Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 16 of 21
Found at i:2508970 original size:18 final size:18
Alignment explanation
Indices: 2508947--2508984 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2508937 AAATCATATA
2508947 ATAATTATTAAATTAAAT
1 ATAATTATTAAATTAAAT
2508965 ATAATTATTAAATTAAAT
1 ATAATTATTAAATTAAAT
2508983 AT
1 AT
2508985 TTGAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTATTAAATTAAAT
Found at i:2509089 original size:16 final size:18
Alignment explanation
Indices: 2509064--2509218 Score: 66
Period size: 17 Copynumber: 9.0 Consensus size: 18
2509054 TTTATTTTTT
2509064 TATT-TATATTTA-A-AA
1 TATTATATATTTATATAA
2509079 TATTATATATTTATATAA
1 TATTATATATTTATATAA
** *
2509097 TATTATCA-CGTTAGTAATAT
1 TATTAT-ATATTTA-T-ATAA
* *
2509117 TATTATATAAATTATAATAG
1 TATTATAT-ATTTAT-ATAA
* *
2509137 TTTTATATATTTATATTA
1 TATTATATATTTATATAA
*
2509155 T-TTTTATATATT-TA-AA
1 TATTATATAT-TTATATAA
*
2509171 -A-T-TATATTTATATTA
1 TATTATATATTTATATAA
*
2509186 TATTAT-TATTTAAATAA
1 TATTATATATTTATATAA
*
2509203 TATT-TAT-TTTTTATAA
1 TATTATATATTTATATAA
2509219 AAAGTTAAAG
Statistics
Matches: 107, Mismatches: 17, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 6 0.06
16 18 0.17
17 25 0.23
18 17 0.16
19 8 0.07
20 21 0.20
21 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATATATTTATATAA
Found at i:2509159 original size:19 final size:19
Alignment explanation
Indices: 2509114--2509196 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
2509104 ACGTTAGTAA
* * *
2509114 TATTATTATATAAATTATAA
1 TATTTTTATAT-ATTTATAT
*
2509134 TAGTTTTATATATTTATAT
1 TATTTTTATATATTTATAT
*
2509153 TATTTTTATATATTTAAAAT
1 TATTTTTATATATTT-ATAT
* *
2509173 TATATTTATAT-TATATTAT
1 TATTTTTATATATTTA-TAT
2509192 TATTT
1 TATTT
2509197 AAATAATATT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.02
19 28 0.55
20 22 0.43
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTTTTATATATTTATAT
Found at i:2509176 original size:33 final size:29
Alignment explanation
Indices: 2509142--2509209 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
2509132 AATAGTTTTA
*
2509142 TATATTTATATTATTTTTATATATTTAAAAT
1 TATATTTATATTA-TATTAT-TATTTAAAAT
2509173 TATATTTATATTATATTATTATTT-AAAT
1 TATATTTATATTATATTATTATTTAAAAT
*
2509201 AATATTTAT
1 TATATTTAT
2509210 TTTTTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 12 0.34
29 5 0.14
30 5 0.14
31 13 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATTTATATTATATTATTATTTAAAAT
Found at i:2509195 original size:11 final size:11
Alignment explanation
Indices: 2509142--2509189 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
2509132 AATAGTTTTA
2509142 TATATTTATAT
1 TATATTTATAT
2509153 TAT-TTT-TA-
1 TATATTTATAT
*
2509161 TATATTTAAAAT
1 TATATTT-ATAT
2509173 TATATTTATAT
1 TATATTTATAT
2509184 TATATT
1 TATATT
2509190 ATTATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 3 0.10
9 5 0.16
10 3 0.10
11 13 0.42
12 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2509205 original size:28 final size:31
Alignment explanation
Indices: 2509143--2509209 Score: 95
Period size: 28 Copynumber: 2.3 Consensus size: 31
2509133 ATAGTTTTAT
* *
2509143 ATATTTATATTATTTTTATATATTTAAAATT
1 ATATTTATATTATTATTATATATTTAAAATA
2509174 ATATTTATATTA-TATTAT-TATTT-AAATA
1 ATATTTATATTATTATTATATATTTAAAATA
2509202 ATATTTAT
1 ATATTTAT
2509210 TTTTTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 12 0.35
29 5 0.15
30 5 0.15
31 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
ATATTTATATTATTATTATATATTTAAAATA
Found at i:2519322 original size:3 final size:3
Alignment explanation
Indices: 2519316--2519349 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2519306 ACCTGTGGTG
2519316 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2519350 GGGAAGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2519926 original size:14 final size:15
Alignment explanation
Indices: 2519898--2519926 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2519888 ATTTTGTATT
2519898 AATAAAATAAATATA
1 AATAAAATAAATATA
2519913 AATAAAAT-AATATA
1 AATAAAATAAATATA
2519927 TTAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAAATAAATATA
Found at i:2523083 original size:19 final size:19
Alignment explanation
Indices: 2523052--2523089 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2523042 AAAATTTCTT
*
2523052 TGTATTGATATTATTTTTA
1 TGTATTGATATTATATTTA
2523071 TGTATT-ATGATTATATTTA
1 TGTATTGAT-ATTATATTTA
2523090 AAATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (19 bp):
TGTATTGATATTATATTTA
Found at i:2523148 original size:32 final size:32
Alignment explanation
Indices: 2523107--2523168 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
2523097 ATTTATATAA
*
2523107 AAATTTTAATATA-TTAATAATTTATATTATCT
1 AAATTTTAATATATTTAAT-ATTTAAATTATCT
2523139 AAATTTTAATATATTTAATATTTAAATTAT
1 AAATTTTAATATATTTAATATTTAAATTAT
2523169 ATTTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (32 bp):
AAATTTTAATATATTTAATATTTAAATTATCT
Found at i:2523188 original size:18 final size:17
Alignment explanation
Indices: 2523082--2523190 Score: 75
Period size: 17 Copynumber: 6.4 Consensus size: 17
2523072 GTATTATGAT
*
2523082 TATATTTAAAATTTT-A
1 TATATTTAATATTTTAA
* * *
2523098 TTTATATAAAAATTTTAA
1 TATAT-TTAATATTTTAA
*
2523116 TATA-TTAATAATTT-A
1 TATATTTAATATTTTAA
*
2523131 TATTATCTAA-ATTTTAA
1 TA-TATTTAATATTTTAA
*
2523148 TATATTTAATATTTAAA
1 TATATTTAATATTTTAA
2523165 TTATATTT-ATATTTTTAA
1 -TATATTTAATA-TTTTAA
2523183 TAATATTT
1 T-ATATTT
2523191 TTTGTATTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.04
16 23 0.32
17 25 0.34
18 22 0.30
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTAATATTTTAA
Found at i:2523291 original size:2 final size:2
Alignment explanation
Indices: 2523284--2523314 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2523274 TTATTTCTCA
*
2523284 AT AT AT AT GT 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
2523315 CATGCGCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2524989 original size:3 final size:3
Alignment explanation
Indices: 2524977--2525015 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2524967 GCAGCTAAAT
*
2524977 CAA CAG CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2525016 ACACTGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.33, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:2525051 original size:9 final size:9
Alignment explanation
Indices: 2524977--2525051 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
2524967 GCAGCTAAAT
2524977 CAACAGCAA
1 CAACAGCAA
*
2524986 CAACAACAA
1 CAACAGCAA
*
2524995 CAACAACAA
1 CAACAGCAA
*
2525004 CAACAACAA
1 CAACAGCAA
2525013 CAAACACTGCAA
1 C-AACA--GCAA
* *
2525025 -AATCACCAG
1 CAA-CAGCAA
*
2525034 CAGCAGCAA
1 CAACAGCAA
2525043 CAACAGCAA
1 CAACAGCAA
2525052 ATGTCATGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
9 41 0.77
10 7 0.13
11 2 0.04
12 3 0.06
ACGTcount: A:0.56, C:0.33, G:0.08, T:0.03
Consensus pattern (9 bp):
CAACAGCAA
Found at i:2526014 original size:20 final size:19
Alignment explanation
Indices: 2525977--2526014 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
2525967 TAATTATAAC
2525977 ATATCAAATAATAATCATA
1 ATATCAAATAATAATCATA
2525996 ATAT-AAATATATAAATCAT
1 ATATCAAATA-AT-AATCAT
2526015 TAAATCTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATATCAAATAATAATCATA
Found at i:2527023 original size:15 final size:15
Alignment explanation
Indices: 2527003--2527069 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
2526993 AAATTAATTA
2527003 AAATATAATATAAAT
1 AAATATAATATAAAT
* *
2527018 AAATATATTAAAAAT
1 AAATATAATATAAAT
*
2527033 -TATATAATATAAAT
1 AAATATAATATAAAT
* * * * *
2527047 TATTATTATTTATAT
1 AAATATAATATAAAT
2527062 AAATATAA
1 AAATATAA
2527070 AATTACTTAA
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
14 11 0.29
15 27 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATAATATAAAT
Found at i:2527046 original size:14 final size:14
Alignment explanation
Indices: 2527005--2527049 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2526995 ATTAATTAAA
*
2527005 ATATAATATAAATAA
1 ATATAATATAAAT-T
* *
2527020 ATATATTAAAAATT
1 ATATAATATAAATT
2527034 ATATAATATAAATT
1 ATATAATATAAATT
2527048 AT
1 AT
2527050 TATTATTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:2527050 original size:24 final size:24
Alignment explanation
Indices: 2526993--2527080 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 24
2526983 ATTAACATAA
*
2526993 AAATTAATTAAAATATAATATAA-AT
1 AAATT-ATTAAAA-ATTATATAATAT
2527018 AAATATATTAAAAATTATATAATAT
1 AAAT-TATTAAAAATTATATAATAT
** *
2527043 AAATTATTATTATTTATATAAATAT
1 AAATTATTAAAAATTATAT-AATAT
2527068 AAAATTACTTAAA
1 -AAATTA-TTAAA
2527081 TATACATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
24 20 0.38
25 22 0.42
26 7 0.13
27 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATTATTAAAAATTATATAATAT
Found at i:2527074 original size:20 final size:20
Alignment explanation
Indices: 2527028--2527074 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2527018 AAATATATTA
2527028 AAAATTATATAATATAAATT
1 AAAATTATATAATATAAATT
** *
2527048 ATTATTAT-TTATATAAATAT
1 AAAATTATATAATATAAAT-T
2527068 AAAATTA
1 AAAATTA
2527075 CTTAAATATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATATAATATAAATT
Found at i:2527291 original size:2 final size:2
Alignment explanation
Indices: 2527284--2527316 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2527274 AGACATACAT
*
2527284 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2527317 GAAATTCACT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2530429 original size:33 final size:33
Alignment explanation
Indices: 2530382--2530449 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2530372 GTAAGTTCTG
*
2530382 AAACAGGAGTCCCTTATGCACTTATTACAATAT
1 AAACAGGAGCCCCTTATGCACTTATTACAATAT
2530415 AAACAGGAGCCCCTTATGCACTTATTACAATAT
1 AAACAGGAGCCCCTTATGCACTTATTACAATAT
2530448 AA
1 AA
2530450 TTTTTAAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (33 bp):
AAACAGGAGCCCCTTATGCACTTATTACAATAT
Found at i:2543359 original size:35 final size:33
Alignment explanation
Indices: 2543297--2543390 Score: 86
Period size: 35 Copynumber: 2.8 Consensus size: 33
2543287 TAGTAAATTT
* * *
2543297 ATAATTTAATATTTTTTATTTAAATTAAAATTAA
1 ATAATTTAAAATTTTATATTTAAATTAAAAAT-A
*
2543331 ATTAATTTAAAATTTTATA-TTATTATTAAAAATA
1 A-TAATTTAAAATTTTATATTTA-AATTAAAAATA
* *
2543365 AT-ATTTAAAA-TTTATTTTTATATTAA
1 ATAATTTAAAATTTTATATTTAAATTAA
2543391 TATTTATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
31 11 0.21
32 11 0.21
33 1 0.02
34 6 0.12
35 23 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
ATAATTTAAAATTTTATATTTAAATTAAAAATA
Found at i:2543759 original size:3 final size:3
Alignment explanation
Indices: 2543751--2543793 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2543741 TTTCCTCATG
2543751 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2543794 TAAAGATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2549117 original size:3 final size:3
Alignment explanation
Indices: 2549109--2549137 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2549099 CACTTAACTT
2549109 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
2549138 CACTGCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:2555534 original size:22 final size:22
Alignment explanation
Indices: 2555490--2555532 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2555480 AAATATCAAT
**
2555490 TTATATAATTTTTATTTTAAAA
1 TTATATAATTTTTATTAAAAAA
2555512 TTATA-AATTTTTATTAAAAAA
1 TTATATAATTTTTATTAAAAAA
2555533 ATAACAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATATAATTTTTATTAAAAAA
Found at i:2558694 original size:38 final size:38
Alignment explanation
Indices: 2558652--2558730 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
2558642 AAATTTTTTA
* * **
2558652 AAATATATTTAAAATAT-TATATTTTTATATTAATATTT
1 AAATATATATAAAATATATA-AATTAAATATTAATATTT
*
2558690 AAATATATATCAAATATATAAATTAAATATTAATATTT
1 AAATATATATAAAATATATAAATTAAATATTAATATTT
2558728 AAA
1 AAA
2558731 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
AAATATATATAAAATATATAAATTAAATATTAATATTT
Found at i:2558705 original size:19 final size:19
Alignment explanation
Indices: 2558678--2558753 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
2558668 TTATATTTTT
* *
2558678 ATATTAATATTTAAA-TAT
1 ATATAAATATTTAAATTAA
*
2558696 ATATCAAATATATAAATTAA
1 ATAT-AAATATTTAAATTAA
*
2558716 ATATTAATATTTAAA--AA
1 ATATAAATATTTAAATTAA
* * *
2558733 ATAAAAAAATTTAAATGAA
1 ATATAAATATTTAAATTAA
2558752 AT
1 AT
2558754 TTTACGAGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
17 14 0.30
18 4 0.09
19 22 0.48
20 6 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
ATATAAATATTTAAATTAA
Found at i:2559865 original size:3 final size:3
Alignment explanation
Indices: 2559857--2559912 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
2559847 TTGAATCTTA
2559857 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2559905 ATT ATT AT
1 ATT ATT AT
2559913 CACTTGTGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2560521 original size:2 final size:2
Alignment explanation
Indices: 2560514--2560551 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2560504 AAACTTATGA
* *
2560514 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2560552 TAAACCAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:2561956 original size:20 final size:22
Alignment explanation
Indices: 2561931--2561971 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
2561921 TTATAATTTT
2561931 TAAATATT-AAATA-AATAAAA
1 TAAATATTAAAATATAATAAAA
2561951 TAAATATTAAAATATAATAAA
1 TAAATATTAAAATATAATAAA
2561972 TTATTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATATTAAAATATAATAAAA
Found at i:2564185 original size:19 final size:21
Alignment explanation
Indices: 2564158--2564196 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2564148 TTATCTGTAA
*
2564158 ATATTTTAA-TAT-ATAAACG
1 ATATATTAATTATGATAAACG
2564177 ATATATTAATTATGATAAAC
1 ATATATTAATTATGATAAAC
2564197 ATGAATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ATATATTAATTATGATAAACG
Found at i:2567103 original size:19 final size:19
Alignment explanation
Indices: 2567081--2567117 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2567071 ATTTACTCTT
*
2567081 ATTTTATTTTTTTAAAATA
1 ATTTTATTTTTTAAAAATA
2567100 ATTTTATTTTTTAAAAAT
1 ATTTTATTTTTTAAAAAT
2567118 TAAATAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATTTTTTAAAAATA
Found at i:2567216 original size:14 final size:14
Alignment explanation
Indices: 2567197--2567234 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2567187 TAAAAGAATT
2567197 TATATTTAATAATA
1 TATATTTAATAATA
2567211 TATATTTAATAATA
1 TATATTTAATAATA
2567225 T-TA-TTAATAA
1 TATATTTAATAA
2567235 ATTAAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.29
13 2 0.08
14 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTTAATAATA
Found at i:2568494 original size:28 final size:28
Alignment explanation
Indices: 2568462--2568519 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
2568452 TTTTTATTTT
2568462 TTATA-AATATTTAAA-TAAATT-AATAA
1 TTATATAA-ATTTAAATTAAATTAAATAA
*
2568488 TTATATAAATTTAAATTATATTAAATAA
1 TTATATAAATTTAAATTAAATTAAATAA
2568516 TTAT
1 TTAT
2568520 TATTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.43
27 7 0.25
28 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTATATAAATTTAAATTAAATTAAATAA
Found at i:2568506 original size:15 final size:16
Alignment explanation
Indices: 2568476--2568522 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2568466 AAATATTTAA
2568476 ATAAATTAATAATTAT
1 ATAAATTAATAATTAT
*
2568492 ATAAATTTA-AATTAT
1 ATAAATTAATAATTAT
*
2568507 ATTAAA-TAATTATTAT
1 A-TAAATTAATAATTAT
2568523 TTATTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATTAATAATTAT
Found at i:2569437 original size:23 final size:22
Alignment explanation
Indices: 2569411--2569493 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 22
2569401 TATTTTAAAT
2569411 ATATAAAAAATAATACGAATATA
1 ATATAAAAAATAATA-GAATATA
*
2569434 ATATCAAAAATTAATTA-AA-ATA
1 ATAT-AAAAAATAA-TAGAATATA
*
2569456 AAATAAAAAATATATATG-ATATGA
1 ATATAAAAAATA-ATA-GAATAT-A
2569480 ATATAAAAATATAA
1 ATATAAAAA-ATAA
2569494 AAAAATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
21 9 0.19
22 8 0.17
23 8 0.17
24 18 0.38
25 5 0.10
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
ATATAAAAAATAATAGAATATA
Found at i:2569499 original size:45 final size:45
Alignment explanation
Indices: 2569413--2569500 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
2569403 TTTTAAATAT
*
2569413 ATAAAAAATAATACGAATATAATATCAAAAATTAATTAAAATAAA
1 ATAAAAAATAATACGAATATAATATCAAAAATTAATAAAAATAAA
*
2569458 ATAAAAAATATATATG-ATATGAATAT-AAAAATATAA-AAAAATA
1 ATAAAAAATA-ATACGAATAT-AATATCAAAAAT-TAATAAAAATA
2569501 TTTATAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 26 0.68
46 12 0.32
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (45 bp):
ATAAAAAATAATACGAATATAATATCAAAAATTAATAAAAATAAA
Found at i:2569695 original size:8 final size:8
Alignment explanation
Indices: 2569684--2569748 Score: 60
Period size: 8 Copynumber: 7.6 Consensus size: 8
2569674 TTAAATTTTT
2569684 AATATTAA
1 AATATTAA
2569692 AATATTAA
1 AATATTAA
2569700 AATA-TAA
1 AATATTAA
2569707 AATATTTTAA
1 AATA--TTAA
2569717 ATATAATTATA
1 A-AT-ATTA-A
*
2569728 AATAATAA
1 AATATTAA
*
2569736 AATATTTA
1 AATATTAA
2569744 AATAT
1 AATAT
2569749 AACATAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 7 0.15
8 24 0.50
9 3 0.06
10 9 0.19
11 4 0.08
12 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
AATATTAA
Found at i:2569707 original size:15 final size:15
Alignment explanation
Indices: 2569684--2569750 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 15
2569674 TTAAATTTTT
*
2569684 AATATTAAAATATTAA
1 AATA-TAAAATATTTA
2569700 AATATAAAATATTTTA
1 AATATAAAATA-TTTA
*
2569716 AATAT--AAT-TATA
1 AATATAAAATATTTA
2569728 AATAATAAAATATTTA
1 AAT-ATAAAATATTTA
2569744 AATATAA
1 AATATAA
2569751 CATAATATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
12 6 0.14
13 2 0.05
14 3 0.07
15 14 0.33
16 18 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAAAATATTTA
Found at i:2571625 original size:27 final size:28
Alignment explanation
Indices: 2571594--2571663 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 28
2571584 TAAAAATTAA
* *
2571594 AAAAATTATGAATAAATTAAAATTTTTT
1 AAAAATTATGAATAAATTAAAATATATT
* * *
2571622 AAAAATTTTTAA-AAATTAATATATATT
1 AAAAATTATGAATAAATTAAAATATATT
*
2571649 -AAAATGATGAATAAA
1 AAAAATTATGAATAAA
2571664 AATATTAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
26 8 0.24
27 15 0.45
28 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAAATTATGAATAAATTAAAATATATT
Found at i:2574706 original size:20 final size:18
Alignment explanation
Indices: 2574684--2574787 Score: 65
Period size: 18 Copynumber: 5.7 Consensus size: 18
2574674 ATCAAAATCT
2574684 ATATAAAATAAATTATTAA
1 ATATAAAATAAA-TATTAA
* *
2574703 TATATCAAA-AATTATATAA
1 -ATATAAAATAAATAT-TAA
* * *
2574722 ATATATATTACATATTAA
1 ATATAAAATAAATATTAA
2574740 ATATAAATATAAA-ATT-A
1 ATATAAA-ATAAATATTAA
2574757 ATA-AAAATAAA-ATATAA
1 ATATAAAATAAATAT-TAA
2574774 ATACATAAAATAAA
1 AT--ATAAAATAAA
2574788 AATAAAATTG
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.11
16 4 0.06
17 7 0.11
18 20 0.30
19 13 0.20
20 15 0.23
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAAATAAATATTAA
Found at i:2574748 original size:6 final size:6
Alignment explanation
Indices: 2574716--2574776 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
2574706 ATCAAAAATT
* * * *
2574716 ATATAA ATATAT AT-TAC ATATTAA ATATAA ATATAA A-ATTA ATAAAA
1 ATATAA ATATAA ATATAA ATA-TAA ATATAA ATATAA ATATAA ATATAA
2574763 ATA-AA ATATAA ATA
1 ATATAA ATATAA ATA
2574777 CATAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.29
6 27 0.60
7 5 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:2574766 original size:21 final size:21
Alignment explanation
Indices: 2574737--2574796 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
2574727 TATTACATAT
*
2574737 TAAATATAAATATAAAATTA-A
1 TAAAAATAAA-ATAAAATTACA
2574758 TAAAAATAAAATATAAA-TACA
1 TAAAAATAAAATA-AAATTACA
2574779 T-AAAATAAAAATAAAATT
1 TAAAAAT-AAAATAAAATT
2574797 GAGAGGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATAAAATAAAATTACA
Found at i:2574781 original size:15 final size:14
Alignment explanation
Indices: 2574738--2574792 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
2574728 ATTACATATT
2574738 AAATATAAAT-ATA
1 AAATATAAATAATA
2574751 AAATTAATAAA-AATA
1 AAA-T-ATAAATAATA
2574766 AAATATAAATACATA
1 AAATATAAATA-ATA
*
2574781 AAATAAAAATAA
1 AAATATAAATAA
2574793 AATTGAGAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.22
14 4 0.11
15 24 0.67
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATATAAATAATA
Found at i:2574792 original size:26 final size:27
Alignment explanation
Indices: 2574738--2574795 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
2574728 ATTACATATT
*
2574738 AAATATAAATATAAAATTAATAAAAATA
1 AAATATAAATACAAAA-TAATAAAAATA
*
2574766 AAATATAAATACATAA-AATAAAAATA
1 AAATATAAATACAAAATAATAAAAATA
2574792 AAAT
1 AAAT
2574796 TGAGAGGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.50
28 14 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (27 bp):
AAATATAAATACAAAATAATAAAAATA
Found at i:2577882 original size:18 final size:16
Alignment explanation
Indices: 2577858--2577914 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 16
2577848 TTTACGAGCT
2577858 AAATAAAAATTAATTAA
1 AAATAAAAATT-ATTAA
*
2577875 TTAAT-AAAATTATTAA
1 -AAATAAAAATTATTAA
2577891 AAATAAAAATAAATATTAA
1 AAATAAAAAT---TATTAA
2577910 AAATA
1 AAATA
2577915 TTTATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 3 0.09
16 10 0.30
17 6 0.18
18 3 0.09
19 11 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAATTATTAA
Found at i:2577897 original size:15 final size:17
Alignment explanation
Indices: 2577857--2577898 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
2577847 TTTTACGAGC
2577857 TAAATAAAAATTAATTAA
1 TAAAT-AAAATTAATTAA
*
2577875 TTAATAAAATT-ATTAA
1 TAAATAAAATTAATTAA
2577891 -AAATAAAA
1 TAAATAAAA
2577899 ATAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 5 0.23
17 6 0.27
18 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATAAAATTAATTAA
Found at i:2577993 original size:53 final size:52
Alignment explanation
Indices: 2577930--2578046 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 52
2577920 ATTATTTTAA
*
2577930 AAAACTAACTACCCAATAAACAATTACACACCTTTTTTAATTTTTTTAATTTT
1 AAAACTAACTACCCAATAAACAATTACACACCTTTTTAAATTTTTTTAA-TTT
2577983 AAAACTAACTACCCAATAAACAATTACACACCTTTTTAAATTTTTTTAATTT
1 AAAACTAACTACCCAATAAACAATTACACACCTTTTTAAATTTTTTTAATTT
*
2578035 AAAAATAACTAC
1 AAAACTAACTAC
2578047 TCTCCTATTA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 14 0.23
53 48 0.77
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (52 bp):
AAAACTAACTACCCAATAAACAATTACACACCTTTTTAAATTTTTTTAATTT
Found at i:2578247 original size:2 final size:2
Alignment explanation
Indices: 2578240--2578265 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2578230 AGATACATAC
2578240 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
2578266 TAGATAATGA
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:2585419 original size:3 final size:3
Alignment explanation
Indices: 2585411--2585440 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2585401 AAAAGCTTGC
*
2585411 TGT TGT TGT TGT TGT TGT TGT TGT AGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
2585441 AGCTGCTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.63
Consensus pattern (3 bp):
TGT
Found at i:2586060 original size:13 final size:13
Alignment explanation
Indices: 2586029--2586071 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2586019 TTATGTATAA
**
2586029 ATTTTAAATGAAT
1 ATTTTAAATTTAT
*
2586042 AATTTAAATTTAT
1 ATTTTAAATTTAT
2586055 ATTTTAAATTTAAT
1 ATTTTAAATTT-AT
2586069 ATT
1 ATT
2586072 ATTTTTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
ATTTTAAATTTAT
Found at i:2588043 original size:27 final size:27
Alignment explanation
Indices: 2588002--2588055 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2587992 CACATGTAAA
*
2588002 ACTGTTCTTACTTATAACTATTTATTT
1 ACTGTTCTAACTTATAACTATTTATTT
* *
2588029 ACTGTTCTAATTTATAATTATTTATTT
1 ACTGTTCTAACTTATAACTATTTATTT
2588056 CCTTACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (27 bp):
ACTGTTCTAACTTATAACTATTTATTT
Found at i:2601777 original size:2 final size:2
Alignment explanation
Indices: 2601764--2601796 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2601754 AAGTAGAAGT
*
2601764 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2601797 GGAAGCATAA
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2607833 original size:62 final size:61
Alignment explanation
Indices: 2607710--2607900 Score: 267
Period size: 61 Copynumber: 3.1 Consensus size: 61
2607700 GTTTGTCACC
* * * * * *
2607710 AGTTAACACCTGTTAGATATGGAAGATTTTTGCATTTTATGATCATCCTCAACTGTTTATT
1 AGTTAAAACCTGTTAGATATGGAAGATTTTTTCGTGTCATCATCATCCTCAACTGTTTATT
*
2607771 AGTTAAAACCTGTTAGATATGGAAGATTTTTTTCGTGTCATCATCATCCTTAACTGTTTATT
1 AGTTAAAACCTGTTAGATATGGAAGA-TTTTTTCGTGTCATCATCATCCTCAACTGTTTATT
* * * *
2607833 AGTTAAAACCTGTTAGATATGGAACATTTTTTCGTGTCATCATCTTCCTCAAGTGTTTGTT
1 AGTTAAAACCTGTTAGATATGGAAGATTTTTTCGTGTCATCATCATCCTCAACTGTTTATT
2607894 A-TTAAAA
1 AGTTAAAA
2607901 TATTAATAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
60 6 0.05
61 57 0.49
62 54 0.46
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (61 bp):
AGTTAAAACCTGTTAGATATGGAAGATTTTTTCGTGTCATCATCATCCTCAACTGTTTATT
Found at i:2610300 original size:33 final size:33
Alignment explanation
Indices: 2610247--2610313 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
2610237 GAAAAATCAC
* *
2610247 TGAAGGTCCGTAAAACAGCTCTTCAGAGAGCAA
1 TGAAGGGCCGTAAAACAGCTCTTCAAAGAGCAA
2610280 TGAAGGGCCGTGAAAA-AGCTCTTCAAAGAGCAA
1 TGAAGGGCCGT-AAAACAGCTCTTCAAAGAGCAA
2610313 T
1 T
2610314 AGCTTTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.18
Consensus pattern (33 bp):
TGAAGGGCCGTAAAACAGCTCTTCAAAGAGCAA
Found at i:2611163 original size:2 final size:2
Alignment explanation
Indices: 2611152--2611204 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
2611142 TGCAGGAATC
2611152 AT AT -T AT AT 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 AT AT AT AT AT
2611193 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2611205 GGCTAGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2617500 original size:25 final size:25
Alignment explanation
Indices: 2617469--2617527 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
2617459 TAGTTCATAT
*
2617469 TATATTTTTATTTTTAA-ATTTAAA
1 TATATTTTTATTTTTAATAATTAAA
* * *
2617493 TTTAATTTAATTTTTAATAATTAAA
1 TATATTTTTATTTTTAATAATTAAA
2617518 TATATTTTTA
1 TATATTTTTA
2617528 GTAATTTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATTTTTATTTTTAATAATTAAA
Found at i:2617514 original size:20 final size:19
Alignment explanation
Indices: 2617491--2617534 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2617481 TTTAAATTTA
*
2617491 AATTTAATTTAATTTTTAAT
1 AATTTAATAT-ATTTTTAAT
* *
2617511 AATTAAATATATTTTTAGT
1 AATTTAATATATTTTTAAT
2617530 AATTT
1 AATTT
2617535 TTTATTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTAATATATTTTTAAT
Found at i:2617698 original size:20 final size:20
Alignment explanation
Indices: 2617611--2617686 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
2617601 CACTAGTAAA
2617611 ATAAAAT-TATAATTATTATT
1 ATAAAATATATAATTA-TATT
* *
2617631 GTAAAATATTTACAATTATATT
1 ATAAAATA--TATAATTATATT
2617653 ATAAAATATATAATTATATT
1 ATAAAATATATAATTATATT
2617673 ATAAAATATA-AATT
1 ATAAAATATATAATT
2617687 TTGTTATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
19 4 0.08
20 27 0.55
22 11 0.22
23 7 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (20 bp):
ATAAAATATATAATTATATT
Found at i:2620928 original size:14 final size:14
Alignment explanation
Indices: 2620866--2620922 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 14
2620856 AATTTCATTA
2620866 ATATAAT-T-TTTT
1 ATATAATATATTTT
*
2620878 ATTATAATATAATTT
1 A-TATAATATATTTT
2620893 AT-TAATAGT-TTTT
1 ATATAATA-TATTTT
2620906 ATATAATATATTTT
1 ATATAATATATTTT
2620920 ATA
1 ATA
2620923 AGATATTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 1 0.03
13 17 0.46
14 15 0.41
15 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATATAATATATTTT
Found at i:2621504 original size:10 final size:10
Alignment explanation
Indices: 2621491--2621526 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
2621481 TAAATATGAT
2621491 TAAATTTAAA
1 TAAATTTAAA
2621501 TAAATTTAAA
1 TAAATTTAAA
2621511 T-AATTTAAA
1 TAAATTTAAA
2621520 -AAATTTA
1 TAAATTTA
2621527 GATCATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:2621577 original size:23 final size:21
Alignment explanation
Indices: 2621546--2621620 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 21
2621536 AATTTAAATT
*
2621546 ATTTTAATTTTACTGTATTTTAA
1 ATTTAAATTTTA-T-TATTTTAA
*
2621569 ATTTAAATTTTATAAATTTTTAA
1 ATTTAAATTTTAT-TA-TTTTAA
** *
2621592 AAGTAAATTTAAATTATTTTAA
1 ATTTAAATTT-TATTATTTTAA
2621614 ATTTAAA
1 ATTTAAA
2621621 GTGAATTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
22 13 0.32
23 26 0.63
24 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTAAATTTTATTATTTTAA
Found at i:2621616 original size:16 final size:16
Alignment explanation
Indices: 2621388--2621620 Score: 103
Period size: 16 Copynumber: 14.6 Consensus size: 16
2621378 TAATAATAAA
2621388 AAATTTAAATT-TTTT
1 AAATTTAAATTATTTT
2621403 AAATTTTAAA-T-TTTT
1 AAA-TTTAAATTATTTT
* * * *
2621418 AAGTTTAGACTATATT
1 AAATTTAAATTATTTT
2621434 AAATTTAAATTATTTT
1 AAATTTAAATTATTTT
2621450 AAAATTTAAATT-TTTT
1 -AAATTTAAATTATTTT
** *
2621466 AAAATTTATTTTATTTA
1 -AAATTTAAATTATTTT
**
2621483 AATATGATTAAATT-TAAAT
1 AA-AT--TTAAATTAT-TTT
* *
2621502 AAATTTAAATAATTTAAA
1 AAATTTAAATTATTT--T
* * **
2621520 AAATTTAGATCA-TAA
1 AAATTTAAATTATTTT
2621535 AAATTTAAATTATTTT
1 AAATTTAAATTATTTT
* *
2621551 -AATTTTACTGTATTTT
1 AAATTTAAAT-TATTTT
*
2621567 AAATTTAAATT-TTAT
1 AAATTTAAATTATTTT
*
2621582 AAATTTTTAAA--A--GT
1 AAA--TTTAAATTATTTT
2621596 AAATTTAAATTATTTT
1 AAATTTAAATTATTTT
2621612 AAATTTAAA
1 AAATTTAAA
2621621 GTGAATTTTA
Statistics
Matches: 163, Mismatches: 33, Indels: 43
0.68 0.14 0.18
Matches are distributed among these distances:
12 6 0.04
14 10 0.06
15 35 0.21
16 61 0.37
17 31 0.19
18 13 0.08
19 7 0.04
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:2621620 original size:22 final size:23
Alignment explanation
Indices: 2621561--2621620 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
2621551 AATTTTACTG
2621561 TATTTTAAATTTAAATTTTATAA
1 TATTTTAAATTTAAATTTTATAA
**
2621584 -ATTTTTAAAAGTAAA-TTTA-AA
1 TA-TTTTAAATTTAAATTTTATAA
2621605 TTATTTTAAATTTAAA
1 -TATTTTAAATTTAAA
2621621 GTGAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 2 0.07
22 16 0.53
23 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTTAAATTTAAATTTTATAA
Found at i:2622865 original size:12 final size:11
Alignment explanation
Indices: 2622845--2622874 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
2622835 AAGATTTGGA
2622845 AAAAAATAAAT
1 AAAAAATAAAT
2622856 AAATAAATAAAT
1 AAA-AAATAAAT
2622868 AAAAAAT
1 AAAAAAT
2622875 GAAGGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:2623105 original size:13 final size:13
Alignment explanation
Indices: 2623069--2623107 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2623059 AATGGTCAAA
2623069 CCCATTGCAGTCT
1 CCCATTGCAGTCT
** *
2623082 CTAATTACAGTCT
1 CCCATTGCAGTCT
2623095 CCCATTGCAGTCT
1 CCCATTGCAGTCT
2623108 ATAATTTACA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (13 bp):
CCCATTGCAGTCT
Found at i:2626187 original size:20 final size:19
Alignment explanation
Indices: 2626157--2626212 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
2626147 ATGTCTCTTT
*
2626157 TTTTTATATATAAAATAAA
1 TTTTAATATATAAAATAAA
2626176 TTATTAATATATTAAAAT-AA
1 TT-TTAATATA-TAAAATAAA
* *
2626196 TTTTAAAATATAGAATA
1 TTTTAATATATAAAATA
2626213 TAATAATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.16
19 9 0.29
20 11 0.35
21 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTTAATATATAAAATAAA
Found at i:2631958 original size:31 final size:33
Alignment explanation
Indices: 2631920--2631992 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 33
2631910 AATTATATTT
* *
2631920 AATTAATTTATT-TTGAT-TTATTAATTTTTAA
1 AATTAATTGATTATTAATATTATTAATTTTTAA
*
2631951 AATTAATTGATTATTAATCAGTTCTTAATTTTTAA
1 AATTAATTGATTATTAAT-A-TTATTAATTTTTAA
2631986 AATTAAT
1 AATTAAT
2631993 AACTTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.31
32 4 0.11
35 20 0.57
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (33 bp):
AATTAATTGATTATTAATATTATTAATTTTTAA
Found at i:2639286 original size:2 final size:2
Alignment explanation
Indices: 2639279--2639312 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2639269 TTTTGTTGGG
2639279 AT 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 AT
2639313 GTTTTTTAGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2639471 original size:26 final size:25
Alignment explanation
Indices: 2639432--2639484 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
2639422 GATTATATAG
**
2639432 ATATATTATTATTAACATAAAAAAAT
1 ATATATTAGAATTAA-ATAAAAAAAT
*
2639458 ATATATTAGAATTAAATAAAAAGAT
1 ATATATTAGAATTAAATAAAAAAAT
2639483 AT
1 AT
2639485 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATTAGAATTAAATAAAAAAAT
Found at i:2644903 original size:23 final size:23
Alignment explanation
Indices: 2644870--2644934 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 23
2644860 AATCCGTATT
2644870 TTTATTATTTTTATAT-TTAA-AA
1 TTTA-TATTTTTATATATTAATAA
2644892 TATTATATTTTTATATATTAATAA
1 T-TTATATTTTTATATATTAATAA
*
2644916 TTTATTTTATTTTATATAT
1 TTTA-TAT-TTTTATATAT
2644935 ATTTATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 12 0.32
23 10 0.27
24 5 0.14
25 10 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATATTTTTATATATTAATAA
Found at i:2645011 original size:16 final size:16
Alignment explanation
Indices: 2644990--2645039 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2644980 TTTTATTATC
2644990 TATTTATTTATATCTA
1 TATTTATTTATATCTA
2645006 TATTTA-TTATTAT-TA
1 TATTTATTTA-TATCTA
*
2645021 TTATTTATTATCTATCTA
1 -TATTTATT-TATATCTA
2645039 T
1 T
2645040 CTATACCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
15 5 0.18
16 15 0.54
17 5 0.18
18 3 0.11
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATTTATATCTA
Found at i:2645013 original size:43 final size:43
Alignment explanation
Indices: 2644966--2645049 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
2644956 TTATGTGTTA
* * * * *
2644966 TTATTATTATTGTTTTTTATTATCTATTTATTTATATCTATAT
1 TTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
2645009 TTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
1 TTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
2645050 CTAACATGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.63
Consensus pattern (43 bp):
TTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
Found at i:2645440 original size:13 final size:13
Alignment explanation
Indices: 2645422--2645447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2645412 ATCTGTCCAA
2645422 CGACTTCATGTGG
1 CGACTTCATGTGG
2645435 CGACTTCATGTGG
1 CGACTTCATGTGG
2645448 GTTTACCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (13 bp):
CGACTTCATGTGG
Found at i:2646119 original size:23 final size:23
Alignment explanation
Indices: 2646102--2646151 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2646092 TATTTATGTT
2646102 TTTTATTATTTATTATTTATAAA
1 TTTTATTATTTATTATTTATAAA
**
2646125 TTTTATTATTTAAAATATTATAAA
1 TTTTATTATTTATTAT-TTATAAA
2646149 TTT
1 TTT
2646152 ATATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATTATTTATTATTTATAAA
Found at i:2646140 original size:15 final size:16
Alignment explanation
Indices: 2646110--2646145 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2646100 TTTTTTATTA
2646110 TTTATTATTTATAAAT
1 TTTATTATTTATAAAT
2646126 TTTATTATTTA-AAAT
1 TTTATTATTTATAAAT
*
2646141 ATTAT
1 TTTAT
2646146 AAATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTATTTATAAAT
Found at i:2646200 original size:6 final size:6
Alignment explanation
Indices: 2646180--2646247 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
2646170 ATTTTATGTT
* *
2646180 TTTATA TTTAT- TTTATA TTTATT TTTATA TTT-TA TTT-TA ATTA-A
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* *
2646224 TTTTAAA TATTATA TATATA TTTA
1 -TTTATA T-TTATA TTTATA TTTA
2646248 AAATATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
5 15 0.30
6 29 0.58
7 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:2646205 original size:12 final size:12
Alignment explanation
Indices: 2646178--2646217 Score: 64
Period size: 11 Copynumber: 3.3 Consensus size: 12
2646168 AAATTTTATG
2646178 TTTTTATATTTA
1 TTTTTATATTTA
2646190 -TTTTATATTTA
1 TTTTTATATTTA
2646201 TTTTTATATTTTA
1 TTTTTATA-TTTA
2646214 TTTT
1 TTTT
2646218 AATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.42
12 7 0.27
13 8 0.31
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:2646206 original size:17 final size:17
Alignment explanation
Indices: 2646180--2646228 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
2646170 ATTTTATGTT
2646180 TTTATATTTAT-TTTATA
1 TTTATATTTATATTT-TA
*
2646197 TTTATTTTTATATTTTA
1 TTTATATTTATATTTTA
*
2646214 TTT-TAATTA-ATTTTA
1 TTTATATTTATATTTTA
2646229 AATATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 6 0.21
16 4 0.14
17 15 0.54
18 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTTATATTTTA
Found at i:2646208 original size:23 final size:23
Alignment explanation
Indices: 2646178--2646227 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2646168 AAATTTTATG
*
2646178 TTTTTATA-TTTATTTTATATTTA
1 TTTTTATATTTTATTTTA-ATTAA
2646201 TTTTTATATTTTATTTTAATTAA
1 TTTTTATATTTTATTTTAATTAA
2646224 TTTT
1 TTTT
2646228 AAATATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTATATTTTATTTTAATTAA
Found at i:2646218 original size:12 final size:11
Alignment explanation
Indices: 2646179--2646247 Score: 68
Period size: 12 Copynumber: 6.0 Consensus size: 11
2646169 AATTTTATGT
2646179 TTTTATATTTA
1 TTTTATATTTA
2646190 TTTTATATTTA
1 TTTTATATTTA
2646201 TTTTTATATTTTA
1 -TTTTATA-TTTA
*
2646214 TTTTA-ATTAA
1 TTTTATATTTA
*
2646224 TTTTAAATATTA
1 TTTTATAT-TTA
*
2646236 TATATATATTTA
1 T-TTTATATTTA
2646248 AAATATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.16
11 14 0.29
12 18 0.37
13 9 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:2646233 original size:24 final size:24
Alignment explanation
Indices: 2646178--2646234 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
2646168 AAATTTTATG
* *
2646178 TTTTTATA-TTTATTTTATATTTA
1 TTTTAATATTTTATTTTATATTAA
*
2646201 TTTTTATATTTTATTTTA-ATTAA
1 TTTTAATATTTTATTTTATATTAA
2646224 TTTTAAATATT
1 TTTT-AATATT
2646235 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTAATATTTTATTTTATATTAA
Found at i:2646314 original size:24 final size:26
Alignment explanation
Indices: 2646280--2646335 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
2646270 TTTGTACATA
*
2646280 TTAAT-TATTTATTTA-T-ATATTTT
1 TTAATATATTTATATATTCATATTTT
2646303 TTAATATATTTATATATTCATATTTT
1 TTAATATATTTATATATTCATATTTT
*
2646329 TTTATAT
1 TTAATAT
2646336 TATGTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 9 0.32
25 1 0.04
26 13 0.46
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTAATATATTTATATATTCATATTTT
Found at i:2647315 original size:19 final size:20
Alignment explanation
Indices: 2647293--2647336 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2647283 TATTTGTATT
* *
2647293 TTTTATTTTTTAATTTTA-A
1 TTTTATTTTTAAATTATATA
2647312 TTTTATTTTTAAATTATATA
1 TTTTATTTTTAAATTATATA
2647332 TTTTA
1 TTTTA
2647337 ATGTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTTTTAAATTATATA
Found at i:2647316 original size:32 final size:32
Alignment explanation
Indices: 2647280--2647346 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2647270 ACTTCACATT
** * * *
2647280 TTTTATTTGTATTTTTTATTTTTTAATTTTAA
1 TTTTATTTGTAAATTATATATTTTAATGTTAA
*
2647312 TTTTATTTTTAAATTATATATTTTAATGTTAA
1 TTTTATTTGTAAATTATATATTTTAATGTTAA
2647344 TTT
1 TTT
2647347 GCATTGTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (32 bp):
TTTTATTTGTAAATTATATATTTTAATGTTAA
Found at i:2659954 original size:60 final size:60
Alignment explanation
Indices: 2659861--2659983 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
2659851 AAGATTTAGA
* *
2659861 TTTGGAATTCCATAATTAGAGTTGCTCATGAGCCGGGCCGGGCCGTAGTTCGAAATTTTG
1 TTTGGAATTCCATAATAAGAGTTGCTCATGAGCCGGGCCGGGCCGTAGTTCGAAAATTTG
2659921 TTTGGAATTCCATAATAAGAGTTGCTCATGAGCCGGGCCGGGCCGTAGTTCGAAAATTTG
1 TTTGGAATTCCATAATAAGAGTTGCTCATGAGCCGGGCCGGGCCGTAGTTCGAAAATTTG
2659981 TTT
1 TTT
2659984 CATCCCTTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (60 bp):
TTTGGAATTCCATAATAAGAGTTGCTCATGAGCCGGGCCGGGCCGTAGTTCGAAAATTTG
Found at i:2678230 original size:19 final size:20
Alignment explanation
Indices: 2678206--2678249 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
2678196 TCTCAATCTG
2678206 AATATTAAAA-AAAATTATA
1 AATATTAAAATAAAATTATA
*
2678225 AATATTAAAATTTAAATTATA
1 AATATTAAAA-TAAAATTATA
2678246 AATA
1 AATA
2678250 ATTATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATTAAAATAAAATTATA
Found at i:2681646 original size:3 final size:3
Alignment explanation
Indices: 2681640--2681674 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2681630 ACTATTAACC
2681640 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
2681675 ACCCATAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:2681837 original size:14 final size:13
Alignment explanation
Indices: 2681820--2681876 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
2681810 TTCTTTATGA
2681820 AATTTTAAGATTTT
1 AATTTTAA-ATTTT
2681834 AATTTTAAATTTT
1 AATTTTAAATTTT
2681847 -ATTTTATATATTTT
1 AATTTTA-A-ATTTT
* *
2681861 AATTTAAAATTAT
1 AATTTTAAATTTT
2681874 AAT
1 AAT
2681877 AAATTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 6 0.16
13 13 0.34
14 14 0.37
15 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
AATTTTAAATTTT
Found at i:2681861 original size:27 final size:26
Alignment explanation
Indices: 2681821--2681871 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2681811 TCTTTATGAA
*
2681821 ATTTTAAGATTTTAATTTTAAATTTT
1 ATTTTAAGATTTTAATTTAAAATTTT
*
2681847 ATTTTATATATTTTAATTTAAAATT
1 ATTTTA-AGATTTTAATTTAAAATT
2681872 ATAATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTTAAGATTTTAATTTAAAATTTT
Found at i:2682157 original size:22 final size:22
Alignment explanation
Indices: 2682103--2682157 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
2682093 CTATGTTTTT
2682103 ATTAA-AT-ATAATTATTAATA
1 ATTAATATAATAATTATTAATA
* *
2682123 ATTAATTTAATAATTTTTAAT-
1 ATTAATATAATAATTATTAATA
*
2682144 ATGTAATATGATAA
1 AT-TAATATAATAA
2682158 CTTTAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.18
21 3 0.11
22 20 0.71
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTAATATAATAATTATTAATA
Found at i:2682276 original size:14 final size:14
Alignment explanation
Indices: 2682257--2682287 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2682247 CAATCAGACA
2682257 ATACTTATTGATAT
1 ATACTTATTGATAT
2682271 ATACTTATTGATAT
1 ATACTTATTGATAT
2682285 ATA
1 ATA
2682288 GATCGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (14 bp):
ATACTTATTGATAT
Found at i:2682342 original size:14 final size:14
Alignment explanation
Indices: 2682325--2682375 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 14
2682315 TTTATATATT
2682325 TATATAAATTTTAA
1 TATATAAATTTTAA
2682339 TATATTAATAATTTATAA
1 TATA-T-A-AATTT-TAA
2682357 TATATAAATTTTAA
1 TATATAAATTTTAA
2682371 TATAT
1 TATAT
2682376 TTATATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.36
15 6 0.18
16 2 0.06
17 6 0.18
18 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:2682348 original size:51 final size:53
Alignment explanation
Indices: 2682293--2682392 Score: 143
Period size: 51 Copynumber: 1.9 Consensus size: 53
2682283 ATATAGATCG
2682293 TAATAATGCATAATATAT-AATATTT-ATATATTTATA-TAAATTTTAATATAT
1 TAATAATGCATAATATATAAAT-TTTAATATATTTATATTAAATTTTAATATAT
** *
2682344 TAATAATTTATAATATATAAATTTTAATATATTTATATTATATTTTAAT
1 TAATAATGCATAATATATAAATTTTAATATATTTATATTAAATTTTAAT
2682393 TTTTTATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 19 0.44
52 14 0.33
53 10 0.23
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (53 bp):
TAATAATGCATAATATATAAATTTTAATATATTTATATTAAATTTTAATATAT
Found at i:2682364 original size:32 final size:33
Alignment explanation
Indices: 2682303--2682386 Score: 113
Period size: 32 Copynumber: 2.6 Consensus size: 33
2682293 TAATAATGCA
2682303 TAATATA-TAATATTTATATATTTATATAAATTT
1 TAATATATTAATATTTATATA-TTATATAAATTT
2682336 TAATATATTAATAATTTATA-A-TATATAAATTT
1 TAATATATTAAT-ATTTATATATTATATAAATTT
*
2682368 TAATATATTTATA-TTATAT
1 TAATATATTAATATTTATAT
2682387 TTTAATTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
30 5 0.11
31 1 0.02
32 22 0.47
33 7 0.15
34 5 0.11
35 7 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TAATATATTAATATTTATATATTATATAAATTT
Found at i:2682411 original size:21 final size:21
Alignment explanation
Indices: 2682364--2682409 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
2682354 TAATATATAA
2682364 ATTTTAATATATTTATATTAT
1 ATTTTAATATATTTATATTAT
* *
2682385 ATTTTAAT-TTTTTATATTTT
1 ATTTTAATATATTTATATTAT
2682405 ATTTT
1 ATTTT
2682410 TATTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTAATATATTTATATTAT
Found at i:2682412 original size:13 final size:15
Alignment explanation
Indices: 2682381--2682410 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2682371 TATATTTATA
2682381 TTATATTTTAATTTT
1 TTATATTTTAATTTT
2682396 TTATATTTT-ATTTT
1 TTATATTTTAATTTT
2682410 T
1 T
2682411 ATTAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATATTTTAATTTT
Found at i:2689470 original size:42 final size:42
Alignment explanation
Indices: 2689411--2689492 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
2689401 TTGTTATGTA
*
2689411 TTACTAAATCCCAGGTTCAATTAAATAGTGCATCTTGGTCGG
1 TTACTAAATCCCAGGTTCAATTAAACAGTGCATCTTGGTCGG
* *
2689453 TTACTAAATCCTAGGTTCAGTTAAACAGTGCATCTTGGTC
1 TTACTAAATCCCAGGTTCAATTAAACAGTGCATCTTGGTC
2689493 AGTGAATGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (42 bp):
TTACTAAATCCCAGGTTCAATTAAACAGTGCATCTTGGTCGG
Found at i:2691292 original size:18 final size:18
Alignment explanation
Indices: 2691250--2691292 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2691240 ATCATTGTTT
* *
2691250 TTATCATTATCATTGTCA
1 TTATCTTTATCAATGTCA
* *
2691268 CTGTCTTTATCAATGTCA
1 TTATCTTTATCAATGTCA
2691286 TTATCTT
1 TTATCTT
2691293 AATCTTTATC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (18 bp):
TTATCTTTATCAATGTCA
Found at i:2694912 original size:35 final size:34
Alignment explanation
Indices: 2694872--2694939 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2694862 TTCAATTAGC
*
2694872 TTTATTTAAATTATTATT-TAATAATAAAAAATATT
1 TTTATTTAAATT-TAATTATAA-AATAAAAAATATT
*
2694907 TTTATTTAAATTTAATTATAAAATATAAAATAT
1 TTTATTTAAATTTAATTATAAAATAAAAAATAT
2694940 CAATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 15 0.50
35 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTATTTAAATTTAATTATAAAATAAAAAATATT
Found at i:2698806 original size:2 final size:2
Alignment explanation
Indices: 2698799--2698830 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2698789 CCAGAATAAG
2698799 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
2698831 TATGTAAATA
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:2703693 original size:5 final size:5
Alignment explanation
Indices: 2703683--2703707 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2703673 TTAATTATTA
2703683 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
2703708 CATGGATTGC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:2705082 original size:20 final size:20
Alignment explanation
Indices: 2705057--2705115 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2705047 ATCGTGAGTG
2705057 TTTATTATATTATTTTTGTA
1 TTTATTATATTATTTTTGTA
* *
2705077 TTTATTA-AATA-TTTTATA
1 TTTATTATATTATTTTTGTA
* * *
2705095 TTCATAATTTTATTTTTGTA
1 TTTATTATATTATTTTTGTA
2705115 T
1 T
2705116 CATATTTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 11 0.37
19 5 0.17
20 14 0.47
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTATTATATTATTTTTGTA
Found at i:2707905 original size:15 final size:15
Alignment explanation
Indices: 2707882--2707928 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2707872 TTTTTAATGA
2707882 TAGCAAGTTACCATT
1 TAGCAAGTTACCATT
** **
2707897 TTTCAAGTTACCGCT
1 TAGCAAGTTACCATT
2707912 TAGCAAGTTACCATT
1 TAGCAAGTTACCATT
2707927 TA
1 TA
2707929 AACAAAAATG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (15 bp):
TAGCAAGTTACCATT
Found at i:2708020 original size:17 final size:16
Alignment explanation
Indices: 2708000--2708051 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2707990 TTTAAAATAT
2708000 TTTTATATTTATATAAA
1 TTTTATATTTA-ATAAA
2708017 TTTTAATATATTAAT-AA
1 TTTT-ATAT-TTAATAAA
*
2708034 TTTT-TATTAAATAAA
1 TTTTATATTTAATAAA
2708049 TTT
1 TTT
2708052 AAAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.13
15 8 0.26
17 10 0.32
18 6 0.19
19 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATATTTAATAAA
Found at i:2708025 original size:18 final size:18
Alignment explanation
Indices: 2707998--2708039 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2707988 TGTTTAAAAT
*
2707998 ATTTTTATAT-TTATATAA
1 ATTTTAATATATTA-ATAA
2708016 ATTTTAATATATTAATAA
1 ATTTTAATATATTAATAA
*
2708034 TTTTTA
1 ATTTTA
2708040 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAATATATTAATAA
Found at i:2711337 original size:22 final size:20
Alignment explanation
Indices: 2711289--2711339 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
2711279 TATCATTAAA
* *
2711289 ATTTTTAAAAATAATTTTTT
1 ATTTTTAAAAAAAATTTATT
2711309 ATATTTTAAAAAAAATATTAATT
1 AT-TTTTAAAAAAAAT-TT-ATT
2711332 ATTTTTAA
1 ATTTTTAA
2711340 TTCGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 12 0.46
22 8 0.31
23 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTAAAAAAAATTTATT
Found at i:2714130 original size:22 final size:22
Alignment explanation
Indices: 2714085--2714127 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2714075 TTGAATATCT
*
2714085 TAATATAAAAATATATAAATAA
1 TAATACAAAAATATATAAATAA
2714107 TAATACAAAAAT-TATAAATAA
1 TAATACAAAAATATATAAATAA
2714128 ATATTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATACAAAAATATATAAATAA
Found at i:2714141 original size:25 final size:23
Alignment explanation
Indices: 2714085--2714141 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
2714075 TTGAATATCT
2714085 TAATA-TAAAAATATATAAATAA
1 TAATACTAAAAATATATAAATAA
2714107 TAATAC-AAAAAT-TATAAATAAA
1 TAATACTAAAAATATATAAAT-AA
2714129 TATTATACTAAAA
1 TA--ATACTAAAA
2714142 CAAAATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 7 0.23
22 15 0.50
24 4 0.13
25 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATACTAAAAATATATAAATAA
Found at i:2717640 original size:15 final size:16
Alignment explanation
Indices: 2717602--2717643 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
2717592 AAATTGATTT
2717602 TATTTTAAAATTTAAAA
1 TATTTT-AAATTTAAAA
*
2717619 TAATTTAAATTT-AAA
1 TATTTTAAATTTAAAA
2717634 TATTTTAAAT
1 TATTTTAAAT
2717644 ATCAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 6 0.26
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTTAAATTTAAAA
Found at i:2717665 original size:22 final size:21
Alignment explanation
Indices: 2717624--2717671 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2717614 TAAAATAATT
* * *
2717624 TAAATTTAAATATTTTAAATA
1 TAAATTTAAAAAATTAAAATA
2717645 TCAAATTTAAAAAATTAAAATA
1 T-AAATTTAAAAAATTAAAATA
2717667 TAAAT
1 TAAAT
2717672 AACTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAAAAAATTAAAATA
Found at i:2718001 original size:22 final size:23
Alignment explanation
Indices: 2717974--2718027 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
2717964 ATTAATTCAC
*
2717974 TAAAATAAATATTATA-TAAAAA
1 TAAAATAAATATCATACTAAAAA
* *
2717996 TAAAATAATTATCATACTAATAA
1 TAAAATAAATATCATACTAAAAA
2718019 TAATAATAA
1 TAA-AATAA
2718028 TTTAGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 14 0.52
23 8 0.30
24 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAATAAATATCATACTAAAAA
Found at i:2721764 original size:16 final size:16
Alignment explanation
Indices: 2721743--2721775 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2721733 AGCTGCAAGA
2721743 GGAGCACAGATCTTAT
1 GGAGCACAGATCTTAT
*
2721759 GGAGCACAGGTCTTAT
1 GGAGCACAGATCTTAT
2721775 G
1 G
2721776 TTTGCTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (16 bp):
GGAGCACAGATCTTAT
Found at i:2729010 original size:10 final size:10
Alignment explanation
Indices: 2728995--2729019 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2728985 TAAACTCTAT
2728995 TTAAATACAA
1 TTAAATACAA
2729005 TTAAATACAA
1 TTAAATACAA
2729015 TTAAA
1 TTAAA
2729020 ACATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAATACAA
Found at i:2729112 original size:228 final size:229
Alignment explanation
Indices: 2728713--2729173 Score: 766
Period size: 228 Copynumber: 2.0 Consensus size: 229
2728703 AAAAAAATTT
* * * *
2728713 TGAATACGATAAAAAAAATTGCGTAATATAAAAATTTAATATAAAATTTATTTAAATACAATTAA
1 TGAATACGATAAAAAAAACTACGTAATATAAAAAATTAATATAAAATCTATTTAAATACAATTAA
* *
2728778 ATATAATTAAAATATAAAAAAAAATATAAATATAATATATATTTATATAAATGATTAAATCTATG
66 ATACAATTAAAACATAAAAAAAAATATAAATATAATATATA-TTATATAAATGATTAAATCTATG
2728843 CAGTCCAAAATCCAAAAGAAAGTTGATGCATTCCATAGGAGATCAAGACTCGATTAATATCAATC
130 CAGTCCAAAATCCAAAAGAAAGTTGATGCATTCCATAGGAGATCAAGACTCGATTAATATCAATC
*
2728908 AACAGCAATGTTCATTGTTTGTGTCTACGTTTGCA
195 AACAGCAATGTTCATTGTTTGTGTCTACGTTTACA
* *
2728943 TGAATACGATAAAAAAAACTACATTACATA-AAAAAATTAATATAAACTCTATTTAAATACAATT
1 TGAATACGATAAAAAAAACTAC-GTA-ATATAAAAAATTAATATAAAATCTATTTAAATACAATT
* *
2729007 AAATACAATTAAAACATAAAAAATAATATAAATAT-ATATATA-TATATAAATTATTAAATCTAT
64 AAATACAATTAAAACATAAAAAAAAATATAAATATAATATATATTATATAAATGATTAAATCTAT
*
2729070 GCAGTCCAAAATCCAAAAGAAAGTTGATTCATTCCATAGGAGATCAAGACTCGATTAATATCAAT
129 GCAGTCCAAAATCCAAAAGAAAGTTGATGCATTCCATAGGAGATCAAGACTCGATTAATATCAAT
2729135 CAACAGCAATGTTCATTGTTTGTGTCTACGTTTACA
194 CAACAGCAATGTTCATTGTTTGTGTCTACGTTTACA
2729171 TGA
1 TGA
2729174 TAAAATCAAT
Statistics
Matches: 217, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
228 122 0.56
230 27 0.12
231 65 0.30
232 3 0.01
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (229 bp):
TGAATACGATAAAAAAAACTACGTAATATAAAAAATTAATATAAAATCTATTTAAATACAATTAA
ATACAATTAAAACATAAAAAAAAATATAAATATAATATATATTATATAAATGATTAAATCTATGC
AGTCCAAAATCCAAAAGAAAGTTGATGCATTCCATAGGAGATCAAGACTCGATTAATATCAATCA
ACAGCAATGTTCATTGTTTGTGTCTACGTTTACA
Found at i:2733343 original size:11 final size:11
Alignment explanation
Indices: 2733316--2733349 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2733306 AAATAATTTT
*
2733316 TAAATA-ATTT
1 TAAATATATTA
2733326 TAAATATATTA
1 TAAATATATTA
2733337 TAAATATATTA
1 TAAATATATTA
2733348 TA
1 TA
2733350 TTTAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATATATTA
Found at i:2745054 original size:23 final size:23
Alignment explanation
Indices: 2745026--2745074 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2745016 TATAATTATT
2745026 TTTAAAAATTAATATTTA-ATATA
1 TTTAAAAATTAATATTTATA-ATA
* *
2745049 TTTAAAATTTATTATTTATAATA
1 TTTAAAAATTAATATTTATAATA
2745072 TTT
1 TTT
2745075 TTTTATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAAAATTAATATTTATAATA
Found at i:2745745 original size:5 final size:5
Alignment explanation
Indices: 2745729--2745762 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2745719 AAAATTACCA
*
2745729 GCCAG GCTAG GCCAG GCCAG GCCAG GCCAG GCCA
1 GCCAG GCCAG GCCAG GCCAG GCCAG GCCAG GCCA
2745763 TCTTTGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.38, G:0.38, T:0.03
Consensus pattern (5 bp):
GCCAG
Found at i:2745907 original size:6 final size:6
Alignment explanation
Indices: 2745896--2745929 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2745886 TTACGGTAGG
2745896 TAAATA TAAATA TAAATA T-AATA T-AATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
2745930 ATTAAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:2745920 original size:17 final size:17
Alignment explanation
Indices: 2745898--2745972 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 17
2745888 ACGGTAGGTA
2745898 AATATAAATATAAATAT
1 AATATAAATATAAATAT
2745915 AATAT-AATATAAATA-
1 AATATAAATATAAATAT
* *
2745930 ATTA-AAGATATTAATAT
1 AATATAA-ATATAAATAT
*
2745947 --TATAAATATAATTAT
1 AATATAAATATAAATAT
*
2745962 AATATATATAT
1 AATATAAATAT
2745973 TAAACATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 14 0.30
16 20 0.43
17 13 0.28
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (17 bp):
AATATAAATATAAATAT
Done.