Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 25 of 25
Found at i:3748772 original size:14 final size:14
Alignment explanation
Indices: 3748753--3748791 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3748743 AATAAAATAT
3748753 AATATAATATTAAA
1 AATATAATATTAAA
3748767 AATATAATA-TAAA
1 AATATAATATTAAA
*
3748780 TATATAAATATT
1 AATAT-AATATT
3748792 TTAAAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 8 0.36
14 13 0.59
15 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATAATATTAAA
Found at i:3748805 original size:33 final size:33
Alignment explanation
Indices: 3748744--3748885 Score: 113
Period size: 32 Copynumber: 4.5 Consensus size: 33
3748734 TAAGATAAGA
3748744 ATAAA-ATATAATATAATATTAAAA---ATATAAT
1 ATAAATATATAA-AT-ATATTAAAATTGATATAAT
* *
3748775 ATAAATATATAAATATTTTAAAATTGATATAAA
1 ATAAATATATAAATATATTAAAATTGATATAAT
* * *
3748808 ATAAAT-TATTAATATATTAAAATTTATAAAAAT
1 ATAAATATATAAATATATTAAAATTGAT-ATAAT
* **
3748841 ATAAATATTTAAATATAATTTTAA-T-ATA-AAT
1 ATAAATATATAAATAT-ATTAAAATTGATATAAT
3748872 A-AAATATATAAATA
1 ATAAATATATAAATA
3748886 AATACACTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
30 20 0.22
31 11 0.12
32 25 0.27
33 23 0.25
34 8 0.09
35 5 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (33 bp):
ATAAATATATAAATATATTAAAATTGATATAAT
Found at i:3748828 original size:32 final size:33
Alignment explanation
Indices: 3748738--3748857 Score: 115
Period size: 32 Copynumber: 3.7 Consensus size: 33
3748728 AGTTAATAAG
3748738 ATAAGAATAAA-ATATAATATAATATTAAAA---AT
1 ATAA-AATAAATATATAA-AT-ATATTAAAATTGAT
* *
3748770 ATAATATAAATATATAAATATTTTAAAATTGAT
1 ATAAAATAAATATATAAATATATTAAAATTGAT
* *
3748803 ATAAAATAAAT-TATTAATATATTAAAATTTAT
1 ATAAAATAAATATATAAATATATTAAAATTGAT
* *
3748835 AAAAATATAAATATTTAAATATA
1 ATAAA-ATAAATATATAAATATA
3748858 ATTTTAATAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
30 8 0.11
31 7 0.10
32 32 0.44
33 18 0.25
34 8 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (33 bp):
ATAAAATAAATATATAAATATATTAAAATTGAT
Found at i:3751842 original size:15 final size:15
Alignment explanation
Indices: 3751822--3751854 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3751812 GCTTCCACCT
3751822 TAGAAAGAAATATGA
1 TAGAAAGAAATATGA
3751837 TAGAAAGAAATATGA
1 TAGAAAGAAATATGA
3751852 TAG
1 TAG
3751855 CTTTGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
TAGAAAGAAATATGA
Found at i:3754974 original size:10 final size:10
Alignment explanation
Indices: 3754961--3755094 Score: 63
Period size: 10 Copynumber: 13.7 Consensus size: 10
3754951 TATTTTTGTG
*
3754961 TTATCTTTTA
1 TTATATTTTA
3754971 TTATATTTTA
1 TTATATTTTA
3754981 -TATA--TTA
1 TTATATTTTA
3754988 -TA-ATTTTA
1 TTATATTTTA
***
3754996 TT-TAAGATA
1 TTATATTTTA
*
3755005 TTAAATATTTA
1 TTATAT-TTTA
*
3755016 TATAAATTTTA
1 T-TATATTTTA
3755027 --ATATTTGTA
1 TTATATTT-TA
3755036 -TATATTTATA
1 TTATATTT-TA
*
3755046 TTATTTTTTA
1 TTATATTTTA
*
3755056 TTTTATTTTAA
1 TTATATTTT-A
3755067 TTAT-TTTATA
1 TTATATTT-TA
3755077 TTATATTTATA
1 TTATATTT-TA
3755088 TTATATT
1 TTATATT
3755095 GTCATTTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 25
0.71 0.10 0.18
Matches are distributed among these distances:
6 1 0.01
7 5 0.05
8 8 0.08
9 12 0.12
10 35 0.36
11 31 0.32
12 5 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TTATATTTTA
Found at i:3755031 original size:18 final size:18
Alignment explanation
Indices: 3754973--3755042 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
3754963 ATCTTTTATT
* *
3754973 ATATTT-TATATATTATA
1 ATATTTATATAAATTTTA
* *
3754990 AT-TTTATTTAAGATATTAA
1 ATATTTATATAA-AT-TTTA
3755009 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
* *
3755027 ATATTTGTATATATTT
1 ATATTTATATAAATTT
3755043 ATATTATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
16 3 0.07
17 5 0.12
18 19 0.46
19 6 0.15
20 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:3755063 original size:21 final size:21
Alignment explanation
Indices: 3755036--3755091 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
3755026 AATATTTGTA
*
3755036 TATATTTATATTATTTTTTAT
1 TATATTTATATTATTTTATAT
*
3755057 TTTATTT-TAATTATTTTATAT
1 TATATTTAT-ATTATTTTATAT
3755078 TATATTTATATTAT
1 TATATTTATATTAT
3755092 ATTGTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TATATTTATATTATTTTATAT
Found at i:3755770 original size:9 final size:9
Alignment explanation
Indices: 3755758--3755783 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3755748 ACTAATTATA
3755758 TAAATTAAT
1 TAAATTAAT
3755767 TAAATTAAT
1 TAAATTAAT
3755776 TAAATTAA
1 TAAATTAA
3755784 ATTTTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAATTAAT
Found at i:3758447 original size:33 final size:32
Alignment explanation
Indices: 3758400--3758486 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 32
3758390 AATAGATAAT
* *
3758400 TTAAAAATAATATAAAATAAA-TATTAAAAAAA
1 TTAAAATTTATATAAAATAAATTATT-AAAAAA
* * **
3758432 TTAAAATTTTATATAATATAAATTATTATAATC
1 TTAAAA-TTTATATAAAATAAATTATTAAAAAA
3758465 TTAAAATTTATATAAATATAAA
1 TTAAAATTTATATAAA-ATAAA
3758487 ATAATTATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 15 0.33
33 26 0.58
34 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TTAAAATTTATATAAAATAAATTATTAAAAAA
Found at i:3758453 original size:17 final size:16
Alignment explanation
Indices: 3758433--3758501 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
3758423 TTAAAAAAAT
*
3758433 TAAAATTTTATATAATA
1 TAAAATTAT-TATAATA
*
3758450 T-AAATTATTATAATCT
1 TAAAATTATTATAAT-A
3758466 TAAAATT-TATATAAATA
1 TAAAATTAT-TAT-AATA
*
3758483 TAAAATAATTATAATA
1 TAAAATTATTATAATA
3758499 TAA
1 TAA
3758502 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
15 6 0.14
16 15 0.35
17 18 0.42
18 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTATTATAATA
Found at i:3759199 original size:14 final size:15
Alignment explanation
Indices: 3759180--3759209 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3759170 AATTTAAGAT
*
3759180 AAAAAATTTTAATAA
1 AAAAAACTTTAATAA
3759195 AAAAAACTTTAATAA
1 AAAAAACTTTAATAA
3759210 TAATATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAACTTTAATAA
Found at i:3760243 original size:23 final size:24
Alignment explanation
Indices: 3760172--3760247 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
3760162 TGTCATGTTC
3760172 ATATTATAATCATGTTAAAATATTAT
1 ATATTATAAT-ATGTTAAAATATT-T
* *
3760198 ATATTTTAATATGTTAATA-ATTT
1 ATATTATAATATGTTAAAATATTT
* *
3760221 ATGTTATAA-ATTTTAAAATATTT
1 ATATTATAATATGTTAAAATATTT
3760244 ATAT
1 ATAT
3760248 ATTCATAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 7 0.17
23 15 0.36
24 3 0.07
25 8 0.19
26 9 0.21
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATTATAATATGTTAAAATATTT
Found at i:3760265 original size:20 final size:20
Alignment explanation
Indices: 3760242--3760283 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3760232 TTTAAAATAT
3760242 TTATATATTCATAATATT-TA
1 TTATATATT-ATAATATTATA
* *
3760262 TTATTTATTATTATATTATA
1 TTATATATTATAATATTATA
3760282 TT
1 TT
3760284 TTAATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATATTATAATATTATA
Found at i:3760276 original size:48 final size:47
Alignment explanation
Indices: 3760172--3760276 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 47
3760162 TGTCATGTTC
* *
3760172 ATATTATAATCATGTTAAAATATTATATATTTTAATATGTTAATAATTT
1 ATATTATAA--ATTTTAAAATATTATATATTATAATATGTTAATAATTT
* *
3760221 ATGTTATAAATTTTAAAATATTTATATATTCATAATAT-TT-ATTATTT
1 ATATTATAAATTTTAAAATA-TTATATATT-ATAATATGTTAATAATTT
3760268 ATTATTATA
1 A-TATTATA
3760277 TTATATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
47 17 0.35
48 17 0.35
49 14 0.29
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (47 bp):
ATATTATAAATTTTAAAATATTATATATTATAATATGTTAATAATTT
Found at i:3760591 original size:3 final size:3
Alignment explanation
Indices: 3760577--3760623 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
3760567 CCTAATTACA
* *
3760577 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TCAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
3760623 T
1 T
3760624 TACAGGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3760814 original size:22 final size:24
Alignment explanation
Indices: 3760770--3760823 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
3760760 GTATAATATT
3760770 ATTTAATTAATAAAAAATTTATTTAA
1 ATTTAATTAATAAAAAA-TTA-TTAA
3760796 ATTTAATT-AT-AAAAA-TATTAA
1 ATTTAATTAATAAAAAATTATTAA
3760817 ATATTAA
1 AT-TTAA
3760824 ATAAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.22
22 6 0.22
24 5 0.19
25 2 0.07
26 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAATTAATAAAAAATTATTAA
Found at i:3764536 original size:18 final size:17
Alignment explanation
Indices: 3764518--3764562 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3764508 AATATATTTA
3764518 AATATTATTATATAATT
1 AATATTATTATATAATT
*
3764535 AATATTA-TATGT--TT
1 AATATTATTATATAATT
3764549 AATATATATTATAT
1 AATAT-TATTATAT
3764563 TTATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 7 0.29
15 2 0.08
16 8 0.33
17 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTATTATATAATT
Found at i:3764553 original size:23 final size:24
Alignment explanation
Indices: 3764526--3764582 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
3764516 TAAATATTAT
3764526 TATATAATTA-ATATTATATGTTTAA
1 TATAT-ATTATAT-TTATATGTTTAA
*
3764551 TATATATTATATTTATATTTTTAA
1 TATATATTATATTTATATGTTTAA
3764575 GTATATAT
1 -TATATAT
3764583 ATTTTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATATTATATTTATATGTTTAA
Found at i:3764604 original size:25 final size:25
Alignment explanation
Indices: 3764510--3764605 Score: 68
Period size: 25 Copynumber: 3.7 Consensus size: 25
3764500 AAAAAAATAA
* **
3764510 TATATTTAAATATTAT-TATATAATT
1 TATATTTATAT-TTATATATATTTTT
* *
3764535 AATATTATATGTTTAATATATATTATATT
1 TATATT-TATATTT-ATATATATT-T-TT
* **
3764564 TATATTTTTAAGTATATATATTTTT
1 TATATTTATATTTATATATATTTTT
3764589 TATATTTATATTTATAT
1 TATATTTATATTTATAT
3764606 GATAATAAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
25 23 0.43
26 6 0.11
27 14 0.26
28 3 0.06
29 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TATATTTATATTTATATATATTTTT
Found at i:3764782 original size:21 final size:21
Alignment explanation
Indices: 3764758--3764818 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 21
3764748 AATTTTTTAA
3764758 ATTTATATCAAATATTATATT
1 ATTTATATCAAATATTATATT
*
3764779 ATTTA-A-CTAAATA-TATGTT
1 ATTTATATC-AAATATTATATT
3764798 -TTTAT-T-AAATATT-TATT
1 ATTTATATCAAATATTATATT
3764815 ATTT
1 ATTT
3764819 TAATATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 6 0.18
20 6 0.18
21 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTATATCAAATATTATATT
Found at i:3765354 original size:2 final size:2
Alignment explanation
Indices: 3765347--3765375 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3765337 GTTGACGTTC
3765347 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3765376 TAAAATTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3766860 original size:24 final size:24
Alignment explanation
Indices: 3766833--3766910 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 24
3766823 TATATTTAAA
3766833 ATATTATTTATTTTTTATATATTT
1 ATATTATTTATTTTTTATATATTT
** *
3766857 ATATTAAGTATATTTTAATATATTAAT
1 ATATTATTTAT-TTTTTATATATT--T
*
3766884 ATATTTATATAATTTTTTATATTATTT
1 ATA-TTAT-TTATTTTTTATA-TATTT
3766911 TTAATTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 9 0.22
25 11 0.27
27 5 0.12
28 10 0.24
29 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (24 bp):
ATATTATTTATTTTTTATATATTT
Found at i:3766870 original size:33 final size:32
Alignment explanation
Indices: 3766817--3766893 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
3766807 ATATTGATAT
* * *
3766817 TATATTTATATTTAAAATATTATTTAT-TTTTTA
1 TATATTTATA-TTAAAATATT-TTAATATATTAA
*
3766850 TATATTTATATTAAGTATATTTTAATATATTAA
1 TATATTTATATTAA-AATATTTTAATATATTAA
3766883 TATATTTATAT
1 TATATTTATAT
3766894 AATTTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 8 0.21
33 30 0.79
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
TATATTTATATTAAAATATTTTAATATATTAA
Found at i:3767181 original size:23 final size:23
Alignment explanation
Indices: 3767132--3767181 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3767122 CAAATAAATT
*
3767132 TAATAATTTTAAATATAATTATA
1 TAATAATTTTAAATATAATAATA
* *
3767155 TAATTATTTTATATATAA-AATA
1 TAATAATTTTAAATATAATAATA
3767177 CTAAT
1 -TAAT
3767182 GATATAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATAATTTTAAATATAATAATA
Found at i:3767221 original size:15 final size:15
Alignment explanation
Indices: 3767183--3767249 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 15
3767173 AATACTAATG
3767183 ATATAATATAAA--T
1 ATATAATATAAATTT
3767196 ATATAA-A-AAATTT
1 ATATAATATAAATTT
3767209 ATATAATATAAA-TT
1 ATATAATATAAATTT
* **
3767223 AT-GAA-ATAAATAA
1 ATATAATATAAATTT
3767236 ATATAATATAAATT
1 ATATAATATAAATT
3767250 ATTAAATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 3 0.07
12 6 0.14
13 17 0.40
14 7 0.17
15 9 0.21
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (15 bp):
ATATAATATAAATTT
Found at i:3767241 original size:27 final size:26
Alignment explanation
Indices: 3767183--3767256 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 26
3767173 AATACTAATG
**
3767183 ATATAATATAAATATATAAA-AAATTT
1 ATATAATATAAAT-TATAAATAAATAA
3767209 ATATAATATAAATTATGAAATAAATAA
1 ATATAATATAAATTAT-AAATAAATAA
3767236 ATATAATATAAATTATTAAAT
1 ATATAATATAAATTA-TAAAT
3767257 TTAGTCTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 3 0.07
26 16 0.37
27 23 0.53
28 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (26 bp):
ATATAATATAAATTATAAATAAATAA
Found at i:3769322 original size:2 final size:2
Alignment explanation
Indices: 3769315--3769346 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3769305 ATTACTTTGG
3769315 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
3769347 TCATTATACC
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:3769917 original size:12 final size:12
Alignment explanation
Indices: 3769900--3769942 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
3769890 GGATTTTTTA
3769900 TTTTTTTAATAT
1 TTTTTTTAATAT
3769912 TTTTTTTAATAT
1 TTTTTTTAATAT
3769924 TTTTGTCTTATATAT
1 TTTT-T-TTA-ATAT
3769939 TTTT
1 TTTT
3769943 ATGTACGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.57
13 1 0.04
14 3 0.11
15 8 0.29
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTTTAATAT
Found at i:3774936 original size:38 final size:38
Alignment explanation
Indices: 3774880--3774973 Score: 161
Period size: 38 Copynumber: 2.5 Consensus size: 38
3774870 AATTTTACAT
*
3774880 TCAGCTCATGCTCTTAATGCAAAAGCAAGTTACCAGAG
1 TCAGCTCATGCTCTTAATGCAAAAGCAAGTAACCAGAG
* *
3774918 TCAGGTCATGCTCTTAATGCAAAAGCGAGTAACCAGAG
1 TCAGCTCATGCTCTTAATGCAAAAGCAAGTAACCAGAG
3774956 TCAGCTCATGCTCTTAAT
1 TCAGCTCATGCTCTTAAT
3774974 TGGCACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (38 bp):
TCAGCTCATGCTCTTAATGCAAAAGCAAGTAACCAGAG
Found at i:3775426 original size:2 final size:2
Alignment explanation
Indices: 3775415--3775452 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3775405 GGAATGTCTA
3775415 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3775453 ATGCAACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3776011 original size:25 final size:23
Alignment explanation
Indices: 3775969--3776024 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
3775959 ATTAATTATA
*
3775969 TAAATATAAATATAATAAAATTT
1 TAAATATAAATATAATAAAATGT
* *
3775992 TAAATATAAATGTGACATAATATGT
1 TAAATATAAATAT-A-ATAAAATGT
3776017 TAAATATA
1 TAAATATA
3776025 TTATATTAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 12 0.43
24 1 0.04
25 15 0.54
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
TAAATATAAATATAATAAAATGT
Found at i:3776053 original size:29 final size:29
Alignment explanation
Indices: 3776009--3776089 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
3775999 AAATGTGACA
3776009 TAATATGTTAAATATATTATATTAGCTGTAT
1 TAATAT-TT-AATATATTATATTAGCTGTAT
* *
3776040 TAATATTTAATATATT-TATTATCTTTAT
1 TAATATTTAATATATTATATTAGCTGTAT
*
3776068 TAAATATATAATAT-TTATATTA
1 T-AATATTTAATATATTATATTA
3776090 TAAATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 13 0.29
29 24 0.53
30 2 0.04
31 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (29 bp):
TAATATTTAATATATTATATTAGCTGTAT
Found at i:3776346 original size:11 final size:12
Alignment explanation
Indices: 3776304--3776348 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
3776294 CTTTAGAAAA
3776304 AAAT-TTAATTAT
1 AAATATTAA-TAT
3776316 AAATA-T-ATAT
1 AAATATTAATAT
3776326 AAATATTAATAT
1 AAATATTAATAT
3776338 AAA-ATTAATAT
1 AAATATTAATAT
3776349 TTTAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.27
11 10 0.33
12 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:3776396 original size:30 final size:29
Alignment explanation
Indices: 3776324--3776410 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 29
3776314 ATAAATATAT
* *
3776324 ATAAATATTAATATAAAATTAATATTTTA
1 ATAAATATAAATATAAAATAAATATTTTA
3776353 ATAATATATTAAATAATAAAATAAAT-TTTTA
1 ATAA-ATA-TAAAT-ATAAAATAAATATTTTA
* * *
3776384 AGTCAATATAAAT-TTAAATAAAAATTT
1 A-TAAATATAAATATAAAATAAATATTT
3776411 ATAAAATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
28 8 0.17
29 7 0.15
30 8 0.17
31 13 0.27
32 12 0.25
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
ATAAATATAAATATAAAATAAATATTTTA
Found at i:3776401 original size:36 final size:35
Alignment explanation
Indices: 3776317--3776404 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 35
3776307 TTTAATTATA
*
3776317 AATATATATAAATATT-AAT-ATAAAATTAATATTTT
1 AATA-ATATAAAT-TTAAATAATAAAATAAATATTTT
3776352 AATAATAT--A-TTAAATAATAAAATAAAT-TTTT
1 AATAATATAAATTTAAATAATAAAATAAATATTTT
3776383 AAGTCAATATAAATTTAAATAA
1 AA-T-AATATAAATTTAAATAA
3776405 AAATTTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
30 2 0.04
31 9 0.20
32 12 0.27
33 5 0.11
34 4 0.09
35 5 0.11
36 8 0.18
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (35 bp):
AATAATATAAATTTAAATAATAAAATAAATATTTT
Found at i:3777112 original size:2 final size:2
Alignment explanation
Indices: 3777105--3777131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3777095 AACATGAACA
3777105 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3777132 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3777175 original size:2 final size:2
Alignment explanation
Indices: 3777131--3777156 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3777121 TCTCTCTCTC
3777131 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
3777157 CTTAAGTTAG
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):
TA
Found at i:3780609 original size:2 final size:2
Alignment explanation
Indices: 3780602--3780636 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3780592 TCAAATTAGA
3780602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3780637 AAACATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3781138 original size:15 final size:15
Alignment explanation
Indices: 3781120--3781181 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
3781110 ATATATTATT
3781120 ATAATTATAAAAATA
1 ATAATTATAAAAATA
* * *
3781135 ATAAATATTAATATA
1 ATAATTATAAAAATA
3781150 ATTAATTATAATAAATA
1 A-TAATTATAA-AAATA
* *
3781167 TTAATAATTAAAAAT
1 ATAATTA-TAAAAAT
3781182 TTAAAATTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 13 0.36
16 16 0.44
17 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATTATAAAAATA
Found at i:3781173 original size:13 final size:13
Alignment explanation
Indices: 3781131--3781174 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3781121 TAATTATAAA
3781131 AATAATAAATATT
1 AATAATAAATATT
*
3781144 AAT-ATAATTAATT
1 AATAATAAAT-ATT
3781157 -ATAATAAATATT
1 AATAATAAATATT
3781169 AATAAT
1 AATAAT
3781175 TAAAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAATAAATATT
Found at i:3781412 original size:12 final size:12
Alignment explanation
Indices: 3781397--3781436 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3781387 TTGCATTAAA
3781397 ATTTATTATTAT
1 ATTTATTATTAT
3781409 ATTT-TTATTAAT
1 ATTTATTATT-AT
*
3781421 ATTTATCATTAT
1 ATTTATTATTAT
3781433 ATTT
1 ATTT
3781437 TTAACTCTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 5 0.20
12 16 0.64
13 4 0.16
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATTATTAT
Found at i:3781412 original size:24 final size:24
Alignment explanation
Indices: 3781385--3781436 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3781375 AAAAAGGTAA
*
3781385 ATTTGCATTAAAATTTATTATTAT
1 ATTTGCATTAAAATTTATCATTAT
** *
3781409 ATTTTTATTAATATTTATCATTAT
1 ATTTGCATTAAAATTTATCATTAT
3781433 ATTT
1 ATTT
3781437 TTAACTCTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTGCATTAAAATTTATCATTAT
Found at i:3781437 original size:24 final size:24
Alignment explanation
Indices: 3781391--3781439 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3781381 GTAAATTTGC
*
3781391 ATTAAAATTTATTATTATATTTTT
1 ATTAAAATTTATCATTATATTTTT
*
3781415 ATTAATATTTATCATTATATTTTT
1 ATTAAAATTTATCATTATATTTTT
3781439 A
1 A
3781440 ACTCTACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTAAAATTTATCATTATATTTTT
Found at i:3790324 original size:2 final size:2
Alignment explanation
Indices: 3790317--3790356 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3790307 GCTATCTTGC
3790317 AT AT 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
3790357 TGTGCTGGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3795408 original size:16 final size:17
Alignment explanation
Indices: 3795382--3795414 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3795372 GAACTCAAGC
*
3795382 TTTATTAATTTTAATTT
1 TTTATTAATTTAAATTT
3795399 TTTA-TAATTTAAATTT
1 TTTATTAATTTAAATTT
3795415 GATTAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTAATTTAAATTT
Found at i:3799003 original size:2 final size:2
Alignment explanation
Indices: 3798996--3799029 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3798986 TTGTCAACAA
3798996 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
3799030 TTTATACAAA
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:3801526 original size:2 final size:2
Alignment explanation
Indices: 3801519--3801556 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3801509 ACAAAATTAC
* *
3801519 AT AT AT AT AT AT AT AT AT AC AC 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
3801557 TTGCTTTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3801800 original size:22 final size:20
Alignment explanation
Indices: 3801775--3801818 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
3801765 GAAAGATGAG
*
3801775 TATTGGATACAAATAAATATTT
1 TATTGAATA-AAATAAAT-TTT
*
3801797 TATTGAATATAATAAATTTT
1 TATTGAATAAAATAAATTTT
3801817 TA
1 TA
3801819 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
TATTGAATAAAATAAATTTT
Found at i:3802186 original size:2 final size:2
Alignment explanation
Indices: 3802174--3802210 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3802164 TTCACTTGCT
*
3802174 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3802211 TCCATTTGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3806126 original size:19 final size:19
Alignment explanation
Indices: 3806085--3806127 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3806075 GCGTGATTTT
* *
3806085 TATTTTAAAAACAATATTC
1 TATTTTAAAAACAATAATA
* *
3806104 TATTTTATAAATAATAATA
1 TATTTTAAAAACAATAATA
3806123 TATTT
1 TATTT
3806128 AAGTTTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTTTAAAAACAATAATA
Found at i:3806594 original size:15 final size:15
Alignment explanation
Indices: 3806571--3806613 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3806561 ATTTAAATCA
3806571 ATTTAATTTAAATATT
1 ATTT-ATTTAAATATT
*
3806587 ATTTATTTATTATATT
1 ATTTATTTA-AATATT
3806603 -TTTATTTAAAT
1 ATTTATTTAAAT
3806614 TTAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTATTTAAATATT
Found at i:3806882 original size:19 final size:19
Alignment explanation
Indices: 3806860--3806915 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3806850 TAAATAAAAG
3806860 TATATTATATTAATATTTA
1 TATATTATATTAATATTTA
* *
3806879 TATATTTTA-TAATTATATA
1 TATATTATATTAA-TATTTA
* *
3806898 TATAATAAATTAATATTT
1 TATATTATATTAATATTT
3806916 TATTAAATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTATATTAATATTTA
Found at i:3806896 original size:15 final size:16
Alignment explanation
Indices: 3806876--3806923 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
3806866 ATATTAATAT
3806876 TTATATATTTTAT-AA
1 TTATATATTTTATAAA
* *
3806891 TTATATATATAATAAA
1 TTATATATTTTATAAA
3806907 TTA-ATATTTTATTAAA
1 TTATATATTTTA-TAAA
3806923 T
1 T
3806924 GAATATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATTTTATAAA
Found at i:3807832 original size:17 final size:16
Alignment explanation
Indices: 3807810--3807844 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3807800 TTATATTAAA
3807810 TAAATATTGATTTAATT
1 TAAATATTGATTT-ATT
*
3807827 TAAATATTTATTTATT
1 TAAATATTGATTTATT
3807843 TA
1 TA
3807845 TAAATTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TAAATATTGATTTATT
Found at i:3807867 original size:30 final size:29
Alignment explanation
Indices: 3807828--3807901 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
3807818 GATTTAATTT
* * * *
3807828 AAATATTTATTTATTTATAAATTAAAGATTA
1 AAAT-TTTATTTA-ATATAAAATAAAAATAA
3807859 AAATTTTATTTGAATATAAAATAAAAATAA
1 AAATTTTATTT-AATATAAAATAAAAATAA
3807889 AAATTTTATTTAA
1 AAATTTTATTTAA
3807902 GTGTGATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 2 0.05
30 31 0.82
31 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
AAATTTTATTTAATATAAAATAAAAATAA
Found at i:3808286 original size:83 final size:84
Alignment explanation
Indices: 3808141--3808306 Score: 244
Period size: 83 Copynumber: 2.0 Consensus size: 84
3808131 CAATCAAAAC
* * * * *
3808141 CCGTGTTCTATCCTCTGCTATCTCTATAGCCACTCTCCCCTTCAGATCTACCAATAATACCTCGC
1 CCGTGTTCGATCCTCTGCTATCTCTATAGACACTCTCCCCTACAGATCAACCAATAACACCTCGC
3808206 CACATCACCATCTTAACTA
66 CACATCACCATCTTAACTA
* * **
3808225 CCGTGTTCGATTCTCTGCT-TCTCTATCGATTCTCTCCCCTACAGATCAACCAATAACACCTCGC
1 CCGTGTTCGATCCTCTGCTATCTCTATAGACACTCTCCCCTACAGATCAACCAATAACACCTCGC
3808289 CACATCACCATCTTAACT
66 CACATCACCATCTTAACT
3808307 CCATCCATCA
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 56 0.77
84 17 0.23
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (84 bp):
CCGTGTTCGATCCTCTGCTATCTCTATAGACACTCTCCCCTACAGATCAACCAATAACACCTCGC
CACATCACCATCTTAACTA
Found at i:3809275 original size:18 final size:18
Alignment explanation
Indices: 3809252--3809293 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3809242 TGGACTTGTC
*
3809252 ATTTTCGTTGAATTATTT
1 ATTTTCGTTGAAGTATTT
*
3809270 ATTTTCTTTGAAGTATTT
1 ATTTTCGTTGAAGTATTT
3809288 ATTTTC
1 ATTTTC
3809294 AACATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (18 bp):
ATTTTCGTTGAAGTATTT
Found at i:3809313 original size:16 final size:16
Alignment explanation
Indices: 3809292--3809323 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3809282 GTATTTATTT
*
3809292 TCAACATATATTTGAA
1 TCAACACATATTTGAA
3809308 TCAACACATATTTGAA
1 TCAACACATATTTGAA
3809324 CTGTGAGAAC
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:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (16 bp):
TCAACACATATTTGAA
Found at i:3810514 original size:76 final size:76
Alignment explanation
Indices: 3810379--3810529 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 76
3810369 CAATGTAATA
* * * * *
3810379 TAAAATTATTTTAAGAAATTTAAATTTTGTAATGTTATATAACTGAATTACTATTATAATTATTT
1 TAAAATTATTTTAAGAAAATCAAATTTTATAATGTTATATAACTAAATTACTATCATAATTATTT
3810444 TATTT-TATTTT
66 T-TTTCTATTTT
* *
3810455 TAAAATTATTTTAA-AAAGATCAAATTTTATAATGTTATATAATTAAATTTCTATCATAATTATT
1 TAAAATTATTTTAAGAAA-ATCAAATTTTATAATGTTATATAACTAAATTACTATCATAATTATT
3810519 TTTTTCTATTT
65 TTTTTCTATTT
3810530 CTCCTAAGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 6 0.09
76 60 0.91
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (76 bp):
TAAAATTATTTTAAGAAAATCAAATTTTATAATGTTATATAACTAAATTACTATCATAATTATTT
TTTTCTATTTT
Found at i:3810834 original size:15 final size:14
Alignment explanation
Indices: 3810803--3810844 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3810793 TAATTTAAGA
*
3810803 TAAAATTTAAATTAT
1 TAAAATTT-ATTTAT
3810818 TAAAATTTATTTGAT
1 TAAAATTTATTT-AT
3810833 T-AAATTTATTTA
1 TAAAATTTATTTA
3810845 CTTAGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 1 0.04
14 13 0.52
15 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TAAAATTTATTTAT
Found at i:3811001 original size:21 final size:22
Alignment explanation
Indices: 3810935--3811007 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 22
3810925 TTTTCATATT
* *
3810935 AATTAAATTTTTTAAAAATTT-
1 AATTAAATTATTTAAATATTTA
* * * *
3810956 AATTAAATTAATTAACTACTGA
1 AATTAAATTATTTAAATATTTA
3810978 AATTAAA-TATTTAAATATTTA
1 AATTAAATTATTTAAATATTTA
*
3810999 AATTTAATT
1 AATTAAATT
3811008 CGATTTATAA
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
21 31 0.79
22 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (22 bp):
AATTAAATTATTTAAATATTTA
Found at i:3811463 original size:19 final size:18
Alignment explanation
Indices: 3811436--3811474 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3811426 TCATATTCAA
* *
3811436 TTTTTTTTAATTTTTAAT
1 TTTTTTTTAAATTTAAAT
3811454 TTTTTATTTAAATTTAAAT
1 TTTTT-TTTAAATTTAAAT
3811473 TT
1 TT
3811475 AAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTTAAATTTAAAT
Found at i:3816674 original size:26 final size:25
Alignment explanation
Indices: 3816621--3816674 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3816611 AATTTTTATG
* *
3816621 ATAAATTATATAAAATATAAAATGA
1 ATAAATTATATAAAAAATAAAATAA
* *
3816646 ATAAATTTTGATAAAAAATAATATAA
1 ATAAATTAT-ATAAAAAATAAAATAA
3816672 ATA
1 ATA
3816675 TGTCATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
ATAAATTATATAAAAAATAAAATAA
Found at i:3816700 original size:17 final size:19
Alignment explanation
Indices: 3816661--3816700 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3816651 TTTTGATAAA
3816661 AAATAATATAAATATGTCAT
1 AAATAATATAAATATGT-AT
3816681 AAAT-ATATAAATATGT-T
1 AAATAATATAAATATGTAT
3816698 AAA
1 AAA
3816701 ATTTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATAATATAAATATGTAT
Found at i:3817924 original size:16 final size:16
Alignment explanation
Indices: 3817905--3817936 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3817895 CAAATTTTGT
*
3817905 GTTTTTTATTTTTTTA
1 GTTTTTTATTCTTTTA
3817921 GTTTTTTATTCTTTTA
1 GTTTTTTATTCTTTTA
3817937 TTAAATTTAT
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:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (16 bp):
GTTTTTTATTCTTTTA
Found at i:3820596 original size:18 final size:18
Alignment explanation
Indices: 3820573--3820608 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3820563 TAATTTAATC
3820573 TAAATAAAAATAAAATTT
1 TAAATAAAAATAAAATTT
*
3820591 TAAATAAAAATATAATTT
1 TAAATAAAAATAAAATTT
3820609 ATTATCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATAAAAATAAAATTT
Found at i:3821736 original size:30 final size:28
Alignment explanation
Indices: 3821702--3821795 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 28
3821692 TTATCACGTC
3821702 TAAATAAATTTTAATTTTTTTAATTTATAT
1 TAAATAAATTTTAA--TTTTTAATTTATAT
*
3821732 TAAATAAATACTTAATTTTTAATTTATAT
1 TAAATAAAT-TTTAATTTTTAATTTATAT
*
3821761 CTAAATAAACTTTTAATATTTAATTTATACT
1 -TAAATAAA-TTTTAATTTTTAATTTATA-T
3821792 TAAA
1 TAAA
3821796 AATTTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
29 14 0.25
30 37 0.65
31 6 0.11
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (28 bp):
TAAATAAATTTTAATTTTTAATTTATAT
Found at i:3822623 original size:32 final size:29
Alignment explanation
Indices: 3822566--3822624 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 29
3822556 TGAAATGTAT
* *
3822566 TAAATTTTTTTATTTTATATTAATATAAG
1 TAAATTTTTTTATTATATATAAATATAAG
3822595 TAAATATTTTTGTATGTATATATAAATATA
1 TAAAT-TTTTT-TAT-TATATATAAATATA
3822625 TACTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 5 0.20
31 3 0.12
32 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
TAAATTTTTTTATTATATATAAATATAAG
Found at i:3822899 original size:189 final size:190
Alignment explanation
Indices: 3822671--3823047 Score: 643
Period size: 189 Copynumber: 2.0 Consensus size: 190
3822661 ATTTACAAAA
* * * *
3822671 TAAAAAAATAAATATAATAGTAAATAATTTTTAATTACTGTAATAATTACATTACTTTTTTTAAT
1 TAAAAAAATAAATATAATAATAAATAATTTGTAATTACTGTAATAACTACAGTACTTTTTTTAAT
3822736 GTTATAATTTATATTATTTCTTAAGATTAAGTTATTAATTAAATAATAATT-ATATGAAAATTAT
66 GTTATAATTTATATTATTTCTTAAGATTAAGTTATTAATTAAATAATAATTCA-ATGAAAATTAT
*
3822800 AAAACATATACTATAAAGTAATTTACTA-TTTATT-CAAAAAATTATTTATGTAACAATTT
130 AAAACATATACTATAAAGTAATTTACTATTTTATTCCAAAAAAATATTTATGTAACAATTT
3822859 TAAAATAAATAAATATAATAATAAATAATTTGTAATTACTGTAATAACTACAGTACTTTTTTTAA
1 TAAAA-AAATAAATATAATAATAAATAATTTGTAATTACTGTAATAACTACAGTACTTTTTTTAA
*
3822924 TGTTATAATTTATATTATTTCTTAAGATTAAGTTATTATTTAAATAATAATTCAATGAAAATTAT
65 TGTTATAATTTATATTATTTCTTAAGATTAAGTTATTAATTAAATAATAATTCAATGAAAATTAT
*
3822989 AAAACATATACTATAAAGTAATTTACTATTTTTTTTCCAAAAAAATATTTATGTAACAA
130 AAAACATATACTATAAAGTAATTTACTA-TTTTATTCCAAAAAAATATTTATGTAACAA
3823048 CATTTTTTCA
Statistics
Matches: 177, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
188 5 0.03
189 145 0.82
190 1 0.01
191 5 0.03
192 21 0.12
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (190 bp):
TAAAAAAATAAATATAATAATAAATAATTTGTAATTACTGTAATAACTACAGTACTTTTTTTAAT
GTTATAATTTATATTATTTCTTAAGATTAAGTTATTAATTAAATAATAATTCAATGAAAATTATA
AAACATATACTATAAAGTAATTTACTATTTTATTCCAAAAAAATATTTATGTAACAATTT
Found at i:3823198 original size:27 final size:27
Alignment explanation
Indices: 3823167--3823220 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3823157 AATTATTAAA
* *
3823167 ATTTAAAATTT-ATTTATTTATATTTT
1 ATTTTAAATTTAATTTATTGATATTTT
*
3823193 ATTTTAAATTTAATTTCTTGATATTTT
1 ATTTTAAATTTAATTTATTGATATTTT
3823220 A
1 A
3823221 GTGAGATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTTAAATTTAATTTATTGATATTTT
Found at i:3823565 original size:23 final size:21
Alignment explanation
Indices: 3823499--3823582 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
3823489 GGAAATTTAA
*
3823499 AAAATT-TTAAATTTTTATTT
1 AAAATTATTTAATTTTTATTT
*
3823519 AAATTTAGTTT-A-TTTTATTT
1 AAAATTA-TTTAATTTTTATTT
3823539 -AAATTATTTAAATTTATTATTT
1 AAAATTATTT-AATTT-TTATTT
*
3823561 AAAATTAATTAATTTTTTATTT
1 AAAATTATTTAA-TTTTTATTT
3823583 TTATATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.06
19 5 0.10
20 14 0.27
21 3 0.06
22 16 0.31
23 11 0.21
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (21 bp):
AAAATTATTTAATTTTTATTT
Found at i:3825890 original size:18 final size:17
Alignment explanation
Indices: 3825807--3825901 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 17
3825797 ATAATATTTA
*
3825807 TATTATTTTATATTTATAT
1 TATT-TTTTATA-TTAAAT
*
3825826 AATTTTTATATATT-AAT
1 TATTTTT-TATATTAAAT
*
3825843 AATTTATATTATA-TAAATT
1 TATTT-T-TTATATTAAA-T
3825862 TAATATTTTTATACTTAAAT
1 T-AT-TTTTTATA-TTAAAT
*
3825882 TATTTTTTATATTATAT
1 TATTTTTTATATTAAAT
3825899 TAT
1 TAT
3825902 AATTTAATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
17 16 0.25
18 20 0.32
19 16 0.25
20 5 0.08
21 6 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTTTATATTAAAT
Found at i:3825931 original size:29 final size:28
Alignment explanation
Indices: 3825879--3825955 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 28
3825869 TTTATACTTA
*
3825879 AATTATTTTTTATATTATATTATAATTT
1 AATTATTTTTTATATTATATTATAATAT
3825907 AATTATTTTTTATTATATTCATATAATATAATA-
1 AATTA--TTTT-TTATATT-ATAT--TATAATAT
*
3825940 AATTATTTTTAATATT
1 AATTATTTTTTATATT
3825956 TTTAGTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 5 0.12
30 10 0.24
31 11 0.27
32 4 0.10
33 5 0.12
34 6 0.15
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
AATTATTTTTTATATTATATTATAATAT
Found at i:3829196 original size:26 final size:26
Alignment explanation
Indices: 3829167--3829228 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
3829157 TAATCATGTC
* *
3829167 ATAATATATTTTTGAATAAAATTAAT
1 ATAATATATTTTGGAATAAAAATAAT
*
3829193 ATAATATA-TTTGGTATAAAAATAAT
1 ATAATATATTTTGGAATAAAAATAAT
*
3829218 AT-TTATATTTT
1 ATAATATATTTT
3829229 AAATTGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 4 0.13
25 19 0.61
26 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (26 bp):
ATAATATATTTTGGAATAAAAATAAT
Found at i:3831353 original size:21 final size:20
Alignment explanation
Indices: 3831324--3831371 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3831314 TTATTTCATA
3831324 TATTTTAATTTTAATTTTAT
1 TATTTTAATTTTAATTTTAT
*
3831344 TATTTATAATTTTTATTTT-T
1 TATTT-TAATTTTAATTTTAT
*
3831364 AATTTTAA
1 TATTTTAA
3831372 ATTAAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.40
21 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTAATTTTAATTTTAT
Found at i:3831364 original size:28 final size:29
Alignment explanation
Indices: 3831312--3831370 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
3831302 TTTTAAAAAG
3831312 TATTATTTCATATATTTTAATTTTAATTT
1 TATTATTTCATATATTTTAATTTTAATTT
*
3831341 TATTATTT-ATA-ATTTTTATTTTTAATTT
1 TATTATTTCATATA-TTTTAATTTTAATTT
3831369 TA
1 TA
3831371 AATTAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 1 0.04
28 19 0.68
29 8 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTATTTCATATATTTTAATTTTAATTT
Found at i:3832060 original size:21 final size:21
Alignment explanation
Indices: 3832031--3832077 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3832021 TTAATATTTT
* *
3832031 TTATAATTTAA-ATTTAATAAA
1 TTATTATTTAATAATTAA-AAA
3832052 TTATTATTTAATAATTAAAAA
1 TTATTATTTAATAATTAAAAA
3832073 TTATT
1 TTATT
3832078 TAAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTATTTAATAATTAAAAA
Found at i:3832075 original size:18 final size:18
Alignment explanation
Indices: 3832054--3832119 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 18
3832044 TTAATAAATT
3832054 ATTATTTAATAATTAAAA
1 ATTATTTAATAATTAAAA
*
3832072 ATTATTTAAAATAATTATAA
1 ATTATTT--AATAATTAAAA
3832092 A-TA-TTAAT-A-TAAAA
1 ATTATTTAATAATTAAAA
3832106 ATATATTT-ATAATT
1 AT-TATTTAATAATT
3832120 TAAATCCATC
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
14 5 0.13
15 1 0.03
16 7 0.18
17 3 0.08
18 10 0.26
19 2 0.05
20 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATTTAATAATTAAAA
Found at i:3832866 original size:65 final size:65
Alignment explanation
Indices: 3832758--3832888 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 65
3832748 TATATTTTAT
** *
3832758 AATTAAATTTAAATAATAATATTTTTATTATTAATTAATAAATT-AAATCAAATCAAATCAAATA
1 AATTAAATTTAAATAATAATATTTTTAAAATTAATTAAAAAATTAAAAT-AAATCAAATCAAATA
3832822 A
65 A
**
3832823 AATTAAATTT-AA-AA-AATATTTTTAAAACTTAATTTATAAAAATTAAAATTTATCAAATCAAA
1 AATTAAATTTAAATAATAATATTTTTAAAA-TTAA-TTA-AAAAATTAAAATAAATCAAATCAAA
3832885 TAA
63 TAA
3832888 A
1 A
3832889 TAATTTTAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
62 11 0.19
63 6 0.11
64 5 0.09
65 31 0.54
66 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (65 bp):
AATTAAATTTAAATAATAATATTTTTAAAATTAATTAAAAAATTAAAATAAATCAAATCAAATAA
Found at i:3833708 original size:27 final size:25
Alignment explanation
Indices: 3833678--3833770 Score: 71
Period size: 28 Copynumber: 3.4 Consensus size: 25
3833668 TATCGTATTA
3833678 ATTATATTTATATATTATATTACATTT
1 ATTATATTTATATATTATATTA-A-TT
* *
3833705 ATTACATTTTTATAATATT-TATTAAAT
1 ATT--ATATTTAT-ATATTATATTAATT
*
3833732 ATTATATTTTTATATTATATTTAAAATT
1 ATTATATTTATATATTATA-TT--AATT
*
3833760 ATTAAATTTAT
1 ATTATATTTAT
3833771 TTAAAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
24 5 0.10
25 8 0.15
26 2 0.04
27 7 0.13
28 13 0.25
29 12 0.23
30 5 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATATTTATATATTATATTAATT
Found at i:3833751 original size:29 final size:26
Alignment explanation
Indices: 3833673--3833754 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
3833663 AAATATATCG
* *
3833673 TATTAATTATATTTATATATTATATT
1 TATTTATTATATTTTTATATTATATT
* *
3833699 ACATTTATTACATTTTTATA--ATATT
1 -TATTTATTATATTTTTATATTATATT
3833724 TATTAAATATTATATTTTTATATTATATT
1 TATT---TATTATATTTTTATATTATATT
3833753 TA
1 TA
3833755 AAATTATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
24 3 0.07
25 5 0.11
27 29 0.66
29 7 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTATTATATTTTTATATTATATT
Found at i:3833790 original size:13 final size:13
Alignment explanation
Indices: 3833763--3833801 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3833753 TAAAATTATT
3833763 AAATTT-ATTTAA
1 AAATTTAATTTAA
*
3833775 AAATTTAATATAA
1 AAATTTAATTTAA
*
3833788 AAAATTAATTTAA
1 AAATTTAATTTAA
3833801 A
1 A
3833802 TACATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTAATTTAA
Found at i:3837880 original size:3 final size:3
Alignment explanation
Indices: 3837874--3837912 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3837864 AATGATGATG
3837874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3837913 GGAAAGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3840079 original size:12 final size:11
Alignment explanation
Indices: 3840057--3840217 Score: 55
Period size: 12 Copynumber: 13.9 Consensus size: 11
3840047 TATGGTATAA
3840057 ATAATTAAAAT
1 ATAATTAAAAT
3840068 ATAATATAAAAT
1 ATAAT-TAAAAT
*
3840080 ATAAAATTAATATAA
1 AT--AATTAA-A-AT
*
3840095 ATAAATAAAA-
1 ATAATTAAAAT
*
3840105 AT-TTTAAAAT
1 ATAATTAAAAT
* *
3840115 -TTA-TATAAT
1 ATAATTAAAAT
*
3840124 ATAAATTATTAAT
1 AT-AATTA-AAAT
*
3840137 ATAATAAAATTTAT
1 ATAATTAAA---AT
3840151 ATAAATTCAAAAT
1 AT-AATT-AAAAT
*
3840164 AT-TTTAAAAT
1 ATAATTAAAAT
*
3840174 -TAATTATAAT
1 ATAATTAAAAT
*
3840184 ATAATAAAATAT
1 ATAATTAAA-AT
*
3840196 ATAAATAAAAT
1 ATAATTAAAAT
3840207 ATAAATTAAAA
1 AT-AATTAAAA
3840218 ATTTTAATTT
Statistics
Matches: 112, Mismatches: 18, Indels: 39
0.66 0.11 0.23
Matches are distributed among these distances:
9 12 0.11
10 14 0.12
11 20 0.18
12 31 0.28
13 18 0.16
14 8 0.07
15 6 0.05
16 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:3840107 original size:20 final size:19
Alignment explanation
Indices: 3840052--3840104 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3840042 TTAAATATGG
*
3840052 TATAAATAATTAAAATATAA
1 TATAAATAAATAAAAT-TAA
*
3840072 TATAAA-ATATAAAATTAA
1 TATAAATAAATAAAATTAA
3840090 TATAAATAAATAAAA
1 TATAAATAAATAAAA
3840105 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.31
19 14 0.48
20 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAATAAATAAAATTAA
Found at i:3840154 original size:14 final size:14
Alignment explanation
Indices: 3840109--3840154 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
3840099 ATAAAAATTT
3840109 TAAAATTTATATAA
1 TAAAATTTATATAA
3840123 TATAAATTATTAATATAA
1 TA-AAA-T-TT-ATATAA
3840141 TAAAATTTATATAA
1 TAAAATTTATATAA
3840155 ATTCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.29
15 5 0.18
16 2 0.07
17 5 0.18
18 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATTTATATAA
Found at i:3840186 original size:33 final size:31
Alignment explanation
Indices: 3840081--3840224 Score: 97
Period size: 27 Copynumber: 5.1 Consensus size: 31
3840071 ATATAAAATA
3840081 TAAAATTAATATAA-ATAAA-TAAAA-ATTT
1 TAAAATTAATATAATATAAATTAAAATATTT
* * **
3840109 TAAAATTTATATAATATAAATTATTAATATAA
1 TAAAATTAATATAATATAAATTA-AAATATTT
3840141 TAAAA-T--T-T-ATATAAATTCAAAATATTT
1 TAAAATTAATATAATATAAATT-AAAATATTT
*
3840168 TAAAATTAATTATAATAT-AA-TAAAATA-TA
1 TAAAATTAA-TATAATATAAATTAAAATATTT
3840197 T-AAA-T-A-A-AATATAAATTAAAA-ATTT
1 TAAAATTAATATAATATAAATTAAAATATTT
3840222 TAA
1 TAA
3840225 TTTTACGCTT
Statistics
Matches: 92, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
23 5 0.05
24 4 0.04
25 7 0.08
26 2 0.02
27 20 0.22
28 19 0.21
29 8 0.09
30 8 0.09
31 5 0.05
32 10 0.11
33 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
TAAAATTAATATAATATAAATTAAAATATTT
Found at i:3840203 original size:60 final size:60
Alignment explanation
Indices: 3840065--3840206 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
3840055 AAATAATTAA
* *
3840065 AATATAATATAAAATATAAAATTAATATAAATAAATAAAAATTTTAAAATTTATATAATAT
1 AATATAATATATAA-ATAAAATTAATATAAATAAATAAAAATTTTAAAATTAATATAATAT
* * ** *
3840126 AA-ATTAT-TAATATAATAAAATTTATATAAATTCA-AAATATTTTAAAATTAATTATAATAT
1 AATATAATAT-ATA-AATAAAATTAATATAAATAAATAAAAATTTTAAAATTAA-TATAATAT
*
3840186 AATAAAATATATAAATAAAAT
1 AATATAATATATAAATAAAAT
3840207 ATAAATTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
59 16 0.24
60 41 0.61
61 9 0.13
62 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (60 bp):
AATATAATATATAAATAAAATTAATATAAATAAATAAAAATTTTAAAATTAATATAATAT
Found at i:3840271 original size:16 final size:16
Alignment explanation
Indices: 3840250--3840281 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3840240 AAAGCCTCTT
*
3840250 AAAAAGGAAAGAAAAA
1 AAAAAGGAAACAAAAA
3840266 AAAAAGGAAACAAAAA
1 AAAAAGGAAACAAAAA
3840282 GAAGTAATTT
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:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGGAAACAAAAA
Found at i:3840775 original size:23 final size:23
Alignment explanation
Indices: 3840727--3840780 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3840717 ATAAATATGT
* * *
3840727 TAAAATAAAATTATTTAACTATA
1 TAAAATAAAATTATATAAATAAA
3840750 TAAAATAAAATTCA-ATAAATAAA
1 TAAAATAAAATT-ATATAAATAAA
3840773 T-AAATAAA
1 TAAAATAAA
3840781 CAACTAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.26
23 19 0.70
24 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAATAAAATTATATAAATAAA
Done.