Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 62 of 199
Found at i:18434729 original size:29 final size:29
Alignment explanation
Indices: 18434687--18434744 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
18434677 GACTGAAATG
18434687 GAGATATAGGAATGGATAATATAAGTACA
1 GAGATATAGGAATGGATAATATAAGTACA
*
18434716 GAGATATAGGAATGGATAATATGAGTACA
1 GAGATATAGGAATGGATAATATAAGTACA
18434745 CACTTGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (29 bp):
GAGATATAGGAATGGATAATATAAGTACA
Found at i:18446809 original size:12 final size:12
Alignment explanation
Indices: 18446792--18446821 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18446782 CCGAACATGC
18446792 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
18446804 CCGTGTGCTAGG
1 CCGTGTGCCAGG
18446816 CCGTGT
1 CCGTGT
18446822 AACAGCCTGA
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:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:18447993 original size:25 final size:25
Alignment explanation
Indices: 18447955--18448024 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
18447945 CTGTACATGT
18447955 ATGCTCACACGAGCTGTGAATCAAA
1 ATGCTCACACGAGCTGTGAATCAAA
* * * *
18447980 ATTCTTACATGAGCTGTGAATCAGA
1 ATGCTCACACGAGCTGTGAATCAAA
18448005 ATGCTCACACGAGCTGTGAA
1 ATGCTCACACGAGCTGTGAA
18448025 AATATGCCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATCAAA
Found at i:18454711 original size:38 final size:38
Alignment explanation
Indices: 18454653--18454759 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 38
18454643 AACATTTACT
* *
18454653 ACACCGACA-TCAAGCTTGCTACGCACTAAGCCTGAATA
1 ACACCGACACT-AAGCCTGCTAAGCACTAAGCCTGAATA
* *
18454691 ACACC-AGCACTAAGCCTGCTAAGCACTAAGCTTGATTA
1 ACACCGA-CACTAAGCCTGCTAAGCACTAAGCCTGAATA
* * *
18454729 ACATCGATACTAAGCCTACTAAGCACTAAGC
1 ACACCGACACTAAGCCTGCTAAGCACTAAGC
18454760 TTGCTAGACA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.02
38 56 0.95
39 2 0.03
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.20
Consensus pattern (38 bp):
ACACCGACACTAAGCCTGCTAAGCACTAAGCCTGAATA
Found at i:18459080 original size:39 final size:39
Alignment explanation
Indices: 18459037--18459117 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
18459027 TAACCACACT
* *
18459037 AATTAGCTCATGTGTTTTAATTGTCTCCTACACGCCACA
1 AATTAGCTCATATGTTTTAATTGTCTCCTACACACCACA
*
18459076 AATTAGCTCATATGTTTTAATTGTCTCCTATACACCACA
1 AATTAGCTCATATGTTTTAATTGTCTCCTACACACCACA
18459115 AAT
1 AAT
18459118 CTCTCAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (39 bp):
AATTAGCTCATATGTTTTAATTGTCTCCTACACACCACA
Found at i:18465644 original size:22 final size:22
Alignment explanation
Indices: 18465602--18465646 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
18465592 ATTAGAAATC
*
18465602 CTACCCAACCAGCCTCTACACT
1 CTACCCAACCAGCCTCAACACT
*
18465624 CTACTCCATCCAGCC-CAACACT
1 CTAC-CCAACCAGCCTCAACACT
18465646 C
1 C
18465647 CATGTGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.27, C:0.51, G:0.04, T:0.18
Consensus pattern (22 bp):
CTACCCAACCAGCCTCAACACT
Found at i:18465862 original size:25 final size:27
Alignment explanation
Indices: 18465834--18465886 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
18465824 ATAGTCATAC
*
18465834 ATAACATA-GAGCAT-GCAGTTATTTT
1 ATAACATAGGAGCATAACAGTTATTTT
*
18465859 ATAACATAGGGGCATAACAGTTATTTT
1 ATAACATAGGAGCATAACAGTTATTTT
18465886 A
1 A
18465887 CCACGTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 11 0.46
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (27 bp):
ATAACATAGGAGCATAACAGTTATTTT
Found at i:18465884 original size:27 final size:26
Alignment explanation
Indices: 18465849--18465914 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
18465839 ATAGAGCATG
18465849 CAGTTATTTTATAACATAGGGGCATAA
1 CAGTTATTTTATAACAT-GGGGCATAA
** * *
18465876 CAGTTATTTTACCACGTGGGGGATAA
1 CAGTTATTTTATAACATGGGGCATAA
*
18465902 CAGTCATTTTATA
1 CAGTTATTTTATA
18465915 TCAGTTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (26 bp):
CAGTTATTTTATAACATGGGGCATAA
Found at i:18474448 original size:9 final size:9
Alignment explanation
Indices: 18474434--18474464 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18474424 GTTAAACGAA
18474434 TCGAGTTAT
1 TCGAGTTAT
*
18474443 TCGAGTTAA
1 TCGAGTTAT
18474452 TCGAGTTAT
1 TCGAGTTAT
18474461 TCGA
1 TCGA
18474465 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18474534 original size:9 final size:9
Alignment explanation
Indices: 18474517--18474553 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
18474507 TGAGTTTTCG
18474517 AATTCGAAT
1 AATTCGAAT
18474526 -ATCTCGAAT
1 AAT-TCGAAT
18474535 AATTCGAAT
1 AATTCGAAT
18474544 AATTCGAAT
1 AATTCGAAT
18474553 A
1 A
18474554 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:18475199 original size:5 final size:5
Alignment explanation
Indices: 18475189--18475215 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18475179 AAATATTTTT
18475189 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
18475216 CAAACGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:18484253 original size:13 final size:13
Alignment explanation
Indices: 18484216--18484263 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
18484206 TTAATTAAAC
18484216 TTAATTAAATTAG-
1 TTAATT-AATTAGT
18484229 TTAATTACATTAGT
1 TTAATTA-ATTAGT
*
18484243 TTACTTAATTAGT
1 TTAATTAATTAGT
18484256 CTTAATTA
1 -TTAATTA
18484264 TAACAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 1 0.03
13 17 0.57
14 12 0.40
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TTAATTAATTAGT
Found at i:18493995 original size:5 final size:5
Alignment explanation
Indices: 18493978--18494010 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
18493968 TTCAATTACA
*
18493978 TTTAG TTTA- TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
18494011 ACATAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:18495555 original size:27 final size:27
Alignment explanation
Indices: 18495525--18495684 Score: 141
Period size: 27 Copynumber: 6.0 Consensus size: 27
18495515 CGTAAACAAG
*
18495525 TCATGAAAGAAATGCTTTTGTGGCGAA
1 TCATGAAAGAAATGCCTTTGTGGCGAA
* *
18495552 TCATGAAAGAAATG-C-ATGTGGTGAA
1 TCATGAAAGAAATGCCTTTGTGGCGAA
* *
18495577 TCATGAAAGAAAAGCCTTTGTGGAGAAA
1 TCATGAAAGAAATGCCTTTGTGGCG-AA
**
18495605 T-ATGAAAGGAAAT-ATTTTGTGGCGAA
1 TCATGAAA-GAAATGCCTTTGTGGCGAA
** *
18495631 TCATGAAAGAAAAACCATTGTGGCGAA
1 TCATGAAAGAAATGCCTTTGTGGCGAA
* * *
18495658 TTATGAAAG-GATAGCCTCTGTGGCGAA
1 TCATGAAAGAAAT-GCCTTTGTGGCGAA
18495685 CCCTACAAGG
Statistics
Matches: 106, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
25 21 0.20
26 9 0.08
27 69 0.65
28 7 0.07
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (27 bp):
TCATGAAAGAAATGCCTTTGTGGCGAA
Found at i:18495640 original size:54 final size:53
Alignment explanation
Indices: 18495525--18495668 Score: 166
Period size: 54 Copynumber: 2.7 Consensus size: 53
18495515 CGTAAACAAG
* * *
18495525 TCATGAAAGAAATGCTTTTGTGGCG-AATCATGAAA-GAAATGCATGTGGTGAA
1 TCATGAAAGAAAAGCCTTTGTGGCGAAAT-ATGAAAGGAAATGCATGTGGCGAA
* ***
18495577 TCATGAAAGAAAAGCCTTTGTGGAGAAATATGAAAGGAAATATTTTGTGGCGAA
1 TCATGAAAGAAAAGCCTTTGTGGCGAAATATGAAAGGAAAT-GCATGTGGCGAA
* * *
18495631 TCATGAAAGAAAAACCATTGTGGCGAATTATGAAAGGA
1 TCATGAAAGAAAAGCCTTTGTGGCGAAATATGAAAGGA
18495669 TAGCCTCTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 28 0.36
53 8 0.10
54 42 0.54
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (53 bp):
TCATGAAAGAAAAGCCTTTGTGGCGAAATATGAAAGGAAATGCATGTGGCGAA
Found at i:18495695 original size:81 final size:79
Alignment explanation
Indices: 18495526--18495680 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 79
18495516 GTAAACAAGT
* ** *
18495526 CATGAAA-GAAATGCTTTTGTGGCGAATCATGAAAGAAATGCATGTGGTGAATCATGAAAGAAAA
1 CATGAAAGGAAAT-ATTTTGTGGCGAATCATGAAAGAAAACCATGTGGCGAATCATGAAAGAAAA
*
18495590 GCCTTTGTGGAGAAA
65 GCCTCTGTGGAGAAA
* * * *
18495605 TATGAAAGGAAATATTTTGTGGCGAATCATGAAAGAAAAACCATTGTGGCGAATTATGAAAGGAT
1 CATGAAAGGAAATATTTTGTGGCGAATCATGAAAG-AAAACCA-TGTGGCGAATCATGAAAGAAA
18495670 AGCCTCTGTGG
64 AGCCTCTGTGG
18495681 CGAACCCTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 27 0.42
80 10 0.16
81 27 0.42
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.25
Consensus pattern (79 bp):
CATGAAAGGAAATATTTTGTGGCGAATCATGAAAGAAAACCATGTGGCGAATCATGAAAGAAAAG
CCTCTGTGGAGAAA
Found at i:18497424 original size:43 final size:42
Alignment explanation
Indices: 18497372--18497518 Score: 213
Period size: 42 Copynumber: 3.5 Consensus size: 42
18497362 GTGCTAAACA
* **
18497372 GAAACCCATAAGGGTTGAACTGAAGCTCGTAAGAGCTGAAGCG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAA-CG
* *
18497415 GAAACCCATAAGGGTTAAATTGAAGCTCAAAAGAGTTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
* * *
18497457 AAAACCCATAAGGGTTAAACTGAAGCTTAAAAGAGCTGAACA
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
18497499 GAAACCCATAAGGGTTAAAC
1 GAAACCCATAAGGGTTAAAC
18497519 AAAAACTTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 58 0.62
43 35 0.38
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
Found at i:18505961 original size:5 final size:5
Alignment explanation
Indices: 18505951--18506016 Score: 123
Period size: 5 Copynumber: 13.2 Consensus size: 5
18505941 AGTTAAAATA
*
18505951 TATAT TATAT TAGAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
18506001 TATAT TATAT TATAT T
1 TATAT TATAT TATAT T
18506017 GTAATGATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 59 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:18506088 original size:15 final size:16
Alignment explanation
Indices: 18506070--18506102 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
18506060 AGCGAAACAG
18506070 AAAGAAAAA-GAAAGA
1 AAAGAAAAAGGAAAGA
18506085 AAAGAAAAAGGAAAGA
1 AAAGAAAAAGGAAAGA
18506101 AA
1 AA
18506103 GGAAGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGGAAAGA
Found at i:18506750 original size:40 final size:40
Alignment explanation
Indices: 18506629--18506768 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
18506619 GACTTCGAGT
* * * *
18506629 CGATAAGACACTGGGTGTCAATTTAATACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * * *
18506670 CGATGAGGCACTGGGTG-CCAA-T-TTACTTTGGTTTAAC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
18506707 CGATGAGACACTGTGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
18506747 CGATGAGGCACTAGGTGTCAAA
1 CGATGAGACACTGGGTGTCAAA
18506769 CTGGTGTGTT
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 16 0.21
38 12 0.16
39 2 0.03
40 32 0.42
41 15 0.19
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:18511326 original size:61 final size:61
Alignment explanation
Indices: 18511250--18511382 Score: 239
Period size: 61 Copynumber: 2.2 Consensus size: 61
18511240 TTGGCACAGC
*
18511250 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACGGAG
1 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACAGAG
* *
18511311 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATGGTGTGTAGGGTTGGACAGAG
1 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACAGAG
18511372 ATGGTGTGTAG
1 ATGGTGTGTAG
18511383 AGGTTGGTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.20, C:0.11, G:0.39, T:0.30
Consensus pattern (61 bp):
ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACAGAG
Found at i:18513209 original size:8 final size:8
Alignment explanation
Indices: 18513196--18513285 Score: 50
Period size: 8 Copynumber: 12.1 Consensus size: 8
18513186 GTTAAAATAT
18513196 ATATTATA
1 ATATTATA
18513204 ATATTATA
1 ATATTATA
18513212 ATATTAT-
1 ATATTATA
*
18513219 ATCTTA-A
1 ATATTATA
*
18513226 TTATTA-A
1 ATATTATA
* *
18513233 GTA-CAT-
1 ATATTATA
*
18513239 ATATTATT
1 ATATTATA
18513247 ATATTATA
1 ATATTATA
* *
18513255 TTA-TATT
1 ATATTATA
18513262 ATATTATA
1 ATATTATA
* *
18513270 TTA-TATT
1 ATATTATA
18513277 ATATTATA
1 ATATTATA
18513285 A
1 A
18513286 GGATAAAATA
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
6 3 0.05
7 24 0.40
8 33 0.55
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (8 bp):
ATATTATA
Found at i:18513214 original size:20 final size:20
Alignment explanation
Indices: 18513191--18513285 Score: 67
Period size: 20 Copynumber: 4.7 Consensus size: 20
18513181 TTAAAGTTAA
18513191 AATATATATTATAATATTAT
1 AATATATATTATAATATTAT
18513211 AATATTATATCT-TAATTATTA-
1 AATA-TATAT-TATAA-TATTAT
* *
18513232 AGTACATATATTATTATATTAT
1 A--ATATATATTATAATATTAT
18513254 -AT-TATATTATATTATATTAT
1 AATATATATTATA--ATATTAT
18513274 -AT-TATATTATAA
1 AATATATATTATAA
18513286 GGATAAAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
18 9 0.15
19 1 0.02
20 22 0.35
21 15 0.24
22 13 0.21
23 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (20 bp):
AATATATATTATAATATTAT
Found at i:18513253 original size:5 final size:5
Alignment explanation
Indices: 18513243--18513284 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
18513233 GTACATATAT
18513243 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
18513285 AGGATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:18513337 original size:11 final size:10
Alignment explanation
Indices: 18513313--18513361 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
18513303 AAATAAAAAG
18513313 ATAGAAAG--
1 ATAGAAAGAA
18513321 ATAGAAACGAA
1 ATAGAAA-GAA
18513332 ATAGAAAGAA
1 ATAGAAAGAA
*
18513342 AAAGAAAGAA
1 ATAGAAAGAA
*
18513352 AGA-AAAGAA
1 ATAGAAAGAA
18513361 A
1 A
18513362 GAAAAAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 14 0.39
11 7 0.19
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (10 bp):
ATAGAAAGAA
Found at i:18513349 original size:4 final size:4
Alignment explanation
Indices: 18513309--18513377 Score: 54
Period size: 4 Copynumber: 17.0 Consensus size: 4
18513299 AATAAAATAA
* *
18513309 AAAG ATAG AAAG ATAG AAACG AAATAG AAAG -AA- AAAG AAAG AAAG AAAAG
1 AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG -AAAG
*
18513359 AAAG AAA- AAGG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG
18513378 GAAGGAGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
3 6 0.12
4 35 0.67
5 7 0.13
6 3 0.06
7 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:18513352 original size:33 final size:33
Alignment explanation
Indices: 18513290--18513376 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
18513280 TTATAAGGAT
* * *
18513290 AAAATAAAG-AATA-AAATAAAAAGATAGAAAG
1 AAAAGAAAGAAATAGAAAGAAAAAGAAAGAAAG
*
18513321 -ATAGAAACGAAATAGAAAGAAAAAGAAAGAAAG
1 AAAAGAAA-GAAATAGAAAGAAAAAGAAAGAAAG
*
18513354 AAAAGAAAGAAAAAGGAAAGAAA
1 AAAAGAAAGAAATA-GAAAGAAA
18513377 GGAAGGAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 5 0.11
31 1 0.02
32 4 0.09
33 21 0.47
34 14 0.31
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (33 bp):
AAAAGAAAGAAATAGAAAGAAAAAGAAAGAAAG
Found at i:18513368 original size:29 final size:28
Alignment explanation
Indices: 18513307--18513377 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
18513297 AGAATAAAAT
* * * *
18513307 AAAAAG-ATAGAAAGATAGAAACGAAAT
1 AAAAAGAAAAGAAAGAAAGAAAAGAAAG
*
18513334 AGAAAGAAAAAGAAAGAAAGAAAAGAAAG
1 AAAAAG-AAAAGAAAGAAAGAAAAGAAAG
*
18513363 AAAAAGGAAAGAAAG
1 AAAAAGAAAAGAAAG
18513378 GAAGGAGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 5 0.14
28 8 0.23
29 22 0.63
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (28 bp):
AAAAAGAAAAGAAAGAAAGAAAAGAAAG
Found at i:18513388 original size:20 final size:20
Alignment explanation
Indices: 18513336--18513388 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
18513326 AACGAAATAG
*
18513336 AAAGAAAAAGAAA-GAAAGA
1 AAAGAAAGAGAAAGGAAAGA
*
18513355 AAAGAAAGAAAAAGGAAAGA
1 AAAGAAAGAGAAAGGAAAGA
* *
18513375 AAGGAAGGAGAAAG
1 AAAGAAAGAGAAAG
18513389 CTACGGCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAGAAAGGAAAGA
Found at i:18514120 original size:21 final size:20
Alignment explanation
Indices: 18514069--18514131 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
18514059 TAGTATATGA
* *
18514069 TGAATTTATTGGATTTATAT
1 TGAATATATTGGATATATAT
*
18514089 TGATTGA-ATTGGTATATATAT
1 TGAAT-ATATTGG-ATATATAT
18514110 TGAATATATT-GAT-TAT-T
1 TGAATATATTGGATATATAT
18514127 TGAAT
1 TGAAT
18514132 TGAAATGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.17
18 3 0.08
19 2 0.06
20 11 0.31
21 14 0.39
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (20 bp):
TGAATATATTGGATATATAT
Found at i:18514271 original size:41 final size:41
Alignment explanation
Indices: 18514227--18514361 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
18514217 GACTTCGAGT
*
18514227 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* * * *
18514268 CGATGAGGCAGTGGGTGCCAATTTACT--TT-GGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* * *
18514305 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* *
18514345 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
18514362 CCTAACTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 22 0.29
38 6 0.08
39 5 0.07
40 19 0.25
41 24 0.32
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (41 bp):
CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
Found at i:18514351 original size:40 final size:40
Alignment explanation
Indices: 18514227--18514361 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
18514217 GACTTCGAGT
* * *
18514227 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * * * *
18514268 CGATGAGGCAGTGGGTG-CCAA-T-TTACTTTGGTTTAAC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
*
18514305 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
18514345 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
18514362 CCTAACTGGT
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 16 0.22
38 12 0.16
39 2 0.03
40 28 0.38
41 15 0.21
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:18523442 original size:40 final size:40
Alignment explanation
Indices: 18523386--18523505 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
18523376 TCAAGATACC
*
18523386 ACAATTTTTTTACTATTTTTAAAAATTTTGAATAATTTTTT
1 ACAATTTTTTTACTATTTCTAAAAATTTT-AATAATTTTTT
* *
18523427 ACAA-TTTTTTACTATTTCTAATAATTTTTATAATTTTTTT
1 ACAATTTTTTTACTATTTCTAAAAATTTTAATAA-TTTTTT
* *** * *
18523467 ATAA-TACCTTACAATTTCTAATAATTTT-ATAATTTTTT
1 ACAATTTTTTTACTATTTCTAAAAATTTTAATAATTTTTT
18523505 A
1 A
18523506 TAGTTGTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 7 0.10
39 8 0.11
40 51 0.73
41 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (40 bp):
ACAATTTTTTTACTATTTCTAAAAATTTTAATAATTTTTT
Found at i:18523615 original size:10 final size:11
Alignment explanation
Indices: 18523590--18523617 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18523580 TTATTTATAT
18523590 TTTTTTGGTAA
1 TTTTTTGGTAA
18523601 TTTTTTGGTAA
1 TTTTTTGGTAA
18523612 TTTTTT
1 TTTTTT
18523618 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (11 bp):
TTTTTTGGTAA
Found at i:18524342 original size:23 final size:23
Alignment explanation
Indices: 18524316--18524361 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18524306 TGAAATCATC
*
18524316 TAATATATAACT-AAGTTAAATAT
1 TAATAT-TAACTGAAATTAAATAT
*
18524339 TAATATTAATTGAAATTAAATAT
1 TAATATTAACTGAAATTAAATAT
18524362 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
TAATATTAACTGAAATTAAATAT
Found at i:18525186 original size:72 final size:72
Alignment explanation
Indices: 18525069--18525210 Score: 257
Period size: 72 Copynumber: 2.0 Consensus size: 72
18525059 TCTCGGATTT
* *
18525069 AAAAAAGGGATCATACCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATACCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
18525134 CTTGATA
66 CTTGATA
*
18525141 AAAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATACCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
18525206 CTTGA
66 CTTGA
18525211 GTTTGAAAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (72 bp):
AAAAAAGGGATCATACCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGATA
Found at i:18525701 original size:2 final size:2
Alignment explanation
Indices: 18525694--18525800 Score: 128
Period size: 2 Copynumber: 54.0 Consensus size: 2
18525684 TAAAAACGTG
* * * *
18525694 TA TA TA TA TA TA TA TA GA TA TG TA TA TA AA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* **
18525735 TA TA TA AA TA TA -A GTA GG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18525777 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
18525801 AATAGGTTAC
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
1 2 0.02
2 85 0.97
3 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:18527703 original size:44 final size:45
Alignment explanation
Indices: 18527650--18527861 Score: 153
Period size: 44 Copynumber: 4.6 Consensus size: 45
18527640 CAGCTTCATT
* *
18527650 CTGCTCCACTGCAACTTCAGGGAGATAATACTTGTATA-TTCAAC
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTATACTTCAAC
* * **
18527694 TTGCCCCACTACAACTTCAAGGG-GATAAGGTTTGT-TACTTCAAC
1 CTGCCCCACTGCAACTTC-AGGGAGATAAGACTTGTATACTTCAAC
* * * * *
18527738 CTGCTCTACTGCAACTTCAGAGAGATAAGACTTGTAGCCTGTCTTCAAT
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTA---T-ACTTCAAC
* * * * * *
18527787 CTGCTCTACAGCAACTTCAGGGAGATAAGA-TTGGTTTATTTTTAAC
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTT-GTATA-CTTCAAC
* * *
18527833 CTACTCCACTGCAATTTCAGGGAGATAAG
1 CTGCCCCACTGCAACTTCAGGGAGATAAG
18527862 GTTTGATATG
Statistics
Matches: 132, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
43 5 0.04
44 54 0.41
45 4 0.03
46 30 0.23
48 3 0.02
49 36 0.27
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (45 bp):
CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTATACTTCAAC
Found at i:18528222 original size:50 final size:50
Alignment explanation
Indices: 18528168--18528852 Score: 574
Period size: 50 Copynumber: 13.7 Consensus size: 50
18528158 TCAAAGAAAT
* * *
18528168 AAGATTCGCTGTTATAGCTTCAATCTATTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * ** * * *
18528218 AAGATTCACTGTTGTAGCTTCAATATGTTCCACTACACTG-CTAGGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
* * *
18528268 AAGATTCACTGTTGCAGCTTCAACCTATTTAACTGCAATGTC-GGGAAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGG-AAGC
* * * * ** *
18528318 AAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCG-CTAGGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
* *
18528368 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATATCAGGGAGGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* ** * * * **
18528418 AAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTAC-ATCGCCAAGGAAAT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAAT-GTCAGGGAAGC
* **
18528468 AAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * * ** ** *
18528518 AAGATTCACTATTGTAGCTTCAATATGTTCCACTGCACCG-CTAGGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
* *
18528568 AAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * * * *** * * **
18528618 AAGACTCGCTACCTT-TAGCTTTAATTTGTTCCGCTGCAACGTTAGGGAAAT
1 AAGATTCGCT--GTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * *
18528669 AAGATTCGCTGTTATAGCTTCAATCTATTTAACTGTAATGTCGGGGAAAC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * * **
18528719 AAGATTCACTGTTGCAGCTTCAATCTATTTAACCGTAATGTTGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * ** * * *
18528769 AAGATTCGCTGTTGTAGCTTCAACCTGTTCT-ACTGTACCGCCAAGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATT-TAACTGCAATGTCAGGGAAGC
18528819 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACT
18528853 TTAGTCTTAA
Statistics
Matches: 493, Mismatches: 127, Indels: 30
0.76 0.20 0.05
Matches are distributed among these distances:
49 10 0.02
50 438 0.89
51 43 0.09
52 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (50 bp):
AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
Found at i:18528290 original size:100 final size:100
Alignment explanation
Indices: 18528167--18528742 Score: 787
Period size: 100 Copynumber: 5.8 Consensus size: 100
18528157 GTCAAAGAAA
*
18528167 TAAGATTCGCTGTTATAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
* *
18528232 TAGCTTCAATATGTTCCACTACACTGCTAGGGAAG
66 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * *
18528267 TAAGATTCACTGTTGCAGCTTCAACCTATTTAACTGCAATGTC-GGGAAAGCAAGATTCACTGTT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAA-CAAGATTCACTGTT
*
18528331 GTAGCTTCAATATGTTTCACTGCACCGCTAGGGAAG
65 GTAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * ** *
18528367 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATATCAGGGAGGCAAGATTCGCTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
* * * * * *
18528432 TAGCTTCAATCTGTTCCACTACATCGCCAAGGAAA
66 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * * *
18528467 TAAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGAAGCAAGATTCACTATTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
18528532 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
66 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * * * *
18528567 TAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGCTACCT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACT--GT
* * * * * *
18528632 T-TAGCTTTAATTTGTTCCGCTGCAACGTTAGGGAAA
64 TGTAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* *
18528668 TAAGATTCGCTGTTATAGCTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGATTCACTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
*
18528733 CAGCTTCAAT
66 TAGCTTCAAT
18528743 CTATTTAACC
Statistics
Matches: 417, Mismatches: 54, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
99 8 0.02
100 318 0.76
101 89 0.21
102 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (100 bp):
TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
Found at i:18528520 original size:200 final size:199
Alignment explanation
Indices: 18528167--18528844 Score: 847
Period size: 200 Copynumber: 3.4 Consensus size: 199
18528157 GTCAAAGAAA
* * * *
18528167 TAAGATTCGCTGTTATAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
* * * * *
18528232 TAGCTTCAATATGTTCCACTACACTGCTAGGGAAGTAAGATTCACTGTTGCAGCTTCAACCTATT
66 TAGCTTCAATCTGTTCCACTACAC-GCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTATT
*
18528297 TAACTGCAATGTCGGGAAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAG
130 TAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAG
18528362 GGAAG
195 GGAAG
* *
18528367 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATATCAGGGAGGCAAGATTCGCTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
* * *
18528432 TAGCTTCAATCTGTTCCACTACATCGCCAAGGAAATAAGATTCGTTGTTGTAGCTTCAATCTATT
66 TAGCTTCAATCTGTTCCACTACA-CGCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTATT
* * *
18528497 TAACTGCAATGTTGGGGAAGCAAGATTCACTATTGTAGCTTCAATATGTTCCACTGCACCGCTAG
130 TAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAG
18528562 GGAAG
195 GGAAG
* * * *
18528567 TAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGCTACCT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCT--GT
* * * * * *
18528632 T-TAGCTTTAATTTGTTCCGCTGCAACGTTAGGGAAATAAGATTCGCTGTTATAGCTTCAATCTA
64 TGTAGCTTCAATCTGTTCCACTAC-ACGCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTA
* * * * * * * * ** *
18528696 TTTAACTGTAATGTCGGGGAAACAAGATTCACTGTTGCAGCTTCAATCTATTTAACCGTAATGTT
128 TTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCT
*
18528761 GGGGAAG
193 AGGGAAG
* * * * ** * * *
18528768 CAAGATTCGCTGTTGTAGCTTCAACCTGTTCT-ACTGTACCGCCAAGGAAGTAAGATTCGCTGTT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATT-TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTT
18528832 GTAGCTTCAATCT
65 GTAGCTTCAATCT
18528845 ATTTAACTTT
Statistics
Matches: 409, Mismatches: 63, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
199 2 0.00
200 246 0.60
201 157 0.38
202 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (199 bp):
TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
TAGCTTCAATCTGTTCCACTACACGCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTATTT
AACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAGG
GAAG
Found at i:18530272 original size:15 final size:15
Alignment explanation
Indices: 18530252--18530301 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
18530242 TGGCCTCTCT
18530252 TTTTTCTTTTTCTTC
1 TTTTTCTTTTTCTTC
18530267 TTTTTCTTTTTCTT-
1 TTTTTCTTTTTCTTC
* *
18530281 TTCTTTCTTCTTCTCC
1 TT-TTTCTTTTTCTTC
18530297 TTTTT
1 TTTTT
18530302 TTAAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTCTTC
Found at i:18530284 original size:11 final size:12
Alignment explanation
Indices: 18530260--18530292 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18530250 CTTTTTTCTT
18530260 TTTCTTCTTTTTC
1 TTTCTTC-TTTTC
18530273 TTT-TTCTTTTC
1 TTTCTTCTTTTC
18530284 TTTCTTCTT
1 TTTCTTCTT
18530293 CTCCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 8 0.42
13 3 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTCTTTTC
Found at i:18530288 original size:21 final size:21
Alignment explanation
Indices: 18530252--18530294 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
18530242 TGGCCTCTCT
*
18530252 TTTTTCTTTTTCTTCTTTTTC
1 TTTTTCTTTTTCTTCTTCTTC
18530273 TTTTTC-TTTTCTTTCTTCTTC
1 TTTTTCTTTTTC-TTCTTCTTC
18530294 T
1 T
18530295 CCTTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTCTTCTTCTTC
Found at i:18533617 original size:3 final size:3
Alignment explanation
Indices: 18533607--18533650 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
18533597 TTAAATTATT
18533607 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18533651 TAAAGAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18533851 original size:17 final size:17
Alignment explanation
Indices: 18533831--18533863 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18533821 GTGAAGAGTC
18533831 AAGGAAAATGAAAGGTT
1 AAGGAAAATGAAAGGTT
*
18533848 AAGGAAGATGAAAGGT
1 AAGGAAAATGAAAGGT
18533864 GAAAAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (17 bp):
AAGGAAAATGAAAGGTT
Found at i:18541173 original size:22 final size:21
Alignment explanation
Indices: 18541148--18541227 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 21
18541138 TACAAATTAA
* *
18541148 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTGC-ATATCAT
18541170 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTGCATATCAT
18541192 ATC-C-AAGATTGCATATCAT
1 ATCTCTAAGATTGCATATCAT
18541211 A--TCTAAGATTGCATATC
1 ATCTCTAAGATTGCATATC
18541228 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.02
19 29 0.55
20 1 0.02
22 12 0.23
23 10 0.19
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCTAAGATTGCATATCAT
Found at i:18541826 original size:44 final size:45
Alignment explanation
Indices: 18541752--18541913 Score: 112
Period size: 45 Copynumber: 3.6 Consensus size: 45
18541742 ATTCTAATCC
* * * * *
18541752 ACCCCACTACAACTTT-AGGGAGACAGGATTT-GTTTATTTAGTCT
1 ACCCCACTGCAA-TTTCAGGGAGATAAGATTTACTTTATTGAGTCT
* *
18541796 ACCCCACTGCAATTTCAGGGGGATAAGATTTACTTTCTTGAGTCT
1 ACCCCACTGCAATTTCAGGGAGATAAGATTTACTTTATTGAGTCT
*** * * ** * *
18541841 GTTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCT
1 ACCCCACTGCAATTTCAGGGAGATAAGATTTACTTTATTGAGTCT
* * * * *
18541886 GCTCCTCCGCAACTTCAGGGAGATAAGA
1 ACCCCACTGCAATTTCAGGGAGATAAGA
18541914 CCTGATATCT
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
43 3 0.03
44 23 0.24
45 71 0.73
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (45 bp):
ACCCCACTGCAATTTCAGGGAGATAAGATTTACTTTATTGAGTCT
Found at i:18541848 original size:45 final size:45
Alignment explanation
Indices: 18541799--18541914 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
18541789 TTAGTCTACC
* * * * *
18541799 CCACTGCAATTTCAGGGGGATAAGATTTACTTTCTTGAGTCTGTT
1 CCACTGCAACTTCAGGGAGATAAGACTCACTTTCTTGAGTCTGCT
* *
18541844 CCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCACTTTCTTGAGTCTGCT
* *
18541889 CCTCCGCAACTTCAGGGAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
18541915 CTGATATCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTCACTTTCTTGAGTCTGCT
Found at i:18542161 original size:44 final size:45
Alignment explanation
Indices: 18542037--18542252 Score: 116
Period size: 44 Copynumber: 4.9 Consensus size: 45
18542027 ATAAGACTGG
* * * * *
18542037 TGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTAC
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* * * * * ** *
18542082 TATCTTCAGTCTGCTCCGCT-ACAACCCAGGGAGGCAAG-GCTAA
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* * *
18542125 TGTCTTTGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTAC
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* **** * * * ** * **
18542170 TATCTTTAACCTGCTCCACT-ACGACCCAGGGAGGCAAG-GCTGG
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* * *
18542213 TATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGA
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGA
18542253 TCTGCTGTCT
Statistics
Matches: 120, Mismatches: 47, Indels: 8
0.69 0.27 0.05
Matches are distributed among these distances:
43 36 0.30
44 51 0.43
45 33 0.28
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (45 bp):
TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
Found at i:18542186 original size:88 final size:88
Alignment explanation
Indices: 18542033--18542474 Score: 643
Period size: 88 Copynumber: 5.0 Consensus size: 88
18542023 TTCGATAAGA
* * * * **
18542033 CTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTACTATCTTCAGTCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
*
18542098 CGCTACAACCCAGGGAGGCAAGG
66 CACTACAACCCAGGGAGGCAAGG
** * * * * *
18542121 CTAATGTCTTTGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTACTATCTTTAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
*
18542186 CACTACGACCCAGGGAGGCAAGG
66 CACTACAACCCAGGGAGGCAAGG
* *
18542209 CTGGTATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
*
18542274 TACTACAACCCAGGGAGGCAAGG
66 CACTACAACCCAGGGAGGCAAGG
* *
18542297 CTGGTATCTTCGATCTACTTCGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
* *
18542362 CACTACGACCCAGGGAGGCAAGA
66 CACTACAACCCAGGGAGGCAAGG
*
18542385 CTGGTATCTTCGATCTGCTTCGCTATCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
* *
18542450 CACAACGAA-CCAGGGAGACAAGG
66 CACTAC-AACCCAGGGAGGCAAGG
18542473 CT
1 CT
18542475 TTGTGATTTC
Statistics
Matches: 317, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 316 1.00
89 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (88 bp):
CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
CACTACAACCCAGGGAGGCAAGG
Found at i:18542293 original size:44 final size:44
Alignment explanation
Indices: 18542152--18542463 Score: 195
Period size: 44 Copynumber: 7.1 Consensus size: 44
18542142 GCTGTCGATG
* * *
18542152 CAGGAAGGCAAGATCTACTATCTTTAACCTGCTCCACTACGACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
* * * * * * * * **
18542196 CAGGGAGGCAAG-GCTGGTATCTTCGATCTGCT-TCGCTGTCAATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCT-ACT-ACGACC
* *
18542240 CAGGAAGGCAAGATCTGCTGTCTTCAACCTGCTCTACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
* * * * * * * * **
18542284 CAGGGAGGCAAG-GCTGGTATCTTCGATCTACT-TCGCTGTCGATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCT-ACT-ACGACC
* *
18542328 TAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
* * * * * **
18542372 CAGGGAGGCAAGA-CTGGTATCTTCGATCTGCT-TCGCTATCGATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCT-ACTA-CGACC
* * *
18542416 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACAACGAAC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
18542460 CAGG
1 CAGG
18542464 GAGACAAGGC
Statistics
Matches: 191, Mismatches: 65, Indels: 24
0.68 0.23 0.09
Matches are distributed among these distances:
42 1 0.01
43 51 0.27
44 86 0.45
45 52 0.27
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
Found at i:18546823 original size:41 final size:41
Alignment explanation
Indices: 18546766--18546992 Score: 357
Period size: 41 Copynumber: 5.5 Consensus size: 41
18546756 TTTAACAATT
* *
18546766 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
18546807 TCACCAGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
18546848 TCA-CGGCACTTCGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
18546888 TCACCGGCACTTAGCTTGGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCT-GCTAGGTTTATAACCTGATTCAGA
* ** *
18546930 TTACTAGAACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
18546971 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
18546993 ACGTATAGTC
Statistics
Matches: 168, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 38 0.23
41 94 0.56
42 36 0.21
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:18546967 original size:83 final size:81
Alignment explanation
Indices: 18546774--18546992 Score: 348
Period size: 83 Copynumber: 2.7 Consensus size: 81
18546764 TTTCACCGGC
* * *
18546774 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCAGCACTTAGCCTGCTAGGTTTATAACC
1 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACC
* *
18546839 TGATTCAGATCACGGC
66 TGATTCAGATCACAGA
* *
18546855 ACTTCGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCTTGGCTAGGTTTATAAC
1 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCT-GCTAGGTTTATAAC
*
18546920 CTGATTCAGATTACTAGA
65 CTGATTCAGATCAC-AGA
18546938 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAG
1 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAG
18546993 ACGTATAGTC
Statistics
Matches: 126, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
81 45 0.36
82 32 0.25
83 49 0.39
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (81 bp):
ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACC
TGATTCAGATCACAGA
Found at i:18550730 original size:22 final size:21
Alignment explanation
Indices: 18550705--18550784 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 21
18550695 TACAAATTAA
* *
18550705 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTGC-ATATCAT
18550727 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTGCATATCAT
18550749 ATC-C-AAGATTGCATATCAT
1 ATCTCTAAGATTGCATATCAT
18550768 A--TCTAAGATTGCATATC
1 ATCTCTAAGATTGCATATC
18550785 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.02
19 29 0.55
20 1 0.02
22 12 0.23
23 10 0.19
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCTAAGATTGCATATCAT
Found at i:18552278 original size:105 final size:106
Alignment explanation
Indices: 18552132--18552343 Score: 297
Period size: 105 Copynumber: 2.0 Consensus size: 106
18552122 ATGGATTGAG
* * *
18552132 ATTTAAGAGGATATTAGGCTATTTGGTTCAACAAGAAATCGAAACCCAGCACGTTAGGGCACGTT
1 ATTTAAAAGGATATTAGGCTATTTGGTTCAACAAGAAATCGAAACCCAGCACATTAGGGCACGAT
* *
18552197 TTCTCGAATTTCCAAATGCAAAATATTG-CCTATTTTGAAA
66 TTCTCGAATTTCCAAACGCAAAATATTGTCCTATTTAGAAA
*
18552237 ATTTAAAAGGATATTTTA-GCTATTTGG-TCGAACGA-AAATCGAAACCCAGCACATTAGGGCAC
1 ATTTAAAAGGATA--TTAGGCTATTTGGTTC-AACAAGAAATCGAAACCCAGCACATTAGGGCAC
* *
18552299 GATTTCTCGGATTTCCAAACGCAAAATATTGTCTTATTTAGAAA
63 GATTTCTCGAATTTCCAAACGCAAAATATTGTCCTATTTAGAAA
18552343 A
1 A
18552344 ATTTTCCTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
105 68 0.72
106 24 0.25
107 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (106 bp):
ATTTAAAAGGATATTAGGCTATTTGGTTCAACAAGAAATCGAAACCCAGCACATTAGGGCACGAT
TTCTCGAATTTCCAAACGCAAAATATTGTCCTATTTAGAAA
Found at i:18552932 original size:12 final size:12
Alignment explanation
Indices: 18552917--18552947 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18552907 ATATAATAAG
18552917 ATATAAAGATAT
1 ATATAAAGATAT
*
18552929 ATATAAAGATGT
1 ATATAAAGATAT
18552941 ATATAAA
1 ATATAAA
18552948 TAGTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (12 bp):
ATATAAAGATAT
Found at i:18553095 original size:3 final size:3
Alignment explanation
Indices: 18553087--18553153 Score: 50
Period size: 3 Copynumber: 23.3 Consensus size: 3
18553077 ATATATAAAT
** * * *
18553087 ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA CT- ATA TTA ATG AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
18553133 ATA AT- ATA ATA GTA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
18553154 GACTTAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 5 0.10
3 45 0.90
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18555293 original size:2 final size:2
Alignment explanation
Indices: 18555286--18555317 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18555276 AGTATACTTC
18555286 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
18555318 GGGATATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18555390 original size:25 final size:25
Alignment explanation
Indices: 18555366--18555413 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
18555356 AAAATGGTTA
*
18555366 TAAGA-AAATGAAAGGTGAAGAG-T
1 TAAGAGAAATGAAAGGTGAAAAGTT
*
18555389 TAAGAGAGATGAAAGGTGAAAAGTT
1 TAAGAGAAATGAAAGGTGAAAAGTT
18555414 GAACATTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 15 0.71
25 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (25 bp):
TAAGAGAAATGAAAGGTGAAAAGTT
Found at i:18558414 original size:18 final size:19
Alignment explanation
Indices: 18558388--18558423 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18558378 ATAAGTGTGT
*
18558388 GATTCAACA-ATATTTAAA
1 GATTAAACAGATATTTAAA
18558406 GATTAAACAGATATTTAA
1 GATTAAACAGATATTTAA
18558424 TAAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (19 bp):
GATTAAACAGATATTTAAA
Found at i:18563912 original size:21 final size:21
Alignment explanation
Indices: 18563870--18563912 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
18563860 GTCGAAAAAT
*
18563870 ATATAAAATTTTATATTATCC
1 ATATAAAAATTTATATTATCC
*
18563891 ATATAATAAATTTA-ATTCTCC
1 ATATAA-AAATTTATATTATCC
18563912 A
1 A
18563913 ATATTTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAAAAATTTATATTATCC
Found at i:18567956 original size:16 final size:16
Alignment explanation
Indices: 18567935--18567974 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
18567925 CGTTTGGTTC
*
18567935 ACTGTAATGGAATAGA
1 ACTGTAATGAAATAGA
18567951 ACTGTAATGAAATAGA
1 ACTGTAATGAAATAGA
*
18567967 GCTGTAAT
1 ACTGTAAT
18567975 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (16 bp):
ACTGTAATGAAATAGA
Found at i:18571445 original size:30 final size:30
Alignment explanation
Indices: 18571409--18571484 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
18571399 TGGTTGACAC
* *
18571409 ATCCCTTTTCATAATTCGATAACCGAAGTT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
* **
18571439 ATCCCTTTTCATAGTTCGACAGTCGAAGCT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
18571469 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
18571485 TGATGGTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCGAAGCT
Found at i:18571569 original size:30 final size:31
Alignment explanation
Indices: 18571528--18571601 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
18571518 CGGTCGTCAC
* **
18571528 CATCCATTTTCATAAT-TTGATAGCCGAAGAT
1 CATCCCTTTTCATAATATCAATAGCCGAAG-T
18571559 -ATCCCTTTTCAT-ATATCAATAGCCGAAGT
1 CATCCCTTTTCATAATATCAATAGCCGAAGT
18571588 CATCCCTTTTCATA
1 CATCCCTTTTCATA
18571602 GTTGGATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 3 0.08
30 34 0.92
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (31 bp):
CATCCCTTTTCATAATATCAATAGCCGAAGT
Found at i:18571621 original size:120 final size:119
Alignment explanation
Indices: 18571408--18571715 Score: 361
Period size: 120 Copynumber: 2.6 Consensus size: 119
18571398 ATGGTTGACA
* * * *
18571408 CATCCCTTTTCATAATTCGATAACCGAAGTTATCCCTTTTCATAGT-TCGACAGTCGAAG-CTAT
1 CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATA-TATCAATAGTCGAAGTC-AT
* ** *
18571471 CCCTTTTCATAATTTGATGGTCGTCACCATCCATTTTAATTTTTCGACGGTCGTCAC
64 CCCTTTTCATAATTGGATAATCGTCACCATCCATTTTAATTGTTC-ACGGTCGTCAC
* * *
18571528 CATCCATTTTCATAATTTGATAGCCGAAGATATCCCTTTTCATATATCAATAGCCGAAGTCATCC
1 CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATATATCAATAGTCGAAGTCATCC
* * * * * * *
18571593 CTTTTCATAGTTGGATAATCGTCCCCATCCCTTTTCATTGTTCATGGTTGTCTC
66 CTTTTCATAATTGGATAATCGTCACCATCCATTTTAATTGTTCACGGTCGTCAC
* * * * *
18571647 CTTCCCTTTTCATAA-TCGATAGCTGAAGCTATCCCTTTTCATAGATCAATAGTCGAAGTTATCC
1 CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATATATCAATAGTCGAAGTCATCC
18571711 CTTTT
66 CTTTT
18571716 TATTCATCGA
Statistics
Matches: 160, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
118 48 0.30
119 22 0.14
120 89 0.56
121 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (119 bp):
CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATATATCAATAGTCGAAGTCATCC
CTTTTCATAATTGGATAATCGTCACCATCCATTTTAATTGTTCACGGTCGTCAC
Found at i:18571681 original size:29 final size:30
Alignment explanation
Indices: 18571649--18571715 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
18571639 GTTGTCTCCT
*
18571649 TCCCTTTTCATA-ATCGATAG-CTGAAGCTA
1 TCCCTTTTCATAGATCAATAGTC-GAAGCTA
*
18571678 TCCCTTTTCATAGATCAATAGTCGAAGTTA
1 TCCCTTTTCATAGATCAATAGTCGAAGCTA
18571708 TCCCTTTT
1 TCCCTTTT
18571716 TATTCATCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 12 0.35
30 21 0.62
31 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (30 bp):
TCCCTTTTCATAGATCAATAGTCGAAGCTA
Found at i:18578677 original size:25 final size:25
Alignment explanation
Indices: 18578645--18578700 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
18578635 ATCATCATCA
*
18578645 AAAT-GCTAAACCACAAGCCAAAAC
1 AAATGGCTAAACCAAAAGCCAAAAC
** *
18578669 AAATGGCTATTCCAAAATCCAAAAC
1 AAATGGCTAAACCAAAAGCCAAAAC
*
18578694 ACATGGC
1 AAATGGC
18578701 CAACATTAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.48, C:0.27, G:0.11, T:0.14
Consensus pattern (25 bp):
AAATGGCTAAACCAAAAGCCAAAAC
Found at i:18579160 original size:30 final size:30
Alignment explanation
Indices: 18579126--18579189 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
18579116 AGCCGAAGCT
*
18579126 ATCCCTGTTCATTATTTGATGGTCATCACC
1 ATCCCTGTTCATTATTCGATGGTCATCACC
* * **
18579156 ATCCCTTTTCATTGTTCGATGGTTTTCACC
1 ATCCCTGTTCATTATTCGATGGTCATCACC
18579186 ATCC
1 ATCC
18579190 TTTTTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.12, T:0.42
Consensus pattern (30 bp):
ATCCCTGTTCATTATTCGATGGTCATCACC
Found at i:18581060 original size:16 final size:14
Alignment explanation
Indices: 18581042--18581087 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
18581032 GGTCTAGTTT
18581042 AGTA-TTGCTTTTG
1 AGTAGTTGCTTTTG
18581055 AGTAG-TGCTTTTG
1 AGTAGTTGCTTTTG
18581068 AGTAG-TGCTTTTG
1 AGTAGTTGCTTTTG
*
18581081 AGAAGTT
1 AGTAGTT
18581088 TTGTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 29 0.97
14 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (14 bp):
AGTAGTTGCTTTTG
Found at i:18581063 original size:13 final size:13
Alignment explanation
Indices: 18581042--18581082 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
18581032 GGTCTAGTTT
*
18581042 AGTATTGCTTTTG
1 AGTAGTGCTTTTG
18581055 AGTAGTGCTTTTG
1 AGTAGTGCTTTTG
18581068 AGTAGTGCTTTTG
1 AGTAGTGCTTTTG
18581081 AG
1 AG
18581083 AAGTTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.17, C:0.07, G:0.29, T:0.46
Consensus pattern (13 bp):
AGTAGTGCTTTTG
Found at i:18583483 original size:80 final size:80
Alignment explanation
Indices: 18583376--18583534 Score: 318
Period size: 80 Copynumber: 2.0 Consensus size: 80
18583366 AGCAAGTGAC
18583376 TAAAAAATTGAAAGAAATACTTAAGCAAATTACGCAAATAAAATATAGCAAACTTAAAAAATATC
1 TAAAAAATTGAAAGAAATACTTAAGCAAATTACGCAAATAAAATATAGCAAACTTAAAAAATATC
18583441 ATAAGAGAAAGGAAG
66 ATAAGAGAAAGGAAG
18583456 TAAAAAATTGAAAGAAATACTTAAGCAAATTACGCAAATAAAATATAGCAAACTTAAAAAATATC
1 TAAAAAATTGAAAGAAATACTTAAGCAAATTACGCAAATAAAATATAGCAAACTTAAAAAATATC
18583521 ATAAGAGAAAGGAA
66 ATAAGAGAAAGGAA
18583535 ATCTAAAACA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (80 bp):
TAAAAAATTGAAAGAAATACTTAAGCAAATTACGCAAATAAAATATAGCAAACTTAAAAAATATC
ATAAGAGAAAGGAAG
Found at i:18585947 original size:72 final size:72
Alignment explanation
Indices: 18585734--18585993 Score: 285
Period size: 72 Copynumber: 3.6 Consensus size: 72
18585724 AATAAACTTT
* * * * *
18585734 ATATCCAAAATC-AAATATAAACAACTATTGATAAAACTA-ATTTAGTATAACTAAGTAGAACAT
1 ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAGACTTAATATAAATAAGTAGAACAT
18585797 AAATTCA
66 AAATTCA
* * * * * *
18585804 ATATCCAAAAAAAAAAAAAACATAAACAATTATTAATAAAAAT-GACCCTAAGCATAAATAAGTA
1 ATATCC----AAAAACAAAACATAAACAACTATTGATAAAACTAGA-CTTAA-TATAAATAAGTA
*
18585868 GACCATAAATTCA
60 GAACATAAATTCA
* *
18585881 ATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAGA-TTACATATAAATAAGTAGAACA
1 ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAGACTTA-ATATAAATAAGTAGAACA
18585945 TAAATTCA
65 TAAATTCA
**
18585953 ATATTAAAAAACAAAACATAAACAACTATTGATAAAACTAG
1 ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAG
18585994 TTTAGCATTG
Statistics
Matches: 155, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
70 6 0.04
72 62 0.40
73 28 0.18
74 6 0.04
75 23 0.15
76 2 0.01
77 28 0.18
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAGACTTAATATAAATAAGTAGAACAT
AAATTCA
Found at i:18599483 original size:9 final size:9
Alignment explanation
Indices: 18599469--18599529 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
18599459 ATAATTTTAT
18599469 TTTTTAAAA
1 TTTTTAAAA
18599478 TTTTTAATAA
1 TTTTTAA-AA
*
18599488 TTTTAAAAA
1 TTTTTAAAA
* *
18599497 TTTTCATAA
1 TTTTTAAAA
**
18599506 TTGTTTGCAA
1 TT-TTTAAAA
*
18599516 TTTTTATAA
1 TTTTTAAAA
18599525 TTTTT
1 TTTTT
18599530 TATTATTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 28 0.67
10 14 0.33
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:18599491 original size:18 final size:18
Alignment explanation
Indices: 18599440--18599507 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
18599430 CATTTTTAAT
18599440 ATTTCTAATAATTTCTTAAATA
1 ATTT-TAATAA-TT-TTAAA-A
*
18599462 ATTTT-AT-TTTTTAAAA
1 ATTTTAATAATTTTAAAA
*
18599478 TTTTTAATAATTTTAAAA
1 ATTTTAATAATTTTAAAA
*
18599496 ATTTTCATAATT
1 ATTTTAATAATT
18599508 GTTTGCAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 5 0.13
17 7 0.18
18 20 0.51
20 2 0.05
21 1 0.03
22 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATAATTTTAAAA
Found at i:18604247 original size:30 final size:30
Alignment explanation
Indices: 18604182--18604249 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
18604172 ATAGTTGGAT
* * * *
18604182 ACCAGATTATTCTAGATTATCATCTTACTTT
1 ACCA-ATTATTCCAGATTATCACCTCACTTC
*
18604213 ACCAATTATTCCAGATTATCGCCTCACTTC
1 ACCAATTATTCCAGATTATCACCTCACTTC
18604243 ACCAATT
1 ACCAATT
18604250 TTTATGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (30 bp):
ACCAATTATTCCAGATTATCACCTCACTTC
Found at i:18605874 original size:19 final size:20
Alignment explanation
Indices: 18605832--18605880 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
18605822 TTAGTATTTG
*
18605832 TAAAATATAATTTGAATATA
1 TAAAATATAATTTAAATATA
* *
18605852 TAAATTATATTTTAAATAT-
1 TAAAATATAATTTAAATATA
18605871 TAAAATATAA
1 TAAAATATAA
18605881 CATTATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAATATAATTTAAATATA
Found at i:18618129 original size:19 final size:18
Alignment explanation
Indices: 18618107--18618151 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
18618097 TCTATTTTAG
18618107 TTATTTTT-TTAGTTGTGAT
1 TTATTTTTGTTAGTTGT--T
18618126 TTATTTATTGTTAGTTGTT
1 TTATTT-TTGTTAGTTGTT
18618145 TTATTTT
1 TTATTTT
18618152 ATTTTTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 2 0.08
21 8 0.33
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (18 bp):
TTATTTTTGTTAGTTGTT
Found at i:18618133 original size:23 final size:21
Alignment explanation
Indices: 18618101--18618157 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
18618091 TAGTTTTCTA
*
18618101 TTTTAGTTATTTTTTTAGTTG
1 TTTTATTTATTTTTTTAGTTG
*
18618122 TGATTTATTTA--TTGTTAGTTG
1 T--TTTATTTATTTTTTTAGTTG
18618143 TTTTATTTTATTTTT
1 TTTTA-TTTATTTTT
18618158 GAGACTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 11 0.39
22 2 0.07
23 7 0.25
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (21 bp):
TTTTATTTATTTTTTTAGTTG
Found at i:18621207 original size:30 final size:30
Alignment explanation
Indices: 18621173--18621233 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
18621163 TCCGGTGATA
* *
18621173 GAAAAATGCAACGCTTGTTCGTTGATCGTT
1 GAAAAATGCAACGCTTATTCATTGATCGTT
*
18621203 GAAAAATGCAACGTTTATTCATTGATCGTT
1 GAAAAATGCAACGCTTATTCATTGATCGTT
18621233 G
1 G
18621234 TAGAGGTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (30 bp):
GAAAAATGCAACGCTTATTCATTGATCGTT
Found at i:18621995 original size:88 final size:86
Alignment explanation
Indices: 18621698--18622107 Score: 328
Period size: 88 Copynumber: 4.7 Consensus size: 86
18621688 TTGTTTCCAA
* ** ** * *
18621698 ATTAAAAGTAAATAAAATCCGTTTCATGATTTATTCCCGCCATTCAACGGATTTTATTCTATTAT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAAC-GATTTTA-T-TA-CA-
* * ***
18621763 TTTTAATTTTATTTCCAAACGGGA-T
61 TTTTGATTTTTTTTCCAAAAATGAGT
* * ** * * *
18621788 ATTAAAGTTAAATAAAACCCGTTTCGGGATTTATTCCCGTCGTTCAATGGATTTTATTCCAATTT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAA-CGATTTTATTAC-ATTT
* *
18621853 TGATTTTATTACCAAAAATGAGT
64 TGATTTTTTTTCCAAAAATGAGT
* * * *
18621876 ATTAAAATTAAAATAAAATCTGTTTCAGGATTTATTCCCACCGTTCAACGAATTTATTACATTTT
1 ATTAAAATT-AAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAACGATTTTATTACATTTT
*
18621941 GATTTTTTTTGCCAAAAATGAGAA
65 GATTTTTTTT-CCAAAAATGAG-T
* *
18621965 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCTGCCGTTTAACAAGATTTTATTTA-ATT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAAC--GATTTTA-TTACATT
* * *
18622029 TT-ATGTTGTTTCC--AAATTAGT
63 TTGATTTTTTTTCCAAAAATGAGT
* * * *
18622050 ATT-AAATTAAATAAAATCTATTTTGAGATTTATTCCCGCTGTTTAACAAGATTTTATT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAAC--GATTTTATT
18622108 TTATTTTATT
Statistics
Matches: 270, Mismatches: 41, Indels: 25
0.80 0.12 0.07
Matches are distributed among these distances:
83 2 0.01
84 49 0.18
85 3 0.01
86 6 0.02
87 32 0.12
88 67 0.25
89 50 0.19
90 58 0.21
91 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (86 bp):
ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAACGATTTTATTACATTTTG
ATTTTTTTTCCAAAAATGAGT
Found at i:18626029 original size:3 final size:3
Alignment explanation
Indices: 18626006--18626077 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
18625996 TATAAACAAA
* * * *
18626006 AAT AA- AAT AAT AA- AACC AAT AAT AAT AGT AAT AAT AGT AAT AAC
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
18626050 AAT AAT AAT ACT AAT AAAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
18626078 TTAAACTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.80
4 5 0.09
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:18626077 original size:24 final size:24
Alignment explanation
Indices: 18626014--18626096 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 24
18626004 AAAATAAAAT
*
18626014 AATAAAACCAATAATAATAGTAATA
1 AATAAAA-CAATAATAATACTAATA
18626039 ATAGTAATAACAATAATAATACTAATA
1 A-A-TAA-AACAATAATAATACTAATA
* * *
18626066 AATAAAATAATATTAA-ACTAAAAA
1 AATAAAACAATAATAATACT-AATA
18626090 AATAAAA
1 AATAAAA
18626097 TAGCACAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
23 3 0.06
24 19 0.38
25 4 0.08
26 2 0.04
27 20 0.40
28 2 0.04
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.25
Consensus pattern (24 bp):
AATAAAACAATAATAATACTAATA
Found at i:18632753 original size:13 final size:14
Alignment explanation
Indices: 18632737--18632774 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18632727 TGTCCATTCA
18632737 ACATTTCATAT-TT
1 ACATTTCATATGTT
*
18632750 ACATTTCATGTGTT
1 ACATTTCATATGTT
*
18632764 CCATTTCATAT
1 ACATTTCATAT
18632775 ATTTGTTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (14 bp):
ACATTTCATATGTT
Found at i:18644096 original size:24 final size:24
Alignment explanation
Indices: 18644069--18644125 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
18644059 AAGATTTAGT
*
18644069 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
18644093 ATTTATTAGCATAATATATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
18644117 ATTGATTAG
1 ATTTATTAG
18644126 AATTAGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:18645486 original size:30 final size:30
Alignment explanation
Indices: 18645450--18645518 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
18645440 TGAAGCAAGT
18645450 AGAGCTACAGATTGATCCAGAATATACAAC
1 AGAGCTACAGATTGATCCAGAATATACAAC
*
18645480 AGAGCTATAGATTGATCCAGAATATACAAC
1 AGAGCTACAGATTGATCCAGAATATACAAC
18645510 AGAGTCTAC
1 AGAG-CTAC
18645519 TCCTCATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (30 bp):
AGAGCTACAGATTGATCCAGAATATACAAC
Found at i:18647478 original size:24 final size:24
Alignment explanation
Indices: 18647422--18647479 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
18647412 GAAGAATTAG
* *
18647422 TATTTATTAGTATGATATATTTAA
1 TATTTATTAGCATAATATATTTAA
* *
18647446 CATTTATTAGCATAATATATTTCA
1 TATTTATTAGCATAATATATTTAA
*
18647470 TATTGATTAG
1 TATTTATTAG
18647480 AATTAGGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (24 bp):
TATTTATTAGCATAATATATTTAA
Found at i:18650518 original size:54 final size:54
Alignment explanation
Indices: 18650427--18650550 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
18650417 TCTTAAATCC
* * * * *
18650427 TGTAACTCACTGAGTT-AGATCACACGGCCGTGTCGCAGGCCATGTGCCAGATCG
1 TGTAACTCACTGACTTGTGA-CACACGGCCATGTCGCAGGCCATGTGCCAGACCA
* * * *
18650481 TGTAACTCTCTGACTTGTGACACATGGCCATGTCGCAGGCCGTGTGCTAGACCA
1 TGTAACTCACTGACTTGTGACACACGGCCATGTCGCAGGCCATGTGCCAGACCA
*
18650535 TGTTACTCACTGACTT
1 TGTAACTCACTGACTT
18650551 CAAATAACAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 56 0.97
55 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (54 bp):
TGTAACTCACTGACTTGTGACACACGGCCATGTCGCAGGCCATGTGCCAGACCA
Found at i:18654536 original size:17 final size:17
Alignment explanation
Indices: 18654514--18654574 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
18654504 GACTTGATTT
*
18654514 TTATTTTTGTTTTTTTA
1 TTATTTGTGTTTTTTTA
18654531 TTATTTGTGTTTTTTT-
1 TTATTTGTGTTTTTTTA
* *
18654547 TTGTGTGTGTGTTTGTTTA
1 TTAT-T-TGTGTTTTTTTA
18654566 TT-TTTGTGT
1 TTATTTGTGT
18654575 ATAGCATTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.21
17 17 0.45
18 11 0.29
19 2 0.05
ACGTcount: A:0.07, C:0.00, G:0.18, T:0.75
Consensus pattern (17 bp):
TTATTTGTGTTTTTTTA
Found at i:18654545 original size:16 final size:15
Alignment explanation
Indices: 18654511--18654574 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 15
18654501 TTGGACTTGA
18654511 TTTTTATTTTTGT-T
1 TTTTTATTTTTGTGT
18654525 TTTTTATTATTTGTGT
1 TTTTTATT-TTTGTGT
*
18654541 TTTTTTTTGTGTGTGTGT
1 TTTTTATT-T-T-TGTGT
18654559 TTGTTTATTTTTGTGT
1 TT-TTTATTTTTGTGT
18654575 ATAGCATTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 8 0.19
15 5 0.12
16 14 0.33
17 2 0.05
18 8 0.19
19 5 0.12
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTTGTGT
Found at i:18657212 original size:19 final size:20
Alignment explanation
Indices: 18657175--18657213 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18657165 TTTTGGATGA
*
18657175 TGAACTAAGTTGTAATAAAC
1 TGAACTAAATTGTAATAAAC
18657195 TGAACTAAATTG-AATAAAC
1 TGAACTAAATTGTAATAAAC
18657214 CTAAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (20 bp):
TGAACTAAATTGTAATAAAC
Found at i:18672775 original size:24 final size:24
Alignment explanation
Indices: 18672748--18672798 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
18672738 TGGTTTGTAT
18672748 TTGTAATATGATTAATAACGCTCG
1 TTGTAATATGATTAATAACGCTCG
18672772 TTGTAATATGATTAATAACGCTCG
1 TTGTAATATGATTAATAACGCTCG
18672796 TTG
1 TTG
18672799 AGTTAATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (24 bp):
TTGTAATATGATTAATAACGCTCG
Found at i:18675405 original size:13 final size:13
Alignment explanation
Indices: 18675387--18675411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18675377 AGAAGAATGG
18675387 AAAAAAGGAAATA
1 AAAAAAGGAAATA
18675400 AAAAAAGGAAAT
1 AAAAAAGGAAAT
18675412 GAAGTAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAAAGGAAATA
Found at i:18676552 original size:21 final size:21
Alignment explanation
Indices: 18676528--18676577 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
18676518 CTTTTTTCTG
*
18676528 TTTT-TTAATTGTTTTTCCTTT
1 TTTTATTAATTGGTTTT-CTTT
*
18676549 TTTTATTATTTGGTTTTCTTT
1 TTTTATTAATTGGTTTTCTTT
18676570 TTTTATTA
1 TTTTATTA
18676578 TTTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTATTAATTGGTTTTCTTT
Found at i:18676578 original size:21 final size:22
Alignment explanation
Indices: 18676540--18676580 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
18676530 TTTTAATTGT
18676540 TTTTCCTTTTTTTATTATTTGG
1 TTTTCCTTTTTTTATTATTTGG
18676562 TTTT-CTTTTTTTATTATTT
1 TTTTCCTTTTTTTATTATTT
18676581 ATTATTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTTCCTTTTTTTATTATTTGG
Found at i:18680707 original size:25 final size:25
Alignment explanation
Indices: 18680679--18680734 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
18680669 GCTCACATGT
*
18680679 GCTTACCATTATTTAG-CTCGGAGGA
1 GCTTACCATTATTCAGCCT-GGAGGA
* *
18680704 GCTTATCGTTATTCAGCCTGGAGGA
1 GCTTACCATTATTCAGCCTGGAGGA
18680729 GCTTAC
1 GCTTAC
18680735 TGTTTATAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (25 bp):
GCTTACCATTATTCAGCCTGGAGGA
Found at i:18687626 original size:12 final size:12
Alignment explanation
Indices: 18687609--18687729 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
18687599 TTATAATAAT
* *
18687609 AATAAACAAATA
1 AATAAAAAAACA
18687621 AATAAAAAAACA
1 AATAAAAAAACA
18687633 AATAAAAAAGA-A
1 AATAAAAAA-ACA
* *
18687645 AA-AGGACAAACA
1 AATA-AAAAAACA
18687657 AAT-AAAAAACA
1 AATAAAAAAACA
* *
18687668 GA-AAAAAGACA
1 AATAAAAAAACA
*
18687679 AACAAATAAAA-A
1 AATAAA-AAAACA
**
18687691 AATAGAAAAAGGA
1 AATA-AAAAAACA
18687704 AATAAAGAAAAACA
1 AAT-AA-AAAAACA
18687718 AATAAAAAAACA
1 AATAAAAAAACA
18687730 TAAAAAGGAC
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
11 17 0.20
12 45 0.54
13 13 0.15
14 9 0.11
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (12 bp):
AATAAAAAAACA
Found at i:18687672 original size:26 final size:25
Alignment explanation
Indices: 18687628--18687703 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 25
18687618 ATAAATAAAA
18687628 AAACAAAT-AAAAAAGAAAAAGGAC
1 AAACAAATAAAAAAAGAAAAAGGAC
*
18687652 AAACAAATAAAAAACAGAAAAAAGAC
1 AAACAAATAAAAAA-AGAAAAAGGAC
18687678 AAACAAATAAAAAAATAGAAAAAGGA
1 AAACAAAT-AAAAAA-AGAAAAAGGA
18687704 AATAAAGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.17
25 5 0.11
26 18 0.39
27 15 0.33
ACGTcount: A:0.76, C:0.08, G:0.11, T:0.05
Consensus pattern (25 bp):
AAACAAATAAAAAAAGAAAAAGGAC
Found at i:18687680 original size:62 final size:62
Alignment explanation
Indices: 18687614--18687741 Score: 152
Period size: 62 Copynumber: 2.1 Consensus size: 62
18687604 ATAATAATAA
* * * *
18687614 ACAAATAAATAAAAAAACAAATAAAAAAGAAA-AAGGACAAACAAAT-AAAAAACAGAAAAAAG
1 ACAAACAAAT-AAAAAA-AAAGAAAAAAGAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAG
* * * *
18687676 ACAAACAAATAAAAAAATAGAAAAAGGAAATAAAGAAAAACAAATAAAAAAACATAAAAAGG
1 ACAAACAAATAAAAAAAAAGAAAAAAGAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAG
18687738 ACAA
1 ACAA
18687742 TAGGCAGCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 11 0.20
61 18 0.32
62 27 0.48
ACGTcount: A:0.77, C:0.08, G:0.09, T:0.07
Consensus pattern (62 bp):
ACAAACAAATAAAAAAAAAGAAAAAAGAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAG
Found at i:18687700 original size:35 final size:34
Alignment explanation
Indices: 18687612--18687736 Score: 105
Period size: 35 Copynumber: 3.7 Consensus size: 34
18687602 TAATAATAAT
* *
18687612 AAACAAATAAATAAAA-AAACAAATAAA-AAAGAA
1 AAACAAATAAA-AAAATAAAAAAAGAAATAAAGAA
** * * *
18687645 AAA-GGACAAACAAATAAAAAACAGAAA-AAAGAC
1 AAACAAATAAAAAAATAAAAAA-AGAAATAAAGAA
*
18687678 AAACAAATAAAAAAATAGAAAAAGGAAATAAAGAA
1 AAACAAATAAAAAAATA-AAAAAAGAAATAAAGAA
* *
18687713 AAACAAATAAAAAAACATAAAAAG
1 AAACAAATAAAAAAATAAAAAAAG
18687737 GACAATAGGC
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
31 3 0.04
32 9 0.13
33 15 0.21
34 18 0.25
35 26 0.37
ACGTcount: A:0.78, C:0.07, G:0.08, T:0.07
Consensus pattern (34 bp):
AAACAAATAAAAAAATAAAAAAAGAAATAAAGAA
Found at i:18687722 original size:61 final size:60
Alignment explanation
Indices: 18687627--18687741 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 60
18687617 AATAAATAAA
* *
18687627 AAAACAAATAAAAAAGAAAAAGGACAAACAAAT-AAAAAACAGAAAAAAGACAAACAAAT
1 AAAACAAATAAAAAAGAAAAAAGAAAAACAAATAAAAAAACAGAAAAAAGACAAACAAAT
* *
18687686 AAAA-AAATAGAAAAAGGAAATAAAGAAAAACAAATAAAAAAACATAAAAAGGACAA
1 AAAACAAATA-AAAAA-GAAA-AAAGAAAAACAAATAAAAAAACAGAAAAAAGACAA
18687742 TAGGCAGCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 5 0.10
59 9 0.19
60 4 0.08
61 12 0.25
62 18 0.38
ACGTcount: A:0.77, C:0.08, G:0.10, T:0.06
Consensus pattern (60 bp):
AAAACAAATAAAAAAGAAAAAAGAAAAACAAATAAAAAAACAGAAAAAAGACAAACAAAT
Found at i:18687737 original size:35 final size:35
Alignment explanation
Indices: 18687668--18687743 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
18687658 ATAAAAAACA
* *
18687668 GAAA-AAAGACAAACAAATAAAAAAATAGAAAAAG
1 GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
*
18687702 GAAATAAAGAAAAACAAATAAAAAAACATAAAAAG
1 GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
18687737 GACAATA
1 GA-AATA
18687744 GGCAGCAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 4 0.11
35 29 0.78
36 4 0.11
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.08
Consensus pattern (35 bp):
GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
Found at i:18689765 original size:26 final size:23
Alignment explanation
Indices: 18689684--18689765 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
18689674 CAGCTTGTAT
* * * **
18689684 GAGCTTATCGTTTCAGCTCTACG
1 GAGCTTACCGTTTTAGCTCGATA
18689707 GAGCTTACCGTTTTAGCTCGATA
1 GAGCTTACCGTTTTAGCTCGATA
*
18689730 CAGCTTACCGTTTATCAGCTCGGA-A
1 GAGCTTACCGTTT-T-AGCTC-GATA
18689755 TGAGCTTACCG
1 -GAGCTTACCG
18689766 ATCATGGCTC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 30 0.62
24 1 0.02
25 6 0.12
26 11 0.23
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGTTTTAGCTCGATA
Found at i:18704768 original size:2 final size:2
Alignment explanation
Indices: 18704761--18704791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18704751 GCGAGTAGTT
18704761 TA TA TA 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 TA TA TA T
18704792 TTAAAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18715990 original size:15 final size:15
Alignment explanation
Indices: 18715966--18715999 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
18715956 TTAACCCGAA
*
18715966 AACCCTAAAAAAAAG
1 AACCCGAAAAAAAAG
*
18715981 AACCCGAAAACAAAG
1 AACCCGAAAAAAAAG
18715996 AACC
1 AACC
18716000 TTTAAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.26, G:0.09, T:0.03
Consensus pattern (15 bp):
AACCCGAAAAAAAAG
Found at i:18724224 original size:12 final size:14
Alignment explanation
Indices: 18724195--18724230 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
18724185 CTCAAATTTT
18724195 AATTTATCATATTC
1 AATTTATCATATTC
18724209 AATTTATCA-A-TC
1 AATTTATCATATTC
18724221 AATTTATCAT
1 AATTTATCAT
18724231 CTCTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.52
13 1 0.05
14 9 0.43
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTATCATATTC
Found at i:18725721 original size:13 final size:13
Alignment explanation
Indices: 18725703--18725728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18725693 TACAACAAAT
18725703 TTAAGTAGAATCA
1 TTAAGTAGAATCA
18725716 TTAAGTAGAATCA
1 TTAAGTAGAATCA
18725729 ACTTTTGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TTAAGTAGAATCA
Found at i:18726656 original size:19 final size:20
Alignment explanation
Indices: 18726618--18726657 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
18726608 AACATTCCTT
*
18726618 AACTTAAGATAACATAAAAA
1 AACTTAAGATAAAATAAAAA
*
18726638 AACTT-AGATAAAATCAAAA
1 AACTTAAGATAAAATAAAAA
18726657 A
1 A
18726658 TCATACTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (20 bp):
AACTTAAGATAAAATAAAAA
Found at i:18726656 original size:20 final size:20
Alignment explanation
Indices: 18726618--18726657 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18726608 AACATTCCTT
*
18726618 AACTTAAGATAACATAAAAA
1 AACTTAAGATAAAATAAAAA
18726638 AACTT-AGATAAAATCAAAAA
1 AACTTAAGATAAAAT-AAAAA
18726658 TCATACTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (20 bp):
AACTTAAGATAAAATAAAAA
Found at i:18733964 original size:37 final size:35
Alignment explanation
Indices: 18733918--18733987 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
18733908 TTCTAGAAAT
18733918 AATATTATTTTAATAGT-TTAATATTAAATTTAATTA
1 AATATTATTTTAATAGTATT-ATATT-AATTTAATTA
*
18733954 AATATTTATTTTAATAGTATTTTATTAATTTAAT
1 AATA-TTATTTTAATAGTATTATATTAATTTAAT
18733988 ATTAAAGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 12 0.39
37 17 0.55
38 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (35 bp):
AATATTATTTTAATAGTATTATATTAATTTAATTA
Found at i:18734334 original size:23 final size:23
Alignment explanation
Indices: 18734291--18734340 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
18734281 TATTTAGAGA
* *
18734291 AATTGTAAAATTACTCCACTGGT
1 AATTGTAAAATTACTACACTGGG
*
18734314 AATTGTAAAATTACTATACTGGG
1 AATTGTAAAATTACTACACTGGG
18734337 AATT
1 AATT
18734341 TTTGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (23 bp):
AATTGTAAAATTACTACACTGGG
Found at i:18735082 original size:34 final size:38
Alignment explanation
Indices: 18735043--18735114 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 38
18735033 TATATTTGTT
*
18735043 TTATAATTGT-T-TATA-ATATTTATAT-TATGAAATA
1 TTATAATTGTATATATATATATATATATATATGAAATA
18735077 TTATAATTGTGATATATATATATATATATATATGAAAT
1 TTATAATTGT-ATATATATATATATATATATATGAAAT
18735115 GATCCACAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 10 0.31
36 1 0.03
37 4 0.12
38 9 0.28
39 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (38 bp):
TTATAATTGTATATATATATATATATATATATGAAATA
Found at i:18739837 original size:24 final size:24
Alignment explanation
Indices: 18739810--18739860 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
18739800 TCCTAACGTG
18739810 ATAGGATTTTATGGGACGTAATGT
1 ATAGGATTTTATGGGACGTAATGT
18739834 ATAGGATTTTATGGGACGTAATGT
1 ATAGGATTTTATGGGACGTAATGT
18739858 ATA
1 ATA
18739861 ATCATCAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (24 bp):
ATAGGATTTTATGGGACGTAATGT
Found at i:18740659 original size:26 final size:26
Alignment explanation
Indices: 18740606--18740672 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
18740596 TACATATATA
* *
18740606 CTCACACGAGCTGTGAAAAGAGTATG
1 CTCACACGAGCTATGAAAAGAGCATG
* * *
18740632 CTCACACGAGCTATGAAATGGGCCTG
1 CTCACACGAGCTATGAAAAGAGCATG
*
18740658 CTCACACTAGCTATG
1 CTCACACGAGCTATG
18740673 GGTCGGAACG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (26 bp):
CTCACACGAGCTATGAAAAGAGCATG
Found at i:18742661 original size:15 final size:15
Alignment explanation
Indices: 18742641--18742672 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18742631 CATTTCATTA
*
18742641 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
18742656 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
18742671 TT
1 TT
18742673 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:18743086 original size:24 final size:24
Alignment explanation
Indices: 18743054--18743100 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
18743044 TAAATATTGA
18743054 GTTAGTCATTGACCATGCGTATGT
1 GTTAGTCATTGACCATGCGTATGT
18743078 GTTAGTCATTGACCATGCGTATG
1 GTTAGTCATTGACCATGCGTATG
18743101 CAACTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (24 bp):
GTTAGTCATTGACCATGCGTATGT
Found at i:18744342 original size:37 final size:37
Alignment explanation
Indices: 18744299--18744402 Score: 89
Period size: 37 Copynumber: 3.0 Consensus size: 37
18744289 AATATTATTT
18744299 TAATAGTTTAATATTATATTTAATTTAATATTTATCC
1 TAATAGTTTAATATTATATTTAATTTAATATTTATCC
***
18744336 TAATAG--T-AT-TT-TA-TTAATTTAATA-TTAAAG
1 TAATAGTTTAATATTATATTTAATTTAATATTTATCC
* *
18744366 TAACTA-TCTTAATATTAAATTTAATTTAATGTTTATC
1 TAA-TAGT-TTAATATTATATTTAATTTAATATTTATC
18744403 TTGTACATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
30 6 0.12
31 13 0.25
32 2 0.04
33 3 0.06
34 4 0.08
35 3 0.06
36 1 0.02
37 16 0.31
38 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (37 bp):
TAATAGTTTAATATTATATTTAATTTAATATTTATCC
Found at i:18760233 original size:18 final size:18
Alignment explanation
Indices: 18760211--18760256 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
18760201 TCAAAATTCA
18760211 AAAATTAAAAAATAATTTT
1 AAAATTAAAAAA-AATTTT
*
18760230 -AAATATATAAAAAATTTT
1 AAAAT-TAAAAAAAATTTT
18760248 AAAATTAAA
1 AAAATTAAA
18760257 TGCTATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTAAAAAAAATTTT
Found at i:18761216 original size:19 final size:21
Alignment explanation
Indices: 18761180--18761218 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18761170 ATAGAAATTT
*
18761180 TGATTTTTTTTATATTTAAAA
1 TGATTTTTTGTATATTTAAAA
18761201 TGATTTTTTGT-T-TTTAAA
1 TGATTTTTTGTATATTTAAA
18761219 TTTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
TGATTTTTTGTATATTTAAAA
Found at i:18761221 original size:25 final size:25
Alignment explanation
Indices: 18761186--18761277 Score: 73
Period size: 25 Copynumber: 3.7 Consensus size: 25
18761176 ATTTTGATTT
*
18761186 TTTTTATATTTAAAATGATTTTTTG
1 TTTTTAAATTTAAAATGATTTTTTG
* * *
18761211 TTTTTAAATTTTAAATAATTTTTTCA
1 TTTTTAAATTTAAAATGATTTTTT-G
* **
18761237 TTTTTATACTTT-AAATTTTTTTTATG
1 TTTTTA-AATTTAAAATGATTTTT-TG
18761263 TTTTT--ATTTAAAATG
1 TTTTTAAATTTAAAATG
18761278 TGAAAAATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 3 0.06
24 4 0.08
25 21 0.40
26 20 0.38
27 5 0.09
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTTAAATTTAAAATGATTTTTTG
Done.