Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 168 of 195
Found at i:27948156 original size:42 final size:42
Alignment explanation
Indices: 27948086--27948311 Score: 184
Period size: 42 Copynumber: 5.2 Consensus size: 42
27948076 TAAAGAGCCT
* *
27948086 TTTATTTT-TCAAAGTTATGGTGCTTCTGTTTAGAGGAGCAA
1 TTTATTTTCCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAA
* * * * *
27948127 TTTATTTTCCCAAAGTTGTAGTGTCTCTGTCTAGAGGAACAA
1 TTTATTTTCCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAA
* * *** *
27948169 TTTATTTTTCTAATTTTTCCAAAGTTGTGGTGCCTCTATTTAGAGTTTCAT
1 TTTA-TTTTC--------CCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAA
** *
27948220 TTTATTTTTTCAAAGTTATGGTACCTCTGTTTAGAGGAGCAA
1 TTTATTTTCCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAA
** * *
27948262 TTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAT
1 TTTATTTTCCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAA
27948304 TTTATTTT
1 TTTATTTT
27948312 TCAAAGTCGT
Statistics
Matches: 148, Mismatches: 27, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
41 8 0.05
42 102 0.69
43 5 0.03
50 4 0.03
51 29 0.20
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTATTTTCCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAA
Found at i:27948234 original size:93 final size:92
Alignment explanation
Indices: 27948089--27948311 Score: 237
Period size: 93 Copynumber: 2.5 Consensus size: 92
27948079 AGAGCCTTTT
* * * **
27948089 ATTTTTCAAAGTTATGGTGCTTCTGTTTAGAGGAGCAATTTATTTTCCCAAAGTTGTAGTGTCTC
1 ATTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCCAAAGTTATAGTACCTC
27948154 TGTCTAGAGGAACAATTTATTTTTCTA
66 TGTCTAGAGGAACAATTTATTTTTCTA
* *** * ** *
27948181 ATTTTTCCAAAGTTGTGGTGCCTCTATTTAGAGTTTCATTTTATTTTTTCAAAGTTATGGTACCT
1 ATTTTT-CAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCCAAAGTTATAGTACCT
* *
27948246 CTGTTTAGAGGAGCAATTTA------T-
65 CTGTCTAGAGGAACAATTTATTTTTCTA
*
27948267 -TTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCATTTTATTTT
1 ATTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTATTTT
27948312 TCAAAGTCGT
Statistics
Matches: 111, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
84 36 0.32
85 5 0.05
87 1 0.01
92 6 0.05
93 63 0.57
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.46
Consensus pattern (92 bp):
ATTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCCAAAGTTATAGTACCTC
TGTCTAGAGGAACAATTTATTTTTCTA
Found at i:27948312 original size:42 final size:42
Alignment explanation
Indices: 27948181--27948318 Score: 197
Period size: 42 Copynumber: 3.3 Consensus size: 42
27948171 TATTTTTCTA
* * ***
27948181 ATTTTTCCAAAGTTGTGGTGCCTCTATTTAGAGTTTCATTTT
1 ATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCATTTT
* * *
27948223 ATTTTTTCAAAGTTATGGTACCTCTGTTTAGAGGAGCAATTT
1 ATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCATTTT
27948265 ATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCATTTT
1 ATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCATTTT
27948307 A-TTTTTCAAAGT
1 ATTTTTTCAAAGT
27948319 CGTTGAACAT
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 11 0.13
42 74 0.87
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.46
Consensus pattern (42 bp):
ATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCATTTT
Found at i:27949372 original size:16 final size:14
Alignment explanation
Indices: 27949346--27949381 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
27949336 AAATTCAGAA
27949346 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
27949360 AATAAATAGAAAAAAT
1 AA-AAATA-AAAAAAT
27949376 AAAAAT
1 AAAAAT
27949382 TTTGAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 9 0.45
16 9 0.45
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:27949680 original size:179 final size:180
Alignment explanation
Indices: 27949374--27949697 Score: 415
Period size: 179 Copynumber: 1.8 Consensus size: 180
27949364 AATAGAAAAA
** * * *
27949374 ATAAAAATTTTGAGAATAAATATTAATTATCCAATGATGAAATTTATATAAATTTCAAATAGTAA
1 ATAAAAATTTTGAGAATAAATACAAATTACCCAAGGATGAAATTTATAGAAATTTCAAATAGTAA
* * * * * *
27949439 ATTTTATATAAAATTTTTAGGTGAGAAATTTTGTCTAAATTTGTCCCAAATGGTGAAATAATTTA
66 ATTCTATATAAAATCTCTAGGTGAGAAATTTTATCTAAATTTATCCCAAATGATGAAATAATTTA
*
27949504 GATAAATTTTCAATATCAATAATTAATATTTATTTTCAAACATAAAAATT
131 GATAAAGTTTCAATATCAATAATTAATATTTATTTTCAAACATAAAAATT
*
27949554 ATAAAAATTTTG-GAATTAAATACAAATTACCCAAGGATGAGATTCT-TAGAAATTTCAAAT-GA
1 ATAAAAATTTTGAGAA-TAAATACAAATTACCCAAGGATGAAATT-TATAGAAATTTCAAATAG-
* * * *
27949616 TAAATTCCTA-A-GAAATCTCTAGGTGAGAAATTTTATTTAAATTTATCCCAAATTATGGAATAA
63 TAAATT-CTATATAAAATCTCTAGGTGAGAAATTTTATCTAAATTTATCCCAAATGATGAAATAA
*
27949679 TTTAGATGAAGTTTCAATA
127 TTTAGATAAAGTTTCAATA
27949698 AAAGTAATTG
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
179 64 0.52
180 55 0.45
181 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (180 bp):
ATAAAAATTTTGAGAATAAATACAAATTACCCAAGGATGAAATTTATAGAAATTTCAAATAGTAA
ATTCTATATAAAATCTCTAGGTGAGAAATTTTATCTAAATTTATCCCAAATGATGAAATAATTTA
GATAAAGTTTCAATATCAATAATTAATATTTATTTTCAAACATAAAAATT
Found at i:27954877 original size:9 final size:9
Alignment explanation
Indices: 27954851--27954890 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
27954841 GTGAAGTTAT
*
27954851 AACAAAAGT
1 AACAAAAGC
27954860 AACAAAAGC
1 AACAAAAGC
27954869 AACAAAAGC
1 AACAAAAGC
27954878 AAACAAAAAGC
1 -AAC-AAAAGC
27954889 AA
1 AA
27954891 AGGAATCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 17 0.61
10 5 0.18
11 6 0.21
ACGTcount: A:0.70, C:0.17, G:0.10, T:0.03
Consensus pattern (9 bp):
AACAAAAGC
Found at i:27957544 original size:4 final size:4
Alignment explanation
Indices: 27957535--27957573 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
27957525 ACTAGTTGAT
27957535 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
27957574 GTTGAATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:27966225 original size:27 final size:27
Alignment explanation
Indices: 27966185--27966248 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
27966175 TCGCTCTGAG
*
27966185 TAAATCTCTTTACCACCAATCTAGCTT
1 TAAATCTCTCTACCACCAATCTAGCTT
27966212 TAAATCTCTCTACCACCAATCTAGCTT
1 TAAATCTCTCTACCACCAATCTAGCTT
27966239 TAAATCTCTC
1 TAAATCTCTC
27966249 AACATTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.31, G:0.03, T:0.36
Consensus pattern (27 bp):
TAAATCTCTCTACCACCAATCTAGCTT
Found at i:27975504 original size:13 final size:13
Alignment explanation
Indices: 27975486--27975510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27975476 ATAGAACTTG
27975486 TAACTAGTTTTAC
1 TAACTAGTTTTAC
27975499 TAACTAGTTTTA
1 TAACTAGTTTTA
27975511 TAATCTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (13 bp):
TAACTAGTTTTAC
Found at i:27976864 original size:21 final size:22
Alignment explanation
Indices: 27976829--27976873 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
27976819 TTATTTTACT
* *
27976829 TTATTTGTTTATTTTTATTTAA
1 TTATTTGTGTATTTTTAATTAA
27976851 TTATTT-TGTATTTTTAATTAA
1 TTATTTGTGTATTTTTAATTAA
27976872 TT
1 TT
27976874 TTAATTTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
TTATTTGTGTATTTTTAATTAA
Found at i:27978854 original size:1 final size:1
Alignment explanation
Indices: 27978848--27978872 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
27978838 CGTTCCAAAT
27978848 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
27978873 GGTGTGCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27979889 original size:3 final size:3
Alignment explanation
Indices: 27979881--27979906 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27979871 TCATCTCGAT
27979881 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
27979907 CAAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:27985831 original size:13 final size:13
Alignment explanation
Indices: 27985815--27985858 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
27985805 AATATTATGA
27985815 AAAAATATAATTT
1 AAAAATATAATTT
* *
27985828 AAAATTTTAA-TT
1 AAAAATATAATTT
27985840 AAATAATATAATTT
1 AAA-AATATAATTT
27985854 AAAAA
1 AAAAA
27985859 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 5 0.20
13 15 0.60
14 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAATATAATTT
Found at i:27985850 original size:26 final size:25
Alignment explanation
Indices: 27985801--27985857 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
27985791 AAACGAAACA
27985801 TTAAAATATTATGAAAAAATATAAT
1 TTAAAATATTATGAAAAAATATAAT
* * *
27985826 TTAAAATTTTAATTAAATAATATAAT
1 TTAAAATATT-ATGAAAAAATATAAT
27985852 TTAAAA
1 TTAAAA
27985858 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAAATATTATGAAAAAATATAAT
Found at i:27989481 original size:33 final size:32
Alignment explanation
Indices: 27989429--27989518 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
27989419 TTAAGTGATC
* * *
27989429 AAATTATATCCAAACAATAAAAAATAAATAATT
1 AAATTATATTCAAATAATAAAAAATAAA-AATA
*
27989462 AAATTATATT--AA-AATAATAAATAAAAATA
1 AAATTATATTCAAATAATAAAAAATAAAAATA
*
27989491 AAATTTTATTCAAATAATGAAAAAATAA
1 AAATTATATTCAAATAAT-AAAAAATAA
27989519 TAAAGTAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 12 0.25
30 12 0.25
31 4 0.08
32 3 0.06
33 17 0.35
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (32 bp):
AAATTATATTCAAATAATAAAAAATAAAAATA
Found at i:27989505 original size:29 final size:30
Alignment explanation
Indices: 27989444--27989522 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
27989434 ATATCCAAAC
* *
27989444 AATAAAAAATAAATAATTAAATTATATTAA
1 AATAATAAATAAATAATAAAATTATATTAA
* *
27989474 AATAATAAATAAA-AATAAAATTTTATTCA
1 AATAATAAATAAATAATAAAATTATATTAA
27989503 AATAATGAAA-AAATAATAAA
1 AATAAT-AAATAAATAATAAA
27989523 GTAATATTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (30 bp):
AATAATAAATAAATAATAAAATTATATTAA
Found at i:27990300 original size:21 final size:21
Alignment explanation
Indices: 27990274--27990363 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
27990264 AAGAAGAAAC
*
27990274 CTGCTGAAGGAAACCAGCAGT
1 CTGCTGAAGGAAACCAACAGT
27990295 CTGCTGTAA-GAAACCAACAGT
1 CTGCTG-AAGGAAACCAACAGT
*
27990316 CTGCTGCAGGAAACCAACAGT
1 CTGCTGAAGGAAACCAACAGT
**
27990337 CTGCTTCAGGAAACCAACAGT
1 CTGCTGAAGGAAACCAACAGT
27990358 CTGCTG
1 CTGCTG
27990364 TTGTCCTTGC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.02
21 60 0.95
22 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (21 bp):
CTGCTGAAGGAAACCAACAGT
Found at i:27994661 original size:18 final size:18
Alignment explanation
Indices: 27994622--27994661 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
27994612 AAGTCTCTAA
*
27994622 ATTTGCAAATCCAAAAAG
1 ATTTGCAAATCCAAAAAC
27994640 ATTTGCAAATCTC-AAAAC
1 ATTTGCAAATC-CAAAAAC
27994658 ATTT
1 ATTT
27994662 AAAAATCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (18 bp):
ATTTGCAAATCCAAAAAC
Found at i:27998473 original size:20 final size:20
Alignment explanation
Indices: 27998428--27998473 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
27998418 AATATTATTT
* *
27998428 AAAATTTTAATAAAAAATAT
1 AAAAATTTAATAAAAAATAA
* *
27998448 ATAAATTTAATAAAAATTAA
1 AAAAATTTAATAAAAAATAA
27998468 AAAAAT
1 AAAAAT
27998474 ATATATTACG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTTAATAAAAAATAA
Found at i:27999562 original size:16 final size:16
Alignment explanation
Indices: 27999543--27999577 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27999533 AATGTAATAT
**
27999543 TAAAATTAATTTTTTA
1 TAAAATTAAAGTTTTA
27999559 TAAAATTAAAGTTTTA
1 TAAAATTAAAGTTTTA
27999575 TAA
1 TAA
27999578 TTTTTAATAT
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TAAAATTAAAGTTTTA
Found at i:28006675 original size:18 final size:18
Alignment explanation
Indices: 28006652--28006693 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
28006642 TGGGACCGAA
28006652 TGATAATGCTTCTGTTGT
1 TGATAATGCTTCTGTTGT
28006670 TGATAATGCTTCTGTTGT
1 TGATAATGCTTCTGTTGT
28006688 TGATAA
1 TGATAA
28006694 CACTTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (18 bp):
TGATAATGCTTCTGTTGT
Found at i:28006699 original size:18 final size:18
Alignment explanation
Indices: 28006660--28006699 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28006650 AATGATAATG
**
28006660 CTTCTGTTGTTGATAATG
1 CTTCTGTTGTTGATAACA
28006678 CTTCTGTTGTTGATAACA
1 CTTCTGTTGTTGATAACA
28006696 CTTC
1 CTTC
28006700 CACAGATCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (18 bp):
CTTCTGTTGTTGATAACA
Found at i:28012120 original size:2 final size:2
Alignment explanation
Indices: 28012113--28012151 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
28012103 GGTATGCTAT
28012113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28012152 AATAAAAGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28015734 original size:16 final size:16
Alignment explanation
Indices: 28015713--28015744 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28015703 CAAGACAAGG
28015713 AGAGATTCAACTTTTT
1 AGAGATTCAACTTTTT
28015729 AGAGATTCAACTTTTT
1 AGAGATTCAACTTTTT
28015745 GAATTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
AGAGATTCAACTTTTT
Found at i:28018740 original size:29 final size:29
Alignment explanation
Indices: 28018708--28018784 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
28018698 CAAACATGAA
*
28018708 TAATATAAATATACATAAATAGACACAAC
1 TAATATAAATATATATAAATAGACACAAC
* ** * *
28018737 TAATATAAATAGATACGAATAGACATAAT
1 TAATATAAATATATATAAATAGACACAAC
*
28018766 TAATATGAATATATATAAA
1 TAATATAAATATATATAAA
28018785 AAATAGAGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (29 bp):
TAATATAAATATATATAAATAGACACAAC
Found at i:28019562 original size:42 final size:42
Alignment explanation
Indices: 28019515--28019600 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
28019505 TAATCACCCA
*
28019515 ATACTTTATATATATATATATATTTTACATTAATTTTTCAAG
1 ATACTTTATATATATATATATATTTCACATTAATTTTTCAAG
28019557 ATACTTTATATATATATATATATTTCACATTAATTTTTCAAG
1 ATACTTTATATATATATATATATTTCACATTAATTTTTCAAG
28019599 AT
1 AT
28019601 TTTTATTTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.51
Consensus pattern (42 bp):
ATACTTTATATATATATATATATTTCACATTAATTTTTCAAG
Found at i:28021203 original size:19 final size:18
Alignment explanation
Indices: 28021179--28021230 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
28021169 ATTAAAATTT
28021179 TTTTCAAAAAATACTAAAA
1 TTTTCAAAAAATA-TAAAA
*
28021198 TTTTCAAAAAATTATAAAT
1 TTTTCAAAAAA-TATAAAA
*
28021217 TTTTTAAAAAATAT
1 TTTTCAAAAAATAT
28021231 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 3 0.10
19 25 0.83
20 2 0.07
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTTCAAAAAATATAAAA
Found at i:28021235 original size:13 final size:12
Alignment explanation
Indices: 28021213--28021244 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
28021203 AAAAAATTAT
28021213 AAATTTTTTAAA
1 AAATTTTTTAAA
28021225 AAATATTTTTAAA
1 AAAT-TTTTTAAA
28021238 AAATTTT
1 AAATTTT
28021245 AAAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTTTTAAA
Found at i:28021326 original size:20 final size:20
Alignment explanation
Indices: 28021281--28021396 Score: 84
Period size: 21 Copynumber: 6.0 Consensus size: 20
28021271 TAAAATTTTT
*
28021281 TTTTAAAA-TTCT-AAAACA
1 TTTTAAAATTTCTAAAAAAA
*
28021299 TTTATAAAATTTATAAAAAAA
1 TTT-TAAAATTTCTAAAAAAA
28021320 TTTTAAAA--T-TAAAAAAA
1 TTTTAAAATTTCTAAAAAAA
** **
28021337 TCTCAAAAATTTAAAAAAAAA
1 T-TTTAAAATTTCTAAAAAAA
*
28021358 TTTAAAAATTTCT--AAAAA
1 TTTTAAAATTTCTAAAAAAA
*
28021376 TTTTCAAAAATTCTAAAAAAA
1 TTTT-AAAATTTCTAAAAAAA
28021397 ATAAAACAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
17 9 0.12
18 17 0.22
19 13 0.17
20 18 0.23
21 21 0.27
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAATTTCTAAAAAAA
Found at i:28021350 original size:19 final size:19
Alignment explanation
Indices: 28021304--28021398 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 19
28021294 AAACATTTAT
**
28021304 AAAATTTATAAAAAAATTTT
1 AAAATTTA-AAAAAAATTCA
28021324 AAAA-TT-AAAAAAATCTCA
1 AAAATTTAAAAAAAAT-TCA
*
28021342 AAAATTTAAAAAAAAATTTA
1 AAAATTT-AAAAAAAATTCA
* **
28021362 AAAATTTCTAAAAATTTTCA
1 AAAATTT-AAAAAAAATTCA
28021382 AAAATTCTAAAAAAAAT
1 AAAATT-TAAAAAAAAT
28021399 AAAACAATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
17 8 0.14
18 5 0.08
19 4 0.07
20 33 0.56
21 9 0.15
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTTAAAAAAAATTCA
Found at i:28021356 original size:12 final size:12
Alignment explanation
Indices: 28021341--28021365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28021331 AAAAAATCTC
28021341 AAAAATTTAAAA
1 AAAAATTTAAAA
28021353 AAAAATTTAAAA
1 AAAAATTTAAAA
28021365 A
1 A
28021366 TTTCTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTTAAAA
Found at i:28021789 original size:12 final size:12
Alignment explanation
Indices: 28021763--28021795 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28021753 AAAATTACGT
28021763 AAATTTTAT-TA
1 AAATTTTATATA
28021774 AAATTTTATATA
1 AAATTTTATATA
28021786 AAA-TTTATAT
1 AAATTTTATAT
28021796 TTATAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATTTTATATA
Found at i:28025201 original size:2 final size:2
Alignment explanation
Indices: 28025189--28025232 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
28025179 TGGGTGGTTC
* *
28025189 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28025231 AT
1 AT
28025233 TAAATACAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28026517 original size:14 final size:14
Alignment explanation
Indices: 28026498--28026524 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28026488 CTTTTTTTTT
28026498 ATAATTATAATTTC
1 ATAATTATAATTTC
28026512 ATAATTATAATTT
1 ATAATTATAATTT
28026525 TAAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTATAATTTC
Found at i:28026568 original size:24 final size:24
Alignment explanation
Indices: 28026541--28026588 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28026531 AAAAATTTAT
*
28026541 ATTTAATATACTGTCAATATATAA
1 ATTTAATATACTGTCAATAAATAA
*
28026565 ATTTTATATACTGTCAATAAATAA
1 ATTTAATATACTGTCAATAAATAA
28026589 GATGATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTTAATATACTGTCAATAAATAA
Found at i:28032502 original size:20 final size:21
Alignment explanation
Indices: 28032469--28032509 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28032459 GGATAGGGCC
28032469 TTTTTTCTTATTTTTCCTTTG
1 TTTTTTCTTATTTTTCCTTTG
* *
28032490 TTTTTT-TTTTTTTTCGTTTG
1 TTTTTTCTTATTTTTCCTTTG
28032510 CTCGGTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTCTTATTTTTCCTTTG
Found at i:28034053 original size:29 final size:29
Alignment explanation
Indices: 28034011--28034070 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28034001 AAAATCAATT
28034011 ATAAAATAATGAAAACTATCTATATAAAA
1 ATAAAATAATGAAAACTATCTATATAAAA
28034040 ATAAAATAATGAAAACTATCTATATAAAA
1 ATAAAATAATGAAAACTATCTATATAAAA
28034069 AT
1 AT
28034071 TATGTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAAATAATGAAAACTATCTATATAAAA
Found at i:28036227 original size:10 final size:10
Alignment explanation
Indices: 28036212--28036236 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28036202 CTATATTTCT
28036212 ATATTTTCAA
1 ATATTTTCAA
28036222 ATATTTTCAA
1 ATATTTTCAA
28036232 ATATT
1 ATATT
28036237 ATATCAAACA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (10 bp):
ATATTTTCAA
Found at i:28044328 original size:60 final size:60
Alignment explanation
Indices: 28044255--28044379 Score: 232
Period size: 60 Copynumber: 2.1 Consensus size: 60
28044245 ATTAAAGCTA
*
28044255 TACAATTAGCTAGATTCGAATTTCATTTTCATATAACTATAACCTTAAACATAAGTGCAT
1 TACAATTAGCTAGATTCAAATTTCATTTTCATATAACTATAACCTTAAACATAAGTGCAT
*
28044315 TACAATTAGCTAGATTCAAATTTCATTTTCTTATAACTATAACCTTAAACATAAGTGCAT
1 TACAATTAGCTAGATTCAAATTTCATTTTCATATAACTATAACCTTAAACATAAGTGCAT
28044375 TACAA
1 TACAA
28044380 GTTTAACCAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (60 bp):
TACAATTAGCTAGATTCAAATTTCATTTTCATATAACTATAACCTTAAACATAAGTGCAT
Found at i:28048899 original size:27 final size:27
Alignment explanation
Indices: 28048849--28048901 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28048839 CGGAAACTAG
* *
28048849 AAAAGAAAAAAAAATAGAAGGAAAATA
1 AAAAGAAAAAAAAATAAAAAGAAAATA
28048876 AAAAGATAAAAAAAA-AAAAAGAAAAT
1 AAAAGA-AAAAAAAATAAAAAGAAAAT
28048902 CTGATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (27 bp):
AAAAGAAAAAAAAATAAAAAGAAAATA
Found at i:28055060 original size:2 final size:2
Alignment explanation
Indices: 28055053--28055135 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
28055043 GCATTTAAAA
28055053 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28055095 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28055136 AAATCAAGAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28058250 original size:63 final size:63
Alignment explanation
Indices: 28058155--28058278 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
28058145 AGATTTTACA
* *
28058155 TTAATGTAGATCTCCCAATAGTTTGGTAAGATTTTATTTAAAAATTATTTATAAAATTTTATT
1 TTAATGCAGATCTCCCAATAGTTTGGTAAGATTTTATTTAAAAATCATTTATAAAATTTTATT
* * * *
28058218 TTAATGCAGATTTCTCAATAGTTTGGTGAGATTTTATTTGAAAATCATTTATAAAATTTTA
1 TTAATGCAGATCTCCCAATAGTTTGGTAAGATTTTATTTAAAAATCATTTATAAAATTTTA
28058279 CTTTGAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.47
Consensus pattern (63 bp):
TTAATGCAGATCTCCCAATAGTTTGGTAAGATTTTATTTAAAAATCATTTATAAAATTTTATT
Found at i:28060938 original size:21 final size:22
Alignment explanation
Indices: 28060904--28060949 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28060894 TTTTTGAATT
* *
28060904 TTTTAAAATATTATTTTTATTA
1 TTTTAAAATATTATTATTAATA
*
28060926 TTTT-AAATTTTATTATTAATA
1 TTTTAAAATATTATTATTAATA
28060947 TTT
1 TTT
28060950 ATGCATGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAAAATATTATTATTAATA
Found at i:28063650 original size:36 final size:36
Alignment explanation
Indices: 28063604--28063675 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
28063594 ATCAGTGCTC
*
28063604 AACAGAATATGAAATTATTAGAAAAAAGACTTAGAG
1 AACAAAATATGAAATTATTAGAAAAAAGACTTAGAG
* *
28063640 AACAAAATATGAAATTATTAGAAGAAAGATTTAGAG
1 AACAAAATATGAAATTATTAGAAAAAAGACTTAGAG
28063676 CCATAGAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.24
Consensus pattern (36 bp):
AACAAAATATGAAATTATTAGAAAAAAGACTTAGAG
Found at i:28067353 original size:35 final size:34
Alignment explanation
Indices: 28067307--28067402 Score: 115
Period size: 34 Copynumber: 2.8 Consensus size: 34
28067297 TGCATTGGTA
28067307 TTTTTG-GAAAAGACATTTGCATTTCATGTA-CAT
1 TTTTTGAGAAAAGACATTTGCATTTCATG-AGCAT
*
28067340 CTTTTTGAGAAAAGACATTTGCATCTCATGAGCAT
1 -TTTTTGAGAAAAGACATTTGCATTTCATGAGCAT
** * *
28067375 AATTTAAGAAAAGACATTTACATTTCAT
1 TTTTTGAGAAAAGACATTTGCATTTCAT
28067403 TTGCATCATA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
34 30 0.56
35 24 0.44
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (34 bp):
TTTTTGAGAAAAGACATTTGCATTTCATGAGCAT
Found at i:28067852 original size:99 final size:97
Alignment explanation
Indices: 28067729--28067931 Score: 309
Period size: 99 Copynumber: 2.1 Consensus size: 97
28067719 AAAAAAAAAA
* *
28067729 TCATTTGCATATTCTCGATGGTGATATCCGAATGTTAAAGTTTGATTTGCATTTTATCGATGATG
1 TCATTTGCATATTCTCGATGGTGATATCCGAATGTTAAAGCTTAATTTGCATTTTATCGATGATG
*
28067794 ATATTTGAGTTTCTTTCAGTGGCGATATCCGAAG
66 ATATTTGAGTTTCCTTCAGTGGCGATA--CGAAG
* * *
28067828 TCATTTGCATATTTTC-AGTGGTGATATCCGAGTGTTAAAGCTTAATTTGCATTTTTTCGATGAT
1 TCATTTGCATATTCTCGA-TGGTGATATCCGAATGTTAAAGCTTAATTTGCATTTTATCGATGAT
*
28067892 GATATTTGAGTTTCCTTCAGTGGTGATACGAAG
65 GATATTTGAGTTTCCTTCAGTGGCGATACGAAG
28067925 TCATTTG
1 TCATTTG
28067932 TATTTTTTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
97 12 0.12
98 1 0.01
99 83 0.86
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (97 bp):
TCATTTGCATATTCTCGATGGTGATATCCGAATGTTAAAGCTTAATTTGCATTTTATCGATGATG
ATATTTGAGTTTCCTTCAGTGGCGATACGAAG
Found at i:28068030 original size:131 final size:132
Alignment explanation
Indices: 28067817--28068072 Score: 399
Period size: 131 Copynumber: 1.9 Consensus size: 132
28067807 TTTCAGTGGC
*
28067817 GATATCCGAAGTCATTTGCATATTTTCAGTGGTGATATCCGAGTGTTAAAGCTTAATTTGCATTT
1 GATATCCGAAGTCATTTGCATATTCTCAGTGGTGATATCCGAGTGTTAAAGCTTAATTTGCATTT
* * * *
28067882 TTTCGATGATGATATTTGAGTTTCCTTCAGTGGTGATA-CGAAGTCATTTGTATTTTTTTTTGTG
66 TCTCGATGATAATATTTGAGTTTCCTTCAGTGGCGATACCGAAGTCATTTGTATATTTTTTTGTG
28067946 AT
131 AT
* *
28067948 GATATCCGAAGTCATTTGCATATTCT-AGATGGTGATATCTGAGTGTTAAAGCTTGATTTGCATT
1 GATATCCGAAGTCATTTGCATATTCTCAG-TGGTGATATCCGAGTGTTAAAGCTTAATTTGCATT
**
28068012 TTCTCGATGATAATATTTGAGTTTCCTTTGGTGGCGATATCCGAAGTCATTTGTATATTTT
65 TTCTCGATGATAATATTTGAGTTTCCTTCAGTGGCGATA-CCGAAGTCATTTGTATATTTT
28068073 GGTGGTGATA
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
130 2 0.02
131 92 0.81
133 19 0.17
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (132 bp):
GATATCCGAAGTCATTTGCATATTCTCAGTGGTGATATCCGAGTGTTAAAGCTTAATTTGCATTT
TCTCGATGATAATATTTGAGTTTCCTTCAGTGGCGATACCGAAGTCATTTGTATATTTTTTTGTG
AT
Found at i:28068107 original size:98 final size:99
Alignment explanation
Indices: 28067948--28068362 Score: 519
Period size: 98 Copynumber: 4.2 Consensus size: 99
28067938 TTTTTGTGAT
* * *
28067948 GATATCCGAAGTCATTTGCATATTCTAGATGGTGATATCTGAGTGTTAAAGCTTGATTTGCATTT
1 GATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCCGAGTGTTAAAGCTTGATTTACATTT
* * * **
28068013 TCTCGATGATAATATTTGAGTTTCCTTTGGTGGC
66 TCTCGATGGTGATATTCGAGTTTCCTTCAGTGGC
* * * * * * *
28068047 GATATCCGAAGTCATTTGTATATT-TTGGTGGTGATATCCGAGTGTTAAAGCTTCAATTGCACTT
1 GATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCCGAGTGTTAAAGCTTGATTTACATTT
* *
28068111 TCTCAATGGTGATATTCGAGTTTCCTTCAGTGGT
66 TCTCGATGGTGATATTCGAGTTTCCTTCAGTGGC
* * * *
28068145 GATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCTGAGTGATAAGGTTTGATTTACATTT
1 GATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCCGAGTGTTAAAGCTTGATTTACATTT
* * **
28068210 TCTTGATGGTGATATTCGAGTTTTCTTTGGTGGC
66 TCTCGATGGTGATATTCGAGTTTCCTTCAGTGGC
* * * * * *
28068244 AATATTCGAAGTCATTTGCATATTCTCAATGGTGATAT-CGAGTATTAAGGTTTGATTTACATTT
1 GATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCCGAGTGTTAAAGCTTGATTTACATTT
*
28068308 TCTCGATGGTGATATTCGAGTTTCCTTCAGTGGT
66 TCTCGATGGTGATATTCGAGTTTCCTTCAGTGGC
*
28068342 GATATCCGAAGTTATTTGCAT
1 GATATCCGAAGTCATTTGCAT
28068363 CTTTTCTGTG
Statistics
Matches: 270, Mismatches: 45, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
98 154 0.57
99 116 0.43
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.41
Consensus pattern (99 bp):
GATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCCGAGTGTTAAAGCTTGATTTACATTT
TCTCGATGGTGATATTCGAGTTTCCTTCAGTGGC
Found at i:28068183 original size:230 final size:229
Alignment explanation
Indices: 28067729--28068183 Score: 657
Period size: 230 Copynumber: 2.0 Consensus size: 229
28067719 AAAAAAAAAA
* * *
28067729 TCATTTGCATATTCTCGATGGTGATATCCGAATGTTAAAGTTTGATTTGCATTTTATCGATGATG
1 TCATTTGCATATTCTAGATGGTGATATCCGAATGTTAAAGCTTGATTTGCATTTTATCGATGATA
28067794 ATATTTGAGTTTCTTTCAGTGGCGATATCCGAAGTCATTTGCATATTTTCAGTGGTGATATCCGA
66 ATATTTGAGTTTCTTTCAGTGGCGATATCCGAAGTCATTTGCATATTTTCAGTGGTGATATCCGA
* * * *
28067859 GTGTTAAAGCTTAATTTGCATTTTTTCGATGATGATATTTGAGTTTCCTTCAGTGGTGATACGAA
131 GTGTTAAAGCTTAATTTGCACTTTCTCAATGATGATATTCGAGTTTCCTTCAGTGGTGATACGAA
* * * *
28067924 GTCATTTGTATTTTTTTTTGTGATGATATCCGAAG
196 GTCATTTGCA-TTATTCTCGTGATGATATCCGAAG
* * *
28067959 TCATTTGCATATTCTAGATGGTGATATCTGAGTGTTAAAGCTTGATTTGCATTTTCTCGATGATA
1 TCATTTGCATATTCTAGATGGTGATATCCGAATGTTAAAGCTTGATTTGCATTTTATCGATGATA
* * *
28068024 ATATTTGAGTTTCCTTT-GGTGGCGATATCCGAAGTCATTTGTATATTTT-GGTGGTGATATCCG
66 ATATTTGAGTTT-CTTTCAGTGGCGATATCCGAAGTCATTTGCATATTTTCAGTGGTGATATCCG
*
28068087 AGTGTTAAAGCTTCAA-TTGCACTTTCTCAATGGTGATATTCGAGTTTCCTTCAGTGGTGATATC
130 AGTGTTAAAGCTT-AATTTGCACTTTCTCAATGATGATATTCGAGTTTCCTTCAGTGGTGATA--
*
28068151 CGAAGTCATTTGCA-TATTCTCGATGGTGATATC
192 CGAAGTCATTTGCATTATTCTCG-TGATGATATC
28068184 TGAGTGATAA
Statistics
Matches: 201, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
229 72 0.36
230 112 0.56
231 17 0.08
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.42
Consensus pattern (229 bp):
TCATTTGCATATTCTAGATGGTGATATCCGAATGTTAAAGCTTGATTTGCATTTTATCGATGATA
ATATTTGAGTTTCTTTCAGTGGCGATATCCGAAGTCATTTGCATATTTTCAGTGGTGATATCCGA
GTGTTAAAGCTTAATTTGCACTTTCTCAATGATGATATTCGAGTTTCCTTCAGTGGTGATACGAA
GTCATTTGCATTATTCTCGTGATGATATCCGAAG
Found at i:28068185 original size:197 final size:197
Alignment explanation
Indices: 28067947--28068362 Score: 591
Period size: 197 Copynumber: 2.1 Consensus size: 197
28067937 TTTTTTGTGA
* *
28067947 TGATATCCGAAGTCATTTGCATATTCTAGATGGTGATATCTGAGTGTTAAAGCTTGATTTGCATT
1 TGATATCCGAAGTCATTTGCATATTCTAGATGGTGATATCTGAGTGATAAAGCTTGATTTACATT
* * * ***
28068012 TTCTCGATGATAATATTTGAGTTTCCTTTGGTGGCGATATCCGAAGTCATTTGTATATT-TTGGT
66 TTCTCGATGATAATATTCGAGTTTCCTTTGGTGGCAATATCCGAAGTCATTTGCATATTCTCAAT
* *
28068076 GGTGATATCCGAGTGTTAAAGCTTCAATTGCACTTTCTCAATGGTGATATTCGAGTTTCCTTCAG
131 GGTGATAT-CGAGTATTAAAGCTTCAATTACACTTTCTCAATGGTGATATTCGAGTTTCCTTCAG
28068141 TGG
195 TGG
* * *
28068144 TGATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCTGAGTGATAAGGTTTGATTTACATT
1 TGATATCCGAAGTCATTTGCATATTCTAGATGGTGATATCTGAGTGATAAAGCTTGATTTACATT
* * * * *
28068209 TTCTTGATGGTGATATTCGAGTTTTCTTTGGTGGCAATATTCGAAGTCATTTGCATATTCTCAAT
66 TTCTCGATGATAATATTCGAGTTTCCTTTGGTGGCAATATCCGAAGTCATTTGCATATTCTCAAT
* * * * * *
28068274 GGTGATATCGAGTATTAAGGTTTGATTTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCAGT
131 GGTGATATCGAGTATTAAAGCTTCAATTACACTTTCTCAATGGTGATATTCGAGTTTCCTTCAGT
28068339 GG
196 GG
*
28068341 TGATATCCGAAGTTATTTGCAT
1 TGATATCCGAAGTCATTTGCAT
28068363 CTTTTCTGTG
Statistics
Matches: 193, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
197 183 0.95
198 10 0.05
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.41
Consensus pattern (197 bp):
TGATATCCGAAGTCATTTGCATATTCTAGATGGTGATATCTGAGTGATAAAGCTTGATTTACATT
TTCTCGATGATAATATTCGAGTTTCCTTTGGTGGCAATATCCGAAGTCATTTGCATATTCTCAAT
GGTGATATCGAGTATTAAAGCTTCAATTACACTTTCTCAATGGTGATATTCGAGTTTCCTTCAGT
GG
Found at i:28068408 original size:197 final size:196
Alignment explanation
Indices: 28067947--28068430 Score: 524
Period size: 197 Copynumber: 2.5 Consensus size: 196
28067937 TTTTTTGTGA
* * ** * *** *
28067947 TGATATCCGAAGTCATTTGCATATTCTAGATGGTGATATCTGAGTGTTAAAGCTTGATTTGCATT
1 TGATATCCGAAGTCATTTGCATATTCTCGATGGTAATATCAAAGT-ATAAAAAATCATTTGCATT
* * * * * ***
28068012 TTCTCGATGATAATATTTGAGTTTCCTTTGGTGGCGATATCCGAAGTCATTTGTATATTTTGGTG
65 TTCTTGATGATGATATTTGAGTTTTCTTTGGTGGCAATATCCGAAGTCATTTGCATATTTCAATG
* *
28068077 GTGATATCCGAGTGTTAAAGCTTCAATTGCACTTTCTCAATGGTGATATTCGAGTTTCCTTCAGT
130 GTGATATCCGAGTATTAAAGCTTCAATTACACTTTCTCAATGGTGATATTCGAGTTTCCTTCAGT
28068142 GG
195 GG
* ** **** * *
28068144 TGATATCCGAAGTCATTTGCATATTCTCGATGGTGATATCTGAGTGATAAGGTTTGATTTACATT
1 TGATATCCGAAGTCATTTGCATATTCTCGATGGTAATATCAAAGT-ATAAAAAATCATTTGCATT
* * *
28068209 TTCTTGATGGTGATATTCGAGTTTTCTTTGGTGGCAATATTCGAAGTCATTTGCATATTCTCAAT
65 TTCTTGATGATGATATTTGAGTTTTCTTTGGTGGCAATATCCGAAGTCATTTGCATATT-TCAAT
* * * * * *
28068274 GGTGATAT-CGAGTATTAAGGTTTGATTTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCAG
129 GGTGATATCCGAGTATTAAAGCTTCAATTACACTTTCTCAATGGTGATATTCGAGTTTCCTTCAG
28068338 TGG
194 TGG
* * * *
28068341 TGATATCCGAAGTTATTTGCATCTTTTCTG-TGGTAATGTACAAACGT-TAAAAAATCATTTGCA
1 TGATATCCGAAGTCATTTGCATATTCTC-GATGGTAATAT-CAAA-GTATAAAAAATCATTTGCA
28068404 TTTTCTTGATGATGATATTTGAGTTTT
63 TTTTCTTGATGATGATATTTGAGTTTT
28068431 TTTCAGTTGT
Statistics
Matches: 244, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
197 229 0.94
198 13 0.05
199 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (196 bp):
TGATATCCGAAGTCATTTGCATATTCTCGATGGTAATATCAAAGTATAAAAAATCATTTGCATTT
TCTTGATGATGATATTTGAGTTTTCTTTGGTGGCAATATCCGAAGTCATTTGCATATTTCAATGG
TGATATCCGAGTATTAAAGCTTCAATTACACTTTCTCAATGGTGATATTCGAGTTTCCTTCAGTG
G
Found at i:28069068 original size:21 final size:19
Alignment explanation
Indices: 28069039--28069088 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
28069029 TTAAATTAAT
*
28069039 AAAATACAAAAAAAAGAACA
1 AAAAGACAAAAAAAAGAA-A
*
28069059 AAAAGAACAATAAAAAGAAA
1 AAAAG-ACAAAAAAAAGAAA
28069079 AAAAGACAAA
1 AAAAGACAAA
28069089 CAACTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 12 0.46
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (19 bp):
AAAAGACAAAAAAAAGAAA
Found at i:28070379 original size:14 final size:14
Alignment explanation
Indices: 28070362--28070392 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28070352 TTTCTTGTTA
28070362 AAAAATTAAATAAT
1 AAAAATTAAATAAT
*
28070376 AAAAATTAACTAAT
1 AAAAATTAAATAAT
28070390 AAA
1 AAA
28070393 TTAAGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAATAAT
Found at i:28076319 original size:20 final size:21
Alignment explanation
Indices: 28076290--28076329 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
28076280 ATGCAATGAC
*
28076290 ATGATGAATGAATGA-TGATG
1 ATGATCAATGAATGAGTGATG
28076310 ATGATCAATGAATGAGTGAT
1 ATGATCAATGAATGAGTGAT
28076330 ATGCATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.30
Consensus pattern (21 bp):
ATGATCAATGAATGAGTGATG
Found at i:28077514 original size:25 final size:25
Alignment explanation
Indices: 28077470--28077525 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
28077460 GTTTTGAGAG
28077470 ATTTTATTTGAAAATCATTTA-TAAA
1 ATTTTATTTGAAAA-CATTTATTAAA
28077495 ATTTTACTTTGAGAAA-ATTTATTAAA
1 ATTTTA-TTTGA-AAACATTTATTAAA
28077521 ATTTT
1 ATTTT
28077526 CAATAGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 11 0.39
26 14 0.50
27 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (25 bp):
ATTTTATTTGAAAACATTTATTAAA
Found at i:28078631 original size:54 final size:59
Alignment explanation
Indices: 28078525--28078638 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 59
28078515 AAATATAAAC
*
28078525 TAAAAATTAAATATAAAGATAAAATAAAACAAGTCATTTTATATATATTATGTATGAAA
1 TAAAAATTAAATATAAAGATAAAATAAAACAAGTCATATTATATATATTATGTATGAAA
*
28078584 TAAAAATTAAATATAAAGATAAAAT-AAGCAAG-C-TATT-T-TATATTATGTATGAAA
1 TAAAAATTAAATATAAAGATAAAATAAAACAAGTCATATTATATATATTATGTATGAAA
28078638 T
1 T
28078639 GTTTAGATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
54 17 0.32
55 1 0.02
56 3 0.06
57 1 0.02
58 6 0.11
59 25 0.47
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (59 bp):
TAAAAATTAAATATAAAGATAAAATAAAACAAGTCATATTATATATATTATGTATGAAA
Found at i:28079056 original size:23 final size:22
Alignment explanation
Indices: 28079026--28079073 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
28079016 TAAAAGTAGT
*
28079026 AATGAAT-ATTTAAAAGAGAATA
1 AATGAATAATCTAAAAGA-AATA
*
28079048 AATGCAATAATCTAAATGAAATA
1 AATG-AATAATCTAAAAGAAATA
28079071 AAT
1 AAT
28079074 TTACTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 8 0.36
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.27
Consensus pattern (22 bp):
AATGAATAATCTAAAAGAAATA
Found at i:28079714 original size:15 final size:16
Alignment explanation
Indices: 28079694--28079729 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
28079684 AGTCGACTAA
28079694 AAATTAAAA-TTAATT
1 AAATTAAAATTTAATT
28079709 AAATTAAAATTTAATT
1 AAATTAAAATTTAATT
*
28079725 CAATT
1 AAATT
28079730 GATTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTAAAATTTAATT
Found at i:28096323 original size:19 final size:19
Alignment explanation
Indices: 28096301--28096347 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
28096291 AATTTTTATG
28096301 AAATTAT-TT-TTTATATATA
1 AAATTATATTATTTA-AT-TA
28096320 AAATTATATTATTTAATTA
1 AAATTATATTATTTAATTA
28096339 AAATTATAT
1 AAATTATAT
28096348 GCATATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 18 0.69
20 4 0.15
21 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATATTATTTAATTA
Found at i:28100957 original size:10 final size:10
Alignment explanation
Indices: 28100933--28100962 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28100923 TATTTTATCA
28100933 ATTAAAATA-
1 ATTAAAATAT
28100942 ATTAAAATAT
1 ATTAAAATAT
28100952 ATTAAAATAT
1 ATTAAAATAT
28100962 A
1 A
28100963 AAATTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:28101325 original size:21 final size:20
Alignment explanation
Indices: 28101301--28101339 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28101291 GCGAATTTAG
28101301 TTTAATCATATATTTAATTCA
1 TTTAATCATAT-TTTAATTCA
* *
28101322 TTTAGTTATATTTTAATT
1 TTTAATCATATTTTAATT
28101340 GTTAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTAATCATATTTTAATTCA
Found at i:28101526 original size:14 final size:13
Alignment explanation
Indices: 28101509--28101540 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
28101499 TTTAAATTTT
28101509 ATAAATAAAATTCA
1 ATAAATAAAATT-A
28101523 ATAAATAAAATTA
1 ATAAATAAAATTA
28101536 ATAAA
1 ATAAA
28101541 AACAATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAAATAAAATTA
Found at i:28102533 original size:29 final size:31
Alignment explanation
Indices: 28102475--28102556 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 31
28102465 CATAATTTAT
*
28102475 ATAATATTT-TCTAAT--TATATAATATAAA
1 ATAATATTTATATAATAATATATAATATAAA
28102503 AT-ATCATTTATA-AATAATATA-AATATAAA
1 ATAAT-ATTTATATAATAATATATAATATAAA
*
28102532 ATAATTTTTATATAATAATAATATA
1 ATAATATTTATATAATAAT-ATATA
28102557 TTTTTTGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
27 2 0.05
28 9 0.20
29 17 0.39
30 12 0.27
31 3 0.07
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATATTTATATAATAATATATAATATAAA
Found at i:28107538 original size:21 final size:21
Alignment explanation
Indices: 28107514--28107555 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28107504 ATCCATAAGC
28107514 TGCATATTAATCTCGAGGTAA
1 TGCATATTAATCTCGAGGTAA
28107535 TGCATATTAATCTCGAGGTAA
1 TGCATATTAATCTCGAGGTAA
28107556 AATTAATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TGCATATTAATCTCGAGGTAA
Found at i:28107562 original size:17 final size:19
Alignment explanation
Indices: 28107516--28107566 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
28107506 CCATAAGCTG
28107516 CATATTAATCTCGAGGTAA
1 CATATTAATCTCGAGGTAA
28107535 TGCATATTAATCTCGAGGTAA
1 --CATATTAATCTCGAGGTAA
28107556 -A-ATTAAT-TCGA
1 CATATTAATCTCGA
28107567 TGAAAGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.13
17 6 0.20
18 1 0.03
21 19 0.63
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (19 bp):
CATATTAATCTCGAGGTAA
Found at i:28116238 original size:59 final size:56
Alignment explanation
Indices: 28116160--28116691 Score: 517
Period size: 59 Copynumber: 8.7 Consensus size: 56
28116150 TTTTTTGTAG
*
28116160 GGAAAATTGATATTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAA-TTT-ATTTT-AA
*
28116219 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA---TATTTTTTGAAAATTTATTT-TAA
*
28116278 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGAAAATTT-ATTTT-AA
* *
28116338 AGAAAATTGATACTTTCAACTTTTCCCCAAAAATACCTTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTT-GAAA---A--TTTATTTTAA
* *
28116403 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTTGGAAATTTATTTTTCTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-----TTTTTT-GAAA---A--TTTATTTT
28116468 AA
55 AA
* * *
28116470 GGAAAATTTATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATT-TTAA
* ** *
28116527 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCC-CAAAA-ATATTTTTTGAAAATTTATTT-TAA
*
28116586 GGAAAATTGATACTTTCTACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTATAA
1 GGAAAATTG--A-----TACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTT-TAA
*
28116650 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTT
28116692 TTGGAATTTT
Statistics
Matches: 417, Mismatches: 26, Indels: 61
0.83 0.05 0.12
Matches are distributed among these distances:
56 6 0.01
57 55 0.13
58 11 0.03
59 112 0.27
60 44 0.11
61 22 0.05
62 12 0.03
64 30 0.07
65 39 0.09
66 21 0.05
67 65 0.16
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTAA
Found at i:28116473 original size:21 final size:21
Alignment explanation
Indices: 28116436--28116480 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
28116426 TCCCTAAAAA
**
28116436 TATTTTTTTTTTTGG-AAATT
1 TATTTTTTTTTAAGGAAAATT
28116456 TATTTTTCTTTTAAGGAAAATT
1 TATTTTT-TTTTAAGGAAAATT
28116478 TAT
1 TAT
28116481 ACTTTCAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TATTTTTTTTTAAGGAAAATT
Found at i:28116654 original size:64 final size:66
Alignment explanation
Indices: 28116537--28116705 Score: 207
Period size: 64 Copynumber: 2.7 Consensus size: 66
28116527 GGAAAATTGA
** * *
28116537 TACTTTCAACTTTTCCCTAAAAATATATTTTTTTTAAATTTATTTCTGAGGAAAATTGATACTTT
1 TACTTTCAACTTTTCCCTAAAAATATATTTTTTGGAAATTTATTTATAAGGAAAATTGATACTTT
28116602 C
66 C
*
28116603 TACTTTCAACTTTTCCC-CAAAA-ATATTTTTTGGAAATTTATTTATAAGGAAAATTG--A----
1 TACTTTCAACTTTTCCCTAAAAATATATTTTTTGGAAATTTATTTATAAGGAAAATTGATACTTT
28116660 -
66 C
28116660 TACTTTCAACTTTTCCCTAAAAATATATTTTTTTGG-AATTT-TTTAT
1 TACTTTCAACTTTTCCCTAAAAATATA-TTTTTTGGAAATTTATTTAT
28116706 TTTTTATTTG
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
57 17 0.18
58 9 0.10
59 8 0.09
60 8 0.09
62 1 0.01
64 30 0.32
65 4 0.04
66 17 0.18
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (66 bp):
TACTTTCAACTTTTCCCTAAAAATATATTTTTTGGAAATTTATTTATAAGGAAAATTGATACTTT
C
Found at i:28116700 original size:123 final size:116
Alignment explanation
Indices: 28116160--28116700 Score: 589
Period size: 123 Copynumber: 4.4 Consensus size: 116
28116150 TTTTTTGTAG
* *
28116160 GGAAAATTGATATTTTCAACTTTTCCC-CAAAA-ATA-TTTTTTGAAAATTTTGATTT-TCAAGG
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTG-AAA-TTT-ATTTCT-AAGG
* *
28116221 AAAATTG-ATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTGAAAATTTATTTCTAA
62 AAAATTGTATACTTTCAACTTTTCCCCAAAAA---TATTTTTTGGAAATTTATTT-TAA
* *
28116278 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTTTGAAATTTTGATTT-TCAAAGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAA-TTT-ATTTCT-AAGGA
28116341 AAATTG-ATACTTTCAACTTTTCCCCAAAAATACCTTTTTTTGGAAATTTATTTTTCTTTTAA
63 AAATTGTATACTTTCAACTTTTCCCCAAAAATA---TTTTTTGGAAATTTA------TTTTAA
*
28116403 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTTGGAAATTTATTTTTCTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TATTTTTTT-GAAATTTA--TTTC---T
*
28116468 AAGGAAAATT-TATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTCTTAA
58 AAGGAAAATTGTATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATT-TTAA
* *
28116527 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTAAATTTATTTCTGAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTTATTTCTAAGGAAAA
28116592 TTGATACTTTCTACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTATAA
66 TTG-TA-----TACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTT-TAA
*
28116650 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAATTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTT
28116701 TTTATTTTTT
Statistics
Matches: 376, Mismatches: 14, Indels: 61
0.83 0.03 0.14
Matches are distributed among these distances:
116 11 0.03
118 28 0.07
119 55 0.15
120 23 0.06
121 7 0.02
122 9 0.02
123 95 0.25
124 39 0.10
125 37 0.10
126 3 0.01
127 2 0.01
128 10 0.03
129 22 0.06
132 34 0.09
133 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTTATTTCTAAGGAAAA
TTGTATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTAA
Found at i:28117199 original size:19 final size:20
Alignment explanation
Indices: 28117159--28117204 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28117149 GAACACCGGT
*
28117159 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
28117179 GCCGGAATCTGGAAA-TTTC
1 GCCGGAATCTGGAAATTTTC
28117198 GCCGGAA
1 GCCGGAA
28117205 GTTGGCAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:28117372 original size:25 final size:25
Alignment explanation
Indices: 28117336--28117383 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28117326 AATCTGGAAA
28117336 TTTCCCAGAAATTTCCAGAAAAATT
1 TTTCCCAGAAATTTCCAGAAAAATT
*
28117361 TTTCGCCA-AAATTTCTAGAAAAA
1 TTTC-CCAGAAATTTCCAGAAAAA
28117384 ATTCTCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (25 bp):
TTTCCCAGAAATTTCCAGAAAAATT
Found at i:28117763 original size:24 final size:26
Alignment explanation
Indices: 28117708--28117765 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
28117698 TAGTATAAAA
28117708 ATAAAATTAAAAAAAAATAATATCAG
1 ATAAAATTAAAAAAAAATAATATCAG
* *
28117734 AT--AATTCAGAAAAAA-AA-ATCAG
1 ATAAAATTAAAAAAAAATAATATCAG
28117756 ATAAAATTAA
1 ATAAAATTAA
28117766 CAGATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
22 7 0.26
23 2 0.07
24 16 0.59
26 2 0.07
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (26 bp):
ATAAAATTAAAAAAAAATAATATCAG
Found at i:28117769 original size:26 final size:26
Alignment explanation
Indices: 28117708--28117779 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 26
28117698 TAGTATAAAA
28117708 ATAAAATTAA-A-AAAAAATAATATCAG
1 ATAAAATTAACAGAAAAAA-AA-ATCAG
28117734 AT--AATT--CAGAAAAAAAAATCAG
1 ATAAAATTAACAGAAAAAAAAATCAG
28117756 ATAAAATTAACAGATAATAAAAAA
1 ATAAAATTAACAGA-AA-AAAAAA
28117780 AAATAACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
22 7 0.18
23 3 0.08
24 14 0.37
26 6 0.16
27 2 0.05
28 6 0.16
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (26 bp):
ATAAAATTAACAGAAAAAAAAATCAG
Found at i:28117829 original size:6 final size:6
Alignment explanation
Indices: 28117814--28117975 Score: 106
Period size: 6 Copynumber: 26.2 Consensus size: 6
28117804 ATATATTACA
*
28117814 AATAAT AATAAA AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
* *
28117862 AAATATAT AACTATAT ACAT-AC AATACAT -ATAA- ATATAAT -CTAAAT
1 -AATA-AT AA-TA-AT A-ATAAT AATA-AT AATAAT A-ATAAT AAT-AAT
* *
28117908 AAAAAT AAATACAC AA-AGAT -ATACAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT -AATA-AT AATA-AT AATA-AT AATAAT AATAAT AATAAT AATAAT
28117958 AATAA- AATACAT AA-AAT A
1 AATAAT AATA-AT AATAAT A
28117976 CAAAAGAGGA
Statistics
Matches: 127, Mismatches: 12, Indels: 35
0.73 0.07 0.20
Matches are distributed among these distances:
5 12 0.09
6 87 0.69
7 17 0.13
8 10 0.08
9 1 0.01
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.29
Consensus pattern (6 bp):
AATAAT
Found at i:28117977 original size:9 final size:9
Alignment explanation
Indices: 28117814--28117975 Score: 106
Period size: 9 Copynumber: 17.4 Consensus size: 9
28117804 ATATATTACA
28117814 AATAATAAT
1 AATAATAAT
*
28117823 AAAAATAAT
1 AATAATAAT
28117832 AATAATAAT
1 AATAATAAT
28117841 AATAATAAT
1 AATAATAAT
28117850 AATAATAAT
1 AATAATAAT
28117859 AATAAATATAT
1 AAT-AATA-AT
28117870 AACTATATACAT
1 AA-TA-ATA-AT
*
28117882 -ACAATACAT
1 AATAATA-AT
28117891 -ATAA-ATAT
1 AATAATA-AT
*
28117899 AAT-CTAAAT
1 AATAAT-AAT
*
28117908 AAAAATAAAT
1 AATAAT-AAT
*
28117918 ACACAA-AGAT
1 A-ATAATA-AT
28117928 -ATACATAAT
1 AATA-ATAAT
28117937 AATAATAAT
1 AATAATAAT
28117946 AATAATAAT
1 AATAATAAT
28117955 AATAATAA-
1 AATAATAAT
28117963 AATACATAA-
1 AATA-ATAAT
28117972 AATA
1 AATA
28117976 CAAAAGAGGA
Statistics
Matches: 128, Mismatches: 11, Indels: 28
0.77 0.07 0.17
Matches are distributed among these distances:
8 9 0.07
9 86 0.67
10 18 0.14
11 9 0.07
12 6 0.05
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.29
Consensus pattern (9 bp):
AATAATAAT
Found at i:28118182 original size:13 final size:13
Alignment explanation
Indices: 28118159--28118290 Score: 76
Period size: 13 Copynumber: 9.8 Consensus size: 13
28118149 TCAACTCAAC
28118159 ATTTTTATTTTTTG
1 ATTTTT-TTTTTTG
*
28118173 ATTTTTTTTTTTTAAA
1 A-TTTTTTTTTTT--G
28118189 ATTTTGTTTTTGTT-
1 ATTTT-TTTTT-TTG
* *
28118203 TTTTGTTTTTTTTT
1 ATTT-TTTTTTTTG
* *
28118217 TTTTGTTTTTTTTT
1 ATTT-TTTTTTTTG
*
28118231 ATTTTTGTTTTT-
1 ATTTTTTTTTTTG
*
28118243 -TTGTTTTTTTTG
1 ATTTTTTTTTTTG
*
28118255 TTTTTTTTTTTTG
1 ATTTTTTTTTTTG
28118268 -TTTTTTGTTTTTG
1 ATTTTTT-TTTTTG
28118281 -TTTTTTTTTT
1 ATTTTTTTTTT
28118291 GCCGAAGTTC
Statistics
Matches: 101, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
11 9 0.09
12 10 0.10
13 32 0.32
14 32 0.32
15 10 0.10
16 6 0.06
17 2 0.02
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (13 bp):
ATTTTTTTTTTTG
Found at i:28118199 original size:1 final size:1
Alignment explanation
Indices: 28118190--28118290 Score: 103
Period size: 1 Copynumber: 101.0 Consensus size: 1
28118180 TTTTTTAAAA
* * * * * * * *
28118190 TTTTGTTTTTGTTTTTTGTTTTTTTTTTTTTGTTTTTTTTTATTTTTGTTTTTTTGTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
28118255 TTTTTTTTTTTTGTTTTTTGTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28118291 GCCGAAGTTC
Statistics
Matches: 78, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.01, C:0.00, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:28118236 original size:37 final size:35
Alignment explanation
Indices: 28118160--28118290 Score: 147
Period size: 35 Copynumber: 3.7 Consensus size: 35
28118150 CAACTCAACA
* * **** *
28118160 TTTTTATTTTTTGATTTTTTTTTTTTAAAATTTTG
1 TTTTTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTT
28118195 TTTTTGTTTTTTGTTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTGTTTTTTGTTTTTTTTTTTTT-TTTTTTTTT
*
28118231 ATTTTTGTTTTTTTGTTTTTTTTGTTTTTTTTTTTTGT
1 -TTTTTG-TTTTTTGTTTTTTTT-TTTTTTTTTTTTTT
28118269 TTTTTG-TTTTTGTTTTTTTTTT
1 TTTTTGTTTTTTGTTTTTTTTTT
28118291 GCCGAAGTTC
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
34 2 0.02
35 38 0.45
36 4 0.05
37 12 0.14
38 23 0.27
39 5 0.06
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.86
Consensus pattern (35 bp):
TTTTTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTT
Found at i:28118291 original size:37 final size:37
Alignment explanation
Indices: 28118190--28118291 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
28118180 TTTTTTAAAA
28118190 TTTTGTTTTTGTTTTTTGTTTTTTTTTT-TTTGTTTTT
1 TTTTGTTTTTG-TTTTTGTTTTTTTTTTGTTTGTTTTT
*
28118227 TTTTATTTTTGTTTTT-TTGTTTTTTTTGTTT-TTTTT
1 TTTTGTTTTTGTTTTTGTT-TTTTTTTTGTTTGTTTTT
28118263 TTTTGTTTTTTGTTTTTGTTTTTTTTTTG
1 TTTTG-TTTTTGTTTTTGTTTTTTTTTTG
28118292 CCGAAGTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
35 2 0.03
36 22 0.37
37 33 0.56
38 2 0.03
ACGTcount: A:0.01, C:0.00, G:0.11, T:0.88
Consensus pattern (37 bp):
TTTTGTTTTTGTTTTTGTTTTTTTTTTGTTTGTTTTT
Found at i:28118424 original size:41 final size:41
Alignment explanation
Indices: 28118299--28118541 Score: 411
Period size: 41 Copynumber: 5.9 Consensus size: 41
28118289 TTGCCGAAGT
*
28118299 TCCTCTAAACAGAGGCACCACGACTTTGGAAA-TAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
* *
28118339 TCCTCTAAACAGAGGTACCACGACTTTGGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGC
28118381 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
28118422 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
28118463 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGC
28118505 TCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAAT
1 TCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAAT
28118542 ACTCCTAGAC
Statistics
Matches: 195, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
40 40 0.21
41 90 0.46
42 65 0.33
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
Found at i:28119808 original size:22 final size:20
Alignment explanation
Indices: 28119780--28119847 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
28119770 TTTGAATCTC
**
28119780 TTTTTTTTCATTTTCTCATTTT
1 TTTTTTTTTTTTTTCTCA--TT
28119802 TTTTTTTTTTTTTTCTCATT
1 TTTTTTTTTTTTTTCTCATT
*
28119822 TTTTCTTTTTTTTTCT--TT
1 TTTTTTTTTTTTTTCTCATT
28119840 TTTTTTTT
1 TTTTTTTT
28119848 CCATCATCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.21
20 17 0.40
22 16 0.38
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTTTTTCTCATT
Found at i:28119821 original size:30 final size:30
Alignment explanation
Indices: 28119780--28119848 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
28119770 TTTGAATCTC
28119780 TTTTTTTTCATTTTCTCATTTTTTTT-TTT
1 TTTTTTTTCATTTTCTCATTTTTTTTCTTT
* *
28119809 TTTTTTTCTCATTTTTTCTTTTTTTTTCTTT
1 TTTTTTT-TCATTTTCTCATTTTTTTTCTTT
28119840 TTTTTTTTC
1 TTTTTTTTC
28119849 CATCATCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 7 0.19
30 19 0.53
31 10 0.28
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (30 bp):
TTTTTTTTCATTTTCTCATTTTTTTTCTTT
Found at i:28119838 original size:10 final size:10
Alignment explanation
Indices: 28119798--28119845 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
28119788 CATTTTCTCA
28119798 TTTTTTTTT-
1 TTTTTTTTTC
28119807 TTTTTTTTTC
1 TTTTTTTTTC
**
28119817 TCATTTTTTC
1 TTTTTTTTTC
28119827 TTTTTTTTTC
1 TTTTTTTTTC
28119837 TTTTTTTTT
1 TTTTTTTTT
28119846 TTCCATCATC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 9 0.26
10 25 0.74
ACGTcount: A:0.02, C:0.08, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:28119857 original size:29 final size:30
Alignment explanation
Indices: 28119798--28119862 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
28119788 CATTTTCTCA
**
28119798 TTTTTTTTTTTTTTTTTTCTCATTTTTTCTT
1 TTTTTTTTTTTTTTTTTTCTCA-TTCATCTT
28119829 TTTTTTTCTTTTTTTTTTTC-CA-TCATCTT
1 TTTTTTT-TTTTTTTTTTTCTCATTCATCTT
28119858 TTTTT
1 TTTTT
28119863 CATCCATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 10 0.32
31 9 0.29
32 12 0.39
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (30 bp):
TTTTTTTTTTTTTTTTTTCTCATTCATCTT
Found at i:28119862 original size:1 final size:1
Alignment explanation
Indices: 28119798--28119847 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
28119788 CATTTTCTCA
* ** * *
28119798 TTTTTTTTTTTTTTTTTTCTCATTTTTTCTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28119848 CCATCATCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.02, C:0.08, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:28123875 original size:57 final size:57
Alignment explanation
Indices: 28123664--28124217 Score: 871
Period size: 57 Copynumber: 9.7 Consensus size: 57
28123654 TTTTTTGTAG
* *
28123664 GGAAAATTGATATTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTG-AAA-TTT-ATTTCT-AA
*
28123723 GGAAAATTGATACTTTCAACTTTT-CCTCAAAA-ATTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTG-AAATTTATTTCTAA
28123779 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTGAAATTTATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCT-AA
28123835 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGAAATTTATTTCTAA
28123892 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAATTTA-TTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAA
28123947 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGAAATTTATTTCTAA
*
28124005 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAA
28124062 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCT--
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTTGAAATTTATTTCTAA
* *
28124119 -GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAA
28124175 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTT
28124218 TGGAATTTTT
Statistics
Matches: 468, Mismatches: 10, Indels: 35
0.91 0.02 0.07
Matches are distributed among these distances:
54 19 0.04
55 42 0.09
56 127 0.27
57 167 0.36
58 71 0.15
59 42 0.09
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAA
Found at i:28123905 original size:113 final size:114
Alignment explanation
Indices: 28123664--28124225 Score: 878
Period size: 113 Copynumber: 4.9 Consensus size: 114
28123654 TTTTTTGTAG
*
28123664 GGAAAATTGATATTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTTGATTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTG-AAA-TTT-ATTTTCAAGGAAA
*
28123728 ATTGATACTTTCAACTTTT-CCTCAAAA-A-TTTTTTTGAAAATTTATTTCTAA
62 ATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTG-AAATTTATTTCTAA
28123779 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTTCAAGGAAAATTG
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTTCAAGGAAAATTG
28123844 ATACTTTCAACTTTTCCC-AAAAATATTTTTTTTGAAATTTATTTCTAA
66 ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
28123892 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAATTTATTCT-AAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTGAAATTTATTTTCAAGGAAAATT
28123955 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
65 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
28124005 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTA-TTTCTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTGAAATTTATTTTC-AAGGAAAAT
28124069 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCT--
64 TGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGAAATTTATTTCTAA
*
28124119 -GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTA-TTTCTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGAAATTTATTTTC-AAGGAAAAT
*
28124182 TGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAATTT
64 TGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTGAAATTT
28124226 TTATTTTTAT
Statistics
Matches: 429, Mismatches: 6, Indels: 26
0.93 0.01 0.06
Matches are distributed among these distances:
112 66 0.15
113 231 0.54
114 44 0.10
115 67 0.16
116 21 0.05
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (114 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTTCAAGGAAAATTG
ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
Found at i:28124009 original size:170 final size:169
Alignment explanation
Indices: 28123664--28124217 Score: 867
Period size: 170 Copynumber: 3.2 Consensus size: 169
28123654 TTTTTTGTAG
* *
28123664 GGAAAATTGATATTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTTGATTT-TCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTG-AAA-TTT-ATTTCT-AAGGAA
28123727 AATTGATACTTTCAACTTTT-CCTCAAAAAT-TTTTTTGAAAATTTATTTCTAAGGAAAATTGAT
62 AATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTG-AAATTTATTTCTAAGGAAAATTGAT
28123790 ACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTT-TCAA
125 ACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCT-AA
28123835 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTGAAATTTATTTCTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGAAATTTATTTCTAAGGAAAAT
28123899 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAATTTA-TTCTAAGGAAAATTGATACTTT
65 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAATTTATTTCTAAGGAAAATTGATACTTT
28123963 CAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
130 CAACTTTTCCC-AAAAATA-TTTTTTTGAAATTTATTTCTAA
*
28124005 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAAGGAAAATT
28124070 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCT---GAAAATTGATACT
66 GATACTTTCAACTTTTCCCTAAAAATA---TTTTTTGAAATTTATTTCTAAGGAAAATTGATACT
*
28124132 TTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
128 TTCAACTTTT-CCCAAAAATATTTTTTTGAAATTTATTTCTAA
28124175 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTT
28124218 TGGAATTTTT
Statistics
Matches: 364, Mismatches: 4, Indels: 30
0.91 0.01 0.08
Matches are distributed among these distances:
168 33 0.09
169 50 0.14
170 181 0.50
171 72 0.20
172 10 0.03
173 14 0.04
174 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (169 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAAGGAAAATT
GATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAATTTATTTCTAAGGAAAATTGATACTTTC
AACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
Found at i:28124713 original size:19 final size:20
Alignment explanation
Indices: 28124680--28124718 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
28124670 GGTGCCAGAT
28124680 TCTGGAAATTTTCGCCGGAA
1 TCTGGAAATTTTCGCCGGAA
28124700 TCTGGAAA-TTTCGCCGGAA
1 TCTGGAAATTTTCGCCGGAA
28124719 GTTGGCCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
TCTGGAAATTTTCGCCGGAA
Found at i:28124867 original size:25 final size:25
Alignment explanation
Indices: 28124831--28124878 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28124821 AATCTGGAAA
28124831 TTTCCCAGAAATTTCCAGAAAAATT
1 TTTCCCAGAAATTTCCAGAAAAATT
*
28124856 TTTCGCCA-AAATTTCTAGAAAAA
1 TTTC-CCAGAAATTTCCAGAAAAA
28124879 ATTCTCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (25 bp):
TTTCCCAGAAATTTCCAGAAAAATT
Found at i:28125320 original size:6 final size:6
Alignment explanation
Indices: 28125309--28125458 Score: 82
Period size: 6 Copynumber: 24.2 Consensus size: 6
28125299 TATTACAAAA
28125309 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAAT ATATAACT ATATACAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AAT-AAT A-ATAA-T A-ATA-AT
* * * * *
28125362 -ACAAT ACAT-AT AA-ATCT AAT-CT AAATAAA AATAAAT ACACAA- AGAT-AT
1 AATAAT A-ATAAT AATA-AT AATAAT -AATAAT AAT-AAT A-ATAAT A-ATAAT
28125410 ACATAAT AATAAT AATAAT AATAAT AATAAT AATAA- AATACAT AA-AAT
1 A-ATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATA-AT AATAAT
28125458 A
1 A
28125459 CAAAAGAGGA
Statistics
Matches: 117, Mismatches: 10, Indels: 35
0.72 0.06 0.22
Matches are distributed among these distances:
5 13 0.11
6 76 0.65
7 17 0.15
8 10 0.09
9 1 0.01
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.29
Consensus pattern (6 bp):
AATAAT
Found at i:28125460 original size:9 final size:9
Alignment explanation
Indices: 28125309--28125458 Score: 82
Period size: 9 Copynumber: 16.1 Consensus size: 9
28125299 TATTACAAAA
28125309 AATAATAAT
1 AATAATAAT
28125318 AATAATAAT
1 AATAATAAT
28125327 AATAATAAT
1 AATAATAAT
28125336 AATAATAAAT
1 AATAAT-AAT
28125346 ATATAACTATAT
1 A-ATAA-TA-AT
*
28125358 ACAT-ACAAT
1 A-ATAATAAT
28125367 ACAT-ATAA-
1 A-ATAATAAT
* *
28125375 ATCTAAT-CT
1 A-ATAATAAT
*
28125384 AAATAAAAAT
1 -AATAATAAT
*
28125394 AAATACACAA-
1 -AATA-ATAAT
28125404 AGAT-ATACAT
1 A-ATAATA-AT
28125414 AATAATAAT
1 AATAATAAT
28125423 AATAATAAT
1 AATAATAAT
28125432 AATAATAAT
1 AATAATAAT
28125441 AATAA-AAT
1 AATAATAAT
28125449 ACATAA-AAT
1 A-ATAATAAT
28125458 A
1 A
28125459 CAAAAGAGGA
Statistics
Matches: 116, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
8 8 0.07
9 75 0.65
10 18 0.16
11 9 0.08
12 6 0.05
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.29
Consensus pattern (9 bp):
AATAATAAT
Found at i:28126700 original size:17 final size:17
Alignment explanation
Indices: 28126678--28126739 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 17
28126668 ATTTATTTAT
28126678 ATATAATATAAAAATTA
1 ATATAATATAAAAATTA
*
28126695 ATATAA-ATTAAAATT-
1 ATATAATATAAAAATTA
* *
28126710 TTATACTAT-AAAA--A
1 ATATAATATAAAAATTA
*
28126724 ATATAATAAAAAAATT
1 ATATAATATAAAAATT
28126740 CCGTGCCTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
14 6 0.18
15 12 0.35
16 10 0.29
17 6 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAATATAAAAATTA
Found at i:28129774 original size:35 final size:36
Alignment explanation
Indices: 28129728--28129798 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
28129718 ATAATTTTGT
28129728 TAGGCAATAGTCATTTTCAAAAAAAA-AAAAAAAAG
1 TAGGCAATAGTCATTTTCAAAAAAAAGAAAAAAAAG
28129763 TAGGCAATAGTCATTTTCAAAAAAAAGGAAAAAAAA
1 TAGGCAATAGTCATTTTCAAAAAAAA-GAAAAAAAA
28129799 AAAGCACTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 26 0.76
37 8 0.24
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.20
Consensus pattern (36 bp):
TAGGCAATAGTCATTTTCAAAAAAAAGAAAAAAAAG
Found at i:28135954 original size:22 final size:22
Alignment explanation
Indices: 28135924--28135970 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
28135914 CGAAAATATA
*
28135924 AAATATATTTTTTAA-TTTTATT
1 AAATATA-TTTATAATTTTTATT
*
28135946 AAATTTATTTATAATTTTTATT
1 AAATATATTTATAATTTTTATT
28135968 AAA
1 AAA
28135971 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATATATTTATAATTTTTATT
Found at i:28137168 original size:20 final size:19
Alignment explanation
Indices: 28137143--28137185 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
28137133 CATCCAATAA
* *
28137143 AAAATAGAATTAGCAAAAAT
1 AAAATAAAATTA-AAAAAAT
28137163 AAAATAAAATTAAAAAAAT
1 AAAATAAAATTAAAAAAAT
28137182 AAAA
1 AAAA
28137186 GGAAAAGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAAAATTAAAAAAAT
Found at i:28141692 original size:2 final size:2
Alignment explanation
Indices: 28141685--28141733 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
28141675 TCAGGTATGG
28141685 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
28141727 CT CT CT C
1 CT CT CT C
28141734 ATGACAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:28148723 original size:2 final size:2
Alignment explanation
Indices: 28148716--28148745 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28148706 CAATTATTAA
*
28148716 TG TG TG TG TG AG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28148746 AGAGAGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:28154250 original size:26 final size:26
Alignment explanation
Indices: 28154198--28154250 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
28154188 ATGTGTTATA
* * * * *
28154198 ATATATAAATTTATAGACTTATTACT
1 ATATATAAATTTAAAAAATCATCACT
28154224 ATATATAAATTTAAAAAATCATCACT
1 ATATATAAATTTAAAAAATCATCACT
28154250 A
1 A
28154251 ATTTTTTTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATATAAATTTAAAAAATCATCACT
Found at i:28155578 original size:17 final size:17
Alignment explanation
Indices: 28155545--28155580 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28155535 CCCTATAATT
*
28155545 AATTAAAACCCATAAAC
1 AATTAAAACCCAAAAAC
*
28155562 AATTAAAACCTAAAAAC
1 AATTAAAACCCAAAAAC
28155579 AA
1 AA
28155581 AACTCTAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (17 bp):
AATTAAAACCCAAAAAC
Found at i:28156760 original size:18 final size:18
Alignment explanation
Indices: 28156679--28156913 Score: 82
Period size: 17 Copynumber: 13.6 Consensus size: 18
28156669 ATGAATTGAA
* *
28156679 AGATTTGTAAGCA-TTTC
1 AGATTCGTAAGAATTTTC
* *
28156696 AGATTTGCAAGAATTTT-
1 AGATTCGTAAGAATTTTC
* *
28156713 AGTTTTGTAAGAACTTTT-
1 AGATTCGTAAGAA-TTTTC
*
28156731 AGATT-GAAAAGAATTTTC
1 AGATTCG-TAAGAATTTTC
*
28156749 AGATTCGCAAGAGA--TTC
1 AGATTCGTAAGA-ATTTTC
* * **
28156766 A-ATTTCATAAAAATTTAA
1 AGA-TTCGTAAGAATTTTC
28156784 AGATTCGTAAGAA-TTTC
1 AGATTCGTAAGAATTTTC
* * *
28156801 ATATTCGCAAAAATTTT-
1 AGATTCGTAAGAATTTTC
* * * *
28156818 AGTTTCATAAAAACTTTC
1 AGATTCGTAAGAATTTTC
* **
28156836 AAATTCACAAGAATTTTC
1 AGATTCGTAAGAATTTTC
* *
28156854 ATATTCGTAAGAA-ATTC
1 AGATTCGTAAGAATTTTC
* * *
28156871 AGGTTCATTAGAATTTT-
1 AGATTCGTAAGAATTTTC
*
28156888 AAATTCGTAAG--TTTTC
1 AGATTCGTAAGAATTTTC
*
28156904 AAATTCGTAA
1 AGATTCGTAA
28156914 AAATGAAAGA
Statistics
Matches: 162, Mismatches: 42, Indels: 29
0.70 0.18 0.12
Matches are distributed among these distances:
15 4 0.02
16 12 0.07
17 80 0.49
18 63 0.39
19 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (18 bp):
AGATTCGTAAGAATTTTC
Found at i:28156800 original size:105 final size:105
Alignment explanation
Indices: 28156672--28156917 Score: 262
Period size: 105 Copynumber: 2.4 Consensus size: 105
28156662 TATTTGTATG
* * * * * ** * * * *
28156672 AATTGAAAGATTTGTAAGCATTTCAGATTTGCAAGAATTTTAGTTTTGTAAGAACTTTTAGATTG
1 AATTTAAAGATTCGTAAGAATTTCAGATTCGCAAAAATTTTAGTTTCATAAAAACTTTCAAATTC
* *
28156737 AAAAGAATTTTCAGATTCGCAAGAGATTCAATTTCATAAA
66 AAAAGAATTTTCAGATTCGCAAGAAATTCAAGTTCATAAA
*
28156777 AATTTAAAGATTCGTAAGAATTTCATATTCGCAAAAATTTTAGTTTCATAAAAACTTTCAAATTC
1 AATTTAAAGATTCGTAAGAATTTCAGATTCGCAAAAATTTTAGTTTCATAAAAACTTTCAAATTC
* * * * * *
28156842 ACAAGAATTTTCATATTCGTAAGAAATTCAGGTTCATTAG
66 AAAAGAATTTTCAGATTCGCAAGAAATTCAAGTTCATAAA
* * * *
28156882 AATTTTAA-ATTCGTAAG-TTTTCAAATTCGTAAAAAT
1 AATTTAAAGATTCGTAAGAATTTCAGATTCGCAAAAAT
28156918 GAAAGATTTG
Statistics
Matches: 117, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
103 16 0.14
104 9 0.08
105 92 0.79
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (105 bp):
AATTTAAAGATTCGTAAGAATTTCAGATTCGCAAAAATTTTAGTTTCATAAAAACTTTCAAATTC
AAAAGAATTTTCAGATTCGCAAGAAATTCAAGTTCATAAA
Found at i:28156909 original size:16 final size:15
Alignment explanation
Indices: 28156884--28156913 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28156874 TTCATTAGAA
28156884 TTTTAAATTCGTAAG
1 TTTTAAATTCGTAAG
28156899 TTTTCAAATTCGTAA
1 TTTT-AAATTCGTAA
28156914 AAATGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (15 bp):
TTTTAAATTCGTAAG
Found at i:28157021 original size:18 final size:18
Alignment explanation
Indices: 28157000--28157058 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
28156990 ATTTGCAAAA
28157000 AATTTTCAAATTCACAAG
1 AATTTTCAAATTCACAAG
*
28157018 AATTTTCAAATTCATAA-
1 AATTTTCAAATTCACAAG
* **
28157035 AAATTTCAAATTTGCAAG
1 AATTTTCAAATTCACAAG
28157053 AATTTT
1 AATTTT
28157059 AGGTTCGCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (18 bp):
AATTTTCAAATTCACAAG
Found at i:28157056 original size:17 final size:17
Alignment explanation
Indices: 28157003--28157057 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
28156993 TGCAAAAAAT
28157003 TTTCAAATTCACAAGAA
1 TTTCAAATTCACAAGAA
* *
28157020 TTTTCAAATTCATAAAAA
1 -TTTCAAATTCACAAGAA
**
28157038 TTTCAAATTTGCAAGAA
1 TTTCAAATTCACAAGAA
28157055 TTT
1 TTT
28157058 TAGGTTCGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTCAAATTCACAAGAA
Found at i:28157479 original size:46 final size:46
Alignment explanation
Indices: 28157330--28157529 Score: 158
Period size: 46 Copynumber: 4.3 Consensus size: 46
28157320 TAATAAAAAG
* * * *
28157330 TTAAAGATTTTCATTCAAAAAAC-TTAGGAATTCACATCCAAAATT
1 TTAAAGATTCTCATTCTAAAAACTTTATGACTTCACATCCAAAATT
* * * * * *
28157375 TCAAAGATTCACATTCGAAAAACCTTTAGTGTC-TCGCAGT-TAAAATT
1 TTAAAGATTCTCATTCTAAAAA-CTTTA-TGACTTCACA-TCCAAAATT
* *
28157422 TCAAAGGTTCTCATTCTAAAAACTTTATGACTTCACATCCAAAATT
1 TTAAAGATTCTCATTCTAAAAACTTTATGACTTCACATCCAAAATT
* * **
28157468 TTAAAGATTCTCATT-TGAAAAATTTTAAGGTTTCACATCC-AAATT
1 TTAAAGATTCTCATTCT-AAAAACTTTATGACTTCACATCCAAAATT
* *
28157513 TTCAAACATTCACATTC
1 TT-AAAGATTCTCATTC
28157530 GATAAATTTT
Statistics
Matches: 123, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
45 30 0.24
46 59 0.48
47 32 0.26
48 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (46 bp):
TTAAAGATTCTCATTCTAAAAACTTTATGACTTCACATCCAAAATT
Found at i:28157549 original size:46 final size:46
Alignment explanation
Indices: 28157359--28157550 Score: 126
Period size: 46 Copynumber: 4.2 Consensus size: 46
28157349 AAACTTAGGA
* * *
28157359 ATTCACATCCAAAATTTCAAAGATTCACATTCGAAAAACCTTT-AGTG
1 ATTCACATCCAAAATTTTAAACATTCACATTCGAAAAA-TTTTAAG-G
* * * ** * * * *
28157406 -TCTCGCAGT-TAAAATTTCAAAGGTTCTCATTCTAAAAACTTT-ATG
1 AT-TCACA-TCCAAAATTTTAAACATTCACATTCGAAAAATTTTAAGG
* * *
28157451 ACTTCACATCCAAAATTTTAAAGATTCTCATTTGAAAAATTTTAAGG
1 A-TTCACATCCAAAATTTTAAACATTCACATTCGAAAAATTTTAAGG
* *
28157498 TTTCACATCC-AAATTTTCAAACATTCACATTCGATAAATTTT-AGAG
1 ATTCACATCCAAAATTTT-AAACATTCACATTCGAAAAATTTTAAG-G
28157544 ATTCACA
1 ATTCACA
28157551 ATTATATTTT
Statistics
Matches: 117, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
45 11 0.09
46 73 0.62
47 32 0.27
48 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (46 bp):
ATTCACATCCAAAATTTTAAACATTCACATTCGAAAAATTTTAAGG
Found at i:28163630 original size:23 final size:24
Alignment explanation
Indices: 28163566--28163639 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
28163556 TCACACCAAG
*
28163566 AAAATATCAAAAAATAAATACCAGTA
1 AAAATATCAAAAAA-ATATA-CAGTA
* * *
28163592 AAAATATCACAGAAATATA-GGTA
1 AAAATATCAAAAAAATATACAGTA
*
28163615 AAAATATCAAAAAAATA-CCAGTA
1 AAAATATCAAAAAAATATACAGTA
28163638 AA
1 AA
28163640 TTTATCGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
23 23 0.59
25 4 0.10
26 12 0.31
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.19
Consensus pattern (24 bp):
AAAATATCAAAAAAATATACAGTA
Found at i:28166131 original size:19 final size:20
Alignment explanation
Indices: 28166093--28166141 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
28166083 AACTTTCCTT
* *
28166093 TTTTTTTTTTGTTTTTTGACC
1 TTTTTTTTTTG-TTTCTGACA
28166114 TTTTTTTTTTG-TTCTGACA
1 TTTTTTTTTTGTTTCTGACA
28166133 TTATTTTTT
1 TT-TTTTTT
28166142 ACTTTTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
21 11 0.44
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTTTTTTTGTTTCTGACA
Found at i:28166188 original size:6 final size:6
Alignment explanation
Indices: 28166179--28166241 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
28166169 AACTTTAACC
* * * * * *
28166179 AAAATT AAAAAT AAAATC ACAATT AAAATT AAAATCCA AAAATC CAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT--T AAAATT AAAATT
28166229 AAAATT AAAATT A
1 AAAATT AAAATT A
28166242 TGGTCTTTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
6 39 0.89
8 5 0.11
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:28167114 original size:22 final size:24
Alignment explanation
Indices: 28167089--28167132 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
28167079 CATGAGTTGG
*
28167089 TAAAGTTT-GAATATT-TTACTTA
1 TAAAATTTAGAATATTATTACTTA
*
28167111 TAAAATTTAGAATTTTATTACT
1 TAAAATTTAGAATATTATTACT
28167133 AGCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 6 0.33
24 5 0.28
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (24 bp):
TAAAATTTAGAATATTATTACTTA
Found at i:28167359 original size:101 final size:103
Alignment explanation
Indices: 28167242--28167440 Score: 282
Period size: 101 Copynumber: 1.9 Consensus size: 103
28167232 AACTTTTCTT
* * *
28167242 AAAAAAAAGAATACCAATGTAA-CTTACTT-CCAATACCACTGTGTT-TTTGTA-TTTTTCATAT
1 AAAAAAAAAAAAACCAATGTAATC-TA-TTACCAATACCAATGT-TTATTTGTATTTTTTCATAT
*
28167303 GATCTTAGATTACATAATAAAGATAATC-AATTTCCATGCA
63 GATCTTAGATTACATAATAAAAATAATCAAATTTCCATGCA
*
28167343 AAAAAAAAAAAAACCAATGTAATCTATTACCAATACTAATGTTTATTTGTATTTTTTTCATATGA
1 AAAAAAAAAAAAACCAATGTAATCTATTACCAATACCAATGTTTATTTGTA-TTTTTTCATATGA
28167408 TCTTAGATTACATAATAAAAATAATCAAATTTC
65 TCTTAGATTACATAATAAAAATAATCAAATTTC
28167441 ATTAAGGATG
Statistics
Matches: 87, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
100 4 0.05
101 39 0.45
102 1 0.01
103 37 0.43
104 6 0.07
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.37
Consensus pattern (103 bp):
AAAAAAAAAAAAACCAATGTAATCTATTACCAATACCAATGTTTATTTGTATTTTTTCATATGAT
CTTAGATTACATAATAAAAATAATCAAATTTCCATGCA
Found at i:28167600 original size:15 final size:16
Alignment explanation
Indices: 28167572--28167608 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28167562 GTATATATAA
28167572 ATTT-TTTTATTATTT
1 ATTTATTTTATTATTT
28167587 ATTTATTTTA-TATTT
1 ATTTATTTTATTATTT
*
28167602 ATATATT
1 ATTTATT
28167609 AATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTATTTTATTATTT
Found at i:28168844 original size:18 final size:20
Alignment explanation
Indices: 28168801--28168844 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
28168791 TAAATTAAAA
*
28168801 AATAAATTTTAAATTTATTT
1 AATAAATTTTAAATTTATAT
*
28168821 ATTAAA-TTT-AATTTATAT
1 AATAAATTTTAAATTTATAT
28168839 AATAAA
1 AATAAA
28168845 AATTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAAATTTTAAATTTATAT
Found at i:28168907 original size:24 final size:23
Alignment explanation
Indices: 28168880--28168943 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 23
28168870 GTTTAATGAG
28168880 ATTATATTTAATATATATATATAA
1 ATTA-ATTTAATATATATATATAA
28168904 ATTAA---AATATATATATA-AA
1 ATTAATTTAATATATATATATAA
*
28168923 ATTAAGTTTAATA-AAATATAT
1 ATTAA-TTTAATATATATATAT
28168944 TTTTTTAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
19 7 0.21
20 12 0.35
22 6 0.18
23 5 0.15
24 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTAATTTAATATATATATATAA
Found at i:28168913 original size:18 final size:19
Alignment explanation
Indices: 28168889--28168927 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
28168879 GATTATATTT
28168889 AATATATATATATAAATTAA
1 AATATATATATA-AAATTAA
28168909 AATATATATATAAAATTAA
1 AATATATATATAAAATTAA
28168928 GTTTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATATATATAAAATTAA
Found at i:28168932 original size:58 final size:59
Alignment explanation
Indices: 28168821--28168934 Score: 160
Period size: 58 Copynumber: 1.9 Consensus size: 59
28168811 AAATTTATTT
* *
28168821 ATTAAATTTAATTTATATAATAAAAATTTAAAAAATATTATTAAATTAAGTTTAATGAG
1 ATTAAATTTAATATATATAATAAAAATTTAAAAAATATTATAAAATTAAGTTTAATGAG
* * *
28168880 ATTATATTTAATATATAT-ATATAAA-TTAAAATATATATATAAAATTAAGTTTAAT
1 ATTAAATTTAATATATATAATAAAAATTTAAAAAATAT-TATAAAATTAAGTTTAAT
28168935 AAAATATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 10 0.20
58 23 0.47
59 16 0.33
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (59 bp):
ATTAAATTTAATATATATAATAAAAATTTAAAAAATATTATAAAATTAAGTTTAATGAG
Found at i:28173823 original size:22 final size:22
Alignment explanation
Indices: 28173795--28173848 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
28173785 GTTCACTATC
28173795 TGGATTGAAGGGAAGTTTATGT
1 TGGATTGAAGGGAAGTTTATGT
*
28173817 TGGATTGAAGGGAGGTTTATGT
1 TGGATTGAAGGGAAGTTTATGT
**
28173839 AAGATTGAAG
1 TGGATTGAAG
28173849 TCATGATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (22 bp):
TGGATTGAAGGGAAGTTTATGT
Found at i:28186310 original size:2 final size:2
Alignment explanation
Indices: 28186300--28186346 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
28186290 GAAAAAAAGA
* * *
28186300 AT AT A- AT AT AT AT AC AT AT AT AT GT AT AT AT AT AT CAT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
28186342 AT AT A
1 AT AT A
28186347 AAAGTGTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28186546 original size:147 final size:150
Alignment explanation
Indices: 28186358--28186659 Score: 370
Period size: 147 Copynumber: 2.0 Consensus size: 150
28186348 AAGTGTGAAC
* * * *
28186358 TCTAAAAGTATTAATAGTGAACGACATAAATATCCTTATAAATTTTAAGAAATAACAAA-TT-TA
1 TCTAAAAGTATTAAAAATGAACAACATAAATATCCTTATAAATTTTAAAAAATAACAAATTTATA
* *
28186421 -C-TTT-TA-AATTTTTTAATTT-TTT-AGTAATGATTATTTGTCA-TAAATATATAGCTTTTAT
66 TCATTTCTAGAATTTTTT-ATTTATTTCA-TAAAGATTATTTGTCATTAAAAATATAGCTTTTA-
28186479 TAGTTAGTTAGTTATTTAAATTTAAA
128 T--TT-GTTAGTTATTTAAATTTAAA
* * *
28186505 TCTAAAAGTGTTAAAAATGAATAACATAAATATCTTTATAAATTTTAAAAAATAACAAATTTATA
1 TCTAAAAGTATTAAAAATGAACAACATAAATATCCTTATAAATTTTAAAAAATAACAAATTTATA
*
28186570 TTTCAATTTCTAGCATTTTTTATTTATTTCATAAAGATTATTTGTCATTAAAAATATAGCTTTTA
66 --TC-ATTTCTAGAATTTTTTATTTATTTCATAAAGATTATTTGTCATTAAAAATATAGCTTTTA
28186635 TTTGTTAGTTATTTAAATTTAAA
128 TTTGTTAGTTATTTAAATTTAAA
28186658 TC
1 TC
28186660 AATTACAAAT
Statistics
Matches: 133, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
147 52 0.39
148 2 0.02
149 2 0.02
152 1 0.01
153 22 0.17
154 5 0.04
155 6 0.05
156 26 0.20
157 17 0.13
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (150 bp):
TCTAAAAGTATTAAAAATGAACAACATAAATATCCTTATAAATTTTAAAAAATAACAAATTTATA
TCATTTCTAGAATTTTTTATTTATTTCATAAAGATTATTTGTCATTAAAAATATAGCTTTTATTT
GTTAGTTATTTAAATTTAAA
Done.