Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 12 of 100
Found at i:3051849 original size:24 final size:24
Alignment explanation
Indices: 3051808--3051872 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 24
3051798 TTAGATGATA
*
3051808 AAAATTATTTTTTA--TTTATTTG
1 AAAATGATTTTTTATTTTTATTTG
3051830 AAAATGATTTTTTATTTTTA-TTG
1 AAAATGATTTTTTATTTTTATTTG
*
3051853 -AAATGATTTTTT-TTATTATT
1 AAAATGATTTTTTATTTTTATT
3051873 AATATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.13
22 26 0.68
23 3 0.08
24 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
AAAATGATTTTTTATTTTTATTTG
Found at i:3051865 original size:23 final size:22
Alignment explanation
Indices: 3051808--3051864 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3051798 TTAGATGATA
*
3051808 AAAATTATTTTTTATTTATTTG
1 AAAATGATTTTTTATTTATTTG
*
3051830 AAAATGATTTTTTATTTTTATTG
1 AAAATGATTTTTTATTTAT-TTG
3051853 -AAATGATTTTTT
1 AAAATGATTTTTT
3051865 TTATTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 29 0.91
23 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
AAAATGATTTTTTATTTATTTG
Found at i:3052037 original size:19 final size:19
Alignment explanation
Indices: 3052010--3052050 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3052000 AAATAAAATC
* *
3052010 AAATCAAATCAAAAAATAA
1 AAATAAAATCAAAAAAGAA
*
3052029 AAATAAAATGAAAAAAGAA
1 AAATAAAATCAAAAAAGAA
3052048 AAA
1 AAA
3052051 CCTGTGATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (19 bp):
AAATAAAATCAAAAAAGAA
Found at i:3053067 original size:26 final size:26
Alignment explanation
Indices: 3053003--3053091 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 26
3052993 AAAAGACTGA
* ** *
3053003 CCTAATTAGGCCCGGACACAAATGGA
1 CCTAATTGGGCCTAGACACAAATGGG
3053029 CCTAATTGGGCCTAGACACAAATGGG
1 CCTAATTGGGCCTAGACACAAATGGG
***
3053055 CCTAATTGGGCCTAGATGTAAATGGG
1 CCTAATTGGGCCTAGACACAAATGGG
*
3053081 CCTAGTTGGGC
1 CCTAATTGGGC
3053092 TTGAATACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.21
Consensus pattern (26 bp):
CCTAATTGGGCCTAGACACAAATGGG
Found at i:3053103 original size:26 final size:26
Alignment explanation
Indices: 3053020--3053106 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
3053010 AGGCCCGGAC
* *
3053020 ACAAATGGACCTAATTGGGCCTAGAC
1 ACAAATGGGCCTAATTGGGCCTAGAT
3053046 ACAAATGGGCCTAATTGGGCCTAGAT
1 ACAAATGGGCCTAATTGGGCCTAGAT
** * *
3053072 GTAAATGGGCCTAGTTGGG-CTTGAAT
1 ACAAATGGGCCTAATTGGGCCTAG-AT
3053098 ACAAATGGG
1 ACAAATGGG
3053107 TATTTACAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
25 3 0.06
26 49 0.94
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (26 bp):
ACAAATGGGCCTAATTGGGCCTAGAT
Found at i:3053588 original size:115 final size:115
Alignment explanation
Indices: 3053445--3053659 Score: 290
Period size: 115 Copynumber: 1.9 Consensus size: 115
3053435 ACCACGAATC
*
3053445 ATAAGAAATAATCTGAACTAAAAAAAGATCAAGTGA-TCAGGATAAAATCACGAGTCAAAATAAA
1 ATAAGAAATAATCTGAACTAAAAAAAGATCAAGTGACT-AGGATAAAATCAAGAGTCAAAATAAA
*
3053509 ACAACTAAG-ACTGAGTCAAGGTCAACAATAAATGATCGGGACAAAGCCATT
65 ACAAC-AAGAACTGAGTCAAGGTCAAAAATAAATGATCGGGACAAAGCCATT
* * *** *
3053560 ATAAGAAATAATCTGAATTGAGCTAAGATCAAGTGACTGGGATAAAATCAAGAGTCAAAATAAAA
1 ATAAGAAATAATCTGAACTAAAAAAAGATCAAGTGACTAGGATAAAATCAAGAGTCAAAATAAAA
** * *
3053625 TGACCAGAACTGAGTCGAGGTCAAAAATAAATGAT
66 CAACAAGAACTGAGTCAAGGTCAAAAATAAATGAT
3053660 TAGAGTAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
114 2 0.02
115 83 0.97
116 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (115 bp):
ATAAGAAATAATCTGAACTAAAAAAAGATCAAGTGACTAGGATAAAATCAAGAGTCAAAATAAAA
CAACAAGAACTGAGTCAAGGTCAAAAATAAATGATCGGGACAAAGCCATT
Found at i:3053913 original size:41 final size:41
Alignment explanation
Indices: 3053852--3053971 Score: 134
Period size: 41 Copynumber: 3.0 Consensus size: 41
3053842 TCTTTACCAT
* *
3053852 ACAT-TTTAGCGAAAAAACCATCCTTAATTAACCTGAATGC
1 ACATCTTTAGCAAAAAAACCATCTTTAATTAACCTGAATGC
* * * *
3053892 ACATCTTTAGCAAAAAAACCATATTTTATCAATCTGAATGC
1 ACATCTTTAGCAAAAAAACCATCTTTAATTAACCTGAATGC
** * * *
3053933 ACGCCTTTAGCAAAGAAACCATCTTTCATTAGCCTGAAT
1 ACATCTTTAGCAAAAAAACCATCTTTAATTAACCTGAAT
3053972 ATTTATCTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
40 4 0.06
41 61 0.94
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (41 bp):
ACATCTTTAGCAAAAAAACCATCTTTAATTAACCTGAATGC
Found at i:3062313 original size:24 final size:22
Alignment explanation
Indices: 3062281--3062329 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
3062271 AAATAATATA
*
3062281 TAAAATAATATAAAATAATTTTTT
1 TAAAATAATA-AAAA-AATATTTT
3062305 TAAAATAATAAAAAAATATTTT
1 TAAAATAATAAAAAAATATTTT
3062327 TAA
1 TAA
3062330 GAAAAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.42
23 4 0.17
24 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATAATAAAAAAATATTTT
Found at i:3066359 original size:13 final size:13
Alignment explanation
Indices: 3066341--3066384 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
3066331 ACAATGGATG
3066341 AAAGATGAGAAAA
1 AAAGATGAGAAAA
*
3066354 AAAGATGATAATGAA
1 AAAGATGAGAA--AA
3066369 AAAGATGAGAAAA
1 AAAGATGAGAAAA
3066382 AAA
1 AAA
3066385 TGAAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 15 0.56
15 12 0.44
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (13 bp):
AAAGATGAGAAAA
Found at i:3066410 original size:17 final size:18
Alignment explanation
Indices: 3066388--3066425 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3066378 AAAAAAATGA
*
3066388 AAAAAGA-AAGAAAGAGG
1 AAAAAGATAAAAAAGAGG
*
3066405 AAAAAGATAAAAAAGATG
1 AAAAAGATAAAAAAGAGG
3066423 AAA
1 AAA
3066426 GAATGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (18 bp):
AAAAAGATAAAAAAGAGG
Found at i:3066419 original size:18 final size:17
Alignment explanation
Indices: 3066376--3066425 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
3066366 GAAAAAGATG
3066376 AGAAAAAAATGA--AAAA
1 AGAAAAAAA-GAGGAAAA
*
3066392 AGAAAGAAAGAGGAAAA
1 AGAAAAAAAGAGGAAAA
*
3066409 AGATAAAAAAGATGAAA
1 AGA-AAAAAAGAGGAAA
3066426 GAATGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 2 0.07
16 8 0.29
17 7 0.25
18 11 0.39
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (17 bp):
AGAAAAAAAGAGGAAAA
Found at i:3066456 original size:26 final size:26
Alignment explanation
Indices: 3066380--3066456 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
3066370 AAGATGAGAA
3066380 AAAAATGA-AAAAAGAA-AGAAAGA-GG
1 AAAAA-GATAAAAAGAAGAGAAA-ATGG
*
3066405 AAAAAGATAAAAAAGATGA-AAGAATGG
1 AAAAAGAT-AAAAAGAAGAGAA-AATGG
3066432 AAAAAGATAAAAAGAAGAGAAAATG
1 AAAAAGATAAAAAGAAGAGAAAATG
3066457 AAGACTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
24 2 0.05
25 5 0.11
26 23 0.52
27 14 0.32
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (26 bp):
AAAAAGATAAAAAGAAGAGAAAATGG
Found at i:3067780 original size:46 final size:46
Alignment explanation
Indices: 3067709--3068033 Score: 434
Period size: 46 Copynumber: 7.1 Consensus size: 46
3067699 TTGATGAAGT
* * * *
3067709 TTTGAATCTTAAATAAGAATCTTTAAGATGTTTTCAAATAAAAATC
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
* *
3067755 TTTAAATCTTAAATGAGAATCTTTAAGACGTTTCCAAATGAGAATC
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
* * * *
3067801 TTTTAATCTTAAATAAAAATCTTTAAGACGTTTTCAAATGAGAACC
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
* *
3067847 TTTGAGTTTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
* * * * * *
3067893 CTTGAGTTTTAAATGAGAATCTTTAAGACGTTCTCAAATAAAAATC
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
* * *
3067939 TTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATA
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
* **
3067985 TTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAATC
1 TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
3068031 TTT
1 TTT
3068034 AAAACATTTT
Statistics
Matches: 249, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 249 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (46 bp):
TTTGAATCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATC
Found at i:3068048 original size:163 final size:163
Alignment explanation
Indices: 3067853--3068196 Score: 503
Period size: 163 Copynumber: 2.1 Consensus size: 163
3067843 AACCTTTGAG
* * * *
3067853 TTTT-AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCCTTGAGTTTTAAATGAGAATCTTT
1 TTTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATCCTTGAGTCTTAAATGAAAATCTTT
*
3067917 AAGACGTTCTCAAATAAAAATCTTTGAGTCTT-AAATGAGAATCTTTAAGACATTTTCAAATGAG
66 AAGACGTTCTCAAATAAAAATCTTTAAGT-TTCAAATGAGAATCTTTAAGACATTTTCAAATGAG
* *
3067981 AATATTTGAGTCTTAAATGAGAATCTTTAAGATA
130 AATATTTGAGTCTTAAATAAGAACCTTTAAGATA
** *
3068015 TTTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATTTTTTAGTCTTAAATGAAAATCTTT
1 TTTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATCCTTGAGTCTTAAATGAAAATCTTT
* * * * * *
3068080 AAGACGTTTTCAAATGAGAATCTTTAAGTTTCAAATGAGAATCTTTAAGATATTTTTAAATGAGC
66 AAGACGTTCTCAAATAAAAATCTTTAAGTTTCAAATGAGAATCTTTAAGACATTTTCAAATGAGA
*
3068145 ATCTTTGAGTCTTAAATAAGAACCTTTAAGATA
131 ATATTTGAGTCTTAAATAAGAACCTTTAAGATA
*
3068178 TTTTCAAATGATAATCTTT
1 TTTTCAAATGAGAATCTTT
3068197 GAGATGTAAA
Statistics
Matches: 162, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
162 6 0.04
163 156 0.96
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (163 bp):
TTTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATCCTTGAGTCTTAAATGAAAATCTTT
AAGACGTTCTCAAATAAAAATCTTTAAGTTTCAAATGAGAATCTTTAAGACATTTTCAAATGAGA
ATATTTGAGTCTTAAATAAGAACCTTTAAGATA
Found at i:3068070 original size:46 final size:46
Alignment explanation
Indices: 3067995--3068196 Score: 226
Period size: 46 Copynumber: 4.3 Consensus size: 46
3067985 TTTGAGTCTT
* *
3067995 AAATGAGAATCTTTAAGATATTTTCAAATGAGAATCTTTAAAACATTTTC
1 AAATGAGAATCTTTAAG---TCTT-AAATGAGAATCTTTAAGACATTTTC
* * * *
3068045 AAATGAGAATTTTTTAGTCTTAAATGAAAATCTTTAAGACGTTTTC
1 AAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACATTTTC
* *
3068091 AAATGAGAATCTTTAAGT-TTCAAATGAGAATCTTTAAGATATTTTT
1 AAATGAGAATCTTTAAGTCTT-AAATGAGAATCTTTAAGACATTTTC
* * * * *
3068137 AAATGAGCATCTTTGAGTCTTAAATAAGAACCTTTAAGATATTTTC
1 AAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACATTTTC
*
3068183 AAATGATAATCTTT
1 AAATGAGAATCTTT
3068197 GAGATGTAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
45 2 0.02
46 109 0.83
47 5 0.04
50 15 0.11
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (46 bp):
AAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACATTTTC
Found at i:3068070 original size:92 final size:89
Alignment explanation
Indices: 3067709--3068171 Score: 380
Period size: 92 Copynumber: 5.0 Consensus size: 89
3067699 TTGATGAAGT
* * * * * * *
3067709 TTTGAATCTTAAATAAGAATCTTTAAGATGTTTTCAAATAAAAATCTTTAAATCTTAAATGAGAA
1 TTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAA
*
3067774 TCTTTAAGACGTTTCCAAATGAGAATC
66 TCTTTAAGTC--TT-CAAATGAGAATC
* * * * * *
3067801 TTTTAATCTTAAATAAAAATCTTTAAGACGTTTTCAAATGAGAACCTTTGAGTTTTAAATGAGAA
1 TTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAA
*
3067866 TCTTTAAGACGTTTTCAAATGAGAATC
66 TCTTT-A-A-GTCTTCAAATGAGAATC
* * * * * * *
3067893 CTTGAGTTTTAAATGAGAATCTTTAAGACGTTCTCAAATAAAAATCTTTGAGTCTTAAATGAGAA
1 TTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAA
* *
3067958 TCTTTAAGACATTTTCAAATGAGAATA
66 TCTTTAAG---TCTTCAAATGAGAATC
** *
3067985 TTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAATCTTTAAAACATTTTCAAATG
1 TTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTT--GA-ATTTT-AAATG
* * *
3068050 AGAATTTTTTAGTCTT-AAATGAAAATC
62 AGAATCTTTAAGTCTTCAAATGAGAATC
*
3068077 TTTAAGACGTTTTCAAATGAGAATCTTT-A-A-G-TTTCAAATGAGAATCTTTAAGATATTTTTA
1 TTT--GA-GTCTT-AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTT--GA-A-TTTTA
* * * *
3068138 AATGAGCATCTTTGAGTCTT-AAATAAGAACC
58 AATGAGAATCTTTAAGTCTTCAAATGAGAATC
3068169 TTT
1 TTT
3068172 AAGATATTTT
Statistics
Matches: 308, Mismatches: 48, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
89 1 0.00
90 1 0.00
91 1 0.00
92 252 0.82
93 10 0.03
94 5 0.02
95 9 0.03
96 29 0.09
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (89 bp):
TTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAA
TCTTTAAGTCTTCAAATGAGAATC
Found at i:3068075 original size:138 final size:133
Alignment explanation
Indices: 3067709--3068121 Score: 418
Period size: 138 Copynumber: 3.0 Consensus size: 133
3067699 TTGATGAAGT
* * * * *
3067709 TTTGAATCTTAAATAAGAATCTTTAAGATGTTTTCAAATAAAAATCTTTAAATCTTAAATGAGAA
1 TTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTTAAATTTTAAATGAGAA
* * * * * * *
3067774 TCTTTAAGACGTTTCCAAATGAGAATCTTTTAATCTTAAATAAAAATCTTTAAGACGTTTTCAAA
66 TTTTTAAGTC--TT--AAATGAAAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC-TTTTCAAA
**
3067839 TGAGAACC
126 TGAGAATA
* * * * *
3067847 TTTGAGTTTTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCCTTGAGTTTTAAATGAGAA
1 TTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTTAAATTTTAAATGAGAA
* * *
3067912 TCTTTAAGACGTTCTCAAATAAAAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAA
66 T-TTTTA-A-G-TCTTAAATGAAAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC-TTTTCAAA
3067977 TGAGAATA
126 TGAGAATA
*
3067985 TTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAATCTTTAAAACATTTTCAAATG
1 TTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTT--AA-ATTTT-AAATG
* *
3068050 AGAATTTTTTAGTCTTAAATGAAAATCTTTAAGACGTTTTCAAATGAGAATCTTTAAG---TTTC
62 AGAATTTTTAAGTCTTAAATGAAAATCTTT--GA-GTCTT-AAATGAGAATCTTTAAGACTTTTC
3068112 AAATGAGAAT
123 AAATGAGAAT
3068122 CTTTAAGATA
Statistics
Matches: 229, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
138 179 0.78
139 4 0.02
140 6 0.03
141 12 0.05
142 28 0.12
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (133 bp):
TTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTTAAATTTTAAATGAGAA
TTTTTAAGTCTTAAATGAAAATCTTTGAGTCTTAAATGAGAATCTTTAAGACTTTTCAAATGAGA
ATA
Found at i:3068172 original size:92 final size:93
Alignment explanation
Indices: 3067995--3068201 Score: 265
Period size: 92 Copynumber: 2.2 Consensus size: 93
3067985 TTTGAGTCTT
* *
3067995 AAATGAGAATCTTTAAGATATTTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATTTTTT
1 AAATGAGAATCTTTAAG--A-TTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATCTTTG
* *
3068060 AGTCTTAAATGAAAATCTTTAAGACGTTTTC
63 AGTCTTAAATGAAAACCTTTAAGACATTTTC
* * * *
3068091 AAATGAGAATCTTTAAG-TTTCAAATGAGAATCTTTAAGATATTTTTAAATGAGCATCTTTGAGT
1 AAATGAGAATCTTTAAGATTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATCTTTGAGT
*
3068155 CTTAAAT-AAGAACCTTTAAGATATTTTC
66 CTTAAATGAA-AACCTTTAAGACATTTTC
* *
3068183 AAATGATAATCTTTGAGAT
1 AAATGAGAATCTTTAAGAT
3068202 GTAAAATCCT
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
91 2 0.02
92 78 0.80
93 1 0.01
96 17 0.17
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (93 bp):
AAATGAGAATCTTTAAGATTTCAAATGAGAATCTTTAAAACATTTTCAAATGAGAATCTTTGAGT
CTTAAATGAAAACCTTTAAGACATTTTC
Found at i:3069888 original size:12 final size:11
Alignment explanation
Indices: 3069875--3069907 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
3069865 AAATTTTTTA
3069875 AAAAATAAAAT
1 AAAAATAAAAT
3069886 -AAAATAAAAT
1 AAAAATAAAAT
3069896 ATAAAATAAAAT
1 A-AAAATAAAAT
3069908 TTTCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3069893 original size:17 final size:17
Alignment explanation
Indices: 3069873--3069907 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3069863 ATAAATTTTT
3069873 TAAAAAATAAAATAAAA
1 TAAAAAATAAAATAAAA
*
3069890 TAAAATATAAAATAAAA
1 TAAAAAATAAAATAAAA
3069907 T
1 T
3069908 TTTCAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAAAATAAAATAAAA
Found at i:3069980 original size:59 final size:59
Alignment explanation
Indices: 3069917--3070144 Score: 205
Period size: 60 Copynumber: 3.8 Consensus size: 59
3069907 TTTTCAAAAA
*
3069917 TAAAAAATATATTTTTAAGAAAAAATTGAAGGTATCAATTTTTCTTAAAAATAAAATTT
1 TAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTT
* * * *
3069976 TAAAAAAATATATTTTTGAGGAAAAGTTGAAATTATCAATTTTTCTTAAAAATAAAATTT
1 T-AAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTT
* * * *
3070036 TCAAAAATATAAAAAAATACTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAATAAAA
1 T-AAAAA-AT------ATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTT-AAAAATAAAA
**
3070101 CCT
57 TTT
* * *
3070104 T--GAAAT-GA--TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 TAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTT
3070145 GTATAAAAGC
Statistics
Matches: 146, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
55 31 0.21
57 1 0.01
59 1 0.01
60 59 0.40
61 2 0.01
64 2 0.01
65 2 0.01
67 36 0.25
68 12 0.08
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (59 bp):
TAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTT
Found at i:3072379 original size:12 final size:12
Alignment explanation
Indices: 3072364--3072432 Score: 79
Period size: 12 Copynumber: 5.7 Consensus size: 12
3072354 TAGTTATTTT
3072364 TTTAATTTTATA
1 TTTAATTTTATA
*
3072376 TTTAATTATATA
1 TTTAATTTTATA
*
3072388 TTTAATTATATA
1 TTTAATTTTATA
3072400 TTT--TTATATATA
1 TTTAATT-T-TATA
3072412 TTTAATTTTATA
1 TTTAATTTTATA
3072424 TTTATATTT
1 TTTA-ATTT
3072433 AAAATAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.04
12 41 0.82
13 5 0.10
14 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:3072384 original size:24 final size:23
Alignment explanation
Indices: 3072352--3072433 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 23
3072342 AAAATTATTT
*
3072352 TTTAGTTATTTTTTTAATTTTATA
1 TTTA-TTATTTATTTAATTTTATA
* *
3072376 TTTAATTATATATTTAATTATATA
1 TTT-ATTATTTATTTAATTTTATA
3072400 TTT-TTATATATATTTAATTTTATA
1 TTTATTAT-T-TATTTAATTTTATA
3072424 TTTA-TATTTA
1 TTTATTATTTA
3072434 AAATAATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
22 6 0.12
23 1 0.02
24 41 0.84
25 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (23 bp):
TTTATTATTTATTTAATTTTATA
Found at i:3073903 original size:5 final size:5
Alignment explanation
Indices: 3073895--3073935 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
3073885 AAAATGGGTT
3073895 TAAAA TAAAA TAAAA TAAAAA TAAAA TAAAA TGAAAA -AAAA
1 TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA T-AAAA TAAAA
3073936 AACCTACGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 21 0.62
6 9 0.26
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:3073915 original size:11 final size:11
Alignment explanation
Indices: 3073895--3073925 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3073885 AAAATGGGTT
3073895 TAAAAT-AAAA
1 TAAAATAAAAA
3073905 TAAAATAAAAA
1 TAAAATAAAAA
3073916 TAAAATAAAA
1 TAAAATAAAA
3073926 TGAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:3073915 original size:16 final size:17
Alignment explanation
Indices: 3073896--3073936 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
3073886 AAATGGGTTT
3073896 AAAATAAAATAAAAT-A
1 AAAATAAAATAAAATGA
3073912 AAAATAAAATAAAATGA
1 AAAATAAAATAAAATGA
3073929 AAAA-AAAA
1 AAAATAAAA
3073937 ACCTACGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAAATGA
Found at i:3074789 original size:19 final size:19
Alignment explanation
Indices: 3074765--3074825 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
3074755 AAAAAAAGTA
3074765 AATAATAA-ATAATAGTATT
1 AATAATAATATAATA-TATT
*
3074784 AATAATAATATACTATATT
1 AATAATAATATAATATATT
*
3074803 -ATAAT-ATAT-AT-TATA
1 AATAATAATATAATATATT
3074818 AATAATAA
1 AATAATAA
3074826 CAAAATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.08
16 6 0.17
17 5 0.14
18 5 0.14
19 12 0.33
20 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AATAATAATATAATATATT
Found at i:3082208 original size:7 final size:7
Alignment explanation
Indices: 3082198--3082222 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3082188 CGTCTTATTT
3082198 CTTAGCC
1 CTTAGCC
3082205 CTTAGCC
1 CTTAGCC
3082212 CTTAGCC
1 CTTAGCC
3082219 CTTA
1 CTTA
3082223 TGGCTAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.40, G:0.12, T:0.32
Consensus pattern (7 bp):
CTTAGCC
Found at i:3084590 original size:19 final size:18
Alignment explanation
Indices: 3084555--3084598 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3084545 TTTGGTTTAA
3084555 ATTT-TTTTAAAATAAAT
1 ATTTATTTTAAAATAAAT
3084572 GATTTATTTTATAAA-AAAT
1 -ATTTATTTTA-AAATAAAT
3084591 ATTTATTT
1 ATTTATTT
3084599 AGATTCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.50
19 9 0.38
20 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTATTTTAAAATAAAT
Found at i:3094266 original size:1 final size:1
Alignment explanation
Indices: 3094260--3094285 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3094250 GTGCAGAGTT
3094260 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3094286 CTATCAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3098027 original size:16 final size:16
Alignment explanation
Indices: 3098006--3098036 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3097996 ATCAATCTCA
3098006 TTAATCTCGGAATTAG
1 TTAATCTCGGAATTAG
*
3098022 TTAATCTTGGAATTA
1 TTAATCTCGGAATTA
3098037 ATTTCTAAAT
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:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (16 bp):
TTAATCTCGGAATTAG
Found at i:3098482 original size:33 final size:32
Alignment explanation
Indices: 3098437--3098513 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
3098427 AGAGATATCA
*
3098437 AGCC-CAATAAACAGAGCTATACTATAGCAGAAT
1 AGCCACAA-AAACA-AGCTATACTATAGAAGAAT
*
3098470 AGCCACAAAAAC-ATCTATACTATAGAAGAAT
1 AGCCACAAAAACAAGCTATACTATAGAAGAAT
* *
3098501 AGTCACCAAAACA
1 AGCCACAAAAACA
3098514 TTAGAGTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 27 0.71
33 8 0.21
34 3 0.08
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (32 bp):
AGCCACAAAAACAAGCTATACTATAGAAGAAT
Found at i:3098488 original size:31 final size:31
Alignment explanation
Indices: 3098453--3098514 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3098443 ATAAACAGAG
*
3098453 CTATACTATAGCAGAATAGCCACAAAAACAT
1 CTATACTATAGAAGAATAGCCACAAAAACAT
* *
3098484 CTATACTATAGAAGAATAGTCACCAAAACAT
1 CTATACTATAGAAGAATAGCCACAAAAACAT
3098515 TAGAGTAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (31 bp):
CTATACTATAGAAGAATAGCCACAAAAACAT
Found at i:3101990 original size:2 final size:2
Alignment explanation
Indices: 3101983--3102013 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3101973 TTTTATAATG
3101983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3102014 GTTTACTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3102116 original size:3 final size:3
Alignment explanation
Indices: 3102108--3102144 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3102098 TATAACATCT
3102108 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3102145 CTATATTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3102178 original size:3 final size:3
Alignment explanation
Indices: 3102170--3102199 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3102160 TACAACATCT
3102170 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3102200 TATATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3102180 original size:62 final size:64
Alignment explanation
Indices: 3102083--3102208 Score: 211
Period size: 62 Copynumber: 2.0 Consensus size: 64
3102073 TTTTTAACCG
* * *
3102083 CTATATTGGATAATCTATAACATCTATAATAATAATAATAATAATAATAATAATA-ATA-ATAA
1 CTATATTGGACAACCTACAACATCTATAATAATAATAATAATAATAATAATAATATATATATAA
3102145 CTATATTGGACAACCTACAACATCTATAATAATAATAATAATAATAATAATAATATATATATAA
1 CTATATTGGACAACCTACAACATCTATAATAATAATAATAATAATAATAATAATATATATATAA
3102209 AAGTAATGCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 52 0.88
63 3 0.05
64 4 0.07
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (64 bp):
CTATATTGGACAACCTACAACATCTATAATAATAATAATAATAATAATAATAATATATATATAA
Found at i:3104577 original size:33 final size:33
Alignment explanation
Indices: 3104530--3104595 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3104520 CTTGACAGAT
3104530 AACTTTCTCATTACCTCAGATTTGCATCAAGGC
1 AACTTTCTCATTACCTCAGATTTGCATCAAGGC
* *
3104563 AACTTTCTCGTTACCTTAGATTTGCATCAAGGC
1 AACTTTCTCATTACCTCAGATTTGCATCAAGGC
3104596 TCAGCACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (33 bp):
AACTTTCTCATTACCTCAGATTTGCATCAAGGC
Found at i:3107406 original size:17 final size:17
Alignment explanation
Indices: 3107384--3107416 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3107374 ATTTAACCTT
3107384 CTGTATAATCACGTCAC
1 CTGTATAATCACGTCAC
3107401 CTGTATAATCACGTCA
1 CTGTATAATCACGTCA
3107417 AATCTACGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (17 bp):
CTGTATAATCACGTCAC
Found at i:3112182 original size:18 final size:19
Alignment explanation
Indices: 3112159--3112209 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
3112149 TATTTAAATA
3112159 TTTATTAATCA-ATTATTT
1 TTTATTAATCATATTATTT
**
3112177 TTTATTTTTCATATTATTT
1 TTTATTAATCATATTATTT
*
3112196 TTTCTTAAT-ATATT
1 TTTATTAATCATATT
3112210 TCAAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTAATCATATTATTT
Found at i:3112870 original size:14 final size:14
Alignment explanation
Indices: 3112851--3112888 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3112841 TTTTAAATGA
3112851 TTTTG-AATATTTAT
1 TTTTGAAAT-TTTAT
3112865 TTTTGAAATTTTAT
1 TTTTGAAATTTTAT
*
3112879 TTTTAAAATT
1 TTTTGAAATT
3112889 ATTTGAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (14 bp):
TTTTGAAATTTTAT
Found at i:3125339 original size:156 final size:156
Alignment explanation
Indices: 3125038--3125365 Score: 389
Period size: 156 Copynumber: 2.1 Consensus size: 156
3125028 ATATAGATAT
* * *
3125038 ATTTATATATATA-AT-T-GTTATTTTTTTCCATAAAAAGCTACAATATGAGAATAAAATAAAAA
1 ATTTATATATATATATATAATTATTTTTTTACATAAAAAGCTACAATATAAGAATAAAATAAAAA
* * * * *
3125100 AAGAGGTTACAAGTATTAAAATTCAAAACTTATATTTATTAAATGTCACATCTTAAAAATTATTG
66 AAGAGGTTACAAATATTAAAATTCAAAACTTAGATTTATTAAATATCACATCTTAAAAATGATTA
3125165 TATAAACTAACTGAATTAAAATTAAA
131 TATAAACTAACTGAATTAAAATTAAA
* *
3125191 ATTTATATATATATATATAATTATTTTTTTACATAGAAAG-TCACAATATAAGAATAAAATAAAG
1 ATTTATATATATATATATAATTATTTTTTTACATAAAAAGCT-ACAATATAAGAATAAAATAAAA
* * ** * * *
3125255 AAAGAGGTTACAAATATTAAAATTTAAAACTTAGATTTGTTGGATATTATC-TTTTAAAAATGGT
65 AAAGAGGTTACAAATATTAAAATTCAAAACTTAGATTTATTAAATATCA-CATCTTAAAAATGAT
* * **
3125319 TATATAAA-TCAATTGAATTAAAGTTTGA
129 TATATAAACT-AACTGAATTAAAATTAAA
*
3125347 ATTTATATATATGTATATA
1 ATTTATATATATATATATA
3125366 TATTTATATA
Statistics
Matches: 147, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
153 13 0.09
154 2 0.01
155 3 0.02
156 128 0.87
157 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.39
Consensus pattern (156 bp):
ATTTATATATATATATATAATTATTTTTTTACATAAAAAGCTACAATATAAGAATAAAATAAAAA
AAGAGGTTACAAATATTAAAATTCAAAACTTAGATTTATTAAATATCACATCTTAAAAATGATTA
TATAAACTAACTGAATTAAAATTAAA
Found at i:3127544 original size:26 final size:26
Alignment explanation
Indices: 3127512--3127602 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 26
3127502 ATTAATTTTA
* *
3127512 ATAAAATTTATTAAACATAATTTATT
1 ATAAAATTTTTTAAACATAATTAATT
*
3127538 ATTAAATTTTTTAAA-ATAA-TAATT
1 ATAAAATTTTTTAAACATAATTAATT
* *
3127562 ATAATAATTTTTTAATCATAATT-ATA
1 ATAA-AATTTTTTAAACATAATTAATT
3127588 ATAATAATTATTTTA
1 ATAA-AATT-TTTTA
3127603 TTTTTATTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
24 7 0.13
25 14 0.25
26 28 0.51
27 6 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAAAATTTTTTAAACATAATTAATT
Found at i:3130848 original size:87 final size:86
Alignment explanation
Indices: 3130682--3131235 Score: 445
Period size: 87 Copynumber: 6.4 Consensus size: 86
3130672 TAAAAACTTC
* * ** *
3130682 TCTAAACAGAGGCTCCAC-ATCTTTTGAAAAATAAATACAGCTCCTCTAAGTAGAAGCTTAACAA
1 TCTAAACAGAGGCTCAACGA-C-TTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAA
* **
3130746 TTTTTTTAAAA-AAATAAAGCTCT
64 -CTTTAAAAAATAAATAAAGCTCT
* * * *
3130769 TCTAAACAGAGGCTCGACGACTTTTGAAAAATAAATAAAGCTCATTTAAACAGAAGCTCAATAAC
1 TCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAAC
*
3130834 TTTAAAAAATAAATAAAGCTCC
65 TTTAAAAAATAAATAAAGCTCT
** * * * * * * *
3130856 TC-AAAGCAGAGATTCAATGACTTTTGAAGAATAAATAAGGCTTCTTTACACA-AAGACTCAACG
1 TCTAAA-CAGAGGCTCAACGAC-TTTGAAAAATAAATAAAGCTCCTCTAAACAGAAG-CTCAACA
* *
3130919 ATTTTAAAAAATAAATAAAGTTCAT
63 ACTTTAAAAAATAAATAAAGCTC-T
** * ** * * * * *
3130944 T-TAAGTAGATGCTCAATAACTTTAAAAAATAAATAAAGCTCCTTTAAGCAGAGGCTTAACAACT
1 TCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAACT
* *
3131008 TTGAAAAATAAATAAAGCTCC
66 TTAAAAAATAAATAAAGCTCT
* ** * * * * * *
3131029 TCTAAACAGAGACTCAACGACTTCAAAAAATAAATAAGGTTCATCTAAGCAGAAACTCAACAGCT
1 TCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAACT
* **
3131094 TTGAAAAATAAATAAAATTAC-
66 TTAAAAAATAAATAAAGCT-CT
* * * * * * * * * *
3131115 TCTAAATAGAAGCTCAACGACTTTAAAAAATAAATAAGGCTCCTCTAAATAGAGGTTTAACGATT
1 TCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAACT
*
3131180 TTCAAAAAATAAATAAGGCTCT
66 TT-AAAAAATAAATAAAGCTCT
3131202 TCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
1 TCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
3131236 GTTCCTCGAT
Statistics
Matches: 372, Mismatches: 84, Indels: 22
0.78 0.18 0.05
Matches are distributed among these distances:
85 1 0.00
86 180 0.48
87 187 0.50
88 4 0.01
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (86 bp):
TCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAACT
TTAAAAAATAAATAAAGCTCT
Found at i:3130873 original size:43 final size:43
Alignment explanation
Indices: 3130753--3131235 Score: 279
Period size: 43 Copynumber: 11.2 Consensus size: 43
3130743 CAATTTTTTT
* * * * *
3130753 AAAA-AAATAAAGCTCTTCTAAA-CAGAGGCTCGACGACTTTTGA
1 AAAATAAATAAAGCTCCT-TAAAGCAGAGACTCAACAAC-TTTAA
* *
3130796 AAAATAAATAAAGCTCATTTAAA-CAGA-AGCTCAATAACTTTAA
1 AAAATAAATAAAGCTC-CTTAAAGCAGAGA-CTCAACAACTTTAA
* * ** *
3130839 AAAATAAATAAAGCTCCTCAAAGCAGAGATTCAATGACTTTTGA
1 AAAATAAATAAAGCTCCTTAAAGCAGAGACTCAACAAC-TTTAA
* * * * * * *
3130883 AGAATAAATAAGGCTTCTTTACA-CAAAGACTCAACGATTTTAA
1 AAAATAAATAAAGC-TCCTTAAAGCAGAGACTCAACAACTTTAA
* * * * *
3130926 AAAATAAATAAAGTTCATTTAAGTAGATG-CTCAATAACTTTAA
1 AAAATAAATAAAGCTCCTTAAAGCAGA-GACTCAACAACTTTAA
* * * *
3130969 AAAATAAATAAAGCTCCTTTAAGCAGAGGCTTAACAACTTTGA
1 AAAATAAATAAAGCTCCTTAAAGCAGAGACTCAACAACTTTAA
* *
3131012 AAAATAAATAAAGCTCCTCTAAA-CAGAGACTCAACGACTTCAA
1 AAAATAAATAAAGCTCCT-TAAAGCAGAGACTCAACAACTTTAA
* * * * * *
3131055 AAAATAAATAAGGTTCATCT-AAGCAGAAACTCAACAGCTTTGA
1 AAAATAAATAAAGCTCCT-TAAAGCAGAGACTCAACAACTTTAA
** * * *
3131098 AAAATAAATAAAATTACTCTAAA-TAGA-AGCTCAACGACTTTAA
1 AAAATAAATAAAGCTCCT-TAAAGCAGAGA-CTCAACAACTTTAA
* * ** * * *
3131141 AAAATAAATAAGGCTCCTCTAAA-TAGAGGTTTAACGATTTTCAA
1 AAAATAAATAAAGCTCCT-TAAAGCAGAGACTCAACAACTTT-AA
* * * * *
3131185 AAAATAAATAAGGCTCTTCTAAA-CAGAGGCTCAACGACTTTGA
1 AAAATAAATAAAGCTCCT-TAAAGCAGAGACTCAACAACTTTAA
3131228 AAAATAAA
1 AAAATAAA
3131236 GTTCCTCGAT
Statistics
Matches: 351, Mismatches: 73, Indels: 32
0.77 0.16 0.07
Matches are distributed among these distances:
42 13 0.04
43 234 0.67
44 97 0.28
45 7 0.02
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (43 bp):
AAAATAAATAAAGCTCCTTAAAGCAGAGACTCAACAACTTTAA
Found at i:3131516 original size:33 final size:33
Alignment explanation
Indices: 3131470--3131534 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
3131460 TCCTAAATTC
* * *
3131470 ATGCACTAGACATTC-TCAAGTGCAATGCATGCT
1 ATGCACTAAACATTCAT-AAATACAATGCATGCT
3131503 ATGCACTAAACATTCATAAATACAATGCATGC
1 ATGCACTAAACATTCATAAATACAATGCATGC
3131535 AAATGTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (33 bp):
ATGCACTAAACATTCATAAATACAATGCATGCT
Found at i:3132044 original size:78 final size:79
Alignment explanation
Indices: 3131851--3132144 Score: 276
Period size: 79 Copynumber: 3.7 Consensus size: 79
3131841 ATCTCATTAA
* * *
3131851 CACTAGCCATTTC-AGAATAAA-TTC-TGTCAACTGATCTACATTATTTTCATTATTTGATTACA
1 CACTAGCAATTTCAAGCATAAATTTCAT-TC-ACTGATCCACATTATTTTCATTATTTGATTACA
* *
3131913 ACTCACAGGTTCCTTAG
64 ACTCATAGCTT-CTTAG
* * * * * *
3131930 CACTAGCAATTT-TAGCATAAATTTTATTCATTGATCCACATTATTTCCATTATCTGATCACAAC
1 CACTAGCAATTTCAAGCATAAATTTCATTCACTGATCCACATTATTTTCATTATTTGATTACAAC
*
3131994 TCATAGCTTCTTAC
66 TCATAGCTTCTTAG
* * * * *
3132008 CACTAGCAATTTCAAG-ATCAATTTCGTTCACTGATCCACATTATTTTTATCATTTGATTATAAC
1 CACTAGCAATTTCAAGCATAAATTTCATTCACTGATCCACATTATTTTCATTATTTGATTACAAC
3132072 TCATAGGCTTCTTAG
66 TCATA-GCTTCTTAG
* ** * * ** * *
3132087 CACTATCAATTTCAAAAAAAAATTT-ATCCGTTGATCCATATTATTTTCATCATTTGAT
1 CACTAGCAATTTCAAGCATAAATTTCATTCACTGATCCACATTATTTTCATTATTTGAT
3132145 CATAGCCCAC
Statistics
Matches: 176, Mismatches: 33, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
78 59 0.34
79 106 0.60
80 10 0.06
81 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (79 bp):
CACTAGCAATTTCAAGCATAAATTTCATTCACTGATCCACATTATTTTCATTATTTGATTACAAC
TCATAGCTTCTTAG
Found at i:3132764 original size:7 final size:7
Alignment explanation
Indices: 3132733--3132805 Score: 56
Period size: 8 Copynumber: 9.4 Consensus size: 7
3132723 AATTTGAGTC
3132733 TTTATTT
1 TTTATTT
*
3132740 TCTTTTTT
1 T-TTATTT
3132748 TTTACCTTT
1 TTTA--TTT
3132757 TTTATTTT
1 TTTA-TTT
3132765 TTTCATTT
1 TTT-ATTT
*
3132773 CTTATTT
1 TTTATTT
3132780 TTTATTTT
1 TTTA-TTT
3132788 TTTCATTT
1 TTT-ATTT
*
3132796 TTCATTT
1 TTTATTT
3132803 TTT
1 TTT
3132806 TTATCCATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
7 16 0.30
8 28 0.53
9 9 0.17
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTATTT
Found at i:3132784 original size:23 final size:23
Alignment explanation
Indices: 3132754--3132805 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
3132744 TTTTTTTACC
3132754 TTTTTTATTTTTTTCATTTCTT-A
1 TTTTTTATTTTTTTCATTT-TTCA
3132777 TTTTTTATTTTTTTCATTTTTCA
1 TTTTTTATTTTTTTCATTTTTCA
3132800 TTTTTT
1 TTTTTT
3132806 TTATCCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTATTTTTTTCATTTTTCA
Found at i:3138997 original size:15 final size:16
Alignment explanation
Indices: 3138969--3139003 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3138959 CAATTTAAGA
3138969 TTATTTTTAAAAAATT
1 TTATTTTTAAAAAATT
* *
3138985 TTATTTTTTAAAATTT
1 TTATTTTTAAAAAATT
3139001 TTA
1 TTA
3139004 AAATTTTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTTTAAAAAATT
Found at i:3139159 original size:14 final size:13
Alignment explanation
Indices: 3139141--3139173 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3139131 TCACTTAGAG
3139141 ATTTTT-TTTAAAA
1 ATTTTTATTT-AAA
3139154 ATTTTTATTTAAA
1 ATTTTTATTTAAA
3139167 ATTTTTA
1 ATTTTTA
3139174 AGAATCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTATTTAAA
Found at i:3139340 original size:20 final size:21
Alignment explanation
Indices: 3139297--3139343 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3139287 CGAAATTAAT
3139297 AAAATA-T-TTTTTTAAATAA
1 AAAATATTATTTTTTAAATAA
3139316 AAAATATTATTTTTTAAAT-A
1 AAAATATTATTTTTTAAATAA
*
3139336 TAAATATT
1 AAAATATT
3139344 TAACTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTATTTTTTAAATAA
Found at i:3139378 original size:24 final size:24
Alignment explanation
Indices: 3139333--3139381 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3139323 TATTTTTTAA
* * **
3139333 ATATAAATATTTAACTGTATAATT
1 ATATAAATATATAAATAAATAATT
3139357 ATATAAATATATAAATAAATAATT
1 ATATAAATATATAAATAAATAATT
3139381 A
1 A
3139382 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATAAATATATAAATAAATAATT
Found at i:3139692 original size:25 final size:25
Alignment explanation
Indices: 3139664--3139712 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3139654 TTCTCACATA
*
3139664 AAAATTTTATAAAAA-TTTATCATTT
1 AAAATTTT-TAAAAAGTCTATCATTT
3139689 AAAATTTTTAAAAAGTCTATCATT
1 AAAATTTTTAAAAAGTCTATCATT
3139713 GGATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATTTTTAAAAAGTCTATCATTT
Found at i:3140485 original size:25 final size:27
Alignment explanation
Indices: 3140433--3140490 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
3140423 CGTGCTTTCT
*
3140433 TCTCTACCTTTTTTTGTATCTCTTTGA
1 TCTCTCCCTTTTTTTGTATCTCTTTGA
3140460 TCTCTCCCTTTTTTT-T-TC-CTTCTGA
1 TCTCTCCCTTTTTTTGTATCTCTT-TGA
3140485 TCTCTC
1 TCTCTC
3140491 GATTAGGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.10
25 11 0.38
26 1 0.03
27 14 0.48
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.59
Consensus pattern (27 bp):
TCTCTCCCTTTTTTTGTATCTCTTTGA
Found at i:3142225 original size:20 final size:19
Alignment explanation
Indices: 3142179--3142227 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
3142169 ATTTAAAGTT
3142179 AATAAAATATTATTTTAAA
1 AATAAAATATTATTTTAAA
**
3142198 AATAAAATATTATTTTTTA
1 AATAAAATATTATTTTAAA
3142217 AATATAAATAT
1 AATA-AAATAT
3142228 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAAATATTATTTTAAA
Found at i:3144647 original size:23 final size:24
Alignment explanation
Indices: 3144604--3144649 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3144594 TATATTGTTA
*
3144604 TTTAAAAAATATATATTAATATAT
1 TTTAAAAAATATATATAAATATAT
3144628 TTTAAAAAAT-T-TCATAAATATA
1 TTTAAAAAATATAT-ATAAATATA
3144650 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 9 0.45
24 10 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAAAAATATATATAAATATAT
Found at i:3144667 original size:15 final size:16
Alignment explanation
Indices: 3144643--3144680 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3144633 AAAATTTCAT
*
3144643 AAATATAAAAAAT-AA
1 AAATAAAAAAAATAAA
*
3144658 AAATAAAAAAACTAAA
1 AAATAAAAAAAATAAA
3144674 AAATAAA
1 AAATAAA
3144681 TCTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAAAAAAATAAA
Found at i:3144781 original size:6 final size:6
Alignment explanation
Indices: 3144772--3144804 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3144762 AAATACTTAT
*
3144772 TAAATA TAAATA TAAAAA TAAATA T-AATA TAAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAA
3144805 AATTCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAATA
Found at i:3144793 original size:18 final size:17
Alignment explanation
Indices: 3144772--3144807 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3144762 AAATACTTAT
3144772 TAAATATAAATATAAAAA
1 TAAATAT-AATATAAAAA
3144790 TAAATATAATATAAAAA
1 TAAATATAATATAAAAA
3144807 T
1 T
3144808 TCAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATATAATATAAAAA
Found at i:3145874 original size:15 final size:15
Alignment explanation
Indices: 3145836--3145892 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3145826 TCGAAATTAA
3145836 TAAAATATTATTTTAAT
1 TAAAATATTATTTT--T
*
3145853 ATGAAATATTATTTTT
1 -TAAAATATTATTTTT
* *
3145869 TAAAATATTAATATT
1 TAAAATATTATTTTT
3145884 TAAATATAT
1 TAAA-ATAT
3145893 ATATATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 16 0.47
16 5 0.15
18 13 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TAAAATATTATTTTT
Found at i:3153522 original size:2 final size:2
Alignment explanation
Indices: 3153515--3153556 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3153505 TATGGGTTGG
3153515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3153557 ACCCATACCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3168557 original size:51 final size:51
Alignment explanation
Indices: 3168481--3168580 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
3168471 GCTTCTTTGT
3168481 TACTTAAGTTCTCCTTCAAGGAGAGGCATCCTGTCAACTACGGGAGGATCG
1 TACTTAAGTTCTCCTTCAAGGAGAGGCATCCTGTCAACTACGGGAGGATCG
*
3168532 TACTTAAGTTCTCCTTCAAGGAGAGGCATCCTGTCAACTGCGGGAGGAT
1 TACTTAAGTTCTCCTTCAAGGAGAGGCATCCTGTCAACTACGGGAGGAT
3168581 ATTACTTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (51 bp):
TACTTAAGTTCTCCTTCAAGGAGAGGCATCCTGTCAACTACGGGAGGATCG
Found at i:3169490 original size:3 final size:3
Alignment explanation
Indices: 3169472--3169505 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3169462 ATTTTCCCTG
*
3169472 TAT T-T TAT TTT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3169506 CAACATGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:3169695 original size:2 final size:2
Alignment explanation
Indices: 3169688--3169725 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3169678 CATCATATTT
3169688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3169726 TCTTGATTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3170701 original size:3 final size:3
Alignment explanation
Indices: 3170687--3170731 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
3170677 AATCGATGAT
*
3170687 AGA AGC AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3170732 CGTAGAGCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3172105 original size:6 final size:6
Alignment explanation
Indices: 3172094--3172118 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3172084 ATATAGATGT
3172094 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
3172119 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:3174508 original size:21 final size:21
Alignment explanation
Indices: 3174468--3174506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3174458 TTTTGATGTT
*
3174468 TTATTTAATTGTTGATTTTAA
1 TTATTTAATTATTGATTTTAA
3174489 TTATTTAATTATT-ATTTT
1 TTATTTAATTATTGATTTT
3174507 TATTTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTATTTAATTATTGATTTTAA
Found at i:3174511 original size:17 final size:19
Alignment explanation
Indices: 3174460--3174511 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
3174450 GGCTTAACTT
* *
3174460 TTGATGTTTTATTTAATTG
1 TTGATTTTTTATTTAATTA
3174479 TTGATTTTAATTATTTAATTA
1 TTGATTTT--TTATTTAATTA
3174500 TT-A-TTTTTATTT
1 TTGATTTTTTATTT
3174512 TTTTGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
19 10 0.34
20 1 0.03
21 12 0.41
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TTGATTTTTTATTTAATTA
Found at i:3200928 original size:20 final size:19
Alignment explanation
Indices: 3200903--3200943 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3200893 AAAAAATAAA
*
3200903 TTTATTAATCTATTCAAAAT
1 TTTATT-ATCTATACAAAAT
*
3200923 TTTATTTTCTATACAAAAT
1 TTTATTATCTATACAAAAT
3200942 TT
1 TT
3200944 AATTTGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTATCTATACAAAAT
Found at i:3200948 original size:19 final size:19
Alignment explanation
Indices: 3200911--3200948 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3200901 AATTTATTAA
* *
3200911 TCTATTCAAAATTTTATTT
1 TCTATACAAAATTTAATTT
3200930 TCTATACAAAATTTAATTT
1 TCTATACAAAATTTAATTT
3200949 GAATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
TCTATACAAAATTTAATTT
Found at i:3201190 original size:77 final size:79
Alignment explanation
Indices: 3201098--3201254 Score: 230
Period size: 78 Copynumber: 2.0 Consensus size: 79
3201088 TTTTGGATAA
*
3201098 AAAATATGTTCTTTATTATGATTTA-T-GATAAAATAATACTTTTAGTAGAAAAAAAC-TTTTTT
1 AAAATATATTCTTTATTATGATTTACTAG-TAAAATAATACTTTTAGTAGAAAAAAACTTTTTTT
3201160 TGTTTTTAAAATGTC
65 TGTTTTTAAAATGTC
* * *
3201175 AAAATATATTTTTTATTATGATTTACTAGTAAAATAATATTTTTAGTAGAAAATAACTTTTTTTT
1 AAAATATATTCTTTATTATGATTTACTAGTAAAATAATACTTTTAGTAGAAAAAAAC--TTTTTT
3201240 TTGTTTTTAAAATGT
64 TTGTTTTTAAAATGT
3201255 ATCGATTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
77 23 0.32
78 27 0.38
79 1 0.01
81 20 0.28
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (79 bp):
AAAATATATTCTTTATTATGATTTACTAGTAAAATAATACTTTTAGTAGAAAAAAACTTTTTTTT
GTTTTTAAAATGTC
Found at i:3202747 original size:11 final size:11
Alignment explanation
Indices: 3202727--3202778 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
3202717 TCGAATTTTT
*
3202727 ATTTATTTTAA
1 ATTTAATTTAA
3202738 ATTTAATTTAA
1 ATTTAATTTAA
*
3202749 TTTTATATTT--
1 ATTTA-ATTTAA
*
3202759 ATTAAATTTAA
1 ATTTAATTTAA
3202770 ATTTAATTT
1 ATTTAATTT
3202779 GATTTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 4 0.12
10 3 0.09
11 22 0.67
12 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:3202783 original size:16 final size:16
Alignment explanation
Indices: 3202727--3202789 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
3202717 TCGAATTTTT
*
3202727 ATTTATTTTAAATTTA
1 ATTTAATTTAAATTTA
*
3202743 ATTTAATTTTATATTT-
1 ATTTAA-TTTAAATTTA
*
3202759 ATTAAATTTAAATTTA
1 ATTTAATTTAAATTTA
*
3202775 ATTTGATTTAAATTT
1 ATTTAATTTAAATTT
3202790 TTGTTTAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 8 0.21
16 23 0.59
17 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAATTTAAATTTA
Found at i:3202891 original size:8 final size:8
Alignment explanation
Indices: 3202874--3202905 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3202864 AATATTATTT
3202874 TATAAATA
1 TATAAATA
*
3202882 TATAATTA
1 TATAAATA
3202890 TATAAATA
1 TATAAATA
3202898 TATAAATA
1 TATAAATA
3202906 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TATAAATA
Found at i:3202893 original size:16 final size:16
Alignment explanation
Indices: 3202855--3202902 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
3202845 TTTGATTCGA
3202855 AATTA-ATAAA-ATAT
1 AATTATATAAATATAT
* *
3202869 TATTTTATAAATATAT
1 AATTATATAAATATAT
3202885 AATTATATAAATATAT
1 AATTATATAAATATAT
3202901 AA
1 AA
3202903 ATAAAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATATAAATATAT
Found at i:3208496 original size:3 final size:3
Alignment explanation
Indices: 3208488--3208519 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3208478 ATGAGAACAA
3208488 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3208520 AAGATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3216641 original size:12 final size:12
Alignment explanation
Indices: 3216624--3216657 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3216614 AGAAACGATT
*
3216624 AAATAAAAATTA
1 AAATAAAAATCA
3216636 AAATAAAAATCA
1 AAATAAAAATCA
3216648 AAATTAAAAA
1 AAA-TAAAAA
3216658 ATCCCATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATAAAAATCA
Found at i:3224034 original size:3 final size:3
Alignment explanation
Indices: 3224021--3224063 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
3224011 TCAATAAAAA
3224021 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3224064 TTACTCTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3225947 original size:19 final size:19
Alignment explanation
Indices: 3225909--3225947 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3225899 CATCTCCCAC
**
3225909 TTTTTTTTCTTTTTCTTTA
1 TTTTTTTTCTTTTTAATTA
*
3225928 TTTTTTTTTTTTTTAATTA
1 TTTTTTTTCTTTTTAATTA
3225947 T
1 T
3225948 AGTATTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTCTTTTTAATTA
Found at i:3228119 original size:13 final size:13
Alignment explanation
Indices: 3228101--3228126 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3228091 ATATATTAAA
3228101 TAAAAATTAAAAT
1 TAAAAATTAAAAT
3228114 TAAAAATTAAAAT
1 TAAAAATTAAAAT
3228127 AGATAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:3229444 original size:6 final size:6
Alignment explanation
Indices: 3229433--3229498 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
3229423 GATATTTGAT
*
3229433 ATTTAA ATTTAA ATTTAA ATTT-- ATTT-A ATTT-G ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
3229477 ATATTAA ATATAT A-TTAA ATTT
1 AT-TTAA ATTTAA ATTTAA ATTT
3229499 GAATCAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
4 4 0.08
5 11 0.22
6 29 0.58
7 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:3229471 original size:32 final size:35
Alignment explanation
Indices: 3229433--3229500 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 35
3229423 GATATTTGAT
*
3229433 ATTTAAATTTAAAT-TTAAAT-T-TATTTAATTTG
1 ATTTAAATTTAAATATTAAATATATATTAAATTTG
3229465 ATTTAAATTTAAATATTAAATATATATTAAATTTG
1 ATTTAAATTTAAATATTAAATATATATTAAATTTG
3229500 A
1 A
3229501 ATCAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.44
33 6 0.19
34 1 0.03
35 11 0.34
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
ATTTAAATTTAAATATTAAATATATATTAAATTTG
Found at i:3229518 original size:35 final size:32
Alignment explanation
Indices: 3229440--3229519 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 32
3229430 GATATTTAAA
* **
3229440 TTTAAATTTAAATTTATTTAATTTGATTTAAAT
1 TTTAAA-TTAAATTTATTAAATTTGATCAAAAT
*
3229473 TTAAATATTAAATATATATTAAATTTGAATCAAAAT
1 TTTAA-ATTAAAT-T-TATTAAATTTG-ATCAAAAT
3229509 TTTAAATTAAA
1 TTTAAATTAAA
3229520 AAACTTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 10 0.26
34 2 0.05
35 16 0.42
36 10 0.26
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTAAATTAAATTTATTAAATTTGATCAAAAT
Found at i:3230959 original size:17 final size:17
Alignment explanation
Indices: 3230933--3230965 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3230923 ATAAATTTTT
3230933 AAAATAAATATATATTA
1 AAAATAAATATATATTA
*
3230950 AAAATTAATATATATT
1 AAAATAAATATATATT
3230966 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATAAATATATATTA
Found at i:3232362 original size:16 final size:16
Alignment explanation
Indices: 3232341--3232371 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3232331 GTGAGCTTCT
3232341 ATTTTAATTTTTTAAA
1 ATTTTAATTTTTTAAA
*
3232357 ATTTTATTTTTTTAA
1 ATTTTAATTTTTTAA
3232372 TTCATCGCAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTAATTTTTTAAA
Found at i:3235210 original size:15 final size:15
Alignment explanation
Indices: 3235192--3235235 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3235182 GCAACAACTA
*
3235192 CAGCAACTGCAACAG
1 CAGCAACAGCAACAG
* *
3235207 CAGCATCAGCAACAT
1 CAGCAACAGCAACAG
*
3235222 CAGCAACAACAACA
1 CAGCAACAGCAACA
3235236 ATGTCATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.45, C:0.34, G:0.14, T:0.07
Consensus pattern (15 bp):
CAGCAACAGCAACAG
Found at i:3236063 original size:10 final size:10
Alignment explanation
Indices: 3236048--3236076 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3236038 TGTTAATCTC
3236048 TCTCTCTCTG
1 TCTCTCTCTG
3236058 TCTCTCTCTG
1 TCTCTCTCTG
3236068 TCTCTCTCT
1 TCTCTCTCT
3236077 TCTAACAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52
Consensus pattern (10 bp):
TCTCTCTCTG
Found at i:3237327 original size:16 final size:17
Alignment explanation
Indices: 3237301--3237335 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3237291 AATCAAACTG
*
3237301 AATTATATATATTTTTT
1 AATTATATATATATTTT
3237318 AATT-TATATATATTTT
1 AATTATATATATATTTT
3237334 AA
1 AA
3237336 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTATATATATATTTT
Found at i:3251455 original size:16 final size:17
Alignment explanation
Indices: 3251434--3251467 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3251424 AAAAGGGAAA
3251434 AAGAAATA-AGCATACC
1 AAGAAATATAGCATACC
*
3251450 AAGAAATATAGCCTACC
1 AAGAAATATAGCATACC
3251467 A
1 A
3251468 TTTACTGCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.15
Consensus pattern (17 bp):
AAGAAATATAGCATACC
Found at i:3266907 original size:2 final size:2
Alignment explanation
Indices: 3266902--3266928 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3266892 AAAAAAAAAA
3266902 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3266929 GAAGCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3278192 original size:13 final size:13
Alignment explanation
Indices: 3278174--3278199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3278164 GTTTAAAAGT
3278174 TTAATTTTAAAAA
1 TTAATTTTAAAAA
3278187 TTAATTTTAAAAA
1 TTAATTTTAAAAA
3278200 GATTTGTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTTTAAAAA
Found at i:3285200 original size:2 final size:2
Alignment explanation
Indices: 3285195--3285224 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3285185 TCTCTCTCTC
3285195 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3285225 TAAAATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3311073 original size:2 final size:2
Alignment explanation
Indices: 3311066--3311107 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3311056 TTGCCCCTCC
3311066 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3311108 TTGCTTCTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3311996 original size:21 final size:20
Alignment explanation
Indices: 3311969--3312020 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3311959 TATGGGTGAT
*
3311969 AAATTAATTTTATTAAATTTA
1 AAATTAATTTTAAT-AATTTA
**
3311990 TTATTAAATTTTAATAATTTA
1 AAATT-AATTTTAATAATTTA
3312011 AAATTAATTT
1 AAATTAATTT
3312021 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.20
21 12 0.48
22 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTAATTTTAATAATTTA
Found at i:3312027 original size:12 final size:12
Alignment explanation
Indices: 3312004--3312035 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3311994 TAAATTTTAA
3312004 TAATTT-AAAAT
1 TAATTTAAAAAT
3312015 TAATTTAAAAAT
1 TAATTTAAAAAT
3312027 TAATTTAAA
1 TAATTTAAA
3312036 TGATTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTTAAAAAT
Found at i:3321925 original size:2 final size:2
Alignment explanation
Indices: 3321918--3321942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3321908 TGCAAGTGAG
3321918 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3321943 GTTGACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3322337 original size:2 final size:2
Alignment explanation
Indices: 3322320--3322354 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3322310 GTTGGAGGAT
* *
3322320 GA GA GG GA GG GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3322355 GAGGAGGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3322860 original size:10 final size:11
Alignment explanation
Indices: 3322845--3322878 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
3322835 GCTCATCCCA
3322845 CTTCTCTCT-T
1 CTTCTCTCTCT
3322855 CTTCTCTCTCT
1 CTTCTCTCTCT
3322866 C-TCTCTCTCT
1 CTTCTCTCTCT
3322876 CTT
1 CTT
3322879 TTTGCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (11 bp):
CTTCTCTCTCT
Found at i:3326397 original size:2 final size:2
Alignment explanation
Indices: 3326385--3326413 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3326375 GTGATACTAC
3326385 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3326414 CTGGTGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3327226 original size:2 final size:2
Alignment explanation
Indices: 3327219--3327248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3327209 AATACCATGC
3327219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3327249 TAAAGGTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3329992 original size:26 final size:27
Alignment explanation
Indices: 3329946--3329998 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3329936 TTATTACTTT
*
3329946 TAAAAAAATTGGGTAATGATTTTTTTG
1 TAAAAAAATTGGGTAATGATTGTTTTG
3329973 TAAAAAAATTGGTGT-A-GATTGTTTTG
1 TAAAAAAATTGG-GTAATGATTGTTTTG
3329999 ATTGATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 13 0.54
28 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (27 bp):
TAAAAAAATTGGGTAATGATTGTTTTG
Found at i:3341053 original size:29 final size:30
Alignment explanation
Indices: 3340988--3341046 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
3340978 TTTTAAATAG
*
3340988 ATATTTTTAACAAAAATATTAATAAAATTT
1 ATATTATTAACAAAAATATTAATAAAATTT
* *
3341018 ATATTATTAA-AAAAATATTGATCAAATTT
1 ATATTATTAACAAAAATATTAATAAAATTT
3341047 TAATTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
ATATTATTAACAAAAATATTAATAAAATTT
Found at i:3342202 original size:39 final size:39
Alignment explanation
Indices: 3342085--3342202 Score: 173
Period size: 39 Copynumber: 3.0 Consensus size: 39
3342075 CCAAAAATCT
* *
3342085 TCATCTTGTTCATTGGTGCTAGATTGAAGTGGGATCTCA
1 TCATCTTGTTCATTGGTGCTAGATTGAAGTTGAATCTCA
* * * *
3342124 CCATGTTGTTCATTGGTGTTAGATTGATGTTGAATCTCA
1 TCATCTTGTTCATTGGTGCTAGATTGAAGTTGAATCTCA
*
3342163 TCATCTTGTTCATTGGTGCTAGATTGACGTTGAATCTCA
1 TCATCTTGTTCATTGGTGCTAGATTGAAGTTGAATCTCA
3342202 T
1 T
3342203 GAAAGTCACG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (39 bp):
TCATCTTGTTCATTGGTGCTAGATTGAAGTTGAATCTCA
Found at i:3350961 original size:205 final size:202
Alignment explanation
Indices: 3350713--3351207 Score: 560
Period size: 202 Copynumber: 2.4 Consensus size: 202
3350703 AGATTTATTA
* * * *
3350713 AAAAATTTATCATTTGAAATTTTTAAGAA-TCTCATTC-TTGGATAATTGTCAAATATTTTCAAC
1 AAAAATTTATCATTTAAAATTTTTAAAAATTCT-A-TCATTGGATAATTATCAAATATTCTC-A-
*
3350776 CAAAAAAAATTTATT-TTTTGT-TTTTCTATTT-TTTTCTCTTGTTTTATTGAAAATAAAT-TTA
62 -AAAAAAAATTTATTATTTTGTATTTT-T-TTTCTCTTC-CTT-TTTTATTGAAAATAAATATTA
*
3350837 ATTATTATTATTAAAACTTTATCTAAATTATTTCACAATTTGGAACAAATTTAGATAAAATTTCT
122 ATTATTATTATTAAAACTTTATCTAAATTATTTCACAATTTGGAACAAATTTAGATAAAATGTCT
3350902 CACCTAAAAATTTTAT
187 CACCTAAAAATTTTAT
* **
3350918 AAAAATTTA-CAATTTAAAATTTTTAAAAATTCTATCATTGGATAATTATTATTTATTCTCAAAA
1 AAAAATTTATC-ATTTAAAATTTTTAAAAATTCTATCATTGGATAATTATCAAATATTCTCAAAA
* * * *
3350982 AATATTTTCTTATTTTGTATTTTTTTTCTCTTCCTTTTTTATTGAAAATAAATATTAATTATTGT
65 AAAAATTTATTATTTTGTATTTTTTTTCTCTTCCTTTTTTATTGAAAATAAATATTAATTATTAT
* * * * *
3351047 TATTGAAACTTTATCTAAATTATTTCATAATTTGGGATAAATTTAGATAAAATGTCTCACTTAAA
130 TATTAAAACTTTATCTAAATTATTTCACAATTTGGAACAAATTTAGATAAAATGTCTCACCTAAA
3351112 AATTTTAT
195 AATTTTAT
* * * * * * **
3351120 AGAAATTTATCATTTGAAAATTTTGAAAATTTC-ATTATTAGATAATTATTAGTTATTCTCAAAA
1 AAAAATTTATCATTT-AAAATTTTTAAAAATTCTATCATTGGATAATTATCAAATATTCTCAAAA
* * *
3351184 AATATTTTTTTA-TTT-TATTTTTTT
65 AAAAATTTATTATTTTGTATTTTTTT
3351208 AAATTTAATC
Statistics
Matches: 256, Mismatches: 25, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
200 9 0.04
201 20 0.08
202 145 0.57
203 27 0.11
204 8 0.03
205 44 0.17
206 3 0.01
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (202 bp):
AAAAATTTATCATTTAAAATTTTTAAAAATTCTATCATTGGATAATTATCAAATATTCTCAAAAA
AAAATTTATTATTTTGTATTTTTTTTCTCTTCCTTTTTTATTGAAAATAAATATTAATTATTATT
ATTAAAACTTTATCTAAATTATTTCACAATTTGGAACAAATTTAGATAAAATGTCTCACCTAAAA
ATTTTAT
Found at i:3351091 original size:202 final size:199
Alignment explanation
Indices: 3350817--3351207 Score: 597
Period size: 202 Copynumber: 1.9 Consensus size: 199
3350807 TTTTCTCTTG
3350817 TTTTATTGAAAATAAATTTAATTATTATTATTAAAACTTTATCTAAATTATTTCACAATTTGGAA
1 TTTTATTGAAAATAAATTTAATTATTATTATTAAAACTTTATCTAAATTATTTCACAATTTGGAA
* *
3350882 CAAATTTAGATAAAATTTCTCACCTAAAAATTTTATAAAAATTTA-CAATTT-AAAATTTTTAAA
66 CAAATTTAGATAAAATGTCTCACCTAAAAATTTTATAAAAATTTATC-ATTTGAAAATTTTGAAA
* *
3350945 AATTCTATCATTGGATAATTATTATTTATTCTCAAAAAATATTTTCTTATTTTGTATTTTTTTTC
130 AATTC-ATCATTAGATAATTATTAGTTATTCTCAAAAAATATTTTCTTA-TTT-TATTTTTTTTC
3351010 TCTTCCTT
192 TCTTCCTT
* * * *
3351018 TTTTATTGAAAATAAATATTAATTATTGTTATTGAAACTTTATCTAAATTATTTCATAATTTGGG
1 TTTTATTGAAAATAAAT-TTAATTATTATTATTAAAACTTTATCTAAATTATTTCACAATTTGGA
* * *
3351083 ATAAATTTAGATAAAATGTCTCACTTAAAAATTTTATAGAAATTTATCATTTGAAAATTTTGAAA
65 ACAAATTTAGATAAAATGTCTCACCTAAAAATTTTATAAAAATTTATCATTTGAAAATTTTGAAA
* * *
3351148 ATTTCATTATTAGATAATTATTAGTTATTCTCAAAAAATATTTTTTTATTTTATTTTTTT
130 AATTCATCATTAGATAATTATTAGTTATTCTCAAAAAATATTTTCTTATTTTATTTTTTT
3351208 AAATTTAATC
Statistics
Matches: 173, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
200 9 0.05
201 20 0.12
202 128 0.74
203 16 0.09
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (199 bp):
TTTTATTGAAAATAAATTTAATTATTATTATTAAAACTTTATCTAAATTATTTCACAATTTGGAA
CAAATTTAGATAAAATGTCTCACCTAAAAATTTTATAAAAATTTATCATTTGAAAATTTTGAAAA
ATTCATCATTAGATAATTATTAGTTATTCTCAAAAAATATTTTCTTATTTTATTTTTTTTCTCTT
CCTT
Found at i:3352552 original size:41 final size:41
Alignment explanation
Indices: 3352495--3353009 Score: 450
Period size: 41 Copynumber: 12.6 Consensus size: 41
3352485 TAAGAAGAAA
* * * *
3352495 CTCAATGACTTTGAAAAATAAAAGGCTCATCTAAATAAAAG
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* *
3352536 CTCAATGACTTTGAAAAATAAAAGGCTCCTCTAAGTAGAGG
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
** * * *
3352577 CTCAACGACTTTAAAAAATAAAAGGCTCTTCTAAGTAGAAG
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* * * * * *
3352618 TTTAACAACTTTGAAAAATAAATAAGGCTTC-TGTAAATAAAGG
1 CTCAATAACTTTGAAAAAT-AA-AAGGC-TCATCTAAGTAGAGG
* * **
3352661 CTCAATGACTTTGAAAAATAAAAAAGCTCATCTAAACAGAGG
1 CTCAATAACTTTGAAAAAT-AAAAGGCTCATCTAAGTAGAGG
* *
3352703 CACAATAACTTTGAAAAATAAAAGGCTCATCTAAGCAGAGG
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* * *
3352744 -TACAATAACTTTGAAAAATAAAAAGCTCTTTTAAGTAGAGG
1 CT-CAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* * * * *
3352785 CACAACAACTTTGAAAAATAAAAAGCTCTTCTAAGCAGAGG
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* * * *
3352826 CACAATAACTTT-AGAAAATAAAAGGCTCCTTTAAGTATAGG
1 CTCAATAACTTTGA-AAAATAAAAGGCTCATCTAAGTAGAGG
* * *
3352867 CAT-AACAACTTTGAAAAATAAAAGGCTCCTCTAAGCAGAGG
1 C-TCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* * * * * *
3352908 --C-ACAACTTTGAAAAATAAAATGCTCCTTTAAGCAGAGA
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* * * * * *
3352946 CACAATAATTTTAAAAAATAAAATGCTCATCTAAATAGAGA
1 CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
* *
3352987 CACAATAATTTTGAAAAATAAAA
1 CTCAATAACTTTGAAAAATAAAA
3353010 AGCTTCTTGA
Statistics
Matches: 402, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
38 34 0.08
40 2 0.00
41 300 0.75
42 33 0.08
43 31 0.08
44 2 0.00
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (41 bp):
CTCAATAACTTTGAAAAATAAAAGGCTCATCTAAGTAGAGG
Found at i:3352844 original size:123 final size:123
Alignment explanation
Indices: 3352497--3353013 Score: 522
Period size: 123 Copynumber: 4.2 Consensus size: 123
3352487 AGAAGAAACT
* * * * ** *
3352497 CAATGACTTTGAAAAATAAAAGGCTCATCTAAATAAAAGCTCAATGACTTTGAAAAATAAAAGGC
1 CAATAACTTTGAAAAATAAAAAGCTCTTCTAAATAAAGGCTCAACAACTTTGAAAAATAAAAAGC
* * * ** * * **
3352562 TCCTCTAAGTAGAGGCTCAACGACTTTAAAAAATAAAAGGCTCTTCTAAGTAGAAGTT
66 TCTTCTAAGCAGAGGCACAATAACTTTAAAAAATAAAAGGCTCATCTAAGTAGAGGCA
* * * **
3352620 TAACAACTTTGAAAAATAAATAAGGCT-TCTGTAAATAAAGGCTCAATGACTTTGAAAAATAAAA
1 CAATAACTTTGAAAAATAAA-AA-GCTCT-TCTAAATAAAGGCTCAACAACTTTGAAAAAT-AAA
* * * * *
3352684 AAGCTCATCTAAACAGAGGCACAATAACTTTGAAAAATAAAAGGCTCATCTAAGCAGAGGTA
62 AAGCTCTTCTAAGCAGAGGCACAATAACTTTAAAAAATAAAAGGCTCATCTAAGTAGAGGCA
* * * *
3352746 CAATAACTTTGAAAAATAAAAAGCTCTTTTAAGTAGAGGCACAACAACTTTGAAAAATAAAAAGC
1 CAATAACTTTGAAAAATAAAAAGCTCTTCTAAATAAAGGCTCAACAACTTTGAAAAATAAAAAGC
* * * *
3352811 TCTTCTAAGCAGAGGCACAATAACTTTAGAAAATAAAAGGCTCCTTTAAGTATAGGCA
66 TCTTCTAAGCAGAGGCACAATAACTTTAAAAAATAAAAGGCTCATCTAAGTAGAGGCA
* * * * ** * *
3352869 TAACAACTTTGAAAAATAAAAGGCTCCTCTAAGCAGAGG--C-ACAACTTTGAAAAATAAAATGC
1 CAATAACTTTGAAAAATAAAAAGCTCTTCTAAATAAAGGCTCAACAACTTTGAAAAATAAAAAGC
* * * * *
3352931 TCCTT-TAAGCAGAGACACAATAATTTTAAAAAATAAAATGCTCATCTAAATAGAGACA
66 T-CTTCTAAGCAGAGGCACAATAACTTTAAAAAATAAAAGGCTCATCTAAGTAGAGGCA
*
3352989 CAATAATTTTGAAAAATAAAAAGCT
1 CAATAACTTTGAAAAATAAAAAGCT
3353014 TCTTGACATT
Statistics
Matches: 332, Mismatches: 56, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
120 87 0.26
121 4 0.01
123 106 0.32
124 29 0.09
125 35 0.11
126 71 0.21
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (123 bp):
CAATAACTTTGAAAAATAAAAAGCTCTTCTAAATAAAGGCTCAACAACTTTGAAAAATAAAAAGC
TCTTCTAAGCAGAGGCACAATAACTTTAAAAAATAAAAGGCTCATCTAAGTAGAGGCA
Found at i:3352993 original size:161 final size:163
Alignment explanation
Indices: 3352507--3353009 Score: 435
Period size: 167 Copynumber: 3.1 Consensus size: 163
3352497 CAATGACTTT
* * * * * * ** * *
3352507 GAAAAATAAAAGGCTCATCTAAATAAAAGCTCAATGACTTTGAAAAATAAAAGGCTCCTCTAAGT
1 GAAAAATAAAAGGCTCCTTTAAGTATAGGCACAACAACTTTGAAAAATAAAAGGCTCATCTAAGC
* * * * * *** *
3352572 AGAGGCTCAACGACTTTAAAAAATAAAAGGCT-CTTCTAAGTAGA-AGTTTAACAACTTTGAAAA
66 AGAGG-ACAACAACTTTGAAAAATAAAAAGCTCCTT-TAAGCAGAGA-CACAACAACTTTAAAAA
* * * * * *
3352635 ATAAATAAGGCTTC-TGTAAATAAAGGCTCAATGACTTT-
128 ATAAA-AA-GC-TCATCTAAACAGAGACACAAT-AATTTA
* * * ** * *
3352673 GAAAAATAAAAAAGCTCATCTAAACAGAGGCACAATAACTTTGAAAAATAAAAGGCTCATCTAAG
1 GAAAAAT-AAAAGGCTCCTTTAAGTATAGGCACAACAACTTTGAAAAATAAAAGGCTCATCTAAG
* * * * *
3352738 CAGAGGTACAATAACTTTGAAAAATAAAAAGCTCTTTTAAGTAGAGGCACAACAACTTTGAAAAA
65 CAGAGG-ACAACAACTTTGAAAAATAAAAAGCTCCTTTAAGCAGAGACACAACAACTTTAAAAAA
* * *
3352803 TAAAAAGCTCTTCTAAGCAGAGGCACAATAACTTTA
129 TAAAAAGCTCATCTAAACAGAGACACAATAA-TTTA
* *
3352839 G-AAAATAAAAGGCTCCTTTAAGTATAGGCATAACAACTTTGAAAAATAAAAGGCTCCTCTAAGC
1 GAAAAATAAAAGGCTCCTTTAAGTATAGGCACAACAACTTTGAAAAATAAAAGGCTCATCTAAGC
* * *
3352903 AGAGG-C-ACAACTTTGAAAAATAAAATGCTCCTTTAAGCAGAGACACAATAATTTTAAAAAATA
66 AGAGGACAACAACTTTGAAAAATAAAAAGCTCCTTTAAGCAGAGACACAACAACTTTAAAAAATA
* * *
3352966 AAATGCTCATCTAAATAGAGACACAATAATTTT
131 AAAAGCTCATCTAAACAGAGACACAATAATTTA
3352999 GAAAAATAAAA
1 GAAAAATAAAA
3353010 AGCTTCTTGA
Statistics
Matches: 282, Mismatches: 48, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
160 4 0.01
161 82 0.29
162 1 0.00
164 57 0.20
165 23 0.08
166 10 0.04
167 103 0.37
168 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (163 bp):
GAAAAATAAAAGGCTCCTTTAAGTATAGGCACAACAACTTTGAAAAATAAAAGGCTCATCTAAGC
AGAGGACAACAACTTTGAAAAATAAAAAGCTCCTTTAAGCAGAGACACAACAACTTTAAAAAATA
AAAAGCTCATCTAAACAGAGACACAATAATTTA
Found at i:3353302 original size:20 final size:20
Alignment explanation
Indices: 3353264--3353302 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3353254 TCACATCCAA
*
3353264 AAGTTCAAAGCTTCTCATTC
1 AAGTTCAAAGCTTCACATTC
*
3353284 AAGTTCAAAGGTTCACATT
1 AAGTTCAAAGCTTCACATT
3353303 TAACAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
AAGTTCAAAGCTTCACATTC
Found at i:3353335 original size:22 final size:22
Alignment explanation
Indices: 3353293--3353335 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3353283 CAAGTTCAAA
**
3353293 GGTTCACATTTAACAAATTTAG
1 GGTTCACATCCAACAAATTTAG
3353315 GGTTCACATCCAA-AAAGTTTA
1 GGTTCACATCCAACAAA-TTTA
3353336 AGCTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
GGTTCACATCCAACAAATTTAG
Found at i:3353976 original size:63 final size:63
Alignment explanation
Indices: 3353909--3354140 Score: 288
Period size: 63 Copynumber: 3.7 Consensus size: 63
3353899 TCTATTTTCT
* * * * *
3353909 ATCACTTGGTCACTACTCATAGGCTTCTCAGCACTAGCCATTTCAAAATAAACTTCGTCCTCC
1 ATCACTTGGTCACTAATCATAGGTTTCTCAGCACTAACCATTTCAAAACAAATTTCGTCCTCC
* * * *
3353972 ATCACTTGGTCATTAATCATAGGTTTTTCAGCACTAACCATTTCAGAACAAATTTCATCCTCC
1 ATCACTTGGTCACTAATCATAGGTTTCTCAGCACTAACCATTTCAAAACAAATTTCGTCCTCC
* * * *
3354035 ATCACTTGGTCA-TCAATCATAGGTTTCTTAGTACTAACCATTTCAAAACAAATTTCGCCCAT-T
1 ATCACTTGGTCACT-AATCATAGGTTTCTCAGCACTAACCATTTCAAAACAAATTTCGTCC-TCC
* * *
3354098 ATCACTTGGTCACCAATTATAGGTTTCTCAGCACTAATCATTT
1 ATCACTTGGTCACTAATCATAGGTTTCTCAGCACTAACCATTT
3354141 TAGAATAAAT
Statistics
Matches: 145, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
62 1 0.01
63 143 0.99
64 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.34
Consensus pattern (63 bp):
ATCACTTGGTCACTAATCATAGGTTTCTCAGCACTAACCATTTCAAAACAAATTTCGTCCTCC
Found at i:3354897 original size:17 final size:15
Alignment explanation
Indices: 3354841--3354914 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 15
3354831 TGAGTCTTTC
*
3354841 TTTTCTTTCATTTTT
1 TTTTTTTTCATTTTT
3354856 ATTTTTTTT--TTTTT
1 -TTTTTTTTCATTTTT
3354870 TTCATTTTTCTCATTTTT
1 TT--TTTTT-TCATTTTT
3354888 TTTTTCTTCTCATTTTT
1 TTTTT-TT-TCATTTTT
*
3354905 AATTTTTTTC
1 -TTTTTTTTC
3354915 TCTTTTCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.04
14 5 0.10
15 5 0.10
16 13 0.27
17 13 0.27
18 11 0.22
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTTCATTTTT
Found at i:3354920 original size:17 final size:16
Alignment explanation
Indices: 3354848--3354920 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 16
3354838 TTCTTTTCTT
3354848 TCATTTTTATTTTTTT-
1 TCATTTTT-TTTTTTTC
3354864 T--TTTTTTTCATTTTTC
1 TCATTTTTTT--TTTTTC
3354880 TCATTTTTTTTTTCTTC
1 TCATTTTTTTTTT-TTC
3354897 TCATTTTTAATTTTTTTC
1 TCATTTTT--TTTTTTTC
3354915 TC-TTTT
1 TCATTTT
3354921 CATTTTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.04
14 5 0.10
15 5 0.10
16 5 0.10
17 15 0.31
18 12 0.24
19 5 0.10
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (16 bp):
TCATTTTTTTTTTTTC
Found at i:3354927 original size:17 final size:17
Alignment explanation
Indices: 3354874--3354927 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
3354864 TTTTTTTTCA
3354874 TTTTTCTCATTTT-TTT
1 TTTTTCTCATTTTATTT
*
3354890 TTTCTTCTCATTTTTAATT
1 TTT-TTCTCA-TTTTATTT
3354909 TTTTTCTC-TTTTCATTT
1 TTTTTCTCATTTT-ATTT
3354926 TT
1 TT
3354928 AATCCATTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 7 0.22
17 11 0.34
18 9 0.28
19 5 0.16
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTCATTTTATTT
Found at i:3354929 original size:23 final size:23
Alignment explanation
Indices: 3354841--3354930 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
3354831 TGAGTCTTTC
*
3354841 TTTTC-TTTCATTTTTATTTTTT
1 TTTTCTTTTCATTTTTAATTTTT
* *
3354863 TTTTTTTTTCATTTTTCTCATTTTTT
1 TTTTCTTTTCA-TTTT-T-AATTTTT
*
3354889 TTTTCTTCTCATTTTTAATTTTT
1 TTTTCTTTTCATTTTTAATTTTT
*
3354912 TTCTCTTTTCATTTTTAAT
1 TTTTCTTTTCATTTTTAAT
3354931 CCATTAGTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
22 4 0.07
23 28 0.48
24 5 0.09
25 5 0.09
26 16 0.28
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTCATTTTTAATTTTT
Found at i:3359431 original size:186 final size:187
Alignment explanation
Indices: 3359223--3359592 Score: 591
Period size: 186 Copynumber: 2.0 Consensus size: 187
3359213 TTTTCTCTTT
*
3359223 TTTTTTATTGAAAATAAATATTAATTATAGTTATTAAAACTTTATCTAAATTATTTTACCATTTG
1 TTTTTTATTGAAAATAAATATTAATTATAGTTATTAAAACTTTATCTAAATTATTTCACCATTTG
* * *
3359288 GGACAAATTTAGATAAAATTTTTCACCTAAGAATTTTATAAAAATTTACCATTTAAAATTT-TAA
66 GAACAAATTTAGATAAAATTTCTCACCTAAAAATTTTATAAAAATTTACCATTTAAAATTTCTAA
* * *
3359352 AAATTTCATCATTGGTTAATTATTATTTATTCTCAAAAAATATTTTTTTGTTTTTCTC
131 AAATTTCATCATTAGATAATTATTATTTATTCT-AAAAAATATTTTTTTATTTTTCTC
* * *
3359410 TTTTTTA-TGAAAATAAATATTAATTATTGTTATTGAAACTTTATTTAAATTATTTCACCATTTG
1 TTTTTTATTGAAAATAAATATTAATTATAGTTATTAAAACTTTATCTAAATTATTTCACCATTTG
* * * *
3359474 GAATAAATTTAGATAAAATTTCTCACCTAAAAATTTTATAAAAATTTACTATTTGAAATTTCTCA
66 GAACAAATTTAGATAAAATTTCTCACCTAAAAATTTTATAAAAATTTACCATTTAAAATTTCTAA
3359539 AAATTTCATCATTAGATAATTATTATTTATTCTAAAAAATATTTTTTTATTTTT
131 AAATTTCATCATTAGATAATTATTATTTATTCTAAAAAATATTTTTTTATTTTT
3359593 TAAAATTTAA
Statistics
Matches: 168, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
186 128 0.76
187 40 0.24
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (187 bp):
TTTTTTATTGAAAATAAATATTAATTATAGTTATTAAAACTTTATCTAAATTATTTCACCATTTG
GAACAAATTTAGATAAAATTTCTCACCTAAAAATTTTATAAAAATTTACCATTTAAAATTTCTAA
AAATTTCATCATTAGATAATTATTATTTATTCTAAAAAATATTTTTTTATTTTTCTC
Found at i:3359927 original size:11 final size:11
Alignment explanation
Indices: 3359908--3359942 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3359898 TCTTCATATT
3359908 TTTTCTTTTTTC
1 TTTT-TTTTTTC
3359920 TTTTTTTTTTC
1 TTTTTTTTTTC
*
3359931 CTTTTTTTTTC
1 TTTTTTTTTTC
3359942 T
1 T
3359943 CTTTACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:3359946 original size:12 final size:12
Alignment explanation
Indices: 3359913--3359946 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
3359903 ATATTTTTTC
3359913 TTTTTTCT-TTT
1 TTTTTTCTCTTT
3359924 TTTTTTC-CTTT
1 TTTTTTCTCTTT
3359935 TTTTTTCTCTTT
1 TTTTTTCTCTTT
3359947 ACAAACCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:3360456 original size:9 final size:8
Alignment explanation
Indices: 3360439--3360463 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3360429 TCGGCAGAAA
3360439 TTATTTTT
1 TTATTTTT
3360447 TTATTTTT
1 TTATTTTT
3360455 TTATTTTT
1 TTATTTTT
3360463 T
1 T
3360464 CCCCATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Done.