Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008741.1 Hibiscus syriacus cultivar Beakdansim tig00111828_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: 100617
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:15852 original size:36 final size:36
Alignment explanation
Indices: 15812--15926 Score: 112
Period size: 36 Copynumber: 3.2 Consensus size: 36
15802 TGATCGGTGA
15812 TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
1 TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
* * *
15848 TGAACCTGCA-AAAAAGAATTACCAGC-CGATC-G-AT
1 TGAACCT--ATATAAGGAATTACCAGCTTGATCAGAAT
* **
15882 GCTGAACCTATATGAGGAATTACCAATTTGATCAGAAT
1 --TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
15920 TGAACCT
1 TGAACCT
15927 GCAGAGACTT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
34 3 0.05
35 12 0.19
36 29 0.47
37 15 0.24
38 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (36 bp):
TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
Found at i:15944 original size:72 final size:72
Alignment explanation
Indices: 15788--15929 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 72
15778 TTAGGTCTAT
* ** * *
15788 AAAGAATTATCAGATGATCGGTGATGAACCTATATAAGGAATTACCAGCTTGATCAGAATTGAAC
1 AAAGAATTACCAGCCGATCGATGATGAACCTATATAAGGAATTACCAACTTGATCAGAATTGAAC
15853 CTGCAAA
66 CTGCAAA
* * *
15860 AAAGAATTACCAGCCGATCGATGCTGAACCTATATGAGGAATTACCAATTTGATCAGAATTGAAC
1 AAAGAATTACCAGCCGATCGATGATGAACCTATATAAGGAATTACCAACTTGATCAGAATTGAAC
15925 CTGCA
66 CTGCA
15930 GAGACTTCAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (72 bp):
AAAGAATTACCAGCCGATCGATGATGAACCTATATAAGGAATTACCAACTTGATCAGAATTGAAC
CTGCAAA
Found at i:17423 original size:24 final size:24
Alignment explanation
Indices: 17396--17502 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
17386 AAACGGAGAT
*
17396 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
17420 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
17444 GTTAGGAATCAAAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
17468 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
17492 ACCAGAAATCA
1 ATCAGAAATCA
17503 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:17502 original size:48 final size:48
Alignment explanation
Indices: 17398--17502 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
17388 ACGGAGATAT
* * ***
17398 CAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAGGT
1 CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAAAC
* * * * *
17446 TAGGAATCAAAACAGATTTCAGATCAGATGTCAAAACAGAATTCAAAC
1 CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAAAC
17494 CAGAAATCA
1 CAGAAATCA
17503 GATAAAATAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (48 bp):
CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAAAC
Found at i:19236 original size:9 final size:9
Alignment explanation
Indices: 19222--19246 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19212 AAAGAAAAAG
19222 AAAATAAAC
1 AAAATAAAC
19231 AAAATAAAC
1 AAAATAAAC
19240 AAAATAA
1 AAAATAA
19247 TAATAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:19809 original size:12 final size:11
Alignment explanation
Indices: 19782--19821 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
19772 TAACAAAATA
*
19782 AATAATATAA-
1 AATAATACAAG
19792 AATAATACAAG
1 AATAATACAAG
19803 TAATAATACAAG
1 -AATAATACAAG
19815 AATAATA
1 AATAATA
19822 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (11 bp):
AATAATACAAG
Found at i:19859 original size:16 final size:16
Alignment explanation
Indices: 19840--19887 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
19830 GAGAAAGTAA
19840 AAAATATAATAATAAT
1 AAAATATAATAATAAT
19856 AAAATATAA-AA-AAT
1 AAAATATAATAATAAT
19870 ATAAATAT-ATAAT-AT
1 A-AAATATAATAATAAT
19885 AAA
1 AAA
19888 TAAGTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.24
15 13 0.45
16 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAATAATAAT
Found at i:20591 original size:37 final size:37
Alignment explanation
Indices: 20493--20594 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
20483 GTGCTTGTGG
* ** * * *
20493 ATCCTATCTTTAGGAGTTTAAATAATAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTAT
* *
20530 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTAT
20567 ATCCTATTTTTAGGAGTTTAAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
20595 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTAT
Found at i:21637 original size:106 final size:106
Alignment explanation
Indices: 21328--22407 Score: 1523
Period size: 106 Copynumber: 10.4 Consensus size: 106
21318 GCATTGTTCC
* * * ** * *
21328 GAGTCCAATATCCTCCG-TCGTGCAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
21392 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * *
21434 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T---AAAAT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*** * *
21493 CCAGCCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * *
21534 GGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
21599 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* **
21640 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
21705 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * * *
21746 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
21811 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* *
21852 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
21917 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * *
21958 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATTGTTTGTTGAGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
22023 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * *
22064 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
22129 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
*
22170 GAGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
22223 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* *
22264 GAGTCCAATATCCTACACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
22329 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* *
22370 GAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCTC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
22408 GGTCCCTTCG
Statistics
Matches: 890, Mismatches: 65, Indels: 38
0.90 0.07 0.04
Matches are distributed among these distances:
94 78 0.09
95 2 0.00
96 2 0.00
99 3 0.00
100 87 0.10
101 9 0.01
102 1 0.00
104 2 0.00
105 7 0.01
106 698 0.78
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
Found at i:22454 original size:74 final size:74
Alignment explanation
Indices: 22333--22481 Score: 262
Period size: 74 Copynumber: 2.0 Consensus size: 74
22323 TGACAACCAG
*
22333 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTA
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTA
22398 AAATTGGCT
66 AAATTGGCT
* * *
22407 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTA
22472 AAATTGGCT
66 AAATTGGCT
22481 C
1 C
22482 TAAAATCAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (74 bp):
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTA
AAATTGGCT
Found at i:22529 original size:180 final size:180
Alignment explanation
Indices: 22227--22586 Score: 594
Period size: 180 Copynumber: 2.0 Consensus size: 180
22217 TGACAACCAG
*
22227 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACACTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTACACTGTGAAGTTG
* ***
22292 AAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 AAATTGGCTCTAAAATCAAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
22357 CTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCT
131 CTTGCGTTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCT
* **
22407 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTACACTGTGAAGTTG
* *
22472 AAATTGGCTCTAAAATCAAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 AAATTGGCTCTAAAATCAAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * *
22537 CTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT
131 CTTGCGTTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCT
22587 TTGAAATTGG
Statistics
Matches: 166, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
180 166 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (180 bp):
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTACACTGTGAAGTTG
AAATTGGCTCTAAAATCAAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCT
Found at i:22601 original size:106 final size:106
Alignment explanation
Indices: 22407--23188 Score: 1251
Period size: 106 Copynumber: 7.4 Consensus size: 106
22397 AAAATTGGCT
*
22407 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
* *** *
22472 AAATTGGCTCTAAAATCAAGAAGTTGTTTGTTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
*
22513 CGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
*
22578 AAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
* * *
22619 CGGTCTCTTCGTCGTGAAGTTAAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
* *
22684 AAATTGGCTCTAAAATTAGGAAGTTGTTTATTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
*
22725 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
* *
22790 AAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
* *
22831 CGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGCGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
*
22896 AAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
* * *
22937 CGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTTTCTGGAGTCCAATATCCTTCGCTTTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
* *
23002 AAATTGGATCTGAAATTGGGAAATTGTTTATTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
*
23043 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
* * * * *
23108 AAATTGGCTCCGAAATTGGAAAATT-ATTGTTGACAACCAG
66 AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
* * * *
23148 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
23189 GGCAAGATAT
Statistics
Matches: 626, Mismatches: 50, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
105 50 0.08
106 576 0.92
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAG
Found at i:24040 original size:22 final size:22
Alignment explanation
Indices: 24014--24069 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
24004 TTGTGTTTGG
*
24014 TCAAAGGTTTTACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
24036 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
24058 TCAAAGGTTTGA
1 TCAAAGGTTTGA
24070 TGGGGTAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:24689 original size:13 final size:14
Alignment explanation
Indices: 24671--24730 Score: 63
Period size: 13 Copynumber: 4.4 Consensus size: 14
24661 TTTTTTATCC
24671 CTTTTTCTT-TTTT
1 CTTTTTCTTCTTTT
*
24684 CTTTTTGTTC-TTT
1 CTTTTTCTTCTTTT
*
24697 CTTTTTGTTCTTCTT
1 CTTTTTCTTCTT-TT
*
24712 -TTTTGCTTCTTTT
1 CTTTTTCTTCTTTT
24725 CTTTTT
1 CTTTTT
24731 TATTTTTTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 23 0.59
14 14 0.36
15 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (14 bp):
CTTTTTCTTCTTTT
Found at i:24694 original size:9 final size:8
Alignment explanation
Indices: 24672--24731 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
24662 TTTTTATCCC
24672 TTTTTC-T
1 TTTTTCTT
24679 TTTTTCTT
1 TTTTTCTT
24687 TTTGTTCTT
1 TTT-TTCTT
*
24696 TCTTTT-TG
1 T-TTTTCTT
*
24704 TTCTTCTT
1 TTTTTCTT
*
24712 TTTTGCTT
1 TTTTTCTT
*
24720 CTTTTCTT
1 TTTTTCTT
24728 TTTT
1 TTTT
24732 ATTTTTTCCC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
7 9 0.22
8 22 0.54
9 8 0.20
10 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:24694 original size:16 final size:15
Alignment explanation
Indices: 24672--24738 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
24662 TTTTTATCCC
24672 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
24687 TTTGTTCTTTCTTT-TT
1 TTT-TTCTTT-TTTCTT
*
24703 GTTCTTCTTTTTTGCTT
1 -TTTTTCTTTTTT-CTT
* *
24720 CTTTTCTTTTTTATT
1 TTTTTCTTTTTTCTT
24735 TTTT
1 TTTT
24739 CCCTTTTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
15 11 0.26
16 24 0.57
17 7 0.17
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:29359 original size:18 final size:18
Alignment explanation
Indices: 29338--29387 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
29328 TAAAATATAT
*
29338 ATAAAAAAGAA-AAAGAAA
1 ATAAAAAA-AATAAACAAA
29356 ATAAAAAAAATAAACAAA
1 ATAAAAAAAATAAACAAA
* *
29374 ATAATAATAATAAA
1 ATAAAAAAAATAAA
29388 GTACGAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (18 bp):
ATAAAAAAAATAAACAAA
Found at i:29447 original size:23 final size:23
Alignment explanation
Indices: 29334--29448 Score: 62
Period size: 23 Copynumber: 5.1 Consensus size: 23
29324 ATAATAAAAT
*
29334 ATATATAAAAAA-GAAAAAG-AA
1 ATATATAAAAAATAAAAAAGTAA
* *
29355 A-ATAAAAAAAATAAACAAAAT-A
1 ATATATAAAAAATAAA-AAAGTAA
* * *
29377 ATA-ATAATAAAGTACGAATAA-TAT
1 ATATATAA-AAAATA--AAAAAGTAA
29401 ATATATAAAAAATAAAAAAGTAA
1 ATATATAAAAAATAAAAAAGTAA
* * * *
29424 ATATATATAAATTAATAAATTAA
1 ATATATAAAAAATAAAAAAGTAA
29447 AT
1 AT
29449 GACGAAAAGA
Statistics
Matches: 70, Mismatches: 14, Indels: 18
0.69 0.14 0.18
Matches are distributed among these distances:
20 9 0.13
21 3 0.04
22 12 0.17
23 30 0.43
24 10 0.14
25 6 0.09
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (23 bp):
ATATATAAAAAATAAAAAAGTAA
Found at i:29737 original size:2 final size:2
Alignment explanation
Indices: 29676--29718 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
29666 CTTGTGTAGA
29676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29718 A
1 A
29719 ATAGTAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29962 original size:12 final size:11
Alignment explanation
Indices: 29934--29974 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
29924 TAACAAAATA
* *
29934 AATAATATAAA
1 AATAATACAAG
29945 AATAATACAAG
1 AATAATACAAG
29956 TAATAATACAAG
1 -AATAATACAAG
29968 AATAATA
1 AATAATA
29975 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:30012 original size:16 final size:16
Alignment explanation
Indices: 29993--30040 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
29983 GAGAAAGTAA
29993 AAAATATAATAATAAT
1 AAAATATAATAATAAT
30009 AAAATATAA-AA-AAT
1 AAAATATAATAATAAT
30023 ATAAATAT-ATAAT-AT
1 A-AAATATAATAATAAT
30038 AAA
1 AAA
30041 TAAGTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.24
15 13 0.45
16 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAATAATAAT
Found at i:30036 original size:22 final size:22
Alignment explanation
Indices: 29993--30040 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
29983 GAGAAAGTAA
29993 AAAATATAATAATAATAAAATAT
1 AAAATATAATAA-AATAAAATAT
* *
30016 AAAAAAT-ATAAATATATAATAT
1 AAAATATAATAAA-ATAAAATAT
30038 AAA
1 AAA
30041 TAAGTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 15 0.68
23 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATATAATAAAATAAAATAT
Found at i:30735 original size:37 final size:37
Alignment explanation
Indices: 30642--30743 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
30632 GTGCTTGTGG
* * ** * * *
30642 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
30679 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
30716 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
30744 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:34126 original size:24 final size:24
Alignment explanation
Indices: 34099--34205 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
34089 AAACGGAGAT
*
34099 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
34123 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
34147 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
**
34171 ATCAGATGTCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
34195 ACCAGAAATCA
1 ATCAGAAATCA
34206 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:34205 original size:48 final size:48
Alignment explanation
Indices: 34101--34207 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
34091 ACGGAGATAT
* * * **
34101 CAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAGGT
1 CAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAGAC
* * * * *
34149 TAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAGAC
1 CAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAGAC
34197 CAGAAATCAGA
1 CAGAAATCAGA
34208 TAAAATATTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.19
Consensus pattern (48 bp):
CAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAGAC
Found at i:34656 original size:17 final size:17
Alignment explanation
Indices: 34634--34669 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34624 CCAATGGTCT
34634 TTATTTCATTTCCACGC
1 TTATTTCATTTCCACGC
34651 TTATTTCATTTCCACGC
1 TTATTTCATTTCCACGC
34668 TT
1 TT
34670 CTACGATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.06, T:0.50
Consensus pattern (17 bp):
TTATTTCATTTCCACGC
Found at i:35928 original size:25 final size:27
Alignment explanation
Indices: 35900--35954 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
35890 TCTTATCTTT
*
35900 TTTTAACATA-AGG-GTATTTTCGTAA
1 TTTTAACATACAGGAGTATTTTCATAA
*
35925 TTTTACCATACAGGAGTATTTTCATAA
1 TTTTAACATACAGGAGTATTTTCATAA
35952 TTT
1 TTT
35955 CTCATCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.35
26 3 0.12
27 14 0.54
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (27 bp):
TTTTAACATACAGGAGTATTTTCATAA
Found at i:43296 original size:19 final size:19
Alignment explanation
Indices: 43272--43309 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43262 AAATATATAA
43272 TAATTTTAAATTTTTAGGG
1 TAATTTTAAATTTTTAGGG
43291 TAATTTTAAATTTTTAGGG
1 TAATTTTAAATTTTTAGGG
43310 AGGACGACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
TAATTTTAAATTTTTAGGG
Found at i:43811 original size:71 final size:67
Alignment explanation
Indices: 43691--43841 Score: 230
Period size: 71 Copynumber: 2.2 Consensus size: 67
43681 TTTCTAAACT
* *
43691 AATTGTTATTTTTTGGTTAATTACTTGTTCAGTACATGGACTATACTTAATTTATCAATGTTGTA
1 AATTATTATTTTTTGGTTAATTACTTGTTCAGTACATGAACTATACTTAATTTATCAATGTTGTA
43756 CA
66 CA
* *
43758 AATTATTATTTTTTGGTTAATTACTTACTTGTTCAGTATATGAACTATGCTTAATTTATCAATGT
1 AATTATTATTTTTTGGTT-A--A-TTACTTGTTCAGTACATGAACTATACTTAATTTATCAATGT
43823 TGTACA
62 TGTACA
43829 AATTATTATTTTT
1 AATTATTATTTTT
43842 CTTTCAATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
67 17 0.22
68 1 0.01
70 1 0.01
71 57 0.75
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.50
Consensus pattern (67 bp):
AATTATTATTTTTTGGTTAATTACTTGTTCAGTACATGAACTATACTTAATTTATCAATGTTGTA
CA
Found at i:44183 original size:61 final size:60
Alignment explanation
Indices: 44114--44278 Score: 233
Period size: 61 Copynumber: 2.7 Consensus size: 60
44104 TATAGGATGA
* *
44114 TGCTTTGTTGAGTCATTCGACTATTAAAAGTTACAAAATGATTCCCC-AAATTATAGGGAAC
1 TGCTTTGTTGAGTC-TTCGACTATTAAAAGTTACAAAATG-GTCCCCTAAATTATAAGGAAC
* *
44175 TGCTTTGTTGAGTCCTTCGACTATTAAAGGTTACAAAATGGTCCCCTAAATTATAAGGAAT
1 TGCTTTGTTGAGT-CTTCGACTATTAAAAGTTACAAAATGGTCCCCTAAATTATAAGGAAC
* *
44236 TGTTTTGTTGAGTTCCTCGACTATTAAAAGTTACAAAATGGTC
1 TGCTTTGTTGAG-TCTTCGACTATTAAAAGTTACAAAATGGTC
44279 AACAACTATT
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
60 5 0.05
61 87 0.93
62 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (60 bp):
TGCTTTGTTGAGTCTTCGACTATTAAAAGTTACAAAATGGTCCCCTAAATTATAAGGAAC
Found at i:45683 original size:21 final size:22
Alignment explanation
Indices: 45640--45683 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
45630 GTTTATAATA
*
45640 TATATATATATATATTTGAAAG
1 TATATATATATATATATGAAAG
* *
45662 TATA-ATATATATGTATGTAAG
1 TATATATATATATATATGAAAG
45683 T
1 T
45684 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (22 bp):
TATATATATATATATATGAAAG
Found at i:55380 original size:256 final size:248
Alignment explanation
Indices: 54814--55431 Score: 744
Period size: 256 Copynumber: 2.4 Consensus size: 248
54804 CTTATTCATA
*
54814 TATTGAATAAAAATATTTTTTTATCATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATA-TTTTTTATTATTTC--G--GGGTCGGGTTTCTAATTCATATATTCGGG-
*
54879 CAGATCGGGTGAAACTTTATTTTGGTCGGGTAGGGTCGGTTTTTTTAAATGTGATATTCAGGTCA
60 --GATCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAATGTGATATTCAGGTCA
*
54944 GATCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATA
123 GATCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATA
*
55009 TTTAAGAATAATTACAATAATACCCCTCTATATGTATTTTTTTCAATTAAATCACTATTTT
188 TTTAAGAATAATTACAATAATACCCCTCTATATATATTTTTTTCAATTAAATCACTATTTT
55070 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCAGGTCGGGTCGGATTTCTAATTCATATATT
1 TATTGAATAAAAATA-TTTTTTATTATTTC-GG---GGTC--G--GG-TTTCTAATTCATATATT
* *
55135 C-GGG-TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTGTTTTTTTTAAAGTGTGATATTCGG
56 CGGGGATCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC-GGTTTTTTTAAA-TGTGATATTCAG
* *
55198 GTCGGGTCGAGTCGGGTTCGGGTTTAGGGTGAAAAATACTTGACCCGACCC-AAAAAATATATAA
119 GTC----AGA-TCGAGTTCGGGTTTAGGGTG-AAAA-A--T-ACCCGACCCGAAAAAATATATAA
* *
55262 TTTTACCTTATATATTTATGAATAATTACAATAATACCCCTCTCTATATATTTGTTTTCCAATTA
174 TTTTACCTTATATATTTAAGAATAATTACAATAATACCCCTCTATATATATTT-TTTT-CAATTA
* * *
55327 AGTCATTGTTTT
237 AATCACTATTTT
55339 TATTGAATAAAAATA-TTTTT-TTATTTC-GGGTCGGGTTTCTAATTCATATATTCTGGTCGGAT
1 TATTGAATAAAAATATTTTTTATTATTTCGGGGTCGGGTTTCTAATTCATATATTC-GG--GGAT
* *
55401 CAGGTGAAACTTTATTTTGGTAGGGTCGGGT
63 CGGGTGAAACTTTATTTTGGTCGGGTCGGGT
55432 TGGGTCTCGG
Statistics
Matches: 320, Mismatches: 15, Indels: 49
0.83 0.04 0.13
Matches are distributed among these distances:
253 1 0.00
255 2 0.01
256 83 0.26
257 14 0.04
258 16 0.05
259 1 0.00
260 6 0.02
261 52 0.16
262 2 0.01
263 19 0.06
264 5 0.02
265 1 0.00
266 7 0.02
267 68 0.21
268 13 0.04
269 30 0.09
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (248 bp):
TATTGAATAAAAATATTTTTTATTATTTCGGGGTCGGGTTTCTAATTCATATATTCGGGGATCGG
GTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAATGTGATATTCAGGTCAGATCGAGT
TCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAAGAA
TAATTACAATAATACCCCTCTATATATATTTTTTTCAATTAAATCACTATTTT
Found at i:57440 original size:70 final size:70
Alignment explanation
Indices: 57327--57479 Score: 252
Period size: 70 Copynumber: 2.2 Consensus size: 70
57317 TGGCAAAGAA
* * *
57327 ACGGTTGACAACACTCCACACCTCTACCGCATTCTCAGCACCAACAAGTTGAGGAAGAAGAGGAA
1 ACGGTTGACAACACCCCACACCTCTACAGCAGTCTCAGCACCAACAAGTTGAGGAAGAAGAGGAA
57392 GGCTC
66 GGCTC
*
57397 ACGGTTGACAACACCCCACACCTCTACAGCAGTCTCAGCACCAACAAGTTGAGGAAGAAGTGGAA
1 ACGGTTGACAACACCCCACACCTCTACAGCAGTCTCAGCACCAACAAGTTGAGGAAGAAGAGGAA
57462 GGCTC
66 GGCTC
* *
57467 ACCGTGGACAACA
1 ACGGTTGACAACA
57480 GCCAAGAAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 77 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.14
Consensus pattern (70 bp):
ACGGTTGACAACACCCCACACCTCTACAGCAGTCTCAGCACCAACAAGTTGAGGAAGAAGAGGAA
GGCTC
Found at i:58497 original size:20 final size:21
Alignment explanation
Indices: 58438--58497 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
58428 CGCTAAATGA
*
58438 TGAACGGTTCAACATTCAGT-GC
1 TGAACGGTTC-ACATTTA-TCGC
58460 TGAACGGTTCATCATTTATCGC
1 TGAACGGTTCA-CATTTATCGC
*
58482 TGAATGGTTC-CATTTA
1 TGAACGGTTCACATTTA
58498 ACAGTAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.18
21 2 0.06
22 26 0.76
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (21 bp):
TGAACGGTTCACATTTATCGC
Found at i:58819 original size:23 final size:22
Alignment explanation
Indices: 58792--58842 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
58782 GTTATGAGCC
58792 AAAATATTTCAAAAAATAAAAT
1 AAAATATTTCAAAAAATAAAAT
*
58814 AGAAATATTTCATAAAATAAAAT
1 A-AAATATTTCAAAAAATAAAAT
58837 AAAATA
1 AAAATA
58843 GAGGACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATATTTCAAAAAATAAAAT
Found at i:59064 original size:4 final size:4
Alignment explanation
Indices: 59055--59079 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
59045 AAGTTATTGT
59055 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
59080 TTAAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:59337 original size:2 final size:2
Alignment explanation
Indices: 59330--59375 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
59320 TTCAACAGTG
59330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59372 AT AT
1 AT AT
59376 GAATATAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59429 original size:18 final size:17
Alignment explanation
Indices: 59382--59423 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
59372 ATATGAATAT
*
59382 AAATTAAT-ATTATTTA
1 AAATTAATAATCATTTA
59398 AAATTAATAATCATTTA
1 AAATTAATAATCATTTA
59415 ATAATTAAT
1 A-AATTAAT
59424 GCTCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTAATAATCATTTA
Found at i:61356 original size:2 final size:2
Alignment explanation
Indices: 61349--61381 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
61339 CCTTTTTAGT
61349 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
61382 TTGGATTTCT
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:72614 original size:3 final size:3
Alignment explanation
Indices: 72606--72649 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
72596 TTAACCCATT
* * * *
72606 CTC CTC CTC TTC CTC CTC CTC CTT CTT CTC CTT CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
72650 TCATGTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (3 bp):
CTC
Found at i:77995 original size:22 final size:22
Alignment explanation
Indices: 77969--78014 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
77959 CGTACACATT
*
77969 AAGTTAAATTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
77991 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
78013 AA
1 AA
78015 CATATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATGATGGACTAA
Found at i:79560 original size:3 final size:3
Alignment explanation
Indices: 79542--79597 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
79532 GCAAATGTAA
* *
79542 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
79588 -AT AATT AAT A
1 AAT AA-T AAT A
79598 TTTATAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:80004 original size:55 final size:55
Alignment explanation
Indices: 79787--80257 Score: 398
Period size: 55 Copynumber: 8.8 Consensus size: 55
79777 CCATTGGGTT
* * * * ** **
79787 TGCTCCCTTTTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCA-ACAAACGTGTC
* * * * *
79842 CGTTCTCTATTCCTTC--AGAGTATAGGAC-T--A-AATCTTCAACAAATGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * *
79891 CGCTCCCCATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAATCAAACGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAA-CAAACGTGTC
* * * *
79943 CGCTCCCTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTCC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGT-C
* * *
79999 T-CTCCCTATTCCTTCAGAAAGTATAGGAC-T---CAATCTTCAACAAATGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * * **
80049 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * * * * ** *
80104 TGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * * **
80159 TGCTCCCTATTGCTTAAGAGAGTATGAGACTTGAACAATCTTCAACATTCGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* ** *
80214 TGCTCTCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCA
80258 TTTGCTTCAC
Statistics
Matches: 349, Mismatches: 52, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.00
49 27 0.08
50 3 0.01
51 65 0.19
52 36 0.10
53 10 0.03
54 1 0.00
55 196 0.56
56 10 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (55 bp):
TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
Found at i:92840 original size:2 final size:2
Alignment explanation
Indices: 92833--92868 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
92823 GGCTAAGGAA
* *
92833 AT AT AT AT AT GT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92869 GATAATCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92953 original size:22 final size:22
Alignment explanation
Indices: 92927--92972 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
92917 CGTACACATT
*
92927 AAGTTAAATTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
92949 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
92971 AA
1 AA
92973 CATATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATGATGGACTAA
Found at i:94501 original size:3 final size:3
Alignment explanation
Indices: 94483--94535 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
94473 GCAAATGTAA
* *
94483 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
94528 AATT AAT A
1 AA-T AAT A
94536 TTTTTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:95720 original size:21 final size:21
Alignment explanation
Indices: 95655--95724 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
95645 AAAACAAAAC
* * *
95655 AAAAGAAAAGAAATGAAAAAA
1 AAAAGAAAATAAATTAATAAA
*
95676 AAAATAAAATAATTATAGTAATAAA
1 AAAAGAAAATAA--AT--TAATAAA
95701 AAAAGAAAATAAATTAATAAA
1 AAAAGAAAATAAATTAATAAA
95722 AAA
1 AAA
95725 CAATAACCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 20 0.50
23 4 0.10
25 16 0.40
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAGAAAATAAATTAATAAA
Found at i:98725 original size:108 final size:109
Alignment explanation
Indices: 98394--98943 Score: 777
Period size: 108 Copynumber: 5.1 Consensus size: 109
98384 CTCGAGCCAA
*
98394 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC-T-TGTGTCTCAAGTCCAATAT
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATAT
* * *
98457 CCTTTGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
66 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* *
98501 TTGTTTGTTGATAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATAT
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATAT
*
98566 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACCGAAAAG
66 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * *
98610 TTGTTTGTTGACAGACAGTCGCCCCTTCGGTGTGAAGTTAAGC-TGTGTGTCTCGAGTCCAATAT
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATAT
* * * **
98674 CCTTCACTGTGAAGTTAAAATTGATTCTGAATGAAACTGAAATT
66 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * * *
98718 TTTTTTGTTAACAGTCAGTCGCCCCTTCGATGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG-TGTCTCGAGTCCAATA
* * * * *
98783 TCCTTTGTTATGAAGTTGAAATTGACTCTGAATAAAATTGAAAAG
65 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * * *
98828 TTGTTTGTTGACAGTCAGTCGCCCTTTGGCTGTGAAGTTGAGCTTGTGTTGTGTCGAGT-CTATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG-TGTCTCGAGTCCAATA
* *
98892 T-ATTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAAG
65 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
98936 TTGTTTGT
1 TTGTTTGT
98944 AACAGTAAAC
Statistics
Matches: 391, Mismatches: 48, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
107 41 0.10
108 142 0.36
109 105 0.27
110 103 0.26
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (109 bp):
TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATAT
CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
Found at i:98904 original size:218 final size:217
Alignment explanation
Indices: 98394--98949 Score: 773
Period size: 218 Copynumber: 2.6 Consensus size: 217
98384 CTCGAGCCAA
* * *
98394 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCT-TGTGTCTCAAGTCCAATATC
1 TTGTTTGTTGACAGTCAGTCGCCCTTTGGCTGTGAAGTTGAGCTGTGTGTCTCGAGTCCAATATC
* * * * *
98458 CTTTGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGATAGTCAGTCGC
66 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTAACAGTCAGTCGC
*
98523 CCCTTCACTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
131 CCCTTCACTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATATCCTTCGCTATGAAGTTGAAATT
*
98588 GACTCTGAATGAAACCGAAAAG
196 GACTCTGAATAAAACCGAAAAG
* * *
98610 TTGTTTGTTGACAGACAGTCGCCCCTTCGG-TGTGAAGTTAAGCTGTGTGTCTCGAGTCCAATAT
1 TTGTTTGTTGACAGTCAGTCG-CCCTTTGGCTGTGAAGTTGAGCTGTGTGTCTCGAGTCCAATAT
* * * ** *
98674 CCTTCACTGTGAAGTTAAAATTGATTCTGAATGAAACTGAAATTTTTTTTGTTAACAGTCAGTCG
65 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTAACAGTCAGTCG
* * *
98739 CCCCTTCGA-TGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATATCCTTTGTTATGAAGTTGAA
130 CCCCTTC-ACTGTGAAGTTGAGCTTGTG-TGTCTCGAGTCCAATATCCTTCGCTATGAAGTTGAA
**
98803 ATTGACTCTGAATAAAATTGAAAAG
193 ATTGACTCTGAATAAAACCGAAAAG
* *
98828 TTGTTTGTTGACAGTCAGTCGCCCTTTGGCTGTGAAGTTGAGCTTGTGTTGTGTCGAGT-CTATA
1 TTGTTTGTTGACAGTCAGTCGCCCTTTGGCTGTGAAGTTGAGC-TGTG-TGTCTCGAGTCCAATA
* *
98892 T-ATTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAAGTTGTTTG-TAACAGT
64 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTAACAGT
98950 AAACTTTTCT
Statistics
Matches: 296, Mismatches: 37, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
216 33 0.11
217 116 0.39
218 129 0.44
219 9 0.03
220 9 0.03
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (217 bp):
TTGTTTGTTGACAGTCAGTCGCCCTTTGGCTGTGAAGTTGAGCTGTGTGTCTCGAGTCCAATATC
CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTAACAGTCAGTCGC
CCCTTCACTGTGAAGTTGAGCTTGTGTGTCTCGAGTCCAATATCCTTCGCTATGAAGTTGAAATT
GACTCTGAATAAAACCGAAAAG
Done.