Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005579.1 Hibiscus syriacus cultivar Beakdansim tig00012946_pilon, whole genome shotgun sequence
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: 288874
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:9491 original size:24 final size:22
Alignment explanation
Indices: 9448--9501 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
9438 GGCGATCCAC
*
9448 AAGATATGTCCTTTGCAATTTC-A
1 AAGA-ATGTCCTTTG-AAATTCAA
9471 AAGAATGTACCTATTGAAATTCAA
1 AAGAATGT-CCT-TTGAAATTCAA
9495 AAGAATG
1 AAGAATG
9502 AGCCAATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.15
23 12 0.44
24 11 0.41
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (22 bp):
AAGAATGTCCTTTGAAATTCAA
Found at i:22444 original size:19 final size:19
Alignment explanation
Indices: 22420--22464 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
22410 CATCATTCAT
22420 GAAAGGTCACAATGTTTGA
1 GAAAGGTCACAATGTTTGA
22439 GAAAGGTCACAATGTTTGA
1 GAAAGGTCACAATGTTTGA
22458 GAAAGGT
1 GAAAGGT
22465 AACCCTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.29, T:0.24
Consensus pattern (19 bp):
GAAAGGTCACAATGTTTGA
Found at i:23923 original size:23 final size:23
Alignment explanation
Indices: 23878--23923 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
23868 GTATACCTAT
*
23878 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
23901 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
23924 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:25254 original size:19 final size:20
Alignment explanation
Indices: 25238--25287 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
25228 ATTTATTTCA
25238 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
25257 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
*
25275 TATTCATTTCTTA
1 T-TTCATTACTTA
25288 AACCCATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:25555 original size:9 final size:9
Alignment explanation
Indices: 25541--25596 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 9
25531 TTGGAGTGCA
25541 AAAAGAAAG
1 AAAAGAAAG
*
25550 AAAAGACA-
1 AAAAGAAAG
25558 AAAAG-AAG
1 AAAAGAAAG
25566 AAAA-AGAAG
1 AAAAGA-AAG
25575 AAAAGAAAAG
1 AAAAG-AAAG
25585 AAAA-AAAG
1 AAAAGAAAG
25593 AAAA
1 AAAA
25597 ATTCAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
7 1 0.03
8 17 0.43
9 14 0.35
10 7 0.17
11 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:25561 original size:17 final size:17
Alignment explanation
Indices: 25539--25588 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
25529 AATTGGAGTG
25539 CAAAAAGAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
25556 CAAAAAG-AAGAAAAAGA
1 CAAAAAGAAAG-AAAAGA
25573 -AGAAAAGAAAAGAAAA
1 CA-AAAAG-AAAGAAAA
25589 AAAGAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.14
17 18 0.62
18 4 0.14
19 3 0.10
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:25597 original size:9 final size:9
Alignment explanation
Indices: 25540--25597 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
25530 ATTGGAGTGC
25540 AAAAAGAAA
1 AAAAAGAAA
*
25549 GAAAAGACAA
1 AAAAAGA-AA
25559 AAAGAAGAAA
1 AAA-AAGAAA
*
25569 AAGAAGAAA
1 AAAAAGAAA
25578 AGAAAAG-AA
1 A-AAAAGAAA
25587 AAAAAGAAA
1 AAAAAGAAA
25596 AA
1 AA
25598 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 5 0.12
9 20 0.49
10 12 0.29
11 4 0.10
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:28522 original size:23 final size:23
Alignment explanation
Indices: 28477--28522 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28467 TTATGCCTAT
*
28477 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
28500 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
28523 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:29851 original size:19 final size:20
Alignment explanation
Indices: 29835--29884 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
29825 ATTTATTTCA
29835 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
29854 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
*
29872 TATTCATTTCTTA
1 T-TTCATTACTTA
29885 AACCCATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:31937 original size:23 final size:25
Alignment explanation
Indices: 31907--31960 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
31897 AAAATCAGAA
*
31907 AAGAAATT-AAAGCAATCCAAAA-G
1 AAGAAATTGAAAGCAATCAAAAAGG
*
31930 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAATTGAAAGCAATCAAAAAGG
31955 AAGAAA
1 AAGAAA
31961 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 8 0.30
24 12 0.44
25 7 0.26
ACGTcount: A:0.61, C:0.11, G:0.17, T:0.11
Consensus pattern (25 bp):
AAGAAATTGAAAGCAATCAAAAAGG
Found at i:31966 original size:6 final size:6
Alignment explanation
Indices: 31955--31983 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
31945 CTCAAAAAGG
31955 AAGAAA AAG-AA AAGAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
31984 GAAAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:31966 original size:25 final size:24
Alignment explanation
Indices: 31915--31966 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
31905 AAAAGAAATT
* **
31915 AAAGCAATCCAAAAGAAGAAATTG
1 AAAGCAATCAAAAAGAAGAAAAAG
*
31939 AAAGCACTCAAAAAGGAAGAAAAAG
1 AAAGCAATCAAAAA-GAAGAAAAAG
31964 AAA
1 AAA
31967 AGAAAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.63, C:0.12, G:0.17, T:0.08
Consensus pattern (24 bp):
AAAGCAATCAAAAAGAAGAAAAAG
Found at i:31969 original size:11 final size:11
Alignment explanation
Indices: 31955--31987 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
31945 CTCAAAAAGG
31955 AAGAAAAAGAA
1 AAGAAAAAGAA
31966 AAGAAAAAGAA
1 AAGAAAAAGAA
*
31977 AA-AGAAAGAA
1 AAGAAAAAGAA
31987 A
1 A
31988 GTTGAAGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:31977 original size:17 final size:16
Alignment explanation
Indices: 31955--31987 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
31945 CTCAAAAAGG
31955 AAGAAAAAGAAAAGAAA
1 AAGAAAAAG-AAAGAAA
31972 AAGAAAAAGAAAGAAA
1 AAGAAAAAGAAAGAAA
31988 GTTGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAGAAA
Found at i:35079 original size:23 final size:24
Alignment explanation
Indices: 35033--35079 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
35023 AGAAAATAAG
***
35033 CACTCAATAAGAAGAAATTGAAAA
1 CACTCAATAAGAAGAAAAAAAAAA
35057 CACTCAA-AAGAAGAAAAAAAAAA
1 CACTCAATAAGAAGAAAAAAAAAA
35080 AAGAAAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.66, C:0.13, G:0.11, T:0.11
Consensus pattern (24 bp):
CACTCAATAAGAAGAAAAAAAAAA
Found at i:39959 original size:24 final size:24
Alignment explanation
Indices: 39913--39964 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
39903 CCTTGGCACT
* * *
39913 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAACTATTGGAACA
* *
39937 TCAAGTGGCATAACTATTGGAACG
1 TCAAGTGGCACAACTATTGGAACA
39961 TCAA
1 TCAA
39965 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAACTATTGGAACA
Found at i:44216 original size:5 final size:5
Alignment explanation
Indices: 44206--44236 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
44196 CTTCAACTTC
*
44206 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
44237 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:44434 original size:24 final size:24
Alignment explanation
Indices: 44389--44434 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
44379 CCACTAAAGC
*
44389 TCTGATACCACTTGATGCAAGGTT
1 TCTGATACCACTTAATGCAAGGTT
* * *
44413 TCTGATGCCGCTTAATGTAAGG
1 TCTGATACCACTTAATGCAAGG
44435 CACTTATACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (24 bp):
TCTGATACCACTTAATGCAAGGTT
Found at i:52742 original size:20 final size:20
Alignment explanation
Indices: 52704--52742 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52694 TGTATAAAGT
**
52704 ATATAAGCTAATATGAATGC
1 ATATAAGCTAATAAAAATGC
*
52724 ATATGAGCTAATAAAAATG
1 ATATAAGCTAATAAAAATG
52743 AATGATAGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (20 bp):
ATATAAGCTAATAAAAATGC
Found at i:66161 original size:23 final size:25
Alignment explanation
Indices: 66112--66162 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
66102 TTCTTTTCTT
*
66112 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTGGAGTGCTTTCAA
*
66137 TTTCTT-CTTTTGGATTGCTTT-AA
1 TTTCTTCCTTTTGGAGTGCTTTCAA
66160 TTT
1 TTT
66163 ATTTTCTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTGGAGTGCTTTCAA
Found at i:67075 original size:20 final size:22
Alignment explanation
Indices: 67035--67080 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
67025 TGCTTGAATG
67035 ATGCACATGGCAGTCTACTTG-A
1 ATGCACATGG-AGTCTACTTGCA
*
67057 ATGCACATGG-GTCTTCTTGCA
1 ATGCACATGGAGTCTACTTGCA
67078 ATG
1 ATG
67081 TTTTGGTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (22 bp):
ATGCACATGGAGTCTACTTGCA
Found at i:69854 original size:2 final size:2
Alignment explanation
Indices: 69849--69880 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69839 TTTTTAATTA
69849 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
69881 GTAGATTATG
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:71961 original size:11 final size:10
Alignment explanation
Indices: 71947--71987 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
71937 TTGCAATTCA
71947 TTTATCTTTT
1 TTTATCTTTT
71957 CTTTATCTTTT
1 -TTTATCTTTT
71968 TTTAATCTTATT
1 TTT-ATCTT-TT
71980 TTTATCTT
1 TTTATCTT
71988 GTTTCCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.11
11 20 0.71
12 5 0.18
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:72327 original size:11 final size:11
Alignment explanation
Indices: 72311--72339 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
72301 ATTTTTTCAA
72311 AAAAAAAAAAC
1 AAAAAAAAAAC
72322 AAAAAAAAAAC
1 AAAAAAAAAAC
72333 AAAAAAA
1 AAAAAAA
72340 GGCAAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:78430 original size:24 final size:24
Alignment explanation
Indices: 78398--78443 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
78388 GGTACAAGTG
78398 CCTTACATCAAGTGGCATCAGAAA
1 CCTTACATCAAGTGGCATCAGAAA
* *
78422 CCTTGCATCAAGTGGTATCAGA
1 CCTTACATCAAGTGGCATCAGA
78444 GCCTTGGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (24 bp):
CCTTACATCAAGTGGCATCAGAAA
Found at i:79573 original size:72 final size:71
Alignment explanation
Indices: 79455--79593 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 71
79445 AATACATCCT
* * * * * *
79455 TTGGCTGAATTCATCCCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
79520 ATGTATC
65 ATGTATC
*
79527 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
79590 AATG
64 AATG
79594 GATGAATTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
71 17 0.29
72 31 0.53
73 10 0.17
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:84362 original size:22 final size:23
Alignment explanation
Indices: 84328--84374 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
84318 CACAAACAAG
**
84328 AAAGCTAAAAAAATGGTTAAATA
1 AAAGCTAAAAAAATGGAAAAATA
*
84351 AAAG-TAATAAAATGGAAAAATA
1 AAAGCTAAAAAAATGGAAAAATA
84373 AA
1 AA
84375 TATGGCAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.66, C:0.02, G:0.13, T:0.19
Consensus pattern (23 bp):
AAAGCTAAAAAAATGGAAAAATA
Found at i:93178 original size:20 final size:20
Alignment explanation
Indices: 93153--93191 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
93143 TAAAGGGAAT
93153 AATAAT-ATAAGTAATGAAAA
1 AATAATAATAAG-AATGAAAA
93173 AATAATAATAAGAATGAAA
1 AATAATAATAAGAATGAAA
93192 TGAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
AATAATAATAAGAATGAAAA
Found at i:94145 original size:30 final size:31
Alignment explanation
Indices: 94106--94165 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
94096 ACATGCTGCC
**
94106 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
94137 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
94166 TAAAGATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:95292 original size:24 final size:25
Alignment explanation
Indices: 95264--95325 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
95254 TTGTGAATCA
95264 CCAAAAGTCATGA-CTATTGGTTCTT
1 CCAAAAGTCATGATCTATTGGTT-TT
*
95289 -CAAAAGTCAT-ATCTTTTGGTTTT
1 CCAAAAGTCATGATCTATTGGTTTT
*
95312 CCAAAAGACATGAT
1 CCAAAAGTCATGAT
95326 TTTGAATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 3 0.09
24 27 0.84
25 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (25 bp):
CCAAAAGTCATGATCTATTGGTTTT
Found at i:97884 original size:30 final size:31
Alignment explanation
Indices: 97843--97902 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
97833 ACATGCTGCC
**
97843 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
97874 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
97903 TAACGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:102663 original size:24 final size:23
Alignment explanation
Indices: 102636--102682 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
102626 AGAAAATCAG
102636 AAAAGAAATTGAAGCACTCAAAAA
1 AAAAGAAATT-AAGCACTCAAAAA
* *
102660 AAAAGAAATTCAGCATTCAAAAA
1 AAAAGAAATTAAGCACTCAAAAA
102683 GAAGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAAGAAATTAAGCACTCAAAAA
Found at i:102714 original size:4 final size:5
Alignment explanation
Indices: 102684--102713 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
102674 ATTCAAAAAG
102684 AAGAA AAGAA AAGAA AAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
102714 GTTGAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:103973 original size:24 final size:24
Alignment explanation
Indices: 103946--104002 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
103936 GACATGACCT
*
103946 TTGACGTTCCAACAATTATGCCAC
1 TTGAAGTTCCAACAATTATGCCAC
103970 TTGAAGTTCCAACAATTATGCCAC
1 TTGAAGTTCCAACAATTATGCCAC
103994 TTGAAGTTC
1 TTGAAGTTC
104003 AAAAAGATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (24 bp):
TTGAAGTTCCAACAATTATGCCAC
Found at i:104037 original size:24 final size:24
Alignment explanation
Indices: 103946--104037 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
103936 GACATGACCT
* *
103946 TTGACGTTCCAACAA-TTATGCCAC
1 TTGAAGTTCC-ACAAGTTGTGCCAC
*
103970 TTGAAGTTCCAACAA-TTATGCCAC
1 TTGAAGTTCC-ACAAGTTGTGCCAC
* * * *
103994 TTGAAGTTCAAAAAGATGTGTCAC
1 TTGAAGTTCCACAAGTTGTGCCAC
*
104018 TTGAAGTGCCACAAGTTGTG
1 TTGAAGTTCCACAAGTTGTG
104038 AGCATTGAGG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.05
24 54 0.95
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (24 bp):
TTGAAGTTCCACAAGTTGTGCCAC
Found at i:111339 original size:90 final size:91
Alignment explanation
Indices: 111185--111366 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
111175 CCTAGAACAC
* * *
111185 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGTATGAGGATCATTTAGGCTCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
111250 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
111276 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
111340 AAGAGCTCTCTCCCTGTTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
111366 C
1 C
111367 ATCATTTCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 61 0.76
91 19 0.24
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:117753 original size:23 final size:24
Alignment explanation
Indices: 117711--117763 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
117701 TTTCTTTCTT
117711 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
117735 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
117758 TTTCTT
1 TTTCTT
117764 TGCTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:128137 original size:19 final size:21
Alignment explanation
Indices: 128113--128164 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
128103 CGGCCAAGAG
*
128113 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
128132 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
128153 CATGTATTTTCA
1 CATGTATTTTCA
128165 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:132100 original size:19 final size:21
Alignment explanation
Indices: 132076--132127 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
132066 CGGCCAAGAG
*
132076 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
132095 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
132116 CATGTATTTTCA
1 CATGTATTTTCA
132128 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:133798 original size:13 final size:13
Alignment explanation
Indices: 133782--133823 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
133772 AGTCTTTTTC
133782 TTTTCTTTTTTGT
1 TTTTCTTTTTTGT
* *
133795 TTTTCTTCTTTCT
1 TTTTCTTTTTTGT
133808 TTTTCTCTTTTTGT
1 TTTTCT-TTTTTGT
133822 TT
1 TT
133824 CTTTTGTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTTGT
Found at i:133799 original size:18 final size:18
Alignment explanation
Indices: 133776--133833 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
133766 TGTAGGAGTC
133776 TTTTTCTTTTCTTTTTTG
1 TTTTTCTTTTCTTTTTTG
*
133794 TTTTTCTTCTTTCTTTTTCTC
1 TTTTTC-T-TTTCTTTTT-TG
*
133815 TTTTT-GTTTCTTTTGTTG
1 TTTTTCTTTTCTTTT-TTG
133833 T
1 T
133834 AGCACTTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 16 0.48
19 2 0.06
20 9 0.27
21 6 0.18
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTTTG
Found at i:133818 original size:27 final size:24
Alignment explanation
Indices: 133774--133823 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 24
133764 GATGTAGGAG
133774 TCTTTTTCTTTTCTTTTTTGTTTT
1 TCTTTTTCTTTTCTTTTTTGTTTT
133798 TCTTCTTTCTTTTTCTCTTTTTGTTT
1 TCTT-TTTC-TTTTCT-TTTTTGTTT
133824 CTTTTGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 6 0.26
27 9 0.39
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (24 bp):
TCTTTTTCTTTTCTTTTTTGTTTT
Found at i:134053 original size:32 final size:32
Alignment explanation
Indices: 133992--134053 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
133982 ACAAAATTAA
*
133992 AAGAAAGAAATGATTAAAATGGAATATGGAAG
1 AAGAAAGAAATGATTAAAAAGGAATATGGAAG
134024 AAGAAAGGAAATGA-TAAGAAAGGAA-ATGGA
1 AAGAAA-GAAATGATTAA-AAAGGAATATGGA
134054 TTGAAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (32 bp):
AAGAAAGAAATGATTAAAAAGGAATATGGAAG
Found at i:137897 original size:33 final size:33
Alignment explanation
Indices: 137855--137923 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
137845 GTTGATGAAT
*
137855 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
137888 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
137921 GAA
1 GAA
137924 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:137928 original size:13 final size:12
Alignment explanation
Indices: 137909--137973 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
137899 TTATTGGCGT
137909 GATATGGTGATG
1 GATATGGTGATG
137921 GAATATGGTGAT-
1 G-ATATGGTGATG
*
137933 GATATAGGCG-T-
1 GATAT-GGTGATG
137944 GATAATGGTGATG
1 GAT-ATGGTGATG
137957 GACTATGGTGAT-
1 GA-TATGGTGATG
137969 GATAT
1 GATAT
137974 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:137964 original size:36 final size:36
Alignment explanation
Indices: 137894--138006 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
137884 AATGGAAGGA
* *
137894 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
137929 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
137965 TGATGATATAGGCGTGATAAT-GTAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGT-GATGGAATATGG
138001 TGATGA
1 TGATGA
138007 AAATAGTATC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 18 0.25
36 54 0.75
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:143165 original size:24 final size:21
Alignment explanation
Indices: 143130--143172 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
143120 GGCACATTAT
*
143130 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
143153 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
143173 GTATTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:144469 original size:26 final size:29
Alignment explanation
Indices: 144406--144483 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
144396 AGACTTGTTG
*
144406 TTGAGTGCTTCAACTTTTCTTTCTTCTTT
1 TTGAGTGCTTGAACTTTTCTTTCTTCTTT
144435 TTGAGTGCTTGAA-TTTT-TTTCTTC-TT
1 TTGAGTGCTTGAACTTTTCTTTCTTCTTT
*
144461 TTGAGTGCTTGCACATTTTCTTT
1 TTGAGTGCTTGAAC-TTTTCTTT
144484 GCTGAATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.32
27 7 0.16
28 8 0.18
29 15 0.34
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.58
Consensus pattern (29 bp):
TTGAGTGCTTGAACTTTTCTTTCTTCTTT
Found at i:153596 original size:21 final size:22
Alignment explanation
Indices: 153574--153617 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
153564 AGAAAAGGAA
*
153574 TTAAGCACTCCAAAAGAAGAATT
1 TTAAGCACTCAAAAAGAAGAA-T
*
153597 TTCAGCACTCAAAAAGAAGAA
1 TTAAGCACTCAAAAAGAAGAA
153618 AAGGAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (22 bp):
TTAAGCACTCAAAAAGAAGAAT
Found at i:159107 original size:16 final size:16
Alignment explanation
Indices: 159073--159121 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
159063 ATAAGTTATC
* * *
159073 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
159089 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
159105 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
159122 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:160464 original size:35 final size:36
Alignment explanation
Indices: 160425--160504 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
160415 AAATGGAATT
* **
160425 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
160460 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
160496 TGGTGATGA
1 TGGTGATGA
160505 ACAGATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
Found at i:162940 original size:25 final size:24
Alignment explanation
Indices: 162894--162943 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
162884 TAGAAAAGGT
*
162894 TAAGAAAAGGATAAGGTAATGAAA
1 TAAGAAAAGGATAAGGAAATGAAA
162918 TAAGAAAAGAAGA-AAGGAAATGAAA
1 TAAGAAAAG--GATAAGGAAATGAAA
162943 T
1 T
162944 GAAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 12 0.52
26 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (24 bp):
TAAGAAAAGGATAAGGAAATGAAA
Found at i:162955 original size:25 final size:24
Alignment explanation
Indices: 162906--162956 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
162896 AGAAAAGGAT
*
162906 AAGGTAATGAAATAAGAAAAGAAGA
1 AAGGAAATGAAAT-AGAAAAGAAGA
162931 AAGGAAATGAAAT-GAAATAGTAAGA
1 AAGGAAATGAAATAGAAA-AG-AAGA
162956 A
1 A
162957 GGTGAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 2 0.09
25 17 0.74
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.14
Consensus pattern (24 bp):
AAGGAAATGAAATAGAAAAGAAGA
Found at i:163606 original size:11 final size:11
Alignment explanation
Indices: 163585--163627 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
163575 AATGGAATTT
163585 GGTGATGATATA
1 GGTG-TGATATA
*
163597 GGCGTGATAT-
1 GGTGTGATATA
163607 GGTGATGATATA
1 GGTG-TGATATA
163619 GGTGTGATA
1 GGTGTGATA
163628 ATGGTGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.11
11 17 0.63
12 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (11 bp):
GGTGTGATATA
Found at i:163612 original size:22 final size:23
Alignment explanation
Indices: 163584--163636 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
163574 AAATGGAATT
163584 TGGTGATGATATAGGCGTGAT-A
1 TGGTGATGATATAGGCGTGATAA
*
163606 TGGTGATGATATAGGTGTGATAA
1 TGGTGATGATATAGGCGTGATAA
163629 TGGTGATG
1 TGGTGATG
163637 GAAGATGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.26, C:0.02, G:0.38, T:0.34
Consensus pattern (23 bp):
TGGTGATGATATAGGCGTGATAA
Found at i:166954 original size:25 final size:24
Alignment explanation
Indices: 166908--166957 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
166898 TAGAAAAGGT
*
166908 TAAGAAAAGGATAAGGTAATGAAA
1 TAAGAAAAGGATAAGGAAATGAAA
166932 TAAGAAAA-GATGAAAGGAAATGAAA
1 TAAGAAAAGGAT--AAGGAAATGAAA
166957 T
1 T
166958 GAAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (24 bp):
TAAGAAAAGGATAAGGAAATGAAA
Found at i:167195 original size:11 final size:10
Alignment explanation
Indices: 167168--167206 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
167158 GTTGTAGGAG
167168 TCTTTTCTTTC
1 TCTTTT-TTTC
*
167179 TGTTTTTTTC
1 TCTTTTTTTC
167189 TTCTTTTTTTC
1 -TCTTTTTTTC
167200 TCTTTTT
1 TCTTTTT
167207 GTTGCTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 11 0.44
11 14 0.56
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (10 bp):
TCTTTTTTTC
Found at i:167612 original size:11 final size:11
Alignment explanation
Indices: 167596--167633 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
167586 AATTTGGTGA
167596 TGATATAGGCG
1 TGATATAGGCG
*
167607 TGATAT-GGTG
1 TGATATAGGCG
167617 ATGATATAGGCG
1 -TGATATAGGCG
167629 TGATA
1 TGATA
167634 ATGGTGATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (11 bp):
TGATATAGGCG
Found at i:167618 original size:22 final size:23
Alignment explanation
Indices: 167590--167642 Score: 99
Period size: 22 Copynumber: 2.3 Consensus size: 23
167580 AAATGGAATT
167590 TGGTGATGATATAGGCGTGAT-A
1 TGGTGATGATATAGGCGTGATAA
167612 TGGTGATGATATAGGCGTGATAA
1 TGGTGATGATATAGGCGTGATAA
167635 TGGTGATG
1 TGGTGATG
167643 GAAGATGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.26, C:0.04, G:0.38, T:0.32
Consensus pattern (23 bp):
TGGTGATGATATAGGCGTGATAA
Found at i:170943 original size:25 final size:24
Alignment explanation
Indices: 170898--170947 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
170888 TAGAAAAGGT
*
170898 TAAGAAAATGATAAGGTAATGAAA
1 TAAGAAAATGATAAGGAAATGAAA
170922 TAAGAAAA-GATGAAAGGAAATGAAA
1 TAAGAAAATGAT--AAGGAAATGAAA
170947 T
1 T
170948 GAAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.18
Consensus pattern (24 bp):
TAAGAAAATGATAAGGAAATGAAA
Found at i:171629 original size:35 final size:36
Alignment explanation
Indices: 171590--171669 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 36
171580 AAATGGAATT
**
171590 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
171625 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
171661 TGGTGATGA
1 TGGTGATGA
171670 ACAGATTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 21 0.50
36 21 0.50
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:172278 original size:12 final size:12
Alignment explanation
Indices: 172261--172293 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
172251 CTTAGGCGTG
172261 ACTTGGCATCAA
1 ACTTGGCATCAA
172273 ACTTGGCATCAA
1 ACTTGGCATCAA
172285 ACTT-GCATC
1 ACTTGGCATC
172294 TAGGTGACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (12 bp):
ACTTGGCATCAA
Found at i:173309 original size:24 final size:24
Alignment explanation
Indices: 173282--173339 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
173272 CCACAAAACA
173282 TGTCTCTTGATATTTCAAAGGAAG
1 TGTCTCTTGATATTTCAAAGGAAG
173306 TGTCTCTTGATATTTCAAAGGAAG
1 TGTCTCTTGATATTTCAAAGGAAG
*
173330 TGTCACTTGA
1 TGTCTCTTGA
173340 AATGCCAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (24 bp):
TGTCTCTTGATATTTCAAAGGAAG
Found at i:182987 original size:27 final size:27
Alignment explanation
Indices: 182957--183015 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
182947 TTGATGACAT
182957 GTCACTTAGATGCAAGATGGATGCCAA
1 GTCACTTAGATGCAAGATGGATGCCAA
182984 GTCACTTAGATGCAAGATGGATGCCAA
1 GTCACTTAGATGCAAGATGGATGCCAA
183011 GTCAC
1 GTCAC
183016 ACCTAGTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (27 bp):
GTCACTTAGATGCAAGATGGATGCCAA
Found at i:185780 original size:35 final size:36
Alignment explanation
Indices: 185732--185815 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
185722 ATTTATAAGT
* * *
185732 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
185767 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
185803 TGGTGATGA-ATAG
1 TGGTGATGATATAG
185816 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:186254 original size:16 final size:16
Alignment explanation
Indices: 186233--186266 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
186223 CCAACTTGAA
186233 GCATGATGATGTTTAG
1 GCATGATGATGTTTAG
186249 GCATGATGATGTTTAG
1 GCATGATGATGTTTAG
186265 GC
1 GC
186267 CGAATAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (16 bp):
GCATGATGATGTTTAG
Found at i:188378 original size:17 final size:17
Alignment explanation
Indices: 188356--188405 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
188346 GTAGGAGTCT
188356 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
188373 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
* *
188391 TTTTTTTTTTGTTGT
1 TTTTCTTTTTCTTGT
188406 AGCACTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:195965 original size:15 final size:15
Alignment explanation
Indices: 195929--195958 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
195919 AGTGCTTCAA
195929 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
195943 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
195958 T
1 T
195959 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:196008 original size:24 final size:24
Alignment explanation
Indices: 195961--196009 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
195951 CTTTTCTTCT
* *
195961 TTTTGAGTGCTGGATTTTTCTTTC
1 TTTTGAGTGCTGCATTTGTCTTTC
195985 TTTTGAGTGCTGCACTTTGT-TTTC
1 TTTTGAGTGCTGCA-TTTGTCTTTC
196009 T
1 T
196010 AATTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.08, C:0.14, G:0.20, T:0.57
Consensus pattern (24 bp):
TTTTGAGTGCTGCATTTGTCTTTC
Found at i:205349 original size:24 final size:23
Alignment explanation
Indices: 205292--205350 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
205282 CTTTTCTTTC
*
205292 CTTTTCTTCTTTTTGAGTGCTGGA
1 CTTTTCTTC-TTTTGAGTGCTGCA
*
205316 TTTTTCCTTCTTTTGAGTGCTGCA
1 CTTTT-CTTCTTTTGAGTGCTGCA
205340 CTTTGTCTTCT
1 CTTT-TCTTCT
205351 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.17, T:0.56
Consensus pattern (23 bp):
CTTTTCTTCTTTTGAGTGCTGCA
Found at i:208132 original size:24 final size:23
Alignment explanation
Indices: 208105--208180 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
208095 GCTTGGAGCC
208105 TCAATGATCACAACTTTTGGAACT
1 TCAATGA-CACAACTTTTGGAACT
* *
208129 TCAAATGACACATCTTTTTGAACT
1 TC-AATGACACAACTTTTGGAACT
* * * *
208153 TCAAGTGGCATAACTGTTGGAACG
1 TCAA-TGACACAACTTTTGGAACT
208177 TCAA
1 TCAA
208181 AGAACATGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.05
24 35 0.83
25 5 0.12
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (23 bp):
TCAATGACACAACTTTTGGAACT
Found at i:213367 original size:6 final size:6
Alignment explanation
Indices: 213344--213434 Score: 51
Period size: 6 Copynumber: 14.5 Consensus size: 6
213334 CCTTGGCTTT
* * * *
213344 TTTTCTC TTTTTG ATTTTC TTTTTC TTTTCTT TTTTTC TTTTCTGAA TTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTT-TC TTTTTC TTTT-T--C TTTTTC
* * *
213397 TTCTTC TTTTTTC TTTTT- TTCTT- TTTGTC TTTTTC TTT
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
213435 CTTTTTGCAC
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
5 7 0.11
6 37 0.58
7 15 0.23
8 1 0.02
9 4 0.06
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:213379 original size:13 final size:13
Alignment explanation
Indices: 213363--213439 Score: 64
Period size: 15 Copynumber: 5.4 Consensus size: 13
213353 TTTGATTTTC
213363 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
*
213376 TTTTTCTTTTCTGAA
1 TTTTTCTTTTCT--T
213391 TTTTTCTTCTTCTTT
1 TTTTTCTT-TTC-TT
*
213406 TTTCTTTTTTTCTT
1 TTT-TTCTTTTCTT
*
213420 TTTGTCTTTTTCTT
1 TTTTTC-TTTTCTT
213434 TCTTTT
1 T-TTTT
213440 TGCACTCTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 13 0.25
14 13 0.25
15 17 0.33
16 7 0.14
17 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:213430 original size:23 final size:23
Alignment explanation
Indices: 213342--213439 Score: 62
Period size: 23 Copynumber: 4.3 Consensus size: 23
213332 TTCCTTGGCT
213342 TTTTTTCTCTTTTTGAT-TTTCTTT-
1 TTTTTT-TCTTTTTG-TCTTT-TTTC
* * * *
213366 TTCTTTTCTTTTTTTCTTTTCTG
1 TTTTTTTCTTTTTGTCTTTTTTC
** *
213389 AATTTTTC-TTCT-TCTTTTTTC
1 TTTTTTTCTTTTTGTCTTTTTTC
213410 TTTTTTTCTTTTTGTC-TTTTTC
1 TTTTTTTCTTTTTGTCTTTTTTC
213432 TTTCTTTT
1 TTT-TTTT
213440 TGCACTCTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
21 13 0.23
22 18 0.32
23 21 0.37
24 5 0.09
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (23 bp):
TTTTTTTCTTTTTGTCTTTTTTC
Found at i:213437 original size:36 final size:34
Alignment explanation
Indices: 213342--213437 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 34
213332 TTCCTTGGCT
213342 TTTTTTCTCTTTTTG-A-TTTTCTTT-TTCTTTTC
1 TTTTTT-TCTTTTTGTATTTTTCTTTCTTCTTTTC
*
213374 TTTTTTTCTTTTCTGAATTTTTC-TTCTTCTTTTTTC
1 TTTTTTTCTTTT-TGTATTTTTCTTTCTTC--TTTTC
*
213410 TTTTTTTCTTTTTGTCTTTTTCTTTCTT
1 TTTTTTTCTTTTTGTATTTTTCTTTCTT
213438 TTTGCACTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
31 6 0.11
32 8 0.15
33 3 0.05
34 8 0.15
35 8 0.15
36 22 0.40
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (34 bp):
TTTTTTTCTTTTTGTATTTTTCTTTCTTCTTTTC
Found at i:213441 original size:18 final size:17
Alignment explanation
Indices: 213349--213441 Score: 65
Period size: 18 Copynumber: 5.5 Consensus size: 17
213339 GCTTTTTTTC
*
213349 TCTTTTTG-ATTTTCTT
1 TCTTTTTGTCTTTTCTT
213365 T-TTCTTT-TCTTTT-TT
1 TCTT-TTTGTCTTTTCTT
213380 TCTTTTCTGAAT-TTTTCTTCT
1 TCTTTT-TG--TCTTTTC-T-T
213401 TCTTTTT-TCTTTT-TT
1 TCTTTTTGTCTTTTCTT
213416 TCTTTTTGTCTTTTTCTT
1 TCTTTTTGTC-TTTTCTT
213434 TCTTTTTG
1 TCTTTTTG
213442 CACTCTAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 26
0.70 0.01 0.29
Matches are distributed among these distances:
15 15 0.24
16 14 0.23
17 5 0.08
18 18 0.29
19 1 0.02
20 2 0.03
21 7 0.11
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.77
Consensus pattern (17 bp):
TCTTTTTGTCTTTTCTT
Found at i:218272 original size:15 final size:15
Alignment explanation
Indices: 218252--218283 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
218242 AAGGGATGCA
218252 AGCAACTAAAATTGG
1 AGCAACTAAAATTGG
218267 AGCAACTAAAATTGG
1 AGCAACTAAAATTGG
218282 AG
1 AG
218284 GAAGGTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (15 bp):
AGCAACTAAAATTGG
Found at i:221868 original size:23 final size:23
Alignment explanation
Indices: 221842--221894 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
221832 AAATCCAGCA
221842 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAG-ACTCGAAAAG
* *
221865 AAGAAATTGAAAGACTCGAAAAG
1 AAGAAAATCAAAGACTCGAAAAG
221888 AAGAAAA
1 AAGAAAA
221895 AGATAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.09
Consensus pattern (23 bp):
AAGAAAATCAAAGACTCGAAAAG
Found at i:224563 original size:11 final size:13
Alignment explanation
Indices: 224531--224560 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
224521 TGGCCAAAGA
224531 TGAAAAGGTATGT
1 TGAAAAGGTATGT
224544 TGAAAAGGTATG-
1 TGAAAAGGTATGT
224556 TGAAA
1 TGAAA
224561 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:227298 original size:22 final size:20
Alignment explanation
Indices: 227273--227312 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
227263 ATGTTTGTTT
227273 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
227295 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
227313 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:228667 original size:13 final size:13
Alignment explanation
Indices: 228645--228674 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
228635 ACTAAACACC
228645 TTTC-ACATACCT
1 TTTCAACATACCT
228657 TTTCAACATACCT
1 TTTCAACATACCT
228670 TTTCA
1 TTTCA
228675 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:231497 original size:11 final size:11
Alignment explanation
Indices: 231481--231505 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
231471 TTTTTTTTCT
231481 TTCACTTGCAC
1 TTCACTTGCAC
231492 TTCACTTGCAC
1 TTCACTTGCAC
231503 TTC
1 TTC
231506 TTTTTGGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:232829 original size:22 final size:20
Alignment explanation
Indices: 232804--232843 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
232794 ATGTTTGTTT
232804 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
232826 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
232844 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:242311 original size:27 final size:26
Alignment explanation
Indices: 242260--242311 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
242250 GCATGATATG
* *
242260 TAATATAATAGTATATATTATAAGGT
1 TAATATAATAGTAAATATTAAAAGGT
242286 TAATATAA-AGTAAATGCATTAAAAGG
1 TAATATAATAGTAAAT--ATTAAAAGG
242312 ATGTTCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (26 bp):
TAATATAATAGTAAATATTAAAAGGT
Found at i:243708 original size:12 final size:11
Alignment explanation
Indices: 243677--243724 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 11
243667 AAAGTGCTAC
243677 AAAA-AAAAAG
1 AAAAGAAAAAG
243687 CAACAAGAAAGAAG
1 -AA-AAGAAA-AAG
243701 AAAAGAAAAGAG
1 AAAAGAAAA-AG
243713 AAAAGAAAAAG
1 AAAAGAAAAAG
243724 A
1 A
243725 CTCCTACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 19 0.58
13 5 0.15
14 3 0.09
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:250939 original size:23 final size:24
Alignment explanation
Indices: 250897--250949 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
250887 TTTTTTTCTT
250897 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
250921 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
250944 TTTCTT
1 TTTCTT
250950 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:256293 original size:13 final size:14
Alignment explanation
Indices: 256275--256304 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
256265 TGTATGAGTA
256275 TTTTCTTC-TTCTT
1 TTTTCTTCTTTCTT
256288 TTTTCTTCTTTCTT
1 TTTTCTTCTTTCTT
256302 TTT
1 TTT
256305 CCTTTTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTCTTTCTT
Found at i:257082 original size:20 final size:21
Alignment explanation
Indices: 257045--257083 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
257035 GATGGTCTTG
*
257045 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
257066 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
257084 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:257463 original size:19 final size:21
Alignment explanation
Indices: 257420--257471 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
257410 GAAACCCCTT
257420 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
257441 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
257460 TGAAGATACATG
1 TGAAAATACATG
257472 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:260632 original size:34 final size:32
Alignment explanation
Indices: 260575--260646 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 32
260565 CTTGGCTTGC
260575 TTTC-TTTTTGAATTTCTCTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTCTTTCTTTT-TGTCT
260606 TTTCTTTTTCTGAATTT-TCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAATTTCTC-T-TTCTTTTTGTCT
260640 TTTCTTT
1 TTTCTTT
260647 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
31 4 0.11
32 6 0.17
33 9 0.25
34 17 0.47
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTCTTTCTTTTTGTCT
Found at i:260644 original size:19 final size:17
Alignment explanation
Indices: 260574--260654 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 17
260564 CCTTGGCTTG
**
260574 CTTTCTTTTTGAATTTCT
1 CTTTCTTTTTGTCTTT-T
260592 CTTTCTTTTCT-TCTTTT
1 CTTTCTTTT-TGTCTTTT
* **
260609 C-TT-TTTCTGAATTTT
1 CTTTCTTTTTGTCTTTT
260624 CTTCTTCTTTTTGTCTTTT
1 C-T-TTCTTTTTGTCTTTT
260643 CTTTCTTTTTGT
1 CTTTCTTTTTGT
260655 ACTTCAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
14 1 0.02
15 8 0.16
16 2 0.04
17 12 0.24
18 15 0.31
19 11 0.22
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (17 bp):
CTTTCTTTTTGTCTTTT
Found at i:261012 original size:20 final size:21
Alignment explanation
Indices: 260975--261013 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
260965 GATGGCCTTG
*
260975 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
260996 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
261014 TTGTATATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:261393 original size:19 final size:21
Alignment explanation
Indices: 261350--261401 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
261340 GAAACCCCTT
261350 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
261371 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
261390 TGAAGATACATG
1 TGAAAATACATG
261402 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:262876 original size:20 final size:21
Alignment explanation
Indices: 262839--262877 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
262829 GATGGCCTTG
*
262839 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
262860 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
262878 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:263257 original size:19 final size:21
Alignment explanation
Indices: 263214--263265 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
263204 GAAACCCCTT
263214 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
263235 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
263254 TGAAGATACATG
1 TGAAAATACATG
263266 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:270581 original size:11 final size:11
Alignment explanation
Indices: 270567--270622 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
270557 CTTTTTTGAA
270567 TTCTTTTTCTT
1 TTCTTTTTCTT
270578 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
270591 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
270604 TGTCTTTTTC-T
1 T-TCTTTTTCTT
270615 TTCTTTTT
1 TTCTTTTT
270623 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:270591 original size:19 final size:18
Alignment explanation
Indices: 270567--270622 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
270557 CTTTTTTGAA
270567 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
270585 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
270604 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
270622 T
1 T
270623 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:275078 original size:24 final size:24
Alignment explanation
Indices: 275036--275087 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
275026 TCACTTCAAG
* **
275036 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGAATCAAGAAACATAACTT
* *
275060 TTGAAGAATCAATAGACATAACTT
1 TTGAAGAATCAAGAAACATAACTT
275084 TTGA
1 TTGA
275088 TAATCCACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACATAACTT
Found at i:284660 original size:24 final size:24
Alignment explanation
Indices: 284633--284683 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
284623 TGTGCATCAC
* *
284633 CAAAAGTCATGTCTATTGATTCTT
1 CAAAAGACATGTCTATTGAATCTT
* *
284657 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACATGTCTATTGAATCTT
284681 CAA
1 CAA
284684 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACATGTCTATTGAATCTT
Done.