Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014424.1 Kokia drynarioides strain JFW-HI SEQ_129462, 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: 134182
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:16846 original size:18 final size:18
Alignment explanation
Indices: 16825--16874 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
16815 TTCAAACTTG
16825 TGACTGCATCTGATTATA
1 TGACTGCATCTGATTATA
* *
16843 TGACTGCATCTAATTATG
1 TGACTGCATCTGATTATA
16861 TGA-TCGCATCTGAT
1 TGACT-GCATCTGAT
16875 CAGGTTGCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (18 bp):
TGACTGCATCTGATTATA
Found at i:44379 original size:25 final size:25
Alignment explanation
Indices: 44350--44402 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
44340 ATATCATGAC
44350 ATATCATCAACTGGATGATGAGAAT
1 ATATCATCAACTGGATGATGAGAAT
44375 ATATCATCAACTGGATGATGAGAAT
1 ATATCATCAACTGGATGATGAGAAT
44400 ATA
1 ATA
44403 CATACGACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (25 bp):
ATATCATCAACTGGATGATGAGAAT
Found at i:48269 original size:12 final size:12
Alignment explanation
Indices: 48252--48276 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48242 TAACCCCTAA
48252 TAAAATTATTTT
1 TAAAATTATTTT
48264 TAAAATTATTTT
1 TAAAATTATTTT
48276 T
1 T
48277 CGACCCAAAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAAATTATTTT
Found at i:52060 original size:23 final size:23
Alignment explanation
Indices: 52034--52081 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
52024 CTGCACACTA
52034 AAATAGTCAATCAATGTTATCGC
1 AAATAGTCAATCAATGTTATCGC
52057 AAATAGTCAATCAATGTTATCGC
1 AAATAGTCAATCAATGTTATCGC
52080 AA
1 AA
52082 TTAGAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (23 bp):
AAATAGTCAATCAATGTTATCGC
Found at i:65206 original size:14 final size:15
Alignment explanation
Indices: 65179--65214 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
65169 TTCCATTTAA
65179 AACAAA-AAGAAAAT
1 AACAAAGAAGAAAAT
65193 AACAAAGAAG-AAAT
1 AACAAAGAAGAAAAT
65207 AA-AAAGAA
1 AACAAAGAA
65215 ACTAAAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 12 0.57
15 3 0.14
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (15 bp):
AACAAAGAAGAAAAT
Found at i:66028 original size:103 final size:103
Alignment explanation
Indices: 65849--66044 Score: 261
Period size: 103 Copynumber: 1.9 Consensus size: 103
65839 CACAAACTAA
* *
65849 GTAGGAGTTGCAATCTTAAACCAGCTAACTCAGAGAGATTTAGGTTGAAATCTTAAATCAGCTAT
1 GTAGGAGTTGCAATCTTAAACCAGCTAACTCAGAGAGATTTAGGTTGAAATCTTAAATCAACTAA
*
65914 CCTTTAAACATCAACTGGGAACATAGGTTCAGAGCTGT
66 CCCTTAAACATCAACTGGGAACATAGGTTCAGAGCTGT
* * * **
65952 GTAGGAGTTGCGATCTTAAATCATCTAACTC-GAAGAGATTTTA-GTTGCGATCTTAAATCAACT
1 GTAGGAGTTGCAATCTTAAACCAGCTAACTCAG-AGAGA-TTTAGGTTGAAATCTTAAATCAACT
** *
66015 AACCCTTAAACATCATTTGGGAACGTAGGT
64 AACCCTTAAACATCAACTGGGAACATAGGT
66045 CCATGATTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
102 1 0.01
103 75 0.94
104 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (103 bp):
GTAGGAGTTGCAATCTTAAACCAGCTAACTCAGAGAGATTTAGGTTGAAATCTTAAATCAACTAA
CCCTTAAACATCAACTGGGAACATAGGTTCAGAGCTGT
Found at i:69982 original size:13 final size:13
Alignment explanation
Indices: 69950--69988 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
69940 TAGCTTTAAC
*
69950 TTAGATTAATTCAGT
1 TTAGATTAA-T-ACT
69965 TTAGATTAATACT
1 TTAGATTAATACT
69978 TTAGATTAATA
1 TTAGATTAATA
69989 TCATTCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.57
14 1 0.04
15 9 0.39
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (13 bp):
TTAGATTAATACT
Found at i:72105 original size:8 final size:8
Alignment explanation
Indices: 72082--72134 Score: 58
Period size: 7 Copynumber: 6.9 Consensus size: 8
72072 AACAACCTAT
72082 AAAAT-AA
1 AAAATAAA
72089 AAAAT-AA
1 AAAATAAA
72096 AAAAT-AA
1 AAAATAAA
72103 AAAATAAA
1 AAAATAAA
*
72111 AAAAAAACA
1 AAAATAA-A
*
72120 AAAATAAG
1 AAAATAAA
72128 AAAATAA
1 AAAATAA
72135 CAATTTTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
7 19 0.46
8 15 0.37
9 7 0.17
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:72123 original size:7 final size:7
Alignment explanation
Indices: 72082--72117 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
72072 AACAACCTAT
72082 AAAATAA
1 AAAATAA
72089 AAAATAA
1 AAAATAA
72096 AAAATAA
1 AAAATAA
72103 AAAATAA
1 AAAATAA
72110 AAAA-AA
1 AAAATAA
72116 AA
1 AA
72118 CAAAAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAATAA
Found at i:72136 original size:17 final size:16
Alignment explanation
Indices: 72088--72137 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
72078 CTATAAAATA
72088 AAAAATAAAAAAT-A-
1 AAAAATAAAAAATAAC
*
72102 AAAAATAAAAAAAAAAC
1 AAAAAT-AAAAAATAAC
72119 AAAAATAAGAAAATAAC
1 AAAAATAA-AAAATAAC
72136 AA
1 AA
72138 TTTTTTGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.20
15 6 0.20
16 3 0.10
17 15 0.50
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.10
Consensus pattern (16 bp):
AAAAATAAAAAATAAC
Found at i:83500 original size:137 final size:138
Alignment explanation
Indices: 83181--83731 Score: 742
Period size: 137 Copynumber: 4.0 Consensus size: 138
83171 TAGAAAAATG
* *
83181 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGACCGAAAATAATTAA
* * * * * *
83246 TATAATTATTTATACTAATAATTTCGATAAAATATATAAAATTAATATTATTTTATAAGAATCAA
66 TATAACTATTTATATTAATAAATTAGATAAAATATATACAATTAATATT-TTGTAT--GAATCAA
83311 ATTCATATATT
128 ATTCATATATT
* *
83322 AATTATATTCTTTCCAAAAGAATATAAATTTTCATGTCTTTTATATTTTGACCGAAAATAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGACCGAAAATAATTAA
* * *
83387 TATAACTATTTATATTAGT-AATTAGGTAAAATATATACAATTAATATTTTTTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTAGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
83451 CATATATT
131 CATATATT
* * * *
83459 AATTATTTTTTTTGCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGACCGAAAATAATTAA
* *
83524 TATAACTGTTTATATTAATAAATTAGGTAAAATATATACAATTAATATTTTGTATG--T-AAATT
66 TATAACTATTTATATTAATAAATTAGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
* *
83586 CATGTACT
131 CATATATT
* *
83594 AATTATATTCTTTCCAAAAGAATATTAATTTCCACGTCTTTTATATTTTGA-CAAAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGACCGAAAA-TAATTA
** * * * *
83658 ATATAAC-AGCTATATTAATAAATTTGATAAAATATGT--AATGAATATTTTGTATGAATC-GAT
65 ATATAACTATTTATATTAATAAATTAGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
83719 TCATATATT
130 TCATATATT
83728 AATT
1 AATT
83732 TTATCTATGT
Statistics
Matches: 369, Mismatches: 36, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
132 16 0.04
134 42 0.11
135 71 0.19
136 1 0.00
137 94 0.25
138 35 0.09
139 6 0.02
140 25 0.07
141 79 0.21
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGACCGAAAATAATTAA
TATAACTATTTATATTAATAAATTAGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:87752 original size:17 final size:17
Alignment explanation
Indices: 87713--87778 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
87703 ATATATATGG
**
87713 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
87730 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
*
87747 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
* *
87764 TAATGCAAGGACAAT
1 AAATGCAATGACAAT
87779 TATACTACAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:87770 original size:34 final size:34
Alignment explanation
Indices: 87713--87778 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
87703 ATATATATGG
*
87713 AAATGCAATGACAATGTAGATGC-AGTGACAATAA
1 AAATGCAATGACAATATAGATGCAAG-GACAATAA
*
87747 AAATGCAATGACATTAATA-ATGCAAGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAAGGACAAT
87779 TATACTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAAGGACAATAA
Found at i:98476 original size:36 final size:37
Alignment explanation
Indices: 98406--98481 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
98396 ACATGTTGCT
* *
98406 GCATGAGCACTTCTAGATTGCACCCAAAACTGTCGTC
1 GCATGAGCACTTCCAAATTGCACCCAAAACTGTCGTC
*
98443 GCATGAGCACTTCCAAATTGCA-CCAAAATTGTCGTC
1 GCATGAGCACTTCCAAATTGCACCCAAAACTGTCGTC
98479 GCA
1 GCA
98482 GGAATATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 16 0.44
37 20 0.56
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (37 bp):
GCATGAGCACTTCCAAATTGCACCCAAAACTGTCGTC
Found at i:101344 original size:37 final size:37
Alignment explanation
Indices: 101289--101365 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
101279 TAATGTCGTT
* * *
101289 GCATGAGCACTTCTAGATTGCGCCCAAAACTGTCACC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTATCACC
* *
101326 GCATGAGCACTTCCAGATTGTACCTAAAACTATCACC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTATCACC
101363 GCA
1 GCA
101366 GGAATATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (37 bp):
GCATGAGCACTTCCAGATTGCACCCAAAACTATCACC
Found at i:101477 original size:38 final size:37
Alignment explanation
Indices: 101398--101479 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
101388 AAGACTGTCC
* *
101398 TTGCATAAATATTTTTCAAATTGCATCCAGAACTATCG
1 TTGCATAAATATTCTTCAAATTGCACCCAGAACTA-CG
101436 TTGCATAAAATATTCTTC-AATTGCACCCAGGAATCTA-G
1 TTGCAT-AAATATTCTTCAAATTGCACCCA-GAA-CTACG
101474 TTGCAT
1 TTGCAT
101480 GAACATGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
38 23 0.59
39 13 0.33
40 3 0.08
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (37 bp):
TTGCATAAATATTCTTCAAATTGCACCCAGAACTACG
Found at i:104593 original size:25 final size:24
Alignment explanation
Indices: 104556--104603 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
104546 CCTATTCTTC
104556 CCCTATATGTCTCACTTCGTCTCACA
1 CCCTATATGTCTC-CTTC-TCTCACA
*
104582 CCCT-TATTTCTCCTTCTCTCAC
1 CCCTATATGTCTCCTTCTCTCAC
104604 CATCATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 4 0.19
25 7 0.33
26 4 0.19
ACGTcount: A:0.15, C:0.42, G:0.04, T:0.40
Consensus pattern (24 bp):
CCCTATATGTCTCCTTCTCTCACA
Found at i:111126 original size:22 final size:21
Alignment explanation
Indices: 111093--111133 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
111083 TATTTGAAAG
* *
111093 ATAATAACTAAGTTAAAATCT
1 ATAAAAACTAAGTGAAAATCT
111114 ATAAAAACATAAGTGAAAAT
1 ATAAAAAC-TAAGTGAAAAT
111134 ACTTGATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
ATAAAAACTAAGTGAAAATCT
Found at i:111947 original size:26 final size:26
Alignment explanation
Indices: 111890--111947 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
111880 CTTCTCCACA
*
111890 TATTTTTTTACTCATGATTCTCTTCT
1 TATTTTTTTACTCATCATTCTCTTCT
* * * * *
111916 TCTTTTTTTATTCATCTTTTTCTTTT
1 TATTTTTTTACTCATCATTCTCTTCT
111942 TATTTT
1 TATTTT
111948 GATTTTCCAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.71
Consensus pattern (26 bp):
TATTTTTTTACTCATCATTCTCTTCT
Found at i:112568 original size:19 final size:19
Alignment explanation
Indices: 112537--112574 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
112527 AGCACACATC
112537 AAAATAAACATAAAAACTA
1 AAAATAAACATAAAAACTA
112556 AAAATGAAA-ATAAAAACTA
1 AAAAT-AAACATAAAAACTA
112575 GATGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.16
Consensus pattern (19 bp):
AAAATAAACATAAAAACTA
Found at i:115823 original size:180 final size:180
Alignment explanation
Indices: 115513--115875 Score: 638
Period size: 180 Copynumber: 2.0 Consensus size: 180
115503 AAGATCAAAA
*
115513 TTTTCTTTATGAAAATCGTCATCTTCCTCCATAGGGATTGATTCTTCATTGGATTGGGGCTCAAT
1 TTTTCTTTATGAAAATCGTCATCTTCCTCCATAAGGATTGATTCTTCATTGGATTGGGGCTCAAT
*
115578 CTCGATTTTCACAAAGCTTTGAACTTCCCCTTCCAAGGATGAAACATCAATGTGCTCGCCGATTC
66 CTCGATTTTCACAAAGCTTTCAACTTCCCCTTCCAAGGATGAAACATCAATGTGCTCGCCGATTC
*
115643 AATCAAACAATTCTTCAAAGAATT-TATTTTTCATTTCCTCATCTATCCCT
131 AATCAAACAATTCTTCAAAGAATTCT-TTTTTCATTTCCTCATCTAGCCCT
*
115693 TTTTCTTTATGAAAATCGTCATCTTCCTCTATAAGGATTGATTCTTCATTGGATTGGGGCTCAAT
1 TTTTCTTTATGAAAATCGTCATCTTCCTCCATAAGGATTGATTCTTCATTGGATTGGGGCTCAAT
* * * *
115758 CTCGATTTTCACAAAGCTTTCAACTTCCCCTTCCAAGGATGAGACATCGATGTGCTTGTCGATTC
66 CTCGATTTTCACAAAGCTTTCAACTTCCCCTTCCAAGGATGAAACATCAATGTGCTCGCCGATTC
115823 AATCAAACAATTCTTCAAAGAATTCTTTTTTCATTTCCTCATCTAGCCCT
131 AATCAAACAATTCTTCAAAGAATTCTTTTTTCATTTCCTCATCTAGCCCT
115873 TTT
1 TTT
115876 CTTGTTCTCA
Statistics
Matches: 174, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
180 173 0.99
181 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (180 bp):
TTTTCTTTATGAAAATCGTCATCTTCCTCCATAAGGATTGATTCTTCATTGGATTGGGGCTCAAT
CTCGATTTTCACAAAGCTTTCAACTTCCCCTTCCAAGGATGAAACATCAATGTGCTCGCCGATTC
AATCAAACAATTCTTCAAAGAATTCTTTTTTCATTTCCTCATCTAGCCCT
Found at i:120755 original size:21 final size:20
Alignment explanation
Indices: 120731--120778 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
120721 AATTTTCCCA
*
120731 CTTTCTCTATGTATTTAAACC
1 CTTTCTCTATGT-TTGAAACC
*
120752 CTTTTTCTCTTTGTTTGAAACC
1 C--TTTCTCTATGTTTGAAACC
120774 CTTTC
1 CTTTC
120779 CTCTTCCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 4 0.17
21 1 0.04
22 8 0.35
23 10 0.43
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.52
Consensus pattern (20 bp):
CTTTCTCTATGTTTGAAACC
Found at i:120775 original size:22 final size:23
Alignment explanation
Indices: 120732--120777 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
120722 ATTTTCCCAC
*
120732 TTTCTCTATGTATTTAAACCCTT
1 TTTCTCTATGTATTGAAACCCTT
*
120755 TTTCTCTTTGT-TTGAAACCCTT
1 TTTCTCTATGTATTGAAACCCTT
120777 T
1 T
120778 CCTCTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.17, C:0.22, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTCTCTATGTATTGAAACCCTT
Found at i:121669 original size:9 final size:11
Alignment explanation
Indices: 121645--121673 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
121635 CTTATAAAAT
121645 AAAAAGAGAAG
1 AAAAAGAGAAG
121656 AAAAAGA-AAG
1 AAAAAGAGAAG
121666 AAAAAGAG
1 AAAAAGAG
121674 GAAATGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAG
Found at i:130807 original size:17 final size:15
Alignment explanation
Indices: 130770--130814 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
130760 TGAATAACGA
*
130770 AAAATAAATAAAAAT
1 AAAATAAATAAAAAC
130785 AAAATAAATAAAACACC
1 AAAATAAATAAAA-A-C
130802 AAAATAAATAAAA
1 AAAATAAATAAAA
130815 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 13 0.48
16 1 0.04
17 13 0.48
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAATAAAAAC
Found at i:130822 original size:17 final size:16
Alignment explanation
Indices: 130769--130822 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
130759 GTGAATAACG
130769 AAAAATAAATAAAAAT
1 AAAAATAAATAAAAAT
*
130785 -AAAATAAATAAAACAC
1 AAAAATAAATAAAA-AT
*
130801 CAAAATAAATAAAATAT
1 AAAAATAAATAAAA-AT
130818 AAAAA
1 AAAAA
130823 AAGCAAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 13 0.41
16 1 0.03
17 18 0.56
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Done.