Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003182.1 Hibiscus syriacus cultivar Beakdansim tig00006697_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: 46855
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:3005 original size:15 final size:15
Alignment explanation
Indices: 2985--3016 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2975 ATCAATACCT
2985 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
3000 TTTTGCATACATTCA
1 TTTTGCATACATGCA
3015 TT
1 TT
3017 ATCCATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:10334 original size:14 final size:14
Alignment explanation
Indices: 10315--10350 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
10305 ATGCTTGAAG
10315 AGAAAAAGAAAGAA
1 AGAAAAAGAAAGAA
*
10329 AGAAAAAAAAAGAA
1 AGAAAAAGAAAGAA
10343 AGAAAAAG
1 AGAAAAAG
10351 GAAAAAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAAGAA
Found at i:11862 original size:83 final size:82
Alignment explanation
Indices: 11718--12020 Score: 401
Period size: 83 Copynumber: 3.5 Consensus size: 82
11708 AACAAATGCC
*
11718 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
11783 ATTGAATTTGGAAGAATA
66 ATTGAATTTGGAAGAA-A
* *
11801 ATGTTCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
*
11866 ATTTAATTTGGAAGAGAA
66 ATTGAATTTGGAAGA-AA
*
11884 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCA-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTA--AA--ATC
* *
11948 AGAACCAGTTATTGAATTTGGAAGAGGA
62 ---A--A-TCATTGAATTTGGAAGA-AA
* *
11976 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGAT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
12021 TTGGTTTGAT
Statistics
Matches: 197, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
83 130 0.66
84 1 0.01
85 2 0.01
86 1 0.01
87 1 0.01
89 1 0.01
91 1 0.01
92 60 0.30
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (82 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
ATTGAATTTGGAAGAAA
Found at i:12043 original size:92 final size:92
Alignment explanation
Indices: 11870--12043 Score: 269
Period size: 92 Copynumber: 1.9 Consensus size: 92
11860 TCAATCATTT
* *
11870 AATTTGGAAGAGAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTT
1 AATTTGGAAGAGAAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
* *
11935 TGGTATGAACCACAGAACCAGTTATTG
66 TGATATAAACCACAGAACCAGTTATTG
* * *
11962 AATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTT
1 AATTTGGAAGAGAAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
12027 TGATATAAAACC-CAGAA
66 TGATAT-AAACCACAGAA
12044 ACAATCATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
92 70 0.95
93 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (92 bp):
AATTTGGAAGAGAAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
TGATATAAACCACAGAACCAGTTATTG
Found at i:12469 original size:52 final size:52
Alignment explanation
Indices: 12405--12509 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
12395 TATCGATATC
12405 TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
*
12457 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
12509 T
1 T
12510 TAACATGTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:13376 original size:112 final size:113
Alignment explanation
Indices: 12807--13575 Score: 1382
Period size: 113 Copynumber: 6.8 Consensus size: 113
12797 GCAAAGATTT
*
12807 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
** * *
12872 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTATGCTA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
*
12920 AAATCCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
** * *
12985 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTTATGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* *
13033 AAATGCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
13098 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
13146 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
13211 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
13259 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
13323 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
13371 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
13435 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* *
13483 AAATCCATCACTCGATGGATCAGCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAG-AAGTTCATAATAAGAAGAACTCATCTGAA
13547 GAAGGAAGAAGAAGTTCATAATGAGAAGA
65 GAAGGAAGAAGAAGTTCATAATGAGAAGA
13576 ACTCATCTGA
Statistics
Matches: 642, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
112 225 0.35
113 417 0.65
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
Found at i:13573 original size:40 final size:38
Alignment explanation
Indices: 13518--13646 Score: 180
Period size: 36 Copynumber: 3.5 Consensus size: 38
13508 TTTCCAGAGA
13518 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTG-AGAA-GAAGAAG
*
13558 AAGTTCATAATGAGAAGAACTCATCT--GAATAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAG
*
13594 AATTTCATAATGAGAAGAACTCATCTGA-AAGAAG-A-
1 AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAG
13629 AA-TTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
13647 TTTGTTCAAC
Statistics
Matches: 84, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
34 16 0.19
35 2 0.02
36 32 0.38
37 8 0.10
40 26 0.31
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (38 bp):
AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAG
Found at i:13575 original size:17 final size:16
Alignment explanation
Indices: 13553--13648 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 16
13543 TGAAGAAGGA
13553 AGAAGAAGTTCATAATG
1 AGAAGAA-TTCATAATG
* *
13570 AGAAGAACTCATCTGAATA
1 AGAAGAATTCA--T-AATG
13589 AGAAGAATTTCATAATG
1 AGAAGAA-TTCATAATG
* *
13606 AGAAGAACTCAT-CTG
1 AGAAGAATTCATAATG
13621 AAAGAAGAAATTCATAATG
1 --AGAAG-AATTCATAATG
13640 AGAAGAATT
1 AGAAGAATT
13649 TGTTCAACCT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
15 2 0.03
16 11 0.17
17 27 0.43
18 8 0.13
19 12 0.19
20 3 0.05
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (16 bp):
AGAAGAATTCATAATG
Found at i:13601 original size:36 final size:35
Alignment explanation
Indices: 13515--13646 Score: 185
Period size: 40 Copynumber: 3.6 Consensus size: 35
13505 GCTTTTCCAG
13515 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAAA-TTCATAATGAGAAGAACTCATCTGAA-AA-GA
13553 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAATAAGA
1 AG-A-AA-TTCATAATGAGAAGAACTCATCTGAA-AAGA
*
13592 AGAATTTCATAATGAGAAGAACTCATCTG-AAAGA
1 AGAAATTCATAATGAGAAGAACTCATCTGAAAAGA
13626 AGAAATTCATAATGAGAAGAA
1 AGAAATTCATAATGAGAAGAA
13647 TTTGTTCAAC
Statistics
Matches: 89, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
34 24 0.27
35 1 0.01
36 24 0.27
37 1 0.01
38 3 0.03
39 5 0.06
40 31 0.35
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.20
Consensus pattern (35 bp):
AGAAATTCATAATGAGAAGAACTCATCTGAAAAGA
Found at i:13714 original size:182 final size:185
Alignment explanation
Indices: 13403--13746 Score: 495
Period size: 182 Copynumber: 1.9 Consensus size: 185
13393 GCTTTTCCAG
*
13403 AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTG
1 AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
13468 TTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGA
66 TTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
13533 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAATAAGA
131 AGAACTCATCTGAAGAA-G-AG-A-AAGTTCATAATGAGAAGAACTCATCTGAATAAGA
* * *
13592 AGAATTTCATAATGAGAAGAACTCATCTG-A-AA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * *
13651 TTCAACC-TTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
66 TTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
*
13715 AGAACTCATTTGAAGAAGAGAAAGTTCATAAT
131 AGAACTCATCTGAAGAAGAGAAAGTTCATAAT
13747 AAAAAGAGCT
Statistics
Matches: 143, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
178 11 0.08
179 1 0.01
180 2 0.01
181 1 0.01
182 66 0.46
183 25 0.17
184 2 0.01
185 1 0.01
186 4 0.03
187 2 0.01
188 1 0.01
189 27 0.19
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (185 bp):
AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAATAAGA
Found at i:14043 original size:27 final size:27
Alignment explanation
Indices: 14001--14064 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
13991 TTAATGTTAT
*
14001 TTATATAATAATTATTATTATTATA-A
1 TTATATAATAATTATTATTAATATATA
14027 TTATAATAATAATTATTATTAATATATA
1 TTAT-ATAATAATTATTATTAATATATA
*
14055 TTATTTAATA
1 TTATATAATA
14065 TTACAAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 25 0.74
28 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATATAATAATTATTATTAATATATA
Found at i:14530 original size:18 final size:19
Alignment explanation
Indices: 14489--14524 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14479 GGAGAGACAG
14489 AAACAGAGCAAAAACAACA
1 AAACAGAGCAAAAACAACA
*
14508 AAACAGAG-AACAACAAC
1 AAACAGAGCAAAAACAAC
14525 CCAACAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (19 bp):
AAACAGAGCAAAAACAACA
Found at i:20120 original size:17 final size:19
Alignment explanation
Indices: 20098--20140 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
20088 TTTTAAATGA
20098 TTTAATA-AT-AAAATATT
1 TTTAATAGATAAAAATATT
20115 TTTAATATGATAAAAATATT
1 TTTAATA-GATAAAAATATT
20135 TCTTAA
1 T-TTAA
20141 AGTTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
19 2 0.09
20 9 0.41
21 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAATAGATAAAAATATT
Found at i:27899 original size:51 final size:50
Alignment explanation
Indices: 27833--27998 Score: 237
Period size: 50 Copynumber: 3.3 Consensus size: 50
27823 CACTTAACAC
* *
27833 TACACCGGTGTAAGTGAATAAAATAAACAAGTGTAGCACTTAACACATTCT
1 TACACCGATGTAAGTGAATAAAATAAA-AAGTGTAGCACTTAACACATACT
*
27884 TACACCGATGTAAGTGAATAAAATAAAAAGTGTAACACTTAACACATAC-
1 TACACCGATGTAAGTGAATAAAATAAAAAGTGTAGCACTTAACACATACT
* **
27933 TACA-CTAGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAATGCATACT
1 TACACCGA-TGTAAGTGAATAAAAT-AAAAAGTGTAGCACTTAACACATACT
27984 TACACCGATGTAAGT
1 TACACCGATGTAAGT
27999 ATGTACATCT
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
48 2 0.02
49 20 0.19
50 42 0.41
51 37 0.36
52 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (50 bp):
TACACCGATGTAAGTGAATAAAATAAAAAGTGTAGCACTTAACACATACT
Found at i:27962 original size:50 final size:49
Alignment explanation
Indices: 27811--27998 Score: 222
Period size: 50 Copynumber: 3.8 Consensus size: 49
27801 TTCATACTAC
* *
27811 AAAAAAATGTAGCACTTAACAC-TAC-AC-CGGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTACACAGTGTAAGTGAATAAAAT
* * *
27857 AAACAAGTGTAGCACTTAACACATTCTTACACCGATGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATAC-TACACAG-TGTAAGTGAATAAAAT
*
27908 -AAAAAGTGTAACACTTAACACATACTACACTAGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTACAC-AGTGTAAGTGAATAAAAT
** *
27957 AAAAAAGTGTAGCACTTAATGCATACTTACACCGATGTAAGT
1 AAAAAAGTGTAGCACTTAACACATAC-TACACAG-TGTAAGT
27999 ATGTACATCT
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
46 20 0.17
47 2 0.02
49 23 0.19
50 48 0.40
51 28 0.23
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.24
Consensus pattern (49 bp):
AAAAAAGTGTAGCACTTAACACATACTACACAGTGTAAGTGAATAAAAT
Found at i:27986 original size:100 final size:96
Alignment explanation
Indices: 27812--27998 Score: 275
Period size: 100 Copynumber: 1.9 Consensus size: 96
27802 TCATACTACA
* * *
27812 AAAAAATGTAGCACTTAACACTACACCGGTGTAAGTGAATAAAATAAACAAGTGTAGCACTTAAC
1 AAAAAATGTAACACTTAACACTACACCAGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAC
*
27877 ACATTCTTACACCGATGTAAGTGAATAAAAT
66 ACATACTTACACCGATGTAAGTGAATAAAAT
*
27908 AAAAAGTGTAACACTTAACACATACTACACTAGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
1 AAAAAATGTAACACTTAACAC-TAC-AC-C-AGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
**
27973 TAATGCATACTTACACCGATGTAAGT
62 TAACACATACTTACACCGATGTAAGT
27999 ATGTACATCT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 19 0.24
97 3 0.04
98 2 0.03
99 1 0.01
100 55 0.69
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (96 bp):
AAAAAATGTAACACTTAACACTACACCAGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAC
ACATACTTACACCGATGTAAGTGAATAAAAT
Found at i:28162 original size:51 final size:52
Alignment explanation
Indices: 28089--28220 Score: 125
Period size: 51 Copynumber: 2.6 Consensus size: 52
28079 AAATAAAAAA
** *
28089 TAAAAA-ATAATAAAAAATAAATATTAAGTTATTTGTATATAAA-T-TTTAT-
1 TAAAAATATAATAAATTATAAATATTAAGTTATTTATAT-TAAACTATTTATG
* * ** *
28138 TAAAAATATATATAATTTATAAATAAT-AGAAACTTATATTAAACTATTTATG
1 TAAAAATATA-ATAAATTATAAATATTAAGTTATTTATATTAAACTATTTATG
28190 TAAAAATATAATAAATTATAAAT-TTAA-TTAT
1 TAAAAATATAATAAATTATAAATATTAAGTTAT
28221 AAATTTAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
49 10 0.16
50 14 0.22
51 30 0.47
52 10 0.16
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (52 bp):
TAAAAATATAATAAATTATAAATATTAAGTTATTTATATTAAACTATTTATG
Found at i:28220 original size:12 final size:12
Alignment explanation
Indices: 28203--28230 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28193 AAATATAATA
28203 AATTATAAATTT
1 AATTATAAATTT
28215 AATTATAAATTT
1 AATTATAAATTT
28227 AATT
1 AATT
28231 TTTTAACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATAAATTT
Found at i:29545 original size:21 final size:20
Alignment explanation
Indices: 29519--29616 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
29509 ATCAGTTTCC
29519 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* ** *
29540 AAAATCGCAATGCGATAGTA
1 AAAATCGCAACGCGATTTTG
** *
29560 AAAATTCGCATTGCGATTTTCC
1 AAAA-TCGCAACGCGATTTT-G
* * *
29582 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
29602 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
29617 ACACATAAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 19 0.32
21 38 0.63
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:29645 original size:20 final size:20
Alignment explanation
Indices: 29584--29812 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
29574 GATTTTCCAG
* ** *
29584 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
29604 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
29624 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
29644 AATCGCAACATGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29664 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
29684 AATCGCAATGCGTATCCGTG
1 AATCGCAACGCGTATCCGTA
*
29704 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29724 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29744 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29764 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29784 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29804 AATCACAAC
1 AATCGCAAC
29813 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:30544 original size:24 final size:24
Alignment explanation
Indices: 30505--30551 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30495 AAATTTGGTC
30505 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
30529 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
30552 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:33083 original size:33 final size:34
Alignment explanation
Indices: 33032--33230 Score: 167
Period size: 33 Copynumber: 5.7 Consensus size: 34
33022 CGGAAATTAC
* *
33032 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
33065 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
33099 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
33138 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* *
33171 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
33204 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
33231 CGAGAGAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 31
0.74 0.08 0.17
Matches are distributed among these distances:
32 2 0.02
33 57 0.43
34 35 0.26
35 1 0.01
36 1 0.01
37 1 0.01
38 14 0.11
39 21 0.16
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:33109 original size:53 final size:52
Alignment explanation
Indices: 33046--33268 Score: 376
Period size: 53 Copynumber: 4.2 Consensus size: 52
33036 GCAACGAGAG
* *
33046 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
33099 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
33152 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
33204 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
33256 AATCGCATTGCGA
1 AATCGCAATGCGA
33269 TTCTCTCGTT
Statistics
Matches: 165, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
52 71 0.43
53 93 0.56
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:33115 original size:19 final size:19
Alignment explanation
Indices: 33046--33268 Score: 234
Period size: 19 Copynumber: 12.7 Consensus size: 19
33036 GCAACGAGAG
33046 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33065 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
33079 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
33099 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33118 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
33132 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
33152 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33171 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
33185 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33204 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33223 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
33237 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
33256 AATCGCATTGCGA
1 AATCGCAATGCGA
33269 TTCTCTCGTT
Statistics
Matches: 172, Mismatches: 10, Indels: 44
0.76 0.04 0.19
Matches are distributed among these distances:
14 42 0.24
15 3 0.02
16 6 0.03
17 8 0.05
18 2 0.01
19 82 0.48
20 29 0.17
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:33189 original size:86 final size:84
Alignment explanation
Indices: 33032--33211 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
33022 CGGAAATTAC
33032 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
33097 AAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
33118 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
33181 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
33204 AATCGCAA
1 AATCGCAA
33212 TGCGAAATGA
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 54 0.63
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:33241 original size:33 final size:33
Alignment explanation
Indices: 33099--33262 Score: 163
Period size: 33 Copynumber: 4.8 Consensus size: 33
33089 CGGAAATGAA
33099 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
33132 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
33165 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
33204 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
33237 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
33263 TTGCGATTCT
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 52 0.49
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:33371 original size:52 final size:53
Alignment explanation
Indices: 33258--33374 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
33248 GAAATTAAAA
*
33258 TCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCCGCATTGCGATTTTAATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
*
33311 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
33363 TCGCATTGCGAT
1 TCGCATTGCGAT
33375 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
Found at i:33382 original size:19 final size:19
Alignment explanation
Indices: 33281--33374 Score: 126
Period size: 19 Copynumber: 5.2 Consensus size: 19
33271 CTCTCGTTGT
33281 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
*
33301 GATTTTAATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
33320 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
33334 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
33353 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
33372 GAT
1 GAT
33375 AGTCATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 6 0.09
19 36 0.55
20 10 0.15
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:33500 original size:14 final size:14
Alignment explanation
Indices: 33481--33517 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33471 CATCAATTAC
33481 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
33495 ACAAATCATCTTTT
1 ACAAATCAACTTTT
33509 ACAAATCAA
1 ACAAATCAA
33518 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:35480 original size:19 final size:19
Alignment explanation
Indices: 35438--35589 Score: 121
Period size: 19 Copynumber: 8.6 Consensus size: 19
35428 TAGTTTACTT
* *
35438 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
35458 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
35477 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
35496 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35515 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
35529 TCGCAA--TGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35546 TCCCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
35560 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35579 TCGCAATGCGA
1 TCGCAACGCGA
35590 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
14 18 0.17
15 1 0.01
16 7 0.07
17 16 0.15
19 53 0.50
20 12 0.11
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:35532 original size:14 final size:14
Alignment explanation
Indices: 35513--35567 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
35503 GCGAAATGAA
*
35513 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
35527 AATCGCAATGAAATG
1 AATCGCAACGAAA-G
*
35542 AAAATCCCAACGAAAG
1 --AATCGCAACGAAAG
35558 AATCGCAACG
1 AATCGCAACG
35568 CGAAATGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 20 0.61
15 1 0.03
16 1 0.03
17 11 0.33
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:35543 original size:31 final size:32
Alignment explanation
Indices: 35456--35584 Score: 134
Period size: 31 Copynumber: 3.8 Consensus size: 32
35446 CGAAACTTAA
* *
35456 AATCGCAACGCGAAATGATAATCGCAACGAGAAACCAA
1 AATCGCAAC-CGAAATGAAAATCGCAAC--G-AA--AG
*
35494 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAAC-CGAAATGAAAATCGCAACGAAAG
* *
35527 AATCGCAA-TGAAATGAAAATCCCAACGAAAG
1 AATCGCAACCGAAATGAAAATCGCAACGAAAG
35558 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAAC-CGAAATGAAAATCGCAA
35585 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
31 28 0.35
33 24 0.30
35 1 0.01
36 1 0.01
38 27 0.33
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (32 bp):
AATCGCAACCGAAATGAAAATCGCAACGAAAG
Found at i:35620 original size:14 final size:14
Alignment explanation
Indices: 35601--35627 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35591 TTTGGTTTCG
35601 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
35615 CGTTGCGATTTTG
1 CGTTGCGATTTTG
35628 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:35627 original size:33 final size:33
Alignment explanation
Indices: 35585--35679 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
35575 AAAATCGCAA
35585 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
35618 TGCGATTTTGGTTTCGCGTTGCGATTCTT-TTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTCGT
**
35651 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
35680 GTTTCGCGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.49
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:35639 original size:19 final size:19
Alignment explanation
Indices: 35585--35713 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
35575 AAAATCGCAA
35585 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
35604 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
35618 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
35637 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
35651 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
35670 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
35689 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
35709 TGCGA
1 TGCGA
35714 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 48 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:35882 original size:93 final size:93
Alignment explanation
Indices: 35758--35947 Score: 346
Period size: 93 Copynumber: 2.1 Consensus size: 93
35748 ATGGATTGCA
* *
35758 TTAC-TTCAATCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAACACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35822 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
35850 TTACTTTCAACCAAAAGACAAAACAAACACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAACACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
35915 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
35943 TTACT
1 TTACT
35948 AAGCAATCTA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 4 0.04
93 90 0.96
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAACACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:37674 original size:20 final size:20
Alignment explanation
Indices: 37645--37723 Score: 106
Period size: 19 Copynumber: 4.0 Consensus size: 20
37635 TGGTTGAAAT
37645 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGAGAATG
***
37665 ACTGTCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAG-AATG
*
37686 AAAATCGCAACGCGA-AATG
1 AAAATCGCAACGAGAGAATG
37705 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
37724 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 18 0.37
20 16 0.33
21 15 0.31
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGAGAGAATG
Found at i:37704 original size:19 final size:19
Alignment explanation
Indices: 37640--37752 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
37630 TCTTTTGGTT
*
37640 GAAAT-AAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
37658 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
37680 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
37699 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
37716 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
37732 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
37751 GA
1 GA
37753 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 3 0.04
19 34 0.45
20 8 0.11
21 12 0.16
22 4 0.05
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:37705 original size:40 final size:40
Alignment explanation
Indices: 37640--37722 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
37630 TCTTTTGGTT
***
37640 GAAATAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATAAAATCGCAACGAGAGAATGAAAATCGCAACGAGA
*
37680 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGAGA
1 GAAAT-AAAATCGCAACGAGAGAATGAAAATCGCAACGAGA
37720 GAA
1 GAA
37723 TCGCAACGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 24 0.63
41 14 0.37
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (40 bp):
GAAATAAAATCGCAACGAGAGAATGAAAATCGCAACGAGA
Found at i:37781 original size:19 final size:19
Alignment explanation
Indices: 37748--37866 Score: 95
Period size: 21 Copynumber: 6.3 Consensus size: 19
37738 AAAATCGCAA
** *
37748 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCTCGT
*
37767 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCTCGT
37786 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCTCGT
37800 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCTCGT
***
37821 TGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCTCGT
37841 TGCGATTTTCATTTATCTCGT
1 TGCGATTTTCA-TT-TCTCGT
37862 TGCGA
1 TGCGA
37867 CTCTTCTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 22 0.27
20 17 0.21
21 27 0.33
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCTCGT
Found at i:37847 original size:41 final size:41
Alignment explanation
Indices: 37790--37867 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
37780 TCGCGTTGCG
*
37790 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
37831 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
37868 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:37852 original size:20 final size:21
Alignment explanation
Indices: 37791--37866 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
37781 CGCGTTGCGA
37791 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
37812 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
37832 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
37853 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
37867 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:37988 original size:33 final size:33
Alignment explanation
Indices: 37946--38016 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
37936 AATACTAACT
37946 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
37979 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
38012 TGAAA
1 TGAAA
38017 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:38423 original size:20 final size:20
Alignment explanation
Indices: 38396--38569 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
38386 CTTTAAATAT
*
38396 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
* * *
38416 CTCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
38438 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38457 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
38477 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
38497 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38517 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
38537 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
38557 CGCGTTGCGATTT
1 CGCGTTGCGATTT
38570 TCATATTCAC
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 116 0.86
21 16 0.12
22 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38526 original size:60 final size:60
Alignment explanation
Indices: 38439--38587 Score: 201
Period size: 60 Copynumber: 2.5 Consensus size: 60
38429 TATGTATTAT
*
38439 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACG-GATACG
1 CGTTGCGATTTACGGATACACGTTGCGATATACGGATACGCATTGCGATTTACGTG-TACG
* * * *
38499 CGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCG
1 CGTTGCGATTTACGGATACACGTTGCGATATACGGATACGCATTGCGATTTACGTGTACG
* ** *
38559 CGTTGCGATTTTCATATTCACGTTGCGAT
1 CGTTGCGATTTACGGATACACGTTGCGAT
38588 TCTGGAAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 78 0.99
61 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACACGTTGCGATATACGGATACGCATTGCGATTTACGTGTACG
Found at i:39291 original size:20 final size:20
Alignment explanation
Indices: 39266--39311 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
39256 AATCTGTAAA
*
39266 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
39286 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
39306 TCGCAA
1 TCGCAA
39312 AGCGCGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:39916 original size:19 final size:20
Alignment explanation
Indices: 39887--39975 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 20
39877 TCACAACGCA
*
39887 ATTTT-AGTTTTGCGTTGAG
1 ATTTTCAGTTTCGCGTTGAG
* * *
39906 ATTTTTATTTTTGCGTTGTA-
1 ATTTTCAGTTTCGCGTTG-AG
* *
39926 ATTTTCA-TTTCGTGTTGCG
1 ATTTTCAGTTTCGCGTTGAG
* *
39945 ATTTTCA-TTTCACGTTGCG
1 ATTTTCAGTTTCGCGTTGAG
*
39964 ATTTTAAGTTTC
1 ATTTTCAGTTTC
39976 AGAAACTACT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
19 36 0.62
20 21 0.36
21 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (20 bp):
ATTTTCAGTTTCGCGTTGAG
Found at i:39935 original size:20 final size:20
Alignment explanation
Indices: 39894--39954 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
39884 GCAATTTTAG
*
39894 TTTTGCGTTGAGATTTTTAT
1 TTTTGCGTTGAGATTTTCAT
39914 TTTTGCGTTGTA-ATTTTCA-
1 TTTTGCGTTG-AGATTTTCAT
* * *
39933 TTTCGTGTTGCGATTTTCAT
1 TTTTGCGTTGAGATTTTCAT
39953 TT
1 TT
39955 CACGTTGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.44
20 18 0.53
21 1 0.03
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
TTTTGCGTTGAGATTTTCAT
Found at i:43637 original size:20 final size:20
Alignment explanation
Indices: 43591--43646 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
43581 ACACTTTCAT
*
43591 AACGCAAAAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
*** *
43611 GTTGCGAAAGTAAAATTCGC
1 AACGCGAAAGTCAAATTCGC
43631 AACGCGAAAGTCAAAT
1 AACGCGAAAGTCAAAT
43647 GCACATTGCG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (20 bp):
AACGCGAAAGTCAAATTCGC
Found at i:43657 original size:20 final size:20
Alignment explanation
Indices: 43597--43657 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
43587 TCATAACGCA
*
43597 AAAGTCAAATTCGCGTTGCG
1 AAAGTCAAATTCGCATTGCG
* **
43617 AAAGTAAAATTCGCAACGCG
1 AAAGTCAAATTCGCATTGCG
* *
43637 AAAGTCAAATGCACATTGCG
1 AAAGTCAAATTCGCATTGCG
43657 A
1 A
43658 TTTTCGCGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
AAAGTCAAATTCGCATTGCG
Found at i:43731 original size:29 final size:29
Alignment explanation
Indices: 43689--43744 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
43679 TTTCACGTTT
*
43689 CGAATTTGATTTTCGCAACAATCGCAATG
1 CGAATTTGACTTTCGCAACAATCGCAATG
43718 CGAATTTGACTTTCGCAACAATCGCAA
1 CGAATTTGACTTTCGCAACAATCGCAA
43745 CAAAAAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAATG
Found at i:44007 original size:18 final size:18
Alignment explanation
Indices: 43984--44019 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43974 AAGTCGGTTG
*
43984 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
44002 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
44020 CCTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Done.