Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 12 of 56
Found at i:2328860 original size:19 final size:18
Alignment explanation
Indices: 2328836--2328882 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
2328826 TAAATTTTTA
2328836 TATTTAAAAATTAATAAAT
1 TATTTAAAAATTAAT-AAT
* * *
2328855 TATTTATATATTAATATT
1 TATTTAAAAATTAATAAT
2328873 TATTTAAAAA
1 TATTTAAAAA
2328883 AATCAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAAAAATTAATAAT
Found at i:2329916 original size:11 final size:11
Alignment explanation
Indices: 2329900--2329926 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2329890 ATGATATATC
2329900 AATAAAATTAA
1 AATAAAATTAA
2329911 AATAAAATTAA
1 AATAAAATTAA
2329922 AATAA
1 AATAA
2329927 TCAAAGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATTAA
Found at i:2330052 original size:14 final size:15
Alignment explanation
Indices: 2330026--2330054 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2330016 GTTTAAATGT
2330026 GTTTTTAATATTTAA
1 GTTTTTAATATTTAA
2330041 GTTTTTAA-ATTTAA
1 GTTTTTAATATTTAA
2330055 AAATAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
GTTTTTAATATTTAA
Found at i:2330534 original size:48 final size:48
Alignment explanation
Indices: 2330460--2330557 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
2330450 CAGATTGCCT
* *
2330460 ATGGCCTAACACCTTGTTTCATTCAGTGATAGTCTGCTCGGATATCCG
1 ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
2330508 ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
1 ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
2330556 AT
1 AT
2330558 ATTCAAAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (48 bp):
ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
Found at i:2330775 original size:50 final size:50
Alignment explanation
Indices: 2330716--2330975 Score: 407
Period size: 50 Copynumber: 5.2 Consensus size: 50
2330706 AGTTGTTGTC
* *
2330716 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2330766 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAAGTGGCCATA
1 ATTGTTGACTATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
2330816 ATTGTTGACGATTCTTCACCAACATTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
2330866 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2330916 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2330966 ATGGTTGACT
1 ATTGTTGACT
2330976 CTAAGTATAT
Statistics
Matches: 194, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
49 2 0.01
50 190 0.98
51 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:2335437 original size:50 final size:50
Alignment explanation
Indices: 2335368--2335627 Score: 418
Period size: 50 Copynumber: 5.2 Consensus size: 50
2335358 AGTTGTTGCC
*
2335368 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2335418 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
1 ATTGTTGACTATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2335468 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* * *
2335518 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
2335568 ATTGTTGA-TAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
2335618 ATTGTTGACT
1 ATTGTTGACT
2335628 CTAAGTATAT
Statistics
Matches: 194, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
49 2 0.01
50 189 0.97
51 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:2339134 original size:19 final size:18
Alignment explanation
Indices: 2339112--2339158 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
2339102 CAAAAATAAA
2339112 ATTTAAAAATTAATATATT
1 ATTTAAAAATTAATAT-TT
* *
2339131 ATTTACATATTAATATTT
1 ATTTAAAAATTAATATTT
*
2339149 AATTAAAAAT
1 ATTTAAAAAT
2339159 ATGAAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAAAAATTAATATTT
Found at i:2340750 original size:12 final size:12
Alignment explanation
Indices: 2340720--2340749 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2340710 GTAGCTCCCC
2340720 TTCTTTTCCTTT
1 TTCTTTTCCTTT
2340732 TTCTTTTCCTTT
1 TTCTTTTCCTTT
2340744 TT-TTTT
1 TTCTTTT
2340750 TTTTAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTCCTTT
Found at i:2344468 original size:13 final size:13
Alignment explanation
Indices: 2344452--2344494 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
2344442 TTAAAGATTA
2344452 TTTAATTATTATT
1 TTTAATTATTATT
* *
2344465 TTTAAATATTAATA
1 TTTAATTATT-ATT
2344479 TTTAATATATTATT
1 TTTAAT-TATTATT
2344493 TT
1 TT
2344495 GATTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 9 0.38
14 11 0.46
15 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATTATTATT
Found at i:2344501 original size:31 final size:29
Alignment explanation
Indices: 2344450--2344536 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 29
2344440 AATTAAAGAT
2344450 TATTTAATTATTA-TTT-TTAAATATTAA
1 TATTTAATTATTATTTTATTAAATATTAA
*
2344477 TATTTAATATATTATTTTGATTAAA-AATAA
1 TATTTAAT-TATTATTTT-ATTAAATATTAA
* *
2344507 TATATTATTTATATATTTTAATAAATATTA
1 TAT-TTAATTAT-TATTTTATTAAATATTA
2344537 GTTTAACATG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 8 0.16
28 5 0.10
29 3 0.06
30 15 0.31
31 18 0.37
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
TATTTAATTATTATTTTATTAAATATTAA
Found at i:2345307 original size:18 final size:19
Alignment explanation
Indices: 2345267--2345312 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2345257 TGTATTTAAA
2345267 TTTAAT-TATAAAATATAT
1 TTTAATATATAAAATATAT
* *
2345285 ATTAATATA-AAAATATTT
1 TTTAATATATAAAATATAT
2345303 TTTAA-ATATA
1 TTTAATATATA
2345313 TTTTTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.13
18 18 0.78
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATATATAAAATATAT
Found at i:2345874 original size:16 final size:15
Alignment explanation
Indices: 2345853--2345895 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
2345843 TATTAAATTC
2345853 AAATATTATATTTATT
1 AAATATTATATTT-TT
2345869 AAATATTAT-TTTTT
1 AAATATTATATTTTT
2345883 ATAATAATTATAT
1 A-AAT-ATTATAT
2345896 ATAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 6 0.25
16 14 0.58
17 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATATTATATTTTT
Found at i:2347469 original size:27 final size:29
Alignment explanation
Indices: 2347416--2347469 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
2347406 AAAAATTCTT
* *
2347416 TAAATATAATAAATATATAAACTTTTATC
1 TAAATAAAATAAATATATAAACATTTATC
*
2347445 TAAATAAAATATATA-ATAAA-ATTTA
1 TAAATAAAATAAATATATAAACATTTA
2347470 AACAACCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 5 0.23
29 13 0.59
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAATAAAATAAATATATAAACATTTATC
Found at i:2347851 original size:14 final size:14
Alignment explanation
Indices: 2347828--2347860 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2347818 TTTTTAAATG
2347828 AATT-AATTTTTTT
1 AATTAAATTTTTTT
2347841 AATTAAATTTTTTT
1 AATTAAATTTTTTT
*
2347855 TATTAA
1 AATTAA
2347861 TCAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTAAATTTTTTT
Found at i:2347872 original size:18 final size:19
Alignment explanation
Indices: 2347828--2347874 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2347818 TTTTTAAATG
*
2347828 AATTAATTTTT-TTAATTA
1 AATTTATTTTTATTAATTA
*
2347846 AATTT-TTTTTATTAA-TC
1 AATTTATTTTTATTAATTA
2347863 AATTTATTTTTA
1 AATTTATTTTTA
2347875 CAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTATTTTTATTAATTA
Found at i:2348154 original size:21 final size:22
Alignment explanation
Indices: 2348120--2348161 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2348110 TAAAAATATT
2348120 AATATTTAAATTTT-ATATAAA
1 AATATTTAAATTTTAATATAAA
2348141 AATA-TTAAATTTTTAATATAA
1 AATATTTAAA-TTTTAATATAA
2348162 TTATCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTTAAATTTTAATATAAA
Found at i:2348761 original size:23 final size:21
Alignment explanation
Indices: 2348735--2348777 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2348725 TTTTACAACA
2348735 ATTTTAAAATATAAATTTATTTG
1 ATTTT-AAATAT-AATTTATTTG
*
2348758 ATTTTAAATATTATTTATTT
1 ATTTTAAATATAATTTATTT
2348778 AATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTAAATATAATTTATTTG
Found at i:2348861 original size:14 final size:14
Alignment explanation
Indices: 2348844--2348898 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
2348834 TATGTATATT
2348844 TTTAAATATATAAA
1 TTTAAATATATAAA
*
2348858 TTTAAATA-ATAGA
1 TTTAAATATATAAA
* *
2348871 -TCAAATATA-ATA
1 TTTAAATATATAAA
*
2348883 TTTAAAAATATAAA
1 TTTAAATATATAAA
2348897 TT
1 TT
2348899 GAATCATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 8 0.25
13 12 0.38
14 12 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
TTTAAATATATAAA
Found at i:2351225 original size:15 final size:16
Alignment explanation
Indices: 2351198--2351228 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2351188 GTTTACATGT
2351198 GTTTTTAATATTTAAA
1 GTTTTTAATATTTAAA
2351214 GTTTTTAA-ATTTAAA
1 GTTTTTAATATTTAAA
2351229 ATAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
GTTTTTAATATTTAAA
Found at i:2351708 original size:46 final size:48
Alignment explanation
Indices: 2351635--2351727 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 48
2351625 GAATTGCCTA
* *
2351635 TGGCCTACACCTTGTTTCATTCCAGTGATAG-CTG-TCGGATATCCGC
1 TGGCCTACACCTTGTTTCAGTCCAGTGATAGTATGCTCGGATATCCGC
2351681 TGGCCTAACACCTTGTTTCAGT-CAGTGATAGTATGCTCGGATATCCG
1 TGGCCT-ACACCTTGTTTCAGTCCAGTGATAGTATGCTCGGATATCCG
2351728 ATATTTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 15 0.36
47 16 0.38
48 11 0.26
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (48 bp):
TGGCCTACACCTTGTTTCAGTCCAGTGATAGTATGCTCGGATATCCGC
Found at i:2352077 original size:96 final size:94
Alignment explanation
Indices: 2351903--2352088 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 94
2351893 GTTGACTATC
* *
2351903 CTTCACCAACCTTTGACAAATAGGGAGGTGACCATAATTGTGCCATCCTCACCAACCTTTGCCAA
1 CTTCACCAACCTTTGACAAAGAAGGAGGTGACCATAATTGTGCCATCCTCACCAACCTTTGCCAA
2351968 TCGAGCGAAGTGGCC-TAATTGTTGACGCTT
66 -CGAGCGAAGTGGCCATAA-TGTTGACGCTT
* * **
2351998 CTTCACCAACCTTTGGACAAAGAAGGAGGTGGCCATAATTGTTTCCAATTTTCA-CAACCTTTGA
1 CTTCACCAACCTTT-GACAAAGAAGGAGGTGACCATAATTG-TGCC-ATCCTCACCAACCTTTG-
* *
2352062 CCAA-GAGGGAGGTGGCCATAATGTTGA
62 CCAACGAGCGAAGTGGCCATAATGTTGA
2352089 AATTCTCACC
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
95 14 0.18
96 40 0.51
97 15 0.19
98 9 0.12
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (94 bp):
CTTCACCAACCTTTGACAAAGAAGGAGGTGACCATAATTGTGCCATCCTCACCAACCTTTGCCAA
CGAGCGAAGTGGCCATAATGTTGACGCTT
Found at i:2352079 original size:47 final size:47
Alignment explanation
Indices: 2351904--2352134 Score: 181
Period size: 47 Copynumber: 4.9 Consensus size: 47
2351894 TTGACTATCC
* * *
2351904 TTCACCAACCTTTGACAAATAGGGAGGTGACCATAATTG-TGCCATC
1 TTCACCAACCTTTGACAAAGAGGGAGGTGGCCATAATTGTTGCCATT
* * * * *
2351950 CTCACCAACCTTTGCCAATCGAGCGAAGTGGCC-TAATTGTTGACGC-TT
1 TTCACCAACCTTTGACAA-AGAGGGAGGTGGCCATAATTGTTG-C-CATT
* *
2351998 CTTCACCAACCTTTGGACAAAGAAGGAGGTGGCCATAATTGTTTCCAATT
1 -TTCACCAACCTTT-GACAAAGAGGGAGGTGGCCATAATTGTTGCC-ATT
* **
2352048 TTCA-CAACCTTTGACCAAGAGGGAGGTGGCCATAA-TGTTGAAATT
1 TTCACCAACCTTTGACAAAGAGGGAGGTGGCCATAATTGTTGCCATT
* * *
2352093 CTCACCCAA-C-TTGACAAATAGAGAGAGGTGG-CATAATGGTTG
1 TTCA-CCAACCTTTGAC-AA-AGAGGGAGGTGGCCATAATTGTTG
2352135 ACTCTAAGTA
Statistics
Matches: 147, Mismatches: 24, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
45 11 0.07
46 33 0.22
47 50 0.34
48 11 0.07
49 28 0.19
50 14 0.10
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (47 bp):
TTCACCAACCTTTGACAAAGAGGGAGGTGGCCATAATTGTTGCCATT
Found at i:2362775 original size:21 final size:21
Alignment explanation
Indices: 2362719--2362775 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
2362709 TGTCCTGGTT
2362719 TTGCTTTCGTTTTCTTGTCCTGC
1 TTGCTTTC-TTTT-TTGTCCTGC
* * * * *
2362742 TCGCATTCATTTTTGTCTTGG
1 TTGCTTTCTTTTTTGTCCTGC
2362763 TTGCTTTCTTTTT
1 TTGCTTTCTTTTT
2362776 ATCCACCCAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 17 0.65
22 3 0.12
23 6 0.23
ACGTcount: A:0.04, C:0.21, G:0.16, T:0.60
Consensus pattern (21 bp):
TTGCTTTCTTTTTTGTCCTGC
Found at i:2366793 original size:22 final size:23
Alignment explanation
Indices: 2366768--2366813 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2366758 TTAAATTAAA
2366768 TTTTAAT-TTG-AATATATATTTT
1 TTTTAATCTTGAAATA-ATATTTT
*
2366790 TTTTACTCTTGAAATAATATTTT
1 TTTTAATCTTGAAATAATATTTT
2366813 T
1 T
2366814 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTAATCTTGAAATAATATTTT
Found at i:2366886 original size:19 final size:20
Alignment explanation
Indices: 2366842--2366888 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2366832 TGTATTTAAA
*
2366842 TTTAATTAT-AAAATATTAT
1 TTTAAATATAAAAATATTAT
*
2366861 ATT-AATATAAAAATATT-T
1 TTTAAATATAAAAATATTAT
2366879 TTTAAATATA
1 TTTAAATATA
2366889 TTTTGTATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATATAAAAATATTAT
Found at i:2367850 original size:19 final size:22
Alignment explanation
Indices: 2367801--2367850 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2367791 ATAATGTTAT
2367801 TATTATTTTTAACTAGCGTGAA
1 TATTATTTTTAACTAGCGTGAA
*
2367823 TATTTATTTTTATCT-GC-T-AA
1 TA-TTATTTTTAACTAGCGTGAA
2367843 TATTATTT
1 TATTATTT
2367851 AAAACATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 1 0.04
22 4 0.15
23 11 0.42
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (22 bp):
TATTATTTTTAACTAGCGTGAA
Found at i:2368662 original size:15 final size:15
Alignment explanation
Indices: 2368642--2368671 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2368632 TGATATATAC
*
2368642 ATATATATATATTAT
1 ATATATATAAATTAT
2368657 ATATATATAAATTAT
1 ATATATATAAATTAT
2368672 CTCATTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATAAATTAT
Found at i:2370425 original size:81 final size:85
Alignment explanation
Indices: 2370327--2370489 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 85
2370317 TACTGCAGAT
*
2370327 TTCGGATACAATGTGAACATTGG-AAAGTGTTGT-GTG-GGTGTTGTTTCTATTATATAATG-CT
1 TTCGGATACAATGTGAACATTGGAAAAGTGTTGTGGTGTGGTG-TGTTTCTATTATATAATGCCC
2370388 ATTGC-ATCCAACATTTTAGA
65 ATTGCTATCCAACATTTTAGA
2370408 TTCGGATACAATGTGAACATTGGAAAAGTGTTGTGGTGTGGTGTGTTTCTATTATATAATGCCCA
1 TTCGGATACAATGTGAACATTGGAAAAGTGTTGTGGTGTGGTGTGTTTCTATTATATAATGCCCA
2370473 TTGCTATCCAACATTTT
66 TTGCTATCCAACATTTT
2370490 TTTTATTTTA
Statistics
Matches: 76, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
81 23 0.30
82 10 0.13
83 21 0.28
84 10 0.13
85 12 0.16
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.39
Consensus pattern (85 bp):
TTCGGATACAATGTGAACATTGGAAAAGTGTTGTGGTGTGGTGTGTTTCTATTATATAATGCCCA
TTGCTATCCAACATTTTAGA
Found at i:2372694 original size:11 final size:11
Alignment explanation
Indices: 2372678--2372704 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2372668 ATGATATATC
2372678 AATAAAATTAA
1 AATAAAATTAA
2372689 AATAAAATTAA
1 AATAAAATTAA
2372700 AATAA
1 AATAA
2372705 TCAAAGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATTAA
Found at i:2373307 original size:48 final size:48
Alignment explanation
Indices: 2373233--2373330 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
2373223 CAGATTGCCT
* *
2373233 ATGGCCTAACACCTTGTTTCATTCAGTGATAGTCTGCTCGGATATCCG
1 ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
2373281 ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
1 ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
2373329 AT
1 AT
2373331 ATTCAAAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (48 bp):
ATGGCCTAACACCTTGTTTCAGTCAGTGATAGTATGCTCGGATATCCG
Found at i:2373548 original size:50 final size:50
Alignment explanation
Indices: 2373489--2373748 Score: 407
Period size: 50 Copynumber: 5.2 Consensus size: 50
2373479 AGTTGTTGTC
* *
2373489 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2373539 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAAGTGGCCATA
1 ATTGTTGACTATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
2373589 ATTGTTGACGATTCTTCACCAACATTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
2373639 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2373689 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2373739 ATGGTTGACT
1 ATTGTTGACT
2373749 CTAAGTATAT
Statistics
Matches: 194, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
49 2 0.01
50 190 0.98
51 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:2378214 original size:50 final size:50
Alignment explanation
Indices: 2378145--2378404 Score: 418
Period size: 50 Copynumber: 5.2 Consensus size: 50
2378135 AGTTGTTGCC
*
2378145 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2378195 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
1 ATTGTTGACTATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
2378245 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* * *
2378295 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
2378345 ATTGTTGA-TAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
2378395 ATTGTTGACT
1 ATTGTTGACT
2378405 CTAAGTATAT
Statistics
Matches: 194, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
49 2 0.01
50 189 0.97
51 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:2383515 original size:12 final size:12
Alignment explanation
Indices: 2383485--2383514 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2383475 GTAGCTCCCC
2383485 TTCTTTTCCTTT
1 TTCTTTTCCTTT
2383497 TTCTTTTCCTTT
1 TTCTTTTCCTTT
2383509 TT-TTTT
1 TTCTTTT
2383515 TTTTAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTCCTTT
Found at i:2387255 original size:15 final size:15
Alignment explanation
Indices: 2387216--2387257 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2387206 AATTAAAGAT
2387216 TATTTAAT-TATT-A
1 TATTTAATATATTAA
* *
2387229 TTTTTAAAATATTAA
1 TATTTAATATATTAA
2387244 TATTTAATATATTA
1 TATTTAATATATTA
2387258 TTTTGATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 6 0.26
14 4 0.17
15 13 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTAATATATTAA
Found at i:2387268 original size:32 final size:26
Alignment explanation
Indices: 2387216--2387310 Score: 73
Period size: 30 Copynumber: 3.3 Consensus size: 26
2387206 AATTAAAGAT
2387216 TATTTAATTATTATTTTTAAAATATTAA
1 TATTTAATTATTATTTTTAAAA-A-TAA
2387244 TATTTAATATATTATTTTGATTAAAAATAA
1 TATTTAAT-TATTA-TTT--TTAAAAATAA
* * *
2387274 TATATTATTTATATATTTTAAATAAATAT
1 TAT-TTAATTAT-TATTTTTAA-AAATAA
2387303 TAGTTTAA
1 TA-TTTAA
2387311 CATGTGCTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
28 11 0.20
29 15 0.27
30 16 0.29
31 7 0.13
32 6 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TATTTAATTATTATTTTTAAAAATAA
Found at i:2388080 original size:18 final size:19
Alignment explanation
Indices: 2388040--2388085 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2388030 TGTATTTAAA
2388040 TTTAAT-TATAAAATATAT
1 TTTAATATATAAAATATAT
* *
2388058 ATTAATATA-AAAATATTT
1 TTTAATATATAAAATATAT
2388076 TTTAA-ATATA
1 TTTAATATATA
2388086 TTTTTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.13
18 18 0.78
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATATATAAAATATAT
Found at i:2388657 original size:16 final size:17
Alignment explanation
Indices: 2388636--2388679 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2388626 ATTAAAATTC
2388636 AAATATTATATTTAT-T
1 AAATATTATATTTATAT
*
2388652 AAATATTAT-TTTTTAT
1 AAATATTATATTTATAT
2388668 AAATAATTATAT
1 AAAT-ATTATAT
2388680 ATAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 5 0.21
18 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATTATATTTATAT
Found at i:2390270 original size:28 final size:28
Alignment explanation
Indices: 2390206--2390270 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
2390196 TTAAAAATTA
* * *
2390206 AAAATTTCTTTAAATATAATAAATATAT
1 AAAATTTATCTAAATAAAATAAATATAT
2390234 AAAATTTTATCTAAATAAAAT-AATATAAT
1 AAAA-TTTATCTAAATAAAATAAATAT-AT
2390263 AAAATTTA
1 AAAATTTA
2390271 AAAAACCCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATTTATCTAAATAAAATAAATATAT
Found at i:2390667 original size:18 final size:17
Alignment explanation
Indices: 2390654--2390686 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2390644 TTTTTTTAAT
2390654 TTAA-AATTTATTTTTA
1 TTAACAATTTATTTTTA
2390670 TTAATCAATTTATTTTT
1 TTAA-CAATTTATTTTT
2390687 TACAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAACAATTTATTTTTA
Found at i:2390980 original size:28 final size:29
Alignment explanation
Indices: 2390911--2390988 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
2390901 TATAAAAATA
2390911 AAATATACCATTATAAAAATATTAATATTTT
1 AAATATA--ATTATAAAAATATTAATATTTT
* *
2390942 AAATTTTATTAT-AAAATATTAAATATTTT
1 AAATATAATTATAAAAATATT-AATATTTT
*
2390971 -AATATAATTATCAAAATA
1 AAATATAATTATAAAAATA
2390989 AACGTATGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 17 0.41
29 19 0.46
31 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATATAATTATAAAAATATTAATATTTT
Found at i:2391628 original size:41 final size:41
Alignment explanation
Indices: 2391560--2391674 Score: 117
Period size: 44 Copynumber: 2.7 Consensus size: 41
2391550 CAACAATTTT
* **
2391560 AAAATATAAATTTATTTGATTTTAAATATTATTT-ATTTAATA
1 AAAATATAAAATT-TTT-ATTTTAAATATTATTTAAAATAATA
*
2391602 AAAATATAAAATTTTTATTTTAAA-ATATATTTAAAATATTA
1 AAAATATAAAATTTTTATTTTAAATAT-TATTTAAAATAATA
*
2391643 AAAATTAATAAATATTTATATTTTAAATATTA
1 AAAA-T-ATAAA-ATTTTTATTTTAAATATTA
2391675 AATTTAAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
39 2 0.03
40 13 0.21
41 12 0.19
42 13 0.21
43 5 0.08
44 15 0.24
45 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (41 bp):
AAAATATAAAATTTTTATTTTAAATATTATTTAAAATAATA
Found at i:2391671 original size:43 final size:39
Alignment explanation
Indices: 2391560--2391672 Score: 102
Period size: 43 Copynumber: 2.7 Consensus size: 39
2391550 CAACAATTTT
**
2391560 AAAATAT-AAATTTATTTGATTTTAAATATTATTTATTTAATA
1 AAAATATAAAATTTA--T-ATTTTAAATA-TATTTAAATAATA
* *
2391602 AAAATATAAAATTTTTATTTTAAAATATATTTAAAATATTA
1 AAAATATAAAATTTATATTTT-AAATATATTT-AAATAATA
2391643 AAAATTAATAAATATTTATATTTTAAATAT
1 AAAA-T-ATAAA-ATTTATATTTTAAATAT
2391673 TAAATTTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
40 10 0.17
41 15 0.25
42 8 0.13
43 17 0.28
44 10 0.17
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
AAAATATAAAATTTATATTTTAAATATATTTAAATAATA
Found at i:2396923 original size:23 final size:23
Alignment explanation
Indices: 2396896--2396944 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2396886 AATTTAGGGG
2396896 ATTTGAATTTTTTTTGGTCGAGT
1 ATTTGAATTTTTTTTGGTCGAGT
* *
2396919 ATTTGAATTTTTTTTTGTTGAGT
1 ATTTGAATTTTTTTTGGTCGAGT
2396942 ATT
1 ATT
2396945 CAGTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (23 bp):
ATTTGAATTTTTTTTGGTCGAGT
Found at i:2396951 original size:22 final size:23
Alignment explanation
Indices: 2396896--2396955 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2396886 AATTTAGGGG
*
2396896 ATTTGAATTTTTTTTGGTCGAGT
1 ATTTCAATTTTTTTTGGTCGAGT
* * *
2396919 ATTTGAATTTTTTTTTGTTGAGT
1 ATTTCAATTTTTTTTGGTCGAGT
*
2396942 A-TTCAGTTTTTTTT
1 ATTTCAATTTTTTTT
2396956 ATTGATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (23 bp):
ATTTCAATTTTTTTTGGTCGAGT
Found at i:2397038 original size:30 final size:30
Alignment explanation
Indices: 2397004--2397061 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2396994 AATTATTGTT
** *
2397004 ATAATTATTTAATTTTATTTTTATTTTAAA
1 ATAATTATTTAATTACAGTTTTATTTTAAA
*
2397034 ATAATTATTTTATTACAGTTTTATTTTA
1 ATAATTATTTAATTACAGTTTTATTTTA
2397062 TTTTAGGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (30 bp):
ATAATTATTTAATTACAGTTTTATTTTAAA
Found at i:2397258 original size:17 final size:16
Alignment explanation
Indices: 2397212--2397269 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
2397202 GTTGTATACT
*
2397212 TATTTAAAATATTTTA
1 TATTTAAATTATTTTA
*
2397228 TATTTAAATAATTTTAA
1 TATTTAAATTATTTT-A
2397245 TATATT-AATTATTTGTA
1 TAT-TTAAATTATTT-TA
2397262 TTATTTAA
1 -TATTTAA
2397270 GTTTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 13 0.38
17 14 0.41
18 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TATTTAAATTATTTTA
Found at i:2399698 original size:2 final size:2
Alignment explanation
Indices: 2399691--2399727 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2399681 TTGAAGTAAA
*
2399691 AT AT AT AT AT AT AT AT AT GT 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 AT AT A
2399728 GTGAAATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2400063 original size:35 final size:34
Alignment explanation
Indices: 2400024--2400098 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
2400014 TTAAATCGAG
* *
2400024 TTTAAAATTTTATTTTATTA-TTATATATTATAATA
1 TTTAAAA-TATATTTTAATAGTTATATATT-TAATA
*
2400059 TTTAAAATATATTTTAATAGTTATATATTTTATA
1 TTTAAAATATATTTTAATAGTTATATATTTAATA
2400093 TTTAAA
1 TTTAAA
2400099 TTTAATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 20 0.56
35 16 0.44
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (34 bp):
TTTAAAATATATTTTAATAGTTATATATTTAATA
Found at i:2400086 original size:16 final size:15
Alignment explanation
Indices: 2400034--2400106 Score: 53
Period size: 19 Copynumber: 4.7 Consensus size: 15
2400024 TTTAAAATTT
*
2400034 TATTTTATTATTATA
1 TATTTTAATATTATA
*
2400049 TATTATAATATTTAAAATA
1 TATTTTAATA-TT---ATA
2400068 TATTTTAATAGTTATA
1 TATTTTAATA-TTATA
2400084 TATTTT-ATATT-TA
1 TATTTTAATATTATA
*
2400097 -AATTTAATAT
1 TATTTTAATAT
2400107 ATTTTTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 4 0.08
13 6 0.12
14 2 0.04
15 11 0.23
16 11 0.23
19 14 0.29
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
TATTTTAATATTATA
Found at i:2400094 original size:34 final size:35
Alignment explanation
Indices: 2400024--2400141 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 35
2400014 TTAAATCGAG
* *
2400024 TTTAAAATTTTATTTTATTATTATATATTATAATA
1 TTTAAAATTATATTTTAATATTATATATTATAATA
*
2400059 TTTAAAA-TATATTTTAATAGTTATATATT-TTATA
1 TTTAAAATTATATTTTAATA-TTATATATTATAATA
* ** * *
2400093 TTTAAATTTAATATATTTTTTATTATTTA-AATAATAA
1 TTTAAAATT-ATAT-TTTAATATTATATATTATAAT-A
2400130 TTT-AAATTATAT
1 TTTAAAATTATAT
2400142 CAATAAGATC
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
34 20 0.30
35 21 0.31
36 17 0.25
37 9 0.13
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTAAAATTATATTTTAATATTATATATTATAATA
Found at i:2400114 original size:40 final size:41
Alignment explanation
Indices: 2400038--2400114 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
2400028 AAATTTTATT
2400038 TTATTATTATATATTATAATATTTAAAATATATTTTAATAG
1 TTATTATTATATATTATAATATTTAAAATATATTTTAATAG
* * *
2400079 TTATATATTTTATATT-TAA-ATTTAATATATTTTTTA
1 TTAT-TATTATATATTATAATATTTAAAATATATTTTA
2400115 TTATTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 15 0.47
41 7 0.22
42 10 0.31
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (41 bp):
TTATTATTATATATTATAATATTTAAAATATATTTTAATAG
Found at i:2400521 original size:36 final size:34
Alignment explanation
Indices: 2400478--2400625 Score: 123
Period size: 34 Copynumber: 4.4 Consensus size: 34
2400468 AGGTTGATAG
*
2400478 TATTA-ATTAAATTTAATAATTTATATTATTTTTA
1 TATTATATTATATTT-ATAATTTATATTATTTTTA
*
2400512 TATTATAATTATATTTAAAATATTATA-TA-TTTTA
1 TATTAT-ATTATATTTATAAT-TTATATTATTTTTA
*
2400546 -A-TATA-TATTTTTATCATATTTATATTATTTTTTA
1 TATTATATTATATTTAT-A-ATTTATATTA-TTTTTA
* *
2400580 TATTATATTATATTT-TATTTTAT-TTATTTTTT
1 TATTATATTATATTTATAATTTATATTATTTTTA
*
2400612 TATAATATATATAT
1 TATTATAT-TATAT
2400626 ATATTCATGC
Statistics
Matches: 94, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
30 7 0.07
31 7 0.07
32 19 0.20
33 9 0.10
34 20 0.21
35 8 0.09
36 18 0.19
37 6 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTATATTATATTTATAATTTATATTATTTTTA
Found at i:2400522 original size:17 final size:16
Alignment explanation
Indices: 2400498--2400610 Score: 90
Period size: 17 Copynumber: 6.8 Consensus size: 16
2400488 ATTTAATAAT
2400498 TTATATTATTTTTATA
1 TTATATTATTTTTATA
*
2400514 TTATAATTATATTTAAAATA
1 TTAT-ATTAT-TTT--TATA
*
2400534 TTATA-TATTTTAATA
1 TTATATTATTTTTATA
*
2400549 -TATATT-TTTATCATA
1 TTATATTATTT-TTATA
2400564 TTTATATTATTTTTTATA
1 -TTATATTA-TTTTTATA
*
2400582 TTATATTATATTTTATT
1 TTATATTAT-TTTTATA
2400599 TTAT-TTATTTTT
1 TTATATTATTTTT
2400611 TTATAATATA
Statistics
Matches: 82, Mismatches: 4, Indels: 23
0.75 0.04 0.21
Matches are distributed among these distances:
14 7 0.09
15 13 0.16
16 9 0.11
17 32 0.39
18 10 0.12
19 4 0.05
20 7 0.09
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTATTTTTATA
Found at i:2400581 original size:12 final size:12
Alignment explanation
Indices: 2400564--2400611 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2400554 TTTTATCATA
2400564 TTTATATTATTT
1 TTTATATTATTT
2400576 TTTATATTA--T
1 TTTATATTATTT
*
2400586 ATTATATT-TTAT
1 TTTATATTATT-T
2400598 TTTAT-TTATTT
1 TTTATATTATTT
2400609 TTT
1 TTT
2400612 TATAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 8 0.27
11 6 0.20
12 16 0.53
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:2400930 original size:23 final size:23
Alignment explanation
Indices: 2400898--2400950 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2400888 ATTTTAAAAA
*
2400898 ATAATATTTAATAATTTTAAATTTT
1 ATAAT-TTTAATA-TTTTAAAATTT
*
2400923 A-AATTTTAATTTTTTAAAATTT
1 ATAATTTTAATATTTTAAAATTT
2400945 ATAATT
1 ATAATT
2400951 CTTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 11 0.44
23 10 0.40
24 3 0.12
25 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAATTTTAATATTTTAAAATTT
Found at i:2401194 original size:2 final size:2
Alignment explanation
Indices: 2401187--2401213 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2401177 TAAATTTATC
2401187 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2401214 AAATACAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2405876 original size:14 final size:14
Alignment explanation
Indices: 2405854--2405896 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2405844 TCATATCACC
* *
2405854 TACAGTTTTCTTAT
1 TACACTTTTCTAAT
2405868 TACACTTTTCTAAT
1 TACACTTTTCTAAT
*
2405882 TA-TCTTTTCTAAT
1 TACACTTTTCTAAT
2405895 TA
1 TA
2405897 TGAAATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (14 bp):
TACACTTTTCTAAT
Found at i:2405890 original size:13 final size:13
Alignment explanation
Indices: 2405872--2405897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2405862 TCTTATTACA
2405872 CTTTTCTAATTAT
1 CTTTTCTAATTAT
2405885 CTTTTCTAATTAT
1 CTTTTCTAATTAT
2405898 GAAATCTTTA
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:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTTCTAATTAT
Found at i:2407138 original size:6 final size:6
Alignment explanation
Indices: 2407127--2407152 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2407117 AAATAACTGC
2407127 GGCGGT GGCGGT GGCGGT GGCGGT GG
1 GGCGGT GGCGGT GGCGGT GGCGGT GG
2407153 AGGATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.69, T:0.15
Consensus pattern (6 bp):
GGCGGT
Found at i:2409025 original size:2 final size:2
Alignment explanation
Indices: 2409020--2409044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2409010 TTTTCCTCAA
2409020 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2409045 AAGGACTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2410937 original size:15 final size:16
Alignment explanation
Indices: 2410919--2410951 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2410909 ATTTTAAAAA
2410919 ATTAAAT-ATATTTAT
1 ATTAAATAATATTTAT
2410934 ATTAAATAAATATTTAT
1 ATTAAAT-AATATTTAT
2410951 A
1 A
2410952 AATAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAATAATATTTAT
Found at i:2411400 original size:2 final size:2
Alignment explanation
Indices: 2411393--2411428 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2411383 ATCTCCTTCA
2411393 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2411429 CCCCCTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2415014 original size:3 final size:3
Alignment explanation
Indices: 2415006--2415033 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2414996 GGTGGTTCTC
2415006 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2415034 CATCGTCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2423196 original size:14 final size:14
Alignment explanation
Indices: 2423176--2423209 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2423166 AATGGTGAGT
*
2423176 TTTTTTTTCTTTTTC
1 TTTTTTTT-TTTTCC
2423191 TTTTTTTTTTTTCC
1 TTTTTTTTTTTTCC
2423205 TTTTT
1 TTTTT
2423210 AAAGTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTCC
Found at i:2423902 original size:75 final size:75
Alignment explanation
Indices: 2423758--2423904 Score: 188
Period size: 75 Copynumber: 2.0 Consensus size: 75
2423748 GAAAATTAAG
* * * * * * *
2423758 AATGATTAAAAGTTGAGTTGCATTAATTAGATTAATTTTATTTTTTATGCTAAATAGTTTGCAAT
1 AATGATTAAAAGTTGAATTGCATGAATTAGATTAATTTTATTTTTGATACAAAATAGGTTACAAT
2423823 AAAAAAAACT
66 AAAAAAAACT
* * * *
2423833 AATGATTAAAATTTGAATTGCATGAATTAGGTTAA-TTTATTTTTGGTACAAAATAGGTTATAAT
1 AATGATTAAAAGTTGAATTGCATGAATTAGATTAATTTTATTTTTGATACAAAATAGGTTACAAT
2423897 AAAAAAAA
66 AAAAAAAA
2423905 TTATAAATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
74 30 0.49
75 31 0.51
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.39
Consensus pattern (75 bp):
AATGATTAAAAGTTGAATTGCATGAATTAGATTAATTTTATTTTTGATACAAAATAGGTTACAAT
AAAAAAAACT
Found at i:2430854 original size:2 final size:2
Alignment explanation
Indices: 2430847--2430873 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2430837 ATAAGAGGGG
2430847 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2430874 GAATCAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2435411 original size:29 final size:30
Alignment explanation
Indices: 2435358--2435429 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
2435348 ATGTCGTTAT
* *
2435358 AAATATTTTATTTTTCAATTATAAAGAAA-A
1 AAATATTTTATTTTACAATGATAAA-AAATA
*
2435388 AAATATTTT-TTTTACAATGGTAAAAAATA
1 AAATATTTTATTTTACAATGATAAAAAATA
2435417 AAATTAATTTTAT
1 AAA-T-ATTTTAT
2435430 ATTTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 3 0.09
29 16 0.46
30 10 0.29
31 5 0.14
32 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATATTTTATTTTACAATGATAAAAAATA
Found at i:2435578 original size:19 final size:20
Alignment explanation
Indices: 2435554--2435602 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2435544 ATCACGTGAA
*
2435554 AAAAAATTTAGATA-AATTT
1 AAAAAATTTAGATATAAATT
*
2435573 AAAAAATTTATATATAAATT
1 AAAAAATTTAGATATAAATT
*
2435593 ACAAAATTTA
1 AAAAAATTTA
2435603 ATGACTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAAATTTAGATATAAATT
Found at i:2435633 original size:17 final size:18
Alignment explanation
Indices: 2435611--2435644 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2435601 TAATGACTAT
2435611 TTTAAATAT-TAAAATAA
1 TTTAAATATATAAAATAA
*
2435628 TTTAAATTTATAAAATA
1 TTTAAATATATAAAATA
2435645 TATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAATATATAAAATAA
Found at i:2435669 original size:26 final size:26
Alignment explanation
Indices: 2435614--2435664 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2435604 TGACTATTTT
*
2435614 AAATATTAAAATAATTTAAATTTATA
1 AAATATTAAAATAAATTAAATTTATA
*
2435640 AAATATATAAAATAAATTAATTTTA
1 AAATAT-TAAAATAAATTAAATTTA
2435665 CAAATCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATATTAAAATAAATTAAATTTATA
Found at i:2444679 original size:15 final size:15
Alignment explanation
Indices: 2444634--2444691 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2444624 TTAAATTAAT
*
2444634 ATTTAATAATAAAAA
1 ATTTAATTATAAAAA
* *
2444649 TATTT-TTTAT-ATAA
1 -ATTTAATTATAAAAA
2444663 ATTTAATTATAAAAA
1 ATTTAATTATAAAAA
2444678 ATATTAA-TATAAAA
1 AT-TTAATTATAAAA
2444692 TTAATATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.12
14 7 0.21
15 15 0.44
16 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTAATTATAAAAA
Found at i:2444688 original size:29 final size:28
Alignment explanation
Indices: 2444634--2444697 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
2444624 TTAAATTAAT
**
2444634 ATTTAATAATAAAAATATTTTTTATATAA
1 ATTTAATAATAAAAATATTTAATATA-AA
*
2444663 ATTTAATTATAAAAA-ATATTAATATAAA
1 ATTTAATAATAAAAATAT-TTAATATAAA
2444691 A-TTAATA
1 ATTTAATA
2444698 TTTGTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 5 0.17
28 5 0.17
29 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTAATAATAAAAATATTTAATATAAA
Found at i:2447211 original size:75 final size:72
Alignment explanation
Indices: 2447116--2447258 Score: 223
Period size: 75 Copynumber: 1.9 Consensus size: 72
2447106 CTGAAGAAGC
*
2447116 ACAATCTTATTGGAAGCAGGAATTTGGGCATTTAGATGATATATGAATTTGACAAATGTGGAAAG
1 ACAATCTTATTGGAAGCAGGAATTTGGACATTTAGATG--ATATGAA-TTGACAAATGTGGAAAG
*
2447181 TTTTAGTGCT
63 TGTTAGTGCT
* *
2447191 ACAATCTTATTGGAAGCAGGAATTTGGACATTTAGATGATATGGATTGAGAAATGTGGAAAGTGT
1 ACAATCTTATTGGAAGCAGGAATTTGGACATTTAGATGATATGAATTGACAAATGTGGAAAGTGT
2447256 TAG
66 TAG
2447259 AGCTTTCTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 21 0.33
73 6 0.09
75 37 0.58
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.33
Consensus pattern (72 bp):
ACAATCTTATTGGAAGCAGGAATTTGGACATTTAGATGATATGAATTGACAAATGTGGAAAGTGT
TAGTGCT
Found at i:2449497 original size:17 final size:17
Alignment explanation
Indices: 2449477--2449516 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2449467 ATTTAATTAA
2449477 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
*
2449494 ATATTTAATATAAATAT
1 ATATTAAATATAAATAT
2449511 AT-TTAA
1 ATATTAA
2449517 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:2452359 original size:2 final size:2
Alignment explanation
Indices: 2452352--2452386 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2452342 AATATTCATC
* *
2452352 TA TA TA TA TA TA TA TA TA TA TA TT TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2452387 TATTAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:2452387 original size:12 final size:12
Alignment explanation
Indices: 2452354--2452402 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
2452344 TATTCATCTA
* *
2452354 TATATATATATA
1 TATATATATTTT
2452366 TATATATATTTT
1 TATATATATTTT
*
2452378 TATATATATTAT
1 TATATATATTTT
2452390 TA-ATATAGTTTT
1 TATATATA-TTTT
2452402 T
1 T
2452403 TAAAACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 5 0.16
12 27 0.84
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TATATATATTTT
Found at i:2452560 original size:20 final size:19
Alignment explanation
Indices: 2452537--2452580 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2452527 TAAAAATTAA
*
2452537 ATAAATAAATTAATCAAAAT
1 ATAAATAAATAAATC-AAAT
* *
2452557 ATAACTAAATAAATCTAAT
1 ATAAATAAATAAATCAAAT
2452576 ATAAA
1 ATAAA
2452581 ATTACTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAATAAATAAATCAAAT
Found at i:2452565 original size:24 final size:24
Alignment explanation
Indices: 2452529--2452584 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2452519 TAAATCATTA
2452529 AAAATTAAATAAATAAAT-TAATC
1 AAAATTAAATAAATAAATCTAATC
* *
2452552 AAAATATAACTAAATAAATCTAATAT
1 AAAAT-TAAATAAATAAATCTAAT-C
2452578 AAAATTA
1 AAAATTA
2452585 CTTAATTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.18
24 12 0.43
25 6 0.21
26 5 0.18
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATTAAATAAATAAATCTAATC
Found at i:2452989 original size:12 final size:12
Alignment explanation
Indices: 2452972--2453004 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2452962 AAATTTTATT
2452972 TTTTTAATTTAA
1 TTTTTAATTTAA
2452984 TTTTTAA-TTAA
1 TTTTTAATTTAA
*
2452995 CTTTTAATTT
1 TTTTTAATTT
2453005 TTATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:2455566 original size:21 final size:22
Alignment explanation
Indices: 2455515--2455555 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2455505 CAATCTGATC
2455515 AAAT-ATATATTATTATTTAAT
1 AAATAATATATTATTATTTAAT
2455536 AAATAATATATT-TTATTTAA
1 AAATAATATATTATTATTTAA
2455556 ATTTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATAATATATTATTATTTAAT
Found at i:2456827 original size:5 final size:5
Alignment explanation
Indices: 2456817--2456842 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2456807 ATTGAGCCGG
2456817 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
2456843 CTCGTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:2457065 original size:34 final size:34
Alignment explanation
Indices: 2457026--2457093 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
2457016 TGTAAATTAA
* * *
2457026 TTTTATTATTTAAAAAT-AATAAATATTTTTATAT
1 TTTTA-TAATTAAAAATGAATAAAAATATTTATAT
*
2457060 TTTTATAATTAAAATTGAATAAAAATATTTATAT
1 TTTTATAATTAAAAATGAATAAAAATATTTATAT
2457094 AAATTGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
TTTTATAATTAAAAATGAATAAAAATATTTATAT
Found at i:2457515 original size:2 final size:2
Alignment explanation
Indices: 2457508--2457539 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2457498 TAATTGTTGA
2457508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2457540 TAGTCTCAAG
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):
AT
Found at i:2457863 original size:2 final size:2
Alignment explanation
Indices: 2457856--2457894 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2457846 CAGCATCTGC
2457856 AT AT AT 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 AT AT AT A
2457895 ACTCAGCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2460448 original size:2 final size:2
Alignment explanation
Indices: 2460441--2460481 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2460431 CTTTGGCCTT
2460441 TA TA TA TA TA 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 TA TA TA TA TA T
2460482 GATTAATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2460816 original size:22 final size:23
Alignment explanation
Indices: 2460791--2460840 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
2460781 ATATTATTTT
2460791 TATTATTAACT-TAT-ATTTGATA
1 TATTATTAA-TATATAATTTGATA
* *
2460813 TATTGTTAATATATAATTTTATA
1 TATTATTAATATATAATTTGATA
2460836 TATTA
1 TATTA
2460841 ATTTATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.48
23 11 0.48
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TATTATTAATATATAATTTGATA
Found at i:2461176 original size:2 final size:2
Alignment explanation
Indices: 2461169--2461197 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2461159 ATACACATGC
2461169 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 A
2461198 AGATAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2461767 original size:22 final size:22
Alignment explanation
Indices: 2461739--2461782 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2461729 TAAAAATTAT
*
2461739 TTTTAT-ATTAATATTTATATAA
1 TTTTATAATTAA-ATTTAAATAA
2461761 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
2461783 AATATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:2463377 original size:3 final size:3
Alignment explanation
Indices: 2463371--2463406 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2463361 TTTTTCACGA
2463371 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2463407 TTGGTGAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2463882 original size:31 final size:31
Alignment explanation
Indices: 2463847--2463912 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
2463837 TAAAATAATT
**
2463847 ATTTAAGCTATAAAATTTTT-ATTTTTATTAA
1 ATTTAA-CTATAAAATTTTTAAAATTTATTAA
* *
2463878 ATTTAATTATAAACTTTTTAAAATTTATTAA
1 ATTTAACTATAAAATTTTTAAAATTTATTAA
2463909 ATTT
1 ATTT
2463913 TCAATAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTTAACTATAAAATTTTTAAAATTTATTAA
Found at i:2463890 original size:30 final size:31
Alignment explanation
Indices: 2463855--2463912 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2463845 TTATTTAAGC
**
2463855 TATAAAATTTTT-ATTTTTATTAAATTTAAT
1 TATAAAATTTTTAAAATTTATTAAATTTAAT
*
2463885 TATAAACTTTTTAAAATTTATTAAATTT
1 TATAAAATTTTTAAAATTTATTAAATTT
2463913 TCAATAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
TATAAAATTTTTAAAATTTATTAAATTTAAT
Found at i:2464887 original size:12 final size:12
Alignment explanation
Indices: 2464870--2464896 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2464860 AACAATGTAT
2464870 GATAATATAATG
1 GATAATATAATG
2464882 GATAATATAATG
1 GATAATATAATG
2464894 GAT
1 GAT
2464897 TCATTCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (12 bp):
GATAATATAATG
Found at i:2466067 original size:14 final size:13
Alignment explanation
Indices: 2466039--2466097 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
2466029 ATTTAATTTT
* *
2466039 TAAATTTAATGAA
1 TAAATTTATTAAA
2466052 TAAAATTTATTAAA
1 T-AAATTTATTAAA
2466066 T-AATTT-TTAAA
1 TAAATTTATTAAA
*
2466077 TAAATTAATTAAA
1 TAAATTTATTAAA
2466090 TTAAATTT
1 -TAAATTT
2466098 TAAATTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.16
12 9 0.24
13 6 0.16
14 17 0.45
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
TAAATTTATTAAA
Found at i:2466087 original size:24 final size:25
Alignment explanation
Indices: 2466054--2466102 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
2466044 TTAATGAATA
* *
2466054 AAATTTATTAAA-TAATTTTTAAAT
1 AAATTAATTAAATTAAATTTTAAAT
2466078 AAATTAATTAAATTAAATTTTAAAT
1 AAATTAATTAAATTAAATTTTAAAT
2466103 TTCATTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATTAATTAAATTAAATTTTAAAT
Found at i:2466585 original size:23 final size:24
Alignment explanation
Indices: 2466541--2466585 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2466531 AAAAAAGAAA
* *
2466541 ATTAATTAATTTTATAAGTTATGT
1 ATTAATAAATTATATAAGTTATGT
2466565 ATTAATAAATTAT-TAAGTTAT
1 ATTAATAAATTATATAAGTTAT
2466586 ATGATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (24 bp):
ATTAATAAATTATATAAGTTATGT
Found at i:2466920 original size:2 final size:2
Alignment explanation
Indices: 2466915--2466950 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2466905 TCTCTCCGCT
*
2466915 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2466951 GCTTGCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:2466924 original size:14 final size:13
Alignment explanation
Indices: 2466905--2466954 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
2466895 TTCGTCAGAG
2466905 TCTCTC-CGCTTC
1 TCTCTCTCGCTTC
*
2466917 TCTCTCTCTCTT-
1 TCTCTCTCGCTTC
*
2466929 TCTCTCTCTCTCTC
1 TCTCTCTCGCT-TC
2466943 TCTCTCTCGCTT
1 TCTCTCTCGCTT
2466955 GCATTTGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 17 0.52
13 6 0.18
14 10 0.30
ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50
Consensus pattern (13 bp):
TCTCTCTCGCTTC
Found at i:2472924 original size:6 final size:7
Alignment explanation
Indices: 2472899--2472923 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2472889 CTCATCAGCC
2472899 TTTTTAT
1 TTTTTAT
2472906 TTTTTAT
1 TTTTTAT
2472913 TTTTTAT
1 TTTTTAT
2472920 TTTT
1 TTTT
2472924 ACCTCTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:2474290 original size:2 final size:2
Alignment explanation
Indices: 2474277--2474315 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2474267 AATCAAAATT
*
2474277 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2474316 AATGCAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2476953 original size:69 final size:70
Alignment explanation
Indices: 2476842--2476979 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 70
2476832 AACATGCTGC
* *
2476842 AAATGCACTCAAGAATCTTACTGGAAGATTTTATGCTGGTTTG-ACTTTTTCTATCTTATATATA
1 AAATGCACTCAAGAATCTTACTGGAAGATTTTATACTGGTTTGAACTTTTCCTATCTTATATATA
2476906 TATAG
66 TATAG
*
2476911 AAATGCACTCAAGAATCTTACTGGAAGATTTTATACTGGTTTGAACTTTTCCTATCTTTTATATA
1 AAATGCACTCAAGAATCTTACTGGAAGATTTTATACTGGTTTGAACTTTTCCTATCTTATATATA
2476976 TATA
66 TATA
2476980 CATATAGATA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
69 42 0.65
70 23 0.35
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (70 bp):
AAATGCACTCAAGAATCTTACTGGAAGATTTTATACTGGTTTGAACTTTTCCTATCTTATATATA
TATAG
Found at i:2477730 original size:70 final size:70
Alignment explanation
Indices: 2477639--2477902 Score: 300
Period size: 70 Copynumber: 3.8 Consensus size: 70
2477629 TTCCGTTTTC
* * * *
2477639 TCATAATACATAATAGCTGCTTGT-TCTGTTAACTTGTCCTTTTGTATTAGCTTCTATATATTGG
1 TCATAATACGTTATAGATGCTTGTGT-TGTTAAGTTGTCCTTTTGTATTAGCTTCTATATATTGG
2477703 GTATTT
65 GTATTT
* *
2477709 TCATAATACGTTATAGATGCTTGTGTTTTTAAGTTGTCCTGTTGTATTAGCTTCTATATATTGGG
1 TCATAATACGTTATAGATGCTTGTGTTGTTAAGTTGTCCTTTTGTATTAGCTTCTATATATTGGG
*
2477774 TGTTT
66 TATTT
* * * * * *
2477779 ACATTATATGTTATAGATGCTTTTGTTGTTAAGTTGTCCTTTTATATTAGCTTCTATCTATT-GG
1 TCATAATACGTTATAGATGCTTGTGTTGTTAAGTTGTCCTTTTGTATTAGCTTCTATATATTGGG
2477843 TGATTT
66 T-ATTT
* * ** * * *
2477849 TTATTATAC-ACAAATGATGCTTGTGTTGTTAAGTTGCCCTTTTGTAATAGCTTC
1 TCATAATACGTTATA-GATGCTTGTGTTGTTAAGTTGTCCTTTTGTATTAGCTTC
2477903 AATCGATTGG
Statistics
Matches: 165, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
69 5 0.03
70 159 0.96
71 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (70 bp):
TCATAATACGTTATAGATGCTTGTGTTGTTAAGTTGTCCTTTTGTATTAGCTTCTATATATTGGG
TATTT
Found at i:2479968 original size:1 final size:1
Alignment explanation
Indices: 2479964--2479989 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2479954 TTTTTTTTTT
2479964 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
2479990 AAATATTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2483121 original size:36 final size:36
Alignment explanation
Indices: 2483065--2483142 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
2483055 GGAAAAAACC
2483065 TCATCAGACTCATCTTCATCCTCAGAATCATCT-TCA
1 TCATCAGACTCATCTTCATCCTCAGAATCA-CTATCA
2483101 TCATCAGAAC-CA-CTTCCATCCTCAGAATCACTATCA
1 TCATCAG-ACTCATCTT-CATCCTCAGAATCACTATCA
2483137 TCATCA
1 TCATCA
2483143 TCATCCTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.13
36 32 0.82
37 2 0.05
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
TCATCAGACTCATCTTCATCCTCAGAATCACTATCA
Found at i:2483132 original size:18 final size:18
Alignment explanation
Indices: 2483068--2483130 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 18
2483058 AAAAACCTCA
*
2483068 TCAGACTCATCTTCATCC
1 TCAGAATCATCTTCATCC
*
2483086 TCAGAATCATCTTCATCA
1 TCAGAATCATCTTCATCC
*
2483104 TCAGAACCA-CTTCCATCC
1 TCAGAATCATCTT-CATCC
2483122 TCAGAATCA
1 TCAGAATCA
2483131 CTATCATCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 3 0.08
18 36 0.92
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.29
Consensus pattern (18 bp):
TCAGAATCATCTTCATCC
Found at i:2483138 original size:18 final size:17
Alignment explanation
Indices: 2483068--2483138 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 17
2483058 AAAAACCTCA
*
2483068 TCAGACTCATCTTCATCC
1 TCAGAATCA-CTTCATCC
*
2483086 TCAGAATCATCTTCATCA
1 TCAGAATCA-CTTCATCC
*
2483104 TCAGAACCACTTCCATCC
1 TCAGAATCACTT-CATCC
2483122 TCAGAATCACTATCATC
1 TCAGAATCACT-TCATC
2483139 ATCATCATCC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 3 0.07
18 42 0.91
19 1 0.02
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.30
Consensus pattern (17 bp):
TCAGAATCACTTCATCC
Found at i:2484834 original size:17 final size:16
Alignment explanation
Indices: 2484809--2484876 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
2484799 GGGTTGGATT
*
2484809 ATTTTGGTTATTTTTAG
1 ATTTAGGTTA-TTTTAG
*
2484826 ATTTAGGTTATTTTAT
1 ATTTAGGTTATTTTAG
2484842 ATTTGAGGTT-TTTT-G
1 ATTT-AGGTTATTTTAG
**
2484857 AATTTATATTATTTTAG
1 -ATTTAGGTTATTTTAG
2484874 ATT
1 ATT
2484877 CGAGTTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 3 0.07
16 24 0.57
17 15 0.36
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (16 bp):
ATTTAGGTTATTTTAG
Found at i:2484845 original size:16 final size:16
Alignment explanation
Indices: 2484808--2484855 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2484798 TGGGTTGGAT
*
2484808 TATTTTGGTTATTTTTA
1 TATTTAGGTTA-TTTTA
*
2484825 GATTTAGGTTATTTTA
1 TATTTAGGTTATTTTA
2484841 TATTTGAGGTT-TTTT
1 TATTT-AGGTTATTTT
2484856 GAATTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.65
Consensus pattern (16 bp):
TATTTAGGTTATTTTA
Found at i:2484855 original size:32 final size:32
Alignment explanation
Indices: 2484819--2484889 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
2484809 ATTTTGGTTA
* * *
2484819 TTTTTAG-ATTTAGGTTATTTTATATTTGAGGT
1 TTTTTAGAATTTAGATTATTTTAGATTCGA-GT
*
2484851 TTTTT-GAATTTATATTATTTTAGATTCGAGT
1 TTTTTAGAATTTAGATTATTTTAGATTCGAGT
2484882 TGTTTTAG
1 T-TTTTAG
2484890 GTTTGAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
31 4 0.12
32 27 0.84
33 1 0.03
ACGTcount: A:0.23, C:0.01, G:0.17, T:0.59
Consensus pattern (32 bp):
TTTTTAGAATTTAGATTATTTTAGATTCGAGT
Found at i:2488781 original size:28 final size:28
Alignment explanation
Indices: 2488749--2488827 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 28
2488739 ATATTTAAAT
2488749 TATATTAATTAAAAATATTAATTTTTTA
1 TATATTAATTAAAAATATTAATTTTTTA
* *
2488777 TATA-T--TTAATAAT-TATAATATTTTA
1 TATATTAATTAAAAATAT-TAATTTTTTA
* *
2488802 TAT-TTAAAT-AAATTATTAATTTTTTA
1 TATATTAATTAAAAATATTAATTTTTTA
2488828 ATTTATTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
24 1 0.03
25 20 0.50
26 12 0.30
27 3 0.08
28 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATATTAATTAAAAATATTAATTTTTTA
Found at i:2488795 original size:25 final size:26
Alignment explanation
Indices: 2488764--2488832 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 26
2488754 TAATTAAAAA
*
2488764 TATTAATTTTTTATATATTTAAT-AAT
1 TATTAATTTTTTATAT-TTAAATAAAT
*
2488790 TA-TAATATTTTATATTTAAATAAAT
1 TATTAATTTTTTATATTTAAATAAAT
2488815 TATTAATTTTTTA-ATTTA
1 TATTAATTTTTTATATTTA
2488833 TTTTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 5 0.13
25 22 0.58
26 11 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TATTAATTTTTTATATTTAAATAAAT
Found at i:2488811 original size:15 final size:15
Alignment explanation
Indices: 2488734--2488811 Score: 52
Period size: 16 Copynumber: 5.1 Consensus size: 15
2488724 TTTTGAATTA
2488734 ATTTAATATTTAAATT
1 ATTTAATATTTAAA-T
**
2488750 ATATTAAT-TAAAAAT
1 AT-TTAATATTTAAAT
* *
2488765 A-TTAATTTTTTATAT
1 ATTTAA-TATTTAAAT
*
2488780 ATTTAATAATTATAAT
1 ATTTAATATTTA-AAT
*
2488796 ATTTTATATTTAAAT
1 ATTTAATATTTAAAT
2488811 A
1 A
2488812 AATTATTAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
13 4 0.09
14 1 0.02
15 15 0.32
16 22 0.47
17 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTAATATTTAAAT
Found at i:2488845 original size:25 final size:24
Alignment explanation
Indices: 2488723--2488859 Score: 73
Period size: 26 Copynumber: 5.5 Consensus size: 24
2488713 GTGTATGAAA
* *
2488723 ATTTTGAATTAATTTAATATTTAA-
1 ATTTT-AATTTATTTAAAATTTAAT
* * *
2488747 ATTAT-ATTAATTAAAAATATTAAT
1 ATTTTAATTTATTTAAAAT-TTAAT
* *
2488771 -TTTTTATATATTTAATAATTATAAT
1 ATTTTAATTTATTTAA-AATT-TAAT
** *
2488796 ATTTTATATTTAAATAAATTATTAAT
1 ATTTTA-ATTTATTTAAAAT-TTAAT
*
2488822 TTTTTAATTTATTTTAAAATTTAAT
1 ATTTTAATTTA-TTTAAAATTTAAT
*
2488847 ATATATAATTTAT
1 AT-TTTAATTTAT
2488860 AAAAATAAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 19
0.70 0.15 0.16
Matches are distributed among these distances:
22 11 0.13
23 7 0.08
24 12 0.14
25 19 0.22
26 28 0.33
27 8 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
ATTTTAATTTATTTAAAATTTAAT
Found at i:2491935 original size:3 final size:3
Alignment explanation
Indices: 2491927--2491954 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2491917 ATGATTCTTT
2491927 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2491955 AGTATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2492318 original size:20 final size:20
Alignment explanation
Indices: 2492295--2492337 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2492285 TAAGTTGATT
*
2492295 TAATTTAAATTAATATTTAA
1 TAATTTAAAATAATATTTAA
*
2492315 TAA-TTAAAATATTATTTAA
1 TAATTTAAAATAATATTTAA
2492334 -AATT
1 TAATT
2492338 AATTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 15 0.75
20 3 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTTAAAATAATATTTAA
Found at i:2492340 original size:22 final size:23
Alignment explanation
Indices: 2492315--2492372 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2492305 TAATATTTAA
*
2492315 TAATTAAAATATTATTTAAA-AT
1 TAATTAAAATATTATATAAATAT
2492337 TAATTATAAA-A-TATATAAATAT
1 TAATTA-AAATATTATATAAATAT
2492359 TAATATAAAATATT
1 TAAT-TAAAATATT
2492373 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 7 0.23
22 16 0.53
23 6 0.20
24 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATTAAAATATTATATAAATAT
Found at i:2492357 original size:32 final size:33
Alignment explanation
Indices: 2492294--2492369 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
2492284 TTAAGTTGAT
*
2492294 TTAATTT-AAATTAATATTTAATAATTAAAATA
1 TTAATTTAAAATTAATATATAATAATTAAAATA
2492326 TT-ATTTAAAATTAAT-TATAA-AATATATAAATA
1 TTAATTTAAAATTAATATATAATAAT-TA-AAATA
*
2492358 TTAATATAAAAT
1 TTAATTTAAAAT
2492370 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 3 0.08
31 10 0.26
32 17 0.45
33 8 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TTAATTTAAAATTAATATATAATAATTAAAATA
Found at i:2492365 original size:21 final size:21
Alignment explanation
Indices: 2492331--2492371 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2492321 AAATATTATT
2492331 TAAAATTAATTATAAAATATA
1 TAAAATTAATTATAAAATATA
2492352 TAAATATTAA-TATAAAATAT
1 TAAA-ATTAATTATAAAATAT
2492372 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAATTAATTATAAAATATA
Found at i:2492581 original size:24 final size:24
Alignment explanation
Indices: 2492542--2492595 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2492532 TAAAATAAAA
** *
2492542 ATTAATTTTATGT-AAATATTTTT
1 ATTAATTTTAAATAAAATAATTTT
2492565 ATATAATTTTAAATAAAATAATTTT
1 AT-TAATTTTAAATAAAATAATTTT
2492590 ATTAAT
1 ATTAAT
2492596 AAAATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.08
24 13 0.50
25 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTAATTTTAAATAAAATAATTTT
Found at i:2492598 original size:17 final size:15
Alignment explanation
Indices: 2492567--2492615 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 15
2492557 ATATTTTTAT
2492567 ATAATTTTAAATAAA
1 ATAATTTTAAATAAA
2492582 ATAATTTTATTAATAAA
1 ATAATTTTA--AATAAA
2492599 ATAATATTTTAAATAAA
1 AT-A-ATTTTAAATAAA
2492616 TTTATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.30
17 14 0.47
18 1 0.03
19 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTTTAAATAAA
Found at i:2494276 original size:19 final size:20
Alignment explanation
Indices: 2494239--2494276 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2494229 TTAATTTTTA
**
2494239 ATTATTTTAAAATTGTATTT
1 ATTATTTTAAAATAATATTT
2494259 ATTA-TTTAAAATAATATT
1 ATTATTTTAAAATAATATT
2494277 AAAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTATTTTAAAATAATATTT
Done.