Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 51 of 204
Found at i:16780815 original size:11 final size:11
Alignment explanation
Indices: 16780765--16780815 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
16780755 TCTTCTTTTT
16780765 TATTATTTTGC
1 TATTATTTTGC
**
16780776 TACCATTTCT-C
1 TATTATTT-TGC
*
16780787 TATTATGTTGC
1 TATTATTTTGC
*
16780798 TATTATTTTGT
1 TATTATTTTGC
16780809 TATTATT
1 TATTATT
16780816 GTTTGGATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
10 1 0.03
11 29 0.94
12 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.61
Consensus pattern (11 bp):
TATTATTTTGC
Found at i:16783588 original size:23 final size:23
Alignment explanation
Indices: 16783556--16783600 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
16783546 CCGATTTGCT
*
16783556 CCCTCCGTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTG
*
16783579 CCCTCTGTTTATTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCT
16783601 TTCCTGCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.31, G:0.07, T:0.60
Consensus pattern (23 bp):
CCCTCCGTTTATTTTCTTTTCTG
Found at i:16783614 original size:61 final size:60
Alignment explanation
Indices: 16783543--16783703 Score: 241
Period size: 66 Copynumber: 2.6 Consensus size: 60
16783533 CTTCTAGCCT
16783543 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTC
1 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTC-TTTCTTTC
*
16783604 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTCTTTT
1 CTGCCGATTTGCTCCCTCCG-----TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTCTTTC
**
16783669 CTGCCGATTTGCTCCCTTTGTTTCTTTTCTTTTCT
1 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCT
16783704 TTTCTACCGA
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
60 15 0.16
61 20 0.22
65 25 0.27
66 32 0.35
ACGTcount: A:0.03, C:0.30, G:0.10, T:0.57
Consensus pattern (60 bp):
CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTCTTTC
Found at i:16783632 original size:38 final size:38
Alignment explanation
Indices: 16783579--16783718 Score: 149
Period size: 38 Copynumber: 4.0 Consensus size: 38
16783569 TTCTTTTCTG
*
16783579 CCCTCTGTTTATTTTCTTTTCTTTCCTGCCGATTTGCT
1 CCCTCTGTTTATTTTCTTTTCTTTTCTGCCGATTTGCT
* *
16783617 CCCTCCGTTTCTTTTCTTTTC-TTT-T--C----TG--
1 CCCTCTGTTTATTTTCTTTTCTTTTCTGCCGATTTGCT
16783645 CCCTCTGTTTATTTTC-TTTCTTTTCTGCCGATTTGCT
1 CCCTCTGTTTATTTTCTTTTCTTTTCTGCCGATTTGCT
* * *
16783682 CCCTTTGTTTCTTTTCTTTTCTTTTCTACCGATTTGC
1 CCCTCTGTTTATTTTCTTTTCTTTTCTGCCGATTTGC
16783719 CAGTTTCTGC
Statistics
Matches: 83, Mismatches: 8, Indels: 22
0.73 0.07 0.19
Matches are distributed among these distances:
27 4 0.05
28 17 0.20
29 1 0.01
30 2 0.02
31 1 0.01
34 1 0.01
35 2 0.02
36 1 0.01
37 16 0.19
38 38 0.46
ACGTcount: A:0.04, C:0.29, G:0.09, T:0.58
Consensus pattern (38 bp):
CCCTCTGTTTATTTTCTTTTCTTTTCTGCCGATTTGCT
Found at i:16783672 original size:27 final size:28
Alignment explanation
Indices: 16783617--16783673 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
16783607 CCGATTTGCT
*
16783617 CCCTCCGTTTCTTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
*
16783645 CCCTCTGTTTATTTTC-TTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
16783672 CC
1 CC
16783674 GATTTGCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.02, C:0.32, G:0.07, T:0.60
Consensus pattern (28 bp):
CCCTCCGTTTATTTTCTTTTCTTTTCTG
Found at i:16783699 original size:65 final size:66
Alignment explanation
Indices: 16783543--16783708 Score: 263
Period size: 65 Copynumber: 2.6 Consensus size: 66
16783533 CTTCTAGCCT
16783543 CTGCCGATTTGCTCCCTCCG-----TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
1 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
16783603 C
66 C
16783604 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTC-TTTCTTT
1 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
*
16783668 T
66 C
**
16783669 CTGCCGATTTGCTCCCTTTGTTTCTTTTCTTTTCTTTTCT
1 CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCT
16783709 ACCGATTTGC
Statistics
Matches: 97, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
61 20 0.21
65 45 0.46
66 32 0.33
ACGTcount: A:0.03, C:0.30, G:0.10, T:0.58
Consensus pattern (66 bp):
CTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
C
Found at i:16784277 original size:7 final size:7
Alignment explanation
Indices: 16784265--16784298 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
16784255 ATTGTCGATA
16784265 CTGTTGT
1 CTGTTGT
16784272 CTGTTGT
1 CTGTTGT
16784279 CTGTTGT
1 CTGTTGT
16784286 CTGTTGT
1 CTGTTGT
*
16784293 TTGTTG
1 CTGTTG
16784299 ATGTGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.29, T:0.59
Consensus pattern (7 bp):
CTGTTGT
Found at i:16787517 original size:2 final size:2
Alignment explanation
Indices: 16787504--16787536 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16787494 GAAAATATGG
*
16787504 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16787537 AACAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16787929 original size:15 final size:15
Alignment explanation
Indices: 16787909--16787944 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16787899 TAGTTACTAG
*
16787909 TAATAATAACGTTAA
1 TAATAATAACGATAA
*
16787924 TAATAATAATGATAA
1 TAATAATAACGATAA
16787939 TAATAA
1 TAATAA
16787945 ATGATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (15 bp):
TAATAATAACGATAA
Found at i:16787949 original size:13 final size:12
Alignment explanation
Indices: 16787923--16787953 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
16787913 AATAACGTTA
16787923 ATAATAATAATG
1 ATAATAATAATG
16787935 ATAATAATAAATG
1 ATAATAAT-AATG
16787948 ATAATA
1 ATAATA
16787954 TATTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:16788277 original size:24 final size:24
Alignment explanation
Indices: 16788250--16788297 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
16788240 CATTTTAAGA
*
16788250 AAGCACGCGGATCCTTCCCTGGGT
1 AAGCACGCGGATCCTACCCTGGGT
16788274 AAGCACGCGGATCCTACCCTGGGT
1 AAGCACGCGGATCCTACCCTGGGT
16788298 CGGGTCACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.19
Consensus pattern (24 bp):
AAGCACGCGGATCCTACCCTGGGT
Found at i:16789825 original size:44 final size:44
Alignment explanation
Indices: 16789766--16790204 Score: 165
Period size: 44 Copynumber: 9.8 Consensus size: 44
16789756 TAGTGTCTTC
* *
16789766 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCTAAATTTT
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTAAATTTT
* * * *
16789810 AATCCGCTCCACTGTAACCTTAGGGAGATAGGATTATCGGCTTCAATCTGATGT
1 AATCTGCTCCACTGTAACCTCAGGGAGATA--A-GATC--C-TAAAT-T--T-T
* * * * * * **
16789864 GATCTACTCTACTGTAACTTCAGAGAGATAAGATTCTTTATTTT
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTAAATTTT
* ** * * *
16789908 AATCCGCTCCACTGTAATTTCAGGGAGATAGGAT--TACTATCTTC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTA-AAT-TTT
* * * * * *
16789952 AATCTGCTCCGCTTTAATCTTAGAGAGATAAGAT-CTGAATTTCTTT
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCT-AA-AT-TTT
** * * * **
16789998 GGTCTACTCCACTGTAACCTCAGGGAGATAGGA-CC-AGA-TGC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTAAATTTT
* * * * *
16790039 GATCTACTCTATTGTAACCTCAGAGAGATAAGATCCTAAATTTT
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTAAATTTT
* * * * * ** ** *
16790083 AAGCCGCTCCACTGTAACTTAAGGGAGATAGGATAGTGTA-TTG
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTAAATTTT
* * * * * *** *
16790126 GACCTGCTCCGCTATAATCTCAGGGAGATAAGATCTCT-GGCTTC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATC-CTAAATTTT
16790170 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
16790205 TGAAATTCTT
Statistics
Matches: 283, Mismatches: 91, Indels: 42
0.68 0.22 0.10
Matches are distributed among these distances:
41 29 0.10
42 3 0.01
43 32 0.11
44 144 0.51
45 2 0.01
46 31 0.11
47 4 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 3 0.01
52 1 0.00
53 1 0.00
54 24 0.08
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTAAATTTT
Found at i:16789952 original size:98 final size:98
Alignment explanation
Indices: 16789777--16789957 Score: 251
Period size: 98 Copynumber: 1.8 Consensus size: 98
16789767 ATCTGCTCCG
*
16789777 CTGTAATCTCAGGGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACCTTAGGGAGATAGG
1 CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACCTTAGGGAGATAGG
*
16789842 ATTATCGGCTTCAATCTGATGTGATCTACTCTA
66 ATTATCAGCTTCAATCTGATGTGATCTACTCTA
* ** *
16789875 CTGTAA-CTTCAGAGAGATAAGATTCTTTATTTTAATCCGCTCCACTGTAA-TTTCAGGGAGATA
1 CTGTAATC-TCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACCTT-AGGGAGATA
*
16789938 GGATTA-CTATCTTCAATCTG
64 GGATTATC-AGCTTCAATCTG
16789958 CTCCGCTTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
97 4 0.05
98 69 0.95
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (98 bp):
CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACCTTAGGGAGATAGG
ATTATCAGCTTCAATCTGATGTGATCTACTCTA
Found at i:16802539 original size:2 final size:2
Alignment explanation
Indices: 16802526--16802558 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16802516 GAAAATATGG
*
16802526 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16802559 AACAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16802949 original size:15 final size:15
Alignment explanation
Indices: 16802929--16802964 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16802919 TAGTTACTAG
*
16802929 TAATAATAACGTTAA
1 TAATAATAACGATAA
*
16802944 TAATAATAATGATAA
1 TAATAATAACGATAA
16802959 TAATAA
1 TAATAA
16802965 ATGATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (15 bp):
TAATAATAACGATAA
Found at i:16802969 original size:13 final size:12
Alignment explanation
Indices: 16802943--16802973 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
16802933 AATAACGTTA
16802943 ATAATAATAATG
1 ATAATAATAATG
16802955 ATAATAATAAATG
1 ATAATAAT-AATG
16802968 ATAATA
1 ATAATA
16802974 TATTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:16803297 original size:24 final size:24
Alignment explanation
Indices: 16803270--16803317 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
16803260 CATTTTAAGA
*
16803270 AAGCACGCGGATCCTTCCCTGGGT
1 AAGCACGCGGATCCTACCCTGGGT
16803294 AAGCACGCGGATCCTACCCTGGGT
1 AAGCACGCGGATCCTACCCTGGGT
16803318 CGGGTCACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.19
Consensus pattern (24 bp):
AAGCACGCGGATCCTACCCTGGGT
Found at i:16804064 original size:13 final size:13
Alignment explanation
Indices: 16804048--16804076 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16804038 CTTTTCCCCT
16804048 GTTCTCTTCTATC
1 GTTCTCTTCTATC
16804061 GTTCTCTTCTATC
1 GTTCTCTTCTATC
16804074 GTT
1 GTT
16804077 TTGGTAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.28, G:0.10, T:0.55
Consensus pattern (13 bp):
GTTCTCTTCTATC
Found at i:16804847 original size:130 final size:120
Alignment explanation
Indices: 16804715--16805127 Score: 722
Period size: 120 Copynumber: 3.4 Consensus size: 120
16804705 AATTATTTTA
* * * *
16804715 AATTTTATTAAATCT-TATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAAATTATCTT
1 AATTTTATTAAAT-TATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATT
* *
16804778 TTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
16804835 AATTTTATTAAATTATATACTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
16804900 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
16804955 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAGTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
16805020 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
16805075 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
16805128 TAAATATGAT
Statistics
Matches: 282, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 1 0.00
120 279 0.99
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:16804875 original size:15 final size:15
Alignment explanation
Indices: 16804849--16804891 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
16804839 TTATTAAATT
16804849 ATATACTTTAATTATA
1 ATATA-TTTAATTATA
*
16804865 ATATATTTAATAATA
1 ATATATTTAATTATA
16804880 AT-TATGTTAATT
1 ATATAT-TTAATT
16804892 TATATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 16 0.67
16 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:16804973 original size:61 final size:61
Alignment explanation
Indices: 16804788--16805095 Score: 264
Period size: 61 Copynumber: 5.1 Consensus size: 61
16804778 TTATAGTATA
*
16804788 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * *
16804849 ATATACTT-TAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTAT
1 ATATA-TTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AAT
*
16804907 C
61 T
16804908 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
16804969 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAGTTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATTA-TTAAGAATTTTATTA-AATT
16805028 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
16805089 ATATATT
1 ATATATT
16805096 TTAATTATAA
Statistics
Matches: 186, Mismatches: 39, Indels: 44
0.69 0.14 0.16
Matches are distributed among these distances:
58 8 0.04
59 57 0.31
60 49 0.26
61 64 0.34
62 8 0.04
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:16804995 original size:15 final size:15
Alignment explanation
Indices: 16804960--16805001 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16804950 TTAAGAATTT
*
16804960 TATTAAATTAT-ATA
1 TATTTAATTATAATA
16804974 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
16804988 TATTTAATAATAAT
1 TATTTAATTATAAT
16805002 TATGTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:16805110 original size:16 final size:16
Alignment explanation
Indices: 16805089--16805130 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
16805079 TTATTAAATT
*
16805089 ATATATTTTAATTATA
1 ATATATTTTAATAATA
16805105 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
16805120 AT-TATGTTTAA
1 ATATAT-TTTAA
16805131 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:16805115 original size:15 final size:15
Alignment explanation
Indices: 16805080--16805121 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16805070 TTAAGAATTT
*
16805080 TATTAAATTAT-ATA
1 TATTTAATTATAATA
16805094 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
16805108 TATTTAATAATAAT
1 TATTTAATTATAAT
16805122 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:16805301 original size:39 final size:40
Alignment explanation
Indices: 16805258--16805362 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 40
16805248 TTCCATTATG
16805258 CTATTACACCTCTATTCCATTCAACCAAACACA-AGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACA-ATAGATTTA
* * *
16805297 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACAATAGATTTA
16805342 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
16805363 ACGCCTCTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 15 0.27
40 5 0.09
43 1 0.02
44 17 0.31
45 17 0.31
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACAATAGATTTA
Found at i:16805356 original size:45 final size:44
Alignment explanation
Indices: 16805256--16805364 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
16805246 TTTTCCATTA
16805256 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * *
16805295 TACTATTACGCCTCTATTCCATTACATTCAACCAAACA-ATTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACA-AGA-T
16805340 TGCTATTACACCTCTATTCCATTAC
1 TGCTATTACACCTCTATTCCATTAC
16805365 GCCTCTTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
43 1 0.02
44 16 0.28
45 24 0.41
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:16808993 original size:16 final size:16
Alignment explanation
Indices: 16808968--16808999 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16808958 TAAAGAACTA
*
16808968 ATTAAGAATAAAAAAT
1 ATTAAAAATAAAAAAT
16808984 ATTAAAAATAAAAAAT
1 ATTAAAAATAAAAAAT
16809000 CCAATTAAGT
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:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
ATTAAAAATAAAAAAT
Found at i:16821487 original size:17 final size:19
Alignment explanation
Indices: 16821467--16821504 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16821457 ATTTTTGTTA
16821467 AAAAT-ATTT-TTTTAAAT
1 AAAATCATTTATTTTAAAT
*
16821484 AAAATCTTTTATTTTAAAT
1 AAAATCATTTATTTTAAAT
16821503 AA
1 AA
16821505 TTTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATCATTTATTTTAAAT
Found at i:16821633 original size:17 final size:16
Alignment explanation
Indices: 16821608--16821657 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
16821598 ATTTATATTT
*
16821608 TAATTATTATTAAATTA
1 TAATCATTA-TAAATTA
16821625 TAATCATTATAAATT-
1 TAATCATTATAAATTA
*
16821640 TAAAT-ATTATATATTA
1 T-AATCATTATAAATTA
16821656 TA
1 TA
16821658 TATTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 11 0.38
16 10 0.34
17 8 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATCATTATAAATTA
Found at i:16821655 original size:22 final size:25
Alignment explanation
Indices: 16821621--16821668 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
16821611 TTATTATTAA
16821621 ATTATAATCATTATAAATTT-AAAT
1 ATTATAATCATTATAAATTTGAAAT
*
16821645 ATTAT-AT-ATTATATATTTGAAAT
1 ATTATAATCATTATAAATTTGAAAT
16821668 A
1 A
16821669 AATTTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 7 0.32
24 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTATAATCATTATAAATTTGAAAT
Found at i:16824258 original size:31 final size:33
Alignment explanation
Indices: 16824222--16824282 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
16824212 TTAAATTTTG
*
16824222 AGTTGGAGTTATTTTGAA-TATG-AATTTTCTT
1 AGTTGGAATTATTTTGAATTATGCAATTTTCTT
16824253 AGTTGGAATTATTTTGAATTATGCAATTTT
1 AGTTGGAATTATTTTGAATTATGCAATTTT
16824283 AGATCTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 17 0.63
32 4 0.15
33 6 0.22
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (33 bp):
AGTTGGAATTATTTTGAATTATGCAATTTTCTT
Found at i:16825309 original size:25 final size:25
Alignment explanation
Indices: 16825268--16825318 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
16825258 CAAATAATTT
16825268 AAAAATATAATATATTCAAAAATAAA
1 AAAAATATAATATATTCAAAAA-AAA
16825294 AAAAATTATAA-A-ATTCAAAAAAAA
1 AAAAA-TATAATATATTCAAAAAAAA
16825318 A
1 A
16825319 TGAAATACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.17
25 9 0.38
26 6 0.25
27 5 0.21
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATATAATATATTCAAAAAAAA
Found at i:16825874 original size:22 final size:22
Alignment explanation
Indices: 16825848--16825892 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16825838 TGTTAACTAT
16825848 TAGCTTATCAGTTAATTAGTTG
1 TAGCTTATCAGTTAATTAGTTG
*
16825870 TAGCTTATCAGTTAGTTAGTTG
1 TAGCTTATCAGTTAATTAGTTG
16825892 T
1 T
16825893 GCAGTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (22 bp):
TAGCTTATCAGTTAATTAGTTG
Found at i:16826928 original size:22 final size:22
Alignment explanation
Indices: 16826902--16826946 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16826892 TGTTAACTGT
16826902 TAGCTTATCAGTTAATTAGTTG
1 TAGCTTATCAGTTAATTAGTTG
*
16826924 TAGCTTATCAGTTAGTTAGTTG
1 TAGCTTATCAGTTAATTAGTTG
16826946 T
1 T
16826947 GCAGTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (22 bp):
TAGCTTATCAGTTAATTAGTTG
Found at i:16831493 original size:22 final size:22
Alignment explanation
Indices: 16831467--16831511 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16831457 TGTTAACTGT
16831467 TAGCTTATCAGTTAATTAGTTG
1 TAGCTTATCAGTTAATTAGTTG
*
16831489 TAGCTTATCAGTTAGTTAGTTG
1 TAGCTTATCAGTTAATTAGTTG
16831511 T
1 T
16831512 GCAGTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (22 bp):
TAGCTTATCAGTTAATTAGTTG
Found at i:16839915 original size:33 final size:33
Alignment explanation
Indices: 16839770--16839926 Score: 93
Period size: 33 Copynumber: 4.6 Consensus size: 33
16839760 TTTAAATGTG
* * *
16839770 AGACCATAGCTGGGCTATGGCATTTTAATGAAA
1 AGACCATAGCTGGGCTATGGCATTCTGATGATA
* * * *
16839803 AGACTATAACTGGGTTATGGCA-TCTTGAACG-TA
1 AGACCATAGCTGGGCTATGGCATTC-TG-ATGATA
* * * * * *
16839836 AGACCATGGTTGGACTATGGCAGTATAGATACATGTGTA
1 AGACCATAGCTGGGCTATGGCA-T-T--CT-GATG-ATA
16839875 AGACCATAGCTGGGCTATGGCATTCTGATGATA
1 AGACCATAGCTGGGCTATGGCATTCTGATGATA
* *
16839908 AGACCATAACTGGGTTATG
1 AGACCATAGCTGGGCTATG
16839927 ACACTACAAA
Statistics
Matches: 90, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
32 1 0.01
33 56 0.62
34 5 0.06
35 1 0.01
36 1 0.01
37 4 0.04
38 1 0.01
39 21 0.23
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (33 bp):
AGACCATAGCTGGGCTATGGCATTCTGATGATA
Found at i:16839961 original size:105 final size:105
Alignment explanation
Indices: 16839770--16839962 Score: 253
Period size: 105 Copynumber: 1.8 Consensus size: 105
16839760 TTTAAATGTG
* * * **
16839770 AGACCATAGCTGGGCTATGGCATTTTAATGAAAAGACTATAACTGGGTTATGGCATCTTGAACGT
1 AGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACATCTCAAACGT
** *
16839835 AAGACCATGGTTGGACTATGGCAGTATAGATACATGTGTA
66 AAGACCATGGCAGGACCATGGCAGTATAGATACATGTGTA
* * **
16839875 AGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACA-CTACAAATT
1 AGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACATCT-CAAACG
*
16839939 TAAGACCATGGCAGGGCCATGGCA
65 TAAGACCATGGCAGGACCATGGCA
16839963 ATGCATGTAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 2 0.03
105 72 0.97
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (105 bp):
AGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACATCTCAAACGT
AAGACCATGGCAGGACCATGGCAGTATAGATACATGTGTA
Found at i:16843799 original size:91 final size:89
Alignment explanation
Indices: 16843686--16843872 Score: 234
Period size: 91 Copynumber: 2.1 Consensus size: 89
16843676 CTTAAGGGCG
* * * * * *
16843686 TAAAAAACCCTCAAACTTTTTCAAAAAGAGTAATTAAG-CCTTGCTTCTTTTTTTTTCACTCAAT
1 TAAAAAACCCTCAAACTCTTTCAAAAAAAGCAATTAAGCCCCTACTT-TTTTTTTTGCACTCAAT
* * *
16843750 TGGGTACTTGAACTT-TCAAAATGTA
65 TGGATACTTGAA-TTGCCAAAATGCA
*
16843775 TAAAAAAGGCCCTCAAACTCTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTTAA
1 TAAAAAA--CCCTCAAACTCTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTCAA
16843840 TTGGATACTTGAATTGCCAAAATGCA
64 TTGGATACTTGAATTGCCAAAATGCA
16843866 TAAAAAA
1 TAAAAAA
16843873 AACCCTTTGA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
89 7 0.08
90 2 0.02
91 69 0.82
92 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (89 bp):
TAAAAAACCCTCAAACTCTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTCAATT
GGATACTTGAATTGCCAAAATGCA
Found at i:16844087 original size:68 final size:67
Alignment explanation
Indices: 16844010--16844217 Score: 213
Period size: 68 Copynumber: 3.1 Consensus size: 67
16844000 AATAGAAGTA
*
16844010 ATAATTTTTTAAAATTTTAATAAAAATATAAAAAAAATATTTAAAAATTATAAAAATAGTAAAAA
1 ATAATTTTTTAAAATTTTAATAAAATTAT-AAAAAAAT-TTTAAAAATTATAAAAATAGTAAAAA
16844075 AATT
64 AATT
* * * * *
16844079 ATAATTTTTTTAAATTTT-ATAAAATTGTAAAATAATTATAAAAGATATATAAATATAG-AAAAA
1 ATAATTTTTTAAAATTTTAATAAAATTATAAAAAAATTTTAAAA-AT-TATAAAAATAGTAAAAA
*
16844142 AAAT
64 AATT
* * * * * * * * *
16844146 AAAAGTTTATAAAGTTTTAAGAAAATTATAAAAAAATGTAAAAAAGTTATAAAATTCGTAAAAAA
1 ATAATTTTTTAAAATTTTAATAAAATTATAAAAAAATTTTAAAAA-TTATAAAAATAGTAAAAAA
16844211 ATT
65 ATT
16844214 ATAA
1 ATAA
16844218 AAATTATCGT
Statistics
Matches: 111, Mismatches: 23, Indels: 11
0.77 0.16 0.08
Matches are distributed among these distances:
66 6 0.05
67 39 0.35
68 49 0.44
69 17 0.15
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (67 bp):
ATAATTTTTTAAAATTTTAATAAAATTATAAAAAAATTTTAAAAATTATAAAAATAGTAAAAAAA
TT
Found at i:16844221 original size:21 final size:20
Alignment explanation
Indices: 16844167--16844222 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
16844157 AAGTTTTAAG
*
16844167 AAAATTATAAAAAAATGTAAA
1 AAAATTAT-AAAAATTGTAAA
*
16844188 AAAGTTAT-AAAATTCGTAAA
1 AAAATTATAAAAATT-GTAAA
16844208 AAAATTATAAAAATT
1 AAAATTATAAAAATT
16844223 ATCGTACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 13 0.43
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAATTATAAAAATTGTAAA
Found at i:16844451 original size:10 final size:9
Alignment explanation
Indices: 16844429--16844535 Score: 53
Period size: 9 Copynumber: 11.9 Consensus size: 9
16844419 AAAAAATACA
*
16844429 TTTTTAAAT
1 TTTTTATAT
16844438 TTTTT-TAT
1 TTTTTATAT
16844446 GATTTTTATAT
1 --TTTTTATAT
*
16844457 TTTTTCTAAT
1 TTTTTAT-AT
16844467 TTTTTA-AT
1 TTTTTATAT
*
16844475 TTTTAATAT
1 TTTTTATAT
*
16844484 TTTATTA-AA
1 TTT-TTATAT
* * *
16844493 GTTTAATAA
1 TTTTTATAT
*
16844502 TTTTTATAA
1 TTTTTATAT
16844511 TTTTTAT-T
1 TTTTTATAT
*
16844519 GATTTT-TAT
1 -TTTTTATAT
16844528 TTTTTATA
1 TTTTTATA
16844536 AATTTTTTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
8 16 0.21
9 42 0.56
10 14 0.19
11 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTTATAT
Found at i:16844452 original size:19 final size:18
Alignment explanation
Indices: 16844428--16844478 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
16844418 TAAAAAATAC
16844428 ATTTTTAAATTTTTT-TA
1 ATTTTTAAATTTTTTCTA
*
16844445 TGATTTTTATATTTTTTCTA
1 --ATTTTTAAATTTTTTCTA
*
16844465 ATTTTTTAATTTTT
1 ATTTTTAAATTTTT
16844479 AATATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.43
19 14 0.50
20 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTAAATTTTTTCTA
Found at i:16844491 original size:18 final size:18
Alignment explanation
Indices: 16844448--16844543 Score: 72
Period size: 18 Copynumber: 5.3 Consensus size: 18
16844438 TTTTTTATGA
**
16844448 TTTTTATATTTTTTCTAAT
1 TTTTTA-ATTTTTAATAAT
16844467 TTTTTAATTTTTAAT-AT
1 TTTTTAATTTTTAATAAT
**
16844484 TTTATTAAAGTTTAATAAT
1 TTT-TTAATTTTTAATAAT
* *
16844503 TTTTATAATTTTTATTGA-
1 TTTT-TAATTTTTAATAAT
*
16844521 TTTTT-ATTTTTTATAAAT
1 TTTTTAATTTTTAAT-AAT
16844539 TTTTT
1 TTTTT
16844544 TGCCACATGT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
16 7 0.11
17 7 0.11
18 27 0.44
19 20 0.33
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTAATTTTTAATAAT
Found at i:16844516 original size:19 final size:19
Alignment explanation
Indices: 16844423--16844527 Score: 76
Period size: 18 Copynumber: 5.6 Consensus size: 19
16844413 TTTTATAAAA
16844423 AATACATTTTTA-AATTTTTT
1 AATA-ATTTTTATAA-TTTTT
* *
16844443 TATGATTTTTAT-ATTTTT
1 AATAATTTTTATAATTTTT
**
16844461 TCTAATTTTT-TAATTTTT
1 AATAATTTTTATAATTTTT
**
16844479 AAT-A-TTTTATTAAAGTTT
1 AATAATTTTTA-TAATTTTT
16844497 AATAATTTTTATAATTTTT
1 AATAATTTTTATAATTTTT
* *
16844516 ATTGATTTTTAT
1 AATAATTTTTAT
16844528 TTTTTATAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
16 4 0.06
17 2 0.03
18 29 0.43
19 25 0.37
20 7 0.10
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (19 bp):
AATAATTTTTATAATTTTT
Found at i:16844806 original size:89 final size:88
Alignment explanation
Indices: 16844638--16844877 Score: 240
Period size: 87 Copynumber: 2.7 Consensus size: 88
16844628 AAGTTAACAA
* * *
16844638 TCAAATGGTCTTTTTAATGCATTTTGACAA-TTTAAGTACCCAATTGAGTGTAAAAAAAAGTAAG
1 TCAAA-GGTCTTTTT-ATGCATTTTGA-AAGTTCAAGTACCTAATTGAGTGCAAAAAAAAGTAAG
*
16844702 GGCTTAATTGCTTTTTTTGAAAAAGGT
63 GGCTTAATAGCTTTTTTTG-AAAAGGT
* *
16844729 T-AAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAATGCAAAAAAAA-T-GGGG
1 TCAAAGGTCTTTTT-ATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGCAAAAAAAAGTAAGGG
* *
16844791 CTTTATAGCTTTTTTTTGAAAATGT
65 CTTAATAGC-TTTTTTTGAAAAGGT
*** * * * *
16844816 TCGGGGGCCTTTTTATGCATTTTAAAAGTTCAAGTA-CTAAATTGAGTGGAAAAAGAAG-AAGG
1 TCAAAGGTCTTTTTATGCATTTTGAAAGTTCAAGTACCT-AATTGAGTGCAAAAAAAAGTAAGG
16844878 CAGGAGCTTA
Statistics
Matches: 125, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
86 2 0.02
87 53 0.42
88 21 0.17
89 45 0.36
90 3 0.02
91 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (88 bp):
TCAAAGGTCTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGCAAAAAAAAGTAAGGGC
TTAATAGCTTTTTTTGAAAAGGT
Found at i:16847612 original size:9 final size:9
Alignment explanation
Indices: 16847600--16847694 Score: 102
Period size: 9 Copynumber: 10.4 Consensus size: 9
16847590 AAATAAAAAA
16847600 AATTCGGGT
1 AATTCGGGT
*
16847609 AATTCGGAT
1 AATTCGGGT
*
16847618 ATTTTTC-GGT
1 A--ATTCGGGT
*
16847628 AATTCGGTT
1 AATTCGGGT
*
16847637 AATTCGGTT
1 AATTCGGGT
16847646 AATTCGGGT
1 AATTCGGGT
*
16847655 AATTCGGTT
1 AATTCGGGT
16847664 AATTCGGGT
1 AATTCGGGT
* *
16847673 AATTTGGAT
1 AATTCGGGT
16847682 AATTCGGGT
1 AATTCGGGT
16847691 AATT
1 AATT
16847695 TTTAACCAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
8 3 0.04
9 62 0.87
10 3 0.04
11 3 0.04
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:16847872 original size:12 final size:12
Alignment explanation
Indices: 16847855--16847879 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16847845 AGTAATTTCG
16847855 GGTCGGTTAACC
1 GGTCGGTTAACC
16847867 GGTCGGTTAACC
1 GGTCGGTTAACC
16847879 G
1 G
16847880 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:16854869 original size:17 final size:17
Alignment explanation
Indices: 16854847--16854882 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
16854837 ACTGTAACAA
16854847 AAACTCTATGGTTTCTC
1 AAACTCTATGGTTTCTC
16854864 AAACTCTATGGTTTCTC
1 AAACTCTATGGTTTCTC
16854881 AA
1 AA
16854883 TGTTCTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (17 bp):
AAACTCTATGGTTTCTC
Found at i:16867385 original size:21 final size:22
Alignment explanation
Indices: 16867343--16867409 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
16867333 TAACAAAAAA
*
16867343 ATTAATATTTTAA-GTAATATTC
1 ATTAATATTTTAATG-AAAATTC
*
16867365 -TTAATAATTTAATGAAAATTC
1 ATTAATATTTTAATGAAAATTC
16867386 ATATTAATATTTTAATGATAAATT
1 --ATTAATATTTTAATGA-AAATT
16867410 AGTTTTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 17 0.46
22 1 0.03
24 14 0.38
25 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (22 bp):
ATTAATATTTTAATGAAAATTC
Found at i:16876254 original size:2 final size:2
Alignment explanation
Indices: 16876243--16876279 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16876233 ATAATAAAAT
16876243 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16876280 AACTTTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16878360 original size:2 final size:2
Alignment explanation
Indices: 16878353--16878379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16878343 AAATTGTTTA
16878353 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
16878380 GTTTAAAAAT
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:16878471 original size:16 final size:16
Alignment explanation
Indices: 16878439--16878468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16878429 AACAGTTTAA
16878439 AAAATAATAGTATAAT
1 AAAATAATAGTATAAT
16878455 AAAATAATA-TATAA
1 AAAATAATAGTATAA
16878469 ATAGGTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATAATAGTATAAT
Found at i:16880226 original size:129 final size:129
Alignment explanation
Indices: 16880009--16880270 Score: 335
Period size: 129 Copynumber: 2.0 Consensus size: 129
16879999 TCTAGTCGGC
* * ** * * *
16880009 AAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTATTACTTTAATCCACTC
1 AAGACCTGATGCAATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACCTTAATCCACCC
* * * ** * *
16880074 TACTACAACTTCAGGGAGGTAGGATTACCAACCTCAATCTGTTCCACTGTAATCTCAGGGAGAT
66 CACTACAACTTCAGGGAGATAGGATTACCAACCTCAATCTGCTCCACTACAACCTCAAGGAGAT
* *
16880138 AAGACCTGATGCAATCCACTCTACTGCAACTTCAGAGAGGTAAGATCTATTACCTTAATCCGCCC
1 AAGACCTGATGCAATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACCTTAATCCACCC
* * ** *
16880203 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCAAGGAGAT
66 CACTACAACTTCAGGGAGATAGGATTACCAACCTCAATCTGCTCCACTACAACCTCAAGGAGAT
16880267 AAGA
1 AAGA
16880271 TTTGCTTCTT
Statistics
Matches: 112, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
129 112 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (129 bp):
AAGACCTGATGCAATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACCTTAATCCACCC
CACTACAACTTCAGGGAGATAGGATTACCAACCTCAATCTGCTCCACTACAACCTCAAGGAGAT
Found at i:16880409 original size:44 final size:43
Alignment explanation
Indices: 16880345--16880457 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 43
16880335 ATGTGATTTT
** *
16880345 CTCCACTACTGCTTAGGGAGATAAGATAT-ATTGTTTTA-ATCTG
1 CTCCACTACAACTTAGGGAGATAAGAT-TGATT-TCTTATATCTG
* *
16880388 CTCCACTACAACTTTAGGGAGATAGGATTGATTTCTTATGTCTG
1 CTCCACTACAAC-TTAGGGAGATAAGATTGATTTCTTATATCTG
**
16880432 CTCCACTACTGCTTAGGGAGATAAGA
1 CTCCACTACAACTTAGGGAGATAAGA
16880458 CTTGTAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 28 0.47
44 31 0.53
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (43 bp):
CTCCACTACAACTTAGGGAGATAAGATTGATTTCTTATATCTG
Found at i:16880676 original size:44 final size:43
Alignment explanation
Indices: 16880626--16880763 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 43
16880616 TAACACAGGA
16880626 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGG
1 AGGCAAGATCTG-TATCTTTAACCAGCTCCACTACAACCGATGG
* * ** * * * *
16880670 AGGCAAGGCTTTGT-T-TTCGATCTGCTTCACTGTCAA-CGCA-GG
1 AGGCAA-GATCTGTATCTTTAACCAGCTCCACT-ACAACCG-ATGG
16880712 AAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGG
1 -AGGCAAGATCTG-TATCTTTAACCAGCTCCACTACAACCGATGG
16880757 AGGCAAG
1 AGGCAAG
16880764 GCTTTGTTTT
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
42 19 0.28
43 12 0.17
44 19 0.28
45 19 0.28
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (43 bp):
AGGCAAGATCTGTATCTTTAACCAGCTCCACTACAACCGATGG
Found at i:16880681 original size:87 final size:87
Alignment explanation
Indices: 16880514--16880773 Score: 394
Period size: 87 Copynumber: 3.0 Consensus size: 87
16880504 TGTAATCTTT
* * * * * * *
16880514 GATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTTCACTAAAACCA
1 GATCTGCTCCACTGTCAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
*
16880579 ATGGAGGCAATGCTTTGTTTTC
66 ATGGAGGCAAGGCTTTGTTTTC
* * *
16880601 GATTTGCTCCGCTGTTAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
1 GATCTGCTCCACTGTCAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
16880666 ATGGAGGCAAGGCTTTGTTTTC
66 ATGGAGGCAAGGCTTTGTTTTC
* * *
16880688 GATCTGCTTCACTGTCAACGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCG
1 GATCTGCTCCACTGTCAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
16880753 ATGGAGGCAAGGCTTTGTTTT
66 ATGGAGGCAAGGCTTTGTTTT
16880774 TTATATTCAC
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 156 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (87 bp):
GATCTGCTCCACTGTCAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
ATGGAGGCAAGGCTTTGTTTTC
Found at i:16882434 original size:26 final size:26
Alignment explanation
Indices: 16882397--16882456 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
16882387 TTAACTTTAA
*
16882397 TTGATTTCTCTTTTTTACTTTTGACT
1 TTGATTTTTCTTTTTTACTTTTGACT
** * *
16882423 TTGATTTTTCTTTTTTGTTTTTTATT
1 TTGATTTTTCTTTTTTACTTTTGACT
16882449 TTGATTTT
1 TTGATTTT
16882457 GACCATTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.73
Consensus pattern (26 bp):
TTGATTTTTCTTTTTTACTTTTGACT
Found at i:16887480 original size:16 final size:16
Alignment explanation
Indices: 16887448--16887477 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16887438 AACAATTTAA
16887448 AAAATAATAGTATAAT
1 AAAATAATAGTATAAT
16887464 AAAATAATA-TATAA
1 AAAATAATAGTATAA
16887478 ATAGGTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATAATAGTATAAT
Found at i:16888296 original size:17 final size:17
Alignment explanation
Indices: 16888252--16888297 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
16888242 TGAAAGACTC
16888252 TTTTTTAT--TCCTTTT
1 TTTTTTATCATCCTTTT
16888267 TTTTCTT-TCCATCCTTTT
1 TTTT-TTAT-CATCCTTTT
16888285 TTTTTTATCATCC
1 TTTTTTATCATCC
16888298 CCCCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.19
16 2 0.08
17 7 0.27
18 12 0.46
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTATCATCCTTTT
Found at i:16894591 original size:49 final size:49
Alignment explanation
Indices: 16894536--16894639 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
16894526 TCATGTGTTA
* * ** * *
16894536 TAATTTTATATAGTGTTGAGTTTTTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGAGTCATGATATTAAACTCAATTT
*
16894585 TAATTTTATAAAGTGTTCACCTTTTGAGTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGAGTCATGATATTAAACTCAATTT
16894634 TAATTT
1 TAATTT
16894640 ATTTTTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGAGTCATGATATTAAACTCAATTT
Found at i:16896137 original size:61 final size:60
Alignment explanation
Indices: 16896041--16896223 Score: 167
Period size: 59 Copynumber: 3.0 Consensus size: 60
16896031 ATTATATTTA
* * * *
16896041 ATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAT
1 ATAAGAATTATTTTAAATAAAATTTTATAGAATTATATATTATGATTTTAGTAAATTCAT
* * ** * * *
16896101 ATAAGAA-TA-TTTAATACTAAGAATTTTATTA-AATTATATATTTTTATTAAAATATATTTA-
1 ATAAGAATTATTTTAA-A-TAA-AATTTTA-TAGAATTATATATTATGATTTTAGTAAATTCAT
* * * *
16896161 ATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAT
1 ATAAGAATTATTTTAAATAAAATTTTATAGAATTATATATTATGATTTTAGTAAATTCAT
16896221 ATA
1 ATA
16896224 TTTTATTAAA
Statistics
Matches: 93, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
58 7 0.08
59 30 0.32
60 19 0.20
61 30 0.32
62 7 0.08
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (60 bp):
ATAAGAATTATTTTAAATAAAATTTTATAGAATTATATATTATGATTTTAGTAAATTCAT
Found at i:16896145 original size:18 final size:17
Alignment explanation
Indices: 16896123--16896257 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 17
16896113 AATACTAAGA
16896123 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
16896140 ATTTTTATTAAA--ATAT
1 A-TTTTATTAAATTATAT
* *
16896156 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
16896170 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* * *
16896189 AGTATTA-TATATTAT-G
1 A-TTTTATTAAATTATAT
*
16896205 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
16896223 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
16896240 ATTATTATTAAATTATAT
1 ATT-TTATTAAATTATAT
16896258 TTAATAATAA
Statistics
Matches: 93, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.02
14 7 0.08
15 9 0.10
16 11 0.12
17 19 0.20
18 40 0.43
19 2 0.02
20 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:16896317 original size:40 final size:37
Alignment explanation
Indices: 16896246--16896319 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
16896236 ATATATTATT
*
16896246 ATTAAATTATATTTAATAATAATTATGTTAAAATATG
1 ATTAAATTATATTTAATAATAATTATATTAAAATATG
16896283 ATTAAATTATTATTTATATTAATAATCT-TATTAAAAT
1 ATTAAATTA-TATTTA-A-TAATAAT-TATATTAAAAT
16896320 TTAATAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
37 9 0.28
38 6 0.19
39 1 0.03
40 15 0.47
41 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATTAAATTATATTTAATAATAATTATATTAAAATATG
Found at i:16896503 original size:46 final size:44
Alignment explanation
Indices: 16896412--16896505 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
16896402 ATTACACCAT
*
16896412 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACAAAAGAATACTATTACGCCTCTATTC
*
16896456 CATTCCATTCAACCAAACAAAAGGATTATCTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACAAAA-GAATA-CTATTACGCCTCTATTC
16896502 CATT
1 CATT
16896506 ACGCCTCTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 21 0.46
45 4 0.09
46 21 0.46
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (44 bp):
CATTCCATTCAACCAAACAAAAGAATACTATTACGCCTCTATTC
Found at i:16896508 original size:16 final size:16
Alignment explanation
Indices: 16896487--16896539 Score: 106
Period size: 16 Copynumber: 3.3 Consensus size: 16
16896477 AGGATTATCT
16896487 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
16896503 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
16896519 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
16896535 ATTAC
1 ATTAC
16896540 AGCGAACCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:16897671 original size:3 final size:3
Alignment explanation
Indices: 16897663--16897694 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16897653 TAAACCTTAT
16897663 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
16897695 TTTGCTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16899392 original size:69 final size:68
Alignment explanation
Indices: 16899263--16899398 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 68
16899253 TTCCCTTGCT
* *
16899263 GTTGATTTCATGTTCTTTTCTGATTTTTATTTCAGTTTTTATGTCATTAAATACTGGTTTAAGTT
1 GTTGATTTCATGCTCTTTTCTGATATTTATTTCAGTTTTTATGTCATTAAATACTGGTTTAAGTT
16899328 GAA
66 GAA
* * *
16899331 GTTGATTTCATGCTCTTTTCCT-A-ATTTATTTCTGTTTTTATATGTCATTAAATATTTGTTTAA
1 GTTGATTTCATGCTCTTTT-CTGATATTTATTTCAG-TTTT-TATGTCATTAAATACTGGTTTAA
16899394 GTTGA
63 GTTGA
16899399 CATTATTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 9 0.15
68 23 0.38
69 28 0.47
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.55
Consensus pattern (68 bp):
GTTGATTTCATGCTCTTTTCTGATATTTATTTCAGTTTTTATGTCATTAAATACTGGTTTAAGTT
GAA
Found at i:16904500 original size:20 final size:20
Alignment explanation
Indices: 16904475--16904533 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
16904465 ACTTACAAGA
16904475 TGTATGGGTAAAAGTGGACT
1 TGTATGGGTAAAAGTGGACT
16904495 TGTATGGGTAGAAA-TGGACT
1 TGTATGGGTA-AAAGTGGACT
* *
16904515 TGTATCGGTATAAGTGGAC
1 TGTATGGGTAAAAGTGGAC
16904534 CTATATGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 30 0.86
21 3 0.09
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.31
Consensus pattern (20 bp):
TGTATGGGTAAAAGTGGACT
Found at i:16904549 original size:20 final size:19
Alignment explanation
Indices: 16904475--16904549 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
16904465 ACTTACAAGA
*
16904475 TGTATGGGTAAAAGTGGACT
1 TGTAT-GGTAGAAGTGGACT
*
16904495 TGTATGGGTAGAAATGGACT
1 TGTAT-GGTAGAAGTGGACT
* *
16904515 TGTATCGGTATAAGTGGACC
1 TGTAT-GGTAGAAGTGGACT
*
16904535 TATATGGTTAGAAGT
1 TGTATGG-TAGAAGT
16904550 CCCCCTAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.04
20 44 0.96
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (19 bp):
TGTATGGTAGAAGTGGACT
Found at i:16905690 original size:28 final size:28
Alignment explanation
Indices: 16905655--16905732 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
16905645 AAAAATAAAA
*
16905655 AATAAAAAATAAAAAAAAATTAAATTTT
1 AATAAAAAATAAAAAAAAATTAAAATTT
*
16905683 AATAAAAAAT-ATAAAAAATATAAAATTT
1 AATAAAAAATAAAAAAAAAT-TAAAATTT
* * *
16905711 ATTAAAAATTAGAAAAAAATTA
1 AATAAAAAATAAAAAAAAATTA
16905733 GAAAAATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
27 8 0.19
28 27 0.64
29 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (28 bp):
AATAAAAAATAAAAAAAAATTAAAATTT
Found at i:16905693 original size:7 final size:7
Alignment explanation
Indices: 16905645--16905670 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16905635 GACACGTGGC
16905645 AAAAATA
1 AAAAATA
16905652 AAAAATA
1 AAAAATA
16905659 AAAAATA
1 AAAAATA
16905666 AAAAA
1 AAAAA
16905671 AAATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:16905728 original size:11 final size:11
Alignment explanation
Indices: 16905714--16905738 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16905704 AAAATTTATT
16905714 AAAAATTAGAA
1 AAAAATTAGAA
16905725 AAAAATTAGAA
1 AAAAATTAGAA
16905736 AAA
1 AAA
16905739 TTGTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:16905829 original size:19 final size:20
Alignment explanation
Indices: 16905802--16905852 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
16905792 AAGTCGTAAG
* *
16905802 AAAATTATAAAAATT-GTAA
1 AAAAATATAAAAATTCATAA
*
16905821 AGAAATAT-AAAATTCATAA
1 AAAAATATAAAAATTCATAA
16905840 AAAAATATAAAAA
1 AAAAATATAAAAA
16905853 AATGTCGTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.23
19 16 0.62
20 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAAATATAAAAATTCATAA
Found at i:16905912 original size:17 final size:18
Alignment explanation
Indices: 16905872--16905912 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
16905862 CTAAAAGAAG
*
16905872 CATTTTATAATTTTTATT
1 CATTTTTTAATTTTTATT
*
16905890 GA-TTTTTAATTTTTA-T
1 CATTTTTTAATTTTTATT
16905906 CATTTTT
1 CATTTTT
16905913 CACCACATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.11
17 16 0.84
18 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (18 bp):
CATTTTTTAATTTTTATT
Found at i:16907815 original size:20 final size:20
Alignment explanation
Indices: 16907792--16907831 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16907782 ACAATATAAT
16907792 ACTTGCATATACATATTTTG
1 ACTTGCATATACATATTTTG
16907812 ACTTGCATATACATATTTTG
1 ACTTGCATATACATATTTTG
16907832 CCTTACTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
ACTTGCATATACATATTTTG
Found at i:16917846 original size:42 final size:42
Alignment explanation
Indices: 16917742--16917862 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 42
16917732 TCATATAAGT
* * **
16917742 TTCCGTTTAACCCTAATGGGTTTTTGTTCAGCTCTTTTAACC
1 TTCCGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACAACC
* * * * *
16917784 TTCAGTTTAACCATTTTGGGTTTCTGTTCAGCTCTTACGAGC
1 TTCCGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACAACC
* * *
16917826 TTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTA
1 TTCCGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTA
16917863 TGTGCTTCTT
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCCGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACAACC
Found at i:16925803 original size:19 final size:18
Alignment explanation
Indices: 16925766--16925804 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16925756 AATTTGAAAC
**
16925766 AAAACATAAATTTTTGGA
1 AAAACATAAATTTCGGGA
16925784 AAAACATGAAATTTCGGGA
1 AAAACAT-AAATTTCGGGA
16925803 AA
1 AA
16925805 CTGGGTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (18 bp):
AAAACATAAATTTCGGGA
Found at i:16931170 original size:40 final size:40
Alignment explanation
Indices: 16931124--16931201 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
16931114 TACTTATCGG
16931124 ATAAGCATTCATACTTTCATAAATATGGCTAAGCATATTT
1 ATAAGCATTCATACTTTCATAAATATGGCTAAGCATATTT
16931164 ATAAGCATTCATACTTTCATAAATATGGCTAAGCATAT
1 ATAAGCATTCATACTTTCATAAATATGGCTAAGCATAT
16931202 CTGTCGATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (40 bp):
ATAAGCATTCATACTTTCATAAATATGGCTAAGCATATTT
Found at i:16933491 original size:103 final size:104
Alignment explanation
Indices: 16933151--16933521 Score: 602
Period size: 105 Copynumber: 3.6 Consensus size: 104
16933141 TGTATATAAA
** * * *
16933151 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
**
16933215 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
16933255 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
* *
16933320 TTGAACTGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
16933360 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
16933425 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
16933463 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
16933522 ATAACGGCTA
Statistics
Matches: 251, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
103 87 0.35
104 68 0.27
105 95 0.38
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:16942529 original size:45 final size:46
Alignment explanation
Indices: 16942480--16942569 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
16942470 AACAATAATA
* *
16942480 GTAACAGTA-TTCAACACACAAAGTGCTGAATCTGTAACAGTAACG
1 GTAACAGTATTTCAACACACAAAGTGCCGAATCGGTAACAGTAACG
**
16942525 GTAACAGTATTTTGACACACAAAGTGCCGAATCGGTAACAGTAAC
1 GTAACAGTATTTCAACACACAAAGTGCCGAATCGGTAACAGTAAC
16942570 AGTAGTCGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 9 0.22
46 31 0.77
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (46 bp):
GTAACAGTATTTCAACACACAAAGTGCCGAATCGGTAACAGTAACG
Found at i:16943991 original size:9 final size:9
Alignment explanation
Indices: 16943977--16944026 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
16943967 CATTTGAATA
16943977 AATAATTAT
1 AATAATTAT
16943986 AATAATTAT
1 AATAATTAT
16943995 AATAATTAT
1 AATAATTAT
16944004 -ATACA-TAT
1 AATA-ATTAT
*
16944012 AATATTTAT
1 AATAATTAT
16944021 ATATAA
1 A-ATAA
16944027 CTTAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 6 0.17
9 26 0.74
10 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:16945182 original size:26 final size:27
Alignment explanation
Indices: 16945102--16945202 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 27
16945092 CCCTTATAGG
* *
16945102 GTAATATTACCGAAATA-CTCCTAGTTT
1 GTAAAATTATCGAAATACCTCC-AGTTT
* *
16945129 GTAAAGTTATCGAAATACC-CTCAATTT
1 GTAAAATTATCGAAATACCTC-CAGTTT
*
16945156 GTAAAATTATTG-AATACCTCCAGTTT
1 GTAAAATTATCGAAATACCTCCAGTTT
* * *
16945182 GAAAAATTACCAAAATACCTC
1 GTAAAATTATCGAAATACCTC
16945203 TATAGGGTAG
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
26 19 0.32
27 38 0.64
28 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCTCCAGTTT
Found at i:16945574 original size:22 final size:22
Alignment explanation
Indices: 16945546--16945605 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
16945536 GTAATCCGAT
16945546 TATGGCTTTGTGCCAACCTAAA
1 TATGGCTTTGTGCCAACCTAAA
* * * * *
16945568 TATGGCTCTGTGCCATCTTGAT
1 TATGGCTTTGTGCCAACCTAAA
16945590 TATGGCTTTGTGCCAA
1 TATGGCTTTGTGCCAA
16945606 TCGTATTTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (22 bp):
TATGGCTTTGTGCCAACCTAAA
Found at i:16946800 original size:37 final size:37
Alignment explanation
Indices: 16946744--16946949 Score: 274
Period size: 37 Copynumber: 5.6 Consensus size: 37
16946734 CTTAGTGTTG
* * *
16946744 TGGCGTGTTATCAATTGGATTAGATCTTATGAGCATT
1 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCATT
16946781 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCATT
1 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCATT
* * *
16946818 TGTCGTGTTTTTGAGTGGATTAGCTCTTATGAGCATT
1 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCATT
* *
16946855 TGGCGTGTTTTTGAGTGGATTAGCTCTTATGAGCATT
1 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCATT
* * *
16946892 TGGCATGTTATTGTGTGGATTAGCTCTTATGAGCGA-T
1 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGC-ATT
16946929 TGGCGTGTT-TCG-GTTGGATTA
1 TGGCGTGTTATCGAG-TGGATTA
16946950 CTTGTGTACT
Statistics
Matches: 155, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
35 1 0.01
36 9 0.06
37 144 0.93
38 1 0.01
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (37 bp):
TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCATT
Found at i:16950989 original size:120 final size:120
Alignment explanation
Indices: 16950776--16951014 Score: 451
Period size: 120 Copynumber: 2.0 Consensus size: 120
16950766 TCTTGTACAT
*
16950776 ATTTTCATGTTGCGATATGTTAGTCTGGTTTACATCTTACTGGAGGCTACACCATGAGTATTCTC
1 ATTTTCATGTTGCGATATGTTAGTCTGGTTTACATCTTACTGGAAGCTACACCATGAGTATTCTC
16950841 ATTGTCATATGATGCCATGGGTCTCTAACACATGTTCTTACATATATTTTCATAA
66 ATTGTCATATGATGCCATGGGTCTCTAACACATGTTCTTACATATATTTTCATAA
*
16950896 ATTTTCATGTTGTGATATGTTAGTCTGGTTTACATCTTACTGGAAGCTACACCATGAGTATTCTC
1 ATTTTCATGTTGCGATATGTTAGTCTGGTTTACATCTTACTGGAAGCTACACCATGAGTATTCTC
*
16950961 ATTGTCATATGATGTCATGGGTCTCTAACACATGTTCTTACATATATTTTCATA
66 ATTGTCATATGATGCCATGGGTCTCTAACACATGTTCTTACATATATTTTCATA
16951015 TCGTGATTTT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (120 bp):
ATTTTCATGTTGCGATATGTTAGTCTGGTTTACATCTTACTGGAAGCTACACCATGAGTATTCTC
ATTGTCATATGATGCCATGGGTCTCTAACACATGTTCTTACATATATTTTCATAA
Found at i:16956277 original size:22 final size:22
Alignment explanation
Indices: 16956252--16956328 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
16956242 CCAAAATATT
16956252 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
16956274 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
16956298 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
16956320 ATCTCCTAA
1 ATCTCCTAA
16956329 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:16956291 original size:46 final size:46
Alignment explanation
Indices: 16956239--16956333 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
16956229 ACAAAGATAG
16956239 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
16956285 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
16956331 AAA
1 AAA
16956334 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:16957957 original size:20 final size:20
Alignment explanation
Indices: 16957934--16957972 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16957924 CGTTCTACGG
16957934 TAATGGCTGCA-AGAAAATTC
1 TAAT-GCTGCACAGAAAATTC
*
16957954 TAATGTTGCACAGAAAATT
1 TAATGCTGCACAGAAAATT
16957973 TATCACAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (20 bp):
TAATGCTGCACAGAAAATTC
Found at i:16968101 original size:27 final size:25
Alignment explanation
Indices: 16968071--16968135 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
16968061 CAAAAATTCA
16968071 AAAAAATTTAAAATTAAAAATATTTTT
1 AAAAAATTTAAAATT-AAAAT-TTTTT
* * *
16968098 -AAAAATTCCAAAATTTATATTTTTT
1 AAAAAATT-TAAAATTAAAATTTTTT
*
16968123 AAAAAAATTAAAA
1 AAAAAATTTAAAA
16968136 AAATCTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.29
26 16 0.52
27 6 0.19
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAAAATTTAAAATTAAAATTTTTT
Found at i:16968113 original size:18 final size:18
Alignment explanation
Indices: 16968055--16968113 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
16968045 TAATCAAAAT
*
16968055 AATTTTCAAAAATTCAAA
1 AATTTTTAAAAATTCAAA
** *
16968073 AAAATTT-AAAATTAAAA
1 AATTTTTAAAAATTCAAA
*
16968090 ATATTTTTAAAAATTCCAA
1 A-ATTTTTAAAAATTCAAA
16968109 AATTT
1 AATTT
16968114 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 10 0.32
18 12 0.39
19 9 0.29
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTTTTAAAAATTCAAA
Found at i:16968957 original size:17 final size:18
Alignment explanation
Indices: 16968935--16968969 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16968925 TTGCACATTG
*
16968935 TGTAA-TTTGGTTTTCTT
1 TGTAATTTTGCTTTTCTT
16968952 TGTAATTTTGCTTTTCTT
1 TGTAATTTTGCTTTTCTT
16968970 CATGACCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.09, G:0.14, T:0.66
Consensus pattern (18 bp):
TGTAATTTTGCTTTTCTT
Found at i:16976284 original size:4 final size:4
Alignment explanation
Indices: 16976267--16976321 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
16976257 AAGACAAGAG
* * * * * *
16976267 ACAT ACAT AAAT ACAT ACGT ACAT ACAT ACAT ACAC ACAC ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
16976315 ACAT ACA
1 ACAT ACA
16976322 CTAGCAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.31, G:0.02, T:0.16
Consensus pattern (4 bp):
ACAT
Found at i:16977726 original size:34 final size:35
Alignment explanation
Indices: 16977671--16977737 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16977661 CAAACACCAG
*
16977671 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
16977706 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
16977738 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:16992597 original size:46 final size:46
Alignment explanation
Indices: 16992544--16992729 Score: 300
Period size: 46 Copynumber: 4.0 Consensus size: 46
16992534 ACAATGCTAT
* * * *
16992544 AACTCAGTATGGTTTCCTTCACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACATTTCAC
*
16992590 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACATTTCAC
*
16992636 AACTCAGTATGGTTTTCGTCACTGAAACACCATACCTACATTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACATTTCAC
* *
16992682 AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTGCATTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACATTTCAC
16992728 AA
1 AA
16992730 TTTTCCATGG
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 132 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACATTTCAC
Found at i:16993991 original size:16 final size:17
Alignment explanation
Indices: 16993945--16993992 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
16993935 AAATTCTTTT
16993945 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
16993962 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
16993979 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
16993993 TTATAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:16999003 original size:46 final size:46
Alignment explanation
Indices: 16998933--16999115 Score: 294
Period size: 46 Copynumber: 4.0 Consensus size: 46
16998923 AAAATGCTAT
* *
16998933 AACTCAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
16998979 AACTCAGTATGGTTTTCTTTACTGAAACACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
16999025 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACATTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
16999071 AACTCAGTATGGCTTTCTTCACTGAAATACCATACCTACTTTTCA
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCA
16999116 AAATTTTCCA
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:17000348 original size:17 final size:17
Alignment explanation
Indices: 17000326--17000373 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
17000316 AAATTCTTTT
17000326 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
17000343 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
17000360 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
17000374 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:17005116 original size:51 final size:50
Alignment explanation
Indices: 17005046--17005241 Score: 227
Period size: 51 Copynumber: 3.9 Consensus size: 50
17005036 CAATGATGTT
* * *
17005046 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATC
* * * *
17005097 CGATACACGTAGTATCCTGCACATAGTACTACACACGTGATCGA-AACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATC
* * *
17005148 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCT-ACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACG-TGACCATATCA-TC
*
17005198 CGGTACACGTAATAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
17005242 CACTTTCATT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
49 2 0.02
50 43 0.36
51 72 0.60
52 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATCATC
Found at i:17005234 original size:101 final size:101
Alignment explanation
Indices: 17005053--17005237 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 101
17005043 GTTCGGTTCA
* *
17005053 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATCCGATACACGTAGTATCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCA-TATCATCCGATACACGTAATAGCCTGCA
17005118 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
*
17005155 CATAGTAGCCTGCACATAGTACTACACATGCT-ACC-TATCATTCCGGTACACGTAATAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATG-TGACCATATCA-TCCGATACACGTAATAGCCTGC
17005218 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
17005238 CCATCACTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
100 5 0.06
101 39 0.50
102 33 0.42
103 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATATCATCCGATACACGTAATAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:17015612 original size:2 final size:2
Alignment explanation
Indices: 17015605--17015636 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17015595 TACATGATAC
17015605 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
17015637 GCATAATAAT
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:17018639 original size:18 final size:17
Alignment explanation
Indices: 17018618--17018660 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
17018608 CTATTTTAAA
17018618 CTTTAATTAATTTTATTT
1 CTTTAATTAA-TTTATTT
*
17018636 CTTTAATT-ATTTCTTT
1 CTTTAATTAATTTATTT
17018652 -TTTAATTAA
1 CTTTAATTAA
17018661 ATTCTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 1 0.04
18 8 0.35
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTAATTAATTTATTT
Found at i:17018657 original size:15 final size:17
Alignment explanation
Indices: 17018619--17018673 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
17018609 TATTTTAAAC
*
17018619 TTTAATT-AATTTTATTT
1 TTTAATTAAATTCTA-TT
*
17018636 CTTTAATT-ATTTCT-TT
1 -TTTAATTAAATTCTATT
17018652 TTTAATTAAATTCTATT
1 TTTAATTAAATTCTATT
17018669 TTTAA
1 TTTAA
17018674 AATTATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.22
16 7 0.22
17 7 0.22
18 11 0.34
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATTAAATTCTATT
Found at i:17019086 original size:2 final size:2
Alignment explanation
Indices: 17019073--17019118 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
17019063 ATAACTAACT
17019073 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17019116 TA T
1 TA T
17019119 GAGAATGAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17019829 original size:20 final size:19
Alignment explanation
Indices: 17019806--17019850 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17019796 ATATAAAATC
17019806 TAAAAATACAAAAAATATAT
1 TAAAAAT-CAAAAAATATAT
* * *
17019826 TAAAAATTAAAAATTATTT
1 TAAAAATCAAAAAATATAT
17019845 TAAAAA
1 TAAAAA
17019851 ATTACATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATCAAAAAATATAT
Found at i:17025017 original size:66 final size:65
Alignment explanation
Indices: 17024904--17025036 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 65
17024894 CAAATTGCTT
* * *
17024904 AACTTAAAGCGGAGGCAGCATCGAGGGAAGCAGAGGCTCAAAGAAAATATGAAGAACTCCAGCTA
1 AACTTAAAGCGGAGGCAGCAGCGAGGGAAGCAGAGGC-CAAAAAAAATATGAAGAACTCCAACTA
17024969 C
65 C
* * *
17024970 AACTTAAAGTGGAGGCAGCAGCGGGGGAAGCAGAGG-CAAGCAAAAAATATGACGAACTCCAACT
1 AACTTAAAGCGGAGGCAGCAGCGAGGGAAGCAGAGGCCAA--AAAAAATATGAAGAACTCCAACT
17025034 AC
64 AC
17025036 A
1 A
17025037 GCTTCAGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
64 3 0.05
66 56 0.95
ACGTcount: A:0.41, C:0.20, G:0.28, T:0.11
Consensus pattern (65 bp):
AACTTAAAGCGGAGGCAGCAGCGAGGGAAGCAGAGGCCAAAAAAAATATGAAGAACTCCAACTAC
Found at i:17026325 original size:23 final size:24
Alignment explanation
Indices: 17026290--17026335 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
17026280 TAATAAAAAT
17026290 ATATTTAAAATATTTTT-TAATTG
1 ATATTTAAAATATTTTTATAATTG
* *
17026313 ATATTTTATATATTTTTATAATT
1 ATATTTAAAATATTTTTATAATT
17026336 AAATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTTAAAATATTTTTATAATTG
Found at i:17034109 original size:15 final size:14
Alignment explanation
Indices: 17034090--17034143 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
17034080 AAATACAAAG
17034090 ATTAAAATTAACAA
1 ATTAAAATTAACAA
17034104 ATTTAAAAAATATAA-AA
1 A-TT--AAAAT-TAACAA
17034121 ATTAAAATTAATCAA
1 ATTAAAATTAA-CAA
17034136 ATTAAAAT
1 ATTAAAAT
17034144 ACAAAGACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 6 0.18
15 12 0.35
16 2 0.06
17 8 0.24
18 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAAATTAACAA
Found at i:17034113 original size:31 final size:30
Alignment explanation
Indices: 17034078--17034155 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
17034068 CCCTTTAACC
17034078 AAAAATACAAAGATTAAAATTAA-CAAATTT
1 AAAAATACAAAGATTAAAATTAATCAAA-TT
* *
17034108 AAAAAATATAAAAATTAAAATTAATCAAATT
1 -AAAAATACAAAGATTAAAATTAATCAAATT
*
17034139 -AAAATACAAAGACTAAA
1 AAAAATACAAAGATTAAA
17034156 TCTGCAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.34
31 23 0.56
32 4 0.10
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (30 bp):
AAAAATACAAAGATTAAAATTAATCAAATT
Found at i:17035307 original size:21 final size:22
Alignment explanation
Indices: 17035282--17035324 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17035272 TATTTTATTT
17035282 TAAAATAT-AATTTATACAATA
1 TAAAATATAAATTTATACAATA
*
17035303 TAAAATATAAATTTATATAATA
1 TAAAATATAAATTTATACAATA
17035325 ATTTGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAATATAAATTTATACAATA
Found at i:17035617 original size:6 final size:6
Alignment explanation
Indices: 17035586--17035628 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
17035576 GTATAAAAAA
*
17035586 TAATAT T-ATAT T-ATAT T-ATGT TAATAT TAATAT TAATAT TAAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAAT
17035629 GTAAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
TAATAT
Found at i:17035635 original size:12 final size:12
Alignment explanation
Indices: 17035586--17035635 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
17035576 GTATAAAAAA
*
17035586 TAATATT-ATAT
1 TAATATTAATGT
17035597 T-ATATT-ATGT
1 TAATATTAATGT
*
17035607 TAATATTAATAT
1 TAATATTAATGT
17035619 TAATATTAATGT
1 TAATATTAATGT
*
17035631 AAATA
1 TAATA
17035636 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 9 0.27
11 6 0.18
12 18 0.55
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (12 bp):
TAATATTAATGT
Found at i:17040441 original size:31 final size:31
Alignment explanation
Indices: 17040406--17040464 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
17040396 AGTTTGGGTG
*
17040406 GTGGTGTCCATGGGAAAGGCGGCACCAAGGA
1 GTGGTGCCCATGGGAAAGGCGGCACCAAGGA
*
17040437 GTGGTGCCCATGGGAAAGGTGGCACCAA
1 GTGGTGCCCATGGGAAAGGCGGCACCAA
17040465 AGTACTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.41, T:0.14
Consensus pattern (31 bp):
GTGGTGCCCATGGGAAAGGCGGCACCAAGGA
Found at i:17040493 original size:32 final size:32
Alignment explanation
Indices: 17040407--17040495 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
17040397 GTTTGGGTGG
*
17040407 TGGTGTCC-ATGGGAAAGGCGGCACC-AAGGAG
1 TGGTG-CCAATGGGAAAGGCGGCACCAAAGGAC
* * *
17040438 TGGTGCCCATGGGAAAGGTGGCACCAAAGTAC
1 TGGTGCCAATGGGAAAGGCGGCACCAAAGGAC
** *
17040470 TGGTGCCAATGTTATAGGCGGCACCA
1 TGGTGCCAATGGGAAAGGCGGCACCA
17040496 GTTCTTAACC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.04
31 21 0.44
32 25 0.52
ACGTcount: A:0.26, C:0.21, G:0.36, T:0.17
Consensus pattern (32 bp):
TGGTGCCAATGGGAAAGGCGGCACCAAAGGAC
Found at i:17042472 original size:3 final size:3
Alignment explanation
Indices: 17042375--17042455 Score: 117
Period size: 3 Copynumber: 26.0 Consensus size: 3
17042365 CTAATCCCGT
17042375 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
17042423 TTA TTA TTC TTG TTA TTGCA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT--A -TTA TTA TTA TTA
17042456 CTTTCCTTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
3 68 0.94
4 1 0.01
5 1 0.01
6 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17042622 original size:2 final size:2
Alignment explanation
Indices: 17042585--17042609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17042575 ATATACTTTA
17042585 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
17042610 CTTACTTATA
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:17043463 original size:19 final size:19
Alignment explanation
Indices: 17043439--17043476 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17043429 ATGAGAATTC
17043439 TTCCTTATGAACCTATGAA
1 TTCCTTATGAACCTATGAA
17043458 TTCCTTATGAACCTATGAA
1 TTCCTTATGAACCTATGAA
17043477 AGTATGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
TTCCTTATGAACCTATGAA
Found at i:17044858 original size:22 final size:22
Alignment explanation
Indices: 17044829--17044945 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 22
17044819 TGCACTAATG
*
17044829 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAACGTGCTA
*
17044851 TACAGAGAGCAC-ATACGTGCTA
1 AACAGAGAGCACTA-ACGTGCTA
* *
17044873 AACGGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTAACGTGCTA
* * *
17044895 GTAATCAAAAAGCACCAACGTGCTAA
1 --AA-CAGAGAGCACTAACGTGCT-A
* *
17044921 TAATCAGAGAGCACCAACATGCTA
1 -AA-CAGAGAGCACTAACGTGCTA
17044945 A
1 A
17044946 TAATCAGAGA
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.01
22 36 0.47
23 1 0.01
24 3 0.04
25 34 0.45
26 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTAACGTGCTA
Found at i:17044952 original size:25 final size:25
Alignment explanation
Indices: 17044890--17044957 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
17044880 AGCACTGACG
* * * *
17044890 TGCTAGTAATCAAAAAGCACCAACG
1 TGCTAATAATCAGAGAGCACCAACA
17044915 TGCTAATAATCAGAGAGCACCAACA
1 TGCTAATAATCAGAGAGCACCAACA
17044940 TGCTAATAATCAGAGAGC
1 TGCTAATAATCAGAGAGC
17044958 GCACTAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (25 bp):
TGCTAATAATCAGAGAGCACCAACA
Found at i:17045848 original size:13 final size:13
Alignment explanation
Indices: 17045830--17045861 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17045820 CCAAAATTCC
17045830 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
17045843 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
*
17045856 CCTTTC
1 CTTTTC
17045862 CCCTTCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:17045939 original size:8 final size:8
Alignment explanation
Indices: 17045920--17045970 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
17045910 TTGTTATATA
17045920 AATATATAT
1 AATAT-TAT
17045929 AATATTAT
1 AATATTAT
17045937 AATATTAT
1 AATATTAT
*
17045945 AATAATAT
1 AATATTAT
*
17045953 AATTAATAT
1 AA-TATTAT
17045962 AATACTTAT
1 AATA-TTAT
17045971 TTATTAAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 22 0.58
9 16 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
AATATTAT
Done.