Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 14 of 29
Found at i:5071135 original size:12 final size:12
Alignment explanation
Indices: 5071118--5071156 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
5071108 TTTTTGATGA
5071118 ACATGTATCGAT
1 ACATGTATCGAT
5071130 ACATGT-TC-AT
1 ACATGTATCGAT
5071140 A-ATGTATCGAT
1 ACATGTATCGAT
5071151 ACATGT
1 ACATGT
5071157 TCATAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 4 0.17
10 5 0.21
11 5 0.21
12 10 0.42
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (12 bp):
ACATGTATCGAT
Found at i:5071146 original size:21 final size:21
Alignment explanation
Indices: 5071120--5071163 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5071110 TTTGATGAAC
5071120 ATGTATCGATACATGTTCATA
1 ATGTATCGATACATGTTCATA
5071141 ATGTATCGATACATGTTCATA
1 ATGTATCGATACATGTTCATA
5071162 AT
1 AT
5071164 CCATATTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATGTTCATA
Found at i:5071302 original size:23 final size:22
Alignment explanation
Indices: 5071276--5071364 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 22
5071266 TTAGTCACAC
*
5071276 GATTCCATATTAACTAGTCATGT
1 GATTCCATATCAACTAGTCA-GT
* ** * *
5071299 GATTCCAAATTTAGTAGTCGCGT
1 GATTCCATATCAACTAGTC-AGT
*
5071322 GATTCCATATCAAATAGTCGAGT
1 GATTCCATATCAACTAGTC-AGT
*
5071345 GATTCAATATCAACTAGTCA
1 GATTCCATATCAACTAGTCA
5071365 CACAATTCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
22 1 0.02
23 53 0.98
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (22 bp):
GATTCCATATCAACTAGTCAGT
Found at i:5071317 original size:46 final size:45
Alignment explanation
Indices: 5071224--5071349 Score: 117
Period size: 46 Copynumber: 2.7 Consensus size: 45
5071214 TCTTAACGGT
** * * *
5071224 TCACGCGATTCCATATTTCCTAGTTACGTGAATCCAAATCGATTAG
1 TCACGCGATTCCATATTAACTAGTCA-GTGATTCCAAATCGAGTAG
* **
5071270 TCACACGATTCCATATTAACTAGTCATGTGATTCCAAATTTAGTAG
1 TCACGCGATTCCATATTAACTAGTCA-GTGATTCCAAATCGAGTAG
* * * *
5071316 TCGCGTGATTCCATATCAAATAGTCGAGTGATTC
1 TCACGCGATTCCATATTAACTAGTC-AGTGATTC
5071350 AATATCAACT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
46 64 0.98
47 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (45 bp):
TCACGCGATTCCATATTAACTAGTCAGTGATTCCAAATCGAGTAG
Found at i:5071372 original size:23 final size:23
Alignment explanation
Indices: 5071346--5071403 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
5071336 TAGTCGAGTG
*
5071346 ATTCAATATCAACTAGTCACACA
1 ATTCAATATCAACCAGTCACACA
* * * * *
5071369 ATTCTATATCCACCATTTACGCA
1 ATTCAATATCAACCAGTCACACA
5071392 ATTCAATATCAA
1 ATTCAATATCAA
5071404 TTAATTACAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (23 bp):
ATTCAATATCAACCAGTCACACA
Found at i:5071971 original size:53 final size:53
Alignment explanation
Indices: 5071914--5072036 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 53
5071904 AAAAACTCAA
* * ** *
5071914 AAAAAAATATTGTTACACACCATGTTCAAAAATTATTGTTGTATATTATGTTG
1 AAAAAAATATTGTTACACACCATATTCAAAAATTATTATTACACATTATGTTG
* ** ** *
5071967 AAAAAAAAATTACTACACGTCATATTTAAAAATTATTATTACACATTATGTTG
1 AAAAAAATATTGTTACACACCATATTCAAAAATTATTATTACACATTATGTTG
5072020 AAAAAAATA-TGTTACAC
1 AAAAAAATATTGTTACAC
5072037 GTCATTTTTA
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
52 6 0.11
53 50 0.89
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (53 bp):
AAAAAAATATTGTTACACACCATATTCAAAAATTATTATTACACATTATGTTG
Found at i:5072023 original size:26 final size:26
Alignment explanation
Indices: 5071915--5072025 Score: 69
Period size: 26 Copynumber: 4.2 Consensus size: 26
5071905 AAAACTCAAA
* * *
5071915 AAAAAATATTGTTACACACCATGTTC
1 AAAAAATATTATTACACATCATGTTG
* * ** * *
5071941 AAAAATTATTGTTGTATATTATGTTG
1 AAAAAATATTATTACACATCATGTTG
* * * * *
5071967 AAAAAAAAATTACTACACGTCATATTT
1 -AAAAAATATTATTACACATCATGTTG
* *
5071994 AAAAATTATTATTACACATTATGTTG
1 AAAAAATATTATTACACATCATGTTG
5072020 AAAAAA
1 AAAAAA
5072026 ATATGTTACA
Statistics
Matches: 58, Mismatches: 26, Indels: 2
0.67 0.30 0.02
Matches are distributed among these distances:
26 43 0.74
27 15 0.26
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (26 bp):
AAAAAATATTATTACACATCATGTTG
Found at i:5072049 original size:26 final size:27
Alignment explanation
Indices: 5071967--5072049 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 27
5071957 TATTATGTTG
* *
5071967 AAAAAAAAATTACTACACGTCATATTT
1 AAAAAAATATTATTACACGTCATATTT
* * * * *
5071994 -AAAAATTATTATTACACATTATGTTG
1 AAAAAAATATTATTACACGTCATATTT
* *
5072020 AAAAAAATA-TGTTACACGTCATTTTT
1 AAAAAAATATTATTACACGTCATATTT
5072046 AAAA
1 AAAA
5072050 TGTTTAACTC
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
26 35 0.83
27 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAAAAATATTATTACACGTCATATTT
Found at i:5072242 original size:114 final size:116
Alignment explanation
Indices: 5072050--5072331 Score: 258
Period size: 115 Copynumber: 2.4 Consensus size: 116
5072040 ATTTTTAAAA
* * * * * *
5072050 TGTTTAACTCTAAAAGTTTAT-GTCTTAGTGAAATACAAAGA-A-G-CCAAGTTACATGCCATGT
1 TGTTTAACTTTAAGAGTTTATATTC-TAGTGAAATACAAAAATAGGACCAAGTTACAGGCCATAT
* ** *
5072111 TAAAAAAAAATTTGTTACGCTGAAAA-AAAAATTATTACACATTAAGTTTA-AGG
65 TAAAAAAAAA--TGTTACACTGAAAATAAAAATTATTACACACCAAGATTATA-G
*
5072164 TGTTTAACTTTAAGAGTTTATATTCTAGTGAAATACAAAAATATGGACCAAGTTATAGGCCATAT
1 TGTTTAACTTTAAGAGTTTATATTCTAGTGAAATACAAAAATA-GGACCAAGTTACAGGCCATAT
* ** * ** *
5072229 T-AAAAAAAA-GTTACATTGAAAATAAAGGTTGTTACATGCCATGATTATAG
65 TAAAAAAAAATGTTACACTGAAAATAAAAATTATTACACACCAAGATTATAG
* *
5072279 TGTTTAA-TTGCAAGAGTTTATATTTTAGTGAAATACAAAAATAGAGACCAAGT
1 TGTTTAACTT-TAAGAGTTTATATTCTAGTGAAATACAAAAATAG-GACCAAGT
5072332 ACCATGTTGA
Statistics
Matches: 139, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
114 48 0.35
115 65 0.47
116 1 0.01
117 9 0.06
118 16 0.12
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (116 bp):
TGTTTAACTTTAAGAGTTTATATTCTAGTGAAATACAAAAATAGGACCAAGTTACAGGCCATATT
AAAAAAAAATGTTACACTGAAAATAAAAATTATTACACACCAAGATTATAG
Found at i:5072654 original size:14 final size:15
Alignment explanation
Indices: 5072635--5072664 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5072625 TGCAAATATG
5072635 GCATGTAACAA-TTT
1 GCATGTAACAACTTT
5072649 GCATGTAACAACTTT
1 GCATGTAACAACTTT
5072664 G
1 G
5072665 AGCAGTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (15 bp):
GCATGTAACAACTTT
Found at i:5074784 original size:15 final size:15
Alignment explanation
Indices: 5074763--5074832 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
5074753 TAGGATATAA
5074763 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
* *
5074778 GTTTAAATTTAAATT
1 ATTTAAATTTAATTT
* **
5074793 ATCT--A-TCCATTAT
1 ATTTAAATTTAATT-T
5074806 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
5074821 GTTTAAATTTAA
1 ATTTAAATTTAA
5074833 ACATAATATC
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
12 3 0.08
13 5 0.12
15 28 0.70
16 4 0.10
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:5082568 original size:19 final size:20
Alignment explanation
Indices: 5082521--5082558 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5082511 TAAATAAATT
5082521 AACTAAAAATTAATTAACAAA
1 AACT-AAAATTAATTAACAAA
5082542 AACTAAAA-TAATTAACA
1 AACTAAAATTAATTAACA
5082559 CTAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
AACTAAAATTAATTAACAAA
Found at i:5086068 original size:65 final size:65
Alignment explanation
Indices: 5085964--5086093 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
5085954 TTGACCCTCA
5085964 CCAAATTTGAGCCATTTAGGGAGGCCTAATGGTGGCTCTCACTAGCTGTTCACTTTTAATAAGGG
1 CCAAATTTGAGCCATTTAGGGAGGCCTAATGGTGGCTCTCACTAGCTGTTCACTTTTAATAAGGG
*
5086029 CCAAATTTGAGCCATTTAGGGAGGCCTAATGGTGTCTCTCACTAGCTGTTCACTTTTAATAAGGG
1 CCAAATTTGAGCCATTTAGGGAGGCCTAATGGTGGCTCTCACTAGCTGTTCACTTTTAATAAGGG
5086094 TCAATGTCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (65 bp):
CCAAATTTGAGCCATTTAGGGAGGCCTAATGGTGGCTCTCACTAGCTGTTCACTTTTAATAAGGG
Found at i:5096130 original size:47 final size:48
Alignment explanation
Indices: 5096058--5096158 Score: 132
Period size: 47 Copynumber: 2.1 Consensus size: 48
5096048 CATTTTTGTC
* * *
5096058 TTAATTTGTAAAAGGAGTTGGTGTCCAGGTTTTTCGTTGGCATAAGGTT
1 TTAA-TTGTAAAAGGAGTTGGTGTCCAGGTTTTTCATTGCCATAAGGGT
* * *
5096107 TTAATTG-AAAATGAGTTGTTGTCCATGTTTTTCATTGCCATAAGGGT
1 TTAATTGTAAAAGGAGTTGGTGTCCAGGTTTTTCATTGCCATAAGGGT
5096154 TTAAT
1 TTAAT
5096159 CGAATGTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 39 0.85
48 3 0.07
49 4 0.09
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.43
Consensus pattern (48 bp):
TTAATTGTAAAAGGAGTTGGTGTCCAGGTTTTTCATTGCCATAAGGGT
Found at i:5097718 original size:21 final size:21
Alignment explanation
Indices: 5097692--5097734 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5097682 CTTATGAATG
*
5097692 TTTCCATTCTAATAGTATCTT
1 TTTCCAGTCTAATAGTATCTT
5097713 TTTCCAGTCTAATAGTATCTT
1 TTTCCAGTCTAATAGTATCTT
5097734 T
1 T
5097735 CCTAGAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTCCAGTCTAATAGTATCTT
Found at i:5101207 original size:39 final size:39
Alignment explanation
Indices: 5101159--5101248 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
5101149 AGAAGAACAG
* *
5101159 GAAAAAGAAAAACAAC-CACCCACT-GAAGA-ACATGAGGAA
1 GAAAAAGAAAAACAACACA-CCA-TAAAAGAGA-ATGAGAAA
*
5101198 GAAAAAGAAAAAGAACACACCATAAAAGAGAATGAGAAA
1 GAAAAAGAAAAACAACACACCATAAAAGAGAATGAGAAA
5101237 GAAAAAGAAAAA
1 GAAAAAGAAAAA
5101249 GAAAAAGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 1 0.02
39 41 0.91
40 3 0.07
ACGTcount: A:0.64, C:0.13, G:0.18, T:0.04
Consensus pattern (39 bp):
GAAAAAGAAAAACAACACACCATAAAAGAGAATGAGAAA
Found at i:5101253 original size:5 final size:6
Alignment explanation
Indices: 5101196--5101261 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
5101186 GAACATGAGG
** * * *
5101196 AAGAAA AAGAAA AAGAACA CACCATAA AAGAGA ATGAGA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAA-A -AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA
5101247 AAGAAA AAGAGAA AA
1 AAGAAA AAGA-AA AA
5101262 AACCCTAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
6 37 0.77
7 7 0.15
8 3 0.06
9 1 0.02
ACGTcount: A:0.73, C:0.06, G:0.18, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:5101998 original size:2 final size:2
Alignment explanation
Indices: 5101991--5102021 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5101981 GAATGGTTGA
5101991 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
5102022 CTCTTGTGTT
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:5107127 original size:17 final size:16
Alignment explanation
Indices: 5107101--5107132 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5107091 TTTAAATTGA
5107101 TTAAATATATAAATAG
1 TTAAATATATAAATAG
5107117 TTAAATAATATAAATA
1 TTAAAT-ATATAAATA
5107133 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:5107484 original size:26 final size:26
Alignment explanation
Indices: 5107455--5107505 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5107445 AAAAGATATG
*
5107455 TATAATAAATAAAATTTTTTAAAATA
1 TATAATAAATAAAAATTTTTAAAATA
5107481 TATAATAAATAAAAATTTTTAAAAT
1 TATAATAAATAAAAATTTTTAAAAT
5107506 TTTTAGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TATAATAAATAAAAATTTTTAAAATA
Found at i:5115659 original size:17 final size:17
Alignment explanation
Indices: 5115637--5115684 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
5115627 AGAGCCATGT
*
5115637 CTTAATATGAATAAACA
1 CTTAATTTGAATAAACA
**
5115654 CTTAATTTGAATAGTCA
1 CTTAATTTGAATAAACA
5115671 CTTAATTTGAATAA
1 CTTAATTTGAATAA
5115685 GGCTTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (17 bp):
CTTAATTTGAATAAACA
Found at i:5122303 original size:2 final size:2
Alignment explanation
Indices: 5122296--5122325 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5122286 TGTCTTTGTA
5122296 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
5122326 TCTCAGTGAA
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:5127578 original size:3 final size:3
Alignment explanation
Indices: 5127570--5127596 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5127560 TATTCATAAC
5127570 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5127597 GTTCTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5128611 original size:10 final size:10
Alignment explanation
Indices: 5128585--5128639 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
5128575 AATAATAAAA
*
5128585 TAATTTTATA
1 TAATTTTATT
5128595 T-ATTTTATT
1 TAATTTTATT
5128604 TAATTTTATT
1 TAATTTTATT
*
5128614 TAA-ATT-TT
1 TAATTTTATT
5128622 TAATTTTTATT
1 TAA-TTTTATT
5128633 TAATTTT
1 TAATTTT
5128640 TTAAATTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 5 0.13
9 10 0.26
10 18 0.47
11 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TAATTTTATT
Found at i:5128625 original size:18 final size:19
Alignment explanation
Indices: 5128602--5128643 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
5128592 ATATATTTTA
5128602 TTTAA-TTTTATTTAAATT
1 TTTAATTTTTATTTAAATT
*
5128620 TTTAATTTTTATTTAATTT
1 TTTAATTTTTATTTAAATT
5128639 TTTAA
1 TTTAA
5128644 ATTTGGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTAATTTTTATTTAAATT
Found at i:5128767 original size:15 final size:16
Alignment explanation
Indices: 5128726--5128769 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
5128716 AGTTAATTAA
*
5128726 TTAATTTATATTATTG
1 TTAATTTATATTTTTG
*
5128742 TT-ATTTATATTTTTT
1 TTAATTTATATTTTTG
5128757 TTAATTT-TATTTT
1 TTAATTTATATTTT
5128770 ATCTGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTAATTTATATTTTTG
Found at i:5128919 original size:15 final size:16
Alignment explanation
Indices: 5128899--5128932 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5128889 TGTTATGTGG
*
5128899 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
5128914 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
5128930 ATT
1 ATT
5128933 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:5129164 original size:14 final size:13
Alignment explanation
Indices: 5129145--5129192 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
5129135 TATGTATATC
5129145 ATATTTAACTATTT
1 ATATTTAA-TATTT
*
5129159 ATATTTTATATATT
1 ATATTTAATAT-TT
5129173 ATAGTTTAATATTT
1 ATA-TTTAATATTT
5129187 AATATT
1 -ATATT
5129193 ATAAACTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 10 0.34
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:5137669 original size:15 final size:15
Alignment explanation
Indices: 5137651--5137691 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
5137641 GTATTTACAG
5137651 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
5137666 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
*
5137681 GCAATGTGATT
1 GTAATGTGATT
5137692 ACAGGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:5137880 original size:26 final size:25
Alignment explanation
Indices: 5137848--5138237 Score: 139
Period size: 28 Copynumber: 14.3 Consensus size: 25
5137838 TTAATATATT
5137848 TATATTTTTATTAATTTTTATATAA
1 TATATTTTTATTAATTTTTATATAA
* *
5137873 TATCATTTTTAAATATATTTTTAATATCA
1 TAT-ATTTTT-ATTA-ATTTTT-ATATAA
* *
5137902 TATATTTTATTTTTTATTTATTATATAA
1 TATA-TTT-TTATTAATTT-TTATATAA
* * *
5137930 TAT-TTTATATTTTATTTTTAATATATT
1 TATATTTTTA-TTAATTTTT-ATATA-A
5137957 TATATTTTTATTAA-TTTTATATAA
1 TATATTTTTATTAATTTTTATATAA
* * *
5137981 TATCATTCTTAAATATATTTTTAATATCA
1 TAT-ATT-TTTATTA-ATTTTT-ATATAA
* *
5138010 TATA-TTTTATT--TTTATTTTATTA
1 TATATTTTTATTAATTT-TTATATAA
* * *
5138033 TAATATTTATATTTATTTTTAATATATT
1 T-ATATTTTTATTAATTTTT-ATATA-A
5138061 TATATTTATATTATTAATTTTTATATAA
1 TATA-TT-T-TTATTAATTTTTATATAA
* *
5138089 TATCATTTTTTAAATT-ATTTTTAATGTCA
1 TAT-A-TTTTT--ATTAATTTTT-ATATAA
* *
5138118 TATATTTTATTTTTATTTATTATTATAA
1 TATATTTT-TATTAATTT-TTA-TATAA
* *
5138146 TAT-TTATATT-TTTATTTTTAATATATT
1 TATATT-T-TTATTAATTTTT-ATATA-A
*
5138173 TATATTTAATTATTATTTTTATATATAA
1 TATATTT--TTATTAATTTT-TATATAA
* * *
5138201 TATCATATTTTAATATATTTTTAATGTCA
1 TAT-AT-TTTTATTA-ATTTTT-ATATAA
5138230 TATATTTT
1 TATATTTT
5138238 ATTTTTATTT
Statistics
Matches: 280, Mismatches: 39, Indels: 90
0.68 0.10 0.22
Matches are distributed among these distances:
23 8 0.03
24 8 0.03
25 20 0.07
26 44 0.16
27 48 0.17
28 70 0.25
29 67 0.24
30 15 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (25 bp):
TATATTTTTATTAATTTTTATATAA
Found at i:5137926 original size:21 final size:21
Alignment explanation
Indices: 5137909--5138086 Score: 83
Period size: 21 Copynumber: 8.5 Consensus size: 21
5137899 TCATATATTT
*
5137909 TATTTTTTATTTATTATATAA
1 TATTTTATATTTATTATATAA
*
5137930 TATTTTATATTTTATT-TTTAA
1 TATTTTATA-TTTATTATATAA
5137951 TATATTTATATTT-TTAT-TAA
1 TAT-TTTATATTTATTATATAA
* *
5137971 T-TTTATATAATATCATTCT-TAA
1 TATTT-TAT-AT-TTATTATATAA
* * *
5137993 -A-TATATTTTTAATATCAT-A
1 TATTTTATATTTATTAT-ATAA
*
5138012 TATTTTATTTTTATTTTATTATAA
1 TATTTTATATTTA--TTA-TATAA
*
5138036 TA-TTTATATTTATT-TTTAA
1 TATTTTATATTTATTATATAA
5138055 TATATTTATATTTA-TATTATTAA
1 TAT-TTTATATTTATTA-TA-TAA
5138078 T-TTTTATAT
1 TATTTTATAT
5138087 AATATCATTT
Statistics
Matches: 122, Mismatches: 14, Indels: 42
0.69 0.08 0.24
Matches are distributed among these distances:
18 6 0.05
19 12 0.10
20 14 0.11
21 49 0.40
22 20 0.16
23 17 0.14
24 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTATATTTATTATATAA
Found at i:5138047 original size:23 final size:22
Alignment explanation
Indices: 5138009--5138196 Score: 94
Period size: 21 Copynumber: 8.5 Consensus size: 22
5137999 TTTTAATATC
*
5138009 ATATATTTTATTTTTATTTTATT
1 ATATA-TTTATATTTATTTTATT
*
5138032 ATAATATTTATATTTATTTT-TA
1 AT-ATATTTATATTTATTTTATT
*
5138054 ATATATTTATATTTATATTATT
1 ATATATTTATATTTATTTTATT
*
5138076 A-ATTTTTATATAATATCATTTT-TT
1 ATATATTTATAT--T-T-ATTTTATT
* * *
5138100 A-A-A-TTATTTTTAATGTCA-T
1 ATATATTTATATTT-ATTTTATT
*
5138119 ATAT-TTTATTTTTATTTATTATT
1 ATATATTTATATTTA-TT-TTATT
*
5138142 ATAATATTTATATTTTTATTTT-TA
1 AT-ATATTTATA--TTTATTTTATT
*
5138166 ATATATTTATATTTA-ATTATT
1 ATATATTTATATTTATTTTATT
5138187 AT-T-TTTATAT
1 ATATATTTATAT
5138197 ATAATATCAT
Statistics
Matches: 130, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
19 13 0.10
20 6 0.05
21 41 0.32
22 12 0.09
23 28 0.22
24 13 0.10
25 11 0.08
26 2 0.02
27 4 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (22 bp):
ATATATTTATATTTATTTTATT
Found at i:5138058 original size:15 final size:15
Alignment explanation
Indices: 5138040--5138220 Score: 79
Period size: 15 Copynumber: 11.5 Consensus size: 15
5138030 TTATAATATT
5138040 TATATTTATTTTTAA
1 TATATTTATTTTTAA
*
5138055 TATATTTATATTT-A
1 TATATTTATTTTTAA
*
5138069 TATTATTAATTTTT-A
1 TA-TATTTATTTTTAA
*
5138084 TATAATATCATTTTTTAA
1 TAT-AT-TTA-TTTTTAA
* *
5138102 -ATTATTT-TTAATGTCA
1 TA-TATTTATT--TTTAA
*
5138118 TATATTTTATTTTTATT
1 TATA-TTTATTTTTA-A
*
5138135 TATTATTATAATATTT-A
1 TA-TATT-T-ATTTTTAA
*
5138152 TATTTTTATTTTTAA
1 TATATTTATTTTTAA
*
5138167 TATATTTATATTTAA
1 TATATTTATTTTTAA
5138182 T-TA-TTATTTTTATA
1 TATATTTATTTTTA-A
*
5138196 TATAATATCATATTTTAA
1 TAT-AT-TTAT-TTTTAA
5138214 TATATTT
1 TATATTT
5138221 TTAATGTCAT
Statistics
Matches: 125, Mismatches: 19, Indels: 43
0.67 0.10 0.23
Matches are distributed among these distances:
13 8 0.06
14 15 0.12
15 43 0.34
16 15 0.12
17 20 0.16
18 14 0.11
19 10 0.08
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (15 bp):
TATATTTATTTTTAA
Found at i:5138203 original size:112 final size:110
Alignment explanation
Indices: 5137837--5138301 Score: 684
Period size: 108 Copynumber: 4.2 Consensus size: 110
5137827 AAAATATAAG
5137837 TTTAATATATTTATATTT-TTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATATC
1 TTTAATATATTTATATTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATATC
5137901 ATATATTTTATTTTTTATTTATTA-TATAATATTT-TATATTTTATT
66 ATATATTTTA-TTTTTATTTATTATTATAATATTTATAT-TTTTATT
*
5137946 TTTAATATATTTATATTT-TTATTAA-TTTTATATAATATCATTCTTAAATATATTTTTAATATC
1 TTTAATATATTTATATTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATATC
5138009 ATATATTTTATTTTTA-TT-TTATTATAATATTTATA--TTTATT
66 ATATATTTTATTTTTATTTATTATTATAATATTTATATTTTTATT
5138050 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTTTTAAAT-TATTTTTAAT
1 TTTAATATATTTATA-TT-TATTATTAATTTTTATATAATATCA-TTTTTAAATATATTTTTAAT
*
5138114 GTCATATATTTTATTTTTATTTATTATTATAATATTTATATTTTTATT
63 ATCATATATTTTATTTTTATTTATTATTATAATATTTATATTTTTATT
*
5138162 TTTAATATATTTATATTTAATTATTATTTTTATATATAATATCATATTTT-AATATATTTTTAAT
1 TTTAATATATTTATATTT-ATTATTAATTTT-TATATAATATCAT-TTTTAAATATATTTTTAAT
*
5138226 GTCATATATTTTATTTTTATTTATTATTATAAT-TTTATATTTTTTCAGTT
63 ATCATATATTTTATTTTTATTTATTATTATAATATTTATA-TTTTT-A-TT
*
5138276 CTTTAATATATTTTTATATTATTATT
1 -TTTAATATATTTATAT-TTATTATT
5138302 TTATTTTAAT
Statistics
Matches: 331, Mismatches: 5, Indels: 34
0.89 0.01 0.09
Matches are distributed among these distances:
104 21 0.06
105 5 0.02
106 13 0.04
107 15 0.05
108 90 0.27
109 35 0.11
110 18 0.05
111 23 0.07
112 85 0.26
113 1 0.00
114 2 0.01
115 21 0.06
116 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (110 bp):
TTTAATATATTTATATTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATATC
ATATATTTTATTTTTATTTATTATTATAATATTTATATTTTTATT
Found at i:5138211 original size:19 final size:20
Alignment explanation
Indices: 5138166--5138217 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
5138156 TTTATTTTTA
* *
5138166 ATATATTTATATTTAATTATT
1 ATAT-TTTATATATAATTATC
5138187 AT-TTTTATATATAA-TATC
1 ATATTTTATATATAATTATC
5138205 ATATTTTA-ATATA
1 ATATTTTATATATA
5138218 TTTTTAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.36
19 15 0.54
20 1 0.04
21 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTATATATAATTATC
Found at i:5138309 original size:29 final size:27
Alignment explanation
Indices: 5138277--5138394 Score: 82
Period size: 29 Copynumber: 4.2 Consensus size: 27
5138267 TTTTCAGTTC
5138277 TTTAATATATTTTTATATTATTATTTTAT
1 TTTAATATATTTTTATATTA-TA-TTTAT
*
5138306 TTTAAT-T-TGTTTTAT-CTATA-TTAT
1 TTTAATATAT-TTTTATATTATATTTAT
* * *
5138330 ATAAATATTAATTTTTATATTTTATTTAT
1 TTTAATA-T-ATTTTTATATTATATTTAT
* *
5138359 TTTAATTTTTATTCTTATATTATATATTAT
1 TTTAA--TATATTTTTATATTATAT-TTAT
5138389 TTTAAT
1 TTTAAT
5138395 TATAATATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
24 8 0.12
26 3 0.04
27 9 0.13
28 12 0.17
29 26 0.38
30 10 0.14
31 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTAATATATTTTTATATTATATTTAT
Found at i:5138331 original size:45 final size:46
Alignment explanation
Indices: 5138181--5138331 Score: 112
Period size: 47 Copynumber: 3.2 Consensus size: 46
5138171 TTTATATTTA
* * *
5138181 ATTATTATTTTTATATA-TAATATCATATTTTAATATATTTTTAATGTCATAT
1 ATTA-TATTTTTATTTATTATTAT-A-ATTTT-ATAT-TTTTTCA-GTC-TAT
* *
5138233 ATTTTATTTTTATTTATTATTATAATTTTATATTTTTTCAGTTCTTT
1 ATTATATTTTTATTTATTATTATAATTTTATATTTTTTCAG-TCTAT
* * *
5138280 AATATATTTTTATATTATTATT-TTATTTTA-ATTTGTTTTA-TCTAT
1 ATTATATTTTTAT-TTATTATTATAATTTTATATTT-TTTCAGTCTAT
5138325 ATTATAT
1 ATTATAT
5138332 AAATATTAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
45 10 0.12
46 4 0.05
47 25 0.30
48 16 0.19
49 4 0.05
50 5 0.06
51 12 0.14
52 8 0.10
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (46 bp):
ATTATATTTTTATTTATTATTATAATTTTATATTTTTTCAGTCTAT
Found at i:5138381 original size:23 final size:23
Alignment explanation
Indices: 5138337--5138381 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5138327 TATATAAATA
*
5138337 TTAATTTTTATATTTTATTTATT
1 TTAATTTTTATATCTTATTTATT
5138360 TTAATTTTTAT-TCTTATATTAT
1 TTAATTTTTATATCTTAT-TTAT
5138382 ATATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTAATTTTTATATCTTATTTATT
Found at i:5138390 original size:24 final size:24
Alignment explanation
Indices: 5138326--5138406 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
5138316 TTTATCTATA
*
5138326 TTATA-TAAATATTAATTTTTATAT
1 TTATATTATATATTAATTTTTAT-T
*
5138350 TT-TATT-TATTTTAATTTTTATT
1 TTATATTATATATTAATTTTTATT
*
5138372 CTTATATTATATATT-ATTTTAATT
1 -TTATATTATATATTAATTTTTATT
*
5138396 ATAATATTATA
1 -TTATATTATA
5138407 AAATATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 17 0.36
24 24 0.51
25 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATTATATATTAATTTTTATT
Found at i:5138403 original size:53 final size:55
Alignment explanation
Indices: 5138291--5138405 Score: 139
Period size: 53 Copynumber: 2.1 Consensus size: 55
5138281 ATATATTTTT
* *
5138291 ATATTATTATTTTATTTTAATTTGTTTTATCTATATTATATAAATATTAATTTTT
1 ATATTATTATTTTATTTTAATTTGTTTTATCTATATTATATAAATATTAATTATA
* * *
5138346 ATATT-TTA-TTTATTTTAATTT-TTAT-TCTTATATTATATATTATTTTAATTATA
1 ATATTATTATTTTATTTTAATTTGTTTTATC-TATATTATATA-AATATTAATTATA
5138399 ATATTAT
1 ATATTAT
5138406 AAAATATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
51 2 0.04
52 14 0.27
53 27 0.52
54 4 0.08
55 5 0.10
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (55 bp):
ATATTATTATTTTATTTTAATTTGTTTTATCTATATTATATAAATATTAATTATA
Found at i:5138405 original size:29 final size:29
Alignment explanation
Indices: 5138344--5138406 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
5138334 ATATTAATTT
* * * *
5138344 TTATATTTTATTTATTTTAATTTTTATTC
1 TTATATTATATTTATTTTAATTTATAATA
5138373 TTATATTATATATTATTTTAA-TTATAATA
1 TTATATTATAT-TTATTTTAATTTATAATA
5138402 TTATA
1 TTATA
5138407 AAATATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATATTATATTTATTTTAATTTATAATA
Found at i:5139437 original size:40 final size:39
Alignment explanation
Indices: 5139393--5139510 Score: 121
Period size: 40 Copynumber: 2.9 Consensus size: 39
5139383 AAGCATAACC
**
5139393 TCACAAAGTCATTGCCTTTTCAAAGTTAAAGCACAACTTT
1 TCACAAAGTC-TTGCCTTTTCAAAGTTAAAGCACAACCCT
*
5139433 TCACAAAGTCTCTACCTTTTC-AAGATTAAAGCACAAACCCT
1 TCACAAAGTCT-TGCCTTTTCAAAG-TTAAAGCAC-AACCCT
* * *
5139474 TCACAAACTCTTTTGTCTTTTCAAGGTTAAAGCACAA
1 TCACAAAGTC--TTGCCTTTTCAAAGTTAAAGCACAA
5139511 TCACTTTACC
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
39 4 0.06
40 27 0.42
41 15 0.23
42 16 0.25
43 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (39 bp):
TCACAAAGTCTTGCCTTTTCAAAGTTAAAGCACAACCCT
Found at i:5139504 original size:42 final size:41
Alignment explanation
Indices: 5139407--5139510 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
5139397 AAAGTCATTG
* ** *
5139407 CCTTTTCAAAGTTAAAGCAC-AACTTTTCACAAAGTCTCTA
1 CCTTTTCAAGGTTAAAGCACAAACCCTTCACAAACTCTCTA
* * *
5139447 CCTTTTCAAGATTAAAGCACAAACCCTTCACAAACTCTTTTG
1 CCTTTTCAAGGTTAAAGCACAAACCCTTCACAAACTC-TCTA
*
5139489 TCTTTTCAAGGTTAAAGCACAA
1 CCTTTTCAAGGTTAAAGCACAA
5139511 TCACTTTACC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 18 0.34
41 13 0.25
42 22 0.42
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.32
Consensus pattern (41 bp):
CCTTTTCAAGGTTAAAGCACAAACCCTTCACAAACTCTCTA
Found at i:5144335 original size:9 final size:10
Alignment explanation
Indices: 5144319--5144344 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5144309 ATTTTCCTTG
5144319 CTTTTTTTTC
1 CTTTTTTTTC
5144329 CTTTTTTTTC
1 CTTTTTTTTC
5144339 CTTTTT
1 CTTTTT
5144345 GAAAAGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
CTTTTTTTTC
Found at i:5156492 original size:28 final size:28
Alignment explanation
Indices: 5156460--5156565 Score: 115
Period size: 28 Copynumber: 3.8 Consensus size: 28
5156450 AAAGCACTAT
*
5156460 TTTTCATAGATCAAGCATAACCTTTGCC
1 TTTTCATAGATCAAGCATAACCATTGCC
* * * *
5156488 TTTTCATTGATTAAGAATAACCATTGCA
1 TTTTCATAGATCAAGCATAACCATTGCC
* *
5156516 TTTTCAAAGATCAAGCACAACCATTGCC
1 TTTTCATAGATCAAGCATAACCATTGCC
* *
5156544 TTTTGA-AGGATTAAGCATAACC
1 TTTTCATA-GATCAAGCATAACC
5156566 TTTACAACAT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
27 1 0.02
28 62 0.98
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (28 bp):
TTTTCATAGATCAAGCATAACCATTGCC
Found at i:5156545 original size:56 final size:56
Alignment explanation
Indices: 5156460--5156565 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 56
5156450 AAAGCACTAT
* * * **
5156460 TTTTCATAGATCAAGCATAACCTTTGCCTTTTCATTGATTAAGAATAACCATTGCA
1 TTTTCAAAGATCAAGCACAACCATTGCCTTTTCAAGGATTAAGAATAACCATTGCA
* *
5156516 TTTTCAAAGATCAAGCACAACCATTGCCTTTTGAAGGATTAAGCATAACC
1 TTTTCAAAGATCAAGCACAACCATTGCCTTTTCAAGGATTAAGAATAACC
5156566 TTTACAACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (56 bp):
TTTTCAAAGATCAAGCACAACCATTGCCTTTTCAAGGATTAAGAATAACCATTGCA
Found at i:5156580 original size:36 final size:37
Alignment explanation
Indices: 5156532--5156604 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
5156522 AAGATCAAGC
5156532 ACAACCATTGCCTTTTGAAGGATTAAGCATAACCTTT
1 ACAACCATTGCCTTTTGAAGGATTAAGCATAACCTTT
* *
5156569 ACAA-CATTGCCTTTTGAAGGTTTAGGCATAACCTTT
1 ACAACCATTGCCTTTTGAAGGATTAAGCATAACCTTT
5156605 TCTCTCTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 30 0.88
37 4 0.12
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (37 bp):
ACAACCATTGCCTTTTGAAGGATTAAGCATAACCTTT
Found at i:5160896 original size:32 final size:33
Alignment explanation
Indices: 5160835--5160898 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5160825 TTTTTAATAT
*
5160835 CATATATTTTATTTTTATTTTTTATTATAATTG
1 CATATATTTTATTTTTATTTTTTAATATAATTG
*
5160868 CATATATTTTGTTTTTA-TTTTTAATATAATT
1 CATATATTTTATTTTTATTTTTTAATATAATT
5160899 TTTTACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (33 bp):
CATATATTTTATTTTTATTTTTTAATATAATTG
Found at i:5162121 original size:33 final size:33
Alignment explanation
Indices: 5162084--5162169 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
5162074 NNNNNNNNNN
**
5162084 TATATTTTATTTTTATTTTTTATTATAATCT-TA
1 TATATTTTATTTTTATTTTTTAACATAAT-TATA
* * *
5162117 TATATTTTATTTTCATTTCTTAACATAATTATC
1 TATATTTTATTTTTATTTTTTAACATAATTATA
*
5162150 TATATTATATATTTTATTTT
1 TATATTTTAT-TTTTATTTT
5162170 AATTTTTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
32 1 0.02
33 35 0.81
34 7 0.16
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (33 bp):
TATATTTTATTTTTATTTTTTAACATAATTATA
Found at i:5164619 original size:10 final size:9
Alignment explanation
Indices: 5164601--5164634 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5164591 TTGTTATTTT
5164601 TATTATATA
1 TATTATATA
5164610 TATGTATATA
1 TAT-TATATA
*
5164620 TATTATATT
1 TATTATATA
5164629 TATTAT
1 TATTAT
5164635 TAAAATGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:5166042 original size:18 final size:17
Alignment explanation
Indices: 5166021--5166105 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
5166011 TTATCAAACA
5166021 AAAAATTATTATAAAAAT
1 AAAAATTATTA-AAAAAT
5166039 AAAAAATT-TTAAAAAAT
1 -AAAAATTATTAAAAAAT
*
5166056 TAAAATATATTAAAAAATTT
1 AAAAAT-TATTAAAAAA--T
* *
5166076 TAAAATTTTTATAAAAAT
1 AAAAATTATTA-AAAAAT
*
5166094 -GAAATTATTAAA
1 AAAAATTATTAAA
5166106 TTTTATAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
16 7 0.12
17 15 0.26
18 12 0.21
19 11 0.19
20 12 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
AAAAATTATTAAAAAAT
Found at i:5166053 original size:10 final size:10
Alignment explanation
Indices: 5166038--5166093 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
5166028 ATTATAAAAA
5166038 TAAAAAATTT
1 TAAAAAATTT
5166048 TAAAAAA--T
1 TAAAAAATTT
* *
5166056 TAAAATATAT
1 TAAAAAATTT
5166066 TAAAAAATTT
1 TAAAAAATTT
*
5166076 T-AAAATTTT
1 TAAAAAATTT
5166085 TATAAAAAT
1 TA-AAAAAT
5166094 GAAATTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 17 0.46
11 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:5166106 original size:25 final size:24
Alignment explanation
Indices: 5166070--5166116 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
5166060 ATATATTAAA
5166070 AAATTTTAAAATTTTTATAAAAATG
1 AAATTTTAAAA-TTTTATAAAAATG
5166095 AAATTATT-AAATTTTATAAAAA
1 AAATT-TTAAAATTTTATAAAAA
5166117 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 8 0.38
26 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATTTTAAAATTTTATAAAAATG
Found at i:5166140 original size:31 final size:30
Alignment explanation
Indices: 5166087--5166144 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
5166077 AAAATTTTTA
5166087 TAAAAATGAAATTATTAAATTTTATAAAAAG
1 TAAAAATGAAATTATTAAATTTT-TAAAAAG
5166118 TAAAAAT-AAATT-TTACAGATTTTTAAA
1 TAAAAATGAAATTATTA-A-ATTTTTAAA
5166145 TTATTGGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 3 0.12
30 10 0.40
31 12 0.48
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
TAAAAATGAAATTATTAAATTTTTAAAAAG
Found at i:5172824 original size:27 final size:25
Alignment explanation
Indices: 5172769--5172837 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 25
5172759 AAAATTACTC
*
5172769 ATAATTATAATTTAATCACATATTA
1 ATAATTATAATTTAATCAAATATTA
*
5172794 ATAATTTATAATTTATTCAAAATATTA
1 ATAA-TTATAATTTAATC-AAATATTA
*
5172821 ATAAATGATAATTTAAT
1 AT-AATTATAATTTAAT
5172838 TATTAATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.11
26 12 0.32
27 19 0.51
28 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (25 bp):
ATAATTATAATTTAATCAAATATTA
Found at i:5172922 original size:18 final size:18
Alignment explanation
Indices: 5172888--5172921 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5172878 AAATATTAAT
*
5172888 AATTTAAATTAATTTTTA
1 AATTTAAAATAATTTTTA
5172906 AATTTAAAAT-ATTTTT
1 AATTTAAAATAATTTTT
5172922 TTTATAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAAAATAATTTTTA
Found at i:5174271 original size:36 final size:36
Alignment explanation
Indices: 5174231--5174302 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
5174221 TCAAATAGTC
* *
5174231 ACAACTTTTCATGTGAAAAAATATAACTTTTCATTT
1 ACAACTTTTCATATGAAAAAACATAACTTTTCATTT
* *
5174267 ACAACTTTTCATATGAAAAGACATAACTTTTTATTT
1 ACAACTTTTCATATGAAAAAACATAACTTTTCATTT
5174303 TGAAAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (36 bp):
ACAACTTTTCATATGAAAAAACATAACTTTTCATTT
Found at i:5178488 original size:115 final size:115
Alignment explanation
Indices: 5178234--5178512 Score: 355
Period size: 115 Copynumber: 2.4 Consensus size: 115
5178224 AATTAAATAA
* * * ** *
5178234 TTTAGTTACATAAGCAATTAATTTAATTATTAAAATTAGTAAAATTCAAGAAATATTTAAATTAA
1 TTTAGTTA-TTAAGCAATTAATTAAATTATTAATATTA-TTTAATTTAAGAAATATTTAAATTAA
* * *
5178299 TTAAAGTTTTATTAAATTAATTGTAATTTAACTACTTGAATTGAAAAAATGT
64 TTAAAGTGTCATTAAATTAATTATAATTTAACTACTTGAATTGAAAAAATGT
* * *
5178351 TTTATTTATTAAGTAATTAATTAAATTAGTAATATTATTTAATTTAA-AAATATTTAAATTAATT
1 TTTAGTTATTAAGCAATTAATTAAATTATTAATATTATTTAATTTAAGAAATATTTAAATTAATT
* * *
5178415 AAGGTGTCATTCAATTAATTAAATAATTTGACTACTTGAATTG-AAAAATGT
66 AAAGTGTCATTAAATTAATT--ATAATTTAACTACTTGAATTGAAAAAATGT
* *
5178466 TTTAGTTATTAAGCAATTAATTAAATTATTAATAATATTTAAATTAA
1 TTTAGTTATTAAGCAATTAATTAAATTATTAATATTATTTAATTTAA
5178513 TTATTAAGGT
Statistics
Matches: 140, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
114 33 0.24
115 57 0.41
116 43 0.31
117 7 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (115 bp):
TTTAGTTATTAAGCAATTAATTAAATTATTAATATTATTTAATTTAAGAAATATTTAAATTAATT
AAAGTGTCATTAAATTAATTATAATTTAACTACTTGAATTGAAAAAATGT
Found at i:5178618 original size:17 final size:17
Alignment explanation
Indices: 5178581--5178613 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5178571 GTGTTATAAG
5178581 TAATTAAGTAATTAATA
1 TAATTAAGTAATTAATA
5178598 TAATTAA-TAA-TAATA
1 TAATTAAGTAATTAATA
5178613 T
1 T
5178614 CTAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAATTAAGTAATTAATA
Found at i:5182032 original size:20 final size:20
Alignment explanation
Indices: 5182003--5182058 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5181993 GTCCTACAGT
*
5182003 AATTATCAATGGAATTCATC
1 AATTACCAATGGAATTCATC
* *
5182023 CATTACCAATGAAATTCATC
1 AATTACCAATGGAATTCATC
*
5182043 AATTACCAATAGAATT
1 AATTACCAATGGAATT
5182059 ATTGATAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (20 bp):
AATTACCAATGGAATTCATC
Found at i:5199353 original size:31 final size:31
Alignment explanation
Indices: 5199317--5199423 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 31
5199307 ATTGTTCTAT
* *
5199317 GGTTATATCTCTATTGCAAAAGGTAATG-AA
1 GGTTATACCTCTATTGTAAAAGGTAATGTAA
* * * *
5199347 TGGTTATACCTCCATTGTGAAAGGTAGTGTGA
1 -GGTTATACCTCTATTGTAAAAGGTAATGTAA
*
5199379 GGTTATACCTCAATTGTAAAAGGTAATGTAA
1 GGTTATACCTCTATTGTAAAAGGTAATGTAA
5199410 GGTTATACCTCTAT
1 GGTTATACCTCTAT
5199424 AAAAAGAGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 63 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (31 bp):
GGTTATACCTCTATTGTAAAAGGTAATGTAA
Found at i:5202918 original size:22 final size:23
Alignment explanation
Indices: 5202892--5202938 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5202882 ATTTCTATGC
*
5202892 ATTACTACAAGAACTAAGCT-AA
1 ATTACTACAAAAACTAAGCTCAA
* *
5202914 ATTACTATAAAAATTAAGCTCAA
1 ATTACTACAAAAACTAAGCTCAA
5202937 AT
1 AT
5202939 AACTCTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTACAAAAACTAAGCTCAA
Found at i:5214284 original size:51 final size:51
Alignment explanation
Indices: 5214229--5214331 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
5214219 TCCAGGGTCC
5214229 TAGACTCAGCTGGCTATATATATAAACCCCTTTTTTCACTTTTTCTTGTTT
1 TAGACTCAGCTGGCTATATATATAAACCCCTTTTTTCACTTTTTCTTGTTT
5214280 TAGACTCAGCTGGCTATATATATAAACCCCTTTTTTCACTTTTTCTTGTTT
1 TAGACTCAGCTGGCTATATATATAAACCCCTTTTTTCACTTTTTCTTGTTT
5214331 T
1 T
5214332 CTTTATTTCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (51 bp):
TAGACTCAGCTGGCTATATATATAAACCCCTTTTTTCACTTTTTCTTGTTT
Found at i:5215002 original size:24 final size:25
Alignment explanation
Indices: 5214982--5215033 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
5214972 ATCAATTATT
5214982 AATCATTAAAATCTA-TTAATTTAA
1 AATCATTAAAATCTATTTAATTTAA
5215006 AATCATTAAAATCTATTTAATTTAA
1 AATCATTAAAATCTATTTAATTTAA
5215031 AAT
1 AAT
5215034 AAAAGTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (25 bp):
AATCATTAAAATCTATTTAATTTAA
Found at i:5215729 original size:2 final size:2
Alignment explanation
Indices: 5215722--5215755 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5215712 CTATATCTTT
5215722 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
5215756 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5215760 original size:2 final size:2
Alignment explanation
Indices: 5215755--5215790 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5215745 ATATATATAT
5215755 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
5215791 GATCACCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5216589 original size:5 final size:5
Alignment explanation
Indices: 5216566--5216721 Score: 52
Period size: 5 Copynumber: 30.4 Consensus size: 5
5216556 ATGTTATAAT
* * *
5216566 TAAAA TAAAA -AATAT TAAAA TAAAA TATACAA TATAA GAATCAA -AAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TA-A-AA TAAAA TAA--AA TAAAA
* * * ** * *
5216614 TAAAA TAAAA TAAAA TATAA GAAAT TAAAA T-TTA TATAA TATAGA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
* * * * * *
5216664 GAAAT TAAAA TAAAA TATATAA TATAA -AAAA TTATA TTAAA -AAAA TAAAAA
1 TAAAA TAAAA TAAAA TA-A-AA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA
5216715 TAAAA TA
1 TAAAA TA
5216722 TATAAGATTA
Statistics
Matches: 110, Mismatches: 27, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
4 12 0.11
5 74 0.67
6 14 0.13
7 10 0.09
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:5216705 original size:27 final size:28
Alignment explanation
Indices: 5216614--5216697 Score: 79
Period size: 30 Copynumber: 3.1 Consensus size: 28
5216604 AATCAAAAAA
*
5216614 TAAAATAAAATA-A-A-ATATAAGAAAT
1 TAAAATAAAATATATAGATAAAAGAAAT
* *
5216639 TAAAATTTATATAATATAGATAAAAGAAAT
1 TAAAA-TAAAAT-ATATAGATAAAAGAAAT
5216669 TAAAATAAAATATATA-ATATAAA-AAAT
1 TAAAATAAAATATATAGATA-AAAGAAAT
5216696 TA
1 TA
5216698 TATTAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
25 5 0.10
26 4 0.08
27 10 0.21
28 9 0.19
29 5 0.10
30 15 0.31
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (28 bp):
TAAAATAAAATATATAGATAAAAGAAAT
Found at i:5216712 original size:50 final size:50
Alignment explanation
Indices: 5216610--5216713 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 50
5216600 TAAGAATCAA
* * * * *
5216610 AAAATAAAATAAAATAAAATATAAGAAATTAAAATTTATATAATATAGAT
1 AAAAGAAAATAAAATAAAATATAAGAAATAAAAAATTATATAATAAAAAT
* *
5216660 AAAAGAAATTAAAATAAAATATATA-ATATAAAAAATTATATTAA-AAAAAT
1 AAAAGAAAATAAAATAAAATATA-AGAAATAAAAAATTATA-TAATAAAAAT
5216710 AAAA
1 AAAA
5216714 ATAAAATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
50 41 0.91
51 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (50 bp):
AAAAGAAAATAAAATAAAATATAAGAAATAAAAAATTATATAATAAAAAT
Found at i:5216732 original size:34 final size:33
Alignment explanation
Indices: 5216670--5216757 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
5216660 AAAAGAAATT
* * *
5216670 AAAATAAAATATATAATATAAAAAATTATATTAAA
1 AAAATAAAA-ATAAAATATATAAAATTATAGT-AA
*
5216705 AAAATAAAAATAAAATATATAAGATTATAGTAA
1 AAAATAAAAATAAAATATATAAAATTATAGTAA
* *
5216738 GAAATGAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
5216758 GACANNNNNN
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 20 0.43
34 18 0.38
35 9 0.19
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAGTAA
Found at i:5218834 original size:16 final size:16
Alignment explanation
Indices: 5218813--5218847 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5218803 AACTTGAAAA
5218813 GGAAGGATTAGCGTTT
1 GGAAGGATTAGCGTTT
5218829 GGAAGGATTAGCGTTT
1 GGAAGGATTAGCGTTT
5218845 GGA
1 GGA
5218848 GAATAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.40, T:0.29
Consensus pattern (16 bp):
GGAAGGATTAGCGTTT
Found at i:5220818 original size:15 final size:16
Alignment explanation
Indices: 5220791--5220823 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5220781 CTAAACAATC
5220791 AATAAATAAGTAAATA
1 AATAAATAAGTAAATA
*
5220807 AATAAA-AAGTAATTA
1 AATAAATAAGTAAATA
5220822 AA
1 AA
5220824 AACAAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AATAAATAAGTAAATA
Found at i:5224914 original size:15 final size:16
Alignment explanation
Indices: 5224894--5224924 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5224884 TATTATACAT
5224894 TTTTCTC-TTACCTTA
1 TTTTCTCATTACCTTA
5224909 TTTTCTCATTACCTTA
1 TTTTCTCATTACCTTA
5224925 CCTATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTCTCATTACCTTA
Found at i:5225665 original size:20 final size:20
Alignment explanation
Indices: 5225636--5225682 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5225626 ATAGTTTTTT
*
5225636 TTTC-TTTTATCTGTGATAG
1 TTTCTTTTTATCTATGATAG
* *
5225655 TTTCTTTTTATCTATGGTAT
1 TTTCTTTTTATCTATGATAG
5225675 TTTCTTTT
1 TTTCTTTT
5225683 AGATTTGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.66
Consensus pattern (20 bp):
TTTCTTTTTATCTATGATAG
Found at i:5227126 original size:20 final size:19
Alignment explanation
Indices: 5227101--5227185 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 19
5227091 AATATTTTAT
*
5227101 AATATTATAATTAAAATAAA
1 AATATTA-AAATAAAATAAA
*
5227121 AATATTAAAATAAAATATAT
1 AATATTAAAATAAAATA-AA
*
5227141 AATA-TAAGAATAAAA-ATTA
1 AATATTAA-AATAAAATA-AA
5227160 AA-A-TAAAATAAAATATAA
1 AATATTAAAATAAAATA-AA
*
5227178 AAAATTAA
1 AATATTAA
5227186 CATTTATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.13
18 9 0.16
19 17 0.31
20 22 0.40
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (19 bp):
AATATTAAAATAAAATAAA
Found at i:5227127 original size:14 final size:15
Alignment explanation
Indices: 5227110--5227404 Score: 76
Period size: 15 Copynumber: 19.1 Consensus size: 15
5227100 TAATATTATA
5227110 ATTAAAATAAAA-AT
1 ATTAAAATAAAATAT
5227124 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
* *
5227139 A-TAATATAAGAATAAAA
1 ATTAAAATAA-AAT--AT
5227156 ATTAAAATAAAATA-
1 ATTAAAATAAAATAT
*
5227170 A--AATATAAAA-A-
1 ATTAAAATAAAATAT
* **
5227181 ATTAACAT-TTATAT
1 ATTAAAATAAAATAT
* ** * *
5227195 AATATAGGTAAAACAA
1 ATTA-AAATAAAATAT
5227211 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
* *
5227226 ATAAAATTATAATAATAA
1 ATTAAA--ATAA-AATAT
*
5227244 ATAAAAATAAAATAT
1 ATTAAAATAAAATAT
* * *
5227259 ATGACATTAAAAATAT
1 ATTAAAAT-AAAATAT
*
5227275 ATTTAAAATATGATATTAT
1 A-TTAAAATA--A-AATAT
*
5227294 ATAAAAATTAATAATAT
1 ATTAAAA-TAA-AATAT
5227311 A--AAAATAAAATAT
1 ATTAAAATAAAATAT
* * *
5227324 ATGATATTAAAAATAT
1 ATTAAAAT-AAAATAT
**
5227340 ATTTAAAATATGATATT
1 A-TTAAAATAAAATA-T
*
5227357 ATATAAAA-ATTAATA-
1 AT-TAAAATA-AAATAT
5227372 A-TATAAATATAAATAT
1 ATTA-AAATA-AAATAT
5227388 ATTAAAAATAAAATAT
1 ATT-AAAATAAAATAT
5227404 A
1 A
5227405 AAATATTATA
Statistics
Matches: 209, Mismatches: 40, Indels: 62
0.67 0.13 0.20
Matches are distributed among these distances:
11 2 0.01
12 9 0.04
13 13 0.06
14 29 0.14
15 44 0.21
16 40 0.19
17 41 0.20
18 24 0.11
19 7 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:5227230 original size:24 final size:23
Alignment explanation
Indices: 5227109--5227231 Score: 65
Period size: 26 Copynumber: 5.0 Consensus size: 23
5227099 ATAATATTAT
*
5227109 AATTAAAATAAAA-ATAT--TAA
1 AATTAAAATAAAATATATAAAAA
*
5227129 AA-TAAAATATATAATATAAGAATAAA
1 AATTAAAATA-A-AATAT-ATAA-AAA
*
5227155 AATTAAAATAAAATAAAATATAAAA
1 AATTAAAATAAAAT-ATATA-AAAA
*
5227180 AATTAACATTTATATAATATAGGTAAAACA
1 AATTAA-A---ATAAAATATA--TAAAA-A
5227210 AATTAAAATAAAATATATAAAA
1 AATTAAAATAAAATATATAAAA
5227232 TTATAATAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
19 7 0.09
20 3 0.04
21 2 0.03
22 2 0.03
23 1 0.01
24 5 0.06
25 14 0.18
26 17 0.22
27 7 0.09
28 2 0.03
29 10 0.13
30 9 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AATTAAAATAAAATATATAAAAA
Found at i:5227236 original size:10 final size:9
Alignment explanation
Indices: 5227217--5227438 Score: 53
Period size: 9 Copynumber: 26.2 Consensus size: 9
5227207 ACAAATTAAA
5227217 ATAAAATAT
1 ATAAAATAT
5227226 ATAAAAT-T
1 ATAAAATAT
*
5227234 ATAATAATAA
1 ATAA-AATAT
5227244 AT-AAA-A-
1 ATAAAATAT
5227250 ATAAAATAT
1 ATAAAATAT
* *
5227259 ATGACAT-T
1 ATAAAATAT
5227267 A-AAAATAT
1 ATAAAATAT
5227275 ATTTAAAATAT
1 A--TAAAATAT
*
5227286 GAT--ATTAT
1 -ATAAAATAT
5227294 ATAAAA-AT
1 ATAAAATAT
*
5227302 -TAATA-AT
1 ATAAAATAT
5227309 AT-AAA-A-
1 ATAAAATAT
5227315 ATAAAATAT
1 ATAAAATAT
* *
5227324 ATGATAT-T
1 ATAAAATAT
5227332 A-AAAATAT
1 ATAAAATAT
5227340 ATTTAAAATAT
1 A--TAAAATAT
**
5227351 GATATTATAT
1 -ATAAAATAT
5227361 A-AAAAT-T
1 ATAAAATAT
* *
5227368 AATAATATAA
1 -ATAAAATAT
5227378 ATATAAATAT
1 ATA-AAATAT
*
5227388 ATTAAA-A-
1 ATAAAATAT
5227395 AT-AAA-AT
1 ATAAAATAT
5227402 ATAAAATATT
1 ATAAAATA-T
*
5227412 ATAATAATAA
1 ATAA-AATAT
5227422 AT-AAA-A-
1 ATAAAATAT
5227428 ATAAAATAT
1 ATAAAATAT
5227437 AT
1 AT
5227439 GACTTTAAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 66
0.64 0.09 0.27
Matches are distributed among these distances:
6 10 0.06
7 33 0.21
8 35 0.22
9 37 0.24
10 22 0.14
11 18 0.11
12 2 0.01
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
ATAAAATAT
Found at i:5227271 original size:21 final size:21
Alignment explanation
Indices: 5227245--5227338 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 21
5227235 TAATAATAAA
*
5227245 TAAAAATAAAATATATGACAT
1 TAAAAATAAAATATATGATAT
*
5227266 TAAAAATATATTTAAAATATGATAT
1 TAAAAATA-A---AATATATGATAT
* * *
5227291 TATATA-AAAAT-TAATAATA-
1 TAAAAATAAAATAT-ATGATAT
5227310 TAAAAATAAAATATATGATAT
1 TAAAAATAAAATATATGATAT
5227331 TAAAAATA
1 TAAAAATA
5227339 TATTTAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
19 5 0.09
20 17 0.30
21 17 0.30
22 1 0.02
23 1 0.02
24 1 0.02
25 14 0.25
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (21 bp):
TAAAAATAAAATATATGATAT
Found at i:5227282 original size:33 final size:33
Alignment explanation
Indices: 5227214--5227575 Score: 135
Period size: 33 Copynumber: 11.2 Consensus size: 33
5227204 AAAACAAATT
* *
5227214 AAAATAAAATATATAAAATTATAATAATA-A-ATA
1 AAAATAAAATATATGATATTA-AA-AATATATATA
* *
5227247 AAAATAAAATATATGACATTAAAAATATAT-TT
1 AAAATAAAATATATGATATTAAAAATATATATA
**
5227279 AAAATATGATAT-T-ATA-TAAAAATTAATAATATA
1 AAAATAAAATATATGATATTAAAAA-T-AT-ATATA
*
5227312 AAAATAAAATATATGATATTAAAAATATAT-TT
1 AAAATAAAATATATGATATTAAAAATATATATA
**
5227344 AAAATATGATAT-T-ATA-TAAAAAT-TA-AT-
1 AAAATAAAATATATGATATTAAAAATATATATA
* * *
5227371 AATATAAATATAAAT-ATATTAAAAATAAAATATA
1 AAAATAAA-ATATATGATATTAAAAAT-ATATATA
* * *
5227405 AAATATTATAATA-AT-A-AATAAAAATAAAATATA
1 AAA-A-TAAAATATATGATATTAAAAAT-ATATATA
* ** *
5227438 TGACTTTAAA-A-AT-ATATTAAGAAATGATATTCTATA
1 -AAAATAAAATATATGATATTAA-AAAT-ATA---TATA
* * * * *
5227474 AAAAT-TAATA-ATAAAAATATAAATATAT-TA
1 AAAATAAAATATATGATATTAAAAATATATATA
**
5227504 AAAATAAAATATAAAATATTATAATAATA-A-ATA
1 AAAATAAAATATATGATATTA-AA-AATATATATA
*
5227537 AAAATAAAATATATGATATTAAAAATATATTTA
1 AAAATAAAATATATGATATTAAAAATATATATA
5227570 AGAAAT
1 A-AAAT
5227576 GCTATTATAT
Statistics
Matches: 251, Mismatches: 43, Indels: 69
0.69 0.12 0.19
Matches are distributed among these distances:
27 5 0.02
28 6 0.02
29 17 0.07
30 20 0.08
31 21 0.08
32 44 0.18
33 82 0.33
34 22 0.09
35 17 0.07
36 17 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (33 bp):
AAAATAAAATATATGATATTAAAAATATATATA
Found at i:5227310 original size:36 final size:36
Alignment explanation
Indices: 5227264--5227376 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
5227254 AATATATGAC
5227264 ATTAAAAATATATTTAAAATATGATATTATATAAAA
1 ATTAAAAATATATTTAAAATATGATATTATATAAAA
* * * *
5227300 ATTAATAATATA---AAAATA--A-AATATAT-GAT
1 ATTAAAAATATATTTAAAATATGATATTATATAAAA
5227329 ATTAAAAATATATTTAAAATATGATATTATATAAAA
1 ATTAAAAATATATTTAAAATATGATATTATATAAAA
*
5227365 ATTAATAATATA
1 ATTAAAAATATA
5227377 AATATAAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
29 12 0.20
30 6 0.10
31 1 0.02
32 6 0.10
33 6 0.10
34 1 0.02
35 6 0.10
36 23 0.38
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (36 bp):
ATTAAAAATATATTTAAAATATGATATTATATAAAA
Found at i:5227322 original size:65 final size:65
Alignment explanation
Indices: 5227223--5227389 Score: 273
Period size: 65 Copynumber: 2.5 Consensus size: 65
5227213 TAAAATAAAA
*
5227223 TATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATGA
1 TATATAAAAAT-TAATAAT--ATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATGA
5227288 TAT
63 TAT
*
5227291 TATATAAAAATTAATAATATAAAAATAAAATATATGATATTAAAAATATATTTAAAATATGATAT
1 TATATAAAAATTAATAATATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATGATAT
*
5227356 TATATAAAAATTAATAATATAAATAT-AAATATAT
1 TATATAAAAATTAATAATATAAAAATAAAATATAT
5227390 TAAAAATAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
64 8 0.08
65 71 0.74
67 7 0.07
68 10 0.10
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (65 bp):
TATATAAAAATTAATAATATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATGATAT
Found at i:5227374 original size:25 final size:24
Alignment explanation
Indices: 5227307--5227375 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
5227297 AAAATTAATA
*
5227307 ATATAAAAATAAAATATATGATATT
1 ATATAAAAATTAAA-ATATGATATT
5227332 A-A-AAATATATTTAAAATATGATATT
1 ATATAAA-A-A-TTAAAATATGATATT
5227357 ATATAAAAATTAATAATAT
1 ATATAAAAATTAA-AATAT
5227376 AAATATAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
23 3 0.08
24 6 0.16
25 19 0.51
26 6 0.16
27 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
ATATAAAAATTAAAATATGATATT
Found at i:5227382 original size:6 final size:6
Alignment explanation
Indices: 5227371--5227437 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
5227361 AAAAATTAAT
* *
5227371 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
5227421 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
5227438 TGACTTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:5227397 original size:26 final size:26
Alignment explanation
Indices: 5227367--5227438 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 26
5227357 ATATAAAAAT
5227367 TAATAATATAAATATAAATATA-TTA
1 TAATAATATAAATATAAATATATTTA
5227392 -AA-AATA-AAATATAAA-ATA-TTA
1 TAATAATATAAATATAAATATATTTA
*
5227413 TAATAATAAATAAAAATAAAATATAT
1 TAATAAT--ATAAATAT-AAATATAT
5227439 GACTTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
21 6 0.16
22 11 0.29
23 7 0.18
24 2 0.05
25 1 0.03
26 5 0.13
27 3 0.08
28 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
TAATAATATAAATATAAATATATTTA
Found at i:5227435 original size:15 final size:16
Alignment explanation
Indices: 5227106--5227549 Score: 97
Period size: 17 Copynumber: 27.2 Consensus size: 16
5227096 TTTATAATAT
*
5227106 TATAATTAAAATAAAA
1 TATAATAAAAATAAAA
*
5227122 -AT-ATTAAAATAAAATA
1 TATAATAAAAAT-AAA-A
5227138 TATAATATAAGAATAAAA
1 TATAATA-AA-AATAAAA
*
5227156 -ATTAAAATAAAATAAAA
1 TA-TAATA-AAAATAAAA
*
5227173 TATAA-AAAATTAACATTTA
1 TATAATAAAAATAA-A---A
* **
5227192 TATAATATAGGTAAAA
1 TATAATAAAAATAAAA
* *
5227208 CA-AATTAAAATAAAA
1 TATAATAAAAATAAAA
5227223 TAT-ATAAAATTATAATAA
1 TATAATAAAA--ATAA-AA
5227241 TA-AATAAAAATAAAA
1 TATAATAAAAATAAAA
* * *
5227256 TAT-ATGACATTAAAAA
1 TATAATAAAAAT-AAAA
* * **
5227272 TATATTTAAAATATGA
1 TATAATAAAAATAAAA
*
5227288 TATTATATAAAAAT-TAA
1 TA-TA-ATAAAAATAAAA
5227305 TA-ATATAAAAATAAAA
1 TATA-ATAAAAATAAAA
* * *
5227321 TAT-ATGATATTAAAAA
1 TATAATAAAAAT-AAAA
* * **
5227337 TATATTTAAAATATGA
1 TATAATAAAAATAAAA
*
5227353 TATTATATAAAAAT--TA
1 TA-TA-ATAAAAATAAAA
*
5227369 -ATAATATAAATATAAA
1 TATAATAAAAATA-AAA
*
5227385 TATATTAAAAATAAAA
1 TATAATAAAAATAAAA
*
5227401 TATAA-AATATTATAATAA
1 TATAATAA-A-AATAA-AA
5227419 TA-AATAAAAATAAAA
1 TATAATAAAAATAAAA
* ***
5227434 TAT-ATGACTTTAAAAA
1 TATAATAAAAAT-AAAA
* * *
5227450 TATATTAAGAAATGATA
1 TATAATAA-AAATAAAA
* *
5227467 T-TCTATAAAAAT--TA
1 TAT-AATAAAAATAAAA
5227481 -ATAATAAAAATATAAA
1 TATAATAAAAATA-AAA
*
5227497 TATATTAAAAATAAAA
1 TATAATAAAAATAAAA
*
5227513 TATAA-AATATTATAATAA
1 TATAATAA-A-AATAA-AA
5227531 TA-AATAAAAATAAAA
1 TATAATAAAAATAAAA
5227546 TATA
1 TATA
5227550 TGATATTAAA
Statistics
Matches: 312, Mismatches: 64, Indels: 104
0.65 0.13 0.22
Matches are distributed among these distances:
13 15 0.05
14 13 0.04
15 67 0.21
16 75 0.24
17 76 0.24
18 46 0.15
19 12 0.04
20 8 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (16 bp):
TATAATAAAAATAAAA
Found at i:5227450 original size:49 final size:48
Alignment explanation
Indices: 5227397--5227565 Score: 140
Period size: 49 Copynumber: 3.2 Consensus size: 48
5227387 TATTAAAAAT
5227397 AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACTTTAA
1 AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGA-TTT-A
* * ***
5227447 AAATATATTAAGAAATGATATTCTATAAAAATTAATAATAAAAATATAAATATATTAAAAA
1 AAA-ATA-T---AAA--ATA-T-TATAATAA-T-A-AATAAAAATA-AAATATATGATTTA
5227508 TAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTA
1 -AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGAT-TTA
5227558 AAAATATA
1 AAAATATA
5227566 TTTAAGAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
49 17 0.18
50 14 0.15
51 4 0.04
52 2 0.02
53 7 0.07
54 1 0.01
55 6 0.06
57 6 0.06
58 1 0.01
59 7 0.07
60 2 0.02
61 5 0.05
62 13 0.14
63 9 0.10
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (48 bp):
AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATTTA
Found at i:5227483 original size:63 final size:60
Alignment explanation
Indices: 5227416--5227615 Score: 204
Period size: 58 Copynumber: 3.4 Consensus size: 60
5227406 AATATTATAA
5227416 TAATAAATAAAAATAAAATATATGACTTTAAAAATATATTAAGAAATGATATTCTATAAAAAT
1 TAAT-AATAAAAATAAAATATATGA-TTTAAAAATATATTAAGAAATGATATT-TATAAAAAT
* * * * *
5227479 TAATAATAAAAATATAA-ATAT-A-TTAAAAATAAAAT-ATAAA--ATA-TTATAATAA-
1 TAATAATAAAAATAAAATATATGATTTAAAAATATATTAAGAAATGATATTTATAAAAAT
*
5227531 T-A-AATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGCTATTATATAAAAAT
1 TAATAATAAAAATAAAATATATGAT-TTAAAAATATA-TTAAGAAATGATATT-TATAAAAAT
5227592 TAATAATAAAAAATATAAATATAT
1 TAATAAT-AAAAATA-AAATATAT
5227616 TAAACTTATA
Statistics
Matches: 111, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
50 12 0.11
51 5 0.05
52 2 0.02
53 7 0.06
54 11 0.10
55 4 0.04
56 4 0.04
57 4 0.04
58 13 0.12
59 1 0.01
60 8 0.07
61 5 0.05
62 13 0.12
63 7 0.06
64 7 0.06
65 8 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (60 bp):
TAATAATAAAAATAAAATATATGATTTAAAAATATATTAAGAAATGATATTTATAAAAAT
Found at i:5227501 original size:112 final size:113
Alignment explanation
Indices: 5227302--5227619 Score: 552
Period size: 112 Copynumber: 2.8 Consensus size: 113
5227292 ATATAAAAAT
5227302 TAATAATATAAAAATAAAATATATGATATTAAAAATATATTTAA-AATATGATATTATATAAAAA
1 TAATAA-ATAAAAATAAAATATATGATATTAAAAATATATTTAAGAA-ATGATATTATATAAAAA
*
5227366 TTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATATTATAA
64 TTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAA
*
5227416 TAATAAATAAAAATAAAATATATGACT-TTAAAAATATA-TTAAGAAATGATATTCTATAAAAAT
1 TAATAAATAAAAATAAAATATATGA-TATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
5227479 TAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAA
65 TAATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAA
*
5227528 TAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGCTATTATATAAAAATT
1 TAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAATT
5227593 AATAATAAAAAATATAAATATATTAAA
66 AATAAT-AAAAATATAAATATATTAAA
5227620 CTTATATTTT
Statistics
Matches: 195, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
111 1 0.01
112 105 0.54
113 62 0.32
114 27 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (113 bp):
TAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAATT
AATAATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAA
Found at i:5227549 original size:23 final size:23
Alignment explanation
Indices: 5227479--5227549 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
5227469 CTATAAAAAT
*
5227479 TAAT-AATAAAAATATAAATATAT
1 TAATAAATAAAAATA-AAATATAA
5227502 TAA-AAATAAAATATAAAATATTATAA
1 TAATAAATAAAA-AT-AAA-A-TATAA
5227528 TAATAAATAAAAATAAAATATA
1 TAATAAATAAAAATAAAATATA
5227550 TGATATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 14 0.34
24 5 0.12
25 5 0.12
26 9 0.22
27 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAATAAATAAAAATAAAATATAA
Found at i:5227789 original size:15 final size:15
Alignment explanation
Indices: 5227769--5227822 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
5227759 TTTTTCCTGT
*
5227769 AATCACATTGCTTGC
1 AATCACATTACTTGC
5227784 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
5227799 AATCACATTACCTGT
1 AATCACATTACTTGC
5227814 AATCACATT
1 AATCACATT
5227823 GCATTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:5236083 original size:2 final size:2
Alignment explanation
Indices: 5236076--5236100 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5236066 CCCTCAAATT
5236076 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5236101 CTTATCAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5248964 original size:16 final size:16
Alignment explanation
Indices: 5248943--5248984 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5248933 AATTCAAATC
5248943 ATTTCAAGTTTGAATT
1 ATTTCAAGTTTGAATT
* *
5248959 ATTTCAAATTTGATTT
1 ATTTCAAGTTTGAATT
*
5248975 GTTTCAAGTT
1 ATTTCAAGTT
5248985 CAAATCACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTCAAGTTTGAATT
Found at i:5258726 original size:45 final size:43
Alignment explanation
Indices: 5258609--5258726 Score: 96
Period size: 45 Copynumber: 2.7 Consensus size: 43
5258599 CATGCTAAGG
* ** *
5258609 TTAGGTTATTACACGTTATGTATAAAAAAATATGATACGTTATGG
1 TTAGGTTATTACACGTCATGT-T-AAAAAATATGATACGACATGA
* * * *
5258654 TTAGGTTGTTACAC-ACTATG-TATAAAAATATGTTGCACGACGTGA
1 TTAGGTTATTACACGTC-ATGTTA-AAAAATATGAT--ACGACATGA
5258699 TTAGGTTATTACACGTCATGTTAAAAAA
1 TTAGGTTATTACACGTCATGTTAAAAAA
5258727 AATATTGTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
42 1 0.02
43 11 0.19
45 42 0.74
46 3 0.05
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (43 bp):
TTAGGTTATTACACGTCATGTTAAAAAATATGATACGACATGA
Found at i:5258808 original size:53 final size:54
Alignment explanation
Indices: 5258707--5258812 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 54
5258697 GATTAGGTTA
* * * *
5258707 TTACACGTCATGTTAAAAAAAATATTGTTGTTATATGCTATGTACAAAAATATG
1 TTACACGTCATGTTAAAAAAAATATTATTATTACACGCTATGTACAAAAATATG
*
5258761 TTACATGTCATGTT-AAAAAAATATTATTATTACACGTCATAT-T-CAAAAATAT
1 TTACACGTCATGTTAAAAAAAATATTATTATTACACG-C-TATGTACAAAAATAT
5258813 TTTATTACAC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
53 27 0.60
54 15 0.33
55 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (54 bp):
TTACACGTCATGTTAAAAAAAATATTATTATTACACGCTATGTACAAAAATATG
Found at i:5258818 original size:30 final size:29
Alignment explanation
Indices: 5258761--5258822 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
5258751 CAAAAATATG
* *
5258761 TTACATGTCATGTTAAAAAAATATTATTA
1 TTACACGTCATATTAAAAAAATATTATTA
*
5258790 TTACACGTCATATT-CAAAAATATT-TTA
1 TTACACGTCATATTAAAAAAATATTATTA
5258817 TTACAC
1 TTACAC
5258823 TTTAATACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 9 0.30
28 9 0.30
29 12 0.40
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (29 bp):
TTACACGTCATATTAAAAAAATATTATTA
Found at i:5271171 original size:12 final size:12
Alignment explanation
Indices: 5271154--5271183 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5271144 TGTTACCAAT
5271154 ATATATATATAA
1 ATATATATATAA
*
5271166 ATATATATGTAA
1 ATATATATATAA
5271178 ATATAT
1 ATATAT
5271184 GCATAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (12 bp):
ATATATATATAA
Found at i:5274855 original size:38 final size:39
Alignment explanation
Indices: 5274772--5274862 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 39
5274762 AGGAACCAAA
*
5274772 TTTTATGTTTTCTTTTCTGAGCACTGTATATATTCACTG
1 TTTTATGTTTTCTTTTCTAAGCACTGTATATATTCACTG
*
5274811 TTTTATGTTTTCTTTTCTAAGCACTGTGTAT-TTCACTG
1 TTTTATGTTTTCTTTTCTAAGCACTGTATATATTCACTG
*
5274849 TTTTATGTTCTCTT
1 TTTTATGTTTTCTT
5274863 CTTGTAACAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 20 0.41
39 29 0.59
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.57
Consensus pattern (39 bp):
TTTTATGTTTTCTTTTCTAAGCACTGTATATATTCACTG
Found at i:5278623 original size:112 final size:112
Alignment explanation
Indices: 5278422--5278644 Score: 437
Period size: 112 Copynumber: 2.0 Consensus size: 112
5278412 GTCCTTTTAT
5278422 CGTAGATAAAAAACATGATAGAACATAATAGTTGACTTACAAATGATGTTACAAAGACACGTGAC
1 CGTAGATAAAAAACATGATAGAACATAATAGTTGACTTACAAATGATGTTACAAAGACACGTGAC
5278487 ACTTGATGTGTCATATACAAGGATGTCAACAAGTAGGGTACCCGCTC
66 ACTTGATGTGTCATATACAAGGATGTCAACAAGTAGGGTACCCGCTC
5278534 CGTAGATAAAAAACATGATAGAACATAATAGTTGACTTACAAATGATGTTACAAAGACACGTGAC
1 CGTAGATAAAAAACATGATAGAACATAATAGTTGACTTACAAATGATGTTACAAAGACACGTGAC
*
5278599 ACTTGATGTGTCATATACAGGGATGTCAACAAGTAGGGTACCCGCT
66 ACTTGATGTGTCATATACAAGGATGTCAACAAGTAGGGTACCCGCT
5278645 AATTTTGAAG
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (112 bp):
CGTAGATAAAAAACATGATAGAACATAATAGTTGACTTACAAATGATGTTACAAAGACACGTGAC
ACTTGATGTGTCATATACAAGGATGTCAACAAGTAGGGTACCCGCTC
Found at i:5279020 original size:34 final size:35
Alignment explanation
Indices: 5278948--5279026 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
5278938 ATATAATTTA
* *
5278948 AACTTAAATAATCAAAAACAAATACCTCAAATATC
1 AACTTAAATAATCAAAAACAAATACCTCAAACAAC
*
5278983 AACTTAAATAA-CTAAAAACAAATA-TTCAAACAAC
1 AACTTAAATAATC-AAAAACAAATACCTCAAACAAC
5279017 AACTTAAATA
1 AACTTAAATA
5279027 TTACTAGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 18 0.45
35 22 0.55
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.23
Consensus pattern (35 bp):
AACTTAAATAATCAAAAACAAATACCTCAAACAAC
Found at i:5279837 original size:28 final size:27
Alignment explanation
Indices: 5279797--5279855 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
5279787 TATTTAAACT
* *
5279797 TATAATACTAAATA-TAAAATTATAATA
1 TATAAAACTAAATAGTAAAA-TACAATA
*
5279824 TATAAAACATAAATAGTTAAATACAATA
1 TATAAAAC-TAAATAGTAAAATACAATA
5279852 TATA
1 TATA
5279856 GGATTGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 16 0.59
29 4 0.15
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (27 bp):
TATAAAACTAAATAGTAAAATACAATA
Found at i:5281270 original size:452 final size:459
Alignment explanation
Indices: 5279964--5281292 Score: 2526
Period size: 460 Copynumber: 2.9 Consensus size: 459
5279954 GAGATATATT
5279964 CAAAATAATTTCCTCTTACATAATCAATATAAATAAAGAAATGATACATTGATAAAAGTTTAAAT
1 CAAAATAATTTCCTCTTACATAATCAATATAAATAAAGAAATGATACATTGATAAAAGTTTAAAT
*
5280029 AATAGCACAACACTACAACTTATATTTAAGCATTGCATAATAATTTATTTATTTTAAAAATTAAA
66 AATAGCACAACACTACAACTTATATTTAAGCATTACATAATAATTTATTTATTTTAAAAATTAAA
5280094 ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGTAAAAATAAAATTCTC
131 ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGTAAAAATAAAATTCTC
5280159 ATATGACATAACAAAAAAGAAAAAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAA
196 ATATGACATAACAAAAAAG-AAAAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAA
5280224 TCTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATGAAAAAAAAAACTTTAAAATTGAT
260 TCTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATGAAAAAAAAAACTTTAAAATTGAT
5280289 ACATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATTAAATAAAAAATTATTTTGAGGG
325 ACATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATTAAATAAAAAATTATTTTGAGGG
5280354 AATACATGTGAATTCTTTATTTTTAAATTTTATATAATATAAATTTTTTTCAAAAATTTTGCCCT
390 AATACATGTGAATTCTTTATTTTTAAATTTTATATAATATAAATTTTTTTCAAAAATTTTGCCCT
5280419 CCCCC
455 CCCCC
5280424 CAAAATAATTTCCTCTTACATAATCAATATAAATAAAGAAATGATACATTGATAAAAGTTTAAAT
1 CAAAATAATTTCCTCTTACATAATCAATATAAATAAAGAAATGATACATTGATAAAAGTTTAAAT
5280489 AATAGCACAACACTACAACTTATATTTAAGCATTACATAATAATTTATTTATTTTAAAAA-TAAA
66 AATAGCACAACACTACAACTTATATTTAAGCATTACATAATAATTTATTTATTTTAAAAATTAAA
5280553 ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGT-AAAATAAAATTCTC
131 ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGTAAAAATAAAATTCTC
5280617 ATATGACATAACAAAAAAG--AAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAAT
196 ATATGACATAACAAAAAAGAAAAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAAT
5280680 CTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATG-AAAAAAAAACTTTAAAATTGATA
261 CTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATGAAAAAAAAAACTTTAAAATTGATA
5280744 CATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATT-AATAAAAAATTA-TTTGAGGGA
326 CATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATTAAATAAAAAATTATTTTGAGGGA
5280807 ATACATGTGAATTCTTTATTTTT-AATTTTATAT-ATATAAATTTTTTTCAAAAATTTTGCCCT-
391 ATACATGTGAATTCTTTATTTTTAAATTTTATATAATATAAATTTTTTTCAAAAATTTTGCCCTC
5280869 CCCC
456 CCCC
5280873 CAAAATAATTTCCTCTTACATAATCAATAT-AATAAAGAAATGATACATTGAT-AAAGTTTAAAT
1 CAAAATAATTTCCTCTTACATAATCAATATAAATAAAGAAATGATACATTGATAAAAGTTTAAAT
5280936 AATAGCACAACACTACAACTTATATTTAAGCATTACATAATAATTTATTTATTTTAAAAATTAAA
66 AATAGCACAACACTACAACTTATATTTAAGCATTACATAATAATTTATTTATTTTAAAAATTAAA
5281001 ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGTAGAAAAT-AAATTCT
131 ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGTA-AAAATAAAATTCT
5281065 CATATGACATAACAAAAAAGAAAAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAA
195 CATATGACATAACAAAAAAGAAAAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAA
5281130 TCTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATGAAAAAAAAAACTTTAAAATTGAT
260 TCTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATGAAAAAAAAAACTTTAAAATTGAT
5281195 ACATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATTAAATAAAAAATTATTTTGA-GG
325 ACATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATTAAATAAAAAATTATTTTGAGGG
5281259 -ATACATGTGAATTCTTTATTTTTAAATTTTATAT
390 AATACATGTGAATTCTTTATTTTTAAATTTTATAT
5281293 CTCCCCCCCC
Statistics
Matches: 859, Mismatches: 1, Indels: 25
0.97 0.00 0.03
Matches are distributed among these distances:
447 71 0.08
448 76 0.09
449 61 0.07
450 34 0.04
451 95 0.11
452 120 0.14
453 36 0.04
454 70 0.08
455 85 0.10
458 33 0.04
459 54 0.06
460 124 0.14
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (459 bp):
CAAAATAATTTCCTCTTACATAATCAATATAAATAAAGAAATGATACATTGATAAAAGTTTAAAT
AATAGCACAACACTACAACTTATATTTAAGCATTACATAATAATTTATTTATTTTAAAAATTAAA
ATCGTAGAAAATAAAATCCATATAATAGAAAAAAGAAGAACATGACAAGTAAAAATAAAATTCTC
ATATGACATAACAAAAAAGAAAAAAAAATATAATTGATGGTTTGTAGAAATTTGGAGAAGAAAAT
CTGTAGAAATTTAAAATATATGAACAAATATAATAGAAATGAAAAAAAAAACTTTAAAATTGATA
CATGTGAAATTATTTTGTTATTCTTTATTTGTATTAATTATTAAATAAAAAATTATTTTGAGGGA
ATACATGTGAATTCTTTATTTTTAAATTTTATATAATATAAATTTTTTTCAAAAATTTTGCCCTC
CCCC
Found at i:5283479 original size:31 final size:30
Alignment explanation
Indices: 5283444--5283505 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
5283434 AATTTTCTTA
*
5283444 TAATTACATATGATTAAAGTAACATAACCTT
1 TAATTACATATGATTAAAATAACAT-ACCTT
5283475 TAATTACATATGATTAAAATAACATACCTT
1 TAATTACATATGATTAAAATAACATACCTT
5283505 T
1 T
5283506 CATCTAAGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (30 bp):
TAATTACATATGATTAAAATAACATACCTT
Found at i:5286523 original size:3 final size:3
Alignment explanation
Indices: 5286517--5286548 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5286507 CATAAGAACC
5286517 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5286549 ACACATTCAT
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:5292148 original size:20 final size:20
Alignment explanation
Indices: 5292110--5292148 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5292100 TATATAATTT
* **
5292110 AAATTATTTTTAATTAAAAA
1 AAATTAATTTTAAACAAAAA
5292130 AAATTAATTTTAAACAAAA
1 AAATTAATTTTAAACAAAA
5292149 TTACCTTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTAATTTTAAACAAAAA
Found at i:5294048 original size:25 final size:23
Alignment explanation
Indices: 5294020--5294076 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
5294010 ATCATTAATT
*
5294020 ATTTGATTTAAATTAAAATATAAAA
1 ATTTAATTTAAA-TAAAATA-AAAA
* *
5294045 ATTTTATTTAAATATAATAAAAA
1 ATTTAATTTAAATAAAATAAAAA
5294068 ATTTAATTT
1 ATTTAATTT
5294077 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 12 0.41
24 6 0.21
25 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAATTTAAATAAAATAAAAA
Found at i:5294067 original size:22 final size:20
Alignment explanation
Indices: 5294032--5294072 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
5294022 TTGATTTAAA
*
5294032 TTAAAATATAAAAATTTTAT
1 TTAAAATATAAAAAATTTAT
5294052 TTAAATATAATAAAAAATTTA
1 TTAAA-AT-ATAAAAAATTTA
5294073 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAATATAAAAAATTTAT
Found at i:5294083 original size:18 final size:20
Alignment explanation
Indices: 5294062--5294103 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5294052 TTAAATATAA
5294062 TAAAAAATTT-A-ATTTTTT
1 TAAAAAATTTAAGATTTTTT
*
5294080 TAAATAATTTAAGATTTTTT
1 TAAAAAATTTAAGATTTTTT
5294100 TAAA
1 TAAA
5294104 GTATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 1 0.05
20 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAAAAATTTAAGATTTTTT
Found at i:5294191 original size:15 final size:15
Alignment explanation
Indices: 5294171--5294217 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5294161 TTTACAATGC
* *
5294171 AATGTGATTATAGGT
1 AATGTGATTACAAGT
*
5294186 AATGTGATTGCAAGT
1 AATGTGATTACAAGT
*
5294201 AATGTGATTGCAAGT
1 AATGTGATTACAAGT
5294216 AA
1 AA
5294218 CATTACAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:5294495 original size:112 final size:110
Alignment explanation
Indices: 5294354--5294576 Score: 410
Period size: 112 Copynumber: 2.0 Consensus size: 110
5294344 AAAATATAAA
*
5294354 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
5294419 TGTCATATATTTTATTTTTATTTATTATTATAATCTTTTATATATTT
66 TGTCATATATTTTATTTTTATTTATTATTATAATC--TTATATATTT
*
5294466 TTTAATATATTTATATTTTTTATTATTAATTTTTGTATAATATCATATCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
5294531 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTT
66 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTT
5294576 T
1 T
5294577 ATTTTTATTT
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
110 11 0.10
112 98 0.90
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (110 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTT
Found at i:5294551 original size:6 final size:6
Alignment explanation
Indices: 5294540--5294625 Score: 57
Period size: 6 Copynumber: 13.7 Consensus size: 6
5294530 ATGTCATATA
* * *
5294540 TTTTAT TTTTAT TTATTAT TATAAT CTTATAT ATTTTAT TTTTAT TTTTA-
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* * * *
5294590 ATATAT TTTTAT ATTATAT ATTTTAT TTTAAT TTTT
1 TTTTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTT
5294626 TTACCTATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
5 3 0.05
6 34 0.56
7 24 0.39
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:5294576 original size:33 final size:30
Alignment explanation
Indices: 5294423--5294618 Score: 108
Period size: 30 Copynumber: 6.7 Consensus size: 30
5294413 TTTTAATGTC
5294423 ATATATTTTATTTTTA--TTT-AT-TA-TT
1 ATATATTTTATTTTTATTTTTAATATATTT
* * *
5294448 ATAATCTTTTATATAT-TTTTTAATATATTT
1 AT-ATATTTTATTTTTATTTTTAATATATTT
* * * *
5294478 ATATTTTTTATTATTAATTTTT-GTATA-AT
1 ATATATTTTATT-TTTATTTTTAATATATTT
* ** * * *
5294507 ATCATATCTTAAATATATTTTT-A-AT-GTC
1 AT-ATATTTTATTTTTATTTTTAATATATTT
*
5294535 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTT-TTAATAT-AT-TT
5294568 ATATATTTTATTTTTATTTTTAATATATTT
1 ATATATTTTATTTTTATTTTTAATATATTT
* *
5294598 TTATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
5294619 AATTTTTTTA
Statistics
Matches: 126, Mismatches: 28, Indels: 28
0.69 0.15 0.15
Matches are distributed among these distances:
25 2 0.02
26 10 0.08
27 16 0.13
28 8 0.06
29 20 0.16
30 28 0.22
31 16 0.13
32 6 0.05
33 20 0.16
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (30 bp):
ATATATTTTATTTTTATTTTTAATATATTT
Found at i:5294605 original size:112 final size:112
Alignment explanation
Indices: 5294354--5294615 Score: 406
Period size: 112 Copynumber: 2.3 Consensus size: 112
5294344 AAAATATAAA
*
5294354 TTTAATATATTTATAT-TTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTA
1 TTTAATATATTTATATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTA
5294418 ATGTCATATATTTTATTTTTATTTATTATTATAATCTTTTATATATTT
66 ATGTCATATATTTTATTTTTATTTATTATTATAATC-TTTATATATTT
*
5294466 TTTAATATATTTATAT-TTTTTATTATTAATTTTTGTATAATATCATATCTTAAATATATTTTTA
1 TTTAATATATTTATATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTA
5294530 ATGTCATATATTTTATTTTTATTTATTATTATAATC-TTATATATTT
66 ATGTCATATATTTTATTTTTATTTATTATTATAATCTTTATATATTT
** *
5294576 TATTTTTATTTTTAATATATTTTTA-TATTATATATTTTAT
1 T-TTAATATATTT-ATATATTTTTATTATTA-AT-TTTTAT
5294616 TTTAATTTTT
Statistics
Matches: 139, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
110 11 0.08
111 8 0.06
112 107 0.77
113 8 0.06
114 5 0.04
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTA
ATGTCATATATTTTATTTTTATTTATTATTATAATCTTTATATATTT
Found at i:5294616 original size:37 final size:37
Alignment explanation
Indices: 5294518--5294625 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 37
5294508 TCATATCTTA
5294518 AATATATTTTTA-ATGTCATATATTTTATTTTTA--TTT
1 AATATATTTTTATAT-T-ATATATTTTATTTTTATTTTT
* * *
5294554 -AT-TATTATAATCTTATATATTTTATTTTTATTTTT
1 AATATATTTTTATATTATATATTTTATTTTTATTTTT
*
5294589 AATATATTTTTATATTATATATTTTATTTTAATTTTT
1 AATATATTTTTATATTATATATTTTATTTTTATTTTT
5294626 TTACCTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
33 16 0.27
34 7 0.12
35 6 0.10
36 2 0.03
37 29 0.48
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (37 bp):
AATATATTTTTATATTATATATTTTATTTTTATTTTT
Found at i:5294627 original size:28 final size:28
Alignment explanation
Indices: 5294569--5294715 Score: 85
Period size: 30 Copynumber: 5.1 Consensus size: 28
5294559 TATAATCTTA
*
5294569 TATATTTTAT-TTTTATTTTTAATATATTTT
1 TATATTATATATTTTA-TTTTAAT-T-TTTT
5294599 TATATTATATATTTTATTTTAATTTTTTT
1 TATATTATATATTTTATTTTAA-TTTTTT
*
5294628 ACCTATATTATATAAATTTTA-TTT--TTTTAT
1 ---TATATTATAT--ATTTTATTTTAATTTTTT
*
5294658 TATATT-T-TATTTTAATTTT--TTATTCT
1 TATATTATATATTTT-ATTTTAATT-TTTT
* *
5294684 TGTATTGTATATTTTATTTTAATATTTTT
1 TATATTATATATTTTATTTTAAT-TTTTT
5294713 TAT
1 TAT
5294716 TTTAATTATA
Statistics
Matches: 96, Mismatches: 6, Indels: 31
0.72 0.05 0.23
Matches are distributed among these distances:
23 5 0.05
24 1 0.01
25 6 0.06
26 9 0.09
27 12 0.12
28 6 0.06
29 10 0.10
30 22 0.23
31 6 0.06
32 10 0.10
33 3 0.03
34 6 0.06
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.69
Consensus pattern (28 bp):
TATATTATATATTTTATTTTAATTTTTT
Found at i:5294647 original size:29 final size:24
Alignment explanation
Indices: 5294606--5294678 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 24
5294596 TTTTATATTA
5294606 TATATTTTATTTTAATTTTTTTACC
1 TATATTTTATTTTAATTTTTTTA-C
*
5294631 TATATTATATAAATTTT-ATTTTTTTAT
1 TATATT-T-T--ATTTTAATTTTTTTAC
5294658 TATATTTTATTTTAATTTTTT
1 TATATTTTATTTTAATTTTTT
5294679 ATTCTTGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
23 5 0.12
24 7 0.17
25 7 0.17
26 2 0.05
27 7 0.17
28 9 0.21
29 5 0.12
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (24 bp):
TATATTTTATTTTAATTTTTTTAC
Found at i:5294647 original size:71 final size:71
Alignment explanation
Indices: 5294518--5294653 Score: 174
Period size: 71 Copynumber: 1.9 Consensus size: 71
5294508 TCATATCTTA
* *
5294518 AATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATTTTT
1 AATATATTTTTAATGTCATATATTTTATTTTAATTTATTATTATAATCTTATAAATTTTATTTTT
5294583 ATTTTT
66 ATTTTT
5294589 AATATATTTTTATAT-T-ATATATTTTATTTTAATTT-TT-TTACCTATAT-TATATAAATTTTA
1 AATATATTTTTA-ATGTCATATATTTTATTTTAATTTATTATTA--TA-ATCT-TATAAATTTTA
5294649 TTTTT
61 TTTTT
5294654 TTATTATATT
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
68 3 0.05
69 2 0.03
70 21 0.36
71 30 0.52
72 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (71 bp):
AATATATTTTTAATGTCATATATTTTATTTTAATTTATTATTATAATCTTATAAATTTTATTTTT
ATTTTT
Found at i:5294709 original size:20 final size:21
Alignment explanation
Indices: 5294686--5294730 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
5294676 TTTATTCTTG
*
5294686 TATTGTATATTTT-ATTTTAA
1 TATTGTATATTTTAATTATAA
* *
5294706 TATTTTTTATTTTAATTATAA
1 TATTGTATATTTTAATTATAA
5294727 TATT
1 TATT
5294731 ATAAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTGTATATTTTAATTATAA
Found at i:5297286 original size:15 final size:15
Alignment explanation
Indices: 5297268--5297304 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5297258 TTTATATATT
*
5297268 TTAATATTTAAATAA
1 TTAATATTAAAATAA
5297283 TTAATATTAAAAT-A
1 TTAATATTAAAATAA
5297297 TT-ATATTA
1 TTAATATTA
5297305 TGTTGTCCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.29
14 3 0.14
15 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATATTAAAATAA
Found at i:5306080 original size:2 final size:2
Alignment explanation
Indices: 5306073--5306100 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5306063 CGATAGATGA
5306073 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
5306101 GGTTTAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.