Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003718.1 Hibiscus syriacus cultivar Beakdansim tig00007951_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: 295015
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:1983 original size:124 final size:123
Alignment explanation
Indices: 1767--2060 Score: 387
Period size: 124 Copynumber: 2.4 Consensus size: 123
1757 GTTGAAGCCA
* * *
1767 CATGTTGAGATGACCAGATTCAGAACAAGTAGGCATTGAGAATGAGCCTTACAATTTGAGGTGAT
1 CATGTTGAGATGACAAGATTCAG-ACAAGGAGGCATTGAGAATGAGCCTTACAATTTAAGGTGAT
* * * * *
1832 GGGGCATTTTGAAGGCTCGTACGGTATAA-ATAATGTTGGGGGCATGATTGAACCCACAT
65 GGGGCATTTTGAAGGCCCATACAGTATAAGATAATGTT-GGGGCACGACTGAACCCACAT
* *
1891 CATGTTGAGATGAAAAGATTCAGACTACGGAGGCA-TGAAGAATGAGCCTTACAATTTAAGGTGA
1 CATGTTGAGATGACAAGATTCAGAC-AAGGAGGCATTG-AGAATGAGCCTTACAATTTAAGGTGA
1955 T-GGGCATTTTGAAGGCCCATACCAGTATAAGATAATGTTGGGGCACGACTGAACCCACAT
64 TGGGGCATTTTGAAGGCCCATA-CAGTATAAGATAATGTTGGGGCACGACTGAACCCACAT
* * **
2015 CATATTGAGATGACAAGATTCAGACCAAGAAGTTATTGAGAATGAG
1 CATGTTGAGATGACAAGATTCAGA-CAAGGAGGCATTGAGAATGAG
2061 TCTCACAACT
Statistics
Matches: 148, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
123 22 0.15
124 115 0.78
125 11 0.07
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.25
Consensus pattern (123 bp):
CATGTTGAGATGACAAGATTCAGACAAGGAGGCATTGAGAATGAGCCTTACAATTTAAGGTGATG
GGGCATTTTGAAGGCCCATACAGTATAAGATAATGTTGGGGCACGACTGAACCCACAT
Found at i:3211 original size:214 final size:215
Alignment explanation
Indices: 2837--3949 Score: 1794
Period size: 214 Copynumber: 5.2 Consensus size: 215
2827 TGAAGCAAAC
* * * * * *
2837 TCATTTGTAAGCCTTTAGGGCAAGATGATAAGTCCTTTGGGCCGTCCATAAGACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGG
2902 ATGTTTTCACATGAATTTGAAAAT-AAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
*
2966 AGAATGTAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
131 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
3031 TGATGCCTAATTCCTTCGGG
196 TGATGCTTAAATCCTTCGGG
* *
3051 TCATCTGTAAGCCTTTAGAGCAAGATGATAAATCCTTCGAGCCATCCGTAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGG
*
3116 ATGTTTTCACATGAATTTG-AAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
* * *
3180 AAAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
131 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
*
3245 TGATGCTTAAATCCTTCGGA
196 TGATGCTTAAATCCTTCGGG
* * * * *
3265 TAATCTATAAGCCTTTAGAGCAAGATGATAAATCCTTC-AGGTCATCCGTAAAACCTTCGGGTAG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGA-GCCATCCATAAAACCTTCGGGTAG
3329 GATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
65 GATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
* *
3394 AAAAATGTGATTTTCAAAATTTCAC-ATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGC
130 AAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
3458 ATGATGCTTAAATCCTTCGGG
195 ATGATGCTTAAATCCTTCGGG
* * * *
3479 TCATCTATAAGCCTTTAGATCAAGATGATAAGTCCTTCGGGCCATCCAT-AAACCTTTGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGG
*
3543 ATG-TTTCACATGAATTTGAAAATG-AAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
* *
3606 AGAATGTAATTTTCAAAATTTTACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
131 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
*
3671 TGATGCTTAAACCCTTCGGG
196 TGATGCTTAAATCCTTCGGG
* *
3691 TCATCTGTAAGCCTTT-GAGCAAGATGACAAGTCCTTC-AGGCCATCCATAAAACCTTCGGGTAT
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGA-GCCATCCATAAAACCTTCGGGTAG
* *
3754 GATATTTTCACATGAATTTGAAAATGAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAACG
65 GATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
*
3819 AAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
130 AAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
*
3884 ATGATGATTAAATCCTTCGGG
195 ATGATGCTTAAATCCTTCGGG
* *
3905 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCAT
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCAT
3950 TTTAAGCCTC
Statistics
Matches: 836, Mismatches: 52, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
211 87 0.10
212 109 0.13
213 43 0.05
214 506 0.61
215 91 0.11
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (215 bp):
TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
TGATGCTTAAATCCTTCGGG
Found at i:3851 original size:426 final size:429
Alignment explanation
Indices: 2837--3949 Score: 1833
Period size: 426 Copynumber: 2.6 Consensus size: 429
2827 TGAAGCAAAC
* * ** * *
2837 TCATTTGTAAGCCTTTAGGGCAAGATGATAAGTCCTTTGGGCCGTCCATAAGACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAAACCTTCGGGTAGG
2902 ATGTTTTCACATGAATTTGAAAAT-AAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
*
2966 AGAATGTAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
131 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* * * *
3031 TGATGCCTAATTCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAATCCTTCGAGCCAT
196 TGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCAT
*
3096 CCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAATGAAAAAATGATGTTTTAAGAAG
261 CCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAATGAAAAAATGATGTTTTAAGAAG
*
3161 ATGGAATTTTTGAAAACAAAAAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCA
326 ATGGAATTTTTGAAAACAAAAAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCA
*
3226 TCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGA
391 TCAATAAGTCTTTCGAGCATGATGCTTAAACCCTTCGGA
* * * * *
3265 TAATCTATAAGCCTTTAGAGCAAGATGATAAATCCTTCAGGTCATCCGTAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAAACCTTCGGGTAGG
3330 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
* *
3395 AAAATGTGATTTTCAAAATTTCAC-ATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCA
131 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
3459 TGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTAGATCAAGATGATAAGTCCTTCGGGCCAT
196 TGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCAT
* *
3524 CCAT-AAACCTTTGGGTAGGATG-TTTCACATGAATTTGAAAATG-AAAAGTGATGTTTTAAGAA
261 CCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTG-AAATGAAAAAATGATGTTTTAAGAA
* * * *
3586 GATGGAATTTTTGAAAACGAAGAATGTAATTTTCAAAATTTTACAATTTATAAGTCCTTCGGGCC
325 GATGGAATTTTTGAAAACAAAAAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCC
* *
3651 ATCAGTAAGTCTTTCGAGCATGATGCTTAAACCCTTCGGG
390 ATCAATAAGTCTTTCGAGCATGATGCTTAAACCCTTCGGA
* *
3691 TCATCTGTAAGCCTTT-GAGCAAGATGACAAGTCCTTCAGGCCATCCATAAAACCTTCGGGTATG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAAACCTTCGGGTAGG
* *
3755 ATATTTTCACATGAATTTGAAAATGAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
*
3820 AGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
131 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
3885 TGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCAT
196 TGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCAT
3950 TTTAAGCCTC
Statistics
Matches: 635, Mismatches: 47, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
425 128 0.20
426 244 0.38
427 22 0.03
428 179 0.28
429 62 0.10
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (429 bp):
TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
TGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCAT
CCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAATGAAAAAATGATGTTTTAAGAAG
ATGGAATTTTTGAAAACAAAAAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCA
TCAATAAGTCTTTCGAGCATGATGCTTAAACCCTTCGGA
Found at i:3915 original size:42 final size:42
Alignment explanation
Indices: 3854--3949 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
3844 AATTTATAAG
* * *
3854 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATTAAA
* * *
3896 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA-TAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATTAAA
*
3937 TCATTCGGGCCAT
1 TCCTTCGGGCCAT
3950 TTTAAGCCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 14 0.30
42 32 0.70
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATTAAA
Found at i:4080 original size:55 final size:55
Alignment explanation
Indices: 3957--4081 Score: 207
Period size: 56 Copynumber: 2.2 Consensus size: 55
3947 CATTTTAAGC
3957 CTCCTTGAAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTCTTGAGTTCTATA
1 CTCC-TGAAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTCTTGAGTTCTATA
*
4013 CTCTCTGAAAGGAATAGGGAGCGAACCCGTTTTCAGAA-ATTTCTTGAGTTCTATA
1 CTC-CTGAAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTCTTGAGTTCTATA
4068 CTCCATGAAAGGAA
1 CTCC-TGAAAGGAA
4082 CATGAAGTAA
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
54 1 0.02
55 29 0.44
56 35 0.53
57 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (55 bp):
CTCCTGAAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTTCTTGAGTTCTATA
Found at i:8671 original size:8 final size:9
Alignment explanation
Indices: 8656--8695 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
8646 TCATTCATCA
*
8656 GAAAAAAAA
1 GAAAAAAAG
8665 GAAAAAAAG
1 GAAAAAAAG
8674 G-AAAAAAG
1 GAAAAAAAG
8682 GAAAAAAAG
1 GAAAAAAAG
8691 GAAAA
1 GAAAA
8696 GACGAGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:8680 original size:17 final size:17
Alignment explanation
Indices: 8658--8695 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
8648 ATTCATCAGA
8658 AAAAAAAGAAAAAAAGG
1 AAAAAAAGAAAAAAAGG
*
8675 AAAAAAGGAAAAAAAGG
1 AAAAAAAGAAAAAAAGG
8692 AAAA
1 AAAA
8696 GACGAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGG
Found at i:8695 original size:7 final size:8
Alignment explanation
Indices: 8659--8695 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
8649 TTCATCAGAA
*
8659 AAAAAAGA
1 AAAAAAGG
8667 AAAAAAGG
1 AAAAAAGG
8675 AAAAAAGG
1 AAAAAAGG
8683 AAAAAAAGG
1 -AAAAAAGG
8692 AAAA
1 AAAA
8696 GACGAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:11890 original size:10 final size:9
Alignment explanation
Indices: 11855--11947 Score: 78
Period size: 10 Copynumber: 9.7 Consensus size: 9
11845 GCTGCTGGAA
*
11855 ACCGGTTTA
1 ACCGGTTTG
*
11864 ACCGGTTTTCA
1 ACCGG-TTT-G
11875 ACCGGTTCTG
1 ACCGGTT-TG
11885 ACCGGTTTG
1 ACCGGTTTG
*
11894 ACCGGTTTCA
1 ACCGGTTT-G
*
11904 ACCGGTTCG
1 ACCGGTTTG
11913 AACCGGTTTG
1 -ACCGGTTTG
*
11923 ACCGGTCTG
1 ACCGGTTTG
*
11932 AATCGGTTTG
1 -ACCGGTTTG
11942 ACCGGT
1 ACCGGT
11948 CCGACCCGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
9 28 0.41
10 34 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:11899 original size:19 final size:20
Alignment explanation
Indices: 11855--11947 Score: 95
Period size: 19 Copynumber: 4.8 Consensus size: 20
11845 GCTGCTGGAA
* * *
11855 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
11875 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
11894 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
11914 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
*
11933 ATCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
11948 CCGACCCGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:11917 original size:29 final size:30
Alignment explanation
Indices: 11854--11928 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
11844 GGCTGCTGGA
*
11854 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
11885 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
11913 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
11929 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:11938 original size:29 final size:28
Alignment explanation
Indices: 11855--11947 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
11845 GCTGCTGGAA
* *
11855 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
11885 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
11913 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTCTCAACCGGTTCG
11942 ACCGGT
1 ACCGGT
11948 CCGACCCGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 7 0.12
29 37 0.65
30 13 0.23
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:11958 original size:5 final size:5
Alignment explanation
Indices: 11948--12029 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
11938 TTTGACCGGT
* *
11948 CCGAC CCGAC CCGAC CTTTGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC
1 CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C--CGAC CCGAC
*
11997 CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C
12030 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.18, C:0.52, G:0.21, T:0.09
Consensus pattern (5 bp):
CCGAC
Found at i:11973 original size:22 final size:22
Alignment explanation
Indices: 11948--12036 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
11938 TTTGACCGGT
*
11948 CCGACCCGACCCGACCTTTGAC
1 CCGACCCGACCCGACCGTTGAC
11970 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
11992 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
12014 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
12036 C
1 C
12037 GTTGACCGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:19213 original size:9 final size:9
Alignment explanation
Indices: 19199--19291 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
19189 GGCTGCTGGA
19199 AACCGGTTT
1 AACCGGTTT
19208 AACCGGTTTT
1 AACCGG-TTT
19218 CAACCGGTTCT
1 -AACCGGTT-T
*
19229 GACCGGTTT
1 AACCGGTTT
*
19238 GACCGGTTT
1 AACCGGTTT
*
19247 CAACC-GTTCG
1 -AACCGGTT-T
19257 AACCGGTTT
1 AACCGGTTT
* *
19266 GACCGGTCTG
1 AACCGGT-TT
*
19276 AATCGGTTT
1 AACCGGTTT
*
19285 GACCGGT
1 AACCGGT
19292 CCGACCCGAC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
9 35 0.53
10 24 0.36
11 7 0.11
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:19224 original size:20 final size:21
Alignment explanation
Indices: 19199--19237 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19189 GGCTGCTGGA
19199 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
19219 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
19238 GACCGGTTTC
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:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:19244 original size:19 final size:20
Alignment explanation
Indices: 19200--19291 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 20
19190 GCTGCTGGAA
* * *
19200 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
19220 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
19239 ACCGGTTTCAACC-GTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
19258 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
*
19277 ATCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
19292 CCGACCCGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.17
19 34 0.57
20 8 0.13
21 8 0.13
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:19264 original size:28 final size:30
Alignment explanation
Indices: 19199--19272 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 30
19189 GGCTGCTGGA
*
19199 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
19230 -ACCGGTTTGACCGGTTTCAACC-GTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
19257 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
19273 CTGAATCGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 1 0.02
28 19 0.46
29 8 0.20
30 13 0.32
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:19289 original size:28 final size:27
Alignment explanation
Indices: 19200--19291 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 27
19190 GCTGCTGGAA
* *
19200 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAA-CGGTT-TG
* * *
19230 ACCGGTTTGACCGGTTTCAACCGTTCG
1 ACCGGTTTGACCGGTCTCAACGGTTTG
*
19257 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTCTCAA-CGGTTTG
19286 ACCGGT
1 ACCGGT
19292 CCGACCCGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 28 0.53
29 11 0.21
30 13 0.25
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (27 bp):
ACCGGTTTGACCGGTCTCAACGGTTTG
Found at i:19302 original size:5 final size:5
Alignment explanation
Indices: 19292--19373 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
19282 TTTGACCGGT
* *
19292 CCGAC CCGAC CCGAC CTTTGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC
1 CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C--CGAC CCGAC
*
19341 CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C
19374 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.18, C:0.52, G:0.21, T:0.09
Consensus pattern (5 bp):
CCGAC
Found at i:19317 original size:22 final size:22
Alignment explanation
Indices: 19292--19380 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
19282 TTTGACCGGT
*
19292 CCGACCCGACCCGACCTTTGAC
1 CCGACCCGACCCGACCGTTGAC
19314 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
19336 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
19358 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
19380 C
1 C
19381 GTTGACCGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:22855 original size:113 final size:113
Alignment explanation
Indices: 22700--23110 Score: 653
Period size: 113 Copynumber: 3.6 Consensus size: 113
22690 ATTTCCAGAG
* *
22700 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTATT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
22765 CAACCTTTTACTTGAATTCATCATTCGATGGATCATCATGGCCAGGTA
66 CAACCTTTTACTCGAATTCATCATTCGATGGATCAGCATTGCCAGGTA
* *
22813 GAGTTCATAATTAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
22878 CAACCTTTTTCTCGAATTCATCACTCGATGGATCAGCATTACCAGGTA
66 CAACCTTTTACTCGAATTCATCATTCGATGGATCAGCATTGCCAGGTA
* * *
22926 GAGTTCATAATGAGAAAAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
22991 CAACCTTTTGCTCGAATTCATCATTCAATGGATCAGCATTGCCAGGTA
66 CAACCTTTTACTCGAATTCATCATTCGATGGATCAGCATTGCCAGGTA
* * *
23039 GAGTTTATAATGAGAAGAACTTATCTGAAG-AGGTAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
23103 CAACCTTT
66 CAACCTTT
23111 GCATGATTCT
Statistics
Matches: 273, Mismatches: 25, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
112 40 0.15
113 233 0.85
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTACTCGAATTCATCATTCGATGGATCAGCATTGCCAGGTA
Found at i:23187 original size:122 final size:119
Alignment explanation
Indices: 22684--23221 Score: 368
Period size: 113 Copynumber: 4.7 Consensus size: 119
22674 TACTCAATGG
* * *
22684 ATCAACATTTCCAGAG-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
* * * * * *
22748 AATGAGAAGAACTTATTCAACCTTTTACTTGAATTC-AT--C----A-TTCGAT-GG
65 AATGAGAAGAACTTGTTCAACC-TTTGCATG-ATTCTATCACAAAGAGATAGATAGC
* ** * * * *
22796 ATCATCATGGCCAG-GTAGAGTTCATAATTAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCA
* * *
22860 TAATGAGAAGAACTTGTTCAACCTTTTTC-TCGAATTC-ATCAC-------TCGAT-GG
64 TAATGAGAAGAACTTGTTCAACC-TTTGCAT-G-ATTCTATCACAAAGAGATAGATAGC
* * * * * *
22909 ATCAGCATTACCAG-GTAGAGTTCATAATGAGAAAAACTCATTTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCA
* ***
22973 TAATAAGAAGAACTTGTTCAACCTTTTGC-TCGAATTC-AT--CATTCA-AT-G---G-
64 TAATGAGAAGAACTTGTTCAACC-TTTGCAT-G-ATTCTATCACAAAGAGATAGATAGC
* * * * *
23022 ATCAGCATTGCCAG-GTAGAGTTTATAATGAGAAGAACTTATCTGAAGAGGTAGAAGAAGTTCAT
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
23086 AATGAGAAGAACTTGTTCAACCTTTGCATGATTCTATCACAGAAGGAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTGCATGATTCTATCACA-AA-GAGATAGAT-AGC
* *
23144 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
23209 ATGAGAAGAACTT
66 ATGAGAAGAACTT
23222 CATAATGAGA
Statistics
Matches: 367, Mismatches: 34, Indels: 40
0.83 0.08 0.09
Matches are distributed among these distances:
110 4 0.01
111 10 0.03
112 50 0.14
113 224 0.61
114 1 0.00
115 2 0.01
116 3 0.01
117 2 0.01
121 1 0.00
122 69 0.19
123 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (119 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTGCATGATTCTATCACAAAGAGATAGATAGC
Found at i:23217 original size:17 final size:17
Alignment explanation
Indices: 23195--23238 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
23185 CTGAAGAGGA
*
23195 AGAAGAAGTTCATAATG
1 AGAAGAACTTCATAATG
23212 AGAAGAACTTCATAATG
1 AGAAGAACTTCATAATG
23229 AGAAGAACTT
1 AGAAGAACTT
23239 GTTCAACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (17 bp):
AGAAGAACTTCATAATG
Found at i:23327 original size:140 final size:139
Alignment explanation
Indices: 23073--23361 Score: 479
Period size: 140 Copynumber: 2.1 Consensus size: 139
23063 CTGAAGAGGT
* * *
23073 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCATGATTCTATCACAGAAGGAGATAG
1 AGAAGAACTTCATAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAG
* * *
23138 ATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAG
66 ATCAGCACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAG
23203 TTCATAATG
131 TTCATAATG
*
23212 AGAAGAACTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAAGAGATA
1 AGAAGAACTTCATAATGAGAAGAACTTGTTCAACC-TTTGCATGACTCTATCACAGAAAGAGATA
* * *
23277 GATCAGCACCAACATTTCTAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAA
65 GATCAGCACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAA
23342 GTTCATAATG
130 GTTCATAATG
23352 AGAAGAACTT
1 AGAAGAACTT
23362 GTTCAACCTT
Statistics
Matches: 139, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
139 34 0.24
140 105 0.76
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (139 bp):
AGAAGAACTTCATAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAG
ATCAGCACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAG
TTCATAATG
Found at i:23365 original size:20 final size:20
Alignment explanation
Indices: 23303--23366 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23293 TCTAGATAAA
23303 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
23323 -ATC-TGAA-GAGGAAGAAAAA
1 GTTCAT-AATGA-GAAGAACTT
23342 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
23362 GTTCA
1 GTTCA
23367 ACCTTTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:23478 original size:20 final size:20
Alignment explanation
Indices: 23416--23479 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23406 CCACAGAAAA
23416 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
23436 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
23455 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
23475 GTTCA
1 GTTCA
23480 ACCTTTTGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:23962 original size:3 final size:3
Alignment explanation
Indices: 23954--24001 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
23944 TTTCCATTTG
**
23954 ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT AAAA ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
24001 A
1 A
24002 CATTACAGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 35 0.90
4 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:25675 original size:25 final size:25
Alignment explanation
Indices: 25633--25680 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
25623 TAGTCATATA
25633 AATATATGTATATATATTGTTTAAAT
1 AATATATGTATATATATT-TTTAAAT
* *
25659 AATA-ATGTTTATTTATTTTTAA
1 AATATATGTATATATATTTTTAA
25681 TATCAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 11 0.55
26 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (25 bp):
AATATATGTATATATATTTTTAAAT
Found at i:37528 original size:41 final size:41
Alignment explanation
Indices: 37471--37551 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
37461 GAATATAAGG
*
37471 GACATAAATCAAGTGCACTGTATTTATAGGTTTAGAAAATA
1 GACATAAATCAAGTGCACTGTATTTAGAGGTTTAGAAAATA
37512 GACATAAATCAAGTGCACTGTATTTAGAGGTTTAGAAAAT
1 GACATAAATCAAGTGCACTGTATTTAGAGGTTTAGAAAAT
37552 GGAACATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (41 bp):
GACATAAATCAAGTGCACTGTATTTAGAGGTTTAGAAAATA
Found at i:42739 original size:5 final size:5
Alignment explanation
Indices: 42733--42837 Score: 138
Period size: 5 Copynumber: 20.8 Consensus size: 5
42723 TTTAGATTCT
* * * * * * *
42733 TTTCT TTTCA TTTCG TTTCT TTTCT TTTCA TTTCG TTTCT TTTCT TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
42783 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA -TTTCA TTTCA TTTCA TTTCA
42834 TTTC
1 TTTC
42838 GGTCACCACA
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
5 87 0.95
6 5 0.05
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (5 bp):
TTTCA
Found at i:42754 original size:20 final size:20
Alignment explanation
Indices: 42729--42837 Score: 155
Period size: 20 Copynumber: 5.4 Consensus size: 20
42719 AAGCTTTAGA
*
42729 TTCTTTTCTTTTCATTTCGT
1 TTCTTTTCTTTTCATTTCAT
*
42749 TTCTTTTCTTTTCATTTCGT
1 TTCTTTTCTTTTCATTTCAT
42769 TTCTTTTCTTTTCATTTCAT
1 TTCTTTTCTTTTCATTTCAT
* *
42789 TTCATTTCATTTCATTTCAT
1 TTCTTTTCTTTTCATTTCAT
*
42809 TTCATTTTCATTTCATTTCAT
1 TTC-TTTTCTTTTCATTTCAT
*
42830 TTCATTTC
1 TTCTTTTC
42838 GGTCACCACA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 64 0.77
21 19 0.23
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (20 bp):
TTCTTTTCTTTTCATTTCAT
Found at i:43766 original size:41 final size:40
Alignment explanation
Indices: 43655--43992 Score: 241
Period size: 41 Copynumber: 8.3 Consensus size: 40
43645 GCTACGAGTC
* * *
43655 TTTAGCGGCGTTTTTATAAAAACGCCACCAAAGAACGAGTCT-
1 TTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC-A-T-TA
* *
43697 TTTGGCGGTGTTTGTATAAAAACGCCACTAAAGTACATTA
1 TTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATTA
* * * *
43737 TTTAACGGCGTTTGTGCTTAAAATGCCACTAAAGTACATTA
1 TTTAGCGGCGTTTGT-ATAAAAACGCCACTAAAGTACATTA
* * * * *
43778 TTTAGCGGTGTTTATATAAAAACGCTACTAAAGTACGAGTC
1 TTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC-ATTA
* * * *
43819 TTT-GATGGTGTTTGTATAAAAACGCCACTAAAATACAATA
1 TTTAG-CGGCGTTTGTATAAAAACGCCACTAAAGTACATTA
** * ** * *
43859 TTTAGTAGCGTTTATATAAAAACAACACTTAAGTACGAGTA
1 TTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC-ATTA
* * * ** *
43900 TTTAGCGACGTTTGTGCTTAAAACGCCACTAAAGTTTGAGTCA
1 TTTAGCGGCGTTTGT-ATAAAAACGCCACTAAAG-TACA-TTA
* ** * *
43943 -TTAGCGGCATTTGTGCAAAAATGCCACTAAAGTACAATA
1 TTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATTA
43982 TTTAGCGGCGT
1 TTTAGCGGCGT
43993 ATGTTCAAAA
Statistics
Matches: 228, Mismatches: 58, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
39 2 0.01
40 71 0.31
41 96 0.42
42 57 0.25
43 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (40 bp):
TTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACATTA
Found at i:43787 original size:81 final size:82
Alignment explanation
Indices: 43701--43934 Score: 265
Period size: 81 Copynumber: 2.9 Consensus size: 82
43691 GAGTCTTTTG
* * * *
43701 GCGGTGTTTGTATAAAAACGCCACTAAAGTAC-ATTATTTAACGGCGTTTGTGCTTAAAATGCCA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAACGGCGTTTGTGCTTAAAACGCCA
43765 CTAAAGTACATTATTTA
66 CTAAAGTACATTATTTA
* * * * * * * *
43782 GCGGTGTTTATATAAAAACGCTACTAAAGTACGAGTCTTTGATGGTGTTTGT-ATAAAAACGCCA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAACGGCGTTTGTGCTTAAAACGCCA
* *
43846 CTAAAATACAATATTTA
66 CTAAAGTACATTATTTA
** ** * * *
43863 GTAGCGTTTATATAAAAACAACACTTAAGTACGAGTATTTAGCGACGTTTGTGCTTAAAACGCCA
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAACGGCGTTTGTGCTTAAAACGCCA
43928 CTAAAGT
66 CTAAAGT
43935 TTGAGTCATT
Statistics
Matches: 123, Mismatches: 28, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
81 93 0.76
82 30 0.24
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (82 bp):
GCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAACGGCGTTTGTGCTTAAAACGCCA
CTAAAGTACATTATTTA
Found at i:43902 original size:122 final size:124
Alignment explanation
Indices: 43647--43912 Score: 313
Period size: 122 Copynumber: 2.2 Consensus size: 124
43637 ATATAAACGC
* * *
43647 TACGAGTCTTTAGCGGCGTTTTTATAAAAACGCCACCAAAGAACGAGTCTTTTGGCGGTGTTTGT
1 TACGAGTATTTAGCGGCGTTTATATAAAAACGCCACCAAAGAACGAGTCTTTTGACGGTGTTTGT
* * * * * * ***
43712 ATAAAAACGCCACTAAAGTACATTATTTAACGGCGTTTGTGCTTAAAATGCCACTAAAG
66 ATAAAAACGCCACTAAAATACAATATTTAACAGCGTTTATGATAAAAACAACACTAAAG
* * * * * *
43771 TAC-ATTATTTAGCGGTGTTTATATAAAAACGCTACTAAAGTACGAGTC-TTTGATGGTGTTTGT
1 TACGAGTATTTAGCGGCGTTTATATAAAAACGCCACCAAAGAACGAGTCTTTTGACGGTGTTTGT
** *
43834 ATAAAAACGCCACTAAAATACAATATTTAGTAGCGTTTAT-ATAAAAACAACACTTAAG
66 ATAAAAACGCCACTAAAATACAATATTTAACAGCGTTTATGATAAAAACAACACTAAAG
*
43892 TACGAGTATTTAGCGACGTTT
1 TACGAGTATTTAGCGGCGTTT
43913 GTGCTTAAAA
Statistics
Matches: 117, Mismatches: 24, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
121 15 0.13
122 61 0.52
123 38 0.32
124 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (124 bp):
TACGAGTATTTAGCGGCGTTTATATAAAAACGCCACCAAAGAACGAGTCTTTTGACGGTGTTTGT
ATAAAAACGCCACTAAAATACAATATTTAACAGCGTTTATGATAAAAACAACACTAAAG
Found at i:44614 original size:58 final size:58
Alignment explanation
Indices: 44519--44630 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
44509 CTCAAAACAC
* *
44519 TTGAAGTTTCTGAGTGTGATGAAATGGAAGAGATGATACAAGGAATATTAGGAGTGTT
1 TTGAAGTTTCTAAGTGTGATGAAATGAAAGAGATGATACAAGGAATATTAGGAGTGTT
*
44577 TTGAAGTTTCTAAGTGTGATGAAATGAAAGAGGTGATACAAGGAATATTAGGAG
1 TTGAAGTTTCTAAGTGTGATGAAATGAAAGAGATGATACAAGGAATATTAGGAG
44631 AAGAAGAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.29
Consensus pattern (58 bp):
TTGAAGTTTCTAAGTGTGATGAAATGAAAGAGATGATACAAGGAATATTAGGAGTGTT
Found at i:46603 original size:31 final size:31
Alignment explanation
Indices: 46561--46678 Score: 227
Period size: 31 Copynumber: 3.8 Consensus size: 31
46551 AGGGTCGAGG
46561 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
46592 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46623 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46654 GTTTACCTATGTTCTTCGGGACATA
1 GTTTACCTATGTTCTTCGGGACATA
46679 AGTAATGTGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:46820 original size:202 final size:201
Alignment explanation
Indices: 46474--46879 Score: 785
Period size: 202 Copynumber: 2.0 Consensus size: 201
46464 AAGAATATGA
46474 ATAAGTAATGTGAACTGTTATAAATGATAATGCCCATGTTATGTGATATAAGAGCTAGGGGTATA
1 ATAAGTAATGTGAACTGTTATAAATGATAATGCCCATGTTATGTGATATAAGAGCTAGGGGTATA
46539 GTTGGCATGCCAAGGGTCGAGGGTTTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGT
66 GTTGGCATGCCAAGGGTCGAGGGTTTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGT
46604 TCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCT
131 TCTTCGGGACATATGGACTG-TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCT
46669 TCGGGAC
195 TCGGGAC
*
46676 ATAAGTAATGTGAACTGTTATAAATGATAATGCCCATGTTATGTGATATGAGAGCTAGGGGTATA
1 ATAAGTAATGTGAACTGTTATAAATGATAATGCCCATGTTATGTGATATAAGAGCTAGGGGTATA
*
46741 GTTGGCATGCCAAGGGTCGAGGGTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGT
66 GTTGGCATGCCAAGGGTCGAGGGTTTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGT
46806 TCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTT
131 TCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTT
46871 CGGGAC
196 CGGGAC
46877 ATA
1 ATA
46880 TGGACTGTTT
Statistics
Matches: 202, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
201 54 0.27
202 148 0.73
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (201 bp):
ATAAGTAATGTGAACTGTTATAAATGATAATGCCCATGTTATGTGATATAAGAGCTAGGGGTATA
GTTGGCATGCCAAGGGTCGAGGGTTTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGT
TCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTT
CGGGAC
Found at i:46979 original size:31 final size:31
Alignment explanation
Indices: 46763--46964 Score: 379
Period size: 31 Copynumber: 6.5 Consensus size: 31
46753 AGGGTCGAGG
46763 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46794 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46825 G-TTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46855 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46886 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
46917 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
46948 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
46965 AGAATCTATG
Statistics
Matches: 168, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
30 30 0.18
31 138 0.82
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:50045 original size:13 final size:13
Alignment explanation
Indices: 50045--50076 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
50035 CCGTTGACCC
50045 GACCCGACCCGTT
1 GACCCGACCCGTT
*
50058 TACCCGACCCGTT
1 GACCCGACCCGTT
50071 GACCCG
1 GACCCG
50077 TTGACCGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:50049 original size:18 final size:18
Alignment explanation
Indices: 50026--50082 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
50016 GGTCACAACT
50026 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
50044 CGACCCGACCCGTTTACC
1 CGACCCGACCCGTTGACC
50062 CGACCCGTTGACCCGTTGACC
1 CGACCC---GACCCGTTGACC
50083 GTTGACCGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:50086 original size:15 final size:16
Alignment explanation
Indices: 50066--50099 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
50056 TTTACCCGAC
50066 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
50081 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
50098 CC
1 CC
50100 ACTATTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:51429 original size:18 final size:18
Alignment explanation
Indices: 51403--51437 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51393 TCGAAAGGAC
*
51403 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
51421 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
51438 CCGGATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:52665 original size:24 final size:24
Alignment explanation
Indices: 52547--52662 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
52537 TTCTATTTGA
52547 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
52571 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
52595 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
52619 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
52643 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
52663 CTGATTTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:52882 original size:2 final size:2
Alignment explanation
Indices: 52875--52900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52865 TTGGATGGGG
52875 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
52901 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63910 original size:17 final size:18
Alignment explanation
Indices: 63888--63927 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
63878 ATAATTCTAA
* *
63888 ATTAAAACCTT-TAATTT
1 ATTAAAACATTCTAAATT
63905 ATTAAAACATTCTAAATT
1 ATTAAAACATTCTAAATT
63923 ATTAA
1 ATTAA
63928 TATACTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAAAACATTCTAAATT
Found at i:66500 original size:32 final size:32
Alignment explanation
Indices: 66464--66528 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
66454 TAAGATAGTT
66464 TCATATGCTATACTTATTCACTAAAGTACTTC
1 TCATATGCTATACTTATTCACTAAAGTACTTC
66496 TCATATGCTATACTTATTCACTAAAGTACTTC
1 TCATATGCTATACTTATTCACTAAAGTACTTC
66528 T
1 T
66529 TCAACTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (32 bp):
TCATATGCTATACTTATTCACTAAAGTACTTC
Found at i:66961 original size:39 final size:39
Alignment explanation
Indices: 66905--66981 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
66895 CTTTAAAGAG
* * * *
66905 TGGTAACTATTTTTTATTACCCTTTAATTTTTATTTGTA
1 TGGTAACTATTTCTTATTACCCCTTAAATTTTACTTGTA
*
66944 TGGTAATTATTTCTTATTACCCCTTAAATTTTACTTGT
1 TGGTAACTATTTCTTATTACCCCTTAAATTTTACTTGT
66982 TTACCTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (39 bp):
TGGTAACTATTTCTTATTACCCCTTAAATTTTACTTGTA
Found at i:73883 original size:20 final size:20
Alignment explanation
Indices: 73846--73907 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 20
73836 ATTCGTTCAT
** *
73846 TTATGTTCGTGAACGTTCGG
1 TTATGTTCGTTTATGTTCGG
73866 TTATGTTCGTTTATGTTCGTTCGG
1 TTATGTTCGTTTA---T-GTTCGG
73890 TTATGTTCGTTTATGTTC
1 TTATGTTCGTTTATGTTC
73908 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 15 0.43
21 1 0.03
24 19 0.54
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.52
Consensus pattern (20 bp):
TTATGTTCGTTTATGTTCGG
Found at i:73886 original size:24 final size:24
Alignment explanation
Indices: 73859--73907 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
73849 TGTTCGTGAA
73859 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
73883 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
73907 C
1 C
73908 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:73887 original size:14 final size:14
Alignment explanation
Indices: 73859--73900 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
73849 TGTTCGTGAA
73859 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
73873 CG-T---TTATGTT
1 CGTTCGGTTATGTT
73883 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
73897 CGTT
1 CGTT
73901 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:73917 original size:24 final size:24
Alignment explanation
Indices: 73865--73920 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
73855 TGAACGTTCG
* *
73865 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
73889 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
73913 TTTATGTT
1 GTTATGTT
73921 TAACACAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:74673 original size:16 final size:16
Alignment explanation
Indices: 74650--74726 Score: 136
Period size: 16 Copynumber: 4.8 Consensus size: 16
74640 GGGTCTCCAA
74650 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
74666 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
74682 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
74698 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
74714 TGTTTATGTTCGT
1 CGTTTATGTTCGT
74727 TTATTTATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 58 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:74707 original size:26 final size:26
Alignment explanation
Indices: 74678--74730 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
74668 TTTATGTTCG
*
74678 TGTTCGT-TTATGTTCGTGTTCGTTTA
1 TGTTCGTGTT-TGTTCATGTTCGTTTA
*
74704 TGTTCGTGTTTGTTTATGTTCGTTTA
1 TGTTCGTGTTTGTTCATGTTCGTTTA
74730 T
1 T
74731 TTATTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.08, C:0.09, G:0.23, T:0.60
Consensus pattern (26 bp):
TGTTCGTGTTTGTTCATGTTCGTTTA
Found at i:81649 original size:30 final size:29
Alignment explanation
Indices: 81615--81679 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
81605 ACACAATTAT
81615 CACCCTAATAGA-AATTAATTACAAAACTAA
1 CACCCTAATA-ACAA-TAATTACAAAACTAA
** *
81645 CACCCTTTTAACAATATTTACAAAACTAA
1 CACCCTAATAACAATAATTACAAAACTAA
81674 CACCCT
1 CACCCT
81680 TTTTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (29 bp):
CACCCTAATAACAATAATTACAAAACTAA
Found at i:81667 original size:29 final size:29
Alignment explanation
Indices: 81633--81705 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
81623 TAGAAATTAA
81633 TTACAAAACTAACACCC-TTTTAACAATAT
1 TTACAAAACTAACACCCTTTTTAA-AATAT
*
81662 TTACAAAACTAACACCCTTTTTTAAATAT
1 TTACAAAACTAACACCCTTTTTAAAATAT
*
81691 TTAAAAAACTAACAC
1 TTACAAAACTAACAC
81706 TCGGTCAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 36 0.88
30 5 0.12
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.32
Consensus pattern (29 bp):
TTACAAAACTAACACCCTTTTTAAAATAT
Found at i:88826 original size:29 final size:29
Alignment explanation
Indices: 88792--88866 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
88782 TAGAAATTAA
88792 TTACAAAACTAACACCC-TTTTAACAATAT
1 TTACAAAACTAACACCCTTTTTAA-AATAT
*
88821 TTACAAAACTAACACCCTTTTTTAAATAT
1 TTACAAAACTAACACCCTTTTTAAAATAT
88850 TTACAAAACTAACACCC
1 TTACAAAACTAACACCC
88867 GGTCAACGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 39 0.89
30 5 0.11
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (29 bp):
TTACAAAACTAACACCCTTTTTAAAATAT
Found at i:97844 original size:567 final size:567
Alignment explanation
Indices: 96769--97900 Score: 1940
Period size: 567 Copynumber: 2.0 Consensus size: 567
96759 GCTGCCAAAA
* * *
96769 ATATTTAAATAACGTAAAAGAATTTTGGATATTTCAATGATAGCAAAAACTAGTACTTAATATTT
1 ATATTTAAATAACGTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
* * *
96834 TAATTAAAGAAAAATTGATATAAATAATTATCGATTTCAGTGATAATACAAAAATAAATATATTT
66 TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAAAAATAAACATATTT
* *
96899 TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGAGAGTGGAGGAATGCCATAAGTTGAAG
131 TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGACAATGGAGGAATGCCATAAGTTGAAG
* * *
96964 TGTGTGTTTAGTTCATCTACGGTTAAAAGCTTTGTTCAACTCAAAGAACTTCTAGTTTCTGATTG
196 TATGTATTTAGTTCATCTACGGTTAAAAGCTTTGTTCAACTCAAAGAACTTCAAGTTTCTGATTG
* * *
97029 TGATGAACTGGAAGAGGTAATGCAAGGAGTATTAGGAGAAGAAAGGATTAGAAGCTTCATAAGTC
261 TGATGAACTGGAAGAGGTAATACAAGGAGTATTAGGAGAAGAAAGGATTAGAAGCTGCACAAGTC
* ** *
97094 TGTTTCCTACACTTGACTACTTGTGGCTCGAACAACTTTCCAAAATCACAAGGTTTTGTAGTGGA
326 TGTTTCCTAAACTTGACTACTTGCAGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
*
97159 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATTTGGGGATGTCGTGGTTTGAG
391 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
*
97224 CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATGACATCTCACTTGATCAAC
456 CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATAACATCTCACTTGATCAAC
97289 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTTGG
521 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTTGG
*
97336 ATATTTAAATAACTTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
1 ATATTTAAATAACGTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
*
97401 TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAGAAATAAACATATTT
66 TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAAAAATAAACATATTT
* * *
97466 TTCATTTGCAGGTTTCATGTTCTGCCTTGGAGACGTTGACAATGGTGGGATGCCATAAGTTGAAG
131 TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGACAATGGAGGAATGCCATAAGTTGAAG
* *
97531 TATGTATTTAGTTCATCTACGGTTAAAAGCTTTGTTCAACTCCAAGAACTTGAAGTTTCTGATTG
196 TATGTATTTAGTTCATCTACGGTTAAAAGCTTTGTTCAACTCAAAGAACTTCAAGTTTCTGATTG
97596 TGATGAACTGGAAGAGGTAATACAAGGAGTATTAGGAGAAGAAAGGATTAGAAGCTGCACAAGTC
261 TGATGAACTGGAAGAGGTAATACAAGGAGTATTAGGAGAAGAAAGGATTAGAAGCTGCACAAGTC
* * * *
97661 TGTTTCCTAAACTTGACTCCTTGCAGCTCGAAGAACTTCCCAAACTCAGAAGGTTTTGTAGTGGA
326 TGTTTCCTAAACTTGACTACTTGCAGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
97726 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
391 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
* * * * *
97791 CACTTTCCATTTGAATAGTACAGATGTTGTTGGAAAGAGCAGCGGTAACATCTCACTTGATCAGC
456 CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATAACATCTCACTTGATCAAC
97856 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTT
521 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTT
97901 AGTTAAATCT
Statistics
Matches: 529, Mismatches: 36, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
567 529 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (567 bp):
ATATTTAAATAACGTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAAAAATAAACATATTT
TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGACAATGGAGGAATGCCATAAGTTGAAG
TATGTATTTAGTTCATCTACGGTTAAAAGCTTTGTTCAACTCAAAGAACTTCAAGTTTCTGATTG
TGATGAACTGGAAGAGGTAATACAAGGAGTATTAGGAGAAGAAAGGATTAGAAGCTGCACAAGTC
TGTTTCCTAAACTTGACTACTTGCAGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATAACATCTCACTTGATCAAC
CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTTGG
Found at i:102740 original size:14 final size:14
Alignment explanation
Indices: 102721--102766 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
102711 TGTTCGTGAA
102721 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
102735 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
102749 CGTTCAGTTATGTT
1 CGTTCGGTTATGTT
102763 CGTT
1 CGTT
102767 ATGTTCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:102771 original size:23 final size:24
Alignment explanation
Indices: 102736--102785 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
102726 GGTTATGTTC
102736 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* *
102760 GTTC-GTTATGTTCTTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
102783 GTT
1 GTT
102786 TAACCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:103532 original size:16 final size:15
Alignment explanation
Indices: 103511--103561 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
103501 GTCTCCAACG
103511 TTTATGTTCGTATTCA
1 TTTATGTTCGT-TTCA
*
103527 TTTATGTTCGTGTTCG
1 TTTATGTTCGT-TTCA
103543 TTTATGTTCGTTT-A
1 TTTATGTTCGTTTCA
103557 TTTAT
1 TTTAT
103562 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTATGTTCGTTTCA
Found at i:110034 original size:29 final size:29
Alignment explanation
Indices: 110000--110068 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
109990 AATTAATTAC
110000 AAAACTAACACCC-TTTTAACAATATTTAA
1 AAAACTAACACCCTTTTTAA-AATATTTAA
*
110029 AAAACTAACACCCTTTTTTAAATATTTAA
1 AAAACTAACACCCTTTTTAAAATATTTAA
110058 AAAACTAACAC
1 AAAACTAACAC
110069 TCAGTCAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 33 0.87
30 5 0.13
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAACTAACACCCTTTTTAAAATATTTAA
Found at i:116759 original size:29 final size:29
Alignment explanation
Indices: 116720--116801 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
116710 ATCCTAATAG
*
116720 AAATTAATTACAAAACTAACACCC-TTTT
1 AAATTATTTACAAAACTAACACCCTTTTT
116748 AACATTATTTACAAAACTAACACCCTTTTTT
1 AA-ATTATTTACAAAACTAACACCC-TTTTT
116779 AAA-TATTTACAAAACTAACACCC
1 AAATTATTTACAAAACTAACACCC
116802 GGTCAACGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.04
29 41 0.82
30 1 0.02
31 6 0.12
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTATTTACAAAACTAACACCCTTTTT
Found at i:122950 original size:19 final size:20
Alignment explanation
Indices: 122928--122979 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
122918 TTTGACCAGT
122928 TTTGACCGGTTC-GAACCGG
1 TTTGACCGGTTCTGAACCGG
*
122947 TTTGACTGG-TCTGAACCGG
1 TTTGACCGGTTCTGAACCGG
122966 TTTGACCGG-TCTGA
1 TTTGACCGGTTCTGA
122980 CCCAACCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 2 0.07
19 28 0.93
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (20 bp):
TTTGACCGGTTCTGAACCGG
Found at i:122975 original size:9 final size:9
Alignment explanation
Indices: 122916--122981 Score: 60
Period size: 10 Copynumber: 7.0 Consensus size: 9
122906 CTGGAAAACT
122916 GGTTTGACC
1 GGTTTGACC
*
122925 AGTTTTGACC
1 -GGTTTGACC
*
122935 GGTTCGAACC
1 GGTTTG-ACC
*
122945 GGTTTGACT
1 GGTTTGACC
*
122954 GGTCTGAACC
1 GGTTTG-ACC
122964 GGTTTGACC
1 GGTTTGACC
*
122973 GGTCTGACC
1 GGTTTGACC
122982 CAACCCGACC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
9 22 0.49
10 23 0.51
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.30
Consensus pattern (9 bp):
GGTTTGACC
Found at i:132943 original size:567 final size:567
Alignment explanation
Indices: 132071--133202 Score: 1922
Period size: 567 Copynumber: 2.0 Consensus size: 567
132061 GCTGCCAAAA
* * *
132071 ATATTTAAATAACGTAAAAGAATTTTGGATATTTCAATGATAGCAAAAACTAGTACTTAATATTT
1 ATATTTAAATAACGTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
* ** * *
132136 TAATTAAAGAAAAATTTATATAAATAATTATCGGTTTCAGTGATAATACAAAAATTAATATATTT
66 TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAAAAATAAACATATTT
* *
132201 TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGAGAGTGGAGGAATGCCATAAGTTGAAG
131 TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGACAATGGAGGAATGCCATAAGTTGAAG
* * *
132266 TGTGTGTTTAGTTCATCTACGATTAAAAGCTTTGTTCAACTCAAAGAACTTCTAGTTTCTGATTG
196 TATGTATTTAGTTCATCTACGATTAAAAGCTTTGTTCAACTCAAAGAACTTCAAGTTTCTGATTG
* *
132331 TGATGAACTGGAAGAGGTAATACAAGGAGTATTACGAGAAGAAAGGATTAGAAGCTTCATAAGTC
261 TGATGAACTGGAAGAGGTAATACAAGGAGTATTACGAGAAGAAAGGATTAGAAGCTGCACAAGTC
* **
132396 TGTTTCCTACACTTGACTACTTGTGGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
326 TGTTTCCTAAACTTGACTACTTGCAGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
*
132461 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATTTGGGGATGTCGTGGTTTGAG
391 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
*
132526 CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATGACATCTCACTTGATCAGC
456 CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATAACATCTCACTTGATCAGC
132591 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTTGG
521 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTTGG
*
132638 ATATTTAAATAACTTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
1 ATATTTAAATAACGTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
*
132703 TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAGAAATAAACATATTT
66 TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAAAAATAAACATATTT
* * *
132768 TTCATTTGCAGGTTTCATGTTCTGCCTTGGAGACGTTGACAATGGTGGGATGCCATAAGTTGAAG
131 TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGACAATGGAGGAATGCCATAAGTTGAAG
* * *
132833 TATGTATTTAGTTCATCTACGGTTAAAAGCTTTGTTCAACTCCAAGAACTTGAAGTTTCTGATTG
196 TATGTATTTAGTTCATCTACGATTAAAAGCTTTGTTCAACTCAAAGAACTTCAAGTTTCTGATTG
*
132898 TGATGAACTGGAAGAGGTAATACAAGGAGTATTAGGAGAAGAAAGGATTAGAAGCTGCACAAGTC
261 TGATGAACTGGAAGAGGTAATACAAGGAGTATTACGAGAAGAAAGGATTAGAAGCTGCACAAGTC
* * * * *
132963 TGTTTCCTAAACTTGACTCCTTGCAGCTCGAAGAACTTCCCAAACTTAGAAGGTTTTGTAGTGGA
326 TGTTTCCTAAACTTGACTACTTGCAGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
133028 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
391 ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
* * * *
133093 CACTTTCCATTTGAATAGTACAGATGTTGTTGGAAAGAGCAGCGGTAACATCTCACTTGATCAGC
456 CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATAACATCTCACTTGATCAGC
133158 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTT
521 CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTT
133203 AGTTAAATCT
Statistics
Matches: 527, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
567 527 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (567 bp):
ATATTTAAATAACGTAAAAGAATCTTGGATATTTCAATGATAACAAAAACCAGTACTTAATATTT
TAATTAAAGAAAAATTAATATAAATAATTATCGAATTCAGTGATAATACAAAAATAAACATATTT
TTCATTTGCAGGTTTCATGTCCTGCCTTGGAGACGTTGACAATGGAGGAATGCCATAAGTTGAAG
TATGTATTTAGTTCATCTACGATTAAAAGCTTTGTTCAACTCAAAGAACTTCAAGTTTCTGATTG
TGATGAACTGGAAGAGGTAATACAAGGAGTATTACGAGAAGAAAGGATTAGAAGCTGCACAAGTC
TGTTTCCTAAACTTGACTACTTGCAGCTCGAACAACTTCCCAAAATCACAAGGTTTTGTAGTGGA
ACTGATATTTCGATTGAATTTACCTCTCTAAGGTATTTACGTATATGGGGATGTCGTGGTTTGAG
CACTTTCCATTTGAATAGTACAAATATTGTTAGAAAGAGCAGCGATAACATCTCACTTGATCAGC
CACAACATCTCTTCCATGCAAAGGTATGTATTAATATCCAATCTTGG
Found at i:138051 original size:14 final size:14
Alignment explanation
Indices: 138032--138073 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
138022 GTTCGTGAAT
138032 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
138046 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
138060 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
138074 ATTTATGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:138837 original size:10 final size:10
Alignment explanation
Indices: 138822--138866 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
138812 GGGTCTCCAA
138822 CGTTTATGTT
1 CGTTTATGTT
138832 CGTTTATGTT
1 CGTTTATGTT
*
138842 CGTGTTCGTGTT
1 CGT-TT-ATGTT
138854 CGTTTATGTT
1 CGTTTATGTT
138864 CGT
1 CGT
138867 GTTCGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 20 0.65
11 4 0.13
12 7 0.23
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:138849 original size:16 final size:16
Alignment explanation
Indices: 138822--138876 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
138812 GGGTCTCCAA
138822 CGTTTATGTTCGT-TT
1 CGTTTATGTTCGTGTT
* **
138837 ATGTTCGTGTTCGTGTT
1 -CGTTTATGTTCGTGTT
138854 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
138870 CGTTTAT
1 CGTTTAT
138877 TTATTAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 30 0.94
17 2 0.06
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:138856 original size:22 final size:22
Alignment explanation
Indices: 138828--138872 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
138818 CCAACGTTTA
138828 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
138850 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
138872 T
1 T
138873 TTATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.13, G:0.27, T:0.56
Consensus pattern (22 bp):
TGTTCGTTTATGTTCGTGTTCG
Found at i:141418 original size:2 final size:2
Alignment explanation
Indices: 141411--141492 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
141401 ATTAGAGATA
141411 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
141453 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
141493 GGGTGGATAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:145349 original size:13 final size:13
Alignment explanation
Indices: 145307--145338 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
145297 AACCCGACCT
145307 GACCCGTTTACCC
1 GACCCGTTTACCC
145320 GACCCGTTTACCC
1 GACCCGTTTACCC
145333 GACCCG
1 GACCCG
145339 ACCCGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.19
Consensus pattern (13 bp):
GACCCGTTTACCC
Found at i:157911 original size:24 final size:24
Alignment explanation
Indices: 157891--157945 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
157881 TATGTTCGTG
157891 AATGTTCGATTATGTTCGTTCGGT
1 AATGTTCGATTATGTTCGTTCGGT
* *
157915 TATGTTCGGTTATGTTCGTTCGGT
1 AATGTTCGATTATGTTCGTTCGGT
*
157939 TATGTTC
1 AATGTTC
157946 TTTCATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.13, G:0.25, T:0.49
Consensus pattern (24 bp):
AATGTTCGATTATGTTCGTTCGGT
Found at i:157917 original size:14 final size:14
Alignment explanation
Indices: 157894--157945 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
157884 GTTCGTGAAT
*
157894 GTTCGATTATGTTC
1 GTTCGGTTATGTTC
157908 GTTCGGTTA---T-
1 GTTCGGTTATGTTC
157918 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
157932 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
157946 TTTCATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.50
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:157945 original size:10 final size:10
Alignment explanation
Indices: 157908--157932 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
157898 GATTATGTTC
157908 GTTCGGTTAT
1 GTTCGGTTAT
157918 GTTCGGTTAT
1 GTTCGGTTAT
157928 GTTCG
1 GTTCG
157933 TTCGGTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.32, T:0.48
Consensus pattern (10 bp):
GTTCGGTTAT
Found at i:157955 original size:14 final size:14
Alignment explanation
Indices: 157900--157958 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
157890 GAATGTTCGA
*
157900 TTATGTTCGTTCGG
1 TTATGTTCGTTCAG
157914 TTATGTTCG----G
1 TTATGTTCGTTCAG
*
157924 TTATGTTCGTTCGG
1 TTATGTTCGTTCAG
* *
157938 TTATGTTCTTTCAT
1 TTATGTTCGTTCAG
157952 TTATGTT
1 TTATGTT
157959 TAACTCAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 10 0.26
14 28 0.74
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
TTATGTTCGTTCAG
Found at i:158707 original size:10 final size:10
Alignment explanation
Indices: 158692--158734 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
158682 GTCTCCAACA
158692 TTTATGTTCG
1 TTTATGTTCG
158702 TTTATGTTCG
1 TTTATGTTCG
*
158712 TGTTCGTGTTCG
1 T-TT-ATGTTCG
158724 TTTATGTTCG
1 TTTATGTTCG
158734 T
1 T
158735 GTTCGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.62
11 4 0.14
12 7 0.24
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:158717 original size:16 final size:16
Alignment explanation
Indices: 158712--158744 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
158702 TTTATGTTCG
158712 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
158728 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
158744 T
1 T
158745 TTATTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTGTTCGTTTA
Found at i:158724 original size:22 final size:22
Alignment explanation
Indices: 158696--158740 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
158686 CCAACATTTA
158696 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
158718 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
158740 T
1 T
158741 TTATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.13, G:0.27, T:0.56
Consensus pattern (22 bp):
TGTTCGTTTATGTTCGTGTTCG
Found at i:161952 original size:2 final size:2
Alignment explanation
Indices: 161945--161985 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
161935 ATTAGAGATA
161945 AT AT AT AT AT AT AT AT A- 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
161986 GGGTGGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:163501 original size:39 final size:39
Alignment explanation
Indices: 163445--163521 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
163435 CTTTAAAGAG
* * * *
163445 TGGTAACTATTTTTTATTACCCTTTAATTTTTATTTGTA
1 TGGTAACTATTTCTTATTACCCCTTAAATTTTACTTGTA
*
163484 TGGTAATTATTTCTTATTACCCCTTAAATTTTACTTGT
1 TGGTAACTATTTCTTATTACCCCTTAAATTTTACTTGT
163522 TTCACCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (39 bp):
TGGTAACTATTTCTTATTACCCCTTAAATTTTACTTGTA
Found at i:165746 original size:14 final size:14
Alignment explanation
Indices: 165727--165772 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
165717 TGTTCGTGAA
165727 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
165741 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
165755 CGTTCAGTTATGTT
1 CGTTCGGTTATGTT
165769 CGTT
1 CGTT
165773 TATGTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:165769 original size:24 final size:24
Alignment explanation
Indices: 165742--165792 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
165732 GGTTATGTTC
165742 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* * *
165766 GTTCGTTTATGTTCTTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
165790 GTT
1 GTT
165793 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:166540 original size:16 final size:15
Alignment explanation
Indices: 166519--166569 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
166509 GTCTCCAACG
166519 TTTATGTTCGTATTCA
1 TTTATGTTCGT-TTCA
*
166535 TTTATGTTCGTGTTCG
1 TTTATGTTCGT-TTCA
166551 TTTATGTTCGTTT-A
1 TTTATGTTCGTTTCA
166565 TTTAT
1 TTTAT
166570 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTATGTTCGTTTCA
Found at i:172636 original size:29 final size:29
Alignment explanation
Indices: 172604--172672 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
172594 AATTAATTAC
*
172604 AAAACTAACACCC-TTTTAACAATATTTTA
1 AAAACTAACACCCTTTTTAA-AATATTTAA
*
172633 AAAACTAACACCCTTTTTTAAATATTTAA
1 AAAACTAACACCCTTTTTAAAATATTTAA
172662 AAAACTAACAC
1 AAAACTAACAC
172673 TCAGTCAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAACTAACACCCTTTTTAAAATATTTAA
Found at i:179409 original size:29 final size:29
Alignment explanation
Indices: 179370--179451 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
179360 ATCCTAATAG
*
179370 AAATTAATTACAAAACTAACACCC-TTTT
1 AAATTATTTACAAAACTAACACCCTTTTT
179398 AACATTATTTACAAAACTAACACCCTTTTTT
1 AA-ATTATTTACAAAACTAACACCC-TTTTT
179429 AAA-TATTTACAAAACTAACACCC
1 AAATTATTTACAAAACTAACACCC
179452 GGTCAACGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.04
29 41 0.82
30 1 0.02
31 6 0.12
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTATTTACAAAACTAACACCCTTTTT
Found at i:184192 original size:3 final size:3
Alignment explanation
Indices: 184184--184230 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
184174 TTTTTACCCA
184184 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
184231 AATATATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:186412 original size:17 final size:17
Alignment explanation
Indices: 186383--186426 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
186373 TTTAATTTTT
*
186383 AATTTTT-TCTTTTCAA
1 AATTTTTATATTTTCAA
*
186399 AATTTTTATATTTTCAT
1 AATTTTTATATTTTCAA
*
186416 AATATTTATAT
1 AATTTTTATAT
186427 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTATATTTTCAA
Found at i:186451 original size:15 final size:14
Alignment explanation
Indices: 186431--186468 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
186421 TTATATGTTT
186431 TATTTTATTTTCAAG
1 TATTTTATTTTC-AG
186446 TATTTTA-TTTCAG
1 TATTTTATTTTCAG
186459 TA-TTTATTTT
1 TATTTTATTTT
186469 TCTGTCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 4 0.18
15 7 0.32
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (14 bp):
TATTTTATTTTCAG
Found at i:186462 original size:13 final size:14
Alignment explanation
Indices: 186431--186467 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
186421 TTATATGTTT
186431 TATTTTATTTTCAAG
1 TATTTTA-TTTCAAG
186446 TATTTTATTTC-AG
1 TATTTTATTTCAAG
186459 TA-TTTATTT
1 TATTTTATTT
186468 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 4 0.18
15 7 0.32
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTTTATTTCAAG
Found at i:198346 original size:83 final size:83
Alignment explanation
Indices: 198208--198391 Score: 343
Period size: 83 Copynumber: 2.2 Consensus size: 83
198198 CATTAACTGA
*
198208 AAGATGAATTTGCTCATA-CATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
198272 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
198290 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
198355 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
198373 AAGATGAATGTGCTCATAG
1 AAGATGAATGTGCTCATAG
198392 TAGAAATAAG
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
82 17 0.17
83 82 0.83
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (83 bp):
AAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
ACCAATCATTGAATTTAG
Found at i:199968 original size:116 final size:115
Alignment explanation
Indices: 199179--199967 Score: 1256
Period size: 116 Copynumber: 6.9 Consensus size: 115
199169 CAAAGATTTA
*
199179 AATCTATCATTTGATGGATCATCATTTCCAGAGAA-AGTTCATAATGAGAAGAA--CTCATCTGA
1 AATCCATCATTTGATGGATCATCATTTCCAG-GAAGAGTTCATAATGAGAAGAACTCTCATCTGA
*
199241 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
199292 AATCCATCATTTGATGGATCATCATTTCCA-GAA-AGTTCATAATGAGAAGAA--CTCATCTGAA
1 AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAA
*
199353 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
199403 AATCCATCATTTGATGGATCATCATTTCCA-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGA
1 AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGA
*
199467 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
* *
199518 AATCCATCATTTGATGGATCATCATTTCCAGAAAAAGTTCATAATGAGAAGAA--CTCATCTGAA
1 AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAA
* **
199581 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTG
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
* * *
199631 AATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGA
1 AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGA
* *
199696 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
* * *
199747 AATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGA
1 AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGA
* *
199812 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
* * *
199863 AATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGA
1 AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGA
*
199928 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
199968 TAATTCTATC
Statistics
Matches: 650, Mismatches: 18, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
111 114 0.18
112 18 0.03
113 132 0.20
114 2 0.00
115 90 0.14
116 294 0.45
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (115 bp):
AATCCATCATTTGATGGATCATCATTTCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTG
Found at i:200292 original size:3 final size:3
Alignment explanation
Indices: 200284--200318 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
200274 TTTTTACCCA
200284 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
200319 AATATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:203772 original size:19 final size:19
Alignment explanation
Indices: 203750--203801 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
203740 TTTGACCAGT
203750 TTTGACCGGT-TCGAACCGG
1 TTTGACCGGTCT-GAACCGG
*
203769 TTTGACTGGTCTGAACCGG
1 TTTGACCGGTCTGAACCGG
*
203788 TTTGACCGATCTGA
1 TTTGACCGGTCTGA
203802 CCCGTCTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGG
Found at i:203827 original size:15 final size:15
Alignment explanation
Indices: 203807--203837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
203797 TCTGACCCGT
203807 CTGACCCAACCCGAC
1 CTGACCCAACCCGAC
*
203822 CTGACCCGACCCGAC
1 CTGACCCAACCCGAC
203837 C
1 C
203838 CGATTGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.55, G:0.16, T:0.06
Consensus pattern (15 bp):
CTGACCCAACCCGAC
Found at i:210988 original size:9 final size:9
Alignment explanation
Indices: 210974--211055 Score: 65
Period size: 9 Copynumber: 8.8 Consensus size: 9
210964 TTCAACCAGT
210974 TTTGACCGG
1 TTTGACCGG
* *
210983 TTTGACTGAT
1 TTTGACCG-G
210993 TTTGACCGG
1 TTTGACCGG
*
211002 TTCGAACCGG
1 TTTG-ACCGG
**
211012 TTTGAGTGG
1 TTTGACCGG
*
211021 TCTGAACCGG
1 TTTG-ACCGG
211031 TTTGACCGG
1 TTTGACCGG
*
211040 TCTGACCGG
1 TTTGACCGG
*
211049 TCTGACC
1 TTTGACC
211056 CAACTCGACC
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
9 36 0.63
10 21 0.37
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.32
Consensus pattern (9 bp):
TTTGACCGG
Found at i:211015 original size:19 final size:20
Alignment explanation
Indices: 210947--211055 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 20
210937 AGGGCTGGAA
* * *
210947 AACCGGTTTGACCAGTTTTC
1 AACCGGTTTGACCGGTTCTG
*
210967 AACCAGTTTTGACCGGTT-TG
1 AACC-GGTTTGACCGGTTCTG
* *
210987 -ACTGATTTTGACCGGTTC-G
1 AACCG-GTTTGACCGGTTCTG
**
211006 AACCGGTTTGAGTGG-TCTG
1 AACCGGTTTGACCGGTTCTG
211025 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
211044 -ACCGGTCTGACC
1 AACCGGTTTGACC
211056 CAACTCGACC
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
18 14 0.19
19 40 0.55
20 8 0.11
21 11 0.15
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:211084 original size:17 final size:17
Alignment explanation
Indices: 211062--211099 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
211052 GACCCAACTC
211062 GACCCGACTCGA-TCGTT
1 GACCCGACTCGACT-GTT
*
211079 GACCCGGCTCGACTGTT
1 GACCCGACTCGACTGTT
211096 GACC
1 GACC
211100 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (17 bp):
GACCCGACTCGACTGTT
Found at i:214470 original size:13 final size:14
Alignment explanation
Indices: 214452--214482 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
214442 TCTTAGATTT
214452 ATTTATA-TTTAAA
1 ATTTATACTTTAAA
214465 ATTTATACTTTAAA
1 ATTTATACTTTAAA
214479 ATTT
1 ATTT
214483 TGGTCAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTATACTTTAAA
Found at i:218925 original size:14 final size:14
Alignment explanation
Indices: 218906--218960 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
218896 GTTCGTGAAT
218906 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
218920 GTTCGGTTA---T-
1 GTTCGGTTATGTTC
218930 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
218944 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
218958 GTT
1 GTT
218961 TATGTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.07, C:0.13, G:0.29, T:0.51
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:218980 original size:24 final size:24
Alignment explanation
Indices: 218904--218967 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
218894 ATGTTCGTGA
218904 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGGTTATGTTCGTTCGGTT
218928 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGGTTATGTTCGTTCGGTT
*
218952 ATGTTCGTTTATGTTC
1 ATGTTCGGTTATGTTC
218968 TTTCATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.09, C:0.12, G:0.27, T:0.52
Consensus pattern (24 bp):
ATGTTCGGTTATGTTCGTTCGGTT
Found at i:219724 original size:10 final size:10
Alignment explanation
Indices: 219709--219751 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
219699 GTCTCCAACA
219709 TTTATGTTCG
1 TTTATGTTCG
219719 TTTATGTTCG
1 TTTATGTTCG
*
219729 TGTTCGTGTTCG
1 T-TT-ATGTTCG
219741 TTTATGTTCG
1 TTTATGTTCG
219751 T
1 T
219752 GTTCGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.62
11 4 0.14
12 7 0.24
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:219734 original size:16 final size:16
Alignment explanation
Indices: 219729--219761 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
219719 TTTATGTTCG
219729 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
219745 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
219761 T
1 T
219762 TTATTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTGTTCGTTTA
Found at i:219741 original size:22 final size:22
Alignment explanation
Indices: 219713--219757 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
219703 CCAACATTTA
219713 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
219735 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
219757 T
1 T
219758 TTATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.13, G:0.27, T:0.56
Consensus pattern (22 bp):
TGTTCGTTTATGTTCGTGTTCG
Found at i:234024 original size:20 final size:21
Alignment explanation
Indices: 233995--234042 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
233985 ATTCTTTACC
*
233995 TTTTAGTTTTAT-TAAGTT-TA
1 TTTTATTTTTATATAA-TTATA
234015 TTTTATTTTTTATATAATTATA
1 TTTTA-TTTTTATATAATTATA
234037 TTTTAT
1 TTTTAT
234043 AAAACTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 10 0.42
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTATTTTTATATAATTATA
Found at i:234041 original size:22 final size:21
Alignment explanation
Indices: 234001--234042 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
233991 TACCTTTTAG
234001 TTTTATTAAGTTTATTTTATT
1 TTTTATTAAGTTTATTTTATT
234022 TTTTATATAA-TTATATTTTAT
1 TTTTAT-TAAGTT-TATTTTAT
234043 AAAACTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTATTAAGTTTATTTTATT
Found at i:235328 original size:24 final size:24
Alignment explanation
Indices: 235301--235416 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
235291 CATAAATCTG
* *
235301 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
235325 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
235349 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAA
*
235373 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
235397 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
235417 TCAAATCGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:235432 original size:48 final size:47
Alignment explanation
Indices: 235301--235434 Score: 162
Period size: 48 Copynumber: 2.8 Consensus size: 47
235291 CATAAATCTG
* * *
235301 GTCAAGTATCATATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATTCAAGTCAA-TATCAGATCAGAATCCAA
* *
235349 GTCAAGTATCAGATCAGAA-TCTATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATTC-AAGTCA-ATATCAGATCAGAATCCAA
* *
235397 GTCAAGTATCAGATCAGAATTCAAATCGAAAATCAGAT
1 GTCAAGTATCAGATCAGAATTCAAGTC-AATATCAGAT
235435 AAAATATTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
47 1 0.01
48 69 0.93
49 4 0.05
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAATTCAAGTCAATATCAGATCAGAATCCAA
Found at i:237772 original size:13 final size:13
Alignment explanation
Indices: 237756--237805 Score: 84
Period size: 13 Copynumber: 3.8 Consensus size: 13
237746 GTCAACGGGT
237756 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
237769 CGGGTCGGG-CAAA
1 CGGGTCGGGTC-AA
237782 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
237795 CGGGTCGGGTC
1 CGGGTCGGGTC
237806 GGGTTGTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.03
13 33 0.94
14 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.48, T:0.14
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:239941 original size:24 final size:24
Alignment explanation
Indices: 239914--240030 Score: 155
Period size: 24 Copynumber: 4.9 Consensus size: 24
239904 ACATAAATCT
* *
239914 GGTCAAGTATCATATCAAAATCCA
1 GGTCAAGTATCAGATCAGAATCCA
239938 GGTCAAGTATCAGATCAGAATCCA
1 GGTCAAGTATCAGATCAGAATCCA
* *
239962 AGTCAAGTATCAGATCAGAATCTA
1 GGTCAAGTATCAGATCAGAATCCA
* *
239986 TGTC-AGATATCATATCAGAATCCA
1 GGTCAAG-TATCAGATCAGAATCCA
*
240010 TGTCAAGTATCAGATCAGAAT
1 GGTCAAGTATCAGATCAGAAT
240031 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GGTCAAGTATCAGATCAGAATCCA
Found at i:242363 original size:15 final size:16
Alignment explanation
Indices: 242333--242366 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
242323 GGTCAACGGT
242333 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
242350 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
242365 GG
1 GG
242367 GTCGAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:242377 original size:13 final size:14
Alignment explanation
Indices: 242358--242396 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
242348 ACGGTCAACG
242358 GGTCAACGGGTCGA
1 GGTCAACGGGTCGA
242372 -GTCAACGGGTC-A
1 GGTCAACGGGTCGA
*
242384 GGTCAATGGGTCG
1 GGTCAACGGGTCG
242397 GGCAAAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.18
Consensus pattern (14 bp):
GGTCAACGGGTCGA
Found at i:242383 original size:8 final size:8
Alignment explanation
Indices: 242323--242369 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
242313 TCAAAGTTTT
242323 GGTCAACGG
1 GGTCAAC-G
242332 TGGTCAACG
1 -GGTCAACG
242341 CCGGTCAAC-
1 --GGTCAACG
242350 GGTCAACG
1 GGTCAACG
242358 GGTCAACG
1 GGTCAACG
242366 GGTC
1 GGTC
242370 GAGTCAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 1 0.03
10 14 0.41
ACGTcount: A:0.21, C:0.28, G:0.36, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:242431 original size:18 final size:18
Alignment explanation
Indices: 242389--242434 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
242379 GGTCAGGTCA
242389 ATGGGTCGGG-CAAAGGG
1 ATGGGTCGGGTCAAAGGG
*
242406 ATGGGTCGGGTCAACGGG
1 ATGGGTCGGGTCAAAGGG
242424 -TCGGGTCGGGT
1 AT-GGGTCGGGT
242435 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.17
Consensus pattern (18 bp):
ATGGGTCGGGTCAAAGGG
Found at i:246628 original size:91 final size:90
Alignment explanation
Indices: 246499--246673 Score: 228
Period size: 91 Copynumber: 1.9 Consensus size: 90
246489 GACCACATCT
* * *
246499 TAATTAAATAAAACAAAACTGATCAAATATTATATTTTTAAATCCAACAAGGAAAAATGTAC-AA
1 TAATTAAATAAAACAAAACTGACCAAATATTATATTTTTAAATCCAACAAGAAAAAATATACAAA
246563 ACTTTAAACGAAAGTGATCAGTCTTA
66 AC-TTAAACGAAAGTGATCAGTCTTA
* * * * **
246589 TAATTAAATAAAA-ATGAAAGTGACCAAATATTATGTTTTTGAATTCAATGAGAAAAAATATACA
1 TAATTAAATAAAACA--AAACTGACCAAATATTATATTTTTAAATCCAACAAGAAAAAATATACA
246653 AAACTTAAACGAAAGTGATCA
64 AAACTTAAACGAAAGTGATCA
246674 ATCATATAGT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
89 1 0.01
90 13 0.18
91 55 0.75
92 4 0.05
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (90 bp):
TAATTAAATAAAACAAAACTGACCAAATATTATATTTTTAAATCCAACAAGAAAAAATATACAAA
ACTTAAACGAAAGTGATCAGTCTTA
Found at i:248675 original size:22 final size:22
Alignment explanation
Indices: 248650--248747 Score: 196
Period size: 22 Copynumber: 4.5 Consensus size: 22
248640 CGCTCTCGCA
248650 CAAATAGCTTCTTTCTCTCTTT
1 CAAATAGCTTCTTTCTCTCTTT
248672 CAAATAGCTTCTTTCTCTCTTT
1 CAAATAGCTTCTTTCTCTCTTT
248694 CAAATAGCTTCTTTCTCTCTTT
1 CAAATAGCTTCTTTCTCTCTTT
248716 CAAATAGCTTCTTTCTCTCTTT
1 CAAATAGCTTCTTTCTCTCTTT
248738 CAAATAGCTT
1 CAAATAGCTT
248748 ATCCTACTAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 76 1.00
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.48
Consensus pattern (22 bp):
CAAATAGCTTCTTTCTCTCTTT
Found at i:251286 original size:20 final size:20
Alignment explanation
Indices: 251192--251560 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
251182 GATTTTCCAT
* ** *
251192 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
251212 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
251232 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
251252 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
251272 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
251292 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
251312 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
251332 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
251352 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
251372 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
251392 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
251412 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
251432 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
251452 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
251472 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
251492 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
251512 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
251532 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
251552 AATCACAAC
1 AATCGCAAC
251561 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:252282 original size:24 final size:24
Alignment explanation
Indices: 252243--252289 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
252233 AAATTTGGTC
252243 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
252267 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
252290 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:252481 original size:12 final size:12
Alignment explanation
Indices: 252464--252488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
252454 ATATAATCCT
252464 GAAGAAGAAAAA
1 GAAGAAGAAAAA
252476 GAAGAAGAAAAA
1 GAAGAAGAAAAA
252488 G
1 G
252489 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:254791 original size:19 final size:19
Alignment explanation
Indices: 254769--255075 Score: 360
Period size: 19 Copynumber: 17.4 Consensus size: 19
254759 CGGAAAATAC
*
254769 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
254788 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
254802 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
254822 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
254836 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
254855 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
254874 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
254888 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
254907 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
254926 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
254940 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
254959 AATCGCAATGCGAAGA-GAA
1 AATCGCAATGCGAA-ATGAA
254978 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
254997 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
255016 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
255030 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
255049 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
255068 AATCGCAA
1 AATCGCAA
255076 CGAGATAATC
Statistics
Matches: 250, Mismatches: 10, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 4 0.02
19 152 0.61
20 14 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Done.