Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009326.1 Hibiscus syriacus cultivar Beakdansim tig00113090_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: 63951
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1969 original size:24 final size:23
Alignment explanation
Indices: 1916--1970 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1906 AGAGGTGGCA
1916 GAGG-TGGCAGTGGTCCCCCTGG
1 GAGGCTGGCAGTGGTCCCCCTGG
* *
1938 GCA-ACTGGCAGTGGTCCATCCTGG
1 G-AGGCTGGCAGTGGTCC-CCCTGG
1962 GAGGCTGGC
1 GAGGCTGGC
1971 TGACTACCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.04
23 14 0.54
24 11 0.42
ACGTcount: A:0.13, C:0.27, G:0.42, T:0.18
Consensus pattern (23 bp):
GAGGCTGGCAGTGGTCCCCCTGG
Found at i:2065 original size:29 final size:30
Alignment explanation
Indices: 2014--2089 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
2004 ATGGTCCAAA
*
2014 AGAA-CAGTTTGCAGCAGTTCACGATCCAGC
1 AGAATCAG-TTGCAGCAGGTCACGATCCAGC
*
2044 AGAATCAGTTGCA-CAGGTCACGATCCAGT
1 AGAATCAGTTGCAGCAGGTCACGATCCAGC
2073 AGAATCAGTTGCAGCAG
1 AGAATCAGTTGCAGCAG
2090 TGCATGGTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 27 0.64
30 12 0.29
31 3 0.07
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.20
Consensus pattern (30 bp):
AGAATCAGTTGCAGCAGGTCACGATCCAGC
Found at i:2390 original size:20 final size:20
Alignment explanation
Indices: 2361--2399 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2351 ATAATTCACC
*
2361 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2381 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
2400 CATGGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:4256 original size:10 final size:10
Alignment explanation
Indices: 4241--4279 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
4231 TAAAATATAT
4241 TATATTTTAA
1 TATATTTTAA
*
4251 TATATTTATAT
1 TATATTT-TAA
4262 TATATTTTAA
1 TATATTTTAA
4272 TATATTTT
1 TATATTTT
4280 TATAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATTTTAA
Found at i:4276 original size:23 final size:21
Alignment explanation
Indices: 4236--4278 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4226 AATGATAAAA
4236 TATATTATATTTTAATATATT
1 TATATTATATTTTAATATATT
4257 TATATTATATTTTAATATATT
1 TATATTATATTTTAATATATT
4278 T
1 T
4279 TTATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATTATATTTTAATATATT
Found at i:4281 original size:23 final size:23
Alignment explanation
Indices: 4236--4300 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 23
4226 AATGATAAAA
4236 TATATTATATTTTAATATA--TT
1 TATATTATATTTTAATATATTTT
4257 TATATTATATTTTAATATATTTT
1 TATATTATATTTTAATATATTTT
* *
4280 TATAATA-ATATTTAAAATATT
1 TATATTATAT-TTTAATATATT
4301 ACAATTTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.49
22 2 0.05
23 18 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTATATTTTAATATATTTT
Found at i:5186 original size:130 final size:130
Alignment explanation
Indices: 4945--5188 Score: 407
Period size: 130 Copynumber: 1.9 Consensus size: 130
4935 CAAATATATC
*
4945 ATATTTTTAAGAGAAATGCACTATACATTCTCAAAGTATGATCTTCATTTTAAATTGGTCCTCAA
1 ATATTTTTAAGAGAAATGCACTATACATTCTCAAAGTATGATCCTCATTTTAAATTGGTCCTCAA
* * **
5010 AGTTTTGAATATTTTAATTTTATCCCTAAACTATGACTCTTTTTCTAAATTAGTCCCTAAAGTTA
66 AGTTTTGAATATTTTAATCTTATCCCTAAACTATGAATCTCATTCTAAATTAGTCCCTAAAGTTA
* **
5075 ATATTTTTAAGAGAACTGCACTATACATTCTTTAAGTATGATCCTCATTTTAAATTGGTCCTCAA
1 ATATTTTTAAGAGAAATGCACTATACATTCTCAAAGTATGATCCTCATTTTAAATTGGTCCTCAA
*
5140 AGTTTTGAATATTTTAATCTTATCCCTAAATTATGAATCTCATTCTAAA
66 AGTTTTGAATATTTTAATCTTATCCCTAAACTATGAATCTCATTCTAAA
5189 AAAAGTCGAC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 105 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (130 bp):
ATATTTTTAAGAGAAATGCACTATACATTCTCAAAGTATGATCCTCATTTTAAATTGGTCCTCAA
AGTTTTGAATATTTTAATCTTATCCCTAAACTATGAATCTCATTCTAAATTAGTCCCTAAAGTTA
Found at i:10922 original size:6 final size:7
Alignment explanation
Indices: 10903--10938 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
10893 GACCCTGAAC
10903 ATAAAAA
1 ATAAAAA
*
10910 ACAAAAA
1 ATAAAAA
10917 ATAAAAA
1 ATAAAAA
10924 ATAAAAA
1 ATAAAAA
10931 ATAAAAA
1 ATAAAAA
10938 A
1 A
10939 ACAATTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (7 bp):
ATAAAAA
Found at i:11023 original size:66 final size:64
Alignment explanation
Indices: 10948--11154 Score: 181
Period size: 73 Copynumber: 3.1 Consensus size: 64
10938 AACAATTTTG
* *
10948 AAAACATATAATA-TAT-TA-A-TTTCTAAAATGTTATTTTAAAAACTATATATTATATGCAT-T
1 AAAACATATAATATTATATATATTTTC-AAAATG---TTTCAAAAACTATATAATATAT--ATAT
11008 TTTCA
60 TTTCA
11013 AAAACTATATAATATTATATATATTTTCAAAATGTTTCAAAAACTATATAATATATATATTTTCA
1 AAAAC-ATATAATATTATATATATTTTCAAAATGTTTCAAAAACTATATAATATATATATTTTCA
** * *
11078 AAAATGTTTTAAAAACTATATATTATATTAGTTTTCAAAATGTTTTAAAAACTATATAATATATA
1 AAAA---CAT-ATAA-TAT-TA-TATA-TA-TTTTCAAAATGTTTCAAAAACTATATAATATATA
11143 TATTTTCA
57 TATTTTCA
11151 AAAA
1 AAAA
11155 ATGTTTTAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
64 2 0.02
65 15 0.12
66 28 0.23
67 4 0.03
68 5 0.04
69 10 0.08
70 6 0.05
71 4 0.03
72 2 0.02
73 45 0.37
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (64 bp):
AAAACATATAATATTATATATATTTTCAAAATGTTTCAAAAACTATATAATATATATATTTTCA
Found at i:11198 original size:74 final size:73
Alignment explanation
Indices: 11024--11295 Score: 361
Period size: 74 Copynumber: 3.7 Consensus size: 73
11014 AAACTATATA
*
11024 ATATTATATATATTTTCAAAATGTTTCAAAAACTATATAATATATATATTTTCAAAAATGTTTTA
1 ATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTA
11089 AAAACTAT
66 AAAACTAT
11097 ATATTATAT-TAGTTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAAATGTTT
1 ATATTATATATA-TTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTC-AAAAATGTTT
11161 TAAAAACTAT
64 TAAAAACTAT
* * *
11171 ATATTATAT-TAGTTTTCAAAATTTTTTAAAAACTATATAATATATAAATGTTTCCAAACATGCT
1 ATATTATATATA-TTTTCAAAATGTTTTAAAAACTATATAATATATATAT-TTT-CAAAAATG-T
* **
11235 TGTCGAAACTAT
62 TTTAAAAACTAT
* ** *
11247 ATATTATATATATATTTTAAAATG-TTTCCAAACTATATACTATATATAT
1 ATATTATATATAT-TTTCAAAATGTTTTAAAAACTATATAATATATATAT
11296 ATATAAATGG
Statistics
Matches: 179, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
72 2 0.01
73 49 0.27
74 67 0.37
75 9 0.05
76 42 0.23
77 10 0.06
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (73 bp):
ATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTA
AAAACTAT
Found at i:11296 original size:36 final size:37
Alignment explanation
Indices: 11007--11297 Score: 321
Period size: 36 Copynumber: 7.7 Consensus size: 37
10997 TTATATGCAT
11007 TTTTCAAAAACTATATAATATTATATATATTTTCAAAATG
1 TTTT-AAAAACTATAT-ATA-TATATATATTTTCAAAATG
*
11047 TTTCAAAAACTATATA-ATATATATATTTTCAAAAATG
1 TTTTAAAAACTATATATATATATATATTTTC-AAAATG
11084 TTTTAAAAACTATATAT-TATAT-TAGTTTTCAAAATG
1 TTTTAAAAACTATATATATATATATA-TTTTCAAAATG
11120 TTTTAAAAACTATATA-ATATATATATTTTCAAAAAATG
1 TTTTAAAAACTATATATATATATATATTTTC--AAAATG
*
11158 TTTTAAAAACTATATAT-TATAT-TAGTTTTCAAAATT
1 TTTTAAAAACTATATATATATATATA-TTTTCAAAATG
*
11194 TTTTAAAAACTATATA-ATATATAAATGTTTCCAAACATG
1 TTTTAAAAACTATATATATATATATAT-TTT-CAAA-ATG
* **
11233 CTTGTCGAAACTATATATTATATATATATTTT-AAAATG
1 -TTTTAAAAACTATATA-TATATATATATTTTCAAAATG
**
11271 -TTTCCAAACTATATACTATATATATAT
1 TTTTAAAAACTATATA-TATATATATAT
11298 ATAAATGGGA
Statistics
Matches: 222, Mismatches: 12, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
36 98 0.44
37 40 0.18
38 40 0.18
39 16 0.07
40 16 0.07
41 3 0.01
42 9 0.04
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTAAAAACTATATATATATATATATTTTCAAAATG
Found at i:11955 original size:84 final size:84
Alignment explanation
Indices: 11887--12693 Score: 820
Period size: 84 Copynumber: 9.7 Consensus size: 84
11877 CTGAGTTTAA
* * *
11887 TCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
11952 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * *
11971 TCGAACTCGAAGGTCTTTTGG-TGACAGATAAACCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * *
12035 TGCCCTCGAAGCTGAGTGTAA
65 TG-CCTTGGAGCTGAGCGTAG
* *
12056 TCGAACTCGAAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
**
12117 CACCTTGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * * *
12137 TCAAACTCGACGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * ** *
12201 TTCCCTCGAAGCTGAATGTAA
65 -TGCCTTGGAGCTGAGCGTAG
* * *
12222 TCGAACTC-AAGGGTC--T--TTGGCACATAACCCTTCTCGACTTAAGCTATACTGCAAATGATG
1 TCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*
12282 TGCCTTGAAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* *
12302 TCGAACTCGAAGGTCTTTGTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
12367 GCCTTAGAGCTAAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * ** * * * * *
12386 TTGAACTCTAAGGTCTTTGG-TAACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
12450 ACCCTCGAAGCTGAGCGTAG
66 -GCCTTGGAGCTGAGCGTAG
* * * * * * **
12470 TCGAACTCGAGGGTC--T--TTGGAAGATAGCCCGTCTCAACTTAAGCTATGCTGCAAATGATAC
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
12531 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
12550 TCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCGATTTAAGTTATGCTGTATATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
12615 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
12634 TCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
12694 TTGTCTTAAA
Statistics
Matches: 580, Mismatches: 120, Indels: 47
0.78 0.16 0.06
Matches are distributed among these distances:
80 62 0.11
81 90 0.16
82 38 0.07
83 70 0.12
84 263 0.45
85 51 0.09
86 6 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:12332 original size:165 final size:164
Alignment explanation
Indices: 11884--12693 Score: 898
Period size: 165 Copynumber: 4.9 Consensus size: 164
11874 GAGCTGAGTT
11884 TAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGA
1 TAATCGAACTCGAAGGTC-T---TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGA
* *
11949 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAAACCTTCTAGCCT
62 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-GTGACAGATAACCCTTCTAGACT
* * **
12014 TGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTG
126 TGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAACG
* * *
12053 TAATCGAACTCGAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGC
1 TAATCGAACTCG-AAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
* * *
12118 ACCTTGGAGCTGAGCGTAGTCAAACTCGACGGTCTTTTGGTGACAGATAACCCTTCTAGACTTGA
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-GTGACAGATAACCCTTCTAGACTTGA
* * *
12183 GTTATGCTGTAAATGATGTTCCCTCGAAGCTGAATG
129 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAACG
*
12219 TAATCGAACTC-AAGGGTCTTTGGCACATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TAATCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
* * * * *
12283 GCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTTGGCAGATAACCCTTCTCGACTTAA
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-TGTGACAGATAACCCTTCTAGACTTGA
* * *
12348 GTTATGCTGCAAATGATATGCCTTAG-AGCT-AAGCG
129 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAA-CG
* * * * * * * *
12383 TAGTTGAACTCTAAGGTCTTTGGTAACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGAT
1 TAATCGAACTCGAAGGTCTTTGG---CAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGAT
* * * * * *
12448 GTACCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTC-TTTG-GA-AGATAGCCCGTCTCA-ACT
63 GT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTGACAGATAACCCTTCT-AGACT
* * ** * * *
12509 TAAGCTATGCTGCAAATGATACG-CCTTGGAGCTGAGCG
126 TGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAACG
* * * * * * *
12547 TAGTCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCGATTTAAGTTATGCTGTATATGA
1 TAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGA
* * *
12612 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTT
62 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTGACAGATAACCCTTCTAGACTT
12677 GAGTTATGCTGCAAATG
127 GAGTTATGCTGCAAATG
12694 TTGTCTTAAA
Statistics
Matches: 551, Mismatches: 70, Indels: 42
0.83 0.11 0.06
Matches are distributed among these distances:
163 5 0.01
164 112 0.20
165 162 0.29
166 152 0.28
167 66 0.12
168 35 0.06
169 13 0.02
170 6 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTGACAGATAACCCTTCTAGACTTGAGT
TATGCTGCAAATGATGTGCCCTCGAAGCTGAACG
Found at i:12512 original size:248 final size:247
Alignment explanation
Indices: 11887--12698 Score: 988
Period size: 248 Copynumber: 3.3 Consensus size: 247
11877 CTGAGTTTAA
* * * * *
11887 TCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTGAGTTATACTGCAAATGATGT
* * * * * * *
11952 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAAACCTTCT-AGCCTTG
65 CCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTC-TTT-G-GA-AGATAACCCTTCTCA-ACTTA
* * * * * *
12016 AGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAAGGTC----TTTGG
125 AGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACTCG-AAGGTCTTTGTTTGG
* * ***
12077 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCACCTTGGAGCTGAGCGTAG
188 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * * *
12137 TCAAACTCGACGGTCTTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTGAGTTATACTGCAAATGATG-
** * * * * *
12202 TCCCTCGAAGCTGAATGTAATCGAACTCAAGGGTCTTTGGCACATAACCCTTCTCGACTTAAGCT
64 TCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGAAGATAACCCTTCTCAACTTAAGCT
*
12267 ATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTTGGCAGATA
129 ATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTTGGCAGATA
* *
12332 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTAAGCGTAG
194 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * * * *
12386 TTGAACTCTAAGGTCTTTGGTAACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTA
1 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATACTGCAAATGATGT-
* *
12451 CCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGAAGATAGCCCGTCTCAACTTAAGCTA
65 CCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGAAGATAACCCTTCTCAACTTAAGCTA
** * *
12516 TGCTGCAAATGATACGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAG-TTGGTAGATA
130 TGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTTGGCAGATA
* * *
12580 ACCCTTCTCGATTTAAGTTATGCTGTATATGATATGCCTTGGAGCTGAGCGTAG
194 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * *
12634 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGTTGTC
1 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATACTGCAAATGATGTC
12699 TTAAAAAATG
Statistics
Matches: 484, Mismatches: 69, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
245 6 0.01
246 24 0.05
247 33 0.07
248 266 0.55
249 71 0.15
250 53 0.11
251 31 0.06
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (247 bp):
TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATACTGCAAATGATGTC
CCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGAAGATAACCCTTCTCAACTTAAGCTAT
GCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTTGGCAGATAAC
CCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
Found at i:14036 original size:95 final size:94
Alignment explanation
Indices: 13869--14064 Score: 277
Period size: 95 Copynumber: 2.1 Consensus size: 94
13859 GGACAGCTTA
* * * * *
13869 ATATATAAACACCTTTATAAGGTTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTG
1 ATATATAAACACCTTTATAAGGCTAGATGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTG
*
13934 CCTTAGAGGGACAGCTCAAGCTTTATTGT
66 CCTTAGAGGGACAACTCAAGCTTTATTGT
* * * *
13963 ATAGTATAATCACCTTTATCAGGCTAGATGAATATTTTCCATAAAGCCAGGGCGTTTAACCACTT
1 ATA-TATAAACACCTTTATAAGGCTAGATGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
14028 G-CTCTAGAGGGACAACTCAAGCTTTATTGT
65 GCCT-TAGAGGGACAACTCAAGCTTTATTGT
14058 ATATATA
1 ATATATA
14065 TAATATTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
94 9 0.10
95 81 0.90
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
ATATATAAACACCTTTATAAGGCTAGATGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTG
CCTTAGAGGGACAACTCAAGCTTTATTGT
Found at i:17990 original size:14 final size:13
Alignment explanation
Indices: 17969--18002 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17959 ATAAATAAAT
17969 AAAAATAAAAGGA
1 AAAAATAAAAGGA
*
17982 AAAACATAAAATGA
1 AAAA-ATAAAAGGA
17996 AAAAATA
1 AAAAATA
18003 TAATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAGGA
Found at i:18083 original size:21 final size:21
Alignment explanation
Indices: 18031--18084 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
18021 ATCAAAGAAA
*
18031 AAAAGAAATAAAAAAATCAAAG
1 AAAATAAAT-AAAAAATCAAAG
**
18053 -AAATGGATAAAAAATCAAAG
1 AAAATAAATAAAAAATCAAAG
18073 AAAATAAATAAA
1 AAAATAAATAAA
18085 TAAAAAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (21 bp):
AAAATAAATAAAAAATCAAAG
Found at i:18087 original size:25 final size:24
Alignment explanation
Indices: 18020--18090 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
18010 AATGAAAATG
*
18020 AATCAAAGAAAAAAAGAAATAAAAA
1 AATCAAAGAAAAAAATAAAT-AAAA
**
18045 AATCAAAG----AAATGGATAAAA
1 AATCAAAGAAAAAAATAAATAAAA
18065 AATCAAAGAAAATAAATAAATAAAA
1 AATCAAAGAAAA-AAATAAATAAAA
18090 A
1 A
18091 GAAAGAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
20 12 0.33
21 5 0.14
25 19 0.53
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (24 bp):
AATCAAAGAAAAAAATAAATAAAA
Found at i:18190 original size:26 final size:26
Alignment explanation
Indices: 18161--18234 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
18151 AAAATGGAAA
*
18161 CAATATGAAGTAAAATA-AATAATACT
1 CAATAT-AAGTAAAACATAATAATACT
* *
18187 CAATATAATTAAAACATAATAATAGT
1 CAATATAAGTAAAACATAATAATACT
*
18213 -AATAATAA-TAATA-ATAATAATA
1 CAAT-ATAAGTAAAACATAATAATA
18235 ATAATAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 9 0.21
25 15 0.36
26 18 0.43
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (26 bp):
CAATATAAGTAAAACATAATAATACT
Found at i:18210 original size:3 final size:3
Alignment explanation
Indices: 18202--18255 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
18192 TAATTAAAAC
*
18202 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18250 A-A ATA A
1 ATA ATA A
18256 GAATTTAGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:23430 original size:9 final size:9
Alignment explanation
Indices: 23416--23440 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23406 AAATCTAGCA
23416 ATCCGAACG
1 ATCCGAACG
23425 ATCCGAACG
1 ATCCGAACG
23434 ATCCGAA
1 ATCCGAA
23441 AGGAAAGGAT
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:0.36, C:0.32, G:0.20, T:0.12
Consensus pattern (9 bp):
ATCCGAACG
Found at i:25834 original size:20 final size:21
Alignment explanation
Indices: 25798--25836 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25788 ATGGTTCGAG
25798 TATCAATATTGGGATGAATAA
1 TATCAATATTGGGATGAATAA
*
25819 TATCGATATT-GGATGAAT
1 TATCAATATTGGGATGAAT
25837 TGGAGCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (21 bp):
TATCAATATTGGGATGAATAA
Found at i:27920 original size:16 final size:17
Alignment explanation
Indices: 27901--27933 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27891 TTTTATAAAA
*
27901 GTTTTCTTTTT-TTTTT
1 GTTTTATTTTTATTTTT
27917 GTTTTATTTTTATTTTT
1 GTTTTATTTTTATTTTT
27934 AAAGATGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (17 bp):
GTTTTATTTTTATTTTT
Found at i:29442 original size:20 final size:20
Alignment explanation
Indices: 29405--29467 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
29395 GAAAACATCG
*
29405 AAGGGATCGATCCTTTTTCAT
1 AAGGGATCGATCC-TTTTCAA
* *
29426 AGGGGATCGATCCTTTTGAA
1 AAGGGATCGATCCTTTTCAA
*
29446 AAGGGATCGATCCTTTACAA
1 AAGGGATCGATCCTTTTCAA
29466 AA
1 AA
29468 CAGAAACTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 24 0.67
21 12 0.33
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTCAA
Found at i:30489 original size:21 final size:21
Alignment explanation
Indices: 30436--30489 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
30426 CTTTTGTTCA
*
30436 AAACACAACTCACTCATTGGAT
1 AAACA-AACTCCCTCATTGGAT
30458 AAACAAACTCCCTCATTGGAT
1 AAACAAACTCCCTCATTGGAT
30479 AAACAAACTCC
1 AAACAAACTCC
30490 ATACAACTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACAAACTCCCTCATTGGAT
Found at i:32425 original size:22 final size:22
Alignment explanation
Indices: 32400--32449 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
32390 TGGACATATG
32400 TATTCATAGGACCTTACTTATA
1 TATTCATAGGACCTTACTTATA
* *
32422 TATTCATAGGACCTTATTTATG
1 TATTCATAGGACCTTACTTATA
32444 TATTCA
1 TATTCA
32450 GTGTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (22 bp):
TATTCATAGGACCTTACTTATA
Found at i:35518 original size:10 final size:9
Alignment explanation
Indices: 35503--35581 Score: 77
Period size: 10 Copynumber: 8.3 Consensus size: 9
35493 CCGGTTTTCA
35503 ACCGGTTCTG
1 ACCGGTT-TG
35513 ACCGGTTTG
1 ACCGGTTTG
*
35522 ACCGGTTTCA
1 ACCGGTTT-G
*
35532 ACCGGTTCG
1 ACCGGTTTG
35541 AACCGGTTTG
1 -ACCGGTTTG
*
35551 ACCGGTCTG
1 ACCGGTTTG
*
35560 AATCGGTTTG
1 -ACCGGTTTG
*
35570 ACCGGTCTG
1 ACCGGTTTG
35579 ACC
1 ACC
35582 CGACCCGACC
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
9 28 0.49
10 29 0.51
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:35527 original size:19 final size:19
Alignment explanation
Indices: 35502--35579 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
35492 ACCGGTTTTC
*
35502 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
35522 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
35541 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
35560 AATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
35579 A
1 A
35580 CCCGACCCGA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.04
19 40 0.78
20 9 0.18
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:35545 original size:29 final size:29
Alignment explanation
Indices: 35485--35581 Score: 117
Period size: 29 Copynumber: 3.3 Consensus size: 29
35475 TGCTGGAAAT
*
35485 CGGTTTAACCGGTTTTCAACCGGTTCTGAC
1 CGGTTTGACCGG-TTTCAACCGGTTCTGAC
35515 CGGTTTGACCGGTTTCAACCGGTTC-GAAC
1 CGGTTTGACCGGTTTCAACCGGTTCTG-AC
* * *
35544 CGGTTTGACCGGTCTGAATCGGTT-TGAC
1 CGGTTTGACCGGTTTCAACCGGTTCTGAC
*
35572 CGGTCTGACC
1 CGGTTTGACC
35582 CGACCCGACC
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 12 0.20
29 37 0.62
30 11 0.18
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (29 bp):
CGGTTTGACCGGTTTCAACCGGTTCTGAC
Found at i:35588 original size:5 final size:5
Alignment explanation
Indices: 35578--35657 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
35568 TGACCGGTCT
* * *
35578 GACCC GACCC GACCGTT GACCC GACCC AACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
35627 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
35658 GTTGACCGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.20, C:0.51, G:0.21, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:35604 original size:22 final size:22
Alignment explanation
Indices: 35578--35664 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
35568 TGACCGGTCT
35578 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
35600 GACCCAACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
35622 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
35644 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
35665 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:35666 original size:7 final size:7
Alignment explanation
Indices: 35654--35684 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
35644 GACCCGACCC
35654 GACCGTT
1 GACCGTT
35661 GACCGTT
1 GACCGTT
35668 GACCGTT
1 GACCGTT
*
35675 GACCATT
1 GACCGTT
35682 GAC
1 GAC
35685 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:42876 original size:29 final size:29
Alignment explanation
Indices: 42834--42900 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
42824 TGCTGGAAAT
*
42834 CGGTTTAACCGGTTTTCAACCGGTTCTG-A-
1 CGGTTTGACCGG-TTTCAACCGGTTC-GAAC
42863 CGGTTTGACCGGTTTCAACCGGTTCGAAC
1 CGGTTTGACCGGTTTCAACCGGTTCGAAC
42892 CGGTTTGAC
1 CGGTTTGAC
42901 GGTCTGAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 1 0.03
28 14 0.40
29 20 0.57
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (29 bp):
CGGTTTGACCGGTTTCAACCGGTTCGAAC
Found at i:42935 original size:5 final size:5
Alignment explanation
Indices: 42925--43004 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
42915 TGACCGGTCT
* * *
42925 GACCC GACCC GACCGTT GACCC GACCC AACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
42974 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
43005 GTTGACCGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.20, C:0.51, G:0.21, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:42951 original size:22 final size:22
Alignment explanation
Indices: 42925--43011 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
42915 TGACCGGTCT
42925 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
42947 GACCCAACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
42969 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
42991 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
43012 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:43013 original size:7 final size:7
Alignment explanation
Indices: 43001--43031 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
42991 GACCCGACCC
43001 GACCGTT
1 GACCGTT
43008 GACCGTT
1 GACCGTT
43015 GACCGTT
1 GACCGTT
*
43022 GACCATT
1 GACCGTT
43029 GAC
1 GAC
43032 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:44942 original size:31 final size:31
Alignment explanation
Indices: 44904--44974 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
44894 AATTTCAAAA
*
44904 ATAACAAATCGA-ATATTAACGTTATCGATTT
1 ATAACAAATCGATA-ATTAACGTTATCAATTT
44935 ATAACAAATCGATAATTAACGTTATCAATTT
1 ATAACAAATCGATAATTAACGTTATCAATTT
44966 ATAACAAAT
1 ATAACAAAT
44975 TGATCACTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (31 bp):
ATAACAAATCGATAATTAACGTTATCAATTT
Found at i:45272 original size:11 final size:12
Alignment explanation
Indices: 45242--45295 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
45232 GTTATTTAAA
45242 CGGGTATTGGGC
1 CGGGTATTGGGC
*
45254 CGGGTATTGGGT
1 CGGGTATTGGGC
45266 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
45277 CGGGAATCGGGC
1 CGGGTATTGGGC
45289 CGGGTAT
1 CGGGTAT
45296 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:45355 original size:24 final size:25
Alignment explanation
Indices: 45293--45373 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 25
45283 TCGGGCCGGG
45293 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
45318 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
45342 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
45367 TATATAT
1 TATATAT
45374 ATAAATAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.09
23 1 0.02
24 23 0.51
25 12 0.27
26 2 0.04
27 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:46262 original size:30 final size:30
Alignment explanation
Indices: 46228--46299 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
46218 CAAAAGTAAC
46228 AAATCGGTCACTACATTATCAATTTATAAT
1 AAATCGGTCACTACATTATCAATTTATAAT
*
46258 AAATCGGTCACTACATTATCGATTTATAAT
1 AAATCGGTCACTACATTATCAATTTATAAT
46288 AAATCGGTCACT
1 AAATCGGTCACT
46300 CACCATTAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATCGGTCACTACATTATCAATTTATAAT
Found at i:47098 original size:196 final size:189
Alignment explanation
Indices: 46857--47232 Score: 558
Period size: 196 Copynumber: 2.0 Consensus size: 189
46847 TTTTTATTAT
* * ** *
46857 TTCGGGTCGGGTTGGATTTCTAATTCATATGTTCGGGTCGGGTCGGATGAAACTTTATTTTTTTC
1 TTCGGGTCAGGTTGGATTTCTAATTCATATATTCAAGTCGGGTCGGATGAAACTTTATTTTGTTC
* *
46922 GGGTCGGGCCGAGTTTTTTAAGTGTGATATTCGGGTCGAGTCAGGTCGGGTTTTTTTAAGTGTGA
66 GGGTC-GGCC-AGGTTTTTAAGTGTGACATTCGGGTCGAGTCAGGTCGGGTTTTTTTAAGTGTGA
46987 TATTCGGGTTGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGA-CCGACCC-GAAAATATATA
129 TATTC-----GGGTCGGGTTCAGGTTTAGGGT-AAAAAAACC-GATCCGACCCGGAAAATATATA
47050 TAA
187 TAA
*
47053 TTCGGGTCAGGTTGGATTTCTAATTCATATATTCAAGTTGGGTCGGATGAAACTTTATTTTGTTC
1 TTCGGGTCAGGTTGGATTTCTAATTCATATATTCAAGTCGGGTCGGATGAAACTTTATTTTGTTC
* *
47118 GGGTCGGTCAGGTTTTTAAGTGTGACATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATA
66 GGGTCGGCCAGGTTTTTAAGTGTGACATTCGGGTCGAGTCAGGTCGGGTTTTTTTAAGTGTGATA
*
47183 TTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAACCGATCCGACCCGGAAAA
131 TTCGGGTCGGGTTCAGGTTTAGGGTAAAAAAACCGATCCGACCCGGAAAA
47233 AAAATTTACC
Statistics
Matches: 167, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
187 2 0.01
188 16 0.10
189 26 0.16
194 56 0.34
195 3 0.02
196 64 0.38
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.35
Consensus pattern (189 bp):
TTCGGGTCAGGTTGGATTTCTAATTCATATATTCAAGTCGGGTCGGATGAAACTTTATTTTGTTC
GGGTCGGCCAGGTTTTTAAGTGTGACATTCGGGTCGAGTCAGGTCGGGTTTTTTTAAGTGTGATA
TTCGGGTCGGGTTCAGGTTTAGGGTAAAAAAACCGATCCGACCCGGAAAATATATATAA
Found at i:48783 original size:16 final size:14
Alignment explanation
Indices: 48754--48780 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48744 TGATATAAAA
48754 AACTATTTTTTATT
1 AACTATTTTTTATT
48768 AACTATTTTTTAT
1 AACTATTTTTTAT
48781 ATTTTTATTT
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
AACTATTTTTTATT
Found at i:50558 original size:31 final size:30
Alignment explanation
Indices: 50512--50573 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
50502 ATCACCCGTG
* *
50512 ATCAATTTTTATAAATTAATAGTATTAATA
1 ATCAATTTTTATAAATCAATAATATTAATA
*
50542 ATCAATTTGTTATAAATCGATAATATTAATA
1 ATCAATTT-TTATAAATCAATAATATTAATA
50573 A
1 A
50574 CCGAATTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
ATCAATTTTTATAAATCAATAATATTAATA
Found at i:50583 original size:31 final size:30
Alignment explanation
Indices: 50514--50585 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
50504 CACCCGTGAT
* * * *
50514 CAATTTTTATAAATTAATAGTATTAATAAT
1 CAATTGTTATAAATCAATAATATTAATAAC
*
50544 CAATTTGTTATAAATCGATAATATTAATAAC
1 CAA-TTGTTATAAATCAATAATATTAATAAC
50575 CGAATTGTTAT
1 C-AATTGTTAT
50586 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 3 0.09
31 30 0.86
32 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (30 bp):
CAATTGTTATAAATCAATAATATTAATAAC
Found at i:51453 original size:51 final size:51
Alignment explanation
Indices: 51377--51482 Score: 167
Period size: 51 Copynumber: 2.1 Consensus size: 51
51367 GGGTACAGCG
* *
51377 CGGTGTAGGGGTCGCGCCTTTGCTTTAATTCTGACACAATTATGCAAGGCA
1 CGGTGTAGGGGGCGCGCCTTTGCTTTAAGTCTGACACAATTATGCAAGGCA
* * *
51428 CGGTGTAGGGGGCGGGCCTTTGCTTTAAGTCTGAGACAATTATGTAAGGCA
1 CGGTGTAGGGGGCGCGCCTTTGCTTTAAGTCTGACACAATTATGCAAGGCA
51479 CGGT
1 CGGT
51483 ACGGGCCGCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (51 bp):
CGGTGTAGGGGGCGCGCCTTTGCTTTAAGTCTGACACAATTATGCAAGGCA
Found at i:57613 original size:21 final size:22
Alignment explanation
Indices: 57588--57645 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
57578 GCAAAAAAAT
*
57588 TAATTAAATAAAATATTAAT-A
1 TAATTAAATAAAATACTAATAA
57609 TAATTAAATAAAATACTAATAA
1 TAATTAAATAAAATACTAATAA
* *
57631 AAATAAAATAAAATA
1 TAATTAAATAAAATA
57646 AAATATACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TAATTAAATAAAATACTAATAA
Found at i:57635 original size:6 final size:5
Alignment explanation
Indices: 57593--57650 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
57583 AAAATTAATT
* * * *
57593 AAATA AAATA TTAATA TAATT AAATA AAATA CTAATAA AAATA AAATA
1 AAATA AAATA -AAATA AAATA AAATA AAATA -AAAT-A AAATA AAATA
57641 AAATA AAATA
1 AAATA AAATA
57651 TACTTAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 33 0.75
6 10 0.23
7 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (5 bp):
AAATA
Found at i:60813 original size:16 final size:15
Alignment explanation
Indices: 60761--60821 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
60751 GAATTTCAGT
* *
60761 CAAACCGAAGTAAACT
1 CAAACCAAAGT-AACC
*
60777 CAAACCAACCG-AACC
1 CAAACCAA-AGTAACC
60792 CAAACCGAAAGTAACC
1 CAAACC-AAAGTAACC
*
60808 CGAACCAAAGTAAC
1 CAAACCAAAGTAAC
60822 TCAGATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 18 0.49
16 18 0.49
17 1 0.03
ACGTcount: A:0.49, C:0.33, G:0.11, T:0.07
Consensus pattern (15 bp):
CAAACCAAAGTAACC
Found at i:60819 original size:15 final size:16
Alignment explanation
Indices: 60788--60858 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 16
60778 AAACCAACCG
60788 AACCCAAACCGAAAGT
1 AACCCAAACCGAAAGT
*
60804 AACCCGAACC-AAAGT
1 AACCCAAACCGAAAGT
* * *** *
60819 AACTCAGATTAAAAAT
1 AACCCAAACCGAAAGT
* *
60835 AATCTAAACCGAAAGT
1 AACCCAAACCGAAAGT
60851 AACCCAAA
1 AACCCAAA
60859 TTAAATAATA
Statistics
Matches: 37, Mismatches: 17, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
15 10 0.27
16 27 0.73
ACGTcount: A:0.52, C:0.25, G:0.10, T:0.13
Consensus pattern (16 bp):
AACCCAAACCGAAAGT
Found at i:60867 original size:30 final size:30
Alignment explanation
Indices: 60831--60890 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
60821 CTCAGATTAA
*
60831 AAATAATCTAAACCGAAAGTAACCCAAATT
1 AAATAATATAAACCGAAAGTAACCCAAATT
* *
60861 AAATAATATGAACCGAAAGTAACCCGAATT
1 AAATAATATAAACCGAAAGTAACCCAAATT
60891 TAATTTATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (30 bp):
AAATAATATAAACCGAAAGTAACCCAAATT
Found at i:62197 original size:19 final size:19
Alignment explanation
Indices: 62173--62269 Score: 90
Period size: 22 Copynumber: 4.9 Consensus size: 19
62163 CCGTTAGATA
*
62173 GGGGAATCGGTACCCCTGG
1 GGGGAATCTGTACCCCTGG
*
62192 GGGGAATCTGT-TCCCT-G
1 GGGGAATCTGTACCCCTGG
*
62209 GGGGAATTTGTACCCCCTGGG
1 GGGGAATCTGTA-CCCCT-GG
*
62230 GGGAGAATTTGTACCCCTGGGG
1 GGG-GAATCTGTACCCCT--GG
62252 GGGGAAATCTGTACCCCT
1 GGGG-AATCTGTACCCCT
62270 AGACAATCTG
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
17 11 0.17
18 4 0.06
19 14 0.21
21 10 0.15
22 27 0.41
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.23
Consensus pattern (19 bp):
GGGGAATCTGTACCCCTGG
Done.