Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 9 of 253
Found at i:2619196 original size:27 final size:26
Alignment explanation
Indices: 2619166--2619228 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
2619156 GGATAATTAA
2619166 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATTAAATAA-CCT
* * * *
2619193 AATAATTATCTTAATATTAATTAACCT
1 AATAA-AATCCTAAAATTAAATAACCT
2619220 AATATAAAT
1 AATA-AAAT
2619229 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAAATAACCT
Found at i:2625227 original size:18 final size:17
Alignment explanation
Indices: 2625200--2625245 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2625190 ATTCTGTTTT
*
2625200 TTATTTATTTATTATTA
1 TTATTTATTTACTATTA
*
2625217 TTATGTTATTTACTGTTA
1 TTAT-TTATTTACTATTA
2625235 TTATTATATTT
1 TTATT-TATTT
2625246 TTTTGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (17 bp):
TTATTTATTTACTATTA
Found at i:2625519 original size:17 final size:16
Alignment explanation
Indices: 2625487--2625524 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2625477 ATATTGTATT
2625487 TATATATATTATTATG
1 TATATATATTATTATG
*
2625503 TATATATTTTAATTATG
1 TATATATATT-ATTATG
2625520 TATAT
1 TATAT
2625525 TTCTAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
TATATATATTATTATG
Found at i:2625542 original size:19 final size:19
Alignment explanation
Indices: 2625518--2625555 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2625508 ATTTTAATTA
*
2625518 TGTATATTTCTAATATCAT
1 TGTATATTTCTAACATCAT
2625537 TGTATATTTCTAACATCAT
1 TGTATATTTCTAACATCAT
2625556 CATTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (19 bp):
TGTATATTTCTAACATCAT
Found at i:2625678 original size:23 final size:25
Alignment explanation
Indices: 2625629--2625678 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
2625619 TCGTTTCTAA
* *
2625629 TATATATGTGTATCGTATATGTTTT
1 TATATATGTGTATCGTATATATCTT
2625654 TATATATGT-TAT-GTATATATCTT
1 TATATATGTGTATCGTATATATCTT
2625677 TA
1 TA
2625679 GTATTATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 3 0.13
25 9 0.39
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.56
Consensus pattern (25 bp):
TATATATGTGTATCGTATATATCTT
Found at i:2626044 original size:21 final size:21
Alignment explanation
Indices: 2626020--2626071 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2626010 ACTATTATTT
* *
2626020 TATTTATTTTTATTCCTAGTA
1 TATTTATTTTTAATACTAGTA
* *
2626041 TATTTATTATTAATATTAGTA
1 TATTTATTTTTAATACTAGTA
*
2626062 TATGTATTTT
1 TATTTATTTT
2626072 ATTATACGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (21 bp):
TATTTATTTTTAATACTAGTA
Found at i:2628619 original size:14 final size:14
Alignment explanation
Indices: 2628600--2628626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2628590 AGCGTTTGAT
2628600 CGAATTGAGTGAAC
1 CGAATTGAGTGAAC
2628614 CGAATTGAGTGAA
1 CGAATTGAGTGAA
2628627 AAATTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (14 bp):
CGAATTGAGTGAAC
Found at i:2628914 original size:10 final size:10
Alignment explanation
Indices: 2628899--2628927 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2628889 TCTCAAAATT
2628899 ATTATTTTAA
1 ATTATTTTAA
2628909 ATTATTTTAA
1 ATTATTTTAA
2628919 ATT-TTTTAA
1 ATTATTTTAA
2628928 CTTTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATTTTAA
Found at i:2628976 original size:18 final size:18
Alignment explanation
Indices: 2628953--2629006 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
2628943 TTTAGAATTT
2628953 ATTTTTGAAAATTTTATA
1 ATTTTTGAAAATTTTATA
* **
2628971 ATTTTTTAAAA-AATATA
1 ATTTTTGAAAATTTTATA
* *
2628988 AATTTTGAAATTTTTATA
1 ATTTTTGAAAATTTTATA
2629006 A
1 A
2629007 ATATTTTGAG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
ATTTTTGAAAATTTTATA
Found at i:2629014 original size:20 final size:19
Alignment explanation
Indices: 2628989--2629060 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
2628979 AAAAATATAA
*
2628989 ATTTTGAAATTTTTATAAAT
1 ATTTT-AAATTTTTAAAAAT
* *
2629009 ATTTT-GAGTTTTAAAAATT
1 ATTTTAAATTTTTAAAAA-T
*
2629028 ATTTTAAATTCTTGAAAAAT
1 ATTTTAAATT-TTTAAAAAT
2629048 ATTTTAAATTTTT
1 ATTTTAAATTTTT
2629061 TTTGTAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.21
19 8 0.19
20 18 0.43
21 7 0.17
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAAAT
Found at i:2631945 original size:22 final size:21
Alignment explanation
Indices: 2631920--2631973 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2631910 ATTTTTTAAA
*
2631920 AATATTTATATTATTTTAATTT
1 AATATTTATATTATTTT-ATAT
2631942 AATATTTATA--ATTTTATAT
1 AATATTTATATTATTTTATAT
2631961 AAT-TTTAT-TTATT
1 AATATTTATATTATT
2631974 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 5 0.17
22 10 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTTATATTATTTTATAT
Found at i:2631971 original size:14 final size:14
Alignment explanation
Indices: 2631922--2631983 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 14
2631912 TTTTTAAAAA
*
2631922 TATTTATATTATTT
1 TATTTATATAATTT
2631936 TAATTTA-AT-ATTT
1 T-ATTTATATAATTT
2631949 ATAATTTTATATAATTT
1 -T-A-TTTATATAATTT
2631966 TATTTAT-TAATTT
1 TATTTATATAATTT
2631979 T-TTTA
1 TATTTA
2631984 CATATACATC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.09
13 11 0.26
14 11 0.26
15 10 0.23
16 3 0.07
17 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTATATAATTT
Found at i:2632604 original size:13 final size:13
Alignment explanation
Indices: 2632588--2632627 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
2632578 TATAAAAAAA
2632588 TTATTTTAATTAT
1 TTATTTTAATTAT
2632601 TTA-TTTAATTAT
1 TTATTTTAATTAT
*
2632613 TTTTTTTAA-TAT
1 TTATTTTAATTAT
2632625 TTA
1 TTA
2632628 AATTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTTAATTAT
Found at i:2638962 original size:6 final size:6
Alignment explanation
Indices: 2638953--2638990 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
2638943 AAATGGAAAT
2638953 TAAAAA TAAAAA TAAAAA T-AAAA T-AAAA T-AAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
2638991 CTCACCCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 15 0.48
6 16 0.52
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:2638969 original size:5 final size:5
Alignment explanation
Indices: 2638955--2638990 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
2638945 ATGGAAATTA
2638955 AAAAT AAAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
2638991 CTCACCCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.63
6 11 0.37
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:2644957 original size:31 final size:31
Alignment explanation
Indices: 2644919--2645036 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
2644909 ACAAATGACA
* * *
2644919 AGTGAAAAGTGGTAGCTTCTGCTACTTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
2644950 AGTGAAAATTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
2644981 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
2645012 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
2645037 AAGTGACAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:2645136 original size:47 final size:46
Alignment explanation
Indices: 2645066--2645313 Score: 157
Period size: 49 Copynumber: 5.3 Consensus size: 46
2645056 TATAAGACCA
* * * * *
2645066 TGGGATATGGTATCGGTGTGATATATGCTACTGTATAAGACCATATC
1 TGGGATATGGCATCAGTGAGATATATGATAC-GTATAAGACCATAGC
* * * *
2645113 TGGGATATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGC
1 TGGGATATGGCATCAGTGAGATATATGATACGTATAAGACCATAGC
* * * * * *
2645159 TGGGTTATGGCATCGATATGTGATATGTGATTACGTGTAAGACCATAAC
1 TGGGATATGGCATC-A-GTGAGATATATGA-TACGTATAAGACCATAGC
* * * * *
2645208 TGGGCTATGGCATC-GATATATGATATGTGATTACGTGTAAGACCATAGT
1 TGGGATATGGCATCAG-T-GA-GATATATGA-TACGTATAAGACCATAGC
* * *
2645257 TGGGCTATGGCATC-----GATATATGAATATGTGTAAGACCATAGC
1 TGGGATATGGCATCAGTGAGATATATG-ATACGTATAAGACCATAGC
*
2645299 TGGGCTATGGCATCA
1 TGGGATATGGCATCA
2645314 TTATGTAAAG
Statistics
Matches: 169, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
42 37 0.22
43 1 0.01
46 25 0.15
47 26 0.15
48 11 0.07
49 69 0.41
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (46 bp):
TGGGATATGGCATCAGTGAGATATATGATACGTATAAGACCATAGC
Found at i:2645202 original size:49 final size:48
Alignment explanation
Indices: 2645132--2645356 Score: 267
Period size: 49 Copynumber: 4.9 Consensus size: 48
2645122 ACATCAGTGA
* *
2645132 GATATGTGATTCGTGTAAGACCATAGCTGGGTTATGGCATCGATATGT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
*
2645180 GATATGTGATTACGTGTAAGACCATAACTGGGCTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
*
2645229 GATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
2645278 GA-A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATC-AT-TAT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
** * **
2645318 G-TA-AAGA-T-GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGA
2645357 GAAAACGAAG
Statistics
Matches: 162, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
40 5 0.03
41 2 0.01
42 56 0.35
43 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
48 12 0.07
49 83 0.51
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
Found at i:2645288 original size:42 final size:42
Alignment explanation
Indices: 2645242--2645356 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 42
2645232 ATGTGATTAC
*
2645242 GTGTAAGACCATAGTTGGGCTATGGCATCGATATATG-AATAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGAT-TATGAAAGAT
*
2645284 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTAAAGAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATG-AAAGAT
**
2645326 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTGGGCTATGGCATCGA
2645357 GAAAACGAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 58 0.89
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGTTGGGCTATGGCATCGATTATGAAAGAT
Found at i:2647942 original size:14 final size:14
Alignment explanation
Indices: 2647923--2647973 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
2647913 AGAAAGAGAT
2647923 GAGAAGATAGAAAA
1 GAGAAGATAGAAAA
*
2647937 GAGAAGAAACGAAATA
1 GAGAAGATA-GAAA-A
*
2647953 GAGAAGATAGAAAT
1 GAGAAGATAGAAAA
2647967 GAGAAGA
1 GAGAAGA
2647974 AACAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 15 0.47
15 8 0.25
16 9 0.28
ACGTcount: A:0.61, C:0.02, G:0.29, T:0.08
Consensus pattern (14 bp):
GAGAAGATAGAAAA
Found at i:2647957 original size:30 final size:30
Alignment explanation
Indices: 2647923--2647982 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2647913 AGAAAGAGAT
*
2647923 GAGAAGATAGAAAAGAGAAGAAACGAAATA
1 GAGAAGATAGAAAAGAGAAGAAACAAAATA
*
2647953 GAGAAGATAGAAATGAGAAGAAACAAAATA
1 GAGAAGATAGAAAAGAGAAGAAACAAAATA
2647983 AAAAAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.25, T:0.08
Consensus pattern (30 bp):
GAGAAGATAGAAAAGAGAAGAAACAAAATA
Found at i:2648098 original size:10 final size:10
Alignment explanation
Indices: 2648085--2648124 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2648075 AGAAAAAGAA
2648085 GAAGAAAATG
1 GAAGAAAATG
*
2648095 GAAGAAAATA
1 GAAGAAAATG
2648105 GAAGAAAAT-
1 GAAGAAAATG
2648114 GAAGGAAAATG
1 GAA-GAAAATG
2648125 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 3 0.11
10 24 0.89
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (10 bp):
GAAGAAAATG
Found at i:2648109 original size:20 final size:20
Alignment explanation
Indices: 2648084--2648123 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2648074 AAGAAAAAGA
2648084 AGAAGAAAATGGAA-GAAAAT
1 AGAAGAAAAT-GAAGGAAAAT
2648104 AGAAGAAAATGAAGGAAAAT
1 AGAAGAAAATGAAGGAAAAT
2648124 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (20 bp):
AGAAGAAAATGAAGGAAAAT
Found at i:2650716 original size:20 final size:20
Alignment explanation
Indices: 2650678--2650717 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2650668 GCATTATGAA
*
2650678 ATTATTAAAAACATAAAAAT
1 ATTATTAAAAAAATAAAAAT
*
2650698 ATTATTAAAAAAATTAAAAT
1 ATTATTAAAAAAATAAAAAT
2650718 TATGTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTATTAAAAAAATAAAAAT
Found at i:2650987 original size:19 final size:19
Alignment explanation
Indices: 2650934--2650987 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
2650924 TATAGAAATC
2650934 AATTTTTAATAAAATTTTAT
1 AATTTTTAAT-AAATTTTAT
** *
2650954 GGTTTTTAATTAATTTTAAT
1 AATTTTTAATAAATTTT-AT
2650974 AATTTTT-ATAAATT
1 AATTTTTAATAAATT
2650988 AGTTTTTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTTTTAATAAATTTTAT
Found at i:2651002 original size:38 final size:36
Alignment explanation
Indices: 2650934--2651031 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 36
2650924 TATAGAAATC
2650934 AATTTTTAATAAAATT-TTATGGTTTTTAATTAATTTTAAT
1 AATTTTTAAT-AAATTATT-T--TTTTTAATT-ATTTTAAT
* *
2650974 AATTTTT-ATAAATTAGTTTTTTTCTAATTTTTTTTAT
1 AATTTTTAATAAATTA-TTTTTTT-TAATTATTTTAAT
*
2651011 GATTTTTAATAAATTATTTTT
1 AATTTTTAATAAATTATTTTT
2651032 ATAAATTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
37 21 0.41
38 18 0.35
39 3 0.06
40 9 0.18
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (36 bp):
AATTTTTAATAAATTATTTTTTTTAATTATTTTAAT
Found at i:2651025 original size:23 final size:23
Alignment explanation
Indices: 2650999--2651050 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2650989 GTTTTTTTCT
* *
2650999 AATTTTTTTTATGATTTTTAAT-A
1 AATTTTTTTTATAAATTTT-ATGA
*
2651022 AATTATTTTTATAAATTTTATGA
1 AATTTTTTTTATAAATTTTATGA
2651045 AATTTT
1 AATTTT
2651051 ATTGTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
AATTTTTTTTATAAATTTTATGA
Found at i:2653649 original size:15 final size:16
Alignment explanation
Indices: 2653619--2653651 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2653609 TTTTTAAGAA
2653619 AAAATATTAAAAAAAG
1 AAAATATTAAAAAAAG
*
2653635 AAAAT-TTAGAAAAAG
1 AAAATATTAAAAAAAG
2653650 AA
1 AA
2653652 TTTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAATATTAAAAAAAG
Found at i:2654029 original size:16 final size:17
Alignment explanation
Indices: 2654005--2654039 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2653995 GTAAAGCTTG
2654005 TATCGATCTATTG-AAT
1 TATCGATCTATTGCAAT
*
2654021 TATCTATCTATTGCAAT
1 TATCGATCTATTGCAAT
2654038 TA
1 TA
2654040 ACAGACCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (17 bp):
TATCGATCTATTGCAAT
Found at i:2654644 original size:19 final size:19
Alignment explanation
Indices: 2654620--2654656 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2654610 TTTTTCCTCT
*
2654620 TTTTGATTTATGTGATAAG
1 TTTTGATCTATGTGATAAG
2654639 TTTTGATCTATGTGATAA
1 TTTTGATCTATGTGATAA
2654657 CGTGACACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (19 bp):
TTTTGATCTATGTGATAAG
Found at i:2655194 original size:114 final size:113
Alignment explanation
Indices: 2654957--2655263 Score: 361
Period size: 114 Copynumber: 2.7 Consensus size: 113
2654947 ATTCAACGAT
* *
2654957 CAAGTTGAG-AAAGTTGTCAAGTTTAGGGACTAAATGTTGACTTATCCCTAATTTTGTATAAAAA
1 CAAGTTGGGAAAAGTTGCCAAGTTTAGGG-CTAAATGTTGACTTATCCCTAATTTTGTAT-AAAA
* *
2655021 AATTAGGTGATAATATGTCATAATCTCATAGTGTCATGTCAACATAGGAC
64 AATTAGGTGATAATATGTCACAATCTCATAATGTCATGTCAACATAGGAC
* * * *
2655071 CAAGTTGGGAAAATTTGCCAAGTTTAGGGCTAAATGTTGACTTATTCCTAA-CTTGTATAAAAAT
1 CAAGTTGGGAAAAGTTGCCAAGTTTAGGGCTAAATGTTGACTTATCCCTAATTTTGTATAAAAAA
* * * *
2655135 TTAGTTGATGATGA-GTCACAATCTCATAATGTTATGTCATCATAGGAAC
66 TTAGGTGATAAT-ATGTCACAATCTCATAATGTCATGTCAACATAGG-AC
* * ** *
2655184 TAAGATTGGGAAAAGTTGTCAAG-TTAGAGATTAAATGTTGAATTATCCCTAATTTTGTATAAAA
1 CAAG-TTGGGAAAAGTTGCCAAGTTTAG-GGCTAAATGTTGACTTATCCCTAATTTTGTAT--AA
2655248 AAAATTAGGTGATAAT
62 AAAATTAGGTGATAAT
2655264 GTGTAATAAT
Statistics
Matches: 162, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
112 43 0.27
113 16 0.10
114 65 0.40
115 23 0.14
117 15 0.09
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (113 bp):
CAAGTTGGGAAAAGTTGCCAAGTTTAGGGCTAAATGTTGACTTATCCCTAATTTTGTATAAAAAA
TTAGGTGATAATATGTCACAATCTCATAATGTCATGTCAACATAGGAC
Found at i:2655311 original size:114 final size:112
Alignment explanation
Indices: 2654961--2655311 Score: 327
Period size: 114 Copynumber: 3.1 Consensus size: 112
2654951 AACGATCAAG
2654961 TTGAGAAAGTTGTCAAGTTTAGGGACTAAATGTTGACTTATCCCTAATTTTGTATAAAAAAATTA
1 TTGA-AAAGTTGTCAAGTTTA-GGACTAAATGTTGACTTATCCCTAATTTTGTATAAAAAAATTA
* *
2655026 GGTGATAATATGTCATAATCTCATAGTGTCATGTCA-ACATAGGACCAAGT-
64 GGTGATAATGTGTCATAATCTCATAGTGTCATGTCATACA-A-GACTAA-TA
* * * * * * *
2655076 TGGGAAAATTTGCCAAGTTTAGGGCTAAATGTTGACTTATTCCTAA-CTTGTAT-AAAAATTTAG
1 T-TGAAAAGTTGTCAAGTTTAGGACTAAATGTTGACTTATCCCTAATTTTGTATAAAAAAATTAG
* * * * * * *
2655139 TTGATGATGAGTCACAATCTCATAATGTTATGTCAT-CATAGGAACTAAGA
65 GTGATAATGTGTCATAATCTCATAGTGTCATGTCATACA-A-G-ACTAATA
* *
2655189 TTGGGAAAAGTTGTCAAG-TTAGAGATTAAATGTTGAATTATCCCTAATTTTGTATAAAAAAAAT
1 TT--GAAAAGTTGTCAAGTTTAG-GACTAAATGTTGACTTATCCCTAATTTTGTAT-AAAAAAAT
* * * * *
2655253 TAGGTGATAATGTGTAATAATTTCAGAGTGTCATGGCATGACAAGATTAATA
62 TAGGTGATAATGTGTCATAATCTCATAGTGTCATGTCAT-ACAAGACTAATA
2655305 TTGAAAA
1 TTGAAAA
2655312 AAAAATACTC
Statistics
Matches: 187, Mismatches: 37, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
112 43 0.23
113 15 0.08
114 60 0.32
115 21 0.11
116 9 0.05
117 36 0.19
118 1 0.01
119 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (112 bp):
TTGAAAAGTTGTCAAGTTTAGGACTAAATGTTGACTTATCCCTAATTTTGTATAAAAAAATTAGG
TGATAATGTGTCATAATCTCATAGTGTCATGTCATACAAGACTAATA
Found at i:2661621 original size:3 final size:3
Alignment explanation
Indices: 2661613--2661650 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2661603 CCGACCACCG
2661613 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
2661651 GAGCTCCACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:2664743 original size:29 final size:30
Alignment explanation
Indices: 2664690--2664769 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
2664680 ATATTAAAAT
* *
2664690 TATATATGAATTATAATTTAATGTGCAATTG
1 TATATATGAATTTTGATTT-ATGTGCAATTG
* *
2664721 TATATATGAATTTTGATTT-TGTGTAATTT
1 TATATATGAATTTTGATTTATGTGCAATTG
2664750 TATATATGAATTTTTGATTT
1 TATATATGAA-TTTTGATTT
2664770 GATATAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.41
30 9 0.20
31 17 0.39
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (30 bp):
TATATATGAATTTTGATTTATGTGCAATTG
Found at i:2664778 original size:30 final size:29
Alignment explanation
Indices: 2664689--2664780 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
2664679 AATATTAAAA
* * **
2664689 TTATATATGAATTATAATTTAATGTGCAATT
1 TTATATATGAATTTTGATTT--TGTATAATT
* *
2664720 GTATATATGAATTTTGATTTTGTGTAATT
1 TTATATATGAATTTTGATTTTGTATAATT
2664749 TTATATATGAATTTTTGA-TTTGATATAATT
1 TTATATATGAA-TTTTGATTTTG-TATAATT
2664779 TT
1 TT
2664781 TGTAATTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 22 0.42
30 14 0.26
31 17 0.32
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (29 bp):
TTATATATGAATTTTGATTTTGTATAATT
Found at i:2665443 original size:2 final size:2
Alignment explanation
Indices: 2665436--2665463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2665426 ACATGGATTT
2665436 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
2665464 AAATCCTTGA
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):
TA
Found at i:2667373 original size:9 final size:10
Alignment explanation
Indices: 2667342--2667386 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
2667332 ATCAATTTTG
2667342 AAAATAA-AC
1 AAAATAATAC
*
2667351 -AAATTATAC
1 AAAATAATAC
*
2667360 AAAAAAATAC
1 AAAATAATAC
2667370 AAAATAA-AC
1 AAAATAATAC
2667379 AAAATAAT
1 AAAATAAT
2667387 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
8 5 0.17
9 11 0.38
10 13 0.45
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAATAC
Found at i:2667400 original size:19 final size:20
Alignment explanation
Indices: 2667378--2667422 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
2667368 ACAAAATAAA
*
2667378 CAAAATAATTT-TTAAAATT-
1 CAAAAT-ATTTATAAAAATTC
2667397 CAAAATATTTATAAAAATTC
1 CAAAATATTTATAAAAATTC
2667417 CAAAAT
1 CAAAAT
2667423 TTATACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAAATATTTATAAAAATTC
Found at i:2667970 original size:2 final size:2
Alignment explanation
Indices: 2667963--2667992 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2667953 AATAGTAATT
2667963 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
2667993 ATAACTATAT
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):
TA
Found at i:2668910 original size:45 final size:46
Alignment explanation
Indices: 2668847--2668933 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 46
2668837 TCTAAACTAA
* *
2668847 AAAAAACTTAATGTTATTTACTTTGAAATAAAA-AATAAAATAATT
1 AAAAAACTTAATCTTATTTACTTTAAAATAAAATAATAAAATAATT
** *
2668892 AAAAAA-TGTAATCTTATTTGTTTTAAAATAAAATAATTAAAT
1 AAAAAACT-TAATCTTATTTACTTTAAAATAAAATAATAAAAT
2668934 TAAATTTGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.03
45 27 0.77
46 7 0.20
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (46 bp):
AAAAAACTTAATCTTATTTACTTTAAAATAAAATAATAAAATAATT
Found at i:2671233 original size:12 final size:13
Alignment explanation
Indices: 2671207--2671236 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2671197 CACTGAAATT
2671207 ATTTTTTATTCAA
1 ATTTTTTATTCAA
2671220 ATTTTTTATT-AA
1 ATTTTTTATTCAA
2671232 ATTTT
1 ATTTT
2671237 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTTATTCAA
Found at i:2679815 original size:118 final size:118
Alignment explanation
Indices: 2679585--2679802 Score: 373
Period size: 118 Copynumber: 1.8 Consensus size: 118
2679575 TATTTCCGGT
2679585 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
2679650 CCTACCCCGGTTACTCAATCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAATCAGTCACGATCTAAGCCATACTCATAACCTCGGC
****
2679703 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
*
2679768 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGC
66 CCTACCCCGGTTACTCAATCAGTCACGATCTAAGC
2679803 TGTACTCGTA
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAATCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:2680643 original size:42 final size:42
Alignment explanation
Indices: 2680597--2680703 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
2680587 GGGATTCTAT
* * *
2680597 GGCTGAAATAGGACTGTTTGGCTGCAGAGATATGACATTCTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGACATTCTG
* * * *
2680639 GGCTGGAATAGAACTGTTAGGCAGCAGGGATATGGCATTTTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGACATTCTG
2680681 GGCTGGAATAGAACTGTTTGGCA
1 GGCTGGAATAGAACTGTTTGGCA
2680704 CCATGGATAG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.27
Consensus pattern (42 bp):
GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGACATTCTG
Found at i:2685314 original size:5 final size:5
Alignment explanation
Indices: 2685304--2685335 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2685294 TTGTGTGTTC
2685304 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2685336 TCACAGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:2685318 original size:9 final size:9
Alignment explanation
Indices: 2685304--2685334 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2685294 TTGTGTGTTC
2685304 TTTATTTTA
1 TTTATTTTA
2685313 TTTATTTTA
1 TTTATTTTA
2685322 TTTTATTTTA
1 -TTTATTTTA
2685332 TTT
1 TTT
2685335 TTCACAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2692193 original size:14 final size:14
Alignment explanation
Indices: 2692174--2692204 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2692164 TGTGCTTAAA
2692174 ATGGCATGATATGT
1 ATGGCATGATATGT
2692188 ATGGCATGATATGT
1 ATGGCATGATATGT
2692202 ATG
1 ATG
2692205 AAATGATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (14 bp):
ATGGCATGATATGT
Found at i:2693620 original size:25 final size:25
Alignment explanation
Indices: 2693591--2693654 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
2693581 ATATAGATAA
2693591 AATTGAAAATTT-T-AGGAAAATTCAT
1 AATTGAAAATTTGTCA--AAAATTCAT
**
2693616 AATTGAAAATTTGTCAAAGCTTCAT
1 AATTGAAAATTTGTCAAAAATTCAT
2693641 AATTGAAAATTTGT
1 AATTGAAAATTTGT
2693655 ATCCTAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 33 0.94
26 1 0.03
27 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (25 bp):
AATTGAAAATTTGTCAAAAATTCAT
Found at i:2697031 original size:20 final size:20
Alignment explanation
Indices: 2697006--2697052 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2696996 AATAAGAAAG
2697006 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
2697026 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
2697046 ATATAAA
1 ATATAAA
2697053 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:2698668 original size:44 final size:44
Alignment explanation
Indices: 2698561--2698888 Score: 183
Period size: 44 Copynumber: 7.5 Consensus size: 44
2698551 TTTAAGTCTA
* * * *
2698561 CTCCACTGTAA-TATCAGGGAGATAAGA-CC-TGA-TGCGATCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGATCCTTTATTTCAATCTG
** * * * *
2698602 CTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTG
* ** * * *
2698646 CTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTG
* ***
2698689 CTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCCT-TTATTTCAATCTG
* ** ** *
2698733 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTCCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCCT-TTATT-T-CAATCTG
* * * * * *
2698779 CTCCACTGTAACCTCAGGGAAATAAGATCC-TGA-TGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTG
** * * *
2698821 CTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTG
2698865 CTCCACTGTAA-TCTCAGGGAGATA
1 CTCCACTGTAACT-TCAGGGAGATA
2698889 GGATTACTAG
Statistics
Matches: 216, Mismatches: 57, Indels: 25
0.72 0.19 0.08
Matches are distributed among these distances:
41 22 0.10
42 35 0.16
43 35 0.16
44 90 0.42
45 2 0.01
46 31 0.14
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTCAATCTG
Found at i:2698706 original size:43 final size:43
Alignment explanation
Indices: 2698640--2698937 Score: 174
Period size: 44 Copynumber: 6.8 Consensus size: 43
2698630 CCTTTATTTT
* * * *
2698640 AATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTC
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATCACTGGCTTC
* * *
2698683 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCACTGGCTTC
* * *
2698727 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTCC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATC---ACTGGCTTC
** * * * *
2698773 GGTCTACTCCACTGTAACCTCAGGGAAATAAGATC-CT-GATGC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCACTGGCTTC
* * ** * *** *
2698815 GATCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTTATTTT
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATCAC-TGGCTTC
* * * *
2698859 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCACTGGCTTC
* **
2698903 AATCTACTCCGTTGTAATCTCAGGGAGATAAGATC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATC
2698938 TGAAATTCTT
Statistics
Matches: 196, Mismatches: 49, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
41 1 0.01
42 32 0.16
43 29 0.15
44 97 0.49
45 2 0.01
46 34 0.17
47 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
AATCTGCTCCACTGTAACTCAGGGAGATAAGATCACTGGCTTC
Found at i:2698711 original size:87 final size:87
Alignment explanation
Indices: 2698595--2698756 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
2698585 AGACCTGATG
* * * * *
2698595 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
2698659 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * * *
2698682 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
2698747 CAGGGAGATA
66 CAGGGAGATA
2698757 AGATCTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 63 0.98
88 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:2698848 original size:132 final size:133
Alignment explanation
Indices: 2698646--2698888 Score: 303
Period size: 132 Copynumber: 1.8 Consensus size: 133
2698636 TTTTAATCCG
* * * * * * * *
2698646 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
1 CTCCACTGTAACCTCAGGGAAATAAGATACTGTATGCGATCTACTCCGCTGTAATCTCAGAGAGA
* *
2698711 TAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGG
66 TAAGATCCT-TGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGG
2698775 TCTA
130 TCTA
* *
2698779 CTCCACTGTAACCTCAGGGAAATAAGATCCTG-ATGCGATCTACTCTGCTGTAA-CTTCAGAGAG
1 CTCCACTGTAACCTCAGGGAAATAAGATACTGTATGCGATCTACTCCGCTGTAATC-TCAGAGAG
* * * *
2698842 ATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATA
65 ATAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATA
2698889 GGATTACTAG
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
131 1 0.01
132 62 0.67
133 29 0.32
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (133 bp):
CTCCACTGTAACCTCAGGGAAATAAGATACTGTATGCGATCTACTCCGCTGTAATCTCAGAGAGA
TAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGT
CTA
Found at i:2711358 original size:20 final size:20
Alignment explanation
Indices: 2711333--2711379 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2711323 AATAAGAAAG
2711333 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
2711353 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
2711373 ATATAAA
1 ATATAAA
2711380 ACAAATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:2711373 original size:25 final size:25
Alignment explanation
Indices: 2711340--2711387 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2711330 AAGATATAAA
* *
2711340 TAATATCAATATAATATAAATATAG
1 TAATATCAATATAAAACAAATATAG
2711365 TAATATCAATATAAAACAAATAT
1 TAATATCAATATAAAACAAATAT
2711388 CTTTGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
TAATATCAATATAAAACAAATATAG
Found at i:2712927 original size:21 final size:21
Alignment explanation
Indices: 2712903--2712947 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2712893 TCGATGCCCC
*
2712903 TTTTGTAA-TTATGTTCAGTTT
1 TTTTGTAATTTATGAT-AGTTT
*
2712924 TTTTTTAATTTATGATAGTTT
1 TTTTGTAATTTATGATAGTTT
2712945 TTT
1 TTT
2712948 CTTAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (21 bp):
TTTTGTAATTTATGATAGTTT
Found at i:2717378 original size:20 final size:21
Alignment explanation
Indices: 2717347--2717391 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2717337 CATAAATTAT
*
2717347 TAAAATATTTATTTAATTACA
1 TAAAATATTTATCTAATTACA
*
2717368 TAAAATA-TTATCTAATTACG
1 TAAAATATTTATCTAATTACA
2717388 TAAA
1 TAAA
2717392 TCAGTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAAATATTTATCTAATTACA
Found at i:2721119 original size:6 final size:6
Alignment explanation
Indices: 2721110--2721146 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
2721100 TCCCACCCGG
*
2721110 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTT TCCCTC T
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC T
2721147 GCACCGTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCCTC
Found at i:2721311 original size:6 final size:6
Alignment explanation
Indices: 2721300--2721339 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
2721290 GCCTTCACCT
2721300 CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA CCCA
1 CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA CCCA
2721340 AGTGGAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCACA
Found at i:2731617 original size:23 final size:22
Alignment explanation
Indices: 2731587--2731638 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
2731577 ATAAATTGTA
*
2731587 TATTTTATAAG-TTTTATATTTTT
1 TATTTTAT-AGTTTTTATA-ATTT
2731610 TATTTTATAGTTTTTATAATTT
1 TATTTTATAGTTTTTATAATTT
2731632 TATTTTA
1 TATTTTA
2731639 GGATAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTTTATAGTTTTTATAATTT
Found at i:2731632 original size:22 final size:23
Alignment explanation
Indices: 2731587--2731638 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
2731577 ATAAATTGTA
*
2731587 TATTTTATAAGTTTTATATTTTT
1 TATTTTATAAGTTTTATATATTT
2731610 TATTTTAT-AGTTTT-TATAATTT
1 TATTTTATAAGTTTTATAT-ATTT
2731632 TATTTTA
1 TATTTTA
2731639 GGATAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.11
22 16 0.59
23 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
TATTTTATAAGTTTTATATATTT
Found at i:2732198 original size:14 final size:13
Alignment explanation
Indices: 2732156--2732202 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 13
2732146 GAAGAGAATG
2732156 AAAAAT-AAAGAA
1 AAAAATAAAAGAA
2732168 AAAAATAAAAGTTAA
1 AAAAATAAAAG--AA
2732183 AAAATATAAAAGAA
1 AAAA-ATAAAAGAA
2732197 AAAAAT
1 AAAAAT
2732203 TAAATTACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 6 0.19
15 6 0.19
16 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAGAA
Found at i:2732206 original size:14 final size:14
Alignment explanation
Indices: 2732162--2732206 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2732152 AATGAAAAAT
2732162 AAAGAAAAAAA-TA
1 AAAGAAAAAAATTA
*
2732175 AAAGTTAAAAAATATA
1 AAAG-AAAAAAAT-TA
2732191 AAAGAAAAAAATTA
1 AAAGAAAAAAATTA
2732205 AA
1 AA
2732207 TTACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.15
14 10 0.37
15 7 0.26
16 6 0.22
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
AAAGAAAAAAATTA
Found at i:2745451 original size:137 final size:136
Alignment explanation
Indices: 2745044--2745451 Score: 443
Period size: 136 Copynumber: 3.0 Consensus size: 136
2745034 TTAAATTTAC
* * * * * *
2745044 TTTGATTTTTCGATTAATCAAGTTGAGTTAATATTATAAGTTAATTTAGTATCAA-TTAAAAATT
1 TTTGATTTTTCGATTAATCAAGCTGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAA-T
* * ** * * *
2745108 TTAAAA-CCTGAATTTTTTTAGTTTATTTCTTTAAATAAATTTATAATTTGTTTTAAATTAGATA
65 TTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTT-TTTTAAATTAGATA
2745172 A-TTTTGA
129 ATTTTTGA
* * * *
2745179 CTTTGATTTTTCGATTATTCAAGCTGAATT-GATATCACAAGTTAATTTGATACCAACTGAAAAG
1 -TTTGATTTTTCGATTAATCAAGCTGAGTTAG-TATCACAAGTTAATTTGGTATCAACTGAAAA-
* * * * *
2745243 A-TT-AAATACTAAAAGTTTTTAATTTATGTCATCAGATAATTTCATAATTTATTTTTAAATCAG
63 ATTTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAA-TT-TTTTTAAATTAG
*
2745306 ATAGTTTTTG-
126 ATAATTTTTGA
* * *
2745316 TTCTGATTTTTCTATCAATCAAGCCGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAAT
1 TT-TGATTTTTCGATTAATCAAGCTGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAAT
*
2745381 TTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTTTTTTAAATTAAATAA
65 TTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTTTTTTAAATTAGAT-A
2745446 ATTTTT
129 ATTTTT
2745452 ATACAATATT
Statistics
Matches: 223, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
135 3 0.01
136 91 0.41
137 81 0.36
138 48 0.22
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (136 bp):
TTTGATTTTTCGATTAATCAAGCTGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAATT
TAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTTTTTTAAATTAGATAAT
TTTTGA
Found at i:2753883 original size:23 final size:22
Alignment explanation
Indices: 2753831--2753883 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2753821 TCCACGTCTT
*
2753831 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
2753853 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
2753876 TTTCTTTT
1 TTTCTTTT
2753884 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:2758736 original size:23 final size:23
Alignment explanation
Indices: 2758705--2758755 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2758695 CAAACCAGTA
2758705 CATGGTGAAATACACGCCACCTC
1 CATGGTGAAATACACGCCACCTC
*
2758728 TATGGTGAAATACACGCCACCTC
1 CATGGTGAAATACACGCCACCTC
2758751 CATGG
1 CATGG
2758756 GCAACAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (23 bp):
CATGGTGAAATACACGCCACCTC
Found at i:2761027 original size:20 final size:21
Alignment explanation
Indices: 2761004--2761051 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2760994 ATTCAAATTG
2761004 AAATACTAAAATTCAAGAT-A
1 AAATACTAAAATTCAAGATAA
* *
2761024 AAAT-CTTGAAATTCAGGATAA
1 AAATAC-TAAAATTCAAGATAA
2761045 AAATACT
1 AAATACT
2761052 GATGTGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 6 0.26
22 1 0.04
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (21 bp):
AAATACTAAAATTCAAGATAA
Found at i:2763839 original size:137 final size:138
Alignment explanation
Indices: 2763659--2763977 Score: 416
Period size: 137 Copynumber: 2.3 Consensus size: 138
2763649 ACTTAAATTT
* *
2763659 ACTTTGATTTTTCGATTAATCAAGCTAAATTAGTATCATAAGTTAATTTGATATCAACT-AAAAG
1 ACTTTGATTTTTCGATTAATCAAGCTGAATTAGTATCATAAGTTAATTTGATACCAACTGAAAAG
* * * * * * *
2763723 TTTTAAAAATTAAAATTTTTTTAATTTGTATCTTTAAATAAATTT-ATAATTTG-TTTTAAATTA
66 -ATTAAAAACTAAAA-GTTTTTAATTTATATCATCAAAT-AATTTCATAATTTGTTTTTAAATCA
2763786 GATAG-TTTCG
128 GATAGTTTTCG
* *
2763796 ACTTTGATTTTTCGATTAATCAAGCTGAATT-GATATCACAAGTTAATTTGATACCAATTGAAAA
1 ACTTTGATTTTTCGATTAATCAAGCTGAATTAG-TATCATAAGTTAATTTGATACCAACTGAAAA
* *
2763860 GATTAAATACTAAAAGTTTTTAATTTATGTCATCAAATAATTTCATAATTTGTTTTTAAATCAGA
65 GATTAAAAACTAAAAGTTTTTAATTTATATCATCAAATAATTTCATAATTTGTTTTTAAATCAGA
*
2763925 TAGTTTTTG
130 TAGTTTTCG
* *
2763934 -CTTTGATTTTTTGATTAATCAAGCTGAGTTAGTATCATAAGTTA
1 ACTTTGATTTTTCGATTAATCAAGCTGAATTAGTATCATAAGTTA
2763978 CAAAAAAATT
Statistics
Matches: 159, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
135 5 0.03
136 27 0.17
137 117 0.74
138 10 0.06
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (138 bp):
ACTTTGATTTTTCGATTAATCAAGCTGAATTAGTATCATAAGTTAATTTGATACCAACTGAAAAG
ATTAAAAACTAAAAGTTTTTAATTTATATCATCAAATAATTTCATAATTTGTTTTTAAATCAGAT
AGTTTTCG
Found at i:2764339 original size:20 final size:21
Alignment explanation
Indices: 2764302--2764340 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2764292 CATGTGACAC
2764302 ATTAAATATTTAATTTATATA
1 ATTAAATATTTAATTTATATA
*
2764323 ATTAAAT-TTTCATTTATA
1 ATTAAATATTTAATTTATA
2764341 ATTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTAAATATTTAATTTATATA
Found at i:2764735 original size:19 final size:20
Alignment explanation
Indices: 2764700--2764749 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2764690 CTTTTAAATA
*
2764700 TAAATAAA-CTTAATA-TTT
1 TAAATAAATCTAAATATTTT
2764718 TAAATAAATCTAAATATTTT
1 TAAATAAATCTAAATATTTT
2764738 TAAATAAATCTA
1 TAAATAAATCTA
2764750 CTTTTATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 15 0.52
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAAATCTAAATATTTT
Found at i:2770395 original size:41 final size:41
Alignment explanation
Indices: 2770338--2770418 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
2770328 ATTAACAAGA
2770338 GATGCTATAGCTTCTAGTTTAATGAATTCACTTTAAAATGC
1 GATGCTATAGCTTCTAGTTTAATGAATTCACTTTAAAATGC
2770379 GATGCTATAGCTTCTAGTTTAATGAATTCACTTTAAAATG
1 GATGCTATAGCTTCTAGTTTAATGAATTCACTTTAAAATG
2770419 GAAATGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (41 bp):
GATGCTATAGCTTCTAGTTTAATGAATTCACTTTAAAATGC
Found at i:2773930 original size:8 final size:8
Alignment explanation
Indices: 2773917--2773943 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2773907 TAATAATTAA
2773917 ATTAAATT
1 ATTAAATT
2773925 ATTAAATT
1 ATTAAATT
2773933 ATTAAATT
1 ATTAAATT
2773941 ATT
1 ATT
2773944 GAATCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTAAATT
Found at i:2774365 original size:2 final size:2
Alignment explanation
Indices: 2774358--2774390 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2774348 TTTCCGAAGC
2774358 AT 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 AT A
2774391 ATAGCTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2779056 original size:18 final size:18
Alignment explanation
Indices: 2779023--2779058 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2779013 TTATATATCG
* *
2779023 TTATTATTAGTCTTTTTA
1 TTATTATTACTATTTTTA
2779041 TTATTATTACTATTTTTA
1 TTATTATTACTATTTTTA
2779059 ATAAATATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTATTACTATTTTTA
Found at i:2781453 original size:18 final size:18
Alignment explanation
Indices: 2781412--2781453 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2781402 ATACATCTAT
*
2781412 AAAATAATAGTATTAATA
1 AAAATAATAGGATTAATA
*
2781430 ACAATAATAAGGATT-ATA
1 AAAATAAT-AGGATTAATA
2781448 AAAATA
1 AAAATA
2781454 CATACATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AAAATAATAGGATTAATA
Found at i:2781909 original size:28 final size:30
Alignment explanation
Indices: 2781873--2781944 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 30
2781863 TATATGAAAA
*
2781873 ATATATATATAATATAATATTAATAAAAATAC
1 ATATATATATAATA-CATATTAA-AAAAATAC
* *
2781905 ATATATATGTAATACATATTAAAAGAATAC
1 ATATATATATAATACATATTAAAAAAATAC
2781935 ATATA-ATATA
1 ATATATATATA
2781945 CATATATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.11
30 12 0.33
31 7 0.19
32 13 0.36
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (30 bp):
ATATATATATAATACATATTAAAAAAATAC
Found at i:2781911 original size:30 final size:29
Alignment explanation
Indices: 2781875--2781950 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
2781865 TATGAAAAAT
2781875 ATATATATAATATAATATTAATAAAAATAC
1 ATATATATAATATAATATTAA-AAAAATAC
* *
2781905 ATATATATGTAATA-CATATTAAAAGAATAC
1 ATATATA--TAATATAATATTAAAAAAATAC
2781935 ATATAATATACATATA
1 ATAT-ATATA-ATATA
2781951 TTCAAAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 2 0.05
30 21 0.55
31 10 0.26
32 5 0.13
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.36
Consensus pattern (29 bp):
ATATATATAATATAATATTAAAAAAATAC
Found at i:2781945 original size:26 final size:27
Alignment explanation
Indices: 2781870--2781949 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 27
2781860 TGATATATGA
*
2781870 AAAATATATATATAATATA-ATATTAAT
1 AAAA-ATACATATAATATACATATTAAT
2781897 AAAAATACATATATATGTAATACATATTAA-
1 AAAAATACATATA-A--T-ATACATATTAAT
*
2781927 AAGAATACATATAATATACATAT
1 AAAAATACATATAATATACATAT
2781950 ATTCAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 16 0.35
27 6 0.13
29 2 0.04
30 15 0.33
31 7 0.15
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAAATACATATAATATACATATTAAT
Found at i:2781951 original size:28 final size:29
Alignment explanation
Indices: 2781869--2781959 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 29
2781859 ATGATATATG
*
2781869 AAAAATATATATATA-AT-ATAATATTAA
1 AAAAATACATATATATATAATAATATTAA
*
2781896 TAAAAATACATATATATGTAATACATATTAA
1 -AAAAATACATATATATATAATA-ATATTAA
* *
2781927 AAGAATACATATA-ATATACAT-ATATTCA
1 AAAAATACATATATATATA-ATAATATTAA
2781955 AAAAA
1 AAAAA
2781960 GATAATAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
28 24 0.45
29 5 0.09
30 17 0.32
31 7 0.13
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATACATATATATATAATAATATTAA
Found at i:2782214 original size:24 final size:24
Alignment explanation
Indices: 2782173--2782218 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2782163 TAGTTATGTA
2782173 ATACATACATAATAATAAAAATAT
1 ATACATACATAATAATAAAAATAT
*
2782197 ATACATAACATAGT-ATAAAAAT
1 ATACAT-ACATAATAATAAAAAT
2782219 TTGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (24 bp):
ATACATACATAATAATAAAAATAT
Found at i:2782375 original size:14 final size:15
Alignment explanation
Indices: 2782342--2782388 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2782332 AGGAATATAT
*
2782342 TAATAATGATAAGA-A
1 TAATAATAATAA-ATA
*
2782357 TAATAGTAAT-AATA
1 TAATAATAATAAATA
2782371 TAATAATAATAAATA
1 TAATAATAATAAATA
2782386 TAA
1 TAA
2782389 AAAACAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 11 0.41
15 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
TAATAATAATAAATA
Found at i:2783444 original size:19 final size:19
Alignment explanation
Indices: 2783422--2783483 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
2783412 GGGTTAGGGT
2783422 GGTTAGGGTATTGGGTATG
1 GGTTAGGGTATTGGGTATG
* *
2783441 GGTTAGTGG-GTTAGGT-TG
1 GGTTAG-GGTATTGGGTATG
* * *
2783459 GTTTAGGTTAGTGGGTATG
1 GGTTAGGGTATTGGGTATG
2783478 GGTTAG
1 GGTTAG
2783484 TGAGCTTCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 1 0.03
18 11 0.34
19 18 0.56
20 2 0.06
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.39
Consensus pattern (19 bp):
GGTTAGGGTATTGGGTATG
Found at i:2783452 original size:36 final size:37
Alignment explanation
Indices: 2783412--2783485 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
2783402 GGGTTGATTA
*
2783412 GGGTTAGGGTGG-TTAGGGTATTGGGTATGGGTTAGT
1 GGGTTAGGGTGGTTTAGGGTAGTGGGTATGGGTTAGT
* *
2783448 GGGTTAGGTTGGTTTAGGTTAGTGGGTATGGGTTAGT
1 GGGTTAGGGTGGTTTAGGGTAGTGGGTATGGGTTAGT
2783485 G
1 G
2783486 AGCTTCTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 11 0.32
37 23 0.68
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.38
Consensus pattern (37 bp):
GGGTTAGGGTGGTTTAGGGTAGTGGGTATGGGTTAGT
Found at i:2789058 original size:40 final size:40
Alignment explanation
Indices: 2788977--2789058 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
2788967 TGGAGATGAA
** * **
2788977 ATTAGCAATATGACAGACAACGTTGGTACTGAATGTTTTT
1 ATTAGCAATATGACAGACAACAATGGGACTGAATGACTTT
*
2789017 ATTAGCAATATGACAGACAACAATGGGACTGACTGACTTT
1 ATTAGCAATATGACAGACAACAATGGGACTGAATGACTTT
2789057 AT
1 AT
2789059 CAACAATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (40 bp):
ATTAGCAATATGACAGACAACAATGGGACTGAATGACTTT
Found at i:2789875 original size:16 final size:16
Alignment explanation
Indices: 2789851--2789881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2789841 ATAATTGAAG
*
2789851 ACAATTTATACCAAAC
1 ACAAATTATACCAAAC
2789867 ACAAATTATACCAAA
1 ACAAATTATACCAAA
2789882 TAAAAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
ACAAATTATACCAAAC
Found at i:2803045 original size:16 final size:16
Alignment explanation
Indices: 2803024--2803054 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2803014 CATATTTGAG
2803024 TTCAGCAACAATTTGC
1 TTCAGCAACAATTTGC
2803040 TTCAGCAACAATTTG
1 TTCAGCAACAATTTG
2803055 ATTAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (16 bp):
TTCAGCAACAATTTGC
Found at i:2803664 original size:14 final size:14
Alignment explanation
Indices: 2803645--2803672 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2803635 TTAGGATTTG
2803645 GATTTGAGGTTCAA
1 GATTTGAGGTTCAA
2803659 GATTTGAGGTTCAA
1 GATTTGAGGTTCAA
2803673 CTTCAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
GATTTGAGGTTCAA
Found at i:2803696 original size:14 final size:14
Alignment explanation
Indices: 2803677--2803720 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2803667 GTTCAACTTC
2803677 AGATTTAGGGTTCA
1 AGATTTAGGGTTCA
* ** *
2803691 AGATTTTGTATTTA
1 AGATTTAGGGTTCA
2803705 AGATTTAGGGTTCA
1 AGATTTAGGGTTCA
2803719 AG
1 AG
2803721 GTTCAAGGTT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTCA
Found at i:2804454 original size:18 final size:18
Alignment explanation
Indices: 2804431--2804466 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2804421 CACCGTTTAT
*
2804431 GACACTATTCACGTATAC
1 GACACTATTCACATATAC
2804449 GACACTATTCACATATAC
1 GACACTATTCACATATAC
2804467 AATAGTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (18 bp):
GACACTATTCACATATAC
Found at i:2806582 original size:28 final size:28
Alignment explanation
Indices: 2806550--2806604 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2806540 CAAGGCTGAC
2806550 TTTT-ATCT-CTTGATTTCAATTTCAATCT
1 TTTTAATCTACTTG-TTT-AATTTCAATCT
*
2806578 TTTTAATTTACTTGTTTAATTTCAATC
1 TTTTAATCTACTTGTTTAATTTCAATC
2806605 ATTTACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTAATCTACTTGTTTAATTTCAATCT
Found at i:2809310 original size:33 final size:33
Alignment explanation
Indices: 2809268--2809334 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2809258 ATTCAGGGAG
2809268 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
1 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
2809301 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
1 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
2809334 T
1 T
2809335 CTAACGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (33 bp):
TTGAAACAAACTTTCTCTATTGATTCCATTAAT
Found at i:2815245 original size:28 final size:28
Alignment explanation
Indices: 2815213--2815267 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2815203 CAAGGCTGAC
2815213 TTTT-ATCT-CTTGATTTCAATTTCAATCT
1 TTTTAATCTACTTG-TTT-AATTTCAATCT
*
2815241 TTTTAATTTACTTGTTTAATTTCAATC
1 TTTTAATCTACTTGTTTAATTTCAATC
2815268 ATTTACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTAATCTACTTGTTTAATTTCAATCT
Found at i:2826244 original size:22 final size:22
Alignment explanation
Indices: 2826200--2826245 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2826190 CATTTGGCGA
* *
2826200 TCCTCCAGTGAATTAAATTTGT
1 TCCTCCAGCGAATTAAATGTGT
* *
2826222 TCCTCTAGCGAATTAAGTGTGT
1 TCCTCCAGCGAATTAAATGTGT
2826244 TC
1 TC
2826246 GGTTGCTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
TCCTCCAGCGAATTAAATGTGT
Found at i:2828109 original size:29 final size:28
Alignment explanation
Indices: 2828077--2828132 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2828067 TTTATTTAAT
** *
2828077 TTTAAAAAGTTATTTGATTAAATTAAAAA
1 TTTAAAAA-TTAAGTGATTAAAATAAAAA
*
2828106 TTTAATAATTAAGTGATTAAAATAAAA
1 TTTAAAAATTAAGTGATTAAAATAAAA
2828133 TAAACTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (28 bp):
TTTAAAAATTAAGTGATTAAAATAAAAA
Found at i:2828245 original size:10 final size:10
Alignment explanation
Indices: 2828230--2828280 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
2828220 CATAAATTAC
2828230 ATAACATATT
1 ATAACATATT
2828240 ATAACATATT
1 ATAACATATT
*
2828250 -T--TAT-TT
1 ATAACATATT
2828256 ATAACATATT
1 ATAACATATT
2828266 ATAACATATTT
1 ATAACATA-TT
2828277 ATAA
1 ATAA
2828281 TATTTAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
6 2 0.06
7 3 0.09
9 3 0.09
10 20 0.59
11 6 0.18
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (10 bp):
ATAACATATT
Found at i:2828277 original size:21 final size:21
Alignment explanation
Indices: 2828230--2828280 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 21
2828220 CATAAATTAC
2828230 ATAACATA-TTATAACATATT
1 ATAACATATTTATAACATATT
2828250 -T----TATTTATAACATATT
1 ATAACATATTTATAACATATT
2828266 ATAACATATTTATAA
1 ATAACATATTTATAA
2828281 TATTTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 11
0.69 0.00 0.31
Matches are distributed among these distances:
15 2 0.08
16 12 0.48
17 1 0.04
19 1 0.04
21 9 0.36
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAACATATTTATAACATATT
Found at i:2828715 original size:22 final size:22
Alignment explanation
Indices: 2828690--2828735 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2828680 ACGTTGGCGA
*
2828690 TCCTCCAGTGAATTAAGTGTGT
1 TCCTCCAGCGAATTAAGTGTGT
*
2828712 TCCTCTAGCGAATTAAGTGTGT
1 TCCTCCAGCGAATTAAGTGTGT
2828734 TC
1 TC
2828736 GGTTGCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (22 bp):
TCCTCCAGCGAATTAAGTGTGT
Found at i:2829956 original size:25 final size:25
Alignment explanation
Indices: 2829927--2829977 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2829917 CATTGAGTTT
2829927 CAAAATCAAACTACGGTTTTCTAAA
1 CAAAATCAAACTACGGTTTTCTAAA
*
2829952 CAAAATCAAACTATGGTTTTCTAAA
1 CAAAATCAAACTACGGTTTTCTAAA
2829977 C
1 C
2829978 TTTGTTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (25 bp):
CAAAATCAAACTACGGTTTTCTAAA
Found at i:2830779 original size:29 final size:31
Alignment explanation
Indices: 2830724--2830784 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2830714 ATTTTATTTT
* *
2830724 TATATAACATAAATTACATAATATATAAAAA
1 TATATAACAAAAATAACATAATATATAAAAA
*
2830755 TATATAAGAAAAATAACAT-AT-TATAAAAA
1 TATATAACAAAAATAACATAATATATAAAAA
2830784 T
1 T
2830785 TAGAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 2 0.07
31 16 0.59
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (31 bp):
TATATAACAAAAATAACATAATATATAAAAA
Found at i:2833474 original size:51 final size:51
Alignment explanation
Indices: 2833362--2833460 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 51
2833352 AATTTCATCT
* *
2833362 CAACATTTACATATTATGTCAATTTTATACTGATTTAACAAATTTAGTCCA
1 CAACATTTACACATTATGTCAATTTGATACTGATTTAACAAATTTAGTCCA
*
2833413 CAACATTTACACATTCTGTCAATTTGAT-CTTGATTTAACAAATTTAGT
1 CAACATTTACACATTATGTCAATTTGATAC-TGATTTAACAAATTTAGT
2833461 TCGTAATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 1 0.02
51 43 0.98
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (51 bp):
CAACATTTACACATTATGTCAATTTGATACTGATTTAACAAATTTAGTCCA
Found at i:2834885 original size:31 final size:31
Alignment explanation
Indices: 2834847--2834915 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2834837 TTACAATTCG
* *
2834847 GTCATTGAACTGTTCGAAAGTATTTATTTAA
1 GTCATTGAACTATTCAAAAGTATTTATTTAA
*
2834878 GTCATTGAACTATTCAAAAGTTTTTATTTAA
1 GTCATTGAACTATTCAAAAGTATTTATTTAA
*
2834909 GTTATTG
1 GTCATTG
2834916 GGCTGTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAAGTATTTATTTAA
Found at i:2837743 original size:13 final size:13
Alignment explanation
Indices: 2837725--2837754 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2837715 TTATTCATTT
2837725 TTTTAACATATTA
1 TTTTAACATATTA
*
2837738 TTTTAACATATTG
1 TTTTAACATATTA
2837751 TTTT
1 TTTT
2837755 GAGCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTAACATATTA
Found at i:2852037 original size:34 final size:35
Alignment explanation
Indices: 2851981--2852049 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
2851971 AGAAAACGTA
*
2851981 AAAAAAAATTAATTAAGTTTTTGTATTAAATTTAT
1 AAAAAAAATTAATTAAGATTTTGTATTAAATTTAT
2852016 AAAAAAAATTAATTAA-ATTTTGTATTAAATTTAT
1 AAAAAAAATTAATTAAGATTTTGTATTAAATTTAT
2852050 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (35 bp):
AAAAAAAATTAATTAAGATTTTGTATTAAATTTAT
Found at i:2852051 original size:16 final size:16
Alignment explanation
Indices: 2852032--2852063 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2852022 AATTAATTAA
2852032 ATTTTGTATTAAATTT
1 ATTTTGTATTAAATTT
*
2852048 ATTTTTTATTAAATTT
1 ATTTTGTATTAAATTT
2852064 TTGTCGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTTTGTATTAAATTT
Found at i:2852904 original size:19 final size:19
Alignment explanation
Indices: 2852880--2852936 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2852870 TTGGAATATT
2852880 TTTTTATAATTTTATTTTA
1 TTTTTATAATTTTATTTTA
*
2852899 TTTTTATAATTTTTTTCTTA
1 TTTTTATAATTTTATT-TTA
2852919 -TTTTATATATTATTATTT
1 TTTTTATA-ATT-TTATTT
2852937 CAATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 22 0.67
20 7 0.21
21 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATAATTTTATTTTA
Found at i:2865050 original size:43 final size:43
Alignment explanation
Indices: 2865002--2865089 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
2864992 AAAATGGTAC
*
2865002 ATGCAAATATAATAATTTAATCAATGTTTGGTTTATAAAATTT
1 ATGCAAATATAATAATCTAATCAATGTTTGGTTTATAAAATTT
2865045 ATGCAAATATAATAATCTAATCAATGTTTGGTTTATAAAATTT
1 ATGCAAATATAATAATCTAATCAATGTTTGGTTTATAAAATTT
2865088 AT
1 AT
2865090 CCATAAATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (43 bp):
ATGCAAATATAATAATCTAATCAATGTTTGGTTTATAAAATTT
Found at i:2865232 original size:76 final size:74
Alignment explanation
Indices: 2865139--2865289 Score: 275
Period size: 76 Copynumber: 2.0 Consensus size: 74
2865129 AATTTGTGGG
2865139 TTGGTTTTTAATTTTTAGGGTTGATAATATCTTTTCCATTAATTGAGTCATACTTACTATACTAG
1 TTGGTTTTTAATTTTTAGGGTTGATAATATCTTTTCCATTAATTGAGTCATACTTACTATACTAG
2865204 AATTTTTTTT
66 -ATTTTTTTT
*
2865214 TTGGTTTTTTAATTTTTAGGGTTGATAATATCTTTTCCATTAATTGTGTCATACTTACTATACTA
1 TTGG-TTTTTAATTTTTAGGGTTGATAATATCTTTTCCATTAATTGAGTCATACTTACTATACTA
2865279 GATTTTTTTT
65 GATTTTTTTT
2865289 T
1 T
2865290 CTTCTTAATT
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
75 14 0.19
76 60 0.81
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (74 bp):
TTGGTTTTTAATTTTTAGGGTTGATAATATCTTTTCCATTAATTGAGTCATACTTACTATACTAG
ATTTTTTTT
Found at i:2868283 original size:20 final size:22
Alignment explanation
Indices: 2868260--2868302 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2868250 ATCAAAAGAA
2868260 TGAAAT-AAT-ATAAAACAATT
1 TGAAATAAATGATAAAACAATT
*
2868280 TGAAATAAATGATTAAACAATT
1 TGAAATAAATGATAAAACAATT
2868302 T
1 T
2868303 TGACTAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 3 0.15
22 11 0.55
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (22 bp):
TGAAATAAATGATAAAACAATT
Found at i:2868554 original size:26 final size:26
Alignment explanation
Indices: 2868525--2868598 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 26
2868515 AATAATTTAA
*
2868525 AAAACAAA-AATGTATATAAAAGTTT
1 AAAACAAACAATATATATAAAAGTTT
* * *
2868550 CAAAATAAACAATATGTATAATAGTTT
1 -AAAACAAACAATATATATAAAAGTTT
* * * *
2868577 AAAAGAAATAACATATGTAAAA
1 AAAACAAACAATATATATAAAA
2868599 TAAAATAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (26 bp):
AAAACAAACAATATATATAAAAGTTT
Found at i:2868664 original size:21 final size:20
Alignment explanation
Indices: 2868640--2868689 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
2868630 TGGTAATAAT
2868640 AATATAAATAAAAACAAAAAA
1 AATATAAAT-AAAACAAAAAA
* **
2868661 AATATATAATATAACAAAACC
1 AATATA-AATAAAACAAAAAA
2868682 AATATAAA
1 AATATAAA
2868690 GTTACCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (20 bp):
AATATAAATAAAACAAAAAA
Found at i:2868793 original size:60 final size:60
Alignment explanation
Indices: 2868729--2868852 Score: 221
Period size: 60 Copynumber: 2.1 Consensus size: 60
2868719 AATAGTAATA
*
2868729 ATATAATAATAATAAAGTAGAGACTAATGATGACAATACATTAATGAGAATAATGATAGC
1 ATATAATAATAATAAAGTAGAAACTAATGATGACAATACATTAATGAGAATAATGATAGC
* *
2868789 ATATAATTATAATAAAGTAGAAACTAATGATGACAATACATTGATGAGAATAATGATAGC
1 ATATAATAATAATAAAGTAGAAACTAATGATGACAATACATTAATGAGAATAATGATAGC
2868849 ATAT
1 ATAT
2868853 TGATAATGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (60 bp):
ATATAATAATAATAAAGTAGAAACTAATGATGACAATACATTAATGAGAATAATGATAGC
Found at i:2869861 original size:18 final size:19
Alignment explanation
Indices: 2869834--2869870 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2869824 AAAAAAAAGA
2869834 AAATACAAAAGAAAAAAAT
1 AAATACAAAAGAAAAAAAT
*
2869853 AAATA-AAAATAAAAAAAT
1 AAATACAAAAGAAAAAAAT
2869871 CAAAAGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (19 bp):
AAATACAAAAGAAAAAAAT
Found at i:2872468 original size:18 final size:19
Alignment explanation
Indices: 2872440--2872479 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2872430 ACGTAAAAAG
2872440 TAAAAAGTAAA-AGATGAAA
1 TAAAAAGTAAATA-ATGAAA
2872459 TAAAAA-TAAATAATGAAA
1 TAAAAAGTAAATAATGAAA
2872477 TAA
1 TAA
2872480 TTTAAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
TAAAAAGTAAATAATGAAA
Found at i:2873115 original size:23 final size:24
Alignment explanation
Indices: 2873089--2873137 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2873079 ATCATGCTTG
* *
2873089 AAGGTTATGGAAAT-GATATGAAA
1 AAGGTAATGGAAATGGATAGGAAA
2873112 AAGGTAATGGAAATGGATAGGAAA
1 AAGGTAATGGAAATGGATAGGAAA
2873136 AA
1 AA
2873138 TATTTGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (24 bp):
AAGGTAATGGAAATGGATAGGAAA
Found at i:2873275 original size:16 final size:14
Alignment explanation
Indices: 2873244--2873290 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
2873234 GAAAATTAAT
2873244 ATAAAATCTAAAATA
1 ATAAAAT-TAAAATA
2873259 ATAATAATTATAAATAA
1 ATAA-AATTA-AAAT-A
2873276 ATAAAATTAAAATA
1 ATAAAATTAAAATA
2873290 A
1 A
2873291 ACCTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 12 0.41
17 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATTAAAATA
Found at i:2877190 original size:23 final size:23
Alignment explanation
Indices: 2877160--2877206 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2877150 GCACGTTTAA
2877160 GAGCTTCTGTCTCTTTTCGTCGT
1 GAGCTTCTGTCTCTTTTCGTCGT
2877183 GAGCTTCTGTCTCTTTTCGTCGT
1 GAGCTTCTGTCTCTTTTCGTCGT
2877206 G
1 G
2877207 CTCGTGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.04, C:0.26, G:0.23, T:0.47
Consensus pattern (23 bp):
GAGCTTCTGTCTCTTTTCGTCGT
Found at i:2878984 original size:17 final size:17
Alignment explanation
Indices: 2878962--2878997 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2878952 TTTATGAGTG
*
2878962 CAATGTGTCTACTAGTA
1 CAATGTGTCTACTACTA
2878979 CAATGTGTCTACTACTA
1 CAATGTGTCTACTACTA
2878996 CA
1 CA
2878998 CCTAACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (17 bp):
CAATGTGTCTACTACTA
Found at i:2882315 original size:21 final size:22
Alignment explanation
Indices: 2882286--2882332 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2882276 CAGAAGGAGT
*
2882286 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2882308 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2882329 GAGT
1 GAGT
2882333 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:2899084 original size:26 final size:25
Alignment explanation
Indices: 2898994--2899092 Score: 99
Period size: 25 Copynumber: 3.8 Consensus size: 25
2898984 AAAGGTATAT
* *
2898994 ACATAGTATTAAAAATATGTACATA
1 ACATAATATTAAAAATATATACATA
* *
2899019 ACATAATGTTAAAAATACATACATA
1 ACATAATATTAAAAATATATACATA
* **
2899044 ATATAGCATTAAAAAATATATACATA
1 ACATAATATT-AAAAATATATACATA
*
2899070 AGATAATATGTAAAATATATATA
1 ACATAATAT-TAAAA-ATATATA
2899093 TGTAATATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
25 27 0.46
26 24 0.41
27 8 0.14
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (25 bp):
ACATAATATTAAAAATATATACATA
Found at i:2899178 original size:23 final size:24
Alignment explanation
Indices: 2899152--2899210 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2899142 AAAAGACATA
*
2899152 TATACGTAATATA-TATAAAAATG
1 TATACATAATATAGTATAAAAATG
* *
2899175 TATACATAATATAGTATTAAAATA
1 TATACATAATATAGTATAAAAATG
*
2899199 T-TACATAGTATA
1 TATACATAATATA
2899211 TACATATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (24 bp):
TATACATAATATAGTATAAAAATG
Found at i:2899522 original size:22 final size:23
Alignment explanation
Indices: 2899476--2899535 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
2899466 GATACTAAAA
* *
2899476 AGAAAATATATAAATATATAGGAT
1 AGAAAATAGAT-AATAAATAGGAT
*
2899500 AGAAAATA-ATAATAAATATGAT
1 AGAAAATAGATAATAAATAGGAT
*
2899522 A-ATAATAGATAATA
1 AGAAAATAGATAATA
2899536 GTAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.16
22 17 0.53
23 2 0.06
24 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (23 bp):
AGAAAATAGATAATAAATAGGAT
Done.