Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold202
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: 2706578
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 14 of 16
Found at i:2199153 original size:20 final size:20
Alignment explanation
Indices: 2199118--2199155 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2199108 TAAATGAAAG
**
2199118 ATAAAATTAATTTTAATGTA
1 ATAAAATTAAAATTAATGTA
2199138 ATAAAATTAAAATTAATG
1 ATAAAATTAAAATTAATG
2199156 GTTAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
ATAAAATTAAAATTAATGTA
Found at i:2199669 original size:15 final size:16
Alignment explanation
Indices: 2199645--2199674 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2199635 TATAAATAAC
2199645 AAATTAATAATAAAAT
1 AAATTAATAATAAAAT
2199661 AAATT-ATAATAAAA
1 AAATTAATAATAAAA
2199675 AGAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAATAATAAAAT
Found at i:2199805 original size:16 final size:17
Alignment explanation
Indices: 2199784--2199816 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2199774 TTTTATGTAT
2199784 TTTTA-TAATATTTTAC
1 TTTTATTAATATTTTAC
2199800 TTTTATTTAATATTTTA
1 TTTTA-TTAATATTTTA
2199817 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTAATATTTTAC
Found at i:2199916 original size:21 final size:21
Alignment explanation
Indices: 2199890--2199929 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2199880 ATAATTAATG
2199890 ATAATT-TATTAATTTATTTAT
1 ATAATTATA-TAATTTATTTAT
*
2199911 ATAATTATATATTTTATTT
1 ATAATTATATAATTTATTT
2199930 TTATTTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATAATTATATAATTTATTTAT
Found at i:2199933 original size:27 final size:30
Alignment explanation
Indices: 2199876--2199935 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
2199866 TTAAAATTGA
2199876 TTATATAATTAATGATAATTTATTAATTTAT
1 TTATATAATTAATGATAATTTATT-ATTTAT
*
2199907 TTATATAATT-AT-ATATTTTATT-TTTAT
1 TTATATAATTAATGATAATTTATTATTTAT
2199934 TT
1 TT
2199936 TCGTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.25
29 9 0.32
30 2 0.07
31 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TTATATAATTAATGATAATTTATTATTTAT
Found at i:2200716 original size:8 final size:8
Alignment explanation
Indices: 2200705--2200773 Score: 52
Period size: 8 Copynumber: 8.1 Consensus size: 8
2200695 TCATTTAAAG
2200705 ATTTATAT
1 ATTTATAT
2200713 ATTTATATT
1 ATTTATA-T
2200722 ATGTTTATAT
1 A--TTTATAT
2200732 ATTT-TATT
1 ATTTATA-T
2200740 ATATTATAT
1 AT-TTATAT
* *
2200749 GTTTAAAAT
1 ATTT-ATAT
2200758 ATTT-TAT
1 ATTTATAT
2200765 ATTTATAT
1 ATTTATAT
2200773 A
1 A
2200774 AATTTTGATA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
7 8 0.16
8 19 0.39
9 12 0.24
10 4 0.08
11 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:2200730 original size:19 final size:18
Alignment explanation
Indices: 2200706--2200741 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
2200696 CATTTAAAGA
2200706 TTTATATATTTATATTATG
1 TTTATATATTT-TATTATG
2200725 TTTATATATTTTATTAT
1 TTTATATATTTTATTAT
2200742 ATTATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTATATATTTTATTATG
Found at i:2200742 original size:23 final size:26
Alignment explanation
Indices: 2200721--2200772 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
2200711 ATATTTATAT
*
2200721 TATGTTT-ATATATTTTATTATATTA
1 TATGTTTAAAATATTTTATTATATTA
2200746 TATGTTTAAAATATTTTA-TAT-TTA
1 TATGTTTAAAATATTTTATTATATTA
2200770 TAT
1 TAT
2200773 AAATTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 10 0.40
26 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (26 bp):
TATGTTTAAAATATTTTATTATATTA
Found at i:2202597 original size:30 final size:29
Alignment explanation
Indices: 2202538--2202595 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2202528 TTTAATATTT
* * *
2202538 TAATTTTTATTGATAATTTATTAATAAAA
1 TAATTTTTATTAATAATATATAAATAAAA
2202567 TAATTTTTATTCAATAATATA-AAATAAAA
1 TAATTTTTATT-AATAATATATAAATAAAA
2202596 ATTAACATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
TAATTTTTATTAATAATATATAAATAAAA
Found at i:2202929 original size:14 final size:14
Alignment explanation
Indices: 2202912--2202963 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
2202902 GAATATACGA
2202912 ATATATCAAAATAT
1 ATATATCAAAATAT
*
2202926 ATATAATAAAAATTATT
1 ATAT-ATCAAAA-TA-T
*
2202943 AATATATCAAAATTT
1 -ATATATCAAAATAT
2202958 ATATAT
1 ATATAT
2202964 AATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 10 0.32
15 7 0.23
16 3 0.10
17 7 0.23
18 4 0.13
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATCAAAATAT
Found at i:2203104 original size:18 final size:18
Alignment explanation
Indices: 2203059--2203107 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2203049 ATACATATAA
2203059 ATATATATAATATAAATT
1 ATATATATAATATAAATT
*
2203077 AT-TAAAATAATA-AAATTT
1 ATAT-ATATAATATAAA-TT
2203095 ATATATATAATAT
1 ATATATATAATAT
2203108 CTTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 4 0.16
18 20 0.80
19 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATATAATATAAATT
Found at i:2204301 original size:3 final size:3
Alignment explanation
Indices: 2204295--2204325 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2204285 TAAATACTAC
2204295 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2204326 GTGAAAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2204605 original size:14 final size:15
Alignment explanation
Indices: 2204581--2204609 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2204571 TAAAATATAA
2204581 AAATTATTTAATATT
1 AAATTATTTAATATT
2204596 AAATTA-TTAATATT
1 AAATTATTTAATATT
2204610 TTAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATTATTTAATATT
Found at i:2204627 original size:13 final size:13
Alignment explanation
Indices: 2204603--2204640 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2204593 ATTAAATTAT
2204603 TAATAT-TTTAAA
1 TAATATATTTAAA
2204615 TAATATATTTAAA
1 TAATATATTTAAA
2204628 TAATAATATTTAA
1 TAAT-ATATTTAA
2204641 TCTTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.25
13 10 0.42
14 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATATTTAAA
Found at i:2204639 original size:14 final size:14
Alignment explanation
Indices: 2204589--2204640 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
2204579 AAAAATTATT
*
2204589 TAATA-TTAAATTAT
1 TAATATTTAAA-TAA
2204603 TAATATTTTAAATAA
1 TAATA-TTTAAATAA
2204618 T-ATATTTAAATAA
1 TAATATTTAAATAA
2204631 TAATATTTAA
1 TAATATTTAA
2204641 TCTTAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 10 0.29
14 16 0.47
15 3 0.09
16 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATATTTAAATAA
Found at i:2204785 original size:16 final size:16
Alignment explanation
Indices: 2204766--2204797 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2204756 TTTGTATATG
2204766 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
*
2204782 AAATATTTTAAATTTA
1 AAATAATTTAAATTTA
2204798 TATTGATTGA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:2205051 original size:18 final size:18
Alignment explanation
Indices: 2205024--2205080 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
2205014 TCACATCATC
*
2205024 AAAATGTATTATTAAAAT
1 AAAATTTATTATTAAAAT
*
2205042 AAAATTTATTATTTTAAAT
1 AAAATTTATTA-TTAAAAT
2205061 AAAATTTATTATTAAAAT
1 AAAATTTATTATTAAAAT
2205079 AA
1 AA
2205081 TAATATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATTTATTATTAAAAT
Found at i:2207067 original size:2 final size:2
Alignment explanation
Indices: 2207060--2207089 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2207050 TCTACAAGAT
2207060 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
2207090 GAGAGAGAGA
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:2207666 original size:20 final size:20
Alignment explanation
Indices: 2207641--2207685 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2207631 TAATTTTTTT
2207641 ATAATTATATTTAAATAAA-A
1 ATAATTATA-TTAAATAAATA
* *
2207661 ATAATTTTATTAATTAAATA
1 ATAATTATATTAAATAAATA
2207681 ATAAT
1 ATAAT
2207686 GTAGGTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTATATTAAATAAATA
Found at i:2212925 original size:11 final size:11
Alignment explanation
Indices: 2212909--2212965 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 11
2212899 TATATACATA
2212909 ATAAAAATAAT
1 ATAAAAATAAT
2212920 ATAAAAATAATT
1 ATAAAAATAA-T
2212932 ATAATATAATATAAT
1 AT-A-A-AA-ATAAT
2212947 ATAAAAATAAT
1 ATAAAAATAAT
2212958 -TAAAAATA
1 ATAAAAATA
2212966 TAATATAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.20
11 15 0.37
12 5 0.12
13 2 0.05
14 2 0.05
15 5 0.12
16 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:2212939 original size:5 final size:5
Alignment explanation
Indices: 2212906--2212976 Score: 60
Period size: 5 Copynumber: 14.4 Consensus size: 5
2212896 TTTTATATAC
* * *
2212906 ATAAT A-AAA ATAAT ATAAAA ATAATT ATAAT ATAAT ATAAT ATAAAA
1 ATAAT ATAAT ATAAT AT-AAT ATAA-T ATAAT ATAAT ATAAT AT-AAT
2212953 ATAAT -TAA- A-AAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT
2212977 TTTTATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 2 0.04
4 7 0.13
5 32 0.60
6 12 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:2212956 original size:38 final size:40
Alignment explanation
Indices: 2212900--2212976 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 40
2212890 TAATAATTTT
*
2212900 ATATACATAATAAAAATAATATAAAAATA-ATTATAATATA
1 ATATACATAATAAAAATAAT-TAAAAATATAATATAATATA
2212940 ATATA-AT-ATAAAAATAATTAAAAATATAATATAATAT
1 ATATACATAATAAAAATAATTAAAAATATAATATAATAT
2212977 TTTTATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 8 0.23
38 20 0.57
39 2 0.06
40 5 0.14
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (40 bp):
ATATACATAATAAAAATAATTAAAAATATAATATAATATA
Found at i:2213136 original size:21 final size:21
Alignment explanation
Indices: 2213082--2213136 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2213072 AATAATTATA
2213082 TAAATA-AATTATATTAATTT
1 TAAATATAATTATATTAATTT
* *
2213102 TAAATTTAAATATA-TAATATT
1 TAAATATAATTATATTAAT-TT
*
2213123 TTAATATAATTATA
1 TAAATATAATTATA
2213137 ATACATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATATAATTATATTAATTT
Found at i:2213159 original size:23 final size:22
Alignment explanation
Indices: 2213127--2213171 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2213117 AATATTTTAA
*
2213127 TATAATTATAATACATAAAATAT
1 TATAAATATAATACA-AAAATAT
*
2213150 TATAAATATAATATAAAAATAT
1 TATAAATATAATACAAAAATAT
2213172 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAATATAATACAAAAATAT
Found at i:2213172 original size:55 final size:55
Alignment explanation
Indices: 2213057--2213185 Score: 138
Period size: 55 Copynumber: 2.4 Consensus size: 55
2213047 AAAATTTATT
* * * * * *
2213057 AAATATTAT-TTTTAAAATAATTATATAAATAAATTATATTAATTTTAAATTTAA
1 AAATATAATATTTTAATATAATTATATAAATAAAATATATTAAATATAAATATAA
* *
2213111 ATATATAATATTTTAATATAATTATAATACATAAAATAT-TATAAATAT-AATATAA
1 AAATATAATATTTTAATATAATTAT-ATAAATAAAATATAT-TAAATATAAATATAA
*
2213166 AAATATATTATTTTAATATA
1 AAATATAATATTTTAATATA
2213186 TAAATTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
54 7 0.11
55 39 0.63
56 16 0.26
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (55 bp):
AAATATAATATTTTAATATAATTATATAAATAAAATATATTAAATATAAATATAA
Found at i:2213518 original size:17 final size:18
Alignment explanation
Indices: 2213498--2213533 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2213488 TTAAATATAA
2213498 TTATAA-TTTAATATATT
1 TTATAATTTTAATATATT
*
2213515 TTATAATTTTATTATATT
1 TTATAATTTTAATATATT
2213533 T
1 T
2213534 ATATTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATAATTTTAATATATT
Found at i:2213534 original size:17 final size:16
Alignment explanation
Indices: 2213486--2213540 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2213476 CACATTAAAA
* *
2213486 AATTAAATATAATTAT
1 AATTTAATATATTTAT
2213502 AATTTAATATATTTTAT
1 AATTTAATATA-TTTAT
*
2213519 AATTTTATTATATTTAT
1 AA-TTTAATATATTTAT
2213536 -ATTTA
1 AATTTA
2213541 GTTAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 4 0.12
16 11 0.32
17 11 0.32
18 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTAATATATTTAT
Found at i:2214036 original size:27 final size:27
Alignment explanation
Indices: 2214006--2214096 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
2213996 ACATAACATA
2214006 AATATAATATTAAAAAAATTAAATTAT
1 AATATAATATTAAAAAAATTAAATTAT
* * *
2214033 AATATATTA-TAAAAATAATAAAATAAT
1 AATATAATATTAAAAA-AATTAAATTAT
* ** *
2214060 AA-ATAAATATATAAATATTTTAAAATAT
1 AATAT-AATAT-TAAAAAAATTAAATTAT
2214088 -ATATAATAT
1 AATATAATAT
2214097 AACTTATTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
26 8 0.16
27 28 0.57
28 8 0.16
29 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATATAATATTAAAAAAATTAAATTAT
Found at i:2214053 original size:19 final size:20
Alignment explanation
Indices: 2214026--2214097 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 20
2214016 TAAAAAAATT
2214026 AAAT-TATAATATATTATAA
1 AAATATATAATATATTATAA
* *
2214045 AAATA-ATAAAATAATA-AA
1 AAATATATAATATATTATAA
*
2214063 TAAATATATAA-ATATTTTAA
1 -AAATATATAATATATTATAA
2214083 AATATATATAATATA
1 AA-ATATATAATATA
2214098 ACTTATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 2 0.05
19 24 0.56
20 14 0.33
21 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATAATATATTATAA
Found at i:2214091 original size:22 final size:22
Alignment explanation
Indices: 2214060--2214128 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 22
2214050 ATAAAATAAT
*
2214060 AAATAAATATATAAATATTTTA
1 AAATATATATATAAATATTTTA
*
2214082 AAATATATATAATATAACT-TATTA
1 AAATATATAT-ATA-AA-TATTTTA
* *
2214106 ATATATTTATA-AAATATTTTA
1 AAATATATATATAAATATTTTA
2214127 AA
1 AA
2214129 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 10 0.27
23 4 0.11
24 14 0.38
25 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATATATATAAATATTTTA
Found at i:2214438 original size:14 final size:15
Alignment explanation
Indices: 2214419--2214453 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2214409 TTACATTATT
2214419 TTTAAATTT-AAAAA
1 TTTAAATTTGAAAAA
*
2214433 TTTAAATTTGAACAA
1 TTTAAATTTGAAAAA
2214448 TTTAAA
1 TTTAAA
2214454 AAATTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TTTAAATTTGAAAAA
Found at i:2214681 original size:17 final size:17
Alignment explanation
Indices: 2214661--2214693 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2214651 TGCATATTAT
*
2214661 ATATATATATATATATA
1 ATATATATAAATATATA
2214678 ATATATATAAATATAT
1 ATATATATAAATATAT
2214694 GTTTTTCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATAAATATATA
Found at i:2214681 original size:19 final size:19
Alignment explanation
Indices: 2214654--2214693 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2214644 TCTTTCGTGC
* *
2214654 ATATTATATATATATATAT
1 ATATAATATATATAAATAT
2214673 ATATAATATATATAAATAT
1 ATATAATATATATAAATAT
2214692 AT
1 AT
2214694 GTTTTTCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATAATATATATAAATAT
Found at i:2214708 original size:2 final size:2
Alignment explanation
Indices: 2214654--2214693 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
2214644 TCTTTCGTGC
*
2214654 AT AT -T AT AT AT AT AT AT AT AT AT A- AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2214694 GTTTTTCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2215045 original size:17 final size:17
Alignment explanation
Indices: 2215025--2215077 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
2215015 ATTTAAAAAT
2215025 ATATTATATAAATTTTA
1 ATATTATATAAATTTTA
*
2215042 ATA-TAT-TAATAATTT-
1 ATATTATATAA-ATTTTA
*
2215057 ACATTATATAAATTTTA
1 ATATTATATAAATTTTA
2215074 ATAT
1 ATAT
2215078 ATTTTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.18
16 14 0.50
17 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATATAAATTTTA
Found at i:2215047 original size:21 final size:23
Alignment explanation
Indices: 2215003--2215055 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 23
2214993 ATAATTTATT
2215003 TATTATAATTAAATTTAAAAATA
1 TATTATAATTAAATTTAAAAATA
*
2215026 TATTAT-A-TAAATTT--TAATA
1 TATTATAATTAAATTTAAAAATA
2215045 TATTAATAATT
1 TATT-ATAATT
2215056 TACATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 8 0.31
20 2 0.08
21 8 0.31
22 2 0.08
23 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTATAATTAAATTTAAAAATA
Found at i:2215052 original size:27 final size:27
Alignment explanation
Indices: 2215022--2215107 Score: 75
Period size: 32 Copynumber: 3.0 Consensus size: 27
2215012 TAAATTTAAA
2215022 AATATATTATATAAATTTTAATATATT
1 AATATATTATATAAATTTTAATATATT
2215049 AATAATTTACATTATATAAATTTTAATATATT
1 AAT-A--T--ATTATATAAATTTTAATATATT
** * *
2215081 TTTATATT-TATATTATTTTATTATATT
1 AATATATTATATA-AATTTTAATATATT
2215108 TTAATTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
26 4 0.08
27 18 0.37
28 1 0.02
29 1 0.02
30 1 0.02
31 1 0.02
32 23 0.47
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
AATATATTATATAAATTTTAATATATT
Found at i:2215106 original size:19 final size:19
Alignment explanation
Indices: 2215068--2215118 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2215058 CATTATATAA
2215068 ATTTTAA-TATATTT-TTAT
1 ATTTTAATTAT-TTTATTAT
2215086 A-TTTATATTATTTTATTAT
1 ATTTTA-ATTATTTTATTAT
2215105 ATTTTAATTATTTT
1 ATTTTAATTATTTT
2215119 TATGTTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.14
18 5 0.17
19 16 0.55
20 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTAATTATTTTATTAT
Found at i:2215629 original size:11 final size:11
Alignment explanation
Indices: 2215613--2215654 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2215603 AAAGAAGATT
2215613 TAATATAAAAA
1 TAATATAAAAA
*
2215624 TAATATAAATA
1 TAATATAAAAA
*
2215635 TAATATTAATAA
1 TAATA-TAAAAA
2215647 -AATATAAA
1 TAATATAAA
2215655 TTATTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.12
11 19 0.73
12 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATATAAAAA
Found at i:2215634 original size:6 final size:6
Alignment explanation
Indices: 2215614--2215691 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
2215604 AAGAAGATTT
* *
2215614 AATATA AAAAT- AATATA AATAT- AATATT AATA-A AATATA AATTATTA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AA-TA-TA
* * *
2215661 AAAATAA AATTTA TATATA AATATA TAATAT
1 AATAT-A AATATA AATATA AATATA -AATAT
2215692 TTTAAATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
5 13 0.23
6 27 0.48
7 12 0.21
8 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AATATA
Found at i:2215705 original size:33 final size:32
Alignment explanation
Indices: 2215627--2215714 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 32
2215617 ATAAAAATAA
2215627 TATAAATATAATATTAATA-AAATATAAATTAT
1 TATAAATATAAT-TTAATATAAATATAAATTAT
* *
2215659 TAAAAATAAAATTTATATATAAATATATAA-TAT
1 TATAAATATAATTTA-ATATAAATATA-AATTAT
*
2215692 TTTAAATATAATTTAA-ATAAATA
1 TATAAATATAATTTAATATAAATA
2215715 AAGTCGAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
31 10 0.21
32 14 0.29
33 22 0.46
34 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TATAAATATAATTTAATATAAATATAAATTAT
Found at i:2215947 original size:27 final size:25
Alignment explanation
Indices: 2215880--2215949 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
2215870 CAAAGCGTTT
2215880 ATTTT-ATTATAAAATATATATTAA
1 ATTTTAATTATAAAATATATATTAA
* *
2215904 ATTTTAATAATAAAAAATATATTTAA
1 ATTTTAATTATAAAATATATA-TTAA
2215930 TATTTTTAATTGATAAAATA
1 -A-TTTTAATT-ATAAAATA
2215950 AGATTTGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.14
25 13 0.35
26 4 0.11
27 1 0.03
28 7 0.19
29 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
ATTTTAATTATAAAATATATATTAA
Found at i:2216105 original size:2 final size:2
Alignment explanation
Indices: 2216098--2216123 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2216088 AAACTACCAA
2216098 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
2216124 TATTCATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2216161 original size:20 final size:20
Alignment explanation
Indices: 2216136--2216176 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2216126 TTCATGTTTA
2216136 TAGTATTAAATAAAAATATT
1 TAGTATTAAATAAAAATATT
2216156 TAGTATTAAATAAAAATATT
1 TAGTATTAAATAAAAATATT
2216176 T
1 T
2216177 TAAAGATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TAGTATTAAATAAAAATATT
Found at i:2216769 original size:14 final size:14
Alignment explanation
Indices: 2216746--2216777 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2216736 AATATATAGG
*
2216746 TTTTATTAATTTTA
1 TTTTAGTAATTTTA
2216760 TTTTAGTAATTTTA
1 TTTTAGTAATTTTA
2216774 TTTT
1 TTTT
2216778 TAAAGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTAGTAATTTTA
Found at i:2217055 original size:20 final size:20
Alignment explanation
Indices: 2217009--2217077 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
2216999 TCATACCCTG
* *
2217009 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* *
2217029 ATATATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
* *
2217049 ATGTATCGATATAT-TCTACA
1 ATGTATCGATACATGTAT-CA
2217069 ATGTATCGA
1 ATGTATCGA
2217078 GATATTATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 2 0.05
20 38 0.95
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:2218026 original size:24 final size:24
Alignment explanation
Indices: 2217994--2218050 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
2217984 AGCCTTTAAC
2217994 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
2218018 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
2218040 CATGCATTTTT
1 CATGCATTTTT
2218051 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:2218057 original size:20 final size:21
Alignment explanation
Indices: 2218003--2218057 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
2217993 CCATGCATTT
**
2218003 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
2218024 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
2218046 -TTTTTAACATGT
1 TTTTTTAACATGT
2218058 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:2225860 original size:15 final size:13
Alignment explanation
Indices: 2225834--2225873 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2225824 AATCATCCTA
2225834 ATTTTTTATTATT
1 ATTTTTTATTATT
2225847 ATTTTTTATT-TT
1 ATTTTTTATTATT
*
2225859 ATTATTTTATGATT
1 ATT-TTTTATTATT
2225873 A
1 A
2225874 CATCCCAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 16 0.67
14 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
ATTTTTTATTATT
Found at i:2228990 original size:24 final size:23
Alignment explanation
Indices: 2228959--2229003 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2228949 TAAAAAATAT
2228959 AAAATTATATAATAAATATTTAAA
1 AAAATTATATAA-AAATATTTAAA
* *
2228983 AAAATTATTTAAATATATTTA
1 AAAATTATATAAAAATATTTA
2229004 TTTTTGCTAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATTATATAAAAATATTTAAA
Found at i:2229254 original size:124 final size:126
Alignment explanation
Indices: 2229068--2229350 Score: 274
Period size: 132 Copynumber: 2.2 Consensus size: 126
2229058 TATAATATTT
* * *
2229068 TAAACATAATTTTAACAAGTAAAATTCTAAAAAAAAATAAATTCATATTTTTTTATCCG-AA-AA
1 TAAACATGATTTTAACAAGTAAAATTATAAAAAAAAATAAATTCATA--TTTTGATCCGAAATAA
* * * *
2229131 ATATA-AA-TTTATTTTAAA-ATTCATATTTTTACTATTTAACGAATTCATATTAAAAATCTAA
64 AAATACAAGTTTATTTTAAAGATT-ATATTTTGAATATTTAACGAATTCATATGAAAAATCTAA
* * * *
2229192 TAAACATGATTTTAACATGTAAAATTATACGAATACAAAATAAATTCGTA-TTTGATCTGAAAAT
1 TAAACATGATTTTAACAAGTAAAATTATA--AA-AAAAAATAAATTCATATTTTGATCCG-AAA-
* * * *
2229256 TTCAAAAATACAAGTTTGTTTTAAAGCTTGTATTTTGAATATTTAATGAATTCATATGAAAAATC
61 -T-AAAAATACAAGTTTATTTTAAAGATTATATTTTGAATATTTAACGAATTCATATGAAAAATC
2229321 TAA
124 TAA
* *
2229324 TAAA-ATGATTTTAAGACGTAAAATTAT
1 TAAACATGATTTTAACAAGTAAAATTAT
2229351 TACAGATAAA
Statistics
Matches: 130, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
124 33 0.25
126 4 0.03
127 14 0.11
130 6 0.05
131 23 0.18
132 48 0.37
133 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (126 bp):
TAAACATGATTTTAACAAGTAAAATTATAAAAAAAAATAAATTCATATTTTGATCCGAAATAAAA
ATACAAGTTTATTTTAAAGATTATATTTTGAATATTTAACGAATTCATATGAAAAATCTAA
Found at i:2233703 original size:26 final size:26
Alignment explanation
Indices: 2233666--2233743 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
2233656 TTTTTAAATT
*
2233666 TAATAATTTTAACTATAATTATAAAA
1 TAATAATATTAACTATAATTATAAAA
*
2233692 TAATAATATTAAC-AAAATTATTAAAA
1 TAATAATATTAACTATAATTA-TAAAA
* * *
2233718 TATTAAAATT-A-TATAAATATAAAA
1 TAATAATATTAACTATAATTATAAAA
2233742 TA
1 TA
2233744 TTTTAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 7 0.16
25 12 0.27
26 25 0.57
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAATATTAACTATAATTATAAAA
Found at i:2233725 original size:17 final size:17
Alignment explanation
Indices: 2233705--2233809 Score: 58
Period size: 17 Copynumber: 5.9 Consensus size: 17
2233695 TAATATTAAC
2233705 AAAATTATTAAAATATT
1 AAAATTATTAAAATATT
2233722 AAAATTA-TATAAATA-T
1 AAAATTATTA-AAATATT
*
2233738 AAAATATTTTAAAAATAAATAT
1 AAAAT-TATT-AAAAT--AT-T
*
2233760 AATATTATT-AAATA-T
1 AAAATTATTAAAATATT
* *
2233775 AAAATTATAATACGAATATA
1 AAAATTAT--TA-AAATATT
2233795 AAAATTA-TAAAATAT
1 AAAATTATTAAAATAT
2233810 AACAATATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 27
0.67 0.07 0.26
Matches are distributed among these distances:
15 8 0.12
16 13 0.19
17 17 0.25
18 5 0.07
19 9 0.13
20 8 0.12
21 3 0.04
22 5 0.07
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (17 bp):
AAAATTATTAAAATATT
Found at i:2233758 original size:22 final size:21
Alignment explanation
Indices: 2233730--2233786 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
2233720 TTAAAATTAT
2233730 ATAAATATAAAATATT-TTAAAA
1 ATAAATAT--AATATTATTAAAA
*
2233752 ATAAATATAATATTATTAAAT
1 ATAAATATAATATTATTAAAA
2233773 ATAAAATTATAATA
1 AT-AAA-TATAATA
2233787 CGAATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 6 0.19
21 7 0.23
22 11 0.35
23 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAATATAATATTATTAAAA
Found at i:2233771 original size:15 final size:15
Alignment explanation
Indices: 2233705--2233811 Score: 68
Period size: 15 Copynumber: 7.1 Consensus size: 15
2233695 TAATATTAAC
2233705 AAAATTATTAAAATATT
1 AAAATTATT-AAATA-T
2233722 AAAATTATATAAATAT
1 AAAATTAT-TAAATAT
2233738 AAAA-TATT---T-T
1 AAAATTATTAAATAT
2233748 AAAA--A-TAAATAT
1 AAAATTATTAAATAT
*
2233760 AATATTATTAAATAT
1 AAAATTATTAAATAT
2233775 AAAATTATAATACGAATAT
1 AAAATTAT--TA--AATAT
*
2233794 AAAAATTATAAAATAT
1 -AAAATTATTAAATAT
2233810 AA
1 AA
2233812 CAATATTTGG
Statistics
Matches: 74, Mismatches: 3, Indels: 28
0.70 0.03 0.27
Matches are distributed among these distances:
8 1 0.01
9 1 0.01
10 5 0.07
11 2 0.03
12 4 0.05
14 2 0.03
15 19 0.26
16 10 0.14
17 15 0.20
18 2 0.03
19 5 0.07
20 8 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (15 bp):
AAAATTATTAAATAT
Found at i:2234228 original size:14 final size:14
Alignment explanation
Indices: 2234194--2234240 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
2234184 AATTTATAAA
2234194 AATTTTATTTAAAATTT
1 AATTTTA-TT-AAA-TT
2234211 AA-TTTATATAAATT
1 AATTTTAT-TAAATT
2234225 AATTTTATTAAATT
1 AATTTTATTAAATT
2234239 AA
1 AA
2234241 AGTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.43
15 9 0.32
16 5 0.18
17 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTATTAAATT
Found at i:2234231 original size:27 final size:28
Alignment explanation
Indices: 2234178--2234229 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2234168 AAATAAAATT
*
2234178 AATTTAAATTTATAAAAATTTTATTTAA
1 AATTTAAATTTATAAAAATTATATTTAA
*
2234206 AATTT-AATTTATATAAATTA-ATTT
1 AATTTAAATTTATAAAAATTATATTT
2234230 TATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 13 0.59
28 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTTAAATTTATAAAAATTATATTTAA
Found at i:2234345 original size:14 final size:15
Alignment explanation
Indices: 2234326--2234360 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2234316 TTAAGTTATT
*
2234326 TATTTTGAAAAA-AA
1 TATTTTAAAAAATAA
2234340 TATTTTAAAAAATAA
1 TATTTTAAAAAATAA
2234355 TATTTT
1 TATTTT
2234361 TTATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TATTTTAAAAAATAA
Found at i:2234785 original size:16 final size:15
Alignment explanation
Indices: 2234760--2234797 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2234750 AAGGCTTCAG
*
2234760 ATTA-TTTTTAATAT
1 ATTATTTTTTAAAAT
2234774 ATATATTTTTTAAAAT
1 AT-TATTTTTTAAAAT
2234790 ATTATTTT
1 ATTATTTT
2234798 ATATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 8 0.38
16 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTTTTTAAAAT
Found at i:2234868 original size:15 final size:15
Alignment explanation
Indices: 2234845--2234883 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2234835 TATTAAAAAT
2234845 TATACTATTTACTAAA
1 TATA-TATTTACTAAA
*
2234861 TATATATTTATTAAA
1 TATATATTTACTAAA
*
2234876 TATTTATT
1 TATATATT
2234884 ACATTATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATTTACTAAA
Found at i:2235094 original size:25 final size:25
Alignment explanation
Indices: 2235066--2235113 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2235056 ATATATTAAA
2235066 TTTTAATA-TATTTTAACAAAAATAC
1 TTTTAATACTA-TTTAACAAAAATAC
* *
2235091 TTTTTATACTATTTATCAAAAAT
1 TTTTAATACTATTTAACAAAAAT
2235114 TAATATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTAATACTATTTAACAAAAATAC
Found at i:2239068 original size:9 final size:9
Alignment explanation
Indices: 2239054--2239078 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2239044 TCCGGCAGGC
2239054 TATGTCACA
1 TATGTCACA
2239063 TATGTCACA
1 TATGTCACA
2239072 TATGTCA
1 TATGTCA
2239079 GGCTAGTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (9 bp):
TATGTCACA
Found at i:2240457 original size:55 final size:56
Alignment explanation
Indices: 2240346--2240457 Score: 174
Period size: 55 Copynumber: 2.0 Consensus size: 56
2240336 ATGGTTTTTC
* *
2240346 ATACGCAAAAGCAACACGACATACAATGTTAATCATATTGGCAGGTATGTATATTT
1 ATACGCAAAAGCAACACGACATACAATGTTAATCATATTAGCAGGTATGTAAATTT
*
2240402 ATAC-CAAAAGCAGCACGACATACAATGTTAATCATATTAGCAGGTATG-ACAATTT
1 ATACGCAAAAGCAACACGACATACAATGTTAATCATATTAGCAGGTATGTA-AATTT
2240457 A
1 A
2240458 CAAGGATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 1 0.02
55 47 0.90
56 4 0.08
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (56 bp):
ATACGCAAAAGCAACACGACATACAATGTTAATCATATTAGCAGGTATGTAAATTT
Found at i:2242937 original size:2 final size:2
Alignment explanation
Indices: 2242930--2242966 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2242920 TCAACATCTC
*
2242930 AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2242967 GTATCAGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2244364 original size:23 final size:22
Alignment explanation
Indices: 2244338--2244387 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
2244328 GATTTTTAAA
2244338 TATTT-TTATAAAATATACATAAT
1 TATTTATT-TAAAATAT-CATAAT
* *
2244361 TATTTATTTAACATATCATATT
1 TATTTATTTAAAATATCATAAT
2244383 TATTT
1 TATTT
2244388 CATAACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 12 0.50
24 2 0.08
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATTTAAAATATCATAAT
Found at i:2244512 original size:3 final size:3
Alignment explanation
Indices: 2244504--2244540 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2244494 AGCCTAAACT
2244504 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2244541 GATGCTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2244815 original size:11 final size:11
Alignment explanation
Indices: 2244799--2244841 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2244789 AATTATGTTA
2244799 ATTATATTAAT
1 ATTATATTAAT
2244810 ATTATATTAAT
1 ATTATATTAAT
* *
2244821 ATAATAGTTTAT
1 ATTATA-TTAAT
2244833 ATT-TATTAA
1 ATTATATTAA
2244842 AAATGTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.11
11 18 0.67
12 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATTATATTAAT
Found at i:2249217 original size:12 final size:12
Alignment explanation
Indices: 2249200--2249225 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2249190 TGGATGGATC
2249200 AGTCAAACTGAG
1 AGTCAAACTGAG
2249212 AGTCAAACTGAG
1 AGTCAAACTGAG
2249224 AG
1 AG
2249226 CTGGTTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (12 bp):
AGTCAAACTGAG
Found at i:2250008 original size:14 final size:15
Alignment explanation
Indices: 2249966--2250015 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
2249956 TTAATTTTTT
*
2249966 ATTATATTTTTAAATA
1 ATTATA-TTTTAAAAA
*
2249982 A-TATATTTAAAAAA
1 ATTATATTTTAAAAA
2249996 ATTA-ATTTTAAAATA
1 ATTATATTTTAAAA-A
2250011 ATTAT
1 ATTAT
2250016 CAGTATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 16 0.57
15 11 0.39
16 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATATTTTAAAAA
Found at i:2250778 original size:13 final size:12
Alignment explanation
Indices: 2250737--2250789 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
2250727 TTTAAAAAAA
2250737 TAAATTTATTTT
1 TAAATTTATTTT
*
2250749 TATAAATTA-TTT
1 TA-AATTTATTTT
*
2250761 TAATTTTATTTT
1 TAAATTTATTTT
*
2250773 TAAATTATATATT
1 TAAATT-TATTTT
2250786 TAAA
1 TAAA
2250790 GAGTTATTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
11 4 0.12
12 15 0.45
13 14 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTATTTT
Found at i:2259100 original size:18 final size:17
Alignment explanation
Indices: 2259066--2259106 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2259056 ATAATTATAA
2259066 TATTTAAATTTAAATAT
1 TATTTAAATTTAAATAT
2259083 TATTTAAATTTAAA-A-
1 TATTTAAATTTAAATAT
2259098 TATTTAAAT
1 TATTTAAAT
2259107 ATATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.38
16 1 0.04
17 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTAAATTTAAATAT
Found at i:2259274 original size:12 final size:11
Alignment explanation
Indices: 2259248--2259282 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2259238 ATGTACGAGC
2259248 CCAAAACCAAA
1 CCAAAACCAAA
2259259 CCAAAACCAGAA
1 CCAAAACCA-AA
*
2259271 CCAAAACTAAA
1 CCAAAACCAAA
2259282 C
1 C
2259283 GCATAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.60, C:0.34, G:0.03, T:0.03
Consensus pattern (11 bp):
CCAAAACCAAA
Found at i:2259512 original size:2 final size:2
Alignment explanation
Indices: 2259505--2259538 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2259495 AGAAAACACG
2259505 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2259539 CTACGCAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2271848 original size:15 final size:15
Alignment explanation
Indices: 2271828--2271856 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2271818 TTATAATTAC
2271828 TTATTAATTTATTTT
1 TTATTAATTTATTTT
2271843 TTATTAATTTATTT
1 TTATTAATTTATTT
2271857 GTATTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTAATTTATTTT
Found at i:2284041 original size:15 final size:16
Alignment explanation
Indices: 2284002--2284041 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2283992 TTGCCATTTC
2284002 CTTTG-TTTTTTCTTT
1 CTTTGTTTTTTTCTTT
*
2284017 CTTT-TCTTTTTCTTT
1 CTTTGTTTTTTTCTTT
2284032 -TTTGTTTTTT
1 CTTTGTTTTTT
2284042 GTTTTTCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (16 bp):
CTTTGTTTTTTTCTTT
Found at i:2284059 original size:20 final size:19
Alignment explanation
Indices: 2284003--2284059 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 19
2283993 TGCCATTTCC
2284003 TTTGTTTTT-TCTTTCTTT
1 TTTGTTTTTCTCTTTCTTT
*
2284021 TCTT-TTTCTT-T-TTTGTTT
1 T-TTGTTT-TTCTCTTTCTTT
2284039 TTTGTTTTTCTGCTTTCTTT
1 TTTGTTTTTCT-CTTTCTTT
2284059 T
1 T
2284060 GATTTCCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 4 0.13
18 15 0.48
19 5 0.16
20 7 0.23
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTGTTTTTCTCTTTCTTT
Found at i:2285330 original size:79 final size:80
Alignment explanation
Indices: 2285190--2285361 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 80
2285180 AAAATCGAGA
* *
2285190 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATTCCCAATTATGAGAAATCAATA-TTTTG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAGTCCCAATTATGAAAAATCAATATTTTTG
* * *
2285254 GGAATAAAGCCGGGG
66 GAAATAAAACCGGAG
* * * * ***
2285269 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGT-GTCCTCGATTGTGAAAAATTGGTATTTTT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAGTCC-CAATTATGAAAAATCAATATTTTT
*
2285333 GGAAATAAAATCGGAG
65 GGAAATAAAACCGGAG
2285349 TTGGAGTATCCCC
1 TTGGAGTATCCCC
2285362 GATTAAAGGA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
78 3 0.04
79 46 0.59
80 29 0.37
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (80 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAGTCCCAATTATGAAAAATCAATATTTTTG
GAAATAAAACCGGAG
Found at i:2285452 original size:51 final size:51
Alignment explanation
Indices: 2285292--2285629 Score: 214
Period size: 51 Copynumber: 6.4 Consensus size: 51
2285282 TCGGAAGTAA
* * * *
2285292 CGGGGTTGGAGTGTCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAAT
* * * *
2285344 CGGAGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAAT
* *** *
2285397 CGGGGTTGGAGTATCCCCGATTATGAAAAGTCAATATTTTGAAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAAT
**** * *** *** ** *
2285448 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAT-TAA-
1 CGGGGTTGGAGTATCCCCGATTATG-AA--AAATT-G-GTAT-TTTGAAAATAAAAT
* * * *
2285503 CGGGGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAA-AAATT-G-GTATTTTGAAAATAAAAT
* * *
2285557 CGGAGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTGAAAATAAAAT
* *
2285608 CGGAGTTGGAATATCCCCGATT
1 CGGGGTTGGAGTATCCCCGATT
2285630 GTGGAGAATT
Statistics
Matches: 215, Mismatches: 60, Indels: 23
0.72 0.20 0.08
Matches are distributed among these distances:
51 78 0.36
52 24 0.11
53 50 0.23
54 37 0.17
55 18 0.08
56 4 0.02
57 4 0.02
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAAT
Found at i:2285511 original size:27 final size:28
Alignment explanation
Indices: 2285448--2285523 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
2285438 AAAATAAAGT
***
2285448 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAGTAA
*
2285476 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAGTAA
*
2285503 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2285524 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAGTAA
Found at i:2287997 original size:20 final size:20
Alignment explanation
Indices: 2287970--2288024 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2287960 TAAAATTTCC
*
2287970 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
2287990 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
2288010 AAATGTATCGATACA
1 AAATGTATCGATACA
2288025 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:2288068 original size:19 final size:18
Alignment explanation
Indices: 2288044--2288111 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2288034 CAGTAGCTAA
2288044 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2288063 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2288078 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2288095 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2288112 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2288084 original size:13 final size:13
Alignment explanation
Indices: 2288066--2288090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2288056 ACAATACTTA
2288066 TGTATCGATACAT
1 TGTATCGATACAT
2288079 TGTATCGATACA
1 TGTATCGATACA
2288091 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2288088 original size:32 final size:32
Alignment explanation
Indices: 2288047--2288109 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2288037 TAGCTAATTA
*
2288047 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2288079 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2288110 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2288173 original size:21 final size:22
Alignment explanation
Indices: 2288147--2288204 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
2288137 GTTGGGACCC
* * *
2288147 TGTATCGATATATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
2288168 TGTATCGATACATTT-CACAAA
1 TGTATCGATACATTTGCACAAA
2288189 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2288205 GAAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:2292466 original size:13 final size:13
Alignment explanation
Indices: 2292448--2292475 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2292438 ATACAAAGGT
2292448 CAATGTATCGATA
1 CAATGTATCGATA
2292461 CAATGTATCGATA
1 CAATGTATCGATA
2292474 CA
1 CA
2292476 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2294448 original size:10 final size:11
Alignment explanation
Indices: 2294428--2294458 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
2294418 GTCCTTTCTT
2294428 TTTTTTCTTTA
1 TTTTTTCTTTA
2294439 TTTTTT-TTTA
1 TTTTTTCTTTA
2294449 TTTTTTCTTT
1 TTTTTTCTTT
2294459 TGATTTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTA
Found at i:2295206 original size:25 final size:24
Alignment explanation
Indices: 2295169--2295216 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2295159 AGAATCAAAT
* *
2295169 ACTATATATAAGATTATATTAATC
1 ACTATATATAAGATAAAATTAATC
*
2295193 ACTATTTAGTAAGATAAAATTAAT
1 ACTATATA-TAAGATAAAATTAAT
2295217 AATCAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (24 bp):
ACTATATATAAGATAAAATTAATC
Found at i:2295499 original size:21 final size:21
Alignment explanation
Indices: 2295469--2295508 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2295459 TATCCAATTC
* *
2295469 AAATCGAAGAAAAAGCTCTTT
1 AAATCAAAGAAAAAACTCTTT
2295490 AAATCAAAGAAAAAACTCT
1 AAATCAAAGAAAAAACTCT
2295509 ACATGTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (21 bp):
AAATCAAAGAAAAAACTCTTT
Found at i:2305721 original size:96 final size:96
Alignment explanation
Indices: 2305557--2305751 Score: 363
Period size: 96 Copynumber: 2.0 Consensus size: 96
2305547 CAGCACAAAT
2305557 ATGCTCACAGATTAAACAGAACCTTAATTAAAAATTCAGTACTTCAAAGTTTAGTACATTATATA
1 ATGCTCACAGATTAAACAGAACCTTAATTAAAAATTCAGTACTTCAAAGTTTAGTACATTATATA
2305622 GGTTGAACTTAAATTTTAATCCAAAAATTTC
66 GGTTGAACTTAAATTTTAATCCAAAAATTTC
** *
2305653 ATGCTCACAGATTAAATGGAACCTTAATTAAAAATTCAGTACTTTAAAGTTTAGTACATTATATA
1 ATGCTCACAGATTAAACAGAACCTTAATTAAAAATTCAGTACTTCAAAGTTTAGTACATTATATA
2305718 GGTTGAACTTAAATTTTAATCCAAAAATTTC
66 GGTTGAACTTAAATTTTAATCCAAAAATTTC
2305749 ATG
1 ATG
2305752 GTTGTCCATG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (96 bp):
ATGCTCACAGATTAAACAGAACCTTAATTAAAAATTCAGTACTTCAAAGTTTAGTACATTATATA
GGTTGAACTTAAATTTTAATCCAAAAATTTC
Found at i:2319863 original size:2 final size:2
Alignment explanation
Indices: 2319856--2319894 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2319846 CCATGAGCGC
2319856 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
2319895 CCCTAACGTG
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:2325383 original size:2 final size:2
Alignment explanation
Indices: 2325359--2325420 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
2325349 AAGTTGTGGC
* * *
2325359 AG AG AG GG AG AG GG AG AG GG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2325401 AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
2325421 GAGGGAGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2327173 original size:16 final size:15
Alignment explanation
Indices: 2327128--2327173 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2327118 ATTATATTAT
*
2327128 ATAATTTATTTTTTA
1 ATAATTTAATTTTTA
*
2327143 AAAATTTTAATTTTTA
1 ATAA-TTTAATTTTTA
2327159 ATAATTTAATATTTT
1 ATAATTTAAT-TTTT
2327174 TTTTATCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATAATTTAATTTTTA
Found at i:2327651 original size:32 final size:33
Alignment explanation
Indices: 2327571--2327654 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 33
2327561 TAACAATCGT
*
2327571 ATATAAGATATTATATATTTATATAAATTTTTTAA
1 ATATAA-ATATT-TATATTTATATAAATTTTTAAA
2327606 ATATAAATAATTTA-ATTTATATAAA-TTTTAAA
1 ATATAAAT-ATTTATATTTATATAAATTTTTAAA
2327638 ATATAATATATTTATAT
1 ATATAA-ATATTTATAT
2327655 AATATTAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
32 17 0.38
33 15 0.33
34 4 0.09
35 9 0.20
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (33 bp):
ATATAAATATTTATATTTATATAAATTTTTAAA
Found at i:2327667 original size:21 final size:20
Alignment explanation
Indices: 2327643--2327702 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
2327633 TTAAAATATA
*
2327643 ATATATTTATATAATATTAAT
1 ATATATTTATATTATATT-AT
2327664 ATATATTTTTATATTATATTAT
1 ATATA--TTTATATTATATTAT
*
2327686 -TATTTTTATATTATATT
1 ATATATTTATATTATATT
2327703 TAAAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 13 0.37
21 8 0.23
22 2 0.06
23 12 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATATTTATATTATATTAT
Found at i:2327674 original size:23 final size:24
Alignment explanation
Indices: 2327637--2327684 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2327627 TAAATTTTAA
2327637 AATATAATATATTTATATAATATT
1 AATATAATATATTTATATAATATT
* *
2327661 AATAT-ATATTTTTATATTATATT
1 AATATAATATATTTATATAATATT
2327684 A
1 A
2327685 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATAATATATTTATATAATATT
Found at i:2327711 original size:19 final size:19
Alignment explanation
Indices: 2327670--2327728 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
2327660 TAATATATAT
* *
2327670 TTTTATATTATA-TTATTAT
1 TTTTATATTATATTTA-AAA
2327689 TTTTATATTATATTTAAAA
1 TTTTATATTATATTTAAAA
* *
2327708 TTTTAAATTA-ATTTTAAA
1 TTTTATATTATATTTAAAA
2327726 TTT
1 TTT
2327729 AAATTGTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.29
19 22 0.63
20 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATATTATATTTAAAA
Found at i:2328402 original size:2 final size:2
Alignment explanation
Indices: 2328395--2328420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2328385 TTATTCTAGA
2328395 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
2328421 GTATGCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2329901 original size:23 final size:23
Alignment explanation
Indices: 2329872--2329918 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2329862 ATTAATTAAT
2329872 TTTGGATTACTATACGATTCTGA
1 TTTGGATTACTATACGATTCTGA
*
2329895 TTTGGATTACTATACGATTTTGA
1 TTTGGATTACTATACGATTCTGA
2329918 T
1 T
2329919 ATCGTATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (23 bp):
TTTGGATTACTATACGATTCTGA
Found at i:2333338 original size:17 final size:17
Alignment explanation
Indices: 2333312--2333346 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2333302 TTGTTATATT
2333312 TAATAGTAATGTATCAA
1 TAATAGTAATGTATCAA
*
2333329 TAATATTAATGTATCAA
1 TAATAGTAATGTATCAA
2333346 T
1 T
2333347 TTTAATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATAGTAATGTATCAA
Found at i:2344325 original size:8 final size:8
Alignment explanation
Indices: 2344302--2344405 Score: 62
Period size: 8 Copynumber: 13.1 Consensus size: 8
2344292 TATTCATATA
*
2344302 ATAATTAT
1 ATAATTTT
2344310 AT-ATTTT
1 ATAATTTT
2344317 ATAATTTT
1 ATAATTTT
2344325 ATAATTTT
1 ATAATTTT
2344333 ATAA--TT
1 ATAATTTT
*
2344339 AT-ATTTAA
1 ATAATTT-T
*
2344347 ATTATTTT
1 ATAATTTT
2344355 AT-ATTTAT
1 ATAATTT-T
2344363 ATTAATTTT
1 A-TAATTTT
2344372 A-AATATATT
1 ATAAT-T-TT
2344381 AATAA-TTT
1 -ATAATTTT
2344389 AT-ATTTT
1 ATAATTTT
2344396 ATATATTTT
1 ATA-ATTTT
2344405 A
1 A
2344406 AGTTATTTAT
Statistics
Matches: 78, Mismatches: 3, Indels: 29
0.71 0.03 0.26
Matches are distributed among these distances:
5 1 0.01
6 5 0.06
7 21 0.27
8 28 0.36
9 16 0.21
10 5 0.06
11 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATAATTTT
Found at i:2344333 original size:16 final size:15
Alignment explanation
Indices: 2344302--2344405 Score: 79
Period size: 16 Copynumber: 6.6 Consensus size: 15
2344292 TATTCATATA
*
2344302 ATAATTATATATTTT
1 ATAATTTTATATTTT
2344317 ATAATTTTATAATTTT
1 ATAATTTTAT-ATTTT
*
2344333 ATAA--TTATATTTAA
1 ATAATTTTATATTT-T
*
2344347 ATTATTTTATATTTAT
1 ATAATTTTATATTT-T
*
2344363 ATTAATTTTAAATATATTA
1 A-TAATTTT--ATAT-TTT
2344382 ATAA-TTTATATTTT
1 ATAATTTTATATTTT
2344396 ATATATTTTA
1 ATA-ATTTTA
2344406 AGTTATTTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
13 4 0.06
14 12 0.17
15 14 0.19
16 23 0.32
17 9 0.12
18 3 0.04
19 5 0.07
20 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATAATTTTATATTTT
Found at i:2344401 original size:22 final size:21
Alignment explanation
Indices: 2344306--2344403 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 21
2344296 CATATAATAA
*
2344306 TTATATATTTTATAATTTTATAAT
1 TTATATA-TTTAT-A-TTTATATT
* *
2344330 TT-TATAATTATATTTAAATT
1 TTATATATTTATATTTATATT
*
2344350 ATTTTATATTTATA-TTA-ATT
1 -TTATATATTTATATTTATATT
*
2344370 TTAAATATATTAATAATTTATATT
1 TT--ATATATTTAT-ATTTATATT
2344394 TTATATATTT
1 TTATATATTT
2344404 TAAGTTATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
19 2 0.03
20 9 0.15
21 14 0.23
22 21 0.35
23 7 0.12
24 7 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATATATTTATATTTATATT
Found at i:2344401 original size:24 final size:25
Alignment explanation
Indices: 2344367--2344415 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2344357 ATTTATATTA
2344367 ATTTTAAATATATTAA-TAATTTAT
1 ATTTTAAATATATTAAGTAATTTAT
* * *
2344391 ATTTTATATATTTTAAGTTATTTAT
1 ATTTTAAATATATTAAGTAATTTAT
2344416 TATATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTTTAAATATATTAAGTAATTTAT
Found at i:2344699 original size:2 final size:2
Alignment explanation
Indices: 2344692--2344726 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2344682 CGACACGTAT
* *
2344692 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2344727 TTTAACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2346328 original size:2 final size:2
Alignment explanation
Indices: 2346317--2346353 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2346307 TTGCATATAT
*
2346317 AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2346354 TATATATATA
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:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:2348488 original size:23 final size:23
Alignment explanation
Indices: 2348457--2348528 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
2348447 TTTACTAACT
*
2348457 TTTTTCTTTCTTTCTTCTTTCTC
1 TTTTCCTTTCTTTCTTCTTTCTC
*
2348480 TTTTCCTTTC-TTCTCTCTCTCTC
1 TTTTCCTTTCTTTCT-TCTTTCTC
**
2348503 TTTTTCCCCTCTTTC-TCTTTCTC
1 -TTTTCCTTTCTTTCTTCTTTCTC
2348526 TTT
1 TTT
2348529 CTGTTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
22 7 0.17
23 23 0.56
24 8 0.20
25 3 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTCCTTTCTTTCTTCTTTCTC
Found at i:2351921 original size:5 final size:5
Alignment explanation
Indices: 2351911--2351935 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2351901 CTGGAAAATT
2351911 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
2351936 TTGATGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:2362666 original size:2 final size:2
Alignment explanation
Indices: 2362659--2362692 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2362649 AAAGCTTAAA
2362659 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2362693 CAACAATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2364656 original size:14 final size:14
Alignment explanation
Indices: 2364626--2364669 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2364616 CCCTTCAGAG
*
2364626 AGAAAAGAAAAAAAA
1 AGAAAA-AAATAAAA
2364641 AGAAAAAAATAAAA
1 AGAAAAAAATAAAA
**
2364655 AGGTAAAAATAAAA
1 AGAAAAAAATAAAA
2364669 A
1 A
2364670 TTATAGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (14 bp):
AGAAAAAAATAAAA
Found at i:2364732 original size:16 final size:15
Alignment explanation
Indices: 2364698--2364801 Score: 88
Period size: 16 Copynumber: 6.8 Consensus size: 15
2364688 CGAGTTCAGA
*
2364698 TAAATTATTTGTA-TT
1 TAAA-TATTTTTAGTT
2364713 TAAATATTTTTAGGTT
1 TAAATATTTTTA-GTT
*
2364729 TAAATTTTTTTAAGTT
1 TAAATATTTTT-AGTT
* *
2364745 TAAATTATTTTGAATT
1 TAAA-TATTTTTAGTT
2364761 TAAA-ATTTTTTA-TT
1 TAAATA-TTTTTAGTT
* *
2364775 TAAATTTTTTTATTT
1 TAAATATTTTTAGTT
2364790 TAAATATTTTTA
1 TAAATATTTTTA
2364802 AATTTAAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.27
15 22 0.30
16 26 0.35
17 6 0.08
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
TAAATATTTTTAGTT
Found at i:2364807 original size:16 final size:16
Alignment explanation
Indices: 2364710--2364810 Score: 93
Period size: 16 Copynumber: 6.5 Consensus size: 16
2364700 AATTATTTGT
*
2364710 ATTTAAATATTTTTAG
1 ATTTAAATATTTTTAA
* *
2364726 GTTTAAATTTTTTTAA
1 ATTTAAATATTTTTAA
* *
2364742 GTTTAAAT-TATTTTGA
1 ATTTAAATAT-TTTTAA
*
2364758 ATTTAAA-ATTTTT-T
1 ATTTAAATATTTTTAA
*
2364772 ATTTAAAT-TTTTTTA
1 ATTTAAATATTTTTAA
*
2364787 TTTTAAATATTTTTAA
1 ATTTAAATATTTTTAA
2364803 ATTTAAAT
1 ATTTAAAT
2364811 TTAATTTATT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.17
15 12 0.17
16 46 0.66
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTTAAATATTTTTAA
Found at i:2364819 original size:46 final size:47
Alignment explanation
Indices: 2364698--2364828 Score: 132
Period size: 47 Copynumber: 2.8 Consensus size: 47
2364688 CGAGTTCAGA
*
2364698 TAAATTATTTGT--ATTT-AAATATTTTTAGGTTTAAATTTTTTTAAGTT
1 TAAATTATTT-TAAATTTAAAAT-TTTTTA-TTTTAAATTTTTTTAAGTT
* *
2364745 TAAATTATTTTGAATTTAAAATTTTTTA-TTTAAATTTTTTT-ATTT
1 TAAATTATTTTAAATTTAAAATTTTTTATTTTAAATTTTTTTAAGTT
2364790 TAAA-TATTTTTAAATTT-AAATTTAATTTATTTTAAATTT
1 TAAATTA-TTTTAAATTTAAAATTT--TTTATTTTAAATTT
2364829 AATTACTTCA
Statistics
Matches: 75, Mismatches: 2, Indels: 14
0.82 0.02 0.15
Matches are distributed among these distances:
44 8 0.11
45 16 0.21
46 18 0.24
47 19 0.25
48 10 0.13
49 4 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (47 bp):
TAAATTATTTTAAATTTAAAATTTTTTATTTTAAATTTTTTTAAGTT
Found at i:2364823 original size:16 final size:16
Alignment explanation
Indices: 2364731--2364832 Score: 68
Period size: 16 Copynumber: 6.2 Consensus size: 16
2364721 TTTAGGTTTA
*
2364731 AATTT-TTTTAAGTTT
1 AATTTATTTTAAATTT
* *
2364746 AAATTATTTTGAATTT
1 AATTTATTTTAAATTT
*
2364762 AAAATTTTTTATTTAAATTT
1 --AA-TTTAT-TTTAAATTT
*
2364782 -TTTTATTTTAAATATT
1 AATTTATTTTAAAT-TT
*
2364798 --TTTAAATTTAAATTT
1 AATTT-ATTTTAAATTT
2364813 AATTTATTTTAAATTT
1 AATTTATTTTAAATTT
2364829 AATT
1 AATT
2364833 ACTTCAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
15 16 0.24
16 36 0.53
17 3 0.04
18 2 0.03
19 3 0.04
20 8 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
AATTTATTTTAAATTT
Found at i:2364824 original size:61 final size:64
Alignment explanation
Indices: 2364699--2364825 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 64
2364689 GAGTTCAGAT
* * *
2364699 AAATTATTTGTATTTAAATATTTTTAGGTTTAAATTTTTTTAAGTTTAAATTATTTTGAATTTA
1 AAATTATTTGTATTTAAATATTTTTAGGTTTAAATATTTTTAAATTTAAATTAATTTGAATTTA
* * *
2364763 AAATT-TTT-TATTTAAATTTTTTTA-TTTTAAATATTTTTAAATTTAAATTTAATTT-ATTTTA
1 AAATTATTTGTATTTAAATATTTTTAGGTTTAAATATTTTTAAATTTAAA-TTAATTTGAATTTA
2364824 AA
1 AA
2364826 TTTAATTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
61 27 0.48
62 21 0.38
63 3 0.05
64 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (64 bp):
AAATTATTTGTATTTAAATATTTTTAGGTTTAAATATTTTTAAATTTAAATTAATTTGAATTTA
Found at i:2370934 original size:47 final size:47
Alignment explanation
Indices: 2370840--2370934 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
2370830 CATCACTAAT
* ** * *
2370840 ACAACTTGTAACTTTTGCATGGATAAAACTACAAACACTCTTTACAA
1 ACAACTTGTAACATTTGCATAAATAAAACTACAAACACTCCTCACAA
** *
2370887 ACAACTTGTAACATTTGCATAAATAAAGTTACAAACCCTCCTCACAA
1 ACAACTTGTAACATTTGCATAAATAAAACTACAAACACTCCTCACAA
2370934 A
1 A
2370935 ATCTATAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.27
Consensus pattern (47 bp):
ACAACTTGTAACATTTGCATAAATAAAACTACAAACACTCCTCACAA
Found at i:2373666 original size:2 final size:2
Alignment explanation
Indices: 2373659--2373689 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2373649 TTTGCTTCAA
2373659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2373690 GTTTCCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2376339 original size:24 final size:24
Alignment explanation
Indices: 2376312--2376365 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
2376302 AATAAATGTG
*
2376312 TTGTTTAAATATATAATATTAT-TT
1 TTGTTTAAATAAAT-ATATTATATT
* *
2376336 TTGTATTTATTAAATATATTATATT
1 TTGT-TTAAATAAATATATTATATT
2376361 TTGTT
1 TTGTT
2376366 CTGCTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTGTTTAAATAAATATATTATATT
Found at i:2383446 original size:10 final size:10
Alignment explanation
Indices: 2383417--2383447 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2383407 CTTCATTGTT
*
2383417 TGTGTGTGTG
1 TGTGTGTGTA
2383427 TGTGTGTGTA
1 TGTGTGTGTA
2383437 TGTGTGTGTA
1 TGTGTGTGTA
2383447 T
1 T
2383448 CTATTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.42, T:0.52
Consensus pattern (10 bp):
TGTGTGTGTA
Found at i:2384475 original size:2 final size:2
Alignment explanation
Indices: 2384468--2384511 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2384458 TCTCGAATTA
* *
2384468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2384510 AT
1 AT
2384512 GAACTAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2385203 original size:39 final size:40
Alignment explanation
Indices: 2385146--2385226 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
2385136 ATGAATTTTT
2385146 TTATAATATATTGCTGATGGAATACATAAATAT-AAAATA
1 TTATAATATATTGCTGATGGAATACATAAATATAAAAATA
* *
2385185 TTATAATATATTGTTGATGGAATAGATAAATATAAAAATA
1 TTATAATATATTGCTGATGGAATACATAAATATAAAAATA
2385225 TT
1 TT
2385227 TTTAAAAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38
Consensus pattern (40 bp):
TTATAATATATTGCTGATGGAATACATAAATATAAAAATA
Done.