Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007742.1 Hibiscus syriacus cultivar Beakdansim tig00110005_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: 174412
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3154 original size:29 final size:29
Alignment explanation
Indices: 3111--3193 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
3101 CTCACCTAAC
3111 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
3141 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
3170 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
3194 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4766 original size:158 final size:158
Alignment explanation
Indices: 4476--4781 Score: 587
Period size: 158 Copynumber: 1.9 Consensus size: 158
4466 GAGGGGTATT
*
4476 CCAATGATCTTGGGCGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
1 CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
4541 ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
66 ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
4606 AAAAAGATGGGAAATTAGCGCGCCATTA
131 AAAAAGATGGGAAATTAGCGCGCCATTA
4634 CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
1 CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
*
4699 ATATTTTCAATTGTAATAGCTTGATTCATATCGGG-TTAGCATAGAGGATAAGGTCGTTAGCGAA
66 ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
4763 AAAAAGATGGGAAATTAGC
131 AAAAAGATGGGAAATTAGC
4782 AACGAACTTG
Statistics
Matches: 146, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
157 48 0.33
158 98 0.67
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (158 bp):
CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
AAAAAGATGGGAAATTAGCGCGCCATTA
Found at i:6542 original size:118 final size:118
Alignment explanation
Indices: 6323--6573 Score: 288
Period size: 118 Copynumber: 2.1 Consensus size: 118
6313 ACAAACGCCG
* **
6323 CAATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCGGCGTTTGTAGTA
1 CAATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCAGCGTTTGTACCA
** * * ** * * * * *
6388 AAAACTGTTGCAATATATTTGATATATAGCGCCGTTTTTAGTTACAAATGCCA
66 AAAACTGCCGCAATAGAATAAATATATAACGACGTTTGTAGTAAAAAATGCCA
* * * *
6441 TAATATGTTTGATATTAATAATCGTTTTGCATAAACATGTTTGATATTTAGCAGCGTTTTTGACC
1 CAATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCAGCGTTTGT-ACC
* * *
6506 ACAAAC-GCCGCAATAGAATAAATATTTAACGACGTTTGTAGTAAAAAATGCCG
65 AAAAACTGCCGCAATAGAATAAATATATAACGACGTTTGTAGTAAAAAATGCCA
*
6559 CAATATATTTGATAT
1 CAATATGTTTGATAT
6574 ATAGCGGCGT
Statistics
Matches: 109, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
118 103 0.94
119 6 0.06
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (118 bp):
CAATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCAGCGTTTGTACCA
AAAACTGCCGCAATAGAATAAATATATAACGACGTTTGTAGTAAAAAATGCCA
Found at i:6585 original size:43 final size:43
Alignment explanation
Indices: 6538--6630 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 43
6528 TATTTAACGA
* * *
6538 CGTTTGTAGTAAAAAATGCCGCAATATATTTGATATATAGCGG
1 CGTTTGTAGTAAAAAATGACACAATAGATTTGATATATAGCGG
* * * *
6581 CGTTTTTAGTTACAAATGACACGATAGATTTGATATATAGCGG
1 CGTTTGTAGTAAAAAATGACACAATAGATTTGATATATAGCGG
*
6624 CTTTTGT
1 CGTTTGT
6631 GGCAGAAACG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (43 bp):
CGTTTGTAGTAAAAAATGACACAATAGATTTGATATATAGCGG
Found at i:21213 original size:21 final size:20
Alignment explanation
Indices: 21157--21214 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
21147 TTGTTGTTTT
**
21157 TTTCTTTCTTTTTTTTCTCA
1 TTTCTTTCTTTTTTTTAACA
*
21177 TGTCTTT-TCTTTTTTTAACA
1 TTTCTTTCT-TTTTTTTAACA
21197 GTTTCTTTCTTTTTTTTA
1 -TTTCTTTCTTTTTTTTA
21215 TTTTCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 15 0.48
21 14 0.45
22 1 0.03
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTCTTTCTTTTTTTTAACA
Found at i:21231 original size:34 final size:33
Alignment explanation
Indices: 21181--21244 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
21171 TTCTCATGTC
** * *
21181 TTTTCTTTTTTTAACAGTTTCTTTCTTTTTTTTA
1 TTTTCTTTTTCGAACAGCTTCTAT-TTTTTTTTA
21215 TTTTCTTTTTCGAACAGCTTCTATTTTTTT
1 TTTTCTTTTTCGAACAGCTTCTATTTTTTT
21245 CATGGAGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 6 0.23
34 20 0.77
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.69
Consensus pattern (33 bp):
TTTTCTTTTTCGAACAGCTTCTATTTTTTTTTA
Found at i:28091 original size:16 final size:15
Alignment explanation
Indices: 28055--28097 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
28045 CAAATATAAT
*
28055 TTAAAATATAAAAAA
1 TTAAATTATAAAAAA
28070 -TAAATTATAAAAATA
1 TTAAATTATAAAAA-A
28085 TTAAATTATAAAA
1 TTAAATTATAAAA
28098 GTAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 1 0.04
16 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAATTATAAAAAA
Found at i:28103 original size:20 final size:20
Alignment explanation
Indices: 28080--28150 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
28070 TAAATTATAA
*
28080 AAATATTAAATTATAAAAGT
1 AAATATTAAAATATAAAAGT
* * **
28100 AAATATAAAAATACAAGTTGT
1 AAATATTAAAATATAA-AAGT
28121 AAATCA-TAAAATATAAAAGT
1 AAAT-ATTAAAATATAAAAGT
28141 AAATATTAAA
1 AAATATTAAA
28151 TTAAAGTATA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.03
20 23 0.59
21 14 0.36
22 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (20 bp):
AAATATTAAAATATAAAAGT
Found at i:28107 original size:28 final size:30
Alignment explanation
Indices: 28055--28112 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
28045 CAAATATAAT
28055 TTAAAATATAAAAAATAAATTATAAAAATA
1 TTAAAATATAAAAAATAAATTATAAAAATA
* *
28085 TTAAATTAT-AAAAGTAAA-TATAAAAATA
1 TTAAAATATAAAAAATAAATTATAAAAATA
28113 CAAGTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 10 0.38
29 8 0.31
30 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (30 bp):
TTAAAATATAAAAAATAAATTATAAAAATA
Found at i:28122 original size:21 final size:23
Alignment explanation
Indices: 28098--28140 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28088 AATTATAAAA
*
28098 GTAAAT-ATAAAA-ATACAAGTT
1 GTAAATCATAAAATATAAAAGTT
28119 GTAAATCATAAAATATAAAAGT
1 GTAAATCATAAAATATAAAAGT
28141 AAATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (23 bp):
GTAAATCATAAAATATAAAAGTT
Found at i:45180 original size:36 final size:36
Alignment explanation
Indices: 45133--45225 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
45123 TTGATTTTTC
45133 AAAGGGACAATTTAAATGGGATAATTTTAAAATATA
1 AAAGGGACAATTTAAATGGGATAATTTTAAAATATA
45169 AAAGGGACAATTTAAATGGGATAATTTTAAAATATA
1 AAAGGGACAATTTAAATGGGATAATTTTAAAATATA
* *
45205 AAAGGGACAAATAAAATGGGA
1 AAAGGGACAATTTAAATGGGA
45226 CAGAGGGAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (36 bp):
AAAGGGACAATTTAAATGGGATAATTTTAAAATATA
Found at i:45368 original size:22 final size:21
Alignment explanation
Indices: 45318--45368 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
45308 TGATTTTATC
45318 GCATA-TTTTTTTTCTTTGTG
1 GCATATTTTTTTTTCTTTGTG
* *
45338 ACACATTTTTGTTTGTCTTT-TG
1 GCATATTTTT-TTT-TCTTTGTG
45360 GCATATTTT
1 GCATATTTT
45369 CCCTACTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 4 0.17
22 12 0.50
23 5 0.21
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.61
Consensus pattern (21 bp):
GCATATTTTTTTTTCTTTGTG
Found at i:46674 original size:20 final size:20
Alignment explanation
Indices: 46645--46687 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
46635 ATTCCACCAC
46645 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
46665 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
46685 ATG
1 ATG
46688 AGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:51570 original size:12 final size:12
Alignment explanation
Indices: 51553--51581 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
51543 CATATTTAAG
51553 ATTCTGTGGTAA
1 ATTCTGTGGTAA
51565 ATTCTGTGGTAA
1 ATTCTGTGGTAA
51577 ATTCT
1 ATTCT
51582 TTAGCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (12 bp):
ATTCTGTGGTAA
Found at i:56084 original size:20 final size:20
Alignment explanation
Indices: 56055--56097 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
56045 ATTCCACCAC
56055 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
56075 ATGCATCTATATGGTTCTAA
1 ATGCAACTATATGCTCCTAA
56095 ATG
1 ATG
56098 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:59935 original size:74 final size:74
Alignment explanation
Indices: 59847--59995 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
59837 AGACATCGGA
59847 AGAGAAAAAGAGTACCCGAAATTGTATTAATCAAATCCATCATGCACATCGAAAATTACAAAGTA
1 AGAGAAAAAGAGTACCCGAAATTGTATTAATCAAATCCATCATGCACATCGAAAATTACAAAGTA
59912 CATTACAAG
66 CATTACAAG
59921 AGAGAAAAAGAGTACCCGAAATTGTATTAATCAAATCCATCATGCACATCGAAAATTACAAAGTA
1 AGAGAAAAAGAGTACCCGAAATTGTATTAATCAAATCCATCATGCACATCGAAAATTACAAAGTA
59986 CATTACAAG
66 CATTACAAG
59995 A
1 A
59996 TAAATGAAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.21
Consensus pattern (74 bp):
AGAGAAAAAGAGTACCCGAAATTGTATTAATCAAATCCATCATGCACATCGAAAATTACAAAGTA
CATTACAAG
Found at i:69536 original size:18 final size:18
Alignment explanation
Indices: 69510--69544 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69500 AATGAAGTAT
69510 ATCAACCTCTTATTGAAA
1 ATCAACCTCTTATTGAAA
* *
69528 ATCAGCCTCTTGTTGAA
1 ATCAACCTCTTATTGAA
69545 GACGTTGGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (18 bp):
ATCAACCTCTTATTGAAA
Found at i:74537 original size:26 final size:26
Alignment explanation
Indices: 74480--74534 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
74470 TTTAAAAAAC
*
74480 AAACTTGAAAATAAAAGAAAAATAAA
1 AAACTTGAAAATAAAAGAAAAAGAAA
*
74506 AAACTTGAAAAGTAAAATAAAAGAGAAA
1 AAACTTGAAAA-TAAAAGAAAA-AGAAA
74534 A
1 A
74535 CTTTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.15
Consensus pattern (26 bp):
AAACTTGAAAATAAAAGAAAAAGAAA
Found at i:78569 original size:21 final size:21
Alignment explanation
Indices: 78545--78588 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
78535 GGAAGCCATT
78545 GATGAAAGATTGGAACTTTGG
1 GATGAAAGATTGGAACTTTGG
78566 GATGAAAGATTGGAACTTTGG
1 GATGAAAGATTGGAACTTTGG
78587 GA
1 GA
78589 AGATGAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (21 bp):
GATGAAAGATTGGAACTTTGG
Found at i:78927 original size:75 final size:75
Alignment explanation
Indices: 78793--78937 Score: 179
Period size: 75 Copynumber: 1.9 Consensus size: 75
78783 TGTTAACAAT
* * *
78793 ATTTGATTTGAATTTAATATTTTTCTAGACTTAATATTATGGTTTAAGTCTTAAGATTTGACACT
1 ATTTGATTTGAATTT-ATATTATTCTAGACTTAATATTATGATTTAAGTATTAAGATTTGACACT
78858 TTAATATTATA
65 TTAATATTATA
* *
78869 ATTTTATTATGAATTT-TATTATTCTAGAGTTAATATTATGATTTGAA-TATTGAA-ATTTGACA
1 ATTTGATT-TGAATTTATATTATTCTAGACTTAATATTATGATTT-AAGTATT-AAGATTTGACA
*
78931 TTTTAAT
63 CTTTAAT
78938 GTTGTTGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
75 42 0.70
76 11 0.18
77 7 0.12
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (75 bp):
ATTTGATTTGAATTTATATTATTCTAGACTTAATATTATGATTTAAGTATTAAGATTTGACACTT
TAATATTATA
Found at i:79736 original size:32 final size:34
Alignment explanation
Indices: 79695--79774 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
79685 TTTAAATAGT
*
79695 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
* *
79727 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATATTTATATAAA
79762 TATTATTTATTTA
1 TATTATTT-TTTA
79775 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 15 0.38
34 3 0.08
35 19 0.47
36 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:79738 original size:34 final size:33
Alignment explanation
Indices: 79662--79769 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 33
79652 GTGGTAAGAA
* *
79662 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
79696 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
79731 ATTTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
79766 ATTT
1 ATTT
79770 ATTTAGAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.43
35 28 0.44
36 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:83607 original size:12 final size:13
Alignment explanation
Indices: 83574--83611 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
83564 AAATACATAA
83574 ATATATTTAATAT
1 ATATATTTAATAT
*
83587 ATTTATTTAATAT
1 ATATATTTAATAT
83600 A-ATATTTAATAT
1 ATATATTTAATAT
83612 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:84506 original size:16 final size:16
Alignment explanation
Indices: 84485--84516 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
84475 AAGAAGGTTC
84485 ACTTAGTGTGATATAA
1 ACTTAGTGTGATATAA
84501 ACTTAGTGTGATATAA
1 ACTTAGTGTGATATAA
84517 GTAATGTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
ACTTAGTGTGATATAA
Found at i:92935 original size:20 final size:20
Alignment explanation
Indices: 92906--92952 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
92896 ATTCCACCTC
*
92906 ATGCAACTATAT-ACTCCTAA
1 ATGCATCTATATGA-TCCTAA
*
92926 ATGCATCTATGTGATCCTAA
1 ATGCATCTATATGATCCTAA
92946 ATG-ATCT
1 ATGCATCT
92953 CTTAGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGCATCTATATGATCCTAA
Found at i:101401 original size:20 final size:20
Alignment explanation
Indices: 101372--101414 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
101362 ATTCCACCAC
101372 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
101392 ATGCATCTATGTGCTCCTAA
1 ATGCAACTATATGCTCCTAA
101412 ATG
1 ATG
101415 AGTTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:103566 original size:21 final size:20
Alignment explanation
Indices: 103538--103576 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
103528 CACTGCAGGA
103538 ATTTATGG-TCTCGACAAAAT
1 ATTTATGGCT-TCGACAAAAT
103558 ATTTCATGGCTTCGACAAA
1 ATTT-ATGGCTTCGACAAA
103577 GACTTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTATGGCTTCGACAAAAT
Found at i:108149 original size:13 final size:14
Alignment explanation
Indices: 108131--108164 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
108121 ACACAGTTTC
*
108131 TTTTCCTTTAAA-A
1 TTTTCCCTTAAATA
108144 TTTTCCCTTAAATA
1 TTTTCCCTTAAATA
108158 TTTTCCC
1 TTTTCCC
108165 CTCAACGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTCCCTTAAATA
Found at i:116049 original size:198 final size:195
Alignment explanation
Indices: 115711--116085 Score: 723
Period size: 198 Copynumber: 1.9 Consensus size: 195
115701 AGATGAACTA
115711 GTTTTATTTTGTAAGGTCACTACTAATCAAATGAGAACTATCCAACCAATAATAGAGGAGTTTTT
1 GTTTTATTTTGTAAGGTCACTACTAATCAAATGAGAACTATCCAACCAATAATAGAGGAGTTTTT
115776 CTTGGAGTCCGGACATAAAGTTAGTGCTGTGAAAACTCGAATTTTCTTCTCAAAGAATAATGCCC
66 CTTGGAGTCCGGACATAAAGTTAGTGCTGTGAAAACTCGAATTTTCTTCTCAAAGAATAATGCCC
115841 CTCAAATTCGGGAGGAAATTATTCGCGGGTTTGCGTTTGCGAAATTTCAGTTTCCTTTGTTACAT
131 CTCAAATTC--G-GGAAATTATTCGCGGGTTTGCGTTTGCGAAATTTCAGTTTCCTTTGTTACAT
115906 ATT
193 ATT
115909 GTTTTATTTTGTAAGGTCACTACTAATCAAATGAGAACTATCCAACCAATAATAGAGGAGTTTTT
1 GTTTTATTTTGTAAGGTCACTACTAATCAAATGAGAACTATCCAACCAATAATAGAGGAGTTTTT
115974 CTTGGAGTCCGGACATAAAGTTAGTGCTGTGAAAACTCGAATTTTCTTCTCAAAGAATAATGCCC
66 CTTGGAGTCCGGACATAAAGTTAGTGCTGTGAAAACTCGAATTTTCTTCTCAAAGAATAATGCCC
116039 CTCAAATTCGGGAAATTATTCGCGGGTTTGCGTTTGCGAAATTTCAG
131 CTCAAATTCGGGAAATTATTCGCGGGTTTGCGTTTGCGAAATTTCAG
116086 GATTAAGGTA
Statistics
Matches: 177, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
195 37 0.21
196 1 0.01
198 139 0.79
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (195 bp):
GTTTTATTTTGTAAGGTCACTACTAATCAAATGAGAACTATCCAACCAATAATAGAGGAGTTTTT
CTTGGAGTCCGGACATAAAGTTAGTGCTGTGAAAACTCGAATTTTCTTCTCAAAGAATAATGCCC
CTCAAATTCGGGAAATTATTCGCGGGTTTGCGTTTGCGAAATTTCAGTTTCCTTTGTTACATATT
Found at i:118041 original size:20 final size:20
Alignment explanation
Indices: 118016--118055 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
118006 CCTAGGTTTG
118016 AATATCAATACTGGAAGAAC
1 AATATCAATACTGGAAGAAC
* * *
118036 AATATCGATATTGGATGAAC
1 AATATCAATACTGGAAGAAC
118056 TAGAATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AATATCAATACTGGAAGAAC
Found at i:121705 original size:20 final size:20
Alignment explanation
Indices: 121672--121715 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
121662 GACGAGTTTA
121672 TTAATTGTCCTTTTAATGCCT
1 TTAATTGTCCTTTTAATG-CT
*
121693 TTAA-TGTCTTTTTAATGCT
1 TTAATTGTCCTTTTAATGCT
121712 TTAA
1 TTAA
121716 CGGTAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 12 0.55
21 4 0.18
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (20 bp):
TTAATTGTCCTTTTAATGCT
Found at i:122177 original size:32 final size:32
Alignment explanation
Indices: 122136--122203 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
122126 TGTGTACATT
* ** *
122136 ATCTTCAATCTCTTACATAACGCACTCCTTTC
1 ATCTTCAATCTCTTACACAACAAAATCCTTTC
122168 ATCTTCAATCTCTTACACAACAAAATCCTTTC
1 ATCTTCAATCTCTTACACAACAAAATCCTTTC
122200 ATCT
1 ATCT
122204 AACCAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.32, G:0.01, T:0.37
Consensus pattern (32 bp):
ATCTTCAATCTCTTACACAACAAAATCCTTTC
Found at i:133919 original size:13 final size:13
Alignment explanation
Indices: 133901--133926 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
133891 AAGGGGGAGA
133901 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
133914 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
133927 TAAAATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:135416 original size:20 final size:20
Alignment explanation
Indices: 135391--135451 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
135381 CCATTAGACA
135391 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
** *
135411 GGGGGAATCTCTTCCCCCTG
1 GGGGGAATCGGTACCCCCTG
135431 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
135451 G
1 G
135452 ACATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.13, C:0.31, G:0.38, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:139377 original size:21 final size:20
Alignment explanation
Indices: 139345--139428 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 20
139335 AAAACCCGTG
*
139345 GGGGGTATCGATTCCCTCAA
1 GGGGGAATCGATTCCCTCAA
*
139365 GGAGGGAATCGATTCACATTCAAA
1 GG-GGGAATCGATTC-C-CTC-AA
*
139389 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCC-TCAA
*
139411 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
139429 TACACTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.08
21 14 0.27
22 14 0.27
23 15 0.29
24 5 0.10
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:139415 original size:22 final size:22
Alignment explanation
Indices: 139345--139426 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
139335 AAAACCCGTG
*
139345 GGGGGTATCGATT-CCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
139365 GGAGGGAATCGATTCACATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
*
139389 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
139411 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
139427 TCTACACTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.04
21 10 0.20
22 17 0.34
23 17 0.34
24 4 0.08
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:145570 original size:23 final size:23
Alignment explanation
Indices: 145543--145586 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
145533 TTTGGCTTTC
*
145543 AAAATCGATTTTTG-TTTTAAAAG
1 AAAATCG-TTTTCGATTTTAAAAG
145566 AAAATCGTTTTCGATTTTAAA
1 AAAATCGTTTTCGATTTTAAA
145587 TTTTGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (23 bp):
AAAATCGTTTTCGATTTTAAAAG
Found at i:146866 original size:21 final size:21
Alignment explanation
Indices: 146841--146923 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
146831 CCGTTAGACA
146841 GGGGGAATTGGTATCCCCTGG
1 GGGGGAATTGGTATCCCCTGG
146862 GGGGGAATCT-GT-TCCCCCT-G
1 GGGGGAAT-TGGTAT-CCCCTGG
*
146882 GGGGGAATCGGTA-CCCCATGG
1 GGGGGAATTGGTATCCCC-TGG
* *
146903 GGGGGAATTTGTACCCCCTGG
1 GGGGGAATTGGTATCCCCTGG
146924 ACATTCTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
19 4 0.08
20 13 0.25
21 30 0.58
22 5 0.10
ACGTcount: A:0.14, C:0.24, G:0.40, T:0.22
Consensus pattern (21 bp):
GGGGGAATTGGTATCCCCTGG
Found at i:146904 original size:41 final size:41
Alignment explanation
Indices: 146841--146923 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
146831 CCGTTAGACA
* *
146841 GGGGGAATTGGTATCCCCTGGGGGGGAATCTGTTCCCCCTG
1 GGGGGAATCGGTATCCCCTGGGGGGGAATCTGTACCCCCTG
*
146882 GGGGGAATCGGTA-CCCCATGGGGGGGAATTTGTACCCCCTG
1 GGGGGAATCGGTATCCCC-TGGGGGGGAATCTGTACCCCCTG
146923 G
1 G
146924 ACATTCTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.14, C:0.24, G:0.40, T:0.22
Consensus pattern (41 bp):
GGGGGAATCGGTATCCCCTGGGGGGGAATCTGTACCCCCTG
Found at i:147665 original size:45 final size:45
Alignment explanation
Indices: 147601--147688 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
147591 TTCTAAAAGT
147601 TGATAACCATAACATCCCATTCTAAAAGTTTGATATTATTTTTAA
1 TGATAACCATAACATCCCATTCTAAAAGTTTGATATTATTTTTAA
*
147646 TGATAACTATAACATCCCATTCTAAAAGTTTGATATTATTTTT
1 TGATAACCATAACATCCCATTCTAAAAGTTTGATATTATTTTT
147689 TAACTTCGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (45 bp):
TGATAACCATAACATCCCATTCTAAAAGTTTGATATTATTTTTAA
Found at i:159532 original size:2 final size:2
Alignment explanation
Indices: 159527--159559 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
159517 CTTTTTTTCT
159527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
159560 TTCACGCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:162664 original size:16 final size:17
Alignment explanation
Indices: 162629--162665 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
162619 TATGGGATAA
162629 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
162646 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
162662 AAAA
1 AAAA
162666 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:162706 original size:17 final size:17
Alignment explanation
Indices: 162684--162716 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
162674 TACTACCATA
*
162684 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
162701 ATATTATATTTTATAT
1 ATATTATATTTTATAT
162717 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:163232 original size:17 final size:17
Alignment explanation
Indices: 163137--163282 Score: 77
Period size: 17 Copynumber: 8.2 Consensus size: 17
163127 AAAATAATGA
* *
163137 AAATAAAAATAAAAAAC
1 AAATAAAGATAAAAAAT
*
163154 AAATGAA-ATAAAAAAAT
1 AAATAAAGAT-AAAAAAT
163171 AAGATAAAGA-AAAAAAT
1 AA-ATAAAGATAAAAAAT
* *
163188 AAAGAAAGAAAATTAAAGAT
1 AAATAAAGATAA--AAA-AT
*
163208 AAAGTAAAGATAAAAAGT
1 AAA-TAAAGATAAAAAAT
163226 AAATAAA-ATGAATAAAAT
1 AAATAAAGAT-AA-AAAAT
* *
163244 AAAGATAAAGAAAAGAAAAG
1 -AA-ATAAAGATAA-AAAAT
163264 AAATAGAA-AT-AAAAAT
1 AAATA-AAGATAAAAAAT
163280 AAA
1 AAA
163283 GATATAAGAA
Statistics
Matches: 102, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
16 17 0.17
17 32 0.31
18 16 0.16
19 13 0.13
20 16 0.16
21 8 0.08
ACGTcount: A:0.75, C:0.01, G:0.10, T:0.14
Consensus pattern (17 bp):
AAATAAAGATAAAAAAT
Found at i:163262 original size:20 final size:20
Alignment explanation
Indices: 163186--163305 Score: 67
Period size: 21 Copynumber: 6.0 Consensus size: 20
163176 AAAGAAAAAA
163186 ATAAAG-AAAGAAAATTAAAG
1 ATAAAGAAAAGAAAA-TAAAG
* *
163206 ATAAAGTAAAGATAA-AAAG
1 ATAAAGAAAAGAAAATAAAG
*
163225 -TAAATAAAATG--AATAAA-
1 ATAAAGAAAA-GAAAATAAAG
*
163242 ATAAAGATAAAGAAAAGAAAAG
1 ATAAAGA-AAAGAAAA-TAAAG
163264 A-AATAGAAATA-AAAATAAAG
1 ATAA-AGAAA-AGAAAATAAAG
163284 ATATAAGAATAAAGAAAATAAA
1 ATA-AAG-A-AAAGAAAATAAA
163306 TAGAATAGAG
Statistics
Matches: 78, Mismatches: 6, Indels: 29
0.69 0.05 0.26
Matches are distributed among these distances:
17 2 0.03
18 16 0.21
19 8 0.10
20 13 0.17
21 21 0.27
22 8 0.10
23 10 0.13
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (20 bp):
ATAAAGAAAAGAAAATAAAG
Found at i:163282 original size:72 final size:72
Alignment explanation
Indices: 163121--163305 Score: 175
Period size: 72 Copynumber: 2.5 Consensus size: 72
163111 GAAACGTGTT
* * *
163121 AGAGAAA-AAATAATGAAAATAAAAATAAAAA-ACAAATGAAATAAAAAAATAAGATAAAGAAAA
1 AGAGAAATAAA-AAT-AAAGTAAAGATAAAAAGA-AAATAAAATAAAAAAATAAGATAAAGAAAA
163184 AAATAAAGAA
63 AAATAAAGAA
* * *
163194 AGA-AAATTAAAGATAAAGTAAAGATAAAAAGTAAATAAAATGAATAAAATAAAGATAAAG-AAA
1 AGAGAAA-TAAAAATAAAGTAAAGATAAAAAGAAAATAAAAT-AAAAAAAT-AAGATAAAGAAAA
*
163257 AGA-AAAGAA
63 AAATAAAGAA
* *
163266 ATAGAAATAAAAATAAAGATATAAGA-ATAAAGAAAATAAA
1 AGAGAAATAAAAATAAAG-TA-AAGATAAAAAGAAAATAAA
163306 TAGAATAGAG
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
72 43 0.46
73 34 0.37
74 16 0.17
ACGTcount: A:0.74, C:0.01, G:0.11, T:0.15
Consensus pattern (72 bp):
AGAGAAATAAAAATAAAGTAAAGATAAAAAGAAAATAAAATAAAAAAATAAGATAAAGAAAAAAA
TAAAGAA
Found at i:163312 original size:18 final size:18
Alignment explanation
Indices: 163255--163319 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 18
163245 AAGATAAAGA
163255 AAAGAAAAGAAATAGAAAT
1 AAAGAAAAGAAATAG-AAT
* *
163274 AAAAATAAAGATATAAGAAT
1 AAAGA-AAAGAAAT-AGAAT
*
163294 AAAGAAAATAAATAGAAT
1 AAAGAAAAGAAATAGAAT
*
163312 AGAGAAAA
1 AAAGAAAA
163320 TAATAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 12 0.32
19 10 0.26
20 14 0.37
21 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAGAAAAGAAATAGAAT
Found at i:163325 original size:44 final size:43
Alignment explanation
Indices: 163230--163351 Score: 119
Period size: 44 Copynumber: 2.8 Consensus size: 43
163220 AAAAGTAAAT
*
163230 AAAATGAATAAAATA-AAG-ATAAAGAAAAGAAA-AGAAATAGA
1 AAAAT-AATAAAATATAAGAATAAAGAAAATAAATAGAAATAGA
*
163271 AATAAAAATAAAGATATAAGAATAAAGAAAATAAATAG-AATAGA
1 AA-AATAATAAA-ATATAAGAATAAAGAAAATAAATAGAAATAGA
* *
163315 GAAAATAATAATAATATATATAATAAA-TAAATAAATA
1 -AAAATAATAA-AATATA-AGAATAAAGAAAATAAATA
163352 ACTAAAAACA
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
41 8 0.12
42 5 0.07
43 3 0.04
44 40 0.59
45 12 0.18
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (43 bp):
AAAATAATAAAATATAAGAATAAAGAAAATAAATAGAAATAGA
Found at i:163330 original size:18 final size:18
Alignment explanation
Indices: 163163--163330 Score: 62
Period size: 18 Copynumber: 9.8 Consensus size: 18
163153 CAAATGAAAT
*
163163 AAAAAAATAAG-ATAAAG
1 AAAATAATAAGAATAAAG
* *
163180 AAAAAAAT-A-AAGAAAG
1 AAAATAATAAGAATAAAG
*
163196 AAAATTA-AAG-ATAAAG
1 AAAATAATAAGAATAAAG
* *
163212 TAAAGATAA-AA-AGTAAAT
1 -AAA-ATAATAAGAATAAAG
163230 AAAATGAATAA-AATAAAG
1 AAAAT-AATAAGAATAAAG
*
163248 ATAAAGAA-AAG-A-AAAG
1 A-AAATAATAAGAATAAAG
* *
163264 -AAATAGA-AATAA-AAAT
1 AAAATA-ATAAGAATAAAG
163280 AAAGAT-ATAAGAATAAAG
1 AAA-ATAATAAGAATAAAG
*
163298 AAAATAA-ATAGAATAGAG
1 AAAATAATA-AGAATAAAG
*
163316 AAAATAATAATAATA
1 AAAATAATAAGAATA
163331 TATATAATAA
Statistics
Matches: 115, Mismatches: 17, Indels: 37
0.68 0.10 0.22
Matches are distributed among these distances:
14 4 0.03
15 3 0.03
16 28 0.24
17 28 0.24
18 48 0.42
19 4 0.03
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (18 bp):
AAAATAATAAGAATAAAG
Found at i:163352 original size:15 final size:16
Alignment explanation
Indices: 163317--163357 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
163307 AGAATAGAGA
163317 AAATAAT-AATAATAT
1 AAATAATAAATAATAT
*
163332 ATATAATAAATAA-AT
1 AAATAATAAATAATAT
163347 AAATAACTAAA
1 AAATAA-TAAA
163358 AACAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAATAATAT
Found at i:163410 original size:26 final size:27
Alignment explanation
Indices: 163367--163421 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
163357 AAACAAGAAT
* * *
163367 AAATAAAAATAAATATAAAGGACATAA
1 AAATAAAAATAAAGATAAAGAAAATAA
*
163394 AAAT-AAAGTAAAGATAAAGAAAATAA
1 AAATAAAAATAAAGATAAAGAAAATAA
163420 AA
1 AA
163422 GAAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (27 bp):
AAATAAAAATAAAGATAAAGAAAATAA
Found at i:163429 original size:17 final size:18
Alignment explanation
Indices: 163409--163446 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
163399 AAGTAAAGAT
163409 AAAGAAAATAAA-AG-AAA
1 AAAGAAAA-AAATAGTAAA
163426 AAAGAAAAAAATAGTAAA
1 AAAGAAAAAAATAGTAAA
163444 AAA
1 AAA
163447 ATATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 10 0.53
18 6 0.32
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAGAAAAAAATAGTAAA
Found at i:163547 original size:3 final size:3
Alignment explanation
Indices: 163539--163588 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
163529 TAGCAAAAAT
163539 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
163585 ATA A
1 ATA A
163589 AAGCATAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:169930 original size:14 final size:14
Alignment explanation
Indices: 169903--169946 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
169893 CACATAAATC
169903 TTAATT-TTAA-AA
1 TTAATTGTTAATAA
169915 TTAATTGTTAATAA
1 TTAATTGTTAATAA
*
169929 TTAATAGTTAAT-A
1 TTAATTGTTAATAA
169942 TTAAT
1 TTAAT
169947 GTTTATCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 6 0.21
13 10 0.34
14 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
TTAATTGTTAATAA
Found at i:171472 original size:21 final size:21
Alignment explanation
Indices: 171448--171514 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
171438 CATTATGAAC
171448 TTCTTCTCTCTTGTGGATGAG
1 TTCTTCTCTCTTGTGGATGAG
* *
171469 TTCTT-T-TCAT-T--ATGAAC
1 TTCTTCTCTCTTGTGGATG-AG
171486 TTCTTCTCTCTTGTGGATGAG
1 TTCTTCTCTCTTGTGGATGAG
171507 TTCTTCTC
1 TTCTTCTC
171515 ATTATGAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
16 3 0.08
17 6 0.17
18 2 0.06
19 6 0.17
20 2 0.06
21 14 0.39
22 3 0.08
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.51
Consensus pattern (21 bp):
TTCTTCTCTCTTGTGGATGAG
Found at i:171488 original size:38 final size:38
Alignment explanation
Indices: 171429--171528 Score: 175
Period size: 38 Copynumber: 2.7 Consensus size: 38
171419 GGATTGAGCA
*
171429 AGTTATTCTCATTATGAACTTCTTCTCTCTTGTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTGGATG
*
171467 AGTTCTTTTCATTATGAACTTCTTCTCTCTTGTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTGGATG
171505 AGTTCTTCTCATTATGAAC-TCTTC
1 AGTTCTTCTCATTATGAACTTCTTC
171529 ACTGAAAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
37 5 0.08
38 54 0.92
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (38 bp):
AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTGGATG
Found at i:172379 original size:15 final size:15
Alignment explanation
Indices: 172359--172399 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
172349 TTAAATGAAA
*
172359 ACTGTCTCAAGAGAT
1 ACTGTCTCAAGAGAG
*
172374 ACTGTCTCAAGGGAG
1 ACTGTCTCAAGAGAG
*
172389 ATTGTCTCAAG
1 ACTGTCTCAAG
172400 CAAGAAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (15 bp):
ACTGTCTCAAGAGAG
Found at i:172483 original size:73 final size:73
Alignment explanation
Indices: 172391--172544 Score: 229
Period size: 73 Copynumber: 2.1 Consensus size: 73
172381 CAAGGGAGAT
*
172391 TGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAA-CATCTCAAGGGAGACAAAACTTTGTTTCA
1 TGTCTCAAGCAAGAAGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTTCA
172455 AGAGAAAAC
66 AGAG-AAAC
* * * * *
172464 TGTCTCAAGCGAGACGAAGTTGATTTTAAGAAAAACCATTTTAAGGGAGACAAAACTTTGTTTCA
1 TGTCTCAAGCAAGAAGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTTCA
*
172529 AGAGAAAT
66 AGAGAAAC
172537 TGTCTCAA
1 TGTCTCAA
172545 AAACTTGTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 42 0.58
74 31 0.42
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (73 bp):
TGTCTCAAGCAAGAAGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTTCA
AGAGAAAC
Found at i:172554 original size:28 final size:29
Alignment explanation
Indices: 172515--172572 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
172505 TAAGGGAGAC
* *
172515 AAAACTTTGTTTCAAGAGAAATTGTCTCA
1 AAAACTTTGTTTAAAGAGAAACTGTCTCA
172544 AAAAC-TTGTTTAAAGAGAAACTGTCTCA
1 AAAACTTTGTTTAAAGAGAAACTGTCTCA
172572 A
1 A
172573 GGGAGACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (29 bp):
AAAACTTTGTTTAAAGAGAAACTGTCTCA
Found at i:172600 original size:36 final size:36
Alignment explanation
Indices: 172544--172759 Score: 162
Period size: 36 Copynumber: 6.1 Consensus size: 36
172534 AATTGTCTCA
* * * *
172544 AAAACTTGTTTAAAGAGAAACTGTCTCAAGGGAGAC
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGGGAGAC
*
172580 AAAATTCGTTTCAAGGGAAACGT-TCTC-----A-A-
1 AAAATTTGTTTCAAGGGAAAC-TATCTCAAGGGAGAC
** *
172609 AATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGAC
1 AAAATT-TGTTTCAAGGGAAACTATCTCAAGGGAGAC
* * * *
172646 AAAATTTGTTTCAATGGAAAATGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGGGAGAC
* * *
172682 AAAATTTGTTTCAAGGGAAACTATCTTAAGTGATA-
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGGGAGAC
* * * *
172717 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAA-ATT-TGTTTCAAGGGAAACTATCTCAAGGGAGAC
172755 AAAAT
1 AAAAT
172760 CTTTTGGTTC
Statistics
Matches: 140, Mismatches: 27, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
29 5 0.04
30 18 0.13
31 1 0.01
35 4 0.03
36 78 0.56
37 31 0.22
38 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
AAAATTTGTTTCAAGGGAAACTATCTCAAGGGAGAC
Found at i:172637 original size:66 final size:64
Alignment explanation
Indices: 172506--172674 Score: 214
Period size: 66 Copynumber: 2.6 Consensus size: 64
172496 AAACCATTTT
* * *
172506 AAGGGAGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAAAACTTGTTTAAAGAGAAACTGTCTC
1 AAGGGAGACAAAA-TTTGTTTCAAGGGAAAGTGTCTCAAAAACTTGTTTAAAGAGAAACTATCTC
* ** *
172571 AAGGGAGACAAAATTCGTTTCAAGGGAAACGT-TCTCAAAATTTTGTGTTTCAAGAGAAACTATC
1 AAGGGAGACAAAATTTGTTTCAAGGGAAA-GTGTCTCAAAA-ACT-TGTTTAAAGAGAAACTATC
172635 TC
63 TC
* *
172637 AAGGGAGACAAAATTTGTTTCAATGGAAAATGTCTCAA
1 AAGGGAGACAAAATTTGTTTCAAGGGAAAGTGTCTCAA
172675 GAGAGACAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 22 0.24
65 16 0.18
66 52 0.58
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (64 bp):
AAGGGAGACAAAATTTGTTTCAAGGGAAAGTGTCTCAAAAACTTGTTTAAAGAGAAACTATCTC
Found at i:172696 original size:21 final size:21
Alignment explanation
Indices: 172635--172696 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
172625 AGAAACTATC
*
172635 TCAAGGGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
172656 TCAA-TG-G--AAAA--TGTC
1 TCAAGAGAGACAAAATTTGTT
172671 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
172692 TCAAG
1 TCAAG
172697 GGAAACTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 1 0.03
17 5 0.16
19 5 0.16
20 1 0.03
21 12 0.39
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:172798 original size:40 final size:40
Alignment explanation
Indices: 172688--173122 Score: 592
Period size: 40 Copynumber: 11.0 Consensus size: 40
172678 AGACAAAATT
* * *
172688 TGTTTCAAGG-GAAACTATCTTAAGT--GATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* * * ** * *
172725 TGTTTCGAGG-GAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* * * * *
172764 TGGTTCAAGGAAAACCAATCTTGAGCGAGGTAAAATCTTT
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
*
172804 TGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* *
172844 TGTTTCAAGGAAAAATC-ATCTTGAATGAGATAAAATCTTA
1 TGTTTCAAGGAAAAA-CAATCTTGAGTGAGATAAAATCTTC
* * *
172884 TGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATATTT
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
*
172924 TGTTTCAAGGAAAAACAATCTTGAGTGTGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
*
172964 TGTTTCAAGGAAAAACAAGCTTGAGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
173004 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* * *
173044 TATTTTAAGGAAAAATAATCTTGAGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
173084 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTT
1 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTT
173123 TTGTATTAAC
Statistics
Matches: 357, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
37 22 0.06
39 20 0.06
40 314 0.88
41 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (40 bp):
TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
Found at i:172860 original size:20 final size:20
Alignment explanation
Indices: 172835--172898 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
172825 TGAATGAGAT
172835 AAAATCTTCTGTTTCAAGGA
1 AAAATCTTCTGTTTCAAGGA
* *
172855 AAAATCATC---TTGAATGAGA
1 AAAATCTTCTGTTTCAA-G-GA
*
172874 TAAAATCTTATGTTTCAAGGA
1 -AAAATCTTCTGTTTCAAGGA
172895 AAAA
1 AAAA
172899 CAATCTTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 2 0.06
20 19 0.58
21 2 0.06
22 1 0.03
23 4 0.12
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAATCTTCTGTTTCAAGGA
Done.