignment explanation
Indices: 28832736--28832792 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
28832726 TTAGGGATTC
**
28832736 CACACGGGCGTGTGTTTTGGAA
1 CACACGGGCGTGTGTAGTGG-A
* * *
28832758 CACACGGCCGTGTCTAGTGGC
1 CACACGGGCGTGTGTAGTGGA
28832779 CACACGGGCGTGTG
1 CACACGGGCGTGTG
28832793 AGACCCTCAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTGTAGTGGA
Found at i:28834906 original size:22 final size:22
Alignment explanation
Indices: 28834880--28834939 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
28834870 ACCCTACCAA
28834880 AGAGCACCGAAGTGCTAAAT-AG
1 AGAGCACCGAAGTGCT-AATCAG
*
28834902 AGAGCACACGAA-TGGTAATCAG
1 AGAGCAC-CGAAGTGCTAATCAG
28834924 AGAGCACCGAAGTGCT
1 AGAGCACCGAAGTGCT
28834940 GAACAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.21
22 22 0.67
23 4 0.12
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.13
Consensus pattern (22 bp):
AGAGCACCGAAGTGCTAATCAG
Found at i:28834965 original size:44 final size:44
Alignment explanation
Indices: 28834880--28834967 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
28834870 ACCCTACCAA
* * *
28834880 AGAGCACCGAAGTGCTAAATAGAGAGCACACGAATGGTAATCAG
1 AGAGCACCGAAGTGCTAAACAAAGAGCACACGAATGCTAATCAG
* * *
28834924 AGAGCACCGAAGTGCTGAACAAAGATCATA-GATATGCTAATCAG
1 AGAGCACCGAAGTGCTAAACAAAGAGCACACGA-ATGCTAATCAG
28834968 TTAATAGGGC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (44 bp):
AGAGCACCGAAGTGCTAAACAAAGAGCACACGAATGCTAATCAG
Found at i:28836113 original size:22 final size:22
Alignment explanation
Indices: 28836067--28836107 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28836057 TTGGGTTTTA
*
28836067 TAATAAGTATAAATAATATACT
1 TAATAAGTATAAATAACATACT
28836089 TAATAAGT-TAAATAACATA
1 TAATAAGTATAAATAACATA
28836108 ATTTAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (22 bp):
TAATAAGTATAAATAACATACT
Found at i:28836301 original size:31 final size:31
Alignment explanation
Indices: 28836275--28836333 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28836265 TAATAGCCGC
* * *
28836275 GAGAGTTAAATAAAAACTTTTAAATAGTTCA
1 GAGACTTAAATAAAAACTTTCAAATAGTCCA
*
28836306 GTGACTTAAATAAAAACTTTCAAATAGT
1 GAGACTTAAATAAAAACTTTCAAATAGT
28836334 TCAATAGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (31 bp):
GAGACTTAAATAAAAACTTTCAAATAGTCCA
Found at i:28840009 original size:8 final size:7
Alignment explanation
Indices: 28839988--28840207 Score: 109
Period size: 7 Copynumber: 30.7 Consensus size: 7
28839978 ACTTTATTTT
28839988 TATATTA
1 TATATTA
28839995 TATATTA
1 TATATTA
28840002 TATGATTA
1 TAT-ATTA
28840010 TATGATTA
1 TAT-ATTA
28840018 TATATTA
1 TATATTA
28840025 TTTATATTA
1 --TATATTA
28840034 CTATTATTA
1 -TA-TATTA
*
28840043 TTTATTA
1 TATATTA
28840050 TATATTA
1 TATATTA
*
28840057 T-TTTTCA
1 TATATT-A
* *
28840064 CAAATTA
1 TATATTA
*
28840071 TTATTATTT
1 -TA-TATTA
*
28840080 TACATTA
1 TATATTA
28840087 T-TATTTA
1 TATA-TTA
28840094 TATATTA
1 TATATTA
28840101 TTATATT-
1 -TATATTA
* *
28840108 TTTACT-
1 TATATTA
*
28840114 TGTATTA
1 TATATTA
28840121 TATATT-
1 TATATTA
28840127 TATTAATTA
1 TA-T-ATTA
*
28840136 TTTA-TA
1 TATATTA
28840142 TATATTA
1 TATATTA
28840149 TATATTA
1 TATATTA
*
28840156 T-T-TTT
1 TATATTA
*
28840161 TACA-TA
1 TATATTA
*
28840167 TATACTTT
1 TATA-TTA
28840175 TATATTA
1 TATATTA
28840182 TATATTA
1 TATATTA
28840189 TAT-TTA
1 TATATTA
*
28840195 TTTTATTA
1 -TATATTA
28840203 TATAT
1 TATAT
28840208 CATTATGTCA
Statistics
Matches: 163, Mismatches: 28, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
5 3 0.02
6 27 0.17
7 74 0.45
8 43 0.26
9 16 0.10
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (7 bp):
TATATTA
Found at i:28840145 original size:21 final size:21
Alignment explanation
Indices: 28840119--28840207 Score: 62
Period size: 23 Copynumber: 4.2 Consensus size: 21
28840109 TTACTTGTAT
28840119 TATATATTTATTAATTATTTA
1 TATATATTTATTAATTATTTA
* *
28840140 TATATATTATATATTATTTTTTACA
1 TATATATT-TAT-TAATTATTT--A
* *
28840165 TATATACTT-TTATATTATATA
1 TATATATTTATTA-ATTATTTA
28840186 T-TATATTTATT--TTA-TTA
1 TATATATTTATTAATTATTTA
28840203 TATAT
1 TATAT
28840208 CATTATGTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
17 3 0.06
18 6 0.11
20 6 0.11
21 12 0.23
22 4 0.08
23 13 0.25
24 1 0.02
25 8 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATATTTATTAATTATTTA
Found at i:28840188 original size:99 final size:103
Alignment explanation
Indices: 28840014--28840205 Score: 238
Period size: 99 Copynumber: 1.9 Consensus size: 103
28840004 TGATTATATG
* *
28840014 ATTATATATTATTTATATTACTATTATTATTTATTATATATTATTTTTCACAAATTATTATTATT
1 ATTATATATTATTTATATTACTATTATTATATATTATATATTATTTTTCACAAATTATTATTATA
28840079 TTACATTATTAT-TTATATATTATTATATTTTTACTTGT
66 TTACATTATTATATT-TATATTATTATATTTTTACTTGT
* *
28840117 ATTATATATT-TATTA-ATTA-T-TTA-TATATATTATATATTATTTTTTACATATATACTT-TT
1 ATTATATATTAT-TTATATTACTATTATTATATATTATATATTATTTTTCACAAAT-TA-TTATT
* *
28840176 ATATTATA-TATTATATTTATTTTATTATAT
63 ATATTACATTATTATATTTATATTATTATAT
28840206 ATCATTATGT
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
99 43 0.54
100 15 0.19
101 3 0.04
102 5 0.06
103 13 0.16
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (103 bp):
ATTATATATTATTTATATTACTATTATTATATATTATATATTATTTTTCACAAATTATTATTATA
TTACATTATTATATTTATATTATTATATTTTTACTTGT
Found at i:28840222 original size:24 final size:22
Alignment explanation
Indices: 28840137--28840262 Score: 81
Period size: 23 Copynumber: 5.8 Consensus size: 22
28840127 TATTAATTAT
*
28840137 TTATATATATTATATATTATTT-
1 TTATATATATTATACATT-TTTA
*
28840159 TT-TACATA-TATAC--TTTTA
1 TTATATATATTATACATTTTTA
**
28840177 -TATTATATATTATATTTATTTTA
1 TTA-TATATATTATACAT-TTTTA
*
28840200 TTATATATCATTATGTCATTTTT-
1 TTATATAT-ATTAT-ACATTTTTA
28840223 TTATAT-TATTATACATTTTTA
1 TTATATATATTATACATTTTTA
28840244 TCTATATATTATTAT-CATT
1 T-TATATA-TATTATACATT
28840263 AAAGGTTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
17 4 0.05
18 1 0.01
19 5 0.06
20 15 0.18
21 11 0.13
22 8 0.10
23 20 0.24
24 17 0.21
25 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.61
Consensus pattern (22 bp):
TTATATATATTATACATTTTTA
Found at i:28840227 original size:21 final size:20
Alignment explanation
Indices: 28840118--28840255 Score: 79
Period size: 21 Copynumber: 6.7 Consensus size: 20
28840108 TTTACTTGTA
*
28840118 TTATATAT-TTATTA-ATTAT
1 TTATATATATTA-TACATTTT
*
28840137 TTATATATATTATATATTATT
1 TTATATATATTATACATT-TT
* *
28840158 TTTTACATA-TATAC-TTTT
1 TTATATATATTATACATTTT
* *
28840176 ATATTATATATTATATTTATTTT
1 TTA-TATATATTATA--CATTTT
*
28840199 ATTATATATCATTATGTCATTTT
1 -TTATATAT-ATTAT-ACATTTT
28840222 TT-TATATTATTATACATTTT
1 TTATATA-TATTATACATTTT
*
28840242 TATCTATATATTAT
1 T-TATATATATTAT
28840256 TATCATTAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
18 3 0.03
19 17 0.18
20 21 0.23
21 24 0.26
22 7 0.08
23 14 0.15
24 7 0.08
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (20 bp):
TTATATATATTATACATTTT
Found at i:28840527 original size:16 final size:16
Alignment explanation
Indices: 28840508--28840574 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
28840498 ATATATTTTA
28840508 TATTTTTTATAATTAT
1 TATTTTTTATAATTAT
* *
28840524 TA-TTCTTATAAATA-
1 TATTTTTTATAATTAT
*
28840538 TATTTTTTATTATATAT
1 TATTTTTTATAAT-TAT
**
28840555 TACATTTTA-AATTTAT
1 TATTTTTTATAA-TTAT
28840571 TATT
1 TATT
28840575 AAATATCACA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
14 2 0.05
15 17 0.46
16 10 0.27
17 8 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTTATAATTAT
Found at i:28840547 original size:15 final size:14
Alignment explanation
Indices: 28840506--28840555 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
28840496 CAATATATTT
28840506 TATATTTTTTATAA
1 TATATTTTTTATAA
28840520 T-TATTATTCTTATAAA
1 TATATT-TT-TTAT-AA
*
28840536 TATATTTTTTATTA
1 TATATTTTTTATAA
28840550 TATATT
1 TATATT
28840556 ACATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 8 0.26
16 5 0.16
17 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTTTTATAA
Found at i:28840573 original size:26 final size:26
Alignment explanation
Indices: 28840539--28840588 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28840529 TTATAAATAT
* * *
28840539 ATTTTTTATTATATATTACATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
28840565 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
28840589 TTTATGCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:28846161 original size:87 final size:87
Alignment explanation
Indices: 28845996--28846238 Score: 261
Period size: 87 Copynumber: 2.8 Consensus size: 87
28845986 CTAGATAATG
* * * * *
28845996 GTACGCAGCAAAGCTGACGTACGTACAGTACAATGCGGTAAACCGCTATACGAATAAGTTGCAGT
1 GTACGCAGCAAAGCTGACGTACGTGCGGTACAGTGCAGTAAACCGCTGTACGAATAAGTTGCAGT
* *** *
28846061 AAAATTGTTAGATCAGACAATA
66 AAAACTACCAGATCAAACAATA
* * * * *
28846083 GTACGTAGCAAAGCTGATGTACATGCGGTACAGTGCAGTAAACCACTGTACGAATAAGTTGTAGT
1 GTACGCAGCAAAGCTGACGTACGTGCGGTACAGTGCAGTAAACCGCTGTACGAATAAGTTGCAGT
* * *
28846148 AAAACTACCAGATCAAATATTG
66 AAAACTACCAGATCAAACAATA
* * * * * * *
28846170 GTAAGCAGCAAAGCTGACGTACGTGTGGTATAGTGCAATACACCGTTGTACAAATAAGTTGCAGT
1 GTACGCAGCAAAGCTGACGTACGTGCGGTACAGTGCAGTAAACCGCTGTACGAATAAGTTGCAGT
28846235 AAAA
66 AAAA
28846239 TTGCCATATC
Statistics
Matches: 126, Mismatches: 30, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
87 126 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (87 bp):
GTACGCAGCAAAGCTGACGTACGTGCGGTACAGTGCAGTAAACCGCTGTACGAATAAGTTGCAGT
AAAACTACCAGATCAAACAATA
Found at i:28849429 original size:47 final size:44
Alignment explanation
Indices: 28849315--28849443 Score: 134
Period size: 47 Copynumber: 2.8 Consensus size: 44
28849305 TCATTTGTGT
*
28849315 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTATGAAA
* * * *
28849361 GCCATTGTAAGACCATTTCTGGGACATGGCATTGG-CATTGAAATGAAA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATT---ATGAAA
*
28849409 GCTAGTGTAAGACATGTCTGGGACATACATCGGCC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
28849444 TCGCAACATA
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
45 4 0.06
46 15 0.22
47 27 0.40
48 21 0.31
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTATGAAA
Found at i:28851870 original size:17 final size:16
Alignment explanation
Indices: 28851836--28851879 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
28851826 ATAACTATGA
*
28851836 TAATAAA-AATAATCC
1 TAATAAATAATAATAC
28851851 TAATAAATACATAATAC
1 TAATAAATA-ATAATAC
28851868 TAATAAATAATA
1 TAATAAATAATA
28851880 TAATAGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.27
16 4 0.15
17 15 0.58
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATAAATAATAATAC
Found at i:28851929 original size:16 final size:16
Alignment explanation
Indices: 28851904--28851934 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28851894 AAACAACACA
28851904 ATTAAAAATAAATAAT
1 ATTAAAAATAAATAAT
*
28851920 ATTAATAATAAATAA
1 ATTAAAAATAAATAA
28851935 ATACAAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAAAATAAATAAT
Found at i:28852949 original size:20 final size:23
Alignment explanation
Indices: 28852920--28852960 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
28852910 GTTTTTCAAA
28852920 AAAAATTGAA-GTAA-TAAATAT
1 AAAAATTGAATGTAATTAAATAT
28852941 AAAAA-TGAATGTAATTAAAT
1 AAAAATTGAATGTAATTAAAT
28852961 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (23 bp):
AAAAATTGAATGTAATTAAATAT
Found at i:28864680 original size:42 final size:40
Alignment explanation
Indices: 28864568--28864684 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 40
28864558 CATAAATAAT
* * *
28864568 TGATGTTTGCTTCAGGGGTTATCGAGACTTGATCTTGGAAA
1 TGAT-TTTGCTTCAAGGGTCATTGAGACTTGATCTTGGAAA
* * * * *
28864609 TGAGTTTGGATCCAAGGGTC-TTCAAGACTTGATCTTGGATGGA
1 TGA-TTTTGCTTCAAGGGTCATT-GAGACTTGATCTTGGA--AA
28864652 TGATTTTGCTTCAAGGGTCATTGAGACTTGATC
1 TGATTTTGCTTCAAGGGTCATTGAGACTTGATC
28864685 CTTAAAATGG
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.02
41 28 0.47
42 24 0.41
43 6 0.10
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (40 bp):
TGATTTTGCTTCAAGGGTCATTGAGACTTGATCTTGGAAA
Found at i:28867184 original size:27 final size:27
Alignment explanation
Indices: 28867154--28867360 Score: 211
Period size: 27 Copynumber: 7.7 Consensus size: 27
28867144 TTAGTTTACC
28867154 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** ** *
28867181 AAATCAATAAAATACCTTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
28867208 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
28867235 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
28867262 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** *
28867289 AAATTACTAAAATA-CCCTTTTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
28867315 AAATTACCGAAATACCCCT-GTAGGGTA
1 AAATTACCAAAATACCCCTGGT-TTGTA
* *
28867342 GAATTACCGAAATACCCCT
1 AAATTACCAAAATACCCCT
28867361 ATAGGGTAGA
Statistics
Matches: 148, Mismatches: 30, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
26 22 0.15
27 126 0.85
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:28867219 original size:54 final size:54
Alignment explanation
Indices: 28867154--28867334 Score: 267
Period size: 54 Copynumber: 3.4 Consensus size: 54
28867144 TTAGTTTACC
* *
28867154 AAATTACCAAAATACCCCTGGTTTGTAAAATCAATAAAATACCTTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCTTTGGTTTATA
* * * *
28867208 AAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCTTTGGTTTATA
*
28867262 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTT--TTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATA-CCTTTGGTTTATA
*
28867315 AAATTACCGAAATACCCCTG
1 AAATTACCAAAATACCCCTG
28867335 TAGGGTAGAA
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
53 23 0.20
54 86 0.76
55 4 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCTTTGGTTTATA
Found at i:28867365 original size:27 final size:27
Alignment explanation
Indices: 28867316--28867691 Score: 466
Period size: 27 Copynumber: 14.3 Consensus size: 27
28867306 TTTTTTATAA
28867316 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28867343 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28867370 AATTATCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28867397 AA-T-------TACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28867416 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28867443 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28867470 AATTATCGCAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28867497 AATTACTGAAATACCCCTATATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28867524 AATTAACGAAATACCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28867551 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28867578 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28867605 AATTATCGCAATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
28867632 AATTACTAAAATACTCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28867659 AATTACC-AAGATA-CCTTGTGGGGTAA
1 AATTACCGAA-ATACCCCTGTAGGGTAG
28867685 AATTACC
1 AATTACC
28867692 ATTTTGCCCC
Statistics
Matches: 306, Mismatches: 34, Indels: 19
0.85 0.09 0.05
Matches are distributed among these distances:
19 16 0.05
20 1 0.00
26 18 0.06
27 271 0.89
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28869496 original size:40 final size:39
Alignment explanation
Indices: 28869432--28869643 Score: 264
Period size: 40 Copynumber: 5.3 Consensus size: 39
28869422 TCTTCGGAAT
* *
28869432 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
*
28869471 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
28869511 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
28869551 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
28869591 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
28869631 TTAGCCCGGATAT
1 TTAGCCCGGATAT
28869644 CATTCAAATG
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
39 10 0.07
40 131 0.89
41 7 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:28869559 original size:80 final size:80
Alignment explanation
Indices: 28869432--28869643 Score: 345
Period size: 80 Copynumber: 2.7 Consensus size: 80
28869422 TCTTCGGAAT
* * * * *
28869432 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
28869496 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
28869511 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
28869576 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
28869591 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
28869644 CATTCAAATG
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
79 4 0.03
80 118 0.97
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:28871442 original size:21 final size:21
Alignment explanation
Indices: 28871398--28871458 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
28871388 TAAAAGCCTT
*
28871398 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTG-CAAC
28871420 CT-ATATATGGCTCTGTGCAAC
1 CTGAT-TATGGCTCTGTGCAAC
*
28871441 CTGATTATGGCTGTGTGC
1 CTGATTATGGCTCTGTGC
28871459 CAAACGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (21 bp):
CTGATTATGGCTCTGTGCAAC
Found at i:28871659 original size:27 final size:27
Alignment explanation
Indices: 28871627--28871748 Score: 165
Period size: 27 Copynumber: 4.5 Consensus size: 27
28871617 TAAGCAGCTT
* * *
28871627 TGCCACATTATCTGTTTCTGGTGGCTA
1 TGCCACAATATCTGTATCTGGTGGCTC
28871654 TGCCACAAATATCTGT-TCTGGTGGCTC
1 TGCCAC-AATATCTGTATCTGGTGGCTC
28871681 TGCCACAATATCTGTATCTGGTGGCTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
28871708 TGACACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
**
28871735 TGTTACAATATCTG
1 TGCCACAATATCTG
28871749 ATAACTGAGC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
26 9 0.10
27 70 0.80
28 8 0.09
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:28871936 original size:31 final size:31
Alignment explanation
Indices: 28871885--28872026 Score: 194
Period size: 31 Copynumber: 4.5 Consensus size: 31
28871875 TTGCATTCAC
* *
28871885 ATTCTGATTTTTTATTCTGTTACCTGATACTA
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
28871917 ATTCTGATTTTGATTCTGTTACCTGATATTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
28871948 ATTTTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
28871979 ATTCTGATTCTGATTCTGTCATCTGATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
28872010 ATTTTGATTTTGATTCT
1 ATTCTGATTTTGATTCT
28872027 AGTTCTGATA
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 91 0.93
32 7 0.07
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:28871948 original size:19 final size:19
Alignment explanation
Indices: 28871920--28871984 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 19
28871910 GATACTAATT
*
28871920 CTGATTTTGATTCTGTTAC
1 CTGATATTGATTCTGTTAC
28871939 CTGATATTGA---T-TT--
1 CTGATATTGATTCTGTTAC
*
28871952 -TGATTTTGATTCTGTTAC
1 CTGATATTGATTCTGTTAC
*
28871970 CTGATACTGATTCTG
1 CTGATATTGATTCTG
28871985 ATTCTGATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
12 8 0.23
15 3 0.09
16 3 0.09
19 21 0.60
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (19 bp):
CTGATATTGATTCTGTTAC
Found at i:28871979 original size:6 final size:6
Alignment explanation
Indices: 28871917--28872035 Score: 77
Period size: 6 Copynumber: 19.3 Consensus size: 6
28871907 CCTGATACTA
* * *
28871917 ATTCTG ATTTTG ATTCTG -TTACCTG ATAT-TG ATTTTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG AT-TCTG ATTCTG ATTCTG ATTCTG
* *
28871966 -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG -TCATCTG ATTCTG ATTTTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
28872016 ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
28872036 AATGTTTCTT
Statistics
Matches: 93, Mismatches: 7, Indels: 26
0.74 0.06 0.21
Matches are distributed among these distances:
5 7 0.08
6 71 0.76
7 11 0.12
8 3 0.03
9 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:28873779 original size:10 final size:10
Alignment explanation
Indices: 28873764--28873788 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28873754 TGGCTACTTC
28873764 GGGCCGAAAG
1 GGGCCGAAAG
28873774 GGGCCGAAAG
1 GGGCCGAAAG
28873784 GGGCC
1 GGGCC
28873789 ATGTGGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.52, T:0.00
Consensus pattern (10 bp):
GGGCCGAAAG
Found at i:28874029 original size:27 final size:27
Alignment explanation
Indices: 28873991--28874172 Score: 213
Period size: 27 Copynumber: 6.7 Consensus size: 27
28873981 TTACTTTACC
*
28873991 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * * *
28874018 AAA-TCCCTAAAATACCCTTGGTCTAAA
1 AAATTACC-AAAATACCCCTGGTTTATA
* *
28874045 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
28874072 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
28874099 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * * *
28874126 AAATTACTAAAATAACCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
28874153 AAATTACCAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
28874173 TAGGGTAGAA
Statistics
Matches: 125, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
26 3 0.02
27 120 0.96
28 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:28874184 original size:27 final size:27
Alignment explanation
Indices: 28874154--28874502 Score: 439
Period size: 27 Copynumber: 13.3 Consensus size: 27
28874144 TTGTTTATAA
*
28874154 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
28874181 AATTACTGGAATACCCATATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28874208 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28874235 AA-T-------TACCCCTGTAGCGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28874254 AATTACCGGAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28874281 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28874308 AATTATC-ACAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
28874335 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28874362 AATTAACGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28874389 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
28874416 AATTATTGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28874443 AATTACCGAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
28874470 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
28874496 AATTACC
1 AATTACC
28874503 ATTTTGCCCC
Statistics
Matches: 283, Mismatches: 29, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.06
20 1 0.00
26 17 0.06
27 247 0.87
28 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28874187 original size:54 final size:54
Alignment explanation
Indices: 28873991--28874172 Score: 274
Period size: 54 Copynumber: 3.4 Consensus size: 54
28873981 TTACTTTACC
** * *
28873991 AAATTACCAAAATACCCCTGGTTTGTAAAATCCCTAAAATACCCTTGGTCTAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * *
28874045 AAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * *
28874099 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATAACCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
28874153 AAATTACCAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
28874173 TAGGGTAGAA
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 115 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
Found at i:28874243 original size:19 final size:19
Alignment explanation
Indices: 28874219--28874260 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
28874209 ATTACCGAAA
*
28874219 TACCCCTGTAGGGTAGAAT
1 TACCCCTGTAGCGTAGAAT
28874238 TACCCCTGTAGCGTAGAAT
1 TACCCCTGTAGCGTAGAAT
28874257 TACC
1 TACC
28874261 GGAATACCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
TACCCCTGTAGCGTAGAAT
Found at i:28874981 original size:22 final size:22
Alignment explanation
Indices: 28874929--28874993 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28874919 TTAAAGTCTT
* *
28874929 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
28874951 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
28874973 CTGATTATGGCTGTGTACCAA
1 CTGATTATGGCTCTGTGCCAA
28874994 ACGTATTTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:28875182 original size:27 final size:27
Alignment explanation
Indices: 28875152--28875280 Score: 152
Period size: 27 Copynumber: 4.8 Consensus size: 27
28875142 ATTCTGTTAA
* * * *
28875152 GTGGCTTTGCCACATTAACTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
* *
28875179 GTGGCTATGCCACAAATATCT-AATCTG
1 GTGGCTCTGCCAC-AATATCTGTATCTG
28875206 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
*
28875233 GTGGCTCTGCCATAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
* **
28875260 GTGACTCTATCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
28875281 ATAATTGAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.08
27 76 0.86
28 5 0.06
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:28875484 original size:6 final size:6
Alignment explanation
Indices: 28875470--28875556 Score: 70
Period size: 6 Copynumber: 14.2 Consensus size: 6
28875460 GATTGTTACT
* * * *
28875470 TGATAC TGATTC TGATTT TGATTC TG-TTACC TGATAC TGATTC CGATTC
1 TGATTC TGATTC TGATTC TGATTC TGATT--C TGATTC TGATTC TGATTC
* *
28875519 TGATTC TG-TCACC TAATTC TGATTC TGATTC TGATTC T
1 TGATTC TGAT--TC TGATTC TGATTC TGATTC TGATTC T
28875557 AGTTTTGATA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
5 3 0.05
6 54 0.84
7 5 0.08
8 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (6 bp):
TGATTC
Found at i:28875505 original size:31 final size:31
Alignment explanation
Indices: 28875417--28875556 Score: 167
Period size: 31 Copynumber: 4.5 Consensus size: 31
28875407 TTGCTTTCAC
* *
28875417 ATTCTGATTTTTTATTCTGTTACCTCATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
* *
28875449 ATTCTAATTTTGA-T-TGTTACTTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
28875478 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * * *
28875509 ATTCCGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
28875540 ATTCTGATTCTGATTCT
1 ATTCTGATTTTGATTCT
28875557 AGTTTTGATA
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
29 25 0.27
30 2 0.02
31 61 0.65
32 6 0.06
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:28881171 original size:31 final size:31
Alignment explanation
Indices: 28881133--28881194 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
28881123 GGTCTTTCCT
*
28881133 AGTTAGAATATCCCTCTATCATAATTTAATA
1 AGTTAGAATATCACTCTATCATAATTTAATA
28881164 AGTTAGAATATCACTCTATCATAATTTAATA
1 AGTTAGAATATCACTCTATCATAATTTAATA
28881195 GCACAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (31 bp):
AGTTAGAATATCACTCTATCATAATTTAATA
Found at i:28881209 original size:31 final size:31
Alignment explanation
Indices: 28881139--28881202 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
28881129 TCCTAGTTAG
* * *
28881139 AATATCCCTCTATCATAATTTAATAAGTTAG
1 AATATCACTCTATCATAATTTAATAAGTCAC
28881170 AATATCACTCTATCATAATTTAAT-AG-CAC
1 AATATCACTCTATCATAATTTAATAAGTCAC
28881199 AATA
1 AATA
28881203 AATCACTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 2 0.07
31 23 0.77
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (31 bp):
AATATCACTCTATCATAATTTAATAAGTCAC
Found at i:28882034 original size:39 final size:40
Alignment explanation
Indices: 28881989--28882072 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
28881979 ACTTCATAAA
* *
28881989 ATCAACATGG-AAAGGAAAAATTAATT-CTAAATTTGCAAT
1 ATCAACATGGTAAA-GAAAAATCAATTCCGAAATTTGCAAT
* *
28882028 ATCAACATGGTAAAGAAAGATCAATTCCGAACTTTGCAAT
1 ATCAACATGGTAAAGAAAAATCAATTCCGAAATTTGCAAT
28882068 ATCAA
1 ATCAA
28882073 TATTGAGGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 20 0.51
40 19 0.49
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (40 bp):
ATCAACATGGTAAAGAAAAATCAATTCCGAAATTTGCAAT
Found at i:28882924 original size:46 final size:46
Alignment explanation
Indices: 28882865--28882957 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
28882855 TAGCCACATC
* *
28882865 ATTTTGAAAGAACAGTTTAGGCTTATGATTAAGAGCATCATCATTT
1 ATTTTGAAAGAACAGTTTAAGCTCATGATTAAGAGCATCATCATTT
* * * * * *
28882911 ATTTTGGATGAACAGTTTAAGCTCGTGCTTAGGAGCATCATCGTTT
1 ATTTTGAAAGAACAGTTTAAGCTCATGATTAAGAGCATCATCATTT
28882957 A
1 A
28882958 GGCTAAACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (46 bp):
ATTTTGAAAGAACAGTTTAAGCTCATGATTAAGAGCATCATCATTT
Found at i:28894129 original size:47 final size:47
Alignment explanation
Indices: 28894068--28894197 Score: 181
Period size: 47 Copynumber: 2.8 Consensus size: 47
28894058 GTGTGAATAA
* * * *
28894068 TACCTTGATTTGGCTACGGGCCATGTTGTAGGTA-TTCAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAG-GAGAAGT
** *
28894115 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCCAGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAGGAGAAGT
28894162 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
28894198 TATCAATTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 69 0.95
48 4 0.05
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAGGAGAAGT
Found at i:28896527 original size:41 final size:41
Alignment explanation
Indices: 28896498--28896588 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
28896488 GGCTTTATGC
28896498 CTAGCAGGCTTACTGCCGATGTATAAAATCAGACTTTGAGT
1 CTAGCAGGCTTACTGCCGATGTATAAAATCAGACTTTGAGT
28896539 CTAGCAGGCTTACTGCCGATGTATAAAATCAGACTTTGAGT
1 CTAGCAGGCTTACTGCCGATGTATAAAATCAGACTTTGAGT
28896580 CTAGCAGGC
1 CTAGCAGGC
28896589 CTCGTGCTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (41 bp):
CTAGCAGGCTTACTGCCGATGTATAAAATCAGACTTTGAGT
Found at i:28898694 original size:23 final size:23
Alignment explanation
Indices: 28898664--28898711 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28898654 AATGATGAAT
28898664 GATTGGTTTACTCAGTATATCCG
1 GATTGGTTTACTCAGTATATCCG
28898687 GATTGGTTTACTCAGTATATCCG
1 GATTGGTTTACTCAGTATATCCG
28898710 GA
1 GA
28898712 CTAACCCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (23 bp):
GATTGGTTTACTCAGTATATCCG
Found at i:28909078 original size:13 final size:14
Alignment explanation
Indices: 28909047--28909078 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28909037 ATTTTTAAAG
28909047 ACTTTTTATTTTCT
1 ACTTTTTATTTTCT
28909061 A-TTTTTATTTTC-
1 ACTTTTTATTTTCT
28909073 ACTTTT
1 ACTTTT
28909079 ATCTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.06
13 15 0.88
14 1 0.06
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (14 bp):
ACTTTTTATTTTCT
Found at i:28916798 original size:46 final size:46
Alignment explanation
Indices: 28916745--28916881 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
28916735 TATATATACA
* * * *
28916745 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
28916791 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
28916837 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
28916882 ATACATGTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:28916915 original size:47 final size:47
Alignment explanation
Indices: 28916855--28917143 Score: 355
Period size: 47 Copynumber: 6.1 Consensus size: 47
28916845 ACACATTTCG
* * * *
28916855 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACGTTTATCA
1 CATTGGCCATTCGGCCTTACCACATATATGCATGTTCACATTCATCA
* *
28916902 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACATATATGCATGTTCACATTCATCA
* * * *
28916949 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACATATATGCATGTTCACATTCATCA
* * * *
28916996 CATTGGCCATTCGGCCATATTACGCATATCTATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCC---TTAC-CACATATATGCATGTTCACATTCATCA
*
28917047 CATTGGCCATTCGGCCTTATCTA-ATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTA-CCACATATATGCATGTTCACATTCATCA
* * * *
28917094 CATTGGCCATTCGGCCTTATCACACATACGCGTGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACATATATGCATGTTCACATTCATCA
28917141 CAT
1 CAT
28917144 AAAATCCTAA
Statistics
Matches: 210, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
46 1 0.00
47 165 0.79
48 4 0.02
49 1 0.00
50 3 0.01
51 36 0.17
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTACCACATATATGCATGTTCACATTCATCA
Found at i:28917047 original size:145 final size:145
Alignment explanation
Indices: 28916881--28917143 Score: 472
Period size: 145 Copynumber: 1.8 Consensus size: 145
28916871 TTACCACATA
* * * *
28916881 TATACATGTTCACGTTTATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCA
1 TATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCTAATATATGCATGTTCACATTCA
*
28916946 TCACATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCACATTGGCCATTCGGC
66 TCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGC
28917011 CATATTACGCATATC
131 CATATTACGCATATC
28917026 TATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCTAATATATGCATGTTCACATTCA
1 TATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCTAATATATGCATGTTCACATTCA
*
28917091 TCACATTGGCCATTCGGCCTTATCACACATACGCGTGTTCACATTCATCACAT
66 TCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
28917144 AAAATCCTAA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 112 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.33
Consensus pattern (145 bp):
TATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCTAATATATGCATGTTCACATTCA
TCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGC
CATATTACGCATATC
Found at i:28917061 original size:98 final size:94
Alignment explanation
Indices: 28916855--28917143 Score: 357
Period size: 98 Copynumber: 3.0 Consensus size: 94
28916845 ACACATTTCG
* * * * * *
28916855 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACGTTTATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCAT
* * *
28916920 ATCTCATATATGCATGTTCACATTCATCA
66 ATCGCATATATACAGGTTCACATTCATCA
* * *
28916949 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCAT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCAT
28917014 ATTACGCATATCTATACAGGTTCACATTCATCA
66 A-T-CGCATA--TATACAGGTTCACATTCATCA
*
28917047 CATTGGCCATTCGGCCTTATCTA-ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCT
1 CATTGGCCATTCGGCCTTATC-ACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCA
* * **
28917111 TATCACACATACGC-GTGTTCACATTCATCA
65 TATCGCATATATACAG-GTTCACATTCATCA
28917141 CAT
1 CAT
28917144 AAAATCCTAA
Statistics
Matches: 169, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
93 1 0.01
94 77 0.46
95 1 0.01
96 9 0.05
97 1 0.01
98 80 0.47
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (94 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCAT
ATCGCATATATACAGGTTCACATTCATCA
Found at i:28920378 original size:40 final size:40
Alignment explanation
Indices: 28920334--28920605 Score: 472
Period size: 40 Copynumber: 6.8 Consensus size: 40
28920324 CCAGCATGAT
*
28920334 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28920374 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28920414 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28920454 TGCTCTTTGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28920494 TGATCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28920534 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28920574 TGCTCTTCGGGACTTAGCCCGGGTATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
28920606 CTCAATTCTC
Statistics
Matches: 221, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 221 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28922145 original size:46 final size:46
Alignment explanation
Indices: 28922092--28922228 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
28922082 TATATATACA
* * * *
28922092 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
28922138 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
28922184 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
28922229 ATACATGTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:28922265 original size:47 final size:47
Alignment explanation
Indices: 28922202--28922490 Score: 398
Period size: 47 Copynumber: 6.1 Consensus size: 47
28922192 ACACATTTCG
* * * *
28922202 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
28922249 CATTGGCCATTTGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
28922296 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
28922343 CATTGGCCATTCGGCCTTATTACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTA-T---CACATATATGCATGTTCACATTCATCA
*
28922394 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
28922441 CATTGGCCATTCGGCCTTATCACACATACGCGTGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
28922488 CAT
1 CAT
28922491 AAAATCCTAA
Statistics
Matches: 214, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
47 172 0.80
48 1 0.00
50 1 0.00
51 40 0.19
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:28922397 original size:145 final size:141
Alignment explanation
Indices: 28922202--28922490 Score: 479
Period size: 145 Copynumber: 2.0 Consensus size: 141
28922192 ACACATTTCG
* * *
28922202 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACGTTCATCACATTGGCCATTTGGCCTT
1 CATTAGCCATTCGGCCTTACCACATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTT
*
28922267 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCGCACATACGCATGTT
66 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
28922332 CACATTCATCA
131 CACATTCATCA
* *
28922343 CATTGGCCATTCGGCCTTATTACGCATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
1 CATTAGCCATTCGGCC---TTAC-CACATATATACAGGTTCACATTCATCACATTGGCCATTCGG
*
28922408 CCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCG
62 CCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
28922473 TGTTCACATTCATCA
127 TGTTCACATTCATCA
28922488 CAT
1 CAT
28922491 AAAATCCTAA
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
141 15 0.11
144 4 0.03
145 118 0.86
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (141 bp):
CATTAGCCATTCGGCCTTACCACATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
CACATTCATCA
Found at i:28922408 original size:98 final size:95
Alignment explanation
Indices: 28922202--28922490 Score: 377
Period size: 98 Copynumber: 3.0 Consensus size: 95
28922192 ACACATTTCG
* * * * *
28922202 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACGTTCATCACATTGGCCATTTGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
28922267 A-TCTCATATATGCATGTTCACATTCATCA
66 ATTCGCATATATACAGGTTCACATTCATCA
* * *
28922296 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
28922361 ATTACGCATATATATACAGGTTCACATTCATCA
66 ATT-CGC--ATATATACAGGTTCACATTCATCA
*
28922394 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * **
28922459 A-TCACACATACGC-GTGTTCACATTCATCA
66 ATTCGCATATATACAG-GTTCACATTCATCA
28922488 CAT
1 CAT
28922491 AAAATCCTAA
Statistics
Matches: 172, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
93 1 0.01
94 80 0.47
95 1 0.01
96 4 0.02
97 1 0.01
98 85 0.49
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (95 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATTCGCATATATACAGGTTCACATTCATCA
Found at i:28927083 original size:31 final size:31
Alignment explanation
Indices: 28927043--28927126 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
28927033 TTTGGGCCAT
*
28927043 GTAGGCCACACAGGCGTGTGGGTCGACACGG
1 GTAGCCCACACAGGCGTGTGGGTCGACACGG
* *
28927074 GTAGCCCACATAGGCATGTGGGTCGACACGG
1 GTAGCCCACACAGGCGTGTGGGTCGACACGG
* *
28927105 GTAGTCCACACGGGCGTGTGGG
1 GTAGCCCACACAGGCGTGTGGG
28927127 ATTTTGGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.19, C:0.25, G:0.40, T:0.15
Consensus pattern (31 bp):
GTAGCCCACACAGGCGTGTGGGTCGACACGG
Found at i:28927215 original size:31 final size:31
Alignment explanation
Indices: 28927180--28927241 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
28927170 GGGCAGTATG
28927180 AGCCACACGAGCGTGTGAGCCCACACGGGCA
1 AGCCACACGAGCGTGTGAGCCCACACGGGCA
* * * *
28927211 AGCCACATGGGTGTGTGGGCCCACACGGGCA
1 AGCCACACGAGCGTGTGAGCCCACACGGGCA
28927242 GGGAGCCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.35, T:0.10
Consensus pattern (31 bp):
AGCCACACGAGCGTGTGAGCCCACACGGGCA
Found at i:28931613 original size:6 final size:6
Alignment explanation
Indices: 28931602--28931630 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28931592 ATGTGCCGAC
28931602 TACTGT TACTGT TACTGT TACTGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTG
28931631 ATTCGACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:28931665 original size:51 final size:45
Alignment explanation
Indices: 28931608--28931712 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
28931598 CGACTACTGT
** *
28931608 TACTGTTACTGTTACTGTTA-CTGATTCGACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACCATTATC-GATTCAACACTTTGTGTGTCGAA
*
28931653 TACTGTTACTGTTACCATTATCGATTCAACACTTTGTGTGTTGAA
1 TACTGTTACTGTTACCATTATCGATTCAACACTTTGTGTGTCGAA
*
28931698 TACTGTTACTATTAC
1 TACTGTTACTGTTAC
28931713 AGATTTGTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 53 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACCATTATCGATTCAACACTTTGTGTGTCGAA
Found at i:28931953 original size:72 final size:73
Alignment explanation
Indices: 28931816--28932101 Score: 210
Period size: 72 Copynumber: 3.8 Consensus size: 73
28931806 AAAGGTATAA
* * * *
28931816 AATAACTGATTATTACTGAATAATTGA-CTGTTACCGAATAATTGACTGTTACT-AGAT-AATAG
1 AATAACTGAATATTACTGAATAATTGATC-ATTACTGAATAATTGATTGTTACTGA-ATAAATAG
*
28931878 ACTGTTACTG
64 ACTGCTACTG
* *
28931888 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGATTGTCACTGAATAAAT-GAC
1 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAATTGATTGTTACTGAATAAATAGAC
*
28931952 TGCTATTG
66 TGCTACTG
* * * *
28931960 AATAACTTAAT-TGCTACTGAAT-ATCTGAT-TTTACTAAATAATTGATTGTTACTGGATAACCG
1 AATAACTGAATAT--TACTGAATAAT-TGATCATTACTGAATAATTGATTGTTACTGAATAA---
*
28932022 ATCAATTGA-TCGATACTG
60 AT--A--GACT-GCTACTG
** * ** * * *
28932040 AATAACTGGTTATTATTGAATAATTGATTGTTACCGAATAAGTGACTGTTACTGAATAAATA
1 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAATTGATTGTTACTGAATAAATA
28932102 ATTGTTCTAA
Statistics
Matches: 170, Mismatches: 26, Indels: 33
0.74 0.11 0.14
Matches are distributed among these distances:
71 1 0.01
72 93 0.55
73 17 0.10
75 3 0.02
77 2 0.01
79 12 0.07
80 41 0.24
81 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (73 bp):
AATAACTGAATATTACTGAATAATTGATCATTACTGAATAATTGATTGTTACTGAATAAATAGAC
TGCTACTG
Found at i:28932107 original size:18 final size:18
Alignment explanation
Indices: 28931816--28932098 Score: 167
Period size: 18 Copynumber: 15.3 Consensus size: 18
28931806 AAAGGTATAA
*
28931816 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* * *
28931834 AATAATTGACTGTTACCG
1 AATAACTGATTGTTACTG
* *
28931852 AATAATTGACTGTTACT-
1 AATAACTGATTGTTACTG
*
28931869 AGATAA-TAGACTGTTACTG
1 A-ATAACT-GATTGTTACTG
* *
28931888 AATAACTGAATATTACTG
1 AATAACTGATTGTTACTG
* **
28931906 AATAATTGATCATTACTG
1 AATAACTGATTGTTACTG
*
28931924 AATAACTGATTGTCACTG
1 AATAACTGATTGTTACTG
* * * *
28931942 AATAAATGACTGCTATTG
1 AATAACTGATTGTTACTG
* *
28931960 AATAACTTAATTGCTACTG
1 AATAAC-TGATTGTTACTG
* *
28931979 AATATCTGATT-TTACTA
1 AATAACTGATTGTTACTG
*
28931996 AATAATTGATTGTTACTG
1 AATAACTGATTGTTACTG
* *
28932014 GATAACCGATCAATTGATCGATACTG
1 AATAA-C--T-GATTG-T---TACTG
* * *
28932040 AATAACTGGTTATTATTG
1 AATAACTGATTGTTACTG
* *
28932058 AATAATTGATTGTTACCG
1 AATAACTGATTGTTACTG
* *
28932076 AATAAGTGACTGTTACTG
1 AATAACTGATTGTTACTG
28932094 AATAA
1 AATAA
28932099 ATAATTGTTC
Statistics
Matches: 205, Mismatches: 46, Indels: 28
0.73 0.16 0.10
Matches are distributed among these distances:
17 15 0.07
18 154 0.75
19 16 0.08
21 2 0.01
22 6 0.03
23 2 0.01
25 1 0.00
26 9 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:28937142 original size:18 final size:19
Alignment explanation
Indices: 28937115--28937162 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
28937105 TTATTTTTTT
28937115 AAAA-ATAAAAATTA-TGA
1 AAAATATAAAAATTATTGA
*
28937132 AAAATATAAAAATTATTTA
1 AAAATATAAAAATTATTGA
28937151 AAAATATAAAAA
1 AAAATATAAAAA
28937163 ATTCCAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
19 14 0.50
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATATAAAAATTATTGA
Found at i:28937628 original size:17 final size:17
Alignment explanation
Indices: 28937580--28937630 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
28937570 AAATTTAAAA
28937580 AATTATTTTTTATTTTTG
1 AATT-TTTTTTATTTTTG
****
28937598 AATTTTAAACATTTTTG
1 AATTTTTTTTATTTTTG
28937615 AATTTTTTTTATTTTT
1 AATTTTTTTTATTTTT
28937631 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (17 bp):
AATTTTTTTTATTTTTG
Found at i:28996513 original size:106 final size:109
Alignment explanation
Indices: 28996385--28996589 Score: 283
Period size: 106 Copynumber: 1.9 Consensus size: 109
28996375 TTTTTATTGT
* * *
28996385 AATTTTTATGTTGCTTTTAATTTATTTTAAAGCTATTTTGTTAGTAA-CT-ATTA-TAAATTGTT
1 AATTTTTATGTTGCTTTTAATTTATTTTAAAGCTATTTTGTTAGTAATATGATTAGTAAAGTATT
28996447 TGTTTAATTTAATGTTTATTGTGATTTGTTAAGTTATGAATGTA
66 TGTTTAATTTAATGTTTATTGTGATTTGTTAAGTTATGAATGTA
* * *
28996491 AATTTTTATGTT-TTTTTAAATTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTAAG
1 AATTTTTATGTTGCTTTT-AATTTATTTTAAAGCTATTTTGTTAGTAA--TATGATTA-GTAAAG
*
28996555 TATTTGTTTAGTTTAATGTTTATTGTGATTTGTTA
62 TATTTGTTTAATTTAATGTTTATTGTGATTTGTTA
28996590 TGAATGTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
105 4 0.05
106 40 0.47
109 1 0.01
110 4 0.05
112 36 0.42
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (109 bp):
AATTTTTATGTTGCTTTTAATTTATTTTAAAGCTATTTTGTTAGTAATATGATTAGTAAAGTATT
TGTTTAATTTAATGTTTATTGTGATTTGTTAAGTTATGAATGTA
Found at i:28996601 original size:106 final size:103
Alignment explanation
Indices: 28996382--28996623 Score: 267
Period size: 106 Copynumber: 2.3 Consensus size: 103
28996372 TAGTTTTTAT
* * *
28996382 TGTAATTTTTATGTTGCTTTTAATTTATTTTAAAGCTATTTTGTTAGTAACTATTATAAATTGTT
1 TGTAATTTTTATGTTGCTTTTAATTTATTTTAAAGCTATTTTGTTAGTAAATATTATAAAGTATT
28996447 TGTTTAATTTAATGTTTATTGTGATTTGTTAAGTTATGAA
66 TGTTTAATTTAATGTTTATTGTGA-TTGTT-AGTTATGAA
* *
28996487 TGTAAATTTTTATGTT-TTTTTAAATTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGT
1 TGT-AATTTTTATGTTGCTTTT-AATTTATTTTAAAGCTATTTTGTTAGTAA---AT-ATTA--T
* *
28996551 TAAGTATTTGTTTAGTTTAATGTTTATTGTGA-T-TT-GTTATGAA
58 AAAGTATTTGTTTAATTTAATGTTTATTGTGATTGTTAGTTATGAA
* * * *
28996594 TGTAATTTTTTTTTTGTTTTTGATTTATTT
1 TGTAATTTTTATGTTGCTTTTAATTTATTT
28996624 GACAATTTTT
Statistics
Matches: 118, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
105 7 0.06
106 58 0.49
107 16 0.14
109 3 0.03
110 5 0.04
112 29 0.25
ACGTcount: A:0.26, C:0.01, G:0.14, T:0.60
Consensus pattern (103 bp):
TGTAATTTTTATGTTGCTTTTAATTTATTTTAAAGCTATTTTGTTAGTAAATATTATAAAGTATT
TGTTTAATTTAATGTTTATTGTGATTGTTAGTTATGAA
Found at i:28997579 original size:21 final size:22
Alignment explanation
Indices: 28997537--28997580 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28997527 TGTGTACAAT
* * *
28997537 AAAAATGAATAAATTTGTGTTA
1 AAAAATGAACAAAATAGTGTTA
28997559 AAAAATGAACAAAATAG-GTTA
1 AAAAATGAACAAAATAGTGTTA
28997580 A
1 A
28997581 TGAGGTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAAATGAACAAAATAGTGTTA
Found at i:29002607 original size:16 final size:16
Alignment explanation
Indices: 29002573--29002609 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29002563 AATTTTTTTG
29002573 AAAA-TAATGAAATAA
1 AAAATTAATGAAATAA
29002588 AAAATTAAT-AAATAA
1 AAAATTAATGAAATAA
29002603 TAAAATT
1 -AAAATT
29002610 GTATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATTAATGAAATAA
Found at i:29007297 original size:103 final size:103
Alignment explanation
Indices: 29007102--29007323 Score: 367
Period size: 103 Copynumber: 2.2 Consensus size: 103
29007092 TGTATATAAA
** * *
29007102 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
29007167 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
29007205 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
29007269 TTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29007308 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
29007324 GATATCCATT
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
103 69 0.62
104 42 0.38
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:29007344 original size:71 final size:71
Alignment explanation
Indices: 29007243--29007393 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 71
29007233 TCATTGGTGG
* *
29007243 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
29007307 GAGGGGT
65 GAGGGGT
***
29007314 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29007379 AGGGGT
66 AGGGGT
29007385 TGCTAAGTG
1 TGCTAAGTG
29007394 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 3 0.04
71 71 0.96
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:29014284 original size:29 final size:29
Alignment explanation
Indices: 29014239--29014297 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
29014229 ATTTCCGAGC
29014239 TTGGGGACAAAAGTGTAATTATGCAAAAGT
1 TTGGGGACAAAAGTGTAATT-TGCAAAAGT
* *
29014269 TTGGGG-CAAAATTGTAATTTTCAAAAGT
1 TTGGGGACAAAAGTGTAATTTGCAAAAGT
29014297 T
1 T
29014298 GGGTGGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 12 0.44
30 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (29 bp):
TTGGGGACAAAAGTGTAATTTGCAAAAGT
Found at i:29014742 original size:25 final size:26
Alignment explanation
Indices: 29014699--29014749 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
29014689 GAAATGTGAA
*
29014699 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
29014725 AGGGGTT-CTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
29014750 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:29014761 original size:101 final size:103
Alignment explanation
Indices: 29014635--29014842 Score: 350
Period size: 101 Copynumber: 2.0 Consensus size: 103
29014625 GGGGTGCTGT
* *
29014635 GTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTTGAAATGTGAA
29014699 AGGGGTTGCTATGTGCTGATT-CCCCGAGGGGTT-CTAA
65 AGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* *
29014736 GTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA
1 GTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA
29014801 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
29014839 GTGC
1 GTGC
29014843 GATATCCATT
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
101 79 0.79
102 13 0.13
103 8 0.08
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.32
Consensus pattern (103 bp):
GTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA
GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:29014894 original size:70 final size:71
Alignment explanation
Indices: 29014762--29014911 Score: 248
Period size: 70 Copynumber: 2.1 Consensus size: 71
29014752 TCATTGGTGG
* *
29014762 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGTTGCTATGTGCTGATTCCCCCG
29014827 AGGGGT
66 AGGGGT
***
29014833 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGTTGCTATGTGCTGATTCCCCCG
29014897 AGGGGT
66 AGGGGT
29014903 TGCTAAGTG
1 TGCTAAGTG
29014912 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.59
71 30 0.41
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:29014916 original size:27 final size:27
Alignment explanation
Indices: 29014870--29014921 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
29014860 TGAAATGAAA
* *
29014870 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGATGATTCCCCCG
29014897 AGGGGTTGCTAAGTGATGATTCCCC
1 AGGGGTTGCTAAGTGATGATTCCCC
29014922 GATTCAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGATGATTCCCCCG
Found at i:29018870 original size:43 final size:42
Alignment explanation
Indices: 29018812--29018921 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
29018802 AAATGCCAAC
* * * * * *
29018812 GTCCTAGACGTGGTCTTACATGTAATCAAATATTGATGCCGCT
1 GTCCCAGACATGGTCTTACACGTAATCAAATA-CGATACCGAT
*
29018855 GTCCCAGACATGGTCTTACACGAAATCAAATACGATACCGAT
1 GTCCCAGACATGGTCTTACACGTAATCAAATACGATACCGAT
* *
29018897 GTCTCAGATATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACACGTAA
29018922 ATCTCAAATC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 29 0.51
43 28 0.49
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAATCAAATACGATACCGAT
Found at i:29018924 original size:43 final size:44
Alignment explanation
Indices: 29018812--29018924 Score: 133
Period size: 43 Copynumber: 2.6 Consensus size: 44
29018802 AAATGCCAAC
* * * * * *
29018812 GTCCTAGACGTGGTCTTACATGT-AATCAAATATTGATGCCGCT
1 GTCCCAGACATGGTCTTACACGTAAATCAAATATCGATACCGAT
29018855 GTCCCAGACATGGTCTTACACG-AAATCAAATA-CGATACCGAT
1 GTCCCAGACATGGTCTTACACGTAAATCAAATATCGATACCGAT
* *
29018897 GTCTCAGATATGGTCTTACACGTAAATC
1 GTCCCAGACATGGTCTTACACGTAAATC
29018925 TCAAATCGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 27 0.45
43 33 0.55
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
GTCCCAGACATGGTCTTACACGTAAATCAAATATCGATACCGAT
Found at i:29026162 original size:42 final size:41
Alignment explanation
Indices: 29026066--29026222 Score: 163
Period size: 43 Copynumber: 3.7 Consensus size: 41
29026056 TACAATACCA
* ** * *
29026066 ATGTCCCAGACGTGGTCTTACACGTAATCAAATATCAATGCC
1 ATGTCCCAGACATGGTCTTACACAAAATTAAATA-CGATGCC
29026108 ATTGTCCCAGACATGGTCTTACACAAAATTAAATACGATGCC
1 A-TGTCCCAGACATGGTCTTACACAAAATTAAATACGATGCC
29026150 GATGTCCCAGACATGGTCTTACACATAAATCTCAAAT-CGATGCC
1 -ATGTCCCAGACATGGTCTTACACA-AAAT-T-AAATACGATGCC
** * *
29026194 AACATCCCAGACACGATCTTACACAAAAT
1 -ATGTCCCAGACATGGTCTTACACAAAAT
29026223 CACACATCAA
Statistics
Matches: 100, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
42 30 0.30
43 38 0.38
44 28 0.28
45 4 0.04
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (41 bp):
ATGTCCCAGACATGGTCTTACACAAAATTAAATACGATGCC
Found at i:29026216 original size:86 final size:85
Alignment explanation
Indices: 29026066--29026222 Score: 208
Period size: 86 Copynumber: 1.8 Consensus size: 85
29026056 TACAATACCA
* * *** * *
29026066 ATGTCCCAGACGTGGTCTTACACGTAATCAAATATCAATGCCATTGTCCCAGACATGGTCTTACA
1 ATGTCCCAGACATGGTCTTACACATAATCAAATATCAATGCCAACATCCCAGACACGATCTTACA
29026131 CAAAATTAAATACGATGCCG
66 CAAAATTAAATACGATGCCG
* *
29026151 ATGTCCCAGACATGGTCTTACACATAAATCTCAA-ATCGATGCCAACATCCCAGACACGATCTTA
1 ATGTCCCAGACATGGTCTTACACAT-AATC-AAATATCAATGCCAACATCCCAGACACGATCTTA
29026215 CACAAAAT
64 CACAAAAT
29026223 CACACATCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 23 0.38
86 36 0.59
87 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (85 bp):
ATGTCCCAGACATGGTCTTACACATAATCAAATATCAATGCCAACATCCCAGACACGATCTTACA
CAAAATTAAATACGATGCCG
Found at i:29038770 original size:73 final size:73
Alignment explanation
Indices: 29038600--29038758 Score: 255
Period size: 73 Copynumber: 2.2 Consensus size: 73
29038590 GCATCTAGGG
** * *
29038600 ACACGCCCGTGTCCTGTGGCCGTGGGAATTAAATTCCAAATTTGAACCTACAGGAGTTTTCACAC
1 ACACGCCCGTGTCCCATGCCCGTGTGAATTAAATTCCAAATTTGAACCTACAGGAGTTTTCACAC
*
29038665 TGCCTGAC
66 GGCCTGAC
*
29038673 ACACGCCCGTGTCCCATGCCCGTGTGAATTAAATTCTAAATTTGAACCTACAGGAGTTTTCACAC
1 ACACGCCCGTGTCCCATGCCCGTGTGAATTAAATTCCAAATTTGAACCTACAGGAGTTTTCACAC
29038738 GGCCTGAC
66 GGCCTGAC
*
29038746 ACACGTCCGTGTC
1 ACACGCCCGTGTC
29038759 TATTGCCCGT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (73 bp):
ACACGCCCGTGTCCCATGCCCGTGTGAATTAAATTCCAAATTTGAACCTACAGGAGTTTTCACAC
GGCCTGAC
Found at i:29048904 original size:47 final size:45
Alignment explanation
Indices: 29048778--29048909 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 45
29048768 CACCAAATTT
*
29048778 GTGAATAGTGTCACAATAATGCAGATAAACTGCCACATAATAAATT
1 GTGAATAGTGTCAC-ATAATGCAGATAAACTGCCACATAATAAATC
* *
29048824 GTTGACA-A--GTCACCAAAATCGCAGATATACTGCCACATAATCAAATC
1 G-TGA-ATAGTGTCA-CATAAT-GCAGATAAACTGCCACATAAT-AAATC
29048871 GTGAATAGTGTCACATTAATGCAGATAAACTGCCACATA
1 GTGAATAGTGTCACA-TAATGCAGATAAACTGCCACATA
29048910 TTTCCACCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
45 9 0.12
46 26 0.36
47 29 0.40
48 8 0.11
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (45 bp):
GTGAATAGTGTCACATAATGCAGATAAACTGCCACATAATAAATC
Found at i:29056210 original size:39 final size:39
Alignment explanation
Indices: 29056143--29056473 Score: 510
Period size: 38 Copynumber: 8.5 Consensus size: 39
29056133 ACAAAGCATG
* * * *
29056143 CGGGACTTTAAGCCCAGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
29056183 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
29056223 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * * *
29056262 CGGGACTTAGCCCGGATAT-ACATCATCACAAATACCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
29056300 CGGGACTTAGCCCGGATAT-ACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
29056338 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
29056377 CGGGACTTAGCCCGGATAT-ACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
29056415 CAGGACTTAGCCCGGATAT-ACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
29056453 CGGGACTTAGCCCAGATATAA
1 CGGGACTTAGCCCGGATATAA
29056474 TTCTCCATTA
Statistics
Matches: 273, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
38 141 0.52
39 111 0.41
40 21 0.08
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:29056333 original size:115 final size:115
Alignment explanation
Indices: 29056143--29056473 Score: 520
Period size: 115 Copynumber: 2.8 Consensus size: 115
29056133 ACAAAGCATG
* * * *
29056143 CGGGACTTTAAGCCCAGATATAATACCAGCACAAA-GCCTGCGGGACTTTAGCCCGGATATAACA
1 CGGGAC-TT-AGCCCGGATAT-ACACCAGCACAAATACCTTCGGGAC-TTAGCCCGGATAT-ACA
29056207 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
61 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
29056262 CGGGACTTAGCCCGGATATACATCATCACAAATACCTTCGGGACTTAGCCCGGATATACACCAGC
1 CGGGACTTAGCCCGGATATACACCAGCACAAATACCTTCGGGACTTAGCCCGGATATACACCAGC
29056327 ACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
66 ACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
29056377 CGGGACTTAGCCCGGATATACACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATACACCAGC
1 CGGGACTTAGCCCGGATATACACCAGCACAAATACCTTCGGGACTTAGCCCGGATATACACCAGC
*
29056442 ACGAATGCCTTCGGGACTTAGCCCAGATATAA
66 ACGAATGCCTTCGGGACTTAGCCCGGATATAA
29056474 TTCTCCATTA
Statistics
Matches: 199, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
115 149 0.75
116 23 0.12
117 19 0.10
118 2 0.01
119 6 0.03
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (115 bp):
CGGGACTTAGCCCGGATATACACCAGCACAAATACCTTCGGGACTTAGCCCGGATATACACCAGC
ACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:29063562 original size:15 final size:15
Alignment explanation
Indices: 29063542--29063571 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29063532 TTCATATGGC
29063542 AATTTAGCCATAATT
1 AATTTAGCCATAATT
29063557 AATTTAGCCATAATT
1 AATTTAGCCATAATT
29063572 GTAATAGTGA
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:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
AATTTAGCCATAATT
Found at i:29064411 original size:30 final size:29
Alignment explanation
Indices: 29064371--29064427 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
29064361 ATTGGGTGAG
*
29064371 AAAAATGATATATGAAATGGTTGTATGGA
1 AAAAATGATATATGAAATGGTTATATGGA
*
29064400 AAAATATGATATATGTAATGGTTATATG
1 AAAA-ATGATATATGAAATGGTTATATG
29064428 AATCAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (29 bp):
AAAAATGATATATGAAATGGTTATATGGA
Found at i:29067793 original size:17 final size:18
Alignment explanation
Indices: 29067754--29067800 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
29067744 TTTCTCAAAA
29067754 TATT-AATT-AATTAATT
1 TATTCAATTAAATTAATT
*
29067770 TATTCAATTAAATTATTT
1 TATTCAATTAAATTAATT
*
29067788 TA-TCAACTAAATT
1 TATTCAATTAAATT
29067801 CTAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 14 0.52
18 9 0.33
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTCAATTAAATTAATT
Found at i:29073552 original size:50 final size:49
Alignment explanation
Indices: 29073495--29073669 Score: 221
Period size: 50 Copynumber: 3.6 Consensus size: 49
29073485 GATATGTGTC
* * *
29073495 AGTGTAAGACCATGTTTGGGACATGGCATCG-GTATCGACAGGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACT-TCGA-ATGTGAGAGCT
* *
29073545 AGTGTAAGACCATGTCTGGGACATGGAATCGACTTCGATATATGAGAG-T
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGA-ATGTGAGAGCT
* * *
29073594 CAGTGTAAGACAATGTCTGGGACATGGCATCGACTTTG-ATGTGTGAGCT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGAATGTGAGAGCT
29073643 AGTGTAAGACCATGTCTGGGACATGGC
1 AGTGTAAGACCATGTCTGGGACATGGC
29073670 GTCGGTATCT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
48 33 0.30
49 2 0.02
50 74 0.67
51 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGAATGTGAGAGCT
Found at i:29083068 original size:5 final size:5
Alignment explanation
Indices: 29083058--29083082 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29083048 AATTGCTCCC
29083058 CTCTT CTCTT CTCTT CTCTT CTCTT
1 CTCTT CTCTT CTCTT CTCTT CTCTT
29083083 ATTTCCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTCTT
Found at i:29083980 original size:19 final size:19
Alignment explanation
Indices: 29083956--29083993 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29083946 TGGGCCACGA
29083956 TGGGCCAAAATGGGC-CGTG
1 TGGGCC-AAATGGGCTCGTG
*
29083975 TGGGCCCAATGGGCTCGTG
1 TGGGCCAAATGGGCTCGTG
29083994 AGCCCCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (19 bp):
TGGGCCAAATGGGCTCGTG
Found at i:29095490 original size:33 final size:33
Alignment explanation
Indices: 29095453--29095532 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
29095443 GAATGCCCTA
* * * *
29095453 TTAAAATTAAGGCTCACCTATCCTTTTAGCCTC
1 TTAAAACTAAGGCTCACCCATCATTGTAGCCTC
* *
29095486 TTAAAGCTAAGGCTGACCCATCATTGTAGCCTC
1 TTAAAACTAAGGCTCACCCATCATTGTAGCCTC
* *
29095519 TTAAATCCAAGGCT
1 TTAAAACTAAGGCT
29095533 TGTCTTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (33 bp):
TTAAAACTAAGGCTCACCCATCATTGTAGCCTC
Found at i:29096735 original size:42 final size:42
Alignment explanation
Indices: 29096688--29096772 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
29096678 GTTTAGTGAC
29096688 TAAATTTTACAAAAGTTAAAATGTTAGGGGTAAATTCATAAT
1 TAAATTTTACAAAAGTTAAAATGTTAGGGGTAAATTCATAAT
29096730 TAAATTTTACAAAAGTTAAAATGTTAGGGGTAAATTCATAAT
1 TAAATTTTACAAAAGTTAAAATGTTAGGGGTAAATTCATAAT
29096772 T
1 T
29096773 TGACATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (42 bp):
TAAATTTTACAAAAGTTAAAATGTTAGGGGTAAATTCATAAT
Found at i:29110085 original size:40 final size:40
Alignment explanation
Indices: 29110041--29110261 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
29110031 AAGTGAATAT
* * * * *
29110041 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAA
29110081 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
29110121 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* *
29110161 ATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* * *
29110201 ATCCGGGTTATGT-CCGAAGGCATT-GTGTGAGTTA-CAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* *
29110238 A-CCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
29110262 TGAACGAGGA
Statistics
Matches: 166, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
36 10 0.06
37 14 0.08
38 8 0.05
39 11 0.07
40 123 0.74
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
Found at i:29110281 original size:76 final size:79
Alignment explanation
Indices: 29110041--29110295 Score: 216
Period size: 80 Copynumber: 3.3 Consensus size: 79
29110031 AAGTGAATAT
* * * * * *
29110041 ATCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATA-CTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCGAAGGCATTCGTGCGAGTTATC-AAATCCGGGCTAAGTCCCGAAGGCAG
** * *
29110105 TCGTGCGAGTTA-TTAA
64 TCGAACGAG-GAGCTAA
* *
29110121 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATCAAATCCGGGCTAAGTCCCGAAGGCAGT
** ** *
29110186 CGTGCGAGTTGTTAA
65 CGAACGAGGAGCTAA
* * * * *
29110201 ATCCGGGTTATGTCCGAAGGCATT-GTGTGAGTTA-CAAA-CCGGGCTATGTCCCGAAGGCATTT
1 ATCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATCAAATCCGGGCTAAGTCCCGAAGGCAGTC
*
29110263 GAACGAGGAGCTAT
66 GAACGAGGAGCTAA
*
29110277 ATCC-GGTTAAATCCGAAGG
1 ATCCGGGTTAAGTCCGAAGG
29110296 TAGTGATTTG
Statistics
Matches: 150, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
75 13 0.09
76 32 0.21
77 3 0.02
78 9 0.06
79 13 0.09
80 80 0.53
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (79 bp):
ATCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATCAAATCCGGGCTAAGTCCCGAAGGCAGTC
GAACGAGGAGCTAA
Found at i:29113837 original size:54 final size:56
Alignment explanation
Indices: 29113755--29113872 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 56
29113745 ACAAGGGATG
29113755 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAA-AAT-AAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
29113809 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
29113865 ATGGGCAA
1 ATGGGCAA
29113873 TAAACTAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 40 0.65
55 3 0.05
56 19 0.31
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:29115059 original size:34 final size:36
Alignment explanation
Indices: 29115011--29115141 Score: 160
Period size: 34 Copynumber: 3.6 Consensus size: 36
29115001 GATATAGATC
*
29115011 CGAAGGC-TTGTGCGAGATACTAAATCCGGGTAAGT
1 CGAAGGCATTGTGCGAGTTACTAAATCCGGGTAAGT
* *
29115046 -GAAGGCATT-TGCGAGTTATTAAATCCGGTTAAGT
1 CGAAGGCATTGTGCGAGTTACTAAATCCGGGTAAGT
29115080 CCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGT
1 --CGAAGGCATTGTGCGAGTTACTAAATCCGGG-TAAGT
*
29115119 CCCGAAGGCATTGTGTGAGTTAC
1 --CGAAGGCATTGTGCGAGTTAC
29115142 ATATAACCGG
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
34 28 0.33
35 2 0.02
37 9 0.11
38 18 0.21
39 27 0.32
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (36 bp):
CGAAGGCATTGTGCGAGTTACTAAATCCGGGTAAGT
Found at i:29115126 original size:39 final size:39
Alignment explanation
Indices: 29115010--29115170 Score: 203
Period size: 39 Copynumber: 4.3 Consensus size: 39
29115000 GGATATAGAT
*
29115010 CCGAAGGC-TTGTGCGAGATACTAAATCCGGG-TAAGT-
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTC
*
29115046 --GAAGGCATT-TGCGAGTTATTAAATCC-GGTTAAGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTC
29115081 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
29115120 CCGAAGGCATTGTGTGAGTTACATATAA-CCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTAC-TA-AATCCGGGTTAAGTC
29115160 CCGAAGGCATT
1 CCGAAGGCATT
29115171 TGAACGAGAG
Statistics
Matches: 110, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
33 2 0.02
34 26 0.24
35 2 0.02
37 9 0.08
38 16 0.15
39 30 0.27
40 23 0.21
41 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:29119819 original size:27 final size:26
Alignment explanation
Indices: 29119763--29119829 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
29119753 CAAGCTAATG
*
29119763 GGGTATTCTTGTAAATTTGAAATTCAA
1 GGGTATTTTTGTAAATTTGAAATT-AA
*
29119790 GGGTATTTTTGTAATTATTGTAAATT-A
1 GGGTATTTTTGTAAAT-TTG-AAATTAA
* *
29119817 GGGTCTTTCTGTA
1 GGGTATTTTTGTA
29119830 TTTTCCCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 26 0.76
28 3 0.09
29 5 0.15
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (26 bp):
GGGTATTTTTGTAAATTTGAAATTAA
Found at i:29119867 original size:28 final size:28
Alignment explanation
Indices: 29119829--29119889 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
29119819 GTCTTTCTGT
29119829 ATTTTCCCAAATCAAGGGTATTTCGATA
1 ATTTTCCCAAATCAAGGGTATTTCGATA
* ** * *
29119857 ATTTTCGCAAATCGGGGGTATTTTGGTA
1 ATTTTCCCAAATCAAGGGTATTTCGATA
29119885 ATTTT
1 ATTTT
29119890 ACAAAATTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (28 bp):
ATTTTCCCAAATCAAGGGTATTTCGATA
Found at i:29119926 original size:24 final size:25
Alignment explanation
Indices: 29119882--29119928 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
29119872 GGGTATTTTG
*
29119882 GTAATTTTACAAAATTAGGGTATCA
1 GTAATTTCACAAAATTAGGGTATCA
*
29119907 GTAATTTCA-AAAATTGGGGTAT
1 GTAATTTCACAAAATTAGGGTAT
29119929 TTTGGTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.36
Consensus pattern (25 bp):
GTAATTTCACAAAATTAGGGTATCA
Found at i:29119951 original size:26 final size:27
Alignment explanation
Indices: 29119922--29119989 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
29119912 TTCAAAAATT
29119922 GGGGTATTTTGGTAA-CTTACAGACT-A
1 GGGGTATTTTGGTAATCTTACA-ACTCA
*
29119948 GGGGTA-TTTGGTAATTTTACAACTCA
1 GGGGTATTTTGGTAATCTTACAACTCA
*
29119974 GGGGTATTTTAGTAAT
1 GGGGTATTTTGGTAAT
29119990 TCTATTCCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 11 0.30
26 18 0.49
27 8 0.22
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (27 bp):
GGGGTATTTTGGTAATCTTACAACTCA
Found at i:29120035 original size:24 final size:27
Alignment explanation
Indices: 29119970--29120046 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 27
29119960 AATTTTACAA
* * *
29119970 CTCAGGGGTATTTTAGTAATTCTATTC
1 CTCAAGGGCATTTCAGTAATTCTATTC
29119997 CTACAAGGGGCATTTCAGTAATTCTA-T-
1 CT-CAA-GGGCATTTCAGTAATTCTATTC
*
29120024 CTCAAGGG-ATTTCAATAATTCTA
1 CTCAAGGGCATTTCAGTAATTCTA
29120047 CCCTATAGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 14 0.32
25 3 0.07
26 3 0.07
27 4 0.09
28 3 0.07
29 17 0.39
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (27 bp):
CTCAAGGGCATTTCAGTAATTCTATTC
Found at i:29127385 original size:21 final size:20
Alignment explanation
Indices: 29127361--29127399 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
29127351 GAGTATTTTG
29127361 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
29127382 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
29127400 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:29136456 original size:40 final size:39
Alignment explanation
Indices: 29136412--29136550 Score: 188
Period size: 40 Copynumber: 3.5 Consensus size: 39
29136402 GCTACTCGTT
*
29136412 CAAATGCCTTCGGGTCATAGCCCGGTATTAGTAACTCGCA
1 CAAATGCCTTCGGGTCTTAGCCCGG-ATTAGTAACTCGCA
* *
29136452 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGTCTTAGCCCGGA-TTAGTAACTCGCA
* * *
29136492 CAAATGCCTTCGGATCTTAGTCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGTCTTAGCCCGG-ATTAGTAACTCGCA
*
29136532 CAAATGCCTTCGGATCTTA
1 CAAATGCCTTCGGGTCTTA
29136551 TCGGATAATG
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 87 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGGTCTTAGCCCGGATTAGTAACTCGCA
Found at i:29137777 original size:53 final size:54
Alignment explanation
Indices: 29137694--29137808 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 54
29137684 TATTAGTTTA
29137694 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACA--TT
*
29137750 TTGCCCATGC-TC-TA-TTTATTTTTCCATTAACACAACATGTTTCATGACATT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATT
29137801 TTGCCCAT
1 TTGCCCAT
29137809 CATCCCTTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
51 10 0.17
53 34 0.59
54 2 0.03
55 2 0.03
56 10 0.17
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.43
Consensus pattern (54 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATT
Found at i:29143614 original size:40 final size:40
Alignment explanation
Indices: 29143577--29143706 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 40
29143567 GCTACTCGTT
*
29143577 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
29143617 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29143657 CAAATGCCTTC-GG-C-TTAGCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
29143694 CAAATGCCTTCGG
1 CAAATGCCTTCGG
29143707 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
37 30 0.37
38 2 0.02
39 2 0.02
40 46 0.56
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:29143719 original size:77 final size:79
Alignment explanation
Indices: 29143577--29143755 Score: 197
Period size: 77 Copynumber: 2.3 Consensus size: 79
29143567 GCTACTCGTT
* *
29143577 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAG-CCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
29143641 GATTTAGTAAC-TCGCA
63 GATATAGTAACTTAGCA
* **
29143657 CAAATGCCTTC-GG-CTTAGCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAA-GCCTTCGGGACTTAGCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
29143719 ATATGGTCACTTAGCA
64 ATATAGTAACTTAGCA
29143735 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGGACTTAGCC
29143756 CGGACATCAT
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
76 3 0.04
77 47 0.55
78 15 0.18
79 9 0.11
80 11 0.13
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAAGCCTTCGGGACTTAGCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCA
Found at i:29144954 original size:56 final size:56
Alignment explanation
Indices: 29144887--29145006 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
29144877 TATTAGTTTA
29144887 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
29144943 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
29144999 TTGCCCAT
1 TTGCCCAT
29145007 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:29146382 original size:43 final size:43
Alignment explanation
Indices: 29146332--29146482 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 43
29146322 TATCCTAGAT
* * *
29146332 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC
* ** * * *
29146375 AGGGTCTTACACAAAATCATATAACGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC
* *
29146418 ATGGTCTTACACGTAATCACAATAT-AATGTCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCAC-ATATCGATGCCAATGTCCCAGAC
* *
29146461 ATGGTTTTACATGTAATCACAT
1 ATGGTCTTACACGTAATCACAT
29146483 CTAGGTAACT
Statistics
Matches: 88, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
42 2 0.02
43 83 0.94
44 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:29161067 original size:10 final size:10
Alignment explanation
Indices: 29161052--29161087 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
29161042 CAAATTCCAA
29161052 AAAAAAAAAC
1 AAAAAAAAAC
29161062 AAAAAAAAAC
1 AAAAAAAAAC
*
29161072 AACAAAAAAAG
1 AA-AAAAAAAC
29161083 AAAAA
1 AAAAA
29161088 GGTTGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:29161068 original size:13 final size:13
Alignment explanation
Indices: 29161050--29161087 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
29161040 ATCAAATTCC
29161050 AAAAAAAAAAACA
1 AAAAAAAAAAACA
*
29161063 AAAAAAAACAACA
1 AAAAAAAAAAACA
29161076 AAAAAAGAAAAA
1 AAAAAA-AAAAA
29161088 GGTTGCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:29163115 original size:64 final size:64
Alignment explanation
Indices: 29162924--29163117 Score: 298
Period size: 64 Copynumber: 3.0 Consensus size: 64
29162914 TATCATTCAT
** * *
29162924 ATCACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGT
1 ATCACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAGC
* *
29162988 ATCACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAACATCCTAATTATTTAACATAAGC
1 ATCACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAGC
* * * *
29163052 ATCACATTTAGTTAAGAGTATTTGATTCATTTTGATCATAACATCCTAATTATTTGTCATAAGC
1 ATCACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAGC
29163116 AT
1 AT
29163118 GATACATGAA
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 118 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (64 bp):
ATCACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAGC
Found at i:29163353 original size:45 final size:44
Alignment explanation
Indices: 29163297--29163396 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 44
29163287 TCATAACAAG
* * *
29163297 TCTTATTTCCCTTAGGTTGCAGTGGAGTAGA-CTGAAGAT-TGAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATC-GAAGATGTG-A-A
29163342 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATGGTGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGAT-GTGAA
29163387 TCTTATCTCC
1 TCTTATCTCC
29163397 ATATATCGGC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
45 45 0.92
46 2 0.04
47 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATGTGAA
Done.