Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 21 of 27
Found at i:3161577 original size:21 final size:21
Alignment explanation
Indices: 3161544--3161585 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3161534 TAAATATTAT
* *
3161544 TATAAAAATATAATTTTTAAA
1 TATAAAAAGATAATTTATAAA
*
3161565 TATATAAAGATAATTTATAAA
1 TATAAAAAGATAATTTATAAA
3161586 ATTATGTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TATAAAAAGATAATTTATAAA
Found at i:3162216 original size:64 final size:64
Alignment explanation
Indices: 3162142--3162331 Score: 344
Period size: 64 Copynumber: 3.0 Consensus size: 64
3162132 TAGCTTGCTC
*
3162142 TTTCTGGTATGCTTTGCCTGTCCATTGTCATCACTTCTTTTGTTATTATTAGTATTATTATTTT
1 TTTCTGGTATGCTTTGCCTGTCCATTGTCATCACTTCTTTTATTATTATTAGTATTATTATTTT
3162206 TTTCTGGTATGCTTTGCCTGTCCATTGTCATCACTTCTTTTATTATTATTAGTATTATTATTTT
1 TTTCTGGTATGCTTTGCCTGTCCATTGTCATCACTTCTTTTATTATTATTAGTATTATTATTTT
* * *
3162270 TTTCTGGTATGCTTTGCCTGTCCATTTTCATCACTTCTATTATTATTATTATTATTATTATT
1 TTTCTGGTATGCTTTGCCTGTCCATTGTCATCACTTCTTTTATTATTATTAGTATTATTATT
3162332 ATTATTATTA
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 122 1.00
ACGTcount: A:0.17, C:0.16, G:0.11, T:0.56
Consensus pattern (64 bp):
TTTCTGGTATGCTTTGCCTGTCCATTGTCATCACTTCTTTTATTATTATTAGTATTATTATTTT
Found at i:3162315 original size:3 final size:3
Alignment explanation
Indices: 3162307--3162355 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3162297 TCATCACTTC
3162307 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3162355 T
1 T
3162356 GTATTCAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3165126 original size:28 final size:31
Alignment explanation
Indices: 3165061--3165127 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 31
3165051 AATTTAAATT
*
3165061 TAATTTAATTTATAAATTTAAATTATTATTA
1 TAATTAAATTTATAAATTTAAATTATTATTA
* *
3165092 -AA-AAAATTTA-AAATTTATATT-TT-TTA
1 TAATTAAATTTATAAATTTAAATTATTATTA
3165118 TAATTAAATT
1 TAATTAAATT
3165128 GAATAGTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
26 3 0.10
27 4 0.13
28 15 0.50
29 6 0.20
30 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TAATTAAATTTATAAATTTAAATTATTATTA
Found at i:3171693 original size:13 final size:14
Alignment explanation
Indices: 3171670--3171698 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3171660 CTTTGCTTTC
3171670 TTTATTTTTTATTT
1 TTTATTTTTTATTT
3171684 TTTA-TTTTTATTT
1 TTTATTTTTTATTT
3171697 TT
1 TT
3171699 AAATCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTATTTTTTATTT
Found at i:3171699 original size:6 final size:7
Alignment explanation
Indices: 3171670--3171698 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3171660 CTTTGCTTTC
3171670 TTTATTT
1 TTTATTT
3171677 TTTATTT
1 TTTATTT
3171684 TTTA-TT
1 TTTATTT
3171690 TTTATTT
1 TTTATTT
3171697 TT
1 TT
3171699 AAATCCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:3172830 original size:2 final size:2
Alignment explanation
Indices: 3172823--3172851 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3172813 AGTTTGTATT
3172823 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 T
3172852 TTGGAGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3173249 original size:6 final size:6
Alignment explanation
Indices: 3173235--3173264 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3173225 ATGAGGCAAG
*
3173235 ATATTA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA
3173265 TATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:3173342 original size:3 final size:3
Alignment explanation
Indices: 3173336--3173378 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3173326 ACTAAACATT
3173336 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3173379 GTTCTGCTGC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3173529 original size:26 final size:26
Alignment explanation
Indices: 3173500--3173566 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
3173490 GTGTGACATT
* **
3173500 ATTTTTTTTAAATTTTTATTTATTTA
1 ATTTTTTTAAAATTTTTACGTATTTA
* * *
3173526 ATTTATTTAAAAATATTACGTATTTA
1 ATTTTTTTAAAATTTTTACGTATTTA
*
3173552 AATTTTTTAAAATTT
1 ATTTTTTTAAAATTT
3173567 ATAATTTTTA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (26 bp):
ATTTTTTTAAAATTTTTACGTATTTA
Found at i:3173572 original size:17 final size:17
Alignment explanation
Indices: 3173547--3173585 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3173537 AATATTACGT
3173547 ATTTA-AATTTTT-TAAA
1 ATTTATAATTTTTAT-AA
3173563 ATTTATAATTTTTATAA
1 ATTTATAATTTTTATAA
3173580 ATTTAT
1 ATTTAT
3173586 GTAACATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 15 0.71
18 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTATAATTTTTATAA
Found at i:3174155 original size:20 final size:19
Alignment explanation
Indices: 3174132--3174173 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3174122 TAAATAAAAG
*
3174132 TATTCAAATTAAATTAAATT
1 TATTCAAATT-AATAAAATT
*
3174152 TATTTAAATTAATAAAATT
1 TATTCAAATTAATAAAATT
3174171 TAT
1 TAT
3174174 ATTTTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTCAAATTAATAAAATT
Found at i:3177308 original size:34 final size:33
Alignment explanation
Indices: 3177260--3177378 Score: 177
Period size: 34 Copynumber: 3.5 Consensus size: 33
3177250 TGGTAAAAAC
3177260 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGCAACCTACCAAAT
*
3177293 CTACCATTTAGTCAACAATGGCAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGCAA-CCTACCAAAT
* *
3177327 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGCAACCTACCAAAT
3177361 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3177379 TCTCCCACTT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
33 19 0.24
34 57 0.73
35 2 0.03
ACGTcount: A:0.42, C:0.29, G:0.07, T:0.23
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGCAACCTACCAAAT
Found at i:3181833 original size:34 final size:33
Alignment explanation
Indices: 3181785--3181903 Score: 168
Period size: 34 Copynumber: 3.5 Consensus size: 33
3181775 TGATAAAAAC
3181785 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGCAACCTACCAAAT
* *
3181818 CTACCATTTAGTCAACAATGGCAAGCC-ATCAAAT
1 C-ACCATTTAATCAACAATGGCAA-CCTACCAAAT
* *
3181852 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGCAACCTACCAAAT
3181886 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3181904 AGTATTGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 19 0.25
34 55 0.72
35 2 0.03
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGCAACCTACCAAAT
Found at i:3182650 original size:34 final size:32
Alignment explanation
Indices: 3182590--3182685 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 32
3182580 ATCATAGTAT
*
3182590 AAAAATAATTAAAACATAATATAAATACGTTACGAA
1 AAAAATAATTAAAA-ATAATA-AAATACATTAC--A
*
3182626 AAAAATAATTAAAAATAATAAAATATATTACA
1 AAAAATAATTAAAAATAATAAAATACATTACA
* *
3182658 AAAAATAA-TAAAAAAAATAACATA-ATTA
1 AAAAATAATTAAAAATAATAAAATACATTA
3182686 TACAAATATA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.07
31 14 0.25
32 9 0.16
34 9 0.16
35 6 0.11
36 14 0.25
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (32 bp):
AAAAATAATTAAAAATAATAAAATACATTACA
Found at i:3182655 original size:19 final size:18
Alignment explanation
Indices: 3182627--3182665 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
3182617 CGTTACGAAA
3182627 AAAATAATTA-AAAATAAT
1 AAAATAATTACAAAA-AAT
3182645 AAAATATATTACAAAAAAT
1 AAAATA-ATTACAAAAAAT
3182664 AA
1 AA
3182666 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAATTACAAAAAAT
Found at i:3182672 original size:12 final size:10
Alignment explanation
Indices: 3182625--3182677 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
3182615 TACGTTACGA
3182625 AAAAAATAAT
1 AAAAAATAAT
*
3182635 TAAAAATAAT
1 AAAAAATAAT
* *
3182645 AAAATATATTAC
1 AAAA-A-ATAAT
3182657 AAAAAATAAT
1 AAAAAATAAT
3182667 AAAAAA-AAT
1 AAAAAATAAT
3182676 AA
1 AA
3182678 CATAATTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 5 0.14
10 21 0.60
11 2 0.06
12 7 0.20
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:3184735 original size:2 final size:2
Alignment explanation
Indices: 3184728--3184762 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3184718 TTAAAACTTT
*
3184728 TA TA TA TA TA TA CA 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 T
3184763 GGAGATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3185147 original size:17 final size:17
Alignment explanation
Indices: 3185127--3185160 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3185117 TATATAAATT
3185127 AATT-AAATTAAATTTTA
1 AATTAAAATT-AATTTTA
3185144 AATTAAAATTAATTTTA
1 AATTAAAATTAATTTTA
3185161 GTTTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAAATTAATTTTA
Found at i:3186193 original size:14 final size:14
Alignment explanation
Indices: 3186171--3186226 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
3186161 TAAATTAAAA
*
3186171 AAATTATAAATATT
1 AAATGATAAATATT
*
3186185 AAATGATAAATTTT
1 AAATGATAAATATT
3186199 AAA-G-T---TATT
1 AAATGATAAATATT
*
3186208 AAATGATAAATTTT
1 AAATGATAAATATT
3186222 AAATG
1 AAATG
3186227 CCACTTTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
9 6 0.18
10 1 0.03
11 1 0.03
12 1 0.03
13 1 0.03
14 23 0.70
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATGATAAATATT
Found at i:3186207 original size:23 final size:23
Alignment explanation
Indices: 3186181--3186224 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3186171 AAATTATAAA
3186181 TATTAAATGATAAATTTTAAAGT
1 TATTAAATGATAAATTTTAAAGT
3186204 TATTAAATGATAAATTTTAAA
1 TATTAAATGATAAATTTTAAA
3186225 TGCCACTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
TATTAAATGATAAATTTTAAAGT
Found at i:3187957 original size:13 final size:13
Alignment explanation
Indices: 3187939--3187985 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
3187929 GTTAATTTTT
*
3187939 AAATAAATTATAA
1 AAATAAATTATTA
3187952 AAATAATATTAATTTA
1 AAATAA-ATT-A-TTA
3187968 AAATAAATTATTA
1 AAATAAATTATTA
3187981 AAATA
1 AAATA
3187986 TTATTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.47
14 4 0.13
15 4 0.13
16 8 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:3187974 original size:29 final size:29
Alignment explanation
Indices: 3187930--3187997 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
3187920 CACATTACTG
*
3187930 TTAATTTTTAAATAAATTATAAAAATAATA
1 TTAA-TTTAAAATAAATTATAAAAATAATA
* *
3187960 TTAATTTAAAATAAATTATTAAAATATTA
1 TTAATTTAAAATAAATTATAAAAATAATA
*
3187989 TTATTTTAA
1 TTAATTTAA
3187998 TTAACAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAATTTAAAATAAATTATAAAAATAATA
Found at i:3192924 original size:14 final size:14
Alignment explanation
Indices: 3192907--3192936 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3192897 TTTTAATTTT
3192907 AATAAAAAATTAAA
1 AATAAAAAATTAAA
*
3192921 AATAAATAATTAAA
1 AATAAAAAATTAAA
3192935 AA
1 AA
3192937 ATTCAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAAAATTAAA
Found at i:3193420 original size:17 final size:18
Alignment explanation
Indices: 3193398--3193440 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
3193388 TATTTTTCAT
3193398 AAAATA-TAAAAAAATAA
1 AAAATATTAAAAAAATAA
* *
3193415 AAAATATTAATATAAT-A
1 AAAATATTAAAAAAATAA
3193432 AAAATATTA
1 AAAATATTA
3193441 GTTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATTAAAAAAATAA
Found at i:3193808 original size:12 final size:12
Alignment explanation
Indices: 3193759--3193819 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
3193749 ACAATAATAC
*
3193759 AAATTTATTATA
1 AAATTTAATATA
*
3193771 TAAATATAATATTA
1 -AAATTTAATA-TA
*
3193785 AAA-ATAAT-TA
1 AAATTTAATATA
3193795 AAATTTAATATA
1 AAATTTAATATA
*
3193807 AAATTTAAAATA
1 AAATTTAATATA
3193819 A
1 A
3193820 TATATATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 5 0.12
11 4 0.10
12 19 0.46
13 11 0.27
14 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATTTAATATA
Found at i:3193834 original size:22 final size:25
Alignment explanation
Indices: 3193800--3193854 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
3193790 AATTAAAATT
3193800 TAATAT-AAAA-TTTAAAA-TAATA
1 TAATATAAAAATTTTAAAATTAATA
*
3193822 T-ATATAAAAATTTTAAAATTTATA
1 TAATATAAAAATTTTAAAATTAATA
3193846 TAATATAAA
1 TAATATAAA
3193855 TTATTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 5 0.18
23 7 0.25
24 5 0.18
25 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATATAAAAATTTTAAAATTAATA
Found at i:3193855 original size:23 final size:22
Alignment explanation
Indices: 3193800--3193861 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
3193790 AATTAAAATT
*
3193800 TAATATAAAATTTAAAATAATA
1 TAATATAAATTTTAAAATAATA
* *
3193822 TATATAAAAATTTTAAAATTTATA
1 TA-ATATAAATTTTAAAA-TAATA
3193846 TAATATAAATTATTAA
1 TAATATAAATT-TTAA
3193862 TATATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 21 0.64
24 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATAAATTTTAAAATAATA
Found at i:3193873 original size:32 final size:33
Alignment explanation
Indices: 3193816--3193898 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
3193806 AAAATTTAAA
* * *
3193816 ATAATATATATAAAAATTTTAAAATTTATATAAT
1 ATAATAT-TTTAAATATATTAAAATTTATATAAT
*
3193850 ATAA-ATTATT-AATATATTAAAATTTATATATT
1 ATAATATT-TTAAATATATTAAAATTTATATAAT
3193882 ATAATATTTTAAATATA
1 ATAATATTTTAAATATA
3193899 ATTATAAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
32 26 0.62
33 12 0.29
34 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
ATAATATTTTAAATATATTAAAATTTATATAAT
Found at i:3193880 original size:14 final size:14
Alignment explanation
Indices: 3193834--3193882 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
3193824 TATAAAAATT
3193834 TTAAAATTTATATAA
1 TTAAAATTTATAT-A
*
3193849 TATAAATTATTAATATA
1 T-TAAA--ATTTATATA
3193866 TTAAAATTTATATA
1 TTAAAATTTATATA
3193880 TTA
1 TTA
3193883 TAATATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 11 0.38
15 1 0.03
16 8 0.28
17 2 0.07
18 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAAATTTATATA
Found at i:3193892 original size:17 final size:16
Alignment explanation
Indices: 3193835--3193897 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
3193825 ATAAAAATTT
* *
3193835 TAAAATTTATATAATA
1 TAAATTTTATATATTA
3193851 TAAATTATTAATATATTA
1 TAAATT-TT-ATATATTA
3193869 -AAA-TTTATATATTA
1 TAAATTTTATATATTA
*
3193883 TAATATTTTAAATAT
1 TAA-ATTTTATATAT
3193898 AATTATAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.21
15 4 0.10
16 7 0.18
17 13 0.33
18 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTTTATATATTA
Found at i:3194218 original size:123 final size:123
Alignment explanation
Indices: 3194071--3194320 Score: 446
Period size: 123 Copynumber: 2.0 Consensus size: 123
3194061 AAATAGGAAA
*
3194071 GAAAGAGAGAGACAGCTCCCCACCGTCACTTCTCTAAAGTACGCCGCGGTGACTCTTTTCTAAAA
1 GAAAGAGAGAGACAGCTCCCCACCGTCACTTCTCTAAAGTACGCCGCGGTGACTCTTTGCTAAAA
*
3194136 TACGCAGATGTCTAGGAATGGAGGAAGTTTCTCCTTATTTAAGTAGAAGAGCAAAAAG
66 TACGCAGATGTCTAGGAATGGAGGAAGTCTCTCCTTATTTAAGTAGAAGAGCAAAAAG
* * *
3194194 GAAAGAGAGAGACAGCTCCTCACCGTGACTTCTCTAAAGTACGCTGCGGTGACTCTTTGCTAAAA
1 GAAAGAGAGAGACAGCTCCCCACCGTCACTTCTCTAAAGTACGCCGCGGTGACTCTTTGCTAAAA
*
3194259 TACGCAGATGTCTAGGAATGGAGGAAGTCTCTCCTTATTTAAGTAGAAGAGGAAAAAG
66 TACGCAGATGTCTAGGAATGGAGGAAGTCTCTCCTTATTTAAGTAGAAGAGCAAAAAG
3194317 GAAA
1 GAAA
3194321 ATAAAAAAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (123 bp):
GAAAGAGAGAGACAGCTCCCCACCGTCACTTCTCTAAAGTACGCCGCGGTGACTCTTTGCTAAAA
TACGCAGATGTCTAGGAATGGAGGAAGTCTCTCCTTATTTAAGTAGAAGAGCAAAAAG
Found at i:3194347 original size:2 final size:2
Alignment explanation
Indices: 3194342--3194381 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3194332 AAGGAAAGAA
3194342 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3194382 GGGCGAAGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3196807 original size:2 final size:2
Alignment explanation
Indices: 3196802--3196830 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3196792 GCACTTATAT
3196802 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3196831 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3196835 original size:2 final size:2
Alignment explanation
Indices: 3196830--3196872 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3196820 ACACACACAC
* *
3196830 AT AT AT AT AT AT AT AT AT AC AT AT A- AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3196871 AT
1 AT
3196873 CAGAATTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3198654 original size:19 final size:21
Alignment explanation
Indices: 3198632--3198671 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3198622 TTTAAATATA
3198632 TAAAAATA-TTATA-AAAAAT
1 TAAAAATATTTATATAAAAAT
*
3198651 TAAATATATTTATATAAAAAT
1 TAAAAATATTTATATAAAAAT
3198672 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAATATTTATATAAAAAT
Found at i:3199179 original size:2 final size:2
Alignment explanation
Indices: 3199172--3199238 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
3199162 TCAACATGGA
* * **
3199172 AT AT AT AT AT AT AT AT AT AT AT AT AA AC AT GG A- 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
3199213 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
3199239 GAATCCAACG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3199206 original size:33 final size:33
Alignment explanation
Indices: 3199164--3199229 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3199154 GGAGGAGGTC
3199164 AACATGGAATATATATATATATATATATATATA
1 AACATGGAATATATATATATATATATATATATA
3199197 AACATGGAATATATATATATATATATATATATA
1 AACATGGAATATATATATATATATATATATATA
3199230 TATATATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (33 bp):
AACATGGAATATATATATATATATATATATATA
Found at i:3200527 original size:13 final size:13
Alignment explanation
Indices: 3200511--3200555 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
3200501 TTATTTATAT
3200511 AATTATTTTAAAA
1 AATTATTTTAAAA
*
3200524 AATTATATTAAATA
1 AATTATTTTAAA-A
3200538 AATTTAATTTTAAAA
1 AA-TT-ATTTTAAAA
3200553 AAT
1 AAT
3200556 ATCAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 11 0.41
14 4 0.15
15 5 0.19
16 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATTTTAAAA
Found at i:3208274 original size:21 final size:21
Alignment explanation
Indices: 3208240--3208307 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
3208230 ATAAACATAA
**
3208240 ATTTTTTATTAATATATAATT
1 ATTTTTTAAAAATATATAATT
*
3208261 ATTTTTTAAAAATATTTAAATT
1 ATTTTTTAAAAATATAT-AATT
* *
3208283 -TTTATTAAATAAATAAATAATT
1 ATTT-TTTAA-AAATATATAATT
3208305 ATT
1 ATT
3208308 AATTTAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 17 0.46
22 12 0.32
23 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTTAAAAATATATAATT
Found at i:3208299 original size:19 final size:19
Alignment explanation
Indices: 3208236--3208300 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
3208226 AAATATAAAC
3208236 ATAAATTTTTTATTAATATATA
1 ATAAA-TTTTTATTAA-ATA-A
* * * *
3208258 ATTATTTTTTA-AAAATAT
1 ATAAATTTTTATTAAATAA
*
3208276 TTAAATTTTTATTAAATAA
1 ATAAATTTTTATTAAATAA
3208295 ATAAAT
1 ATAAAT
3208301 AATTATTAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 5
0.68 0.21 0.11
Matches are distributed among these distances:
18 8 0.25
19 13 0.41
20 2 0.06
21 6 0.19
22 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAAATTTTTATTAAATAA
Found at i:3208354 original size:18 final size:16
Alignment explanation
Indices: 3208313--3208359 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
3208303 TTATTAATTT
*
3208313 AAATATTA-AAATTAA
1 AAATATTATATATTAA
*
3208328 AAATATTATTTATTAA
1 AAATATTATATATTAA
3208344 ATAATATTTATATATT
1 A-AATA-TTATATATT
3208360 TTTATAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 8 0.31
16 6 0.23
17 4 0.15
18 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTATATATTAA
Found at i:3208454 original size:14 final size:12
Alignment explanation
Indices: 3208425--3208449 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3208415 TTTCAGCAGG
3208425 TAGTGAAAAAAA
1 TAGTGAAAAAAA
3208437 TAGTGAAAAAAA
1 TAGTGAAAAAAA
3208449 T
1 T
3208450 TTAGTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (12 bp):
TAGTGAAAAAAA
Found at i:3208476 original size:11 final size:11
Alignment explanation
Indices: 3208456--3208488 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3208446 AAATTTAGTA
3208456 TTTATATATTT
1 TTTATATATTT
3208467 TATT-TATATTT
1 T-TTATATATTT
3208478 TTTATATATTT
1 TTTATATATTT
3208489 AAAGTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATATATTT
Found at i:3208602 original size:22 final size:22
Alignment explanation
Indices: 3208571--3208626 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3208561 ATTTTTATCG
*
3208571 TGTTTAAATTATTTTTGTA-TTA
1 TGTTTTAATTATTTTT-TATTTA
3208593 TGTTTTAATTATTTTTTATTTA
1 TGTTTTAATTATTTTTTATTTA
* *
3208615 TATTTTATTTAT
1 TGTTTTAATTAT
3208627 ATCGTGTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TGTTTTAATTATTTTTTATTTA
Found at i:3208627 original size:11 final size:11
Alignment explanation
Indices: 3208590--3208628 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3208580 TATTTTTGTA
* *
3208590 TTATGTTTTAA
1 TTATATTTTAT
*
3208601 TTATTTTTTAT
1 TTATATTTTAT
3208612 TTATATTTTAT
1 TTATATTTTAT
3208623 TTATAT
1 TTATAT
3208629 CGTGTGTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TTATATTTTAT
Found at i:3208912 original size:22 final size:24
Alignment explanation
Indices: 3208877--3208922 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
3208867 TGATATATTT
3208877 ATATATTTATATTATTTTTATATA
1 ATATATTTATATTATTTTTATATA
*
3208901 ATAT-TTTA-ATTATTTTTTTATA
1 ATATATTTATATTATTTTTATATA
3208923 TTTCATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 4 0.19
24 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATATTTATATTATTTTTATATA
Found at i:3208978 original size:17 final size:16
Alignment explanation
Indices: 3208951--3209005 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
3208941 TCGATTTATC
3208951 TTATATTTTACATAAT
1 TTATATTTTACATAAT
*
3208967 TTATAGTTTTACATAGT
1 TTATA-TTTTACATAAT
3208984 TTATAATTTTA-ATAAT
1 TTAT-ATTTTACATAAT
*
3209000 ATATAT
1 TTATAT
3209006 ATAATGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 2 0.06
16 12 0.35
17 19 0.56
18 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (16 bp):
TTATATTTTACATAAT
Found at i:3210152 original size:17 final size:18
Alignment explanation
Indices: 3210126--3210167 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3210116 TTAATTTCAA
*
3210126 ATTT-AATTACATAAAAT
1 ATTTAAATTACAAAAAAT
3210143 -TTTAAATTACAAAAAAT
1 ATTTAAATTACAAAAAAT
3210160 ATTTAAAT
1 ATTTAAAT
3210168 AAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTAAATTACAAAAAAT
Found at i:3210305 original size:13 final size:13
Alignment explanation
Indices: 3210287--3210311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3210277 TTTATTATTT
3210287 TTTTAATTTAATA
1 TTTTAATTTAATA
3210300 TTTTAATTTAAT
1 TTTTAATTTAAT
3210312 TTATTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAATTTAATA
Found at i:3210961 original size:8 final size:8
Alignment explanation
Indices: 3210948--3211017 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
3210938 TTTAAAAATA
3210948 ATTTATAT
1 ATTTATAT
3210956 ATTTATATTTT
1 ATTTATA---T
3210967 ATTTATAT
1 ATTTATAT
*
3210975 ATTTTTAT
1 ATTTATAT
3210983 ATTATATTAT
1 ATT-TA-TAT
* *
3210993 ATTTTTAAA
1 ATTTAT-AT
3211002 ATATTATAT
1 AT-TTATAT
3211011 ATTTATA
1 ATTTATA
3211018 AAAATTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 24 0.49
9 8 0.16
10 9 0.18
11 8 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTATAT
Found at i:3210969 original size:11 final size:11
Alignment explanation
Indices: 3210955--3210997 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
3210945 ATAATTTATA
3210955 TATTTATATTT
1 TATTTATATTT
*
3210966 TATTTATATAT
1 TATTTATATTT
*
3210977 T-TTTATATTA
1 TATTTATATTT
3210987 TA-TTATATTT
1 TATTTATATTT
3210997 T
1 T
3210998 TAAAATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 16 0.59
11 11 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTATATTT
Found at i:3210970 original size:19 final size:19
Alignment explanation
Indices: 3210948--3211017 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
3210938 TTTAAAAATA
*
3210948 ATTTATATATTTATATTTT
1 ATTTATATATTTATATATT
*
3210967 ATTTATATATTTTTATATT
1 ATTTATATATTTATATATT
* *
3210986 ATATTATAT-TTT-TAAAAT
1 AT-TTATATATTTATATATT
3211004 A-TTATATATTTATA
1 ATTTATATATTTATA
3211018 AAAATTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.14
17 3 0.07
18 7 0.16
19 22 0.50
20 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTATATATTTATATATT
Found at i:3210987 original size:15 final size:15
Alignment explanation
Indices: 3210948--3210989 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
3210938 TTTAAAAATA
*
3210948 ATTTATATATT-TAT
1 ATTTTTATATTATAT
3210962 A-TTTTAT-TTATAT
1 ATTTTTATATTATAT
3210975 ATTTTTATATTATAT
1 ATTTTTATATTATAT
3210990 TATATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.08
13 9 0.38
14 7 0.29
15 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTATATTATAT
Found at i:3211007 original size:16 final size:16
Alignment explanation
Indices: 3210972--3211020 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
3210962 ATTTTATTTA
*
3210972 TATATTTTTATATTATAT
1 TATATTTTTA-A-AATAT
3210990 TATATTTTTAAAATAT
1 TATATTTTTAAAATAT
3211006 TATATATTTATAAAA
1 TATAT-TTT-TAAAA
3211021 ATTTTAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.32
17 4 0.14
18 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTTTTAAAATAT
Found at i:3211062 original size:20 final size:21
Alignment explanation
Indices: 3211005--3211085 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
3210995 TTTTAAAATA
* *
3211005 TTATAT-ATTTATAA-AAATT
1 TTATATAAATTATAATATATT
3211024 TTA-ATAAATTAATAATATATT
1 TTATATAAATT-ATAATATATT
3211045 TTATATAAATTA-AATATATT
1 TTATATAAATTATAATATATT
* *
3211065 TT-TATATATTATATTATATT
1 TTATATAAATTATAATATATT
3211085 T
1 T
3211086 AATTATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
20 22 0.42
21 8 0.15
22 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATATAAATTATAATATATT
Found at i:3211076 original size:28 final size:28
Alignment explanation
Indices: 3211038--3211095 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
3211028 TAAATTAATA
*
3211038 ATATATTTTATATAAATTAAATATATTTTT
1 ATATATTATAT-TAAATTAAAT-TATTTTT
* *
3211068 ATATATTATATTATATTTAATTATTTTT
1 ATATATTATATTAAATTAAATTATTTTT
3211096 TATTATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 8 0.32
30 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATATTATATTAAATTAAATTATTTTT
Found at i:3211394 original size:2 final size:2
Alignment explanation
Indices: 3211385--3211426 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3211375 ATTTACAGGT
*
3211385 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3211426 T
1 T
3211427 GTTTTAGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3211596 original size:16 final size:15
Alignment explanation
Indices: 3211547--3211595 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3211537 TTTTTATTAT
3211547 AATATTTTAAATA-A
1 AATATTTTAAATATA
*
3211561 AGATATTTTTAA-AT-
1 A-ATATTTTAAATATA
3211575 AATATATTTAAATATA
1 AATAT-TTTAAATATA
3211591 AATAT
1 AATAT
3211596 AAATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 11 0.39
16 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATTTTAAATATA
Found at i:3214838 original size:12 final size:11
Alignment explanation
Indices: 3214805--3214845 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
3214795 ATAAAATAAA
3214805 TATATAAATTTT
1 TATA-AAATTTT
3214817 T-TAAAATTTT
1 TATAAAATTTT
3214827 TATAATAATTTT
1 TATAA-AATTTT
3214839 TATAAAA
1 TATAAAA
3214846 AATAAACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.30
11 7 0.26
12 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATAAAATTTT
Found at i:3215403 original size:16 final size:17
Alignment explanation
Indices: 3215369--3215407 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3215359 TTTTTAAACT
3215369 TATTTTTTAAAATAAAA
1 TATTTTTTAAAATAAAA
3215386 TATTATTTT-AAA-AAAA
1 TATT-TTTTAAAATAAAA
3215402 TATTTT
1 TATTTT
3215408 CTCATCCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 8 0.38
17 7 0.33
18 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTTTTAAAATAAAA
Found at i:3219544 original size:43 final size:43
Alignment explanation
Indices: 3219490--3219575 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
3219480 ATGGCCTGTT
3219490 TTGTTTACAAAATACTTGGTACTTGATATTGAAATATGTTTTC
1 TTGTTTACAAAATACTTGGTACTTGATATTGAAATATGTTTTC
3219533 TTGTTTACAAAATACTTGGTACTTGATATTGAAATATGTTTTC
1 TTGTTTACAAAATACTTGGTACTTGATATTGAAATATGTTTTC
3219576 ATTATCACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (43 bp):
TTGTTTACAAAATACTTGGTACTTGATATTGAAATATGTTTTC
Found at i:3219567 original size:22 final size:22
Alignment explanation
Indices: 3219499--3219568 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
3219489 TTTGTTTACA
3219499 AAATACTTGGTACTTGATATTG
1 AAATACTTGGTACTTGATATTG
* * *
3219521 AAATA--TGTTTTCTTG-T-TTACA
1 AAATACTTG-GTACTTGATATT--G
3219542 AAATACTTGGTACTTGATATTG
1 AAATACTTGGTACTTGATATTG
3219564 AAATA
1 AAATA
3219569 TGTTTTCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 10 0.29
22 15 0.43
23 3 0.09
24 2 0.06
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
AAATACTTGGTACTTGATATTG
Found at i:3219586 original size:43 final size:43
Alignment explanation
Indices: 3219496--3219587 Score: 150
Period size: 43 Copynumber: 2.1 Consensus size: 43
3219486 TGTTTTGTTT
* *
3219496 ACAAAATACTTGGTACTTGATATTGAAATATGTTTTCTTGTTT
1 ACAAAATACTTGGTACTTGATATTGAAATATGTTTTCTTGATC
3219539 ACAAAATACTTGGTACTTGATATTGAAATATGTTTTCATT-ATC
1 ACAAAATACTTGGTACTTGATATTGAAATATGTTTTC-TTGATC
3219582 ACAAAA
1 ACAAAA
3219588 GATTATGACA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (43 bp):
ACAAAATACTTGGTACTTGATATTGAAATATGTTTTCTTGATC
Found at i:3221051 original size:15 final size:15
Alignment explanation
Indices: 3221033--3221066 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3221023 AAAAAAAAAG
*
3221033 AAAACAGGCAAATGT
1 AAAACAAGCAAATGT
3221048 AAAACAAGCAAATGT
1 AAAACAAGCAAATGT
3221063 AAAA
1 AAAA
3221067 TGAATAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.12
Consensus pattern (15 bp):
AAAACAAGCAAATGT
Found at i:3221146 original size:20 final size:19
Alignment explanation
Indices: 3221113--3221154 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
3221103 CGATCGTAAT
*
3221113 TATAAATATGATGAATGAA
1 TATAAATATAATGAATGAA
3221132 TATATAATATAATGAATGAA
1 TATA-AATATAATGAATGAA
3221152 TAT
1 TAT
3221155 TAACGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (19 bp):
TATAAATATAATGAATGAA
Found at i:3224601 original size:37 final size:37
Alignment explanation
Indices: 3224551--3224637 Score: 108
Period size: 35 Copynumber: 2.4 Consensus size: 37
3224541 GAGATAAAAA
* * *
3224551 AATTAAAAAATTATATATTTTTATTTATATTTTTTAT
1 AATTAAAATATTATATATTTTTATATAAATTTTTTAT
3224588 AATTAAAATA-T-TATATTTTTATATAAATTTTTTAT
1 AATTAAAATATTATATATTTTTATATAAATTTTTTAT
3224623 ATATTAATAAT-TTAT
1 A-ATTAA-AATATTAT
3224638 TTTATTTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
35 23 0.53
36 6 0.14
37 13 0.30
38 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (37 bp):
AATTAAAATATTATATATTTTTATATAAATTTTTTAT
Found at i:3224603 original size:35 final size:35
Alignment explanation
Indices: 3224564--3224661 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 35
3224554 TAAAAAATTA
3224564 TATATTTTTATTTATATTTTTTATA-ATTAAAATAT
1 TATATTTTTATTTATATTTTTTATATATTAAAA-AT
* * *
3224599 TATATTTTTATATAAATTTTTTATATATTAATAAT
1 TATATTTTTATTTATATTTTTTATATATTAAAAAT
*
3224634 T-TA-TTTTATTTCATATATATTTATATAT
1 TATATTTTTATTT-ATAT-TTTTTATATAT
3224662 ATATATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 7 0.13
34 5 0.09
35 36 0.67
36 6 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
TATATTTTTATTTATATTTTTTATATATTAAAAAT
Found at i:3231905 original size:13 final size:13
Alignment explanation
Indices: 3231887--3231914 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3231877 ATACAAAGAT
3231887 CAATGTATCGATA
1 CAATGTATCGATA
3231900 CAATGTATCGATA
1 CAATGTATCGATA
3231913 CA
1 CA
3231915 TTGAGTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3231929 original size:33 final size:33
Alignment explanation
Indices: 3231869--3231934 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3231859 AATTTCCCAG
*
3231869 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATATATCGATACA
**
3231902 ATGTATCGATACATTGAGT-AATATATCGATACA
1 ATGTATCGATACAAAGA-TCAATATATCGATACA
3231935 TTTCCTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATATATCGATACA
Found at i:3233020 original size:32 final size:31
Alignment explanation
Indices: 3232983--3233054 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
3232973 TTATTTTTAT
*
3232983 TTATATA-AATTATTATAAATTTATATAAATAG
1 TTATATATAATAATT-T-AATTTATATAAATAG
* *
3233015 TTATATATTAATAATTTATTTTATATAAATAT
1 TTATATA-TAATAATTTAATTTATATAAATAG
3233047 TTATATAT
1 TTATATAT
3233055 TCATATATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 27 0.77
33 1 0.03
34 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TTATATATAATAATTTAATTTATATAAATAG
Found at i:3233027 original size:284 final size:283
Alignment explanation
Indices: 3232497--3233071 Score: 961
Period size: 284 Copynumber: 2.0 Consensus size: 283
3232487 TTTTGTATAG
* * *
3232497 TTTGTTATTTGATTCAATTTAAAAAAAATTATATATTTGTATCATGTTCGTGTCATATCTCCATT
1 TTTGTCATTTGATTCAATTTAAAAAAAATTATATATTTGTATCATATTCATGTCATATCTCCATT
* *
3232562 CACGACATATTTTGCATGATTTATCATAATAATTTAATTTAAAGTATTATATCTCAATTCATGAC
66 CACGACATATTTTACATGATTTATCATAATAATTTAATTTAAAGTATTATATCTCAATTCATAAC
*
3232627 ATTTTTTCATAATTTGTTATAGTGATTTAATTAAAAAAATTATGTCTTTTTACGTGTTTGTGTTA
131 ATTTTTTCATAATTTGTTATAGTGATTTAATTAAAAAAATTATATCTTTTTACGTGTTTGTGTTA
*
3232692 TTTTTGTTTATAAAAATTATTATAAATTTATATAAATAGTTATACATTAATAATTTATTTTATAT
196 TTTTTATTTATAAAAATTATTATAAATTTATATAAATAGTTATACATTAATAATTTATTTTATAT
*
3232757 AAATATTTATATATTAATGTATT
261 AAATATTTATATATTAATATATT
* * * *
3232780 TTTGTCATTTGATTCAATTTTAAAAAAACTTATATGTTTGTTTTATATTCATGTCATATCTCCAT
1 TTTGTCATTTGATTCAA-TTTAAAAAAAATTATATATTTGTATCATATTCATGTCATATCTCCAT
* *
3232845 TCCCGACATATTTTACATGATTTATCATAATAATTTAATTTAAAGTATTATATCTGAATTCATAA
65 TCACGACATATTTTACATGATTTATCATAATAATTTAATTTAAAGTATTATATCTCAATTCATAA
* *
3232910 TATTTTTTCATAATTTGTTATAGTGATTTAATTAAAATAATTATATCTTTTTACGTGTTTGTGTT
130 CATTTTTTCATAATTTGTTATAGTGATTTAATTAAAAAAATTATATCTTTTTACGTGTTTGTGTT
* *
3232975 ATTTTTATTTATATAAATTATTATAAATTTATATAAATAGTTATATATTAATAATTTATTTTATA
195 ATTTTTATTTATAAAAATTATTATAAATTTATATAAATAGTTATACATTAATAATTTATTTTATA
*
3233040 TAAATATTTATATATTCATATATT
260 TAAATATTTATATATTAATATATT
*
3233064 CTTGTCAT
1 TTTGTCAT
3233072 GTTCATATTA
Statistics
Matches: 271, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
283 16 0.06
284 255 0.94
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (283 bp):
TTTGTCATTTGATTCAATTTAAAAAAAATTATATATTTGTATCATATTCATGTCATATCTCCATT
CACGACATATTTTACATGATTTATCATAATAATTTAATTTAAAGTATTATATCTCAATTCATAAC
ATTTTTTCATAATTTGTTATAGTGATTTAATTAAAAAAATTATATCTTTTTACGTGTTTGTGTTA
TTTTTATTTATAAAAATTATTATAAATTTATATAAATAGTTATACATTAATAATTTATTTTATAT
AAATATTTATATATTAATATATT
Found at i:3233060 original size:20 final size:19
Alignment explanation
Indices: 3232974--3233061 Score: 66
Period size: 20 Copynumber: 4.9 Consensus size: 19
3232964 GTGTTTGTGT
*
3232974 TATTTTTAT-TTATATAAA
1 TATTTATATATTATATAAA
*
3232992 T-TATTATAAATTTATATAAA
1 TAT-TTATATA-TTATATAAA
*
3233012 TAGTTATATATTA-AT--A
1 TATTTATATATTATATAAA
3233028 -ATTTAT-T-TTATATAAA
1 TATTTATATATTATATAAA
3233044 TATTTATATATTCATATA
1 TATTTATATATT-ATATA
3233062 TTCTTGTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 5 0.09
16 2 0.04
17 7 0.13
18 8 0.15
19 5 0.09
20 21 0.39
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
TATTTATATATTATATAAA
Found at i:3233354 original size:20 final size:22
Alignment explanation
Indices: 3233329--3233381 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
3233319 TCAAAATTTT
3233329 ATAAAATATTATTAT-A-TTAG
1 ATAAAATATTATTATGAGTTAG
*
3233349 ATAAAA-A-TATTATGAGTTAT
1 ATAAAATATTATTATGAGTTAG
3233369 ATAAAATATTATT
1 ATAAAATATTATT
3233382 TAAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 15 0.54
21 1 0.04
22 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
ATAAAATATTATTATGAGTTAG
Found at i:3233361 original size:18 final size:19
Alignment explanation
Indices: 3233329--3233380 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
3233319 TCAAAATTTT
* *
3233329 ATAAAATATTATTATATTAG
1 ATAAAATATTATGA-GTTAG
*
3233349 ATAAAAATATTATGAGTTAT
1 AT-AAAATATTATGAGTTAG
3233369 ATAAAATATTAT
1 ATAAAATATTAT
3233381 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.36
20 7 0.25
21 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (19 bp):
ATAAAATATTATGAGTTAG
Found at i:3233378 original size:32 final size:34
Alignment explanation
Indices: 3233342--3233413 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
3233332 AAATATTATT
*
3233342 ATATTAGATAAAAATATT-AT-GAGTTATATAAA
1 ATATTAGATAAAAATATTCATACAGTTATATAAA
** *
3233374 ATATTATTTAAAAATTTTCATCACAGTTATATAAA
1 ATATTAGATAAAAATATTCAT-ACAGTTATATAAA
3233409 ATATT
1 ATATT
3233414 GCCTAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 15 0.45
33 2 0.06
35 16 0.48
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (34 bp):
ATATTAGATAAAAATATTCATACAGTTATATAAA
Found at i:3233486 original size:19 final size:20
Alignment explanation
Indices: 3233439--3233490 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3233429 CTAGAACTAA
3233439 ATAAAATATTA-CACATTAC
1 ATAAAATATTATCACATTAC
*
3233458 ATACAAATATTATGA-ATTAC
1 ATA-AAATATTATCACATTAC
3233478 ATAAAATATTATC
1 ATAAAATATTATC
3233491 TAAGTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.41
20 16 0.55
21 1 0.03
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAATATTATCACATTAC
Found at i:3233558 original size:13 final size:15
Alignment explanation
Indices: 3233538--3233574 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
3233528 AAAATACTCG
3233538 ATTTTTATTAAAT-T
1 ATTTTTATTAAATAT
3233552 A-TTTTATT-AATAT
1 ATTTTTATTAAATAT
3233565 ATTTTTATTA
1 ATTTTTATTA
3233575 CCCATAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.15
13 9 0.45
14 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTATTAAATAT
Found at i:3244586 original size:26 final size:27
Alignment explanation
Indices: 3244528--3244590 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
3244518 AAAGAATTAT
3244528 TTTTTAAAATAAAAAATCATTTAAAAG
1 TTTTTAAAATAAAAAATCATTTAAAAG
* *
3244555 TATTTTAAAATAAAATAAT-TTTTATAA-
1 T-TTTTAAAATAAAA-AATCATTTAAAAG
3244582 TTTTTAAAA
1 TTTTTAAAA
3244591 ATTAAAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.25
27 2 0.06
28 19 0.59
29 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TTTTTAAAATAAAAAATCATTTAAAAG
Found at i:3247243 original size:55 final size:55
Alignment explanation
Indices: 3247159--3247268 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
3247149 TGAATATAAA
* *
3247159 AAAGTGTGTGCCCAGAGTAAGTTGAACATAAATGAGCTTAATTCAAATCAAGCTT
1 AAAGTGTATGCCCAGAGTAAGTTGAACATAAATGAGCTTAATGCAAATCAAGCTT
* *
3247214 AAAGTGTATGCCCAGAGTAAGTTGAACATAAATTAGCTTAATGCAAATGAAGCTT
1 AAAGTGTATGCCCAGAGTAAGTTGAACATAAATGAGCTTAATGCAAATCAAGCTT
3247269 TGGGAAGGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (55 bp):
AAAGTGTATGCCCAGAGTAAGTTGAACATAAATGAGCTTAATGCAAATCAAGCTT
Found at i:3247378 original size:16 final size:17
Alignment explanation
Indices: 3247357--3247390 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3247347 ACATGTGTAA
3247357 AATTAATTAAT-TTTTT
1 AATTAATTAATATTTTT
3247373 AATTAATTAATATTTTT
1 AATTAATTAATATTTTT
3247390 A
1 A
3247391 TTTTTATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTAATTAATATTTTT
Found at i:3247551 original size:26 final size:26
Alignment explanation
Indices: 3247515--3247567 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3247505 AAAATCAAGC
3247515 TATCTGTTAATACAAATAGACATAAT
1 TATCTGTTAATACAAATAGACATAAT
3247541 TATCTGTTAATACAAATAGACATAAT
1 TATCTGTTAATACAAATAGACATAAT
3247567 T
1 T
3247568 TTAGGCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (26 bp):
TATCTGTTAATACAAATAGACATAAT
Found at i:3252860 original size:20 final size:20
Alignment explanation
Indices: 3252809--3252871 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
3252799 GTAATTTTAG
* *
3252809 ATTATTAAAATCATTTAAAA
1 ATTATTAAAATTATATAAAA
* *
3252829 GACTAATAAAATTATATAAAA
1 -ATTATTAAAATTATATAAAA
*
3252850 ATTATTAAAATTATATCAAA
1 ATTATTAAAATTATATAAAA
3252870 AT
1 AT
3252872 AATAACTAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (20 bp):
ATTATTAAAATTATATAAAA
Found at i:3252861 original size:9 final size:10
Alignment explanation
Indices: 3252834--3252871 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
3252824 TAAAAGACTA
3252834 ATAAAATTAT
1 ATAAAATTAT
3252844 ATAAAAATTAT
1 AT-AAAATTAT
3252855 -TAAAATTAT
1 ATAAAATTAT
3252864 ATCAAAAT
1 AT-AAAAT
3252872 AATAACTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.32
10 4 0.16
11 13 0.52
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAAATTAT
Found at i:3252871 original size:31 final size:32
Alignment explanation
Indices: 3252836--3252908 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
3252826 AAAGACTAAT
* *
3252836 AAAATTATATAA-AAATTATTAAAATTATATC
1 AAAATTATATAACAAACTACTAAAATTATATC
*
3252867 AAAA-TA-ATAACTAAGCTACTAAAATTATATC
1 AAAATTATATAAC-AAACTACTAAAATTATATC
3252898 AAATATTATAT
1 AAA-ATTATAT
3252909 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.12
30 2 0.06
31 23 0.68
32 1 0.03
33 2 0.06
34 2 0.06
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAATTATATAACAAACTACTAAAATTATATC
Found at i:3256914 original size:2 final size:2
Alignment explanation
Indices: 3256907--3256953 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3256897 GTGCTTTGAA
3256907 AT 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 AT
3256949 AT AT A
1 AT AT A
3256954 GCCTTTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3257246 original size:22 final size:23
Alignment explanation
Indices: 3257209--3257253 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3257199 GATATCAATT
3257209 AATTTAATTAATAAAATTATAAAA
1 AATTTAA-TAATAAAATTATAAAA
3257233 AATTTAA-AATAAAATTATAAA
1 AATTTAATAATAAAATTATAAA
3257254 TATTTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.67
24 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATTTAATAATAAAATTATAAAA
Found at i:3257254 original size:12 final size:12
Alignment explanation
Indices: 3257218--3257255 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
3257208 TAATTTAATT
3257218 AATAAAATTATA
1 AATAAAATTATA
*
3257230 AA-AAATTTA-A
1 AATAAAATTATA
3257240 AATAAAATTATA
1 AATAAAATTATA
3257252 AATA
1 AATA
3257256 TTTTGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.14
11 12 0.55
12 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAAATTATA
Found at i:3269125 original size:2 final size:2
Alignment explanation
Indices: 3269120--3269144 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3269110 AGAGAAAGGC
3269120 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
3269145 TATCATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3269905 original size:36 final size:36
Alignment explanation
Indices: 3269865--3269935 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
3269855 CAATGCCAGT
3269865 AACATAGTTTTTAAGAAACAATAAAGGAGAGGAAAC
1 AACATAGTTTTTAAGAAACAATAAAGGAGAGGAAAC
3269901 AACATAGTTTTTAAGAAACAATAAAGGAGAGGAAA
1 AACATAGTTTTTAAGAAACAATAAAGGAGAGGAAA
3269936 TATAAGCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20
Consensus pattern (36 bp):
AACATAGTTTTTAAGAAACAATAAAGGAGAGGAAAC
Found at i:3272277 original size:10 final size:10
Alignment explanation
Indices: 3272262--3272286 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3272252 TTATTGTCTT
3272262 TTTTTTTTTC
1 TTTTTTTTTC
3272272 TTTTTTTTTC
1 TTTTTTTTTC
3272282 TTTTT
1 TTTTT
3272287 AAGATAGGGA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:3275552 original size:13 final size:13
Alignment explanation
Indices: 3275534--3275569 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3275524 TTTTATTTTT
**
3275534 TTAAATATTTATA
1 TTAAATATAAATA
3275547 TTAAATATAAATA
1 TTAAATATAAATA
3275560 TTAAATATAA
1 TTAAATATAA
3275570 CTTTTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:3276975 original size:17 final size:18
Alignment explanation
Indices: 3276941--3276983 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3276931 TGAATTGTAG
**
3276941 TTAATTTTTTTTTGAAAT
1 TTAATTTTGGTTTGAAAT
3276959 TTAATTTTGGTTT-AAAT
1 TTAATTTTGGTTTGAAAT
*
3276976 TTAGTTTT
1 TTAATTTT
3276984 ACAGTCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
TTAATTTTGGTTTGAAAT
Found at i:3277046 original size:23 final size:22
Alignment explanation
Indices: 3277018--3277087 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
3277008 ATAATAAAAT
3277018 AATTAAAAATTATTTTTAATTA
1 AATTAAAAATTATTTTTAATTA
* *
3277040 ATATTAATATATT-TTTATAATTA
1 A-ATTAA-AAATTATTTTTAATTA
* *
3277063 AATT-TAAATTATTTATTTATTA
1 AATTAAAAATTATTT-TTAATTA
3277085 AAT
1 AAT
3277088 AATGATTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 12 0.32
23 15 0.39
24 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTAAAAATTATTTTTAATTA
Found at i:3280073 original size:2 final size:2
Alignment explanation
Indices: 3280066--3280114 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3280056 GCTTAGTTTG
3280066 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3280108 AC AC AC A
1 AC AC AC A
3280115 TATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3284349 original size:2 final size:2
Alignment explanation
Indices: 3284342--3284376 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3284332 ATGCCAAACC
3284342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3284377 GTCTTAGTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3288513 original size:21 final size:21
Alignment explanation
Indices: 3288487--3288597 Score: 82
Period size: 22 Copynumber: 5.1 Consensus size: 21
3288477 TATCAACATT
*
3288487 AAATAATATAAATATAATGTA
1 AAATAATATAAATATAATATA
3288508 AAATAATTAATTTAATATATAATATA
1 AAATAA-T-A--TAA-ATATAATATA
* *
3288534 AAAAAATATAAAAATAATAT-
1 AAATAATATAAATATAATATA
* *
3288554 AAAT-ATATAAATATATTAAA
1 AAATAATATAAATATAATATA
* **
3288574 AAATTAAAATTTATATAATATA
1 AAA-TAATATAAATATAATATA
3288596 AA
1 AA
3288598 TTATTAATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
19 12 0.17
20 6 0.09
21 15 0.21
22 17 0.24
23 1 0.01
24 1 0.01
25 4 0.06
26 14 0.20
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (21 bp):
AAATAATATAAATATAATATA
Found at i:3288543 original size:10 final size:11
Alignment explanation
Indices: 3288487--3288556 Score: 61
Period size: 11 Copynumber: 6.1 Consensus size: 11
3288477 TATCAACATT
3288487 AAATAATATAA
1 AAATAATATAA
* *
3288498 ATATAATGTAAA
1 AAATAATAT-AA
*
3288510 ATAATTAATTTAA
1 A-AA-TAATATAA
*
3288523 TATATAATATAA
1 -AAATAATATAA
3288535 AAA-AATATAA
1 AAATAATATAA
3288545 AAATAATATAA
1 AAATAATATAA
3288556 A
1 A
3288557 TATATAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
10 10 0.21
11 17 0.36
12 10 0.21
13 4 0.09
14 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (11 bp):
AAATAATATAA
Found at i:3288543 original size:17 final size:18
Alignment explanation
Indices: 3288521--3288575 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
3288511 TAATTAATTT
3288521 AATATATAATATAA-AAA
1 AATATATAATATAATAAA
* *
3288538 AATATA-AAAATAATATA
1 AATATATAATATAATAAA
*
3288555 AATATATAAATATATTAAA
1 AATATAT-AATATAATAAA
3288574 AA
1 AA
3288576 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.20
17 14 0.47
19 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATATAATATAATAAA
Found at i:3288569 original size:8 final size:8
Alignment explanation
Indices: 3288521--3288635 Score: 58
Period size: 8 Copynumber: 13.8 Consensus size: 8
3288511 TAATTAATTT
3288521 AATATATA
1 AATATATA
* *
3288529 ATATAAAAA
1 A-ATATATA
*
3288538 AATATAAA
1 AATATATA
3288546 AATAATATA
1 AAT-ATATA
3288555 AATATATA
1 AATATATA
3288563 AATATATTA
1 AATATA-TA
*
3288572 AA-AAATTA
1 AATATA-TA
*
3288580 AA-ATTTA
1 AATATATA
*
3288587 TATAATATA
1 AAT-ATATA
*
3288596 AAT-TATT
1 AATATATA
3288603 AATATATTAA
1 AATATA-T-A
3288613 AATTTATATA
1 AA--TATATA
3288623 AATATAT-
1 AATATATA
3288630 AATATA
1 AATATA
3288636 ATTCGTTAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
7 15 0.18
8 36 0.42
9 24 0.28
10 5 0.06
11 1 0.01
12 4 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATATATA
Found at i:3288581 original size:17 final size:18
Alignment explanation
Indices: 3288521--3288604 Score: 63
Period size: 19 Copynumber: 4.9 Consensus size: 18
3288511 TAATTAATTT
3288521 AATATATAATATA--AAAA
1 AATATA-AATATATTAAAA
* *
3288538 AATATAAAAATAATATAAA
1 AATATAAATATATTA-AAA
*
3288557 TATATAAATATATTAAAA
1 AATATAAATATATTAAAA
* *
3288575 AAT-TAAA-AT-TTATAT
1 AATATAAATATATTAAAA
3288590 AATATAAAT-TATTAA
1 AATATAAATATATTAA
3288605 TATATTAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.13
16 12 0.23
17 13 0.25
18 6 0.11
19 15 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAAATATATTAAAA
Found at i:3288612 original size:32 final size:34
Alignment explanation
Indices: 3288521--3288635 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 34
3288511 TAATTAATTT
* *
3288521 AATATATAATATA--AAAAAATATAAAAATAATATAA
1 AATATA-AATATATTAAAAAAT-TAAAATTTATAT-A
3288556 ATATATAAATATATTAAAAAATTAAAATTTATAT-
1 A-ATATAAATATATTAAAAAATTAAAATTTATATA
* *
3288590 AATATAAAT-TATTAATATATTAAAATTTATATA
1 AATATAAATATATTAAAAAATTAAAATTTATATA
3288623 AATATATAATATA
1 AATATA-AATATA
3288636 ATTCGTTAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
32 21 0.30
33 14 0.20
34 4 0.06
35 9 0.13
36 15 0.21
37 7 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AATATAAATATATTAAAAAATTAAAATTTATATA
Found at i:3294192 original size:38 final size:38
Alignment explanation
Indices: 3294149--3294282 Score: 187
Period size: 38 Copynumber: 3.5 Consensus size: 38
3294139 TAGCCACCGA
* **
3294149 CCAATTTCAAATTGAATTCTCTAGTCGTCAACCGTTGG
1 CCAATTTCAAATTGAATTCTCTAGCCGTCAACCGTCAG
* * *
3294187 CCAATTTTAAATTGAATTCTCTAGCCGTCAGCCGCCAG
1 CCAATTTCAAATTGAATTCTCTAGCCGTCAACCGTCAG
* * *
3294225 CCAATTTCAAATTGAATTCTCTAACCGTCAACCATCAA
1 CCAATTTCAAATTGAATTCTCTAGCCGTCAACCGTCAG
3294263 CCAATTTCAAATTGAATTCT
1 CCAATTTCAAATTGAATTCT
3294283 TTAAACTCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 84 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (38 bp):
CCAATTTCAAATTGAATTCTCTAGCCGTCAACCGTCAG
Found at i:3294502 original size:17 final size:17
Alignment explanation
Indices: 3294460--3294530 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
3294450 TTCGTGTCTC
3294460 ATTT-ATATTATATTAT
1 ATTTAATATTATATTAT
**
3294476 ATTTTTTATTATATTAT
1 ATTTAATATTATATTAT
*
3294493 ATTTAATA-T-TGTTAT
1 ATTTAATATTATATTAT
3294508 ATTTAAT-TTATATTAT
1 ATTTAATATTATATTAT
*
3294524 ATATAAT
1 ATTTAAT
3294531 TGAATATCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.28
16 16 0.35
17 17 0.37
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (17 bp):
ATTTAATATTATATTAT
Found at i:3296004 original size:3 final size:3
Alignment explanation
Indices: 3295996--3296028 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3295986 TCACTTTTGA
3295996 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3296029 CACTTCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3298136 original size:27 final size:29
Alignment explanation
Indices: 3298112--3298186 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 29
3298102 TATGTTTAAA
*
3298112 ATATTATATATTTATATAAATTTTAATAC
1 ATATTATATATTTATATAAATTTTAACAC
* *
3298141 GTTATTAATTTATATTATATAAATTTTAACAC
1 -ATATT-ATATAT-TTATATAAATTTTAACAC
3298173 AT-TTATATATTTAT
1 ATATTATATATTTAT
3298187 GTTATATTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.11
29 5 0.13
30 6 0.16
31 6 0.16
32 17 0.45
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (29 bp):
ATATTATATATTTATATAAATTTTAACAC
Found at i:3298185 original size:33 final size:32
Alignment explanation
Indices: 3298112--3298193 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
3298102 TATGTTTAAA
*
3298112 ATATTATATATTTATATAAATTTTAATACGTTAT
1 ATATT-TATA-TTATATAAATTTTAACACGTTAT
*
3298146 -TAATTTATATTATATAAATTTTAACACATTTAT
1 AT-ATTTATATTATATAAATTTTAACAC-GTTAT
*
3298179 ATATTTATGTTATAT
1 ATATTTATATTATAT
3298194 TCGTATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 17 0.40
33 21 0.50
34 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (32 bp):
ATATTTATATTATATAAATTTTAACACGTTAT
Found at i:3300252 original size:2 final size:2
Alignment explanation
Indices: 3300245--3300278 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3300235 AAACAATACA
*
3300245 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3300279 TCACAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3305528 original size:20 final size:18
Alignment explanation
Indices: 3305505--3305550 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
3305495 ACATATTATT
3305505 AATATAATAAAATTTATATA
1 AATATAATAAAA--TATATA
3305525 AATATAAAATAAAATATATA
1 AATAT--AATAAAATATATA
3305545 AATATA
1 AATATA
3305551 TATTAATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.04
20 16 0.67
22 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:3305551 original size:22 final size:22
Alignment explanation
Indices: 3305487--3305552 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
3305477 AAAATTAATT
* *
3305487 TATAAAAT-ACATAT-TATTAA
1 TATAAAATAAAATATATATAAA
*
3305507 TAT--AATAAAATTTATATAAA
1 TATAAAATAAAATATATATAAA
3305527 TATAAAATAAAATATATA-AATA
1 TATAAAATAAAATATATATAA-A
3305549 TATA
1 TATA
3305553 TTAATACTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 11 0.30
21 2 0.05
22 17 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAAATAAAATATATATAAA
Found at i:3306100 original size:16 final size:16
Alignment explanation
Indices: 3306051--3306102 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
3306041 TCTTATATTT
3306051 AATAATA-TTTAAATA
1 AATAATATTTTAAATA
* *
3306066 AATATTATTTTTAATTA
1 AATAATA-TTTTAAATA
*
3306083 AATAATATTTTGAATA
1 AATAATATTTTAAATA
3306099 AATA
1 AATA
3306103 TTTAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 6 0.20
16 11 0.37
17 13 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AATAATATTTTAAATA
Found at i:3307875 original size:2 final size:2
Alignment explanation
Indices: 3307868--3307893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3307858 ATGTTGTGTA
3307868 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
3307894 TTGGAGTTCA
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:3309441 original size:39 final size:39
Alignment explanation
Indices: 3309398--3309477 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
3309388 TGTTGGTCAC
3309398 AACATGTCTCTAGTCAATACCCAACATCATCCCAAAAGA
1 AACATGTCTCTAGTCAATACCCAACATCATCCCAAAAGA
*
3309437 AACATGTCTCTAGTCAATACCCAACATCATCTCAAAAGA
1 AACATGTCTCTAGTCAATACCCAACATCATCCCAAAAGA
3309476 AA
1 AA
3309478 AAAAAAAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.42, C:0.29, G:0.07, T:0.21
Consensus pattern (39 bp):
AACATGTCTCTAGTCAATACCCAACATCATCCCAAAAGA
Found at i:3311081 original size:2 final size:2
Alignment explanation
Indices: 3311074--3311098 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3311064 ATCTATTATG
3311074 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3311099 CCCTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3313089 original size:23 final size:22
Alignment explanation
Indices: 3313046--3313107 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
3313036 AAAAAAAAAG
*
3313046 ATTATATATATTAAGATTCATATT
1 ATTAAATATATTAA-ATTCAT-TT
*
3313070 -TTAAATCTATTAAATATCATTT
1 ATTAAATATATTAAAT-TCATTT
3313092 ATTAAATATAATTAAA
1 ATTAAATAT-ATTAAA
3313108 CGAATCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 4 0.12
23 22 0.69
24 6 0.19
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTAAATATATTAAATTCATTT
Found at i:3313202 original size:3 final size:3
Alignment explanation
Indices: 3313194--3313246 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
3313184 AAAGCAATTG
* * *
3313194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TGA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3313242 TTA TT
1 TTA TT
3313247 GAATTTAGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3317091 original size:26 final size:26
Alignment explanation
Indices: 3317062--3317139 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 26
3317052 CCGCTCAATC
3317062 TTTTTTTAATTATATAATATATAATA
1 TTTTTTTAATTATATAATATATAATA
* * * *
3317088 TTTTTATATTTATATATTATGTAAT-
1 TTTTTTTAATTATATAATATATAATA
* * * *
3317113 TTATATTAAATAAATAATATA-AATA
1 TTTTTTTAATTATATAATATATAATA
3317138 TT
1 TT
3317140 AAAAATTATA
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 21 0.54
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTTTTTAATTATATAATATATAATA
Found at i:3321134 original size:18 final size:16
Alignment explanation
Indices: 3321111--3321153 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
3321101 TTAATTATTT
3321111 TTTAAATATATAAAATAA
1 TTTAAATATA-AAAAT-A
*
3321129 TTTAAAAATAAAAATA
1 TTTAAATATAAAAATA
*
3321145 TTTATATAT
1 TTTAAATAT
3321154 TCAATATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATATAAAAATA
Found at i:3321147 original size:16 final size:18
Alignment explanation
Indices: 3321111--3321148 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3321101 TTAATTATTT
*
3321111 TTTAAATATATAAAATAA
1 TTTAAAAATATAAAATAA
3321129 TTTAAAAATA-AAAAT-A
1 TTTAAAAATATAAAATAA
3321145 TTTA
1 TTTA
3321149 TATATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAATATAAAATAA
Found at i:3321502 original size:13 final size:13
Alignment explanation
Indices: 3321484--3321511 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3321474 GATCTTCGAT
3321484 TTAAATATAAATA
1 TTAAATATAAATA
3321497 TTAAATATAAATA
1 TTAAATATAAATA
3321510 TT
1 TT
3321512 TATTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAATATAAATA
Done.