Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:135211 original size:87 final size:85
Alignment explanation
Indices: 135065--135286 Score: 381
Period size: 87 Copynumber: 2.6 Consensus size: 85
135055 ACAAATTAAA
* * *
135065 TAATTAATCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGTTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTA
135130 TTGTGCTTGATAATGTTTCCAG
66 TTGTGCTTGATAAT-TTT-CAG
*
135152 TAATTAACCTATTTTATTATAAAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTA
135217 TTGTGCTTGATAATTTTCAG
66 TTGTGCTTGATAATTTTCAG
*
135237 TAATCAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG
135287 CTATCTATTA
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
85 51 0.40
86 3 0.02
87 75 0.58
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (85 bp):
TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTA
TTGTGCTTGATAATTTTCAG
Found at i:135312 original size:46 final size:46
Alignment explanation
Indices: 135252--135460 Score: 159
Period size: 46 Copynumber: 4.7 Consensus size: 46
135242 AACCTATTTT
135252 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTATCTATTAC
* * * *
135298 ATTATATAAGCGCTATCTATTACATTATATAAGCGATATCTAATAT
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTATCTATTAC
* * * ** * * * *
135344 GTTAT-T--GTGTTTGAAAATGTTTTCAGTA-ATTAA-C-TTAT-T-TT--
1 ATTATATAAGCG-CT--ACCT-ATTACATTATA-TAAGCGCTATCTATTAC
*
135385 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTATCTATTAC
* *
135431 ATTATATAAGAGCTACCTATTACATCATAT
1 ATTATATAAGCGCTACCTATTACATTATAT
135461 TTTTACCTGT
Statistics
Matches: 122, Mismatches: 26, Indels: 30
0.69 0.15 0.17
Matches are distributed among these distances:
40 9 0.07
41 8 0.07
42 3 0.02
43 5 0.04
44 6 0.05
45 4 0.03
46 78 0.64
47 9 0.07
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (46 bp):
ATTATATAAGCGCTACCTATTACATTATATAAGCGCTATCTATTAC
Found at i:135348 original size:23 final size:23
Alignment explanation
Indices: 135252--135339 Score: 158
Period size: 23 Copynumber: 3.8 Consensus size: 23
135242 AACCTATTTT
*
135252 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTATCTATTAC
135275 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
135298 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
*
135321 ATTATATAAGCGATATCTA
1 ATTATATAAGCGCTATCTA
135340 ATATGTTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTATTAC
Found at i:135416 original size:133 final size:131
Alignment explanation
Indices: 135158--135460 Score: 471
Period size: 133 Copynumber: 2.3 Consensus size: 131
135148 CCAGTAATTA
** * *
135158 ACCTATTTTATTATAAAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGC
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
*
135223 TTGATAATTTTCAGTAATCAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGC
66 TTGAAAATTTTCAGTAATCAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGC
135288 T
131 T
* * * *
135289 ATCTATTACATTATATAAGCGCTATCTATTACATTATATAAGCGATATCTAATATGTTATTGTGT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
* *
135354 TTGAAAATGTTTTCAGTAATTAACTTATTTTATTATATAAGCGCTACCTATTACATTATATAAGC
66 TTGAAAA--TTTTCAGTAATCAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGC
135419 GCT
129 GCT
* *
135422 ACCTATTACATTATATAAGAGCTACCTATTACATCATAT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATAT
135461 TTTTACCTGT
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
131 63 0.41
133 92 0.59
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (131 bp):
ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
TTGAAAATTTTCAGTAATCAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGC
T
Found at i:135438 original size:25 final size:23
Alignment explanation
Indices: 135385--135460 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
135375 AACTTATTTT
135385 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
135408 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
135431 ATTATATAAGAGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
135454 ATCATAT
1 ATTATAT
135461 TTTTACCTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:141224 original size:103 final size:103
Alignment explanation
Indices: 141048--141368 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
141038 TAATGTCCAT
*
141048 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATTAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
141113 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
141151 AAGAACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATAAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
* *
141216 GACCTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
141254 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
*
141319 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
141357 AAGGACCACATA
1 AAGGACCACATA
141369 GACCCTCTAC
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:141937 original size:21 final size:21
Alignment explanation
Indices: 141919--141976 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
141909 TCGTTTGAGG
141919 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
141940 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
141961 GCGTATCGATTCCCCT
1 GGGTATCGATTCCCCT
141977 AGCCCAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:148038 original size:23 final size:23
Alignment explanation
Indices: 148012--148062 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
148002 CAGCTCATAT
*
148012 AATTGCACCTAAGTACCACGTAG
1 AATTGCACCGAAGTACCACGTAG
* *
148035 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGAAGTACCACGTAG
148058 AATTG
1 AATTG
148063 TACTGTAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTACCACGTAG
Found at i:148216 original size:103 final size:103
Alignment explanation
Indices: 148091--148411 Score: 590
Period size: 103 Copynumber: 3.1 Consensus size: 103
148081 TAATGTCCAT
*
148091 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
148156 GACTTCA-ATCACGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACA-CATGTTCCAAAGAATACATATATGTCCCG
*
148194 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
148259 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
148297 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
148362 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
148400 AAGGACCACATA
1 AAGGACCACATA
148412 GACCCTCTAC
Statistics
Matches: 211, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 210 1.00
104 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:148978 original size:21 final size:21
Alignment explanation
Indices: 148954--148996 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
148944 TCATATTCGT
*
148954 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
148975 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
148996 T
1 T
148997 AGCCCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:149925 original size:19 final size:18
Alignment explanation
Indices: 149892--149988 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 18
149882 ATCAAGAACA
149892 AAAAAGAAGAAGAAAAAAG
1 AAAAAGAA-AAGAAAAAAG
149911 AGAAAA-ACAAAGAAAAAAG
1 A-AAAAGA-AAAGAAAAAAG
* *
149930 CAAAAAGAAAATAAAAAAC
1 -AAAAAGAAAAGAAAAAAG
*
149949 AAAAAGAAAATAAAAAAG
1 AAAAAGAAAAGAAAAAAG
*
149967 CAAAAA-TAAAGAAAAAAG
1 -AAAAAGAAAAGAAAAAAG
149985 AAAA
1 AAAA
149989 CAAGACGCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.06
18 27 0.40
19 30 0.44
20 7 0.10
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAG
Found at i:149928 original size:12 final size:11
Alignment explanation
Indices: 149891--149988 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 11
149881 AATCAAGAAC
149891 AAAAAAGAAGAA
1 AAAAAAGAA-AA
149903 GAAAAAAGAGAAA
1 -AAAAAAGA-AAA
*
149916 AACAAAGAAAA
1 AAAAAAGAAAA
* *
149927 AAGCAAA-AAGA
1 AA-AAAAGAAAA
*
149938 AAATAA-AAAA
1 AAAAAAGAAAA
*
149948 CAAAAAGAAAA
1 AAAAAAGAAAA
*
149959 TAAAAAAGCAAA
1 -AAAAAAGAAAA
*
149971 AATAAAGAAAA
1 AAAAAAGAAAA
149982 AAGAAAA
1 AA-AAAA
149989 CAAGACGCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
10 9 0.13
11 25 0.37
12 23 0.34
13 10 0.15
14 1 0.01
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:149934 original size:8 final size:7
Alignment explanation
Indices: 149891--149993 Score: 52
Period size: 7 Copynumber: 14.1 Consensus size: 7
149881 AATCAAGAAC
149891 AAAAAAG
1 AAAAAAG
*
149898 -AAGAAG
1 AAAAAAG
149904 AAAAAAG
1 AAAAAAG
*
149911 -AGAAA-
1 AAAAAAG
*
149916 AACAAAG
1 AAAAAAG
149923 AAAAAAG
1 AAAAAAG
*
149930 CAAAAAG
1 AAAAAAG
149937 AAAATAA-
1 AAAA-AAG
*
149944 AAAACAAA
1 AAAA-AAG
*
149952 AAGAAAAT
1 AA-AAAAG
149960 AAAAAAG
1 AAAAAAG
149967 CAAAAATAAAG
1 ---AAA-AAAG
149978 AAAAAAG
1 AAAAAAG
149985 AAAACAAG
1 AAAA-AAG
149993 A
1 A
149994 CGCTTATACA
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
6 13 0.17
7 38 0.51
8 15 0.20
9 2 0.03
10 3 0.04
11 4 0.05
ACGTcount: A:0.80, C:0.05, G:0.13, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:149949 original size:30 final size:31
Alignment explanation
Indices: 149891--149993 Score: 88
Period size: 32 Copynumber: 3.3 Consensus size: 31
149881 AATCAAGAAC
* *
149891 AAAAAAG-AAGAAGAAAAAAGAGAAAAACAAAG
1 AAAAAAGAAAAAAG-AAAAATA-AAAAACAAAG
*
149923 AAAAAAGCAAAAAG-AAAATAAAAAACAAA-
1 AAAAAAGAAAAAAGAAAAATAAAAAACAAAG
*
149952 AAGAAAATAAAAAAGCAAAAATAAAGAAA-AAAG
1 AA-AAAAGAAAAAAG-AAAAATAAA-AAACAAAG
149985 AAAACAAGA
1 AAAA-AAGA
149994 CGCTTATACA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
29 2 0.03
30 19 0.32
31 5 0.08
32 20 0.34
33 13 0.22
ACGTcount: A:0.80, C:0.05, G:0.13, T:0.03
Consensus pattern (31 bp):
AAAAAAGAAAAAAGAAAAATAAAAAACAAAG
Found at i:149983 original size:37 final size:37
Alignment explanation
Indices: 149892--149985 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 37
149882 ATCAAGAACA
* *
149892 AAAAAGAAGAAGAAAAAAGAGAAAAACAAAGAAAAAAGC
1 AAAAAG-A-AAGAAAAAAGACAAAAAAAAAGAAAAAAGC
*
149931 AAAAAGAAA-ATAAAAA-ACAAAAAGAAAATAAAAAAGC
1 AAAAAGAAAGA-AAAAAGACAAAAA-AAAAGAAAAAAGC
*
149968 AAAAATAAAGAAAAAAGA
1 AAAAAGAAAGAAAAAAGA
149986 AAACAAGACG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
36 7 0.15
37 31 0.66
38 3 0.06
39 6 0.13
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (37 bp):
AAAAAGAAAGAAAAAAGACAAAAAAAAAGAAAAAAGC
Found at i:151597 original size:43 final size:43
Alignment explanation
Indices: 151523--151605 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
151513 CGAAGGGGCC
* *
151523 ATCCACGATTTCAACTCCACGAATGAGGATATCGTGCCCACAA
1 ATCCACGATTTCAACTCCACGAACGAGGATATCATGCCCACAA
* * *
151566 ATCCACGATTTCAACTTCACG-GCGAATGATATCATGCCCA
1 ATCCACGATTTCAACTCCACGAACG-AGGATATCATGCCCA
151606 TCTACACAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGAACGAGGATATCATGCCCACAA
Found at i:152106 original size:37 final size:37
Alignment explanation
Indices: 152034--152277 Score: 221
Period size: 37 Copynumber: 6.9 Consensus size: 37
152024 CAAAATAAAG
*
152034 TTTTGTCTCTCTTGAGACAGTTTCTATTG-AA-AAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA
*
152069 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA
*
152106 -------TCT-TTGA-ATATGTTT-TCTTTGAAAC-AAA
1 TTTTGTCTCTCTTGAGACA-GTTTCTC-TTGAAACAAAA
* * * * * * *
152134 TTTCGTCTC-CATTAAGACAATTTCTTTTGGAACTAAG
1 TTTTGTCTCTC-TTGAGACAGTTTCTCTTGAAACAAAA
* * *
152171 CTTTGTCTCTATTGAGACAGTTTCTCTTGAAAC-ATA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA
* *
152207 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAG
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA
152244 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
152278 CCAACCTTTG
Statistics
Matches: 166, Mismatches: 25, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.04
29 15 0.09
30 3 0.02
35 29 0.17
36 45 0.27
37 68 0.41
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA
Found at i:152249 original size:73 final size:73
Alignment explanation
Indices: 152119--152277 Score: 205
Period size: 73 Copynumber: 2.2 Consensus size: 73
152109 TTGAATATGT
** * *
152119 TTTCT-TTGAAACAAATTTCGTCTCCATTAAGACAATTTCTTTTGGAACTAAGCTTTGTCTCTAT
1 TTTCTCTTGAAACAAATTTCGTCTCCATTAAGACAATTTCCCTTGAAACAAAGCTTTGTCTCTAT
152183 TGAGACAG
66 TGAGACAG
* * * * * *
152191 TTTCTCTTGAAACATATTTTGTCTCTC-TTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTCGTCTC-CATTAAGACAATTTCCCTTGAAACAAAGCTTTGTCTCTA
152255 TTGAGACAG
65 TTGAGACAG
152264 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
152278 CCAACCTTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
72 5 0.07
73 69 0.92
74 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCCATTAAGACAATTTCCCTTGAAACAAAGCTTTGTCTCTAT
TGAGACAG
Found at i:152334 original size:67 final size:70
Alignment explanation
Indices: 152225--152379 Score: 194
Period size: 67 Copynumber: 2.3 Consensus size: 70
152215 CTCTTGAGAC
* * * * **
152225 AGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG-AA-AC-ACCAACCTTT
1 AGTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGTAACACAAAAAACCTTT
152287 G-AAT
66 GTAAT
*
152291 ATGTTTCTCTTTAAACAAAATTTTGCCTCCCTGTG-GACAGTTTCTCTTGTAACACAAAAAACCT
1 A-GTTTCTCTTGAAACAAAATTTTGCCTCCCT-TGAGACAGTTTCTCTTGTAACACAAAAAACCT
152355 TTGTAAT
64 TTGTAAT
152362 AGTTTCTCTTGAAACAAA
1 AGTTTCTCTTGAAACAAA
152380 CAAAAACCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
66 1 0.01
67 39 0.52
68 4 0.05
69 2 0.03
70 25 0.33
71 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGTAACACAAAAAACCTTT
GTAAT
Found at i:152370 original size:33 final size:32
Alignment explanation
Indices: 152329--152422 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 32
152319 CCCTGTGGAC
* *
152329 AGTTTCTCTTGTAACACAAAAAACCTTTGTAAT
1 AGTTTCTCTTGAAACACAAAAAACCTTTG-AAA
*
152362 AGTTTCTCTTGAAACAAACAAAAACCTTTGAAA
1 AGTTTCTCTTGAAACACA-AAAAACCTTTGAAA
* *
152395 ATGTTTCTCTTGAAATACAAAAGACCTT
1 A-GTTTCTCTTGAAACACAAAAAACCTT
152423 CGAGTTCGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (32 bp):
AGTTTCTCTTGAAACACAAAAAACCTTTGAAA
Found at i:152370 original size:173 final size:172
Alignment explanation
Indices: 152034--152377 Score: 396
Period size: 173 Copynumber: 2.0 Consensus size: 172
152024 CAAAATAAAG
*
152034 TTTTGTCTCTCTTGAGACAGTTTCTATTGAAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1 TTTTGTCTCTCTTGAGACAGTTTCCATTGAAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
* * *
152099 AACAAAATCTTTGAATATGTTTTCTTTGAAACAAATTTCGTCTCCATTAAGACAATTTCTTTTGG
66 AACAAAACCTTTGAATATGTTTTCTTTGAAACAAATTTCGCCTCCATTAAGACAATTTCTCTTGG
*****
152164 AACTAAGCTTTGTCTCTATTGAGACAGTTTCTCTTGAAACATA
131 AACTAA-CAAAAACTCTATTGAGACAGTTTCTCTTGAAACATA
* *
152207 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 TTTTGTCTCTCTTGAGACAGTTTCCATTGAAA-AAA-TTTTGTCTCTCTTGAGACAGTTTCCCTT
* * * * *
152272 GAAACACCAACCTTTGAATATGTTTCTCTTT-AAACAAAATTTTGCCTCCCTGT-GGACAGTTTC
64 GAAACA-AAACCTTTGAATATGTTT-TCTTTGAAAC-AAATTTCGCCTCCAT-TAAGACAATTTC
* *
152335 TCTTGTAAC--ACAAAAAAC-CT-TTGTA-ATAGTTTCTCTTGAAACA
125 TCTTGGAACTAAC-AAAAACTCTATTG-AGACAGTTTCTCTTGAAACA
152378 AACAAAAACC
Statistics
Matches: 145, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
173 50 0.34
174 7 0.05
175 35 0.24
176 20 0.14
177 32 0.22
178 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (172 bp):
TTTTGTCTCTCTTGAGACAGTTTCCATTGAAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAAACCTTTGAATATGTTTTCTTTGAAACAAATTTCGCCTCCATTAAGACAATTTCTCTTGG
AACTAACAAAAACTCTATTGAGACAGTTTCTCTTGAAACATA
Found at i:152390 original size:34 final size:32
Alignment explanation
Indices: 152329--152409 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 32
152319 CCCTGTGGAC
* * *
152329 AGTTTCTCTTGTAACACAAAAAACCTTTGTAAT
1 AGTTTCTCTTGAAACAAAAAAAACCTTTG-AAA
152362 AGTTTCTCTTGAAACAAACAAAAACCTTTGAAA
1 AGTTTCTCTTGAAACAAA-AAAAACCTTTGAAA
152395 ATGTTTCTCTTGAAA
1 A-GTTTCTCTTGAAA
152410 TACAAAAGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 19 0.44
34 24 0.56
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (32 bp):
AGTTTCTCTTGAAACAAAAAAAACCTTTGAAA
Found at i:154140 original size:8 final size:8
Alignment explanation
Indices: 154127--154156 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
154117 TTTTTTCGGT
154127 TTATTTTA
1 TTATTTTA
154135 TTA-TTTA
1 TTATTTTA
154142 TTATTTTA
1 TTATTTTA
154150 TTATTTT
1 TTATTTT
154157 CTTGTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTTA
Found at i:154145 original size:15 final size:15
Alignment explanation
Indices: 154127--154155 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
154117 TTTTTTCGGT
154127 TTATTTTATTATTTA
1 TTATTTTATTATTTA
154142 TTATTTTATTATTT
1 TTATTTTATTATTT
154156 TCTTGTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTATTATTTA
Found at i:154293 original size:20 final size:19
Alignment explanation
Indices: 154243--154283 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
154233 AGGTAAGCAA
*
154243 TTTAAATTAAATTTTAAAT
1 TTTAAATTAAATTATAAAT
154262 TTTAAATTTAAATTAT-AAT
1 TTTAAA-TTAAATTATAAAT
154281 TTT
1 TTT
154284 TGCAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAATTAAATTATAAAT
Found at i:160885 original size:23 final size:23
Alignment explanation
Indices: 160859--160912 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
160849 AAATGCACTA
160859 AAGTGCCACGTAGAATTACACCG
1 AAGTGCCACGTAGAATTACACCG
* * *
160882 AAGTACCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTACACCG
*
160905 GAGTGCCA
1 AAGTGCCA
160913 TATAAAATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTACACCG
Found at i:162506 original size:20 final size:20
Alignment explanation
Indices: 162469--162506 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
162459 TTCCCCTTGA
*
162469 AGTGCATCGATACTTTCTAC
1 AGTGCATCGATACATTCTAC
*
162489 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
162507 TTAACATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:162605 original size:64 final size:61
Alignment explanation
Indices: 162517--162674 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 61
162507 TTAACATGTA
* *
162517 CATCGATGCACTACCCATGCATCGATACACAAAT-CACCTTCGATGTTTTCATTTTAAGGGGGTG
1 CATCGATGCACT-CCTATGCATCGATACACAAATGCA--TTCGATGTTTCCATTTTAA-GGGGTG
* * * *
162581 CATCGATGCACTCCTTATGTATCGATGCACTAACTGCATTCGATGTTTCCATTTTAATGGGTG
1 CATCGATGCACTCC-TATGCATCGATACAC-AAATGCATTCGATGTTTCCATTTTAAGGGGTG
*
162644 CATCGATGCACTTCCTGTGCATCGATACACA
1 CATCGATGCAC-TCCTATGCATCGATACACA
162675 CTGAACAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 30 0.37
64 45 0.56
65 3 0.04
66 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (61 bp):
CATCGATGCACTCCTATGCATCGATACACAAATGCATTCGATGTTTCCATTTTAAGGGGTG
Found at i:165662 original size:23 final size:23
Alignment explanation
Indices: 165646--165727 Score: 155
Period size: 23 Copynumber: 3.6 Consensus size: 23
165636 CGTATAAATA
165646 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
165669 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
165692 CACCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
165715 CACCGAAGTGCCA
1 CACCGAAGTGCCA
165728 TATAAAATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:167222 original size:20 final size:20
Alignment explanation
Indices: 167197--167234 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
167187 TTCCCCTTGA
167197 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
167217 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
167235 GTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:169995 original size:60 final size:60
Alignment explanation
Indices: 169928--170047 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
169918 TCAATCCCAT
* * *
169928 CTCAAATTAT-AATTATCATTTTAAATT-ATTCATTATAA-TTTTCAATATTCTAATTTCATC
1 CTCAAATTATGAATT-TCATTTTAAATTAATT-ATTA-AATTTTTAAATAATATAATTTCATC
*
169988 CTCAAATTATGAATTTCTTTTTAAATTAATTATTAAATTTTTAAATAATATAATTTCATC
1 CTCAAATTATGAATTTCATTTTAAATTAATTATTAAATTTTTAAATAATATAATTTCATC
170048 TCAGACTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
59 2 0.04
60 44 0.83
61 7 0.13
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (60 bp):
CTCAAATTATGAATTTCATTTTAAATTAATTATTAAATTTTTAAATAATATAATTTCATC
Found at i:173264 original size:14 final size:14
Alignment explanation
Indices: 173245--173272 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
173235 AAGTGAAAGA
173245 ATAGTTATATAATT
1 ATAGTTATATAATT
173259 ATAGTTATATAATT
1 ATAGTTATATAATT
173273 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:174729 original size:20 final size:20
Alignment explanation
Indices: 174704--174745 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
174694 TCGAGTAAAA
*
174704 ATTAAAATATGA-TCATTTAT
1 ATTAAAAT-TGATTAATTTAT
174724 ATTAAAATTGATTAATTTAT
1 ATTAAAATTGATTAATTTAT
174744 AT
1 AT
174746 CGTTTCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTAAAATTGATTAATTTAT
Found at i:176931 original size:78 final size:78
Alignment explanation
Indices: 176787--176958 Score: 258
Period size: 78 Copynumber: 2.2 Consensus size: 78
176777 TCATCAGATG
* * * *
176787 AGTTC-TCTCATTATGAACTCTCCACTGGCAATGTTGATCCACCTCTTTCTGTGATGGAATTAGG
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAGG
176851 CAAAGATTGAA-A
66 CAAAGATTGAACA
* * *
176863 ATTTTCTTCTCATTATGAATTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCGG
1 A-GTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAG
176928 GCAAAGATTGAACA
65 GCAAAGATTGAACA
176942 AGTTCTTCTCATTATGA
1 AGTTCTTCTCATTATGA
176959 GCTTCTTCTC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
76 1 0.01
77 3 0.04
78 79 0.93
79 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (78 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAGG
CAAAGATTGAACA
Found at i:177401 original size:17 final size:16
Alignment explanation
Indices: 177362--177402 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
177352 TTTTGCTTAT
*
177362 TTATCTGTATTGAGTC
1 TTATCTTTATTGAGTC
177378 TTCATCTTTATTGAGTC
1 TT-ATCTTTATTGAGTC
177395 ATTATCTT
1 -TTATCTT
177403 GTCGAATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.54
Consensus pattern (16 bp):
TTATCTTTATTGAGTC
Found at i:177834 original size:39 final size:39
Alignment explanation
Indices: 177780--177859 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
177770 TGAAAAAGTG
177780 TCAGGATTGATGGGTTGGTTTCAGATTAGCTTTCTATTT
1 TCAGGATTGATGGGTTGGTTTCAGATTAGCTTTCTATTT
177819 TCAGGATTGATGGGTTGGTTTCAGATTAGCTTTCTATTT
1 TCAGGATTGATGGGTTGGTTTCAGATTAGCTTTCTATTT
177858 TC
1 TC
177860 TAAGGTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.11, G:0.25, T:0.46
Consensus pattern (39 bp):
TCAGGATTGATGGGTTGGTTTCAGATTAGCTTTCTATTT
Found at i:180365 original size:20 final size:20
Alignment explanation
Indices: 180323--180366 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
180313 TTATCGTTCG
* *
180323 ATGTTATATTAAATGAATGA
1 ATGTTATATTAAATCAATAA
**
180343 ATGTTATATTACTTCAATAA
1 ATGTTATATTAAATCAATAA
180363 ATGT
1 ATGT
180367 AAGTACATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (20 bp):
ATGTTATATTAAATCAATAA
Found at i:180953 original size:34 final size:34
Alignment explanation
Indices: 180915--180980 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
180905 AGAAATAAGT
180915 TAGTGCATGTAAGATAATCGAAAAAGATAAAAGG
1 TAGTGCATGTAAGATAATCGAAAAAGATAAAAGG
180949 TAGTGCATGTAAGATAATCGAAAAAGATAAAA
1 TAGTGCATGTAAGATAATCGAAAAAGATAAAA
180981 AAGACTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (34 bp):
TAGTGCATGTAAGATAATCGAAAAAGATAAAAGG
Found at i:183756 original size:3 final size:3
Alignment explanation
Indices: 183748--183802 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
183738 GGGTTTGTAA
* * *
183748 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT GAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
183796 AAT AAT A
1 AAT AAT A
183803 TAAGGCGAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:184828 original size:15 final size:15
Alignment explanation
Indices: 184808--184838 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
184798 AAAATTTAAG
184808 TTAGTCCCCTCAAAC
1 TTAGTCCCCTCAAAC
184823 TTAGTCCCCTCAAAC
1 TTAGTCCCCTCAAAC
184838 T
1 T
184839 ATATCACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.39, G:0.06, T:0.29
Consensus pattern (15 bp):
TTAGTCCCCTCAAAC
Found at i:185015 original size:30 final size:30
Alignment explanation
Indices: 184979--185038 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
184969 AATCTCTCTC
184979 CTTGGACACTTTTTTTCTCTGCTATTGTGG
1 CTTGGACACTTTTTTTCTCTGCTATTGTGG
185009 CTTGGACACTTTTTTTCTCTGCTATTGTGG
1 CTTGGACACTTTTTTTCTCTGCTATTGTGG
185039 TGCGATCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (30 bp):
CTTGGACACTTTTTTTCTCTGCTATTGTGG
Found at i:185469 original size:11 final size:11
Alignment explanation
Indices: 185439--185471 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
185429 AGTTGCCATT
*
185439 GTTAAAAAAAA
1 GTTAAAAAGAA
185450 GTTAAAAAGAA
1 GTTAAAAAGAA
185461 GTTAAAAAGAA
1 GTTAAAAAGAA
185472 TCAAAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (11 bp):
GTTAAAAAGAA
Found at i:188346 original size:36 final size:36
Alignment explanation
Indices: 188299--188488 Score: 272
Period size: 36 Copynumber: 5.3 Consensus size: 36
188289 GAAAACGAAC
* *
188299 ACTTGGATCGGAAATGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
* * *
188335 ACTTGAATCGGAAGTGTCGATACTTTCTTCCGTTCA
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
188371 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
* * *
188407 ATTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
* * *
188443 ATTTGAATCGGAAGTGACGATACTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
*
188479 ATTTGAATCG
1 ACTTGAATCG
188489 TCGGTGCACC
Statistics
Matches: 139, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 139 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
Found at i:190022 original size:19 final size:19
Alignment explanation
Indices: 189994--190030 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
189984 ACATTAGCAG
*
189994 TGCATGTTCTAGAATGCAA
1 TGCATATTCTAGAATGCAA
190013 TGCATATTCTAGAATGCA
1 TGCATATTCTAGAATGCA
190031 TATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATATTCTAGAATGCAA
Found at i:191561 original size:2 final size:2
Alignment explanation
Indices: 191554--191620 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
191544 AAACTCTCAC
191554 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
191596 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
191621 AATTCATTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:193037 original size:2 final size:2
Alignment explanation
Indices: 193030--193056 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
193020 AGCTTCAAAG
193030 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 T
193057 GAATAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:193121 original size:14 final size:14
Alignment explanation
Indices: 193098--193128 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
193088 TTACTTCTCT
193098 TAATTGTTAAGTAA
1 TAATTGTTAAGTAA
*
193112 TAATTTTTAAGTAA
1 TAATTGTTAAGTAA
193126 TAA
1 TAA
193129 AGCATTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATTGTTAAGTAA
Found at i:198532 original size:23 final size:23
Alignment explanation
Indices: 198506--198566 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
198496 CTCATATAAA
*
198506 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
198529 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
198552 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
198567 TTTAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:198691 original size:62 final size:61
Alignment explanation
Indices: 198625--198810 Score: 174
Period size: 62 Copynumber: 3.0 Consensus size: 61
198615 CATATACTAG
198625 GGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
1 GGATCAAGTATG-GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
* * * * * *
198687 GGATCACA--AT-GTC-C-CGAAGGAC--CACATATCATTCCTTAAGAAT-CATATACATATGCC
1 GGATCA-AGTATGGTCTCAC-CA-GACTTCACACAT-GTTCC-AAAGAATACATAT--ATGTCCC
198744 -AA
59 GAA
198746 GGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
1 GGATCAAGTATG-GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
198808 GGA
1 GGA
198811 CCACAATGTC
Statistics
Matches: 95, Mismatches: 12, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
57 7 0.07
58 12 0.13
59 20 0.21
60 7 0.07
61 7 0.07
62 23 0.24
63 12 0.13
64 7 0.07
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (61 bp):
GGATCAAGTATGGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
Found at i:198700 original size:18 final size:18
Alignment explanation
Indices: 198677--198712 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
198667 GAATACATAT
*
198677 ATGTCCCGAAGGATCACA
1 ATGTCCCGAAGGACCACA
198695 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
198713 TATCATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:198748 original size:59 final size:59
Alignment explanation
Indices: 198680--198861 Score: 153
Period size: 59 Copynumber: 3.0 Consensus size: 59
198670 TACATATATG
198680 TCCCGAAGGATCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATA
1 TCCCGAAGGATCACAATGTCCCGAA-GACCACATATCATTCCTTAAGAATCATATACATA
* * * * *
198740 TGCC-AAGGATCA-AGTATGTGTCTCAC-CAGACTTCACACAT-GTTCC-AAAGAATACATAT--
1 TCCCGAAGGATCACA--A--TGTC-C-CGAAGAC--CACATATCATTCCTTAAGAAT-CATATAC
*
198798 ATG
57 ATA
*
198801 TCCCGAAGGACCACAATGTCCCGAATGACCACATATCATTCCTTAAGAATCATATACATA
1 TCCCGAAGGATCACAATGTCCCGAA-GACCACATATCATTCCTTAAGAATCATATACATA
198861 T
1 T
198862 ACTAGGGATC
Statistics
Matches: 92, Mismatches: 13, Indels: 34
0.66 0.09 0.24
Matches are distributed among these distances:
57 7 0.08
58 12 0.13
59 21 0.23
60 7 0.08
61 6 0.07
62 20 0.22
63 12 0.13
64 7 0.08
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (59 bp):
TCCCGAAGGATCACAATGTCCCGAAGACCACATATCATTCCTTAAGAATCATATACATA
Found at i:198787 original size:121 final size:121
Alignment explanation
Indices: 198573--198936 Score: 620
Period size: 121 Copynumber: 3.0 Consensus size: 121
198563 GCCATTTAAT
** *
198573 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
*
198638 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGATCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* * *
198694 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
198759 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
198815 AATGTCCCGAATGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
* * * *
198880 GACTCACTAGACTTCACACATGTTCCAAAGGATACATATATATCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
198936 A
1 A
198937 TAGACCCTCG
Statistics
Matches: 228, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 228 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (121 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:198821 original size:18 final size:18
Alignment explanation
Indices: 198798--198833 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
198788 GAATACATAT
198798 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
*
198816 ATGTCCCGAATGACCACA
1 ATGTCCCGAAGGACCACA
198834 TATCATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:200166 original size:21 final size:21
Alignment explanation
Indices: 200140--200183 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
200130 ATTTTATTCG
* *
200140 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
200161 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
200182 CT
1 CT
200184 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:205205 original size:24 final size:24
Alignment explanation
Indices: 205178--205234 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
205168 ACTTTGGGAT
205178 GCAAATGGATAGGATTCAAACATG
1 GCAAATGGATAGGATTCAAACATG
205202 GCAAATGGATAGGATTCAAACATG
1 GCAAATGGATAGGATTCAAACATG
*
205226 GAAAATGGA
1 GCAAATGGA
205235 CAACAAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (24 bp):
GCAAATGGATAGGATTCAAACATG
Found at i:210041 original size:36 final size:36
Alignment explanation
Indices: 209959--210100 Score: 223
Period size: 36 Copynumber: 4.0 Consensus size: 36
209949 TGAACAAGAA
*
209959 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT-
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
209994 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
* *
210030 GAACGGAAGGAAGCATCGACACTTTCGATTCAAATC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
* * *
210066 GAACGGAAAGAGGCATCGGCACTTTTGATTCAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
210101 GTTCATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 34 0.35
36 64 0.65
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
Found at i:231448 original size:28 final size:28
Alignment explanation
Indices: 231416--231484 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
231406 TGTAATAAAG
* *
231416 AAAAGGAAAATAAA-AAGAAAATAACAAA
1 AAAAGAAAAATAAATAACAAAA-AACAAA
*
231444 AAAAGTAAAAA-AAATAACAAAAATCAAA
1 AAAAG-AAAAATAAATAACAAAAAACAAA
231472 AAACAGAAAAATA
1 AAA-AGAAAAATA
231485 GCAAATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.78, C:0.06, G:0.07, T:0.09
Consensus pattern (28 bp):
AAAAGAAAAATAAATAACAAAAAACAAA
Found at i:231474 original size:21 final size:20
Alignment explanation
Indices: 231422--231474 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
231412 AAAGAAAAGG
*
231422 AAAATAAAAAGAAAATAACA
1 AAAATAAAAAAAAAATAACA
231442 AAAA-AAGTAAAAAAAATAACA
1 AAAATAA--AAAAAAAATAACA
*
231463 AAAATCAAAAAA
1 AAAATAAAAAAA
231475 CAGAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
21 16 0.57
22 1 0.04
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.09
Consensus pattern (20 bp):
AAAATAAAAAAAAAATAACA
Found at i:235465 original size:20 final size:20
Alignment explanation
Indices: 235440--235479 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
235430 TATGTCTTAT
235440 ATAATCT-TAAAATTTATACA
1 ATAATCTATAAAA-TTATACA
*
235460 ATAATCTATGAAATTATACA
1 ATAATCTATAAAATTATACA
235480 TAAATTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAATCTATAAAATTATACA
Found at i:236610 original size:36 final size:34
Alignment explanation
Indices: 236528--236610 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 34
236518 TTACAAATTG
* *
236528 TAAAATATTTATATATTTTCTTTAAAAAATTAAAT
1 TAAAA-ATTTATATATTTTCTTTAAAAAATAAAAA
* *
236563 TCATAATATTTATATAATTTTTTTTACAAAAATAAAAA
1 T-A-AAAATTTATAT-ATTTTCTTTA-AAAAATAAAAA
236601 TAAAAATTTA
1 TAAAAATTTA
236611 ACCTTCGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
35 1 0.03
36 16 0.41
37 12 0.31
38 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (34 bp):
TAAAAATTTATATATTTTCTTTAAAAAATAAAAA
Found at i:236624 original size:14 final size:14
Alignment explanation
Indices: 236605--236633 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
236595 TAAAAATAAA
236605 AATTTAACCTTCGT
1 AATTTAACCTTCGT
236619 AATTTAACCTTCGT
1 AATTTAACCTTCGT
236633 A
1 A
236634 GAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
AATTTAACCTTCGT
Found at i:237457 original size:27 final size:27
Alignment explanation
Indices: 237417--237527 Score: 98
Period size: 32 Copynumber: 3.8 Consensus size: 27
237407 AAATAATAAT
* *
237417 AAAACTTTAGTATTATGACTATTTTTT-
1 AAAA-TTTATTATTATGATTATTTTTTG
237444 AAATATTTATTATTATGATTATTTCTTTTG
1 AAA-ATTTATTATTATGATTA-TT-TTTTG
237474 AAAATATTATTATTATGATTATTTTTTTTTTG
1 AAAAT-TTATTATTATGATTA----TTTTTTG
*
237506 AAAATATTATTATGATGATTAT
1 AAAAT-TTATTATTATGATTAT
237528 AGGTGCACAG
Statistics
Matches: 73, Mismatches: 3, Indels: 15
0.80 0.03 0.16
Matches are distributed among these distances:
27 17 0.23
28 4 0.05
29 6 0.08
30 18 0.25
32 25 0.34
33 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (27 bp):
AAAATTTATTATTATGATTATTTTTTG
Found at i:237510 original size:32 final size:31
Alignment explanation
Indices: 237444--237527 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 31
237434 ACTATTTTTT
237444 AAATATTTATTATTATGATTA-TTTCTTTTGA
1 AAATA-TTATTATTATGATTATTTTCTTTTGA
*
237475 AAATATTATTATTATGATTATTTTTTTTTTGA
1 AAATATTATTATTATGATTA-TTTTCTTTTGA
*
237507 AAATATTATTATGATGATTAT
1 AAATATTATTATTATGATTAT
237528 AGGTGCACAG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
30 15 0.31
31 6 0.12
32 28 0.57
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (31 bp):
AAATATTATTATTATGATTATTTTCTTTTGA
Found at i:244039 original size:2 final size:2
Alignment explanation
Indices: 244032--244069 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
244022 GGTATTTTAA
244032 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
244070 TGATTACTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253065 original size:16 final size:17
Alignment explanation
Indices: 253044--253080 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
253034 ATTTCACAAA
253044 TATTTTA-AAA-TAATGT
1 TATTTTAGAAATTAAT-T
253060 TATTTTAGAAATTAATT
1 TATTTTAGAAATTAATT
253077 TATT
1 TATT
253081 GGGTTCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TATTTTAGAAATTAATT
Found at i:264934 original size:15 final size:15
Alignment explanation
Indices: 264914--264945 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
264904 TCTCTTCTTA
264914 TTCTATTTTTCTTTC
1 TTCTATTTTTCTTTC
264929 TTCTATTTTTCTTTC
1 TTCTATTTTTCTTTC
264944 TT
1 TT
264946 GTCCCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTATTTTTCTTTC
Found at i:264944 original size:12 final size:14
Alignment explanation
Indices: 264908--264941 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
264898 GTTTCTTCTC
*
264908 TTCTTATTCTATTT
1 TTCTTCTTCTATTT
264922 TTCTTTCTTCTATTT
1 TTC-TTCTTCTATTT
264937 TTCTT
1 TTCTT
264942 TCTTGTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTCTTCTATTT
Found at i:265785 original size:21 final size:21
Alignment explanation
Indices: 265760--265816 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
265750 ATACTCAAGG
*
265760 GAGTATTAATACTACCTGAAA
1 GAGTATCAATACTACCTGAAA
*
265781 GAGTATCAATACTACGTGAAA
1 GAGTATCAATACTACCTGAAA
265802 GAGTATCAATACTAC
1 GAGTATCAATACTAC
265817 ATTAAGGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (21 bp):
GAGTATCAATACTACCTGAAA
Found at i:277612 original size:20 final size:20
Alignment explanation
Indices: 277583--277778 Score: 189
Period size: 20 Copynumber: 9.7 Consensus size: 20
277573 GTTTCCAGAT
277583 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
277603 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
277623 TTCGCGTTGCGATTTTTTGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
277646 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
277666 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
*
277686 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
277706 TCGCAACGAGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
277726 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
277746 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
277766 TCGCAATGCGATT
1 TCGCAATGCGATT
277779 TTCAAAGCGC
Statistics
Matches: 145, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.02
20 117 0.81
21 11 0.08
22 9 0.06
23 3 0.02
24 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:277968 original size:22 final size:22
Alignment explanation
Indices: 277943--277999 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
277933 CACTCTCTAA
*
277943 GACGACATCCGTCCCCATCTCC
1 GACGAAATCCGTCCCCATCTCC
*
277965 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCCGTCCCCATCTCC
*
277987 GGCGAAATCCGTC
1 GACGAAATCCGTC
278000 TATCTCCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.42, G:0.18, T:0.18
Consensus pattern (22 bp):
GACGAAATCCGTCCCCATCTCC
Found at i:278447 original size:20 final size:20
Alignment explanation
Indices: 278399--278449 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
278389 TTAGTTTCGC
** *
278399 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
278419 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
278439 GTTGCGATTTT
1 GTTGCGATTTT
278450 AAGTTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:278456 original size:20 final size:20
Alignment explanation
Indices: 278382--278457 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
278372 AGAATCGCAA
**
278382 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCAGTTTCATGT
** * *
278401 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCAGTTTCATGT
*
278421 TGCGATTTTCATTTTCATGT
1 TGCGATTTTCAGTTTCATGT
*
278441 TGCGATTTTAAGTTTCA
1 TGCGATTTTCAGTTTCA
278458 GAAACTTTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.15
20 40 0.85
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCAGTTTCATGT
Found at i:280186 original size:18 final size:18
Alignment explanation
Indices: 280163--280212 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
280153 TTTACTCGTA
280163 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
280181 ATTTCACTTAGATTAATC
1 ATTTCACTTAGATTAACC
280199 ATTTCACTTAGATT
1 ATTTCACTTAGATT
280213 GGTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:280455 original size:20 final size:19
Alignment explanation
Indices: 280430--280496 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
280420 GTGATTCTCT
280430 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
280450 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
280470 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
280488 TGTTGCGAT
1 CGTTGCGAT
280497 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 12 0.28
19 1 0.02
20 30 0.70
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:281075 original size:21 final size:21
Alignment explanation
Indices: 280984--281087 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
280974 GACTCACCTG
* *
280984 TCATCGTTCAAGAGGCCTC-C
1 TCATCGTTCAAGAGGCCACTA
* *
281004 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCACTA
** * * *
281026 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCACTA
* *
281047 CCACCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGGCCACTA
* *
281068 TCATCGTTGAAGAGGTCACT
1 TCATCGTTCAAGAGGCCACT
281088 CCCAATATTC
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTA
Found at i:281090 original size:42 final size:41
Alignment explanation
Indices: 280984--281091 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
280974 GACTCACCTG
* *
280984 TCATCGTTCAAGAGG-CCTCCCCTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGTCCT-CCC-ACCGTTCAAGAGGCCACTA
**
281026 TCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGGT--CCTCCCACCGTTCAAGAGGCCACTA
*
281068 TCATCGTTGAAGAGGTCACTCCCA
1 TCATCGTTCAAGAGGTC-CTCCCA
281092 ATATTCTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
41 2 0.04
42 44 0.81
43 5 0.09
44 3 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (41 bp):
TCATCGTTCAAGAGGTCCTCCCACCGTTCAAGAGGCCACTA
Found at i:281245 original size:13 final size:13
Alignment explanation
Indices: 281227--281260 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
281217 GAAGTGGAGA
281227 GGAAACAACTACC
1 GGAAACAACTACC
281240 GGAAACAACTACC
1 GGAAACAACTACC
281253 GGAAACAA
1 GGAAACAA
281261 TTCTGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.26, G:0.18, T:0.06
Consensus pattern (13 bp):
GGAAACAACTACC
Found at i:282507 original size:14 final size:14
Alignment explanation
Indices: 282470--282531 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
282460 TTGCTTGTTT
*
282470 AATTGATTTATAAA
1 AATTGATTTGTAAA
282484 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
282498 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
282513 TATTGATGTGTAAA
1 AATTGATTTGTAAA
282527 TAATT
1 -AATT
282532 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:282655 original size:20 final size:20
Alignment explanation
Indices: 282630--282682 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
282620 AGGTACACTT
* *
282630 TCGCAATGCTAAACTCAAAA
1 TCGCAATGCGAAACACAAAA
*
282650 TCGCAATGCGAAAGACAAAA
1 TCGCAATGCGAAACACAAAA
*
282670 TCGCAACGCGAAA
1 TCGCAATGCGAAA
282683 GTCAATTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAATGCGAAACACAAAA
Found at i:282699 original size:19 final size:20
Alignment explanation
Indices: 282677--282719 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
282667 AAATCGCAAC
*
282677 GCGAAAGTC-AATTCGCATT
1 GCGAAAGTCTAATACGCATT
* *
282696 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCATT
282716 GCGA
1 GCGA
282720 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCATT
Found at i:282755 original size:20 final size:20
Alignment explanation
Indices: 282726--283016 Score: 321
Period size: 20 Copynumber: 14.8 Consensus size: 20
282716 GCGATTTTCT
* *
282726 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* * *
282746 CGTTGTGATACTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
* * *
282766 CCTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
282786 CGTTGCGAATA-TCAAATTCG
1 CGTTGCG-ATAGTCAAATTCG
282806 CGTTGCGTATA-TCAAATTCG
1 CGTTGCG-ATAGTCAAATTCG
282826 CGTTGCGAATA-TCAAATTCG
1 CGTTGCG-ATAGTCAAATTCG
*
282846 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
282866 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
282886 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
282906 TGTTGCGATATTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
282926 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
282940 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
282960 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
282980 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
283000 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
283017 GAATGTGTAA
Statistics
Matches: 230, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.05
16 1 0.00
18 1 0.00
19 3 0.01
20 211 0.92
21 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:283239 original size:140 final size:140
Alignment explanation
Indices: 282987--283256 Score: 531
Period size: 140 Copynumber: 1.9 Consensus size: 140
282977 TCGCGTTACG
282987 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
283052 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
283117 AATACACGTA
131 AATACACGTA
283127 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
283192 TAGCAATGTTCAAACTCAAGTTACTAATTCATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
283257 TACAACGTTT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 129 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACGTA
Found at i:283331 original size:12 final size:12
Alignment explanation
Indices: 283313--283351 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
283303 GTGATGCCGG
*
283313 TTGTGATTGTGA
1 TTGTGATTTTGA
*
283325 TTTTGATTTTGA
1 TTGTGATTTTGA
*
283337 TTGCGATTTTGA
1 TTGTGATTTTGA
283349 TTG
1 TTG
283352 CCTTTTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.03, G:0.26, T:0.56
Consensus pattern (12 bp):
TTGTGATTTTGA
Found at i:283337 original size:18 final size:18
Alignment explanation
Indices: 283316--283350 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
283306 ATGCCGGTTG
*
283316 TGATTGTGATTTTGATTT
1 TGATTGCGATTTTGATTT
283334 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
283351 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:285596 original size:24 final size:24
Alignment explanation
Indices: 285562--285615 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
285552 CTGAAACATC
285562 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
285586 ATCAAAGTCCGGGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
285610 ATCAAA
1 ATCAAA
285616 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:286451 original size:20 final size:20
Alignment explanation
Indices: 286426--286505 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
286416 GAAATTCAGT
*
286426 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
286446 GTTGCGATAGTCAAAATCTC
1 GTTGCGATAGTCAGAATCGC
286466 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
286486 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
286506 ATTACGATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:286472 original size:40 final size:40
Alignment explanation
Indices: 286426--286503 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
286416 GAAATTCAGT
*
286426 GTTGCGACAGTCAGAATCGCGTTGCGATAGTCAAAATCTC
1 GTTGCGACAGTCAGAATCGCATTGCGATAGTCAAAATCTC
* *
286466 GTTGCGATAGTCAGAATCGCATTGCGATAGTCATAATC
1 GTTGCGACAGTCAGAATCGCATTGCGATAGTCAAAATC
286504 GCATTACGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (40 bp):
GTTGCGACAGTCAGAATCGCATTGCGATAGTCAAAATCTC
Found at i:286506 original size:20 final size:20
Alignment explanation
Indices: 286427--286553 Score: 114
Period size: 20 Copynumber: 6.3 Consensus size: 20
286417 AAATTCAGTG
* * *
286427 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
* * *
286447 TTGCGATAGTCAAAATCTCG
1 TTGCGATAGTCATAATCGCA
*
286467 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCATAATCGCA
286487 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* * *
286507 TTACGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* *
286527 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
286547 TTGCGAT
1 TTGCGAT
286554 TTACATATTC
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
19 1 0.01
20 94 0.99
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:286531 original size:60 final size:61
Alignment explanation
Indices: 286457--286613 Score: 158
Period size: 60 Copynumber: 2.6 Consensus size: 61
286447 TTGCGATAGT
* *
286457 CAAAATCTCGTTGCGATAGTCAGAATCGCATTGCGATAGT-CATAATCGCATTACG-ATTTA
1 CAAAATCGCATTGCGATAGTCAGAATCGCATTGCGAT-GTACATAATCGCATTACGAATTTA
* * * * * * * *
286517 CATATTCGCATTGCGAT-TTACATATTCGCATTGCGATTTACATATTCGCATTACGAATTTG
1 CAAAATCGCATTGCGATAGT-CAGAATCGCATTGCGATGTACATAATCGCATTACGAATTTA
* * *
286578 GAAAATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 CAAAATCGCATTGCGATAGTCAGAATCGCATTGCGA
286614 ATATGGAAAC
Statistics
Matches: 75, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
59 2 0.03
60 42 0.56
61 30 0.40
62 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (61 bp):
CAAAATCGCATTGCGATAGTCAGAATCGCATTGCGATGTACATAATCGCATTACGAATTTA
Found at i:286554 original size:20 final size:20
Alignment explanation
Indices: 286482--286568 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
286472 ATAGTCAGAA
* *
286482 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGAT-TTACATAT
*
286502 TCGCATTACGATTTACATAT
1 TCGCATTGCGATTTACATAT
286522 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
286542 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
286562 TCGCATT
1 TCGCATT
286569 ACGAATTTGG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 1 0.02
20 61 0.98
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:287424 original size:35 final size:35
Alignment explanation
Indices: 287377--287462 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
287367 AAAACAGTCA
* * *
287377 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
287412 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
287447 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
287463 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:287456 original size:21 final size:21
Alignment explanation
Indices: 287431--287473 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
287421 TTCTAAACCC
287431 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
287452 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
287473 T
1 T
287474 TAAGGTAATA
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:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:287628 original size:16 final size:18
Alignment explanation
Indices: 287596--287629 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
287586 TATTAATGTA
287596 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
287614 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
287630 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:288300 original size:130 final size:130
Alignment explanation
Indices: 288097--288344 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
288087 AATTTTCTTC
* * *
288097 TAATTAGGAGGTGACATATGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACATGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
288162 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTCATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * * *
288227 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACATGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
288292 CCTAATTAAATGATTAATTCATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTCATTAAATTTTATTTAATTTAGGACCAAATTGAT
288345 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACATGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTCATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:293530 original size:2 final size:2
Alignment explanation
Indices: 293525--293554 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
293515 GTGTGCATAC
293525 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
293555 GAGAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:293724 original size:41 final size:39
Alignment explanation
Indices: 293696--293960 Score: 379
Period size: 41 Copynumber: 6.5 Consensus size: 39
293686 ATTCGCGTTG
293696 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
293737 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
293778 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
293819 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
* *
293860 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCG--TTTC
*
293901 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG--TTTC
293942 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
293961 CTACAGTTGT
Statistics
Matches: 218, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
40 1 0.00
41 216 0.99
42 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGTTTC
Found at i:293854 original size:123 final size:123
Alignment explanation
Indices: 293696--293960 Score: 487
Period size: 123 Copynumber: 2.2 Consensus size: 123
293686 ATTCGCGTTG
293696 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-AA
293760 AATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
65 AATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
293819 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAA
* *
293884 GTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
66 ATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
293942 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
293961 CTACAGTTGT
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
123 137 0.99
124 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (123 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAA
ATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:293967 original size:82 final size:82
Alignment explanation
Indices: 293696--293960 Score: 487
Period size: 82 Copynumber: 3.2 Consensus size: 82
293686 ATTCGCGTTG
293696 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
293761 ATCGCGTTGCGATTTTC
66 ATCGCGTTGCGATTTTC
293778 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
293843 ATCGCGTTGCGATTTTC
66 ATCGCGTTGCGATTTTC
* *
293860 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAA
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAA
*
293924 ATTCGCGTTGCGATTTTC
65 AATCGCGTTGCGATTTTC
293942 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
293961 CTACAGTTGT
Statistics
Matches: 179, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
82 178 0.99
83 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCGTTGCGATTTTC
Found at i:294089 original size:6 final size:6
Alignment explanation
Indices: 294078--294127 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
294068 GACACGTATT
*
294078 ACCACG ACCACG ACCACG ACCACG ACCACG ACAACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
294125 ACC
1 ACC
294128 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:294281 original size:13 final size:13
Alignment explanation
Indices: 294263--294292 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
294253 TTGAGCATTA
294263 CCAACACTTGTTC
1 CCAACACTTGTTC
294276 CCAACACTTGTTC
1 CCAACACTTGTTC
294289 CCAA
1 CCAA
294293 TCACATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.40, G:0.07, T:0.27
Consensus pattern (13 bp):
CCAACACTTGTTC
Found at i:294490 original size:6 final size:6
Alignment explanation
Indices: 294459--294517 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
294449 TCTTGTCTCG
294459 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
294503 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
294518 AATACGTGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:294650 original size:42 final size:41
Alignment explanation
Indices: 294601--294723 Score: 140
Period size: 41 Copynumber: 3.0 Consensus size: 41
294591 TCAACGAATT
*
294601 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGTGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
294643 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
* * * * *
294684 TGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAA
294724 TTAGAGATCG
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 58 0.78
42 16 0.22
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:294671 original size:41 final size:41
Alignment explanation
Indices: 294626--294723 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
294616 ACAACTGTAG
* * *
294626 ACTATCGCAACGTGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
294667 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
294708 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
294724 TTAGAGATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
Found at i:294675 original size:21 final size:21
Alignment explanation
Indices: 294649--294722 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
294639 GAAATGGAAA
294649 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
294670 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* *
294690 ACCACAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
294711 ATCGCAACGCGA
1 ATCGCAACGCGA
294723 ATTAGAGATC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:294735 original size:19 final size:19
Alignment explanation
Indices: 294711--294780 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
294701 ATTTTCAACT
*
294711 ATCGCAACGCGAATTAGAG
1 ATCGCAATGCGAATTAGAG
* *
294730 ATCGCATTGC-AATAGTGGAG
1 ATCGCAATGCGAAT--TAGAG
294750 ATCGCAATGCGAATTAGAG
1 ATCGCAATGCGAATTAGAG
*
294769 ATCGCATTGCGA
1 ATCGCAATGCGA
294781 TTTTGTTGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.07
19 23 0.55
20 13 0.31
21 3 0.07
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (19 bp):
ATCGCAATGCGAATTAGAG
Found at i:294752 original size:20 final size:19
Alignment explanation
Indices: 294719--294780 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
294709 CTATCGCAAC
294719 GCGAATTAGAGATCGCATT
1 GCGAATTAGAGATCGCATT
* *
294738 GC-AATAGTGGAGATCGCAAT
1 GCGAAT--TAGAGATCGCATT
294758 GCGAATTAGAGATCGCATT
1 GCGAATTAGAGATCGCATT
294777 GCGA
1 GCGA
294781 TTTTGTTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.08
19 17 0.47
20 13 0.36
21 3 0.08
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (19 bp):
GCGAATTAGAGATCGCATT
Found at i:295536 original size:3 final size:3
Alignment explanation
Indices: 295528--295557 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
295518 GCAAAATATG
295528 TAA TAA TAA TAA GTAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TA
295558 TTTATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:295543 original size:13 final size:13
Alignment explanation
Indices: 295522--295557 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
295512 GGTGCTGCAA
*
295522 AATATGTAATAAT
1 AATAAGTAATAAT
295535 AATAAGTAATAAT
1 AATAAGTAATAAT
295548 AATAA-TAATA
1 AATAAGTAATA
295558 TTTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
AATAAGTAATAAT
Found at i:295853 original size:48 final size:47
Alignment explanation
Indices: 295801--295918 Score: 173
Period size: 48 Copynumber: 2.5 Consensus size: 47
295791 ATTCCGATGT
* *
295801 CTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGATTTGTTCCGCTTA
1 CTCTGAAGGGAATATCAAATCTTG-AGAAGAGAAATCTGTTCCGCTTA
*
295849 CTCTGAAGGGAATATCAAATCTTTGAGAATAGAAATCTGTTCCGCTTA
1 CTCTGAAGGGAATATCAAATC-TTGAGAAGAGAAATCTGTTCCGCTTA
* *
295897 CTCTGAAGGGACTATCAGATCT
1 CTCTGAAGGGAATATCAAATCT
295919 GAGGAAGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
47 1 0.02
48 60 0.94
49 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (47 bp):
CTCTGAAGGGAATATCAAATCTTGAGAAGAGAAATCTGTTCCGCTTA
Found at i:296046 original size:113 final size:113
Alignment explanation
Indices: 295837--296393 Score: 812
Period size: 113 Copynumber: 4.9 Consensus size: 113
295827 GAAGAGAGAT
* * * * *
295837 TTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTTGAGAATAGAAATC-TGTTCCGCTTACTCT
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGA-CATGTTCCGCTTACTCT
* * *
295901 GAAGGGACTATCAGATCTGAGGAAGTTGATCCATTGAATCGAAGCAGAC
65 GAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAAGCAGAC
* * *
295950 TTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGATAGACATGCTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
* *
296015 AAGGGAATATCATATCTGGGGGAGTTAATCCATTGAATCGAAGCAGAC
66 AAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAAGCAGAC
* * *
296063 TTGTTCCACTTACTCTGAAGGGAATATCAAATATTAGAAAAAAGAGACATGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
** * *
296128 AAGGGAATATCTCATCTGGGGGAGTTAATCCATTGAATCAAAGCAGAC
66 AAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAAGCAGAC
* *
296176 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
* * * *
296241 AAGGGAATATCACAGCTGGGGGAGTTGATCCATTGAATC-AGGATAGAC
66 AAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAAG-CAGAC
* *
296289 TTGTTCCACTTACTTTGAAGGGAATATCAAATCTTGGATAAGAGAGACATGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
* *
296354 AAGGGAATATCAGATCTGGAGGAATTGATCCATTGAATCG
66 AAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCG
296394 GGACCGAACC
Statistics
Matches: 407, Mismatches: 34, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
112 3 0.01
113 404 0.99
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (113 bp):
TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
AAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAAGCAGAC
Found at i:297392 original size:162 final size:162
Alignment explanation
Indices: 297075--297398 Score: 616
Period size: 161 Copynumber: 2.0 Consensus size: 162
297065 TTAATCAGGA
297075 TGCTTGAAACGCAGTTAAAAATATCTATTTATTTATAAATAAAGAGTTTTTGGATGAATACATGA
1 TGCTTGAAACGCAGTTAAAAATATCTATTTATTTATAAATAAAGAGTTTTTGGATGAATACATGA
297140 CAAACTTTTAATTGGAATAATCAAAAGAAAACACAGTAGGCATTATCAAACATCAATAGTAAATG
66 CAAACTTTTAATTGGAATAATCAAAAGAAAACACAGTAGGCATTATCAAACATCAATAGTAAATG
297205 CTTTTGAATTGGCACGCCAATAAGAGGACCCG
131 CTTTTGAATTGGCACGCCAATAAGAGGACCCG
297237 TGCTTGAAACGCAGTTAAAAATATCTATTTATTTATAAATAAAGAG-TTTTGGATGAATACATGA
1 TGCTTGAAACGCAGTTAAAAATATCTATTTATTTATAAATAAAGAGTTTTTGGATGAATACATGA
297301 CAAACTTTTAATTGGAATAATCAAAAGAAAACACAGTAGGCATTATCAAACATCAATAGTACAAA
66 CAAACTTTTAATTGGAATAATCAAAAGAAAACACAGTAGGCATTATCAAACATCAATAGT--AAA
297366 TGCTTTTGAATTGGCACGCC-ATAAGAGGACCCG
129 TGCTTTTGAATTGGCACGCCAATAAGAGGACCCG
297399 AGTGTAGCTT
Statistics
Matches: 160, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
161 78 0.49
162 59 0.37
163 23 0.14
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (162 bp):
TGCTTGAAACGCAGTTAAAAATATCTATTTATTTATAAATAAAGAGTTTTTGGATGAATACATGA
CAAACTTTTAATTGGAATAATCAAAAGAAAACACAGTAGGCATTATCAAACATCAATAGTAAATG
CTTTTGAATTGGCACGCCAATAAGAGGACCCG
Found at i:297754 original size:12 final size:11
Alignment explanation
Indices: 297716--297765 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
297706 ATGAACCCTC
297716 CTTTTATTTTCT
1 CTTTTATTTT-T
297728 CTTTTA-TTTT
1 CTTTTATTTTT
*
297738 CTTTCATTTTT
1 CTTTTATTTTT
*
297749 CTTTTCTTTTT
1 CTTTTATTTTT
297760 CCTTTT
1 -CTTTT
297766 TTAGTCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 6 0.18
11 16 0.48
12 11 0.33
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (11 bp):
CTTTTATTTTT
Found at i:297773 original size:17 final size:17
Alignment explanation
Indices: 297739--297786 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
297729 TTTTATTTTC
**
297739 TTTCATTTTTCTTTTCTT
1 TTTCATTTTT-TAGTCTT
*
297757 TTTCCTTTTTTAGTCTT
1 TTTCATTTTTTAGTCTT
*
297774 TTTTATTTTTTAG
1 TTTCATTTTTTAG
297787 GCGAAATACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTCATTTTTTAGTCTT
Found at i:304418 original size:24 final size:25
Alignment explanation
Indices: 304381--304427 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
304371 TTTGTTCCCA
*
304381 TTCTTTCTTAATC-TCCTTATCCTG
1 TTCTTTCTTAATCTTCCTCATCCTG
* *
304405 TTCTTTTTTTATCTTCCTCATCC
1 TTCTTTCTTAATCTTCCTCATCC
304428 AAATCAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.11, C:0.30, G:0.02, T:0.57
Consensus pattern (25 bp):
TTCTTTCTTAATCTTCCTCATCCTG
Found at i:304907 original size:11 final size:11
Alignment explanation
Indices: 304893--304922 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
304883 TGCAATGTAG
304893 ATGCAATATGA
1 ATGCAATATGA
*
304904 ATGCAAGATGA
1 ATGCAATATGA
304915 ATGCAATA
1 ATGCAATA
304923 CAAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:308030 original size:40 final size:41
Alignment explanation
Indices: 307986--308065 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
307976 CAAACAAAAC
307986 TTATTTAAAACAAAAC-AAGGGATCAAAAACCAAATTAGAT
1 TTATTTAAAACAAAACAAAGGGATCAAAAACCAAATTAGAT
*
308026 TTATTTAAAACAAAACAAAGGGATCAAAAATCAAATTAGA
1 TTATTTAAAACAAAACAAAGGGATCAAAAACCAAATTAGA
308066 ACGAACTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 16 0.42
41 22 0.58
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.23
Consensus pattern (41 bp):
TTATTTAAAACAAAACAAAGGGATCAAAAACCAAATTAGAT
Found at i:314734 original size:10 final size:10
Alignment explanation
Indices: 314719--314775 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
314709 ACGAGCTATG
314719 CGAGGGCATC
1 CGAGGGCATC
*
314729 CGAGGGCAAC
1 CGAGGGCATC
*
314739 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
314752 CGAGGGAATC
1 CGAGGGCATC
*
314762 CGAGGGCAAC
1 CGAGGGCATC
314772 CGAG
1 CGAG
314776 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:314747 original size:33 final size:33
Alignment explanation
Indices: 314695--314779 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
314685 GACCATCCGA
* * * *
314695 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
314728 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
314761 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
314780 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.26, C:0.28, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:314835 original size:10 final size:10
Alignment explanation
Indices: 314816--314883 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
314806 CCTACCCTCG
*
314816 CTCGGTTGCC
1 CTCGGATGCC
314826 CTCGGATGCC
1 CTCGGATGCC
*
314836 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
314848 GTTCGGATGGC
1 -CTCGGATGCC
*
314859 CTCGGATGCT
1 CTCGGATGCC
*
314869 CTCGGATGGC
1 CTCGGATGCC
314879 CTCGG
1 CTCGG
314884 TCGAATGGCC
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
10 35 0.78
11 3 0.07
12 2 0.04
13 5 0.11
ACGTcount: A:0.09, C:0.34, G:0.32, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:314897 original size:34 final size:33
Alignment explanation
Indices: 314825--314902 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
314815 GCTCGGTTGC
* *
314825 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
1 CCTCGGATGCCCTCGCATAGCTCGGTCGAATGG
* * *
314858 CCTCGGATGCTCTCGGATGGCCTCGGTCGAATGG
1 CCTCGGATGCCCTCGCATAG-CTCGGTCGAATGG
314892 CCTCGGATGCC
1 CCTCGGATGCC
314903 AGCGTGTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
33 17 0.45
34 21 0.55
ACGTcount: A:0.12, C:0.33, G:0.32, T:0.23
Consensus pattern (33 bp):
CCTCGGATGCCCTCGCATAGCTCGGTCGAATGG
Done.