Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000105.1 Hibiscus syriacus cultivar Beakdansim tig00000189_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: 103267
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1094 original size:46 final size:47
Alignment explanation
Indices: 1035--1140 Score: 162
Period size: 46 Copynumber: 2.3 Consensus size: 47
1025 GACAATACGC
*
1035 ACGAATAAATGCATACTTAG-AAAAG-AAAAAAACAAGAATAGAACAT
1 ACGAATAATTGCATACTTAGAAAAAGAAAAAAAACAAGAATA-AACAT
*
1081 ACGAATAATTGCATACTTAGAAAAAGAAAAAAAAACAAGAATACACAT
1 ACGAATAATTGCATACTTAGAAAAAG-AAAAAAAACAAGAATAAACAT
1129 ACGAATAATTGC
1 ACGAATAATTGC
1141 GGTGATTATC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
46 19 0.35
47 5 0.09
48 16 0.29
49 15 0.27
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (47 bp):
ACGAATAATTGCATACTTAGAAAAAGAAAAAAAACAAGAATAAACAT
Found at i:6037 original size:17 final size:17
Alignment explanation
Indices: 6015--6048 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6005 TCCATAAATC
*
6015 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
*
6032 CAAAATCAAACATTCCA
1 CAAAATCAAACAATCCA
6049 AAATATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:8048 original size:19 final size:20
Alignment explanation
Indices: 7997--8055 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
7987 GATTCCCCTG
7997 TGGGGGAATCGGTTCCCTTCAA
1 TGGGGGAATCGGTT-CC-TCAA
*
8019 AGGGGGAATCGGTTCCTC-A
1 TGGGGGAATCGGTTCCTCAA
* *
8038 TGGGGGGATCGATTCCTC
1 TGGGGGAATCGGTTCCTC
8056 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 16 0.48
20 2 0.06
21 2 0.06
22 13 0.39
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (20 bp):
TGGGGGAATCGGTTCCTCAA
Found at i:11880 original size:22 final size:21
Alignment explanation
Indices: 11838--11877 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11828 GAGTTTGTTT
*
11838 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
11859 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
11878 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:14525 original size:32 final size:32
Alignment explanation
Indices: 14489--14553 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
14479 TTGTTAAATG
* * *
14489 AAAGGAGTTTGTTGTATAAGAGATTGAAGATA
1 AAAGGAGTGTGTTATATAAGAGATTAAAGATA
*
14521 AAAGGAGTGTGTTATGTAAGAGATTAAAGATA
1 AAAGGAGTGTGTTATATAAGAGATTAAAGATA
14553 A
1 A
14554 TGTGCACAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.29
Consensus pattern (32 bp):
AAAGGAGTGTGTTATATAAGAGATTAAAGATA
Found at i:18196 original size:24 final size:24
Alignment explanation
Indices: 18164--18221 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
18154 GACAAGATGC
18164 AGCTGTTTTTTCAATGGGTACATG
1 AGCTGTTTTTTCAATGGGTACATG
*
18188 AGCTGTTTTTTGAATGGGTACATG
1 AGCTGTTTTTTCAATGGGTACATG
18212 AGCTGTTTTT
1 AGCTGTTTTT
18222 AGGCTACACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (24 bp):
AGCTGTTTTTTCAATGGGTACATG
Found at i:18723 original size:17 final size:18
Alignment explanation
Indices: 18699--18751 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 18
18689 CATCATAAAA
18699 TCTATTTTCCCCTTTTCT
1 TCTATTTTCCCCTTTTCT
*
18717 T-TATTTTCCTCTTTTCT
1 TCTATTTTCCCCTTTTCT
*
18734 TCTA-TTTCCCCTCTTCT
1 TCTATTTTCCCCTTTTCT
18751 T
1 T
18752 ATATCTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTATTTTCCCCTTTTCT
Found at i:20018 original size:20 final size:20
Alignment explanation
Indices: 19993--20045 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
19983 GATTTTCCAT
*
19993 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAACATAAA
*
20013 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATAAA
20033 AATCGCAACGCGA
1 AATCGCAACGCGA
20046 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATAAA
Found at i:20076 original size:61 final size:61
Alignment explanation
Indices: 20011--20278 Score: 168
Period size: 61 Copynumber: 4.5 Consensus size: 61
20001 CGCGAATATA
** * **
20011 AAAATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGCGATACGT-AAAATCGCAACGAGTATCCGT
* * * *
20072 AAAATCGCAATGCGTATC-CGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
1 AAAATCGCAACGCG-AACACGTAAATCGCAACG-CGATACGTAAAATCGCAACGAGTATCCGT
* * * *
20134 -AAATCGCAACGAGAATACGTAAATCGCAACGCG----G--AAATCGCAACGAGAATACGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGCGATACGTAAAATCGCAACGAGTATCCGT
* * ** * * * * *
20188 -AAATCGCAATGCGTATC-CGTAAATCGCAATACGAATACGT-AAATTGCAATGCGAATACGT
1 AAAATCGCAACGCG-AACACGTAAATCGCAACGCG-ATACGTAAAATCGCAACGAGTATCCGT
* *
20248 -AAATCGCAATGCGAATC-TGTAAATCGCAACG
1 AAAATCGCAACGCGAA-CACGTAAATCGCAACG
20279 AGATTCTGAC
Statistics
Matches: 165, Mismatches: 30, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
54 42 0.25
55 1 0.01
56 1 0.01
59 2 0.01
60 44 0.27
61 50 0.30
62 24 0.15
63 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (61 bp):
AAAATCGCAACGCGAACACGTAAATCGCAACGCGATACGTAAAATCGCAACGAGTATCCGT
Found at i:20098 original size:20 final size:20
Alignment explanation
Indices: 20054--20278 Score: 196
Period size: 20 Copynumber: 11.4 Consensus size: 20
20044 GATTCTGACT
* * *
20054 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGAATACGT-AA
* * *
20075 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
20095 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGAATACGT-AA
* *
20116 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
*
20136 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATACGTAA
20156 ATCGCAACGCG-----G-AA
1 ATCGCAACGCGAATACGTAA
*
20170 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATACGTAA
* * *
20190 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
**
20210 ATCGCAATACGAATACGTAA
1 ATCGCAACGCGAATACGTAA
* *
20230 ATTGCAATGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
*
20250 ATCGCAATGCGAAT-CTGTAA
1 ATCGCAACGCGAATAC-GTAA
20270 ATCGCAACG
1 ATCGCAACG
20279 AGATTCTGAC
Statistics
Matches: 171, Mismatches: 23, Indels: 21
0.80 0.11 0.10
Matches are distributed among these distances:
14 12 0.07
15 1 0.01
19 2 0.01
20 123 0.72
21 33 0.19
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATACGTAA
Found at i:20099 original size:41 final size:40
Alignment explanation
Indices: 20054--20276 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
20044 GATTCTGACT
* *
20054 ATCGCAACGAGTATCCGTAAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
* *
20095 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
*
20136 ATCGCAACGAGAATACGTAAATCGCAA--CG----CGGAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
20170 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
* * * *
20210 ATCGCAA-TACGAATACGTAAATTGCAATGCGAATACGTAA
1 ATCGCAACGA-GAATACGTAAATCGCAATGCGTATCCGTAA
* *
20250 ATCGCAATGCGAAT-CTGTAAATCGCAA
1 ATCGCAACGAGAATAC-GTAAATCGCAA
20277 CGAGATTCTG
Statistics
Matches: 159, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
34 31 0.19
36 2 0.01
38 2 0.01
39 2 0.01
40 68 0.43
41 54 0.34
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
Found at i:20215 original size:74 final size:75
Alignment explanation
Indices: 20093--20236 Score: 229
Period size: 74 Copynumber: 1.9 Consensus size: 75
20083 GCGTATCCGT
20093 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGA-GAATACGTAAA
1 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAA-GACGAATACGTAAA
20157 TCGCAACGCGG
65 TCGCAACGCGG
* * *
20168 AAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAATACGAATACGTAAAT
1 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAGACGAATACGTAAAT
*
20232 TGCAA
66 CGCAA
20237 TGCGAATACG
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 1 0.02
74 44 0.69
75 19 0.30
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (75 bp):
AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAGACGAATACGTAAAT
CGCAACGCGG
Found at i:20286 original size:20 final size:19
Alignment explanation
Indices: 20031--20284 Score: 110
Period size: 20 Copynumber: 12.9 Consensus size: 19
20021 CGCGAACATA
*
20031 TAAATCGCAACGCGATTC-
1 TAAATCGCAACGAGATTCG
* *
20049 TGACTATCGCAACGAGTATCCG
1 T-A-AATCGCAACGAG-ATTCG
* * *
20071 TAAAATCGCAATGCGTATCCG
1 T-AAATCGCAACGAG-ATTCG
* *
20092 TAAATCGCAACGACAATACG
1 TAAATCGCAACGA-GATTCG
* *
20112 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGAG-ATTCG
*
20133 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
20153 TAAATCGCAAC--G---CG
1 TAAATCGCAACGAGATTCG
* *
20167 GAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
* * *
20187 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGAG-ATTCG
*
20207 TAAATCGCAATACGA-ATACG
1 TAAATCGC-A-ACGAGATTCG
* *
20227 TAAATTGCAATGCGA-ATACG
1 TAAATCGCAA--CGAGATTCG
* * *
20247 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGAGATTC-G
20267 TAAATCGCAACGAGATTC
1 TAAATCGCAACGAGATTC
20285 TGACTATCGC
Statistics
Matches: 182, Mismatches: 35, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
14 12 0.07
16 1 0.01
18 4 0.02
19 4 0.02
20 121 0.66
21 36 0.20
22 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (19 bp):
TAAATCGCAACGAGATTCG
Found at i:21114 original size:24 final size:24
Alignment explanation
Indices: 21087--21133 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
21077 GTATTCGAAA
21087 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
21111 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
21134 TTTTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:23704 original size:19 final size:19
Alignment explanation
Indices: 23680--23831 Score: 127
Period size: 19 Copynumber: 8.7 Consensus size: 19
23670 GCAACGAGAG
23680 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23699 AATCGCAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
* *
23713 AATCGCAACGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
23733 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
23752 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
23766 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
23785 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
23799 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
23818 AATCGCAACGCGAA
1 AATCGCAATGCGAA
23832 TTTAGTTTCG
Statistics
Matches: 105, Mismatches: 12, Indels: 32
0.70 0.08 0.21
Matches are distributed among these distances:
14 31 0.30
15 2 0.02
16 5 0.05
17 7 0.07
18 2 0.02
19 46 0.44
20 12 0.11
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:23704 original size:33 final size:34
Alignment explanation
Indices: 23647--23740 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
23637 CTTAATGTCT
* ** *
23647 ATCGCAACGCGGAAATTACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAAA
* *
23681 ATCGCAATGC-GAAATGAAAATCGCAACGTGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAAA
**
23714 ATCGCAACGCGGAAATGACTATCGCAA
1 ATCGCAACGCGGAAATGAAAATCGCAA
23741 TGCGAAATGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAAA
Found at i:23714 original size:14 final size:14
Alignment explanation
Indices: 23695--23722 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23685 CAATGCGAAA
23695 TGAAAATCGCAACG
1 TGAAAATCGCAACG
23709 TGAAAATCGCAACG
1 TGAAAATCGCAACG
23723 CGGAAATGAC
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:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:23729 original size:14 final size:14
Alignment explanation
Indices: 23696--23729 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23686 AATGCGAAAT
*
23696 GAAAATCGCAACGT
1 GAAAATCGCAACGC
23710 GAAAATCGCAACGC
1 GAAAATCGCAACGC
*
23724 GGAAAT
1 GAAAAT
23730 GACTATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:23738 original size:53 final size:52
Alignment explanation
Indices: 23680--23792 Score: 172
Period size: 53 Copynumber: 2.2 Consensus size: 52
23670 GCAACGAGAG
* *
23680 AATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCGCAACGCGGAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGC-GAAATGAA
* * *
23733 TATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
23785 AATCGCAA
1 AATCGCAA
23793 CGAGGGAATC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
52 14 0.26
53 40 0.74
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
Found at i:23773 original size:33 final size:33
Alignment explanation
Indices: 23734--23827 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
23724 GGAAATGACT
23734 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
23767 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
23800 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
23828 CGAATTTAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:23803 original size:86 final size:85
Alignment explanation
Indices: 23640--23831 Score: 267
Period size: 86 Copynumber: 2.2 Consensus size: 85
23630 CAATCATCTT
* * **
23640 AATGTCTATCGCAACGCGGAAATTACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
*
23705 AACGTGAAAATCGCAACGCGGA
65 AACGAGAAAATCGCAACGC-GA
*
23727 AATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 AATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
** *
23792 ACGAGGGAATCGCAATGCGA
66 ACGAGAAAATCGCAACGCGA
**
23812 AATGAAAATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
23832 TTTAGTTTCG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 19 0.20
86 59 0.63
87 15 0.16
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (85 bp):
AATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
ACGAGAAAATCGCAACGCGA
Found at i:23849 original size:19 final size:19
Alignment explanation
Indices: 23827--23889 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
23817 AAATCGCAAC
* *
23827 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAATTTCGCGTT
23846 GCGATTTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
23865 GCGATTTTAATTTCGCATT
1 GCGATTTTAATTTCGCGTT
23884 GCGATT
1 GCGATT
23890 CTCTAGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:24047 original size:14 final size:14
Alignment explanation
Indices: 24028--24064 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
24018 CATCAATTAA
24028 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
24042 ACAAATCATCTTTT
1 ACAAATCAACTTTT
*
24056 ACAATTCAA
1 ACAAATCAA
24065 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:25478 original size:21 final size:21
Alignment explanation
Indices: 25412--25478 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
25402 GTGAATCGGG
*
25412 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * *
25432 CCTCTTCAACGAT--GACGGTGGC
1 -CTCTTGAACGGTGGGA-GG-GGA
25454 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
25475 CTCT
1 CTCT
25479 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
19 2 0.06
21 26 0.76
22 4 0.12
23 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:26967 original size:33 final size:33
Alignment explanation
Indices: 26930--27036 Score: 151
Period size: 33 Copynumber: 3.2 Consensus size: 33
26920 GGAAATTACT
* * * *
26930 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGTGAAAATTGCAACGCGAAATGAAA
26963 ATCGCAACGTGAAAATTGCAACGCGAAATGAAA
1 ATCGCAACGTGAAAATTGCAACGCGAAATGAAA
**
26996 ATCGCAACGTGAAAATTGCAACGCGGAAATGACT
1 ATCGCAACGTGAAAATTGCAACGC-GAAATGAAA
27030 ATCGCAA
1 ATCGCAA
27037 TGCGAAATGA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 53 0.79
34 14 0.21
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAACGTGAAAATTGCAACGCGAAATGAAA
Found at i:26977 original size:14 final size:14
Alignment explanation
Indices: 26958--27018 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
26948 CAATGCGAAA
26958 TGAAAATCGCAACG
1 TGAAAATCGCAACG
*
26972 TGAAAATTGCAACGCG
1 TGAAAATCGCAA--CG
26988 AAATGAAAATCGCAACG
1 ---TGAAAATCGCAACG
*
27005 TGAAAATTGCAACG
1 TGAAAATCGCAACG
27019 CGGAAATGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 24 0.62
16 2 0.05
17 2 0.05
19 11 0.28
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:27045 original size:53 final size:52
Alignment explanation
Indices: 26972--27090 Score: 157
Period size: 53 Copynumber: 2.3 Consensus size: 52
26962 AATCGCAACG
* * *
26972 TGAAAATTGCAACGCGAAATGAAAATCGCAACGTGAAAATTGCAACGCGGAAA
1 TGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAACGC-GAAA
** * * *
27025 TGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAA
1 TGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAA
27077 TGAAAATCGCAACG
1 TGAAAATCGCAACG
27091 AGGGAATCGC
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
52 15 0.27
53 40 0.73
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
TGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAA
Found at i:27069 original size:33 final size:33
Alignment explanation
Indices: 27030--27123 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
27020 GGAAATGACT
27030 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
27063 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
27096 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
27124 CGAATTTAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:27188 original size:33 final size:33
Alignment explanation
Indices: 27140--27212 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
27130 TAGTTTCGCG
* *
27140 TTGCGATTTTGTCGTTGCGATTTTAATTTCACA
1 TTGCGATTCTCTCGTTGCGATTTTAATTTCACA
* *
27173 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTAATTTCACA
27206 TTGCGAT
1 TTGCGAT
27213 AGTCATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTAATTTCACA
Found at i:27211 original size:19 final size:19
Alignment explanation
Indices: 27154--27212 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
27144 GATTTTGTCG
* *
27154 TTGCGATTTTAATTTCACA
1 TTGCGATTTTCATTTCGCA
*
27173 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
27187 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27206 TTGCGAT
1 TTGCGAT
27213 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.19
16 6 0.19
17 6 0.19
19 13 0.42
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:27338 original size:14 final size:14
Alignment explanation
Indices: 27319--27355 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
27309 CATCAATTAA
27319 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
27333 ACAAATCATCTTTT
1 ACAAATCAACTTTT
27347 ACAAATCAA
1 ACAAATCAA
27356 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:28768 original size:21 final size:21
Alignment explanation
Indices: 28702--28768 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
28692 GTGAATCGGG
*
28702 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * *
28722 CCTCTTCAACGAT--GACGGTGGC
1 -CTCTTGAACGGTGGGA-GG-GGA
28744 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
28765 CTCT
1 CTCT
28769 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
19 2 0.06
21 26 0.76
22 4 0.12
23 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:30811 original size:20 final size:20
Alignment explanation
Indices: 30786--30867 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
30776 TTTTGGTTGA
30786 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
30806 AATGAAAATCACAACGCG-G
1 AATGAAAATCGCAACGAGAG
** * *
30825 AAATGACTATCGCCACGCGA-
1 -AATGAAAATCGCAACGAGAG
30845 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
30865 AAT
1 AAT
30868 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
19 16 0.33
20 33 0.67
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:30876 original size:33 final size:33
Alignment explanation
Indices: 30833--30924 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
30823 GGAAATGACT
*
30833 ATCGCCACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
30866 ATCGCAACGCGAAATTAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
30899 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
30925 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:30889 original size:19 final size:19
Alignment explanation
Indices: 30784--30929 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
30774 TCTTTTGGTT
*
30784 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
30803 GAGAATGAAAATCACAACGC
1 GA-AATGAAAATCGCAACGC
** *
30823 GGAAATGACTATCGCCACGC
1 -GAAATGAAAATCGCAACGC
30843 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
30860 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
30876 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
30893 G--A-GAGAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
30909 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
30928 GA
1 GA
30930 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
14 18 0.19
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 37 0.38
20 28 0.29
21 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:30958 original size:19 final size:20
Alignment explanation
Indices: 30936--31046 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
30926 GCGATTTTGG
30936 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
30955 TTTCGCGTTGCGA--TTC--
1 TTTCGCGTTGCGATTTTCAT
*
30971 --TCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* **
30989 TTCTCTCGTTGCGATAGTCAT
1 TT-TCGCGTTGCGATTTTCAT
*
31010 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
31030 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
31047 AAGTTTAGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 13 0.17
20 30 0.39
21 18 0.23
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:31642 original size:20 final size:21
Alignment explanation
Indices: 31612--31822 Score: 208
Period size: 20 Copynumber: 10.4 Consensus size: 21
31602 TTAAAAATCG
*
31612 CGTTACGATTTACGGATACGT
1 CGTTGCGATTTACGGATACGT
*
31633 -GTTGCGATTTATGGATAC-T
1 CGTTGCGATTTACGGATACGT
*
31652 CGTTGTGATTTACGGATACG-
1 CGTTGCGATTTACGGATACGT
* * *
31672 CGTTGCAATTTTACGTAT-TGT
1 CGTTGCGA-TTTACGGATACGT
*
31693 CGTTGTGATTTACGGATACG-
1 CGTTGCGATTTACGGATACGT
* * *
31713 CATTGCGATTTACGTATTC-T
1 CGTTGCGATTTACGGATACGT
* *
31733 CGTTGCGATTTACAGTTACG-
1 CGTTGCGATTTACGGATACGT
* *
31753 CGTTGCGATTTACGTATTC-T
1 CGTTGCGATTTACGGATACGT
31773 CGTTGCGATTTACGGATACG-
1 CGTTGCGATTTACGGATACGT
31793 CGTTGCGATTTTACGGATAC-T
1 CGTTGCGA-TTTACGGATACGT
31814 CGTTGCGAT
1 CGTTGCGAT
31823 AGTCAGAATC
Statistics
Matches: 152, Mismatches: 27, Indels: 23
0.75 0.13 0.11
Matches are distributed among these distances:
19 1 0.01
20 117 0.77
21 34 0.22
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTACGGATACGT
Found at i:31677 original size:40 final size:40
Alignment explanation
Indices: 31612--31883 Score: 278
Period size: 40 Copynumber: 6.8 Consensus size: 40
31602 TTAAAAATCG
* * * * *
31612 CGTTACGATTTACGGATACGTGTTGCGATTTATGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
31652 CGTTGTGATTTACGGATACGCGTTGCAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* *
31693 CGTTGTGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* *
31733 CGTTGCGATTTACAGTTACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* *
31773 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* * ** * *
31814 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTACGTATTCT
* ** *
31854 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
31884 ATGGAAAATC
Statistics
Matches: 196, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 128 0.65
41 66 0.34
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:31753 original size:81 final size:80
Alignment explanation
Indices: 31612--31883 Score: 296
Period size: 81 Copynumber: 3.4 Consensus size: 80
31602 TTAAAAATCG
* * * * *
31612 CGTTACGATTTACGGATACGTGTTGCGATTTATGGATACTCGTTGTGATTTACGGATACGCGTTG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACGCGTTG
*
31677 CAATTTTACGTATTGT
66 CAA-TTTACGTATTCT
* * * * *
31693 CGTTGTGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAGTTACGCGTTG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACGCGTTG
*
31758 CGATTTACGTATTCT
66 CAATTTACGTATTCT
*
31773 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACTCGTTGCGAT-TTACAGATA-CGCG
* ** * *
31836 TTGCGATTTATATGTTCG
63 TTGCAATTTACGTATTCT
* ** *
31854 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
31884 ATGGAAAATC
Statistics
Matches: 162, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
80 40 0.25
81 121 0.75
82 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (80 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACGCGTTG
CAATTTACGTATTCT
Found at i:31854 original size:20 final size:20
Alignment explanation
Indices: 31831--31883 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
31821 ATAGTCAGAA
*
31831 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
31851 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
31871 TCGCGTTGCGATT
1 TCGCGTTGCGATT
31884 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:31982 original size:20 final size:19
Alignment explanation
Indices: 31933--31986 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
31923 ATTCTTCATA
31933 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
31952 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
31973 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
31987 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:38745 original size:19 final size:19
Alignment explanation
Indices: 38674--38747 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
38664 AACGTTTGGG
*
38674 GAAAAGTATCGAAACTTTAT
1 GAAAAGTATCGAAACTCT-T
*
38694 GGAAAA-T-TTGAAACTCTT
1 -GAAAAGTATCGAAACTCTT
* *
38712 GAGATAGTTTCGAAACTCTT
1 GA-AAAGTATCGAAACTCTT
38732 GAAAAGTATCGAAACT
1 GAAAAGTATCGAAACT
38748 TTTTGGGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 2 0.05
18 3 0.07
19 21 0.48
20 13 0.30
21 5 0.11
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.30
Consensus pattern (19 bp):
GAAAAGTATCGAAACTCTT
Found at i:42199 original size:36 final size:36
Alignment explanation
Indices: 42159--42369 Score: 395
Period size: 36 Copynumber: 5.9 Consensus size: 36
42149 ACGGTGCTGG
* *
42159 ACATTAATACACGAATGTACCAAAGCTGATTTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
42195 ACATTGATACACGAATGTACCAAAGCTGACATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
42231 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
42267 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
42303 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
42339 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
42370 ATGGATAAAT
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 171 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:48719 original size:36 final size:36
Alignment explanation
Indices: 48679--48889 Score: 332
Period size: 36 Copynumber: 5.9 Consensus size: 36
48669 ACAGTGATGG
* *
48679 ACATTGATACACAAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * *
48715 ACATTGATACATGAATGTACCAAATCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
48751 ACATTGATACACGAATGTACCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
48787 ACATTGATACACGAATGTACCAAAGCTTATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
48823 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
** *
48859 ACATTGATACATAAATGTACCAAAGTTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
48890 ATGTATAAAT
Statistics
Matches: 163, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 163 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:49403 original size:12 final size:12
Alignment explanation
Indices: 49386--49411 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49376 AATTACCCTT
49386 AATAAATCTTAA
1 AATAAATCTTAA
49398 AATAAATCTTAA
1 AATAAATCTTAA
49410 AA
1 AA
49412 ATTATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAATCTTAA
Found at i:49809 original size:16 final size:16
Alignment explanation
Indices: 49783--49815 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
49773 TTACAGGCTA
49783 AAAAATATATAACTTTT
1 AAAAATATATAA-TTTT
49800 AAAAAT-TATAATTTT
1 AAAAATATATAATTTT
49815 A
1 A
49816 TGTCCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAATATATAATTTT
Found at i:52264 original size:488 final size:489
Alignment explanation
Indices: 51322--52308 Score: 1924
Period size: 488 Copynumber: 2.0 Consensus size: 489
51312 CAGATTTTTA
51322 CTTCAAGATTCACGTCGGCTTACAAGGACAATTCTTTGCTACCAACTCGGATTATGTCGTTTCAA
1 CTTCAAGATTCACGTCGGCTTACAAGGACAATTCTTTGCTACCAACTCGGATTATGTCGTTTCAA
51387 CAATAACTGATTTCGATCTCAGTTTCCTCTTAGCAAACAATTTTGCTAAGTGTGTTCTCGGGAAG
66 CAATAACTGATTTCGATCTCAGTTTCCTCTTAGCAAACAATTTTGCTAAGTGTGTTCTCGGGAAG
51452 TCAAATATGCTCCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAACATCCAGACTAATGT
131 TCAAATATGCTCCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAACATCCAGACTAATGT
51517 CAAAATTGTTTTAATTTGAAAAGTAAGGTAAAAAAACAAAGAGAAAAAATCCGAAGCGATTTAAG
196 CAAAATTGTTTTAATTTGAAAAGTAAGGTAAAAAAACAAAGAGAAAAAATCCGAAGCGATTTAAG
*
51582 TACCTTAAAATTCTCACGTTTGGAATTGAGCCTTCGCTTTAGTCTTCGGCTTGAAAGAAAATTAG
261 TACCTTAAAATTCTCACGTTTGGAATTGAGCCTTCGATTTAGTCTTCGGCTTGAAAGAAAATTAG
51647 CTAAGCATGGCCAAATTCATACTTAGCATAATTGAAAACGAAATTTTAAAAGAAAATAGGAGAAG
326 CTAAGCATGGCCAAATTCATACTTAGCATAATTGAAAACGAAATTTTAAAAGAAAATAGGAGAAG
51712 TATGCACAGAATAGAGAGAAAGCTAGAGAGAAAAAGATGATTTAATTCTCAGATGAGAGAGATGT
391 TATGCACAGAATAGAGAGAAAGCTAGAGAGAAAAAGATGATTTAATTCTCAGATGAGAGAGATGT
51777 GTTTCTAGGCTCACCCTTAGAGGGTATTTATAGC
456 GTTTCTAGGCTCACCCTTAGAGGGTATTTATAGC
51811 CTTCAAGATTCACGTCGGCTTACAAGGACAATTCTTTGCTACCAACTCGGATTATGTCGTTTCAA
1 CTTCAAGATTCACGTCGGCTTACAAGGACAATTCTTTGCTACCAACTCGGATTATGTCGTTTCAA
51876 CAATAACTGATTTCGATCTCAGTTTCCTCTTAGCAAACAATTTTGCTAAGTGTGTTCTCGGGAAG
66 CAATAACTGATTTCGATCTCAGTTTCCTCTTAGCAAACAATTTTGCTAAGTGTGTTCTCGGGAAG
* *
51941 TCGAATATGCTCCAATAAGCAAATCCTTCTTCAAACGTTAACCATAACAACATCCAGACTAATGT
131 TCAAATATGCTCCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAACATCCAGACTAATGT
52006 CAAAATTGTTTTAATTTGAAAAGTAAGGT-AAAAAACAAAGAGAAAAAATCCGAAGCGATTTAAG
196 CAAAATTGTTTTAATTTGAAAAGTAAGGTAAAAAAACAAAGAGAAAAAATCCGAAGCGATTTAAG
*
52070 TACCTTACAATTCTCACGTTTGGAATTGAGCCTTCGATTTAGTCTTCGGCTTGAAAGAAAATTAG
261 TACCTTAAAATTCTCACGTTTGGAATTGAGCCTTCGATTTAGTCTTCGGCTTGAAAGAAAATTAG
52135 CTAAGCATGGCCAAATTCATACTTAGCATAATTGAAAACGAAATTTTAAAAGAAAATAGGAGAAG
326 CTAAGCATGGCCAAATTCATACTTAGCATAATTGAAAACGAAATTTTAAAAGAAAATAGGAGAAG
52200 TATGCACAGAATAGAGAGAAAGCTAGAGAGAAAAAGATGATTTAATTCTCAGATGAGAGAGATGT
391 TATGCACAGAATAGAGAGAAAGCTAGAGAGAAAAAGATGATTTAATTCTCAGATGAGAGAGATGT
52265 GTTTCTAGGCTCACCCTTAGAGGGTATTTATAGC
456 GTTTCTAGGCTCACCCTTAGAGGGTATTTATAGC
52299 CTTCAA-ATTC
1 CTTCAAGATTC
52309 CTAAAAATAA
Statistics
Matches: 494, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
487 4 0.01
488 268 0.54
489 222 0.45
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (489 bp):
CTTCAAGATTCACGTCGGCTTACAAGGACAATTCTTTGCTACCAACTCGGATTATGTCGTTTCAA
CAATAACTGATTTCGATCTCAGTTTCCTCTTAGCAAACAATTTTGCTAAGTGTGTTCTCGGGAAG
TCAAATATGCTCCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAACATCCAGACTAATGT
CAAAATTGTTTTAATTTGAAAAGTAAGGTAAAAAAACAAAGAGAAAAAATCCGAAGCGATTTAAG
TACCTTAAAATTCTCACGTTTGGAATTGAGCCTTCGATTTAGTCTTCGGCTTGAAAGAAAATTAG
CTAAGCATGGCCAAATTCATACTTAGCATAATTGAAAACGAAATTTTAAAAGAAAATAGGAGAAG
TATGCACAGAATAGAGAGAAAGCTAGAGAGAAAAAGATGATTTAATTCTCAGATGAGAGAGATGT
GTTTCTAGGCTCACCCTTAGAGGGTATTTATAGC
Found at i:52422 original size:45 final size:43
Alignment explanation
Indices: 52368--52476 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 43
52358 AAAAACACTT
*
52368 AAAATTATTTAAACTAAAATACCTAAAACAAAGATAAACA-AAAA
1 AAAACTATTTAAACTAAAATACCTAAAACAAA-ATAAA-ATAAAA
* * * * **
52412 AAATACTATTTAAAATAATAT-CCTAAACCTAAATAAAATACTA
1 AAA-ACTATTTAAACTAAAATACCTAAAACAAAATAAAATAAAA
*
52455 AAACCTATTTAAACTAAAATAC
1 AAAACTATTTAAACTAAAATAC
52477 AAAGATAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
42 15 0.29
43 11 0.21
44 12 0.23
45 14 0.27
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.26
Consensus pattern (43 bp):
AAAACTATTTAAACTAAAATACCTAAAACAAAATAAAATAAAA
Found at i:59456 original size:15 final size:15
Alignment explanation
Indices: 59435--59474 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
59425 TAAATTTTAG
*
59435 AAAATGAATTATTGG
1 AAAATGAATTATTGA
*
59450 AATATGAATT-TTGA
1 AAAATGAATTATTGA
59464 AAAATGAATTA
1 AAAATGAATTA
59475 CATTTCTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (15 bp):
AAAATGAATTATTGA
Found at i:59781 original size:31 final size:29
Alignment explanation
Indices: 59713--59843 Score: 70
Period size: 31 Copynumber: 4.3 Consensus size: 29
59703 AATATTATTT
*
59713 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
59743 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * * *
59776 TTATATTAATTATTTATTAAAGTAATAGT-G
1 TTATATT--TTATTAATAAAAATATTAATAA
* * *
59806 TTATATTATATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
*
59834 GTATATTTTA
1 TTATATTTTA
59844 AATATCTTTA
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
27 9 0.12
28 12 0.16
30 8 0.11
31 22 0.29
32 6 0.08
33 19 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:59862 original size:23 final size:23
Alignment explanation
Indices: 59813--59863 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
59803 GTGTTATATT
**
59813 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
59836 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
59859 ATATT
1 ATATT
59864 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:61476 original size:23 final size:23
Alignment explanation
Indices: 61450--61495 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
61440 AATGCAAATT
61450 AATGAATCTATGAAATCTTTAAC
1 AATGAATCTATGAAATCTTTAAC
61473 AATGAATCTATGAAATCTTTAAC
1 AATGAATCTATGAAATCTTTAAC
61496 GTGATTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (23 bp):
AATGAATCTATGAAATCTTTAAC
Found at i:71072 original size:21 final size:21
Alignment explanation
Indices: 71030--71072 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
71020 AAGGTCTCAC
* *
71030 TTTATTGGGTTTTGCTTTTTA
1 TTTATTGGGTTATGCTTATTA
71051 TTTATTGGGTTGATGC-TATTA
1 TTTATTGGGTT-ATGCTTATTA
71072 T
1 T
71073 CTCTAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.14, C:0.05, G:0.21, T:0.60
Consensus pattern (21 bp):
TTTATTGGGTTATGCTTATTA
Found at i:72423 original size:72 final size:72
Alignment explanation
Indices: 72333--72573 Score: 378
Period size: 72 Copynumber: 3.3 Consensus size: 72
72323 CAAGCCCCAG
*
72333 ATGATTGTG-CCAGCCATCATGATCACC-TGGACCATGGACATAAACATGAACATGCTCATAGTC
1 ATGATTGTGCCCA-TCATCATGATCACCAT-GACCATGGACATAAACATGAACATGCTCATAGTC
72396 ATGACAACC
64 ATGACAACC
* * *
72405 ATGATTCTGCCCATCATCATGATCACCATGACCATGGACATGAACGTGAACATGCTCATAGTCAT
1 ATGATTGTGCCCATCATCATGATCACCATGACCATGGACATAAACATGAACATGCTCATAGTCAT
72470 GACAACC
66 GACAACC
* *
72477 ATGATTGTGCCCACCATCATGATCACCATGACCATGGACATAAACATGATCATGCTCATAGTCAT
1 ATGATTGTGCCCATCATCATGATCACCATGACCATGGACATAAACATGAACATGCTCATAGTCAT
*
72542 GACCACC
66 GACAACC
*
72549 TTGATTGTGCCCATCATCATGATCA
1 ATGATTGTGCCCATCATCATGATCA
72574 AGGCCTGCAC
Statistics
Matches: 155, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
72 151 0.97
73 4 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (72 bp):
ATGATTGTGCCCATCATCATGATCACCATGACCATGGACATAAACATGAACATGCTCATAGTCAT
GACAACC
Found at i:75700 original size:9 final size:9
Alignment explanation
Indices: 75686--75712 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
75676 TATGGACTTT
75686 GAGCAGTTG
1 GAGCAGTTG
75695 GAGCAGTTG
1 GAGCAGTTG
75704 GAGCAGTTG
1 GAGCAGTTG
75713 TACATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (9 bp):
GAGCAGTTG
Found at i:81733 original size:24 final size:24
Alignment explanation
Indices: 81693--81741 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
81683 TTTTTTATAT
*
81693 ATAATAATATTACATATTTAATTA
1 ATAATAATATTACATATTAAATTA
* *
81717 ATAATAATTTTATATATTAAATTA
1 ATAATAATATTACATATTAAATTA
81741 A
1 A
81742 ACTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATAATATTACATATTAAATTA
Found at i:82568 original size:2 final size:2
Alignment explanation
Indices: 82563--82605 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
82553 ATAATGTGTG
82563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82605 T
1 T
82606 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:86410 original size:21 final size:22
Alignment explanation
Indices: 86384--86428 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
86374 CCATTCCTAA
86384 TCCAAGCAAATATT-TTTCTTT
1 TCCAAGCAAATATTATTTCTTT
* * *
86405 TCCAAGTAACTCTTATTTCTTT
1 TCCAAGCAAATATTATTTCTTT
86427 TC
1 TC
86429 TTTCTTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.49
Consensus pattern (22 bp):
TCCAAGCAAATATTATTTCTTT
Found at i:89380 original size:21 final size:21
Alignment explanation
Indices: 89356--89395 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
89346 TTTATTTTAT
89356 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
89377 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
89396 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:89443 original size:33 final size:33
Alignment explanation
Indices: 89390--89488 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
89380 TTTGTTTCAA
89390 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
89422 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
89455 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
89488 T
1 T
89489 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:89517 original size:13 final size:13
Alignment explanation
Indices: 89474--89528 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
89464 TTGGAAGTAT
89474 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
89487 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
89501 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
89514 TTAAGTATTTGAA
1 TTAAGTATTTCAA
89527 TT
1 TT
89529 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:89751 original size:21 final size:21
Alignment explanation
Indices: 89725--89781 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
89715 TAGAGCGTGG
*
89725 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
89746 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
89767 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
89782 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:97516 original size:27 final size:27
Alignment explanation
Indices: 97477--97544 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
97467 TTGTAGGAAT
97477 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
97502 TATAGATATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
97529 TATAGAGATATGATTT
1 TATAGAGATATGATTT
97545 TGTAAATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 6 0.15
27 33 0.85
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:101292 original size:27 final size:26
Alignment explanation
Indices: 101216--101296 Score: 128
Period size: 26 Copynumber: 3.1 Consensus size: 26
101206 TAGGAATTAT
101216 AGAGATGATTGTTACCATTCCTATAG
1 AGAGATGATTGTTACCATTCCTATAG
* *
101242 ATATATGATTGTTA-CATTCCTATAG
1 AGAGATGATTGTTACCATTCCTATAG
101267 AGAGATGATTTGTTACCATTCCTATAG
1 AGAGATGA-TTGTTACCATTCCTATAG
101294 AGA
1 AGA
101297 TGATTTTGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
25 17 0.35
26 18 0.37
27 14 0.29
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (26 bp):
AGAGATGATTGTTACCATTCCTATAG
Found at i:101297 original size:25 final size:25
Alignment explanation
Indices: 101213--101302 Score: 114
Period size: 25 Copynumber: 3.6 Consensus size: 25
101203 GTGTAGGAAT
101213 TATAGAGATGA-TTGTTACCATTCC
1 TATAGAGATGATTTGTTACCATTCC
*
101237 TATAGATAT-ATGATTGTTA-CATTCC
1 TATAGAGATGAT--TTGTTACCATTCC
101262 TATAGAGAGATGATTTGTTACCATTCC
1 TAT--AGAGATGATTTGTTACCATTCC
101289 TATAGAGATGATTT
1 TATAGAGATGATTT
101303 TGTAAAGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.02
24 8 0.14
25 20 0.35
26 12 0.21
27 14 0.25
28 2 0.04
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (25 bp):
TATAGAGATGATTTGTTACCATTCC
Found at i:101304 original size:26 final size:27
Alignment explanation
Indices: 101219--101305 Score: 110
Period size: 26 Copynumber: 3.3 Consensus size: 27
101209 GAATTATAGA
* *
101219 GATGATTGTTACCATTCCTATAGATAT
1 GATGTTTGTTACCATTCCTATAGAGAT
*
101246 -ATGATTGTTA-CATTCCTATAGAGA-
1 GATGTTTGTTACCATTCCTATAGAGAT
101270 GATGATTTGTTACCATTCCTATAGAGAT
1 GATG-TTTGTTACCATTCCTATAGAGAT
101298 GAT-TTTGT
1 GATGTTTGT
101306 AAAGAGAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
25 16 0.30
26 21 0.39
27 14 0.26
28 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (27 bp):
GATGTTTGTTACCATTCCTATAGAGAT
Found at i:101539 original size:20 final size:19
Alignment explanation
Indices: 101514--101605 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 19
101504 TTTTCCTAAT
101514 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAAT-CGTAAA
101534 TCGCAATGCGAAT-GTAAA
1 TCGCAATGCGAATCGTAAA
** *
101552 TCGCAACACGAATC-TGACTA
1 TCGCAATGCGAATCGT-A-AA
101572 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAAT-CGTAAA
*
101592 TCGCAACGCGAATC
1 TCGCAATGCGAATC
101606 TGACTATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 17 0.28
19 2 0.03
20 38 0.63
21 2 0.03
22 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (19 bp):
TCGCAATGCGAATCGTAAA
Found at i:101604 original size:40 final size:38
Alignment explanation
Indices: 101533--101622 Score: 153
Period size: 40 Copynumber: 2.3 Consensus size: 38
101523 GAATACGTAA
101533 ATCGCAATGCGAATGTAAATCGCAACACGAATCTGACT
1 ATCGCAATGCGAATGTAAATCGCAACACGAATCTGACT
*
101571 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
1 ATCGCAATGCGAAT--GTAAATCGCAACACGAATCTGACT
101611 ATCGCAATGCGA
1 ATCGCAATGCGA
101623 TTTACATAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 14 0.29
40 35 0.71
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (38 bp):
ATCGCAATGCGAATGTAAATCGCAACACGAATCTGACT
Found at i:101614 original size:20 final size:20
Alignment explanation
Indices: 101551--101622 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
101541 GCGAATGTAA
*
101551 ATCGCAACACGAATCTGACT
1 ATCGCAACGCGAATCTGACT
* *
101571 ATCGCAATGCGAATAC-GTA-A
1 ATCGCAACGCGAAT-CTG-ACT
101591 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
*
101611 ATCGCAATGCGA
1 ATCGCAACGCGA
101623 TTTACATAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.05
20 38 0.90
21 2 0.05
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Found at i:101821 original size:22 final size:22
Alignment explanation
Indices: 101796--101861 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
101786 GGTGACATCC
101796 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
101818 GTCCCCATCTCCAACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
101840 GTCTCCATCTCTGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
101862 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:102215 original size:20 final size:19
Alignment explanation
Indices: 102190--102237 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
102180 GCGATTCTGT
*
102190 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATC-AATTCG
*
102210 CGTTGCGATAATCATTTCG
1 CGTTGCGATAATCAATTCG
*
102229 TGTTGCGAT
1 CGTTGCGAT
102238 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAATCAATTCG
Found at i:102233 original size:19 final size:19
Alignment explanation
Indices: 102191--102257 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
102181 CGATTCTGTC
* * *
102191 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAATC-ATTTCGT
102211 GTTGCGATAATCATTTCGT
1 GTTGCGATAATCATTTCGT
**
102230 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAATCA-TTTCGT
*
102250 GTAGCGAT
1 GTTGCGAT
102258 TTTCATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.40
20 24 0.60
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.40
Consensus pattern (19 bp):
GTTGCGATAATCATTTCGT
Found at i:102269 original size:21 final size:20
Alignment explanation
Indices: 102206--102281 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
102196 GATAGTCAAA
* **
102206 TTCGCGTTGCGATAATCA-T
1 TTCGTGTTGCGATTTTCATT
102225 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
102245 TTCGTGTAGCGATTTTCATTT
1 TTCGTGTTGCGATTTTCA-TT
*
102266 TTCGTGTTGCAATTTT
1 TTCGTGTTGCGATTTT
102282 AAGTTTCAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
19 15 0.31
20 18 0.37
21 16 0.33
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Done.