Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014042.1 Kokia drynarioides strain JFW-HI SEQ_129073, 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: 199966
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:3311 original size:30 final size:29
Alignment explanation
Indices: 3271--3345 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 29
3261 TTAAATTAGT
3271 AAAA-ATAAAA-TTATACTTTAATCCTATTA
1 AAAATATAAAATTTATA-TTTAATCCT-TTA
*
3300 AAAATATAAAATTTTTATTTAATCCTTTA
1 AAAATATAAAATTTATATTTAATCCTTTA
* *
3329 TAAAT-TACAATTT-TATT
1 AAAATATAAAATTTATATT
3346 ATCATAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.10
28 7 0.17
29 11 0.27
30 15 0.37
31 4 0.10
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATATAAAATTTATATTTAATCCTTTA
Found at i:4120 original size:20 final size:20
Alignment explanation
Indices: 4097--4134 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4087 AAAAACATTA
4097 CATAAAATTTCAAA-ACTTTT
1 CATAAAA-TTCAAACACTTTT
*
4117 CATAATATTCAAACACTT
1 CATAAAATTCAAACACTT
4135 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (20 bp):
CATAAAATTCAAACACTTTT
Found at i:4881 original size:10 final size:10
Alignment explanation
Indices: 4868--4901 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
4858 TTTTTATTAA
4868 TTTTTAATTT
1 TTTTTAATTT
4878 TTTTTAATTT
1 TTTTTAATTT
*
4888 TATTTAATATT
1 TTTTTAAT-TT
4899 TTT
1 TTT
4902 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:9784 original size:20 final size:20
Alignment explanation
Indices: 9746--9784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9736 TAAAAAGAAC
*
9746 TTTTCCCTAAAAAAGTGCTT
1 TTTTCCCTAAAAAACTGCTT
* *
9766 TTTTCCTTAAAACACTGCT
1 TTTTCCCTAAAAAACTGCT
9785 AAACAAATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCCTAAAAAACTGCTT
Found at i:12359 original size:13 final size:13
Alignment explanation
Indices: 12341--12374 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
12331 CTAAATACAA
12341 ATATTTAATGATT
1 ATATTTAATGATT
12354 ATATTTAATGATT
1 ATATTTAATGATT
12367 ATATTTAA
1 ATATTTAA
12375 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
ATATTTAATGATT
Found at i:13142 original size:21 final size:22
Alignment explanation
Indices: 13118--13158 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13108 TTGCCTGCCA
13118 TGTCGCGACATGGA-TCCTGTG
1 TGTCGCGACATGGACTCCTGTG
* *
13139 TGTCTCGACATTGACTCCTG
1 TGTCGCGACATGGACTCCTG
13159 AACGCGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (22 bp):
TGTCGCGACATGGACTCCTGTG
Found at i:22613 original size:21 final size:22
Alignment explanation
Indices: 22560--22603 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
22550 CGATACTTAT
*
22560 GACAGTTCTACCGATACAAGTGA
1 GACA-TTCTACCGATACAAGTCA
22583 GACATT-TACCGATACAAGTCA
1 GACATTCTACCGATACAAGTCA
22604 TGCTTCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 2 0.10
23 4 0.20
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (22 bp):
GACATTCTACCGATACAAGTCA
Found at i:27833 original size:36 final size:37
Alignment explanation
Indices: 27793--27930 Score: 178
Period size: 36 Copynumber: 3.8 Consensus size: 37
27783 ATCGTTATTC
* * *
27793 ATTTTATTCATTATTGACCCTG-AGGTCATGATGCTT
1 ATTTTACTCCTTATTGACCCTGAAGATCATGATGCTT
27829 ATTTTACT-CTCTATTGACCCTG-AGATCATGATGCTT
1 ATTTTACTCCT-TATTGACCCTGAAGATCATGATGCTT
*
27865 ATTTTACTCCTTATTGA-CCTGAAGATCATGATGCTC
1 ATTTTACTCCTTATTGACCCTGAAGATCATGATGCTT
* *
27901 ATTTTACTCCTTGTTGACCC-GAAGGTCATG
1 ATTTTACTCCTTATTGACCCTGAAGATCATG
27931 CCTGTAACCA
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
35 5 0.05
36 83 0.90
37 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (37 bp):
ATTTTACTCCTTATTGACCCTGAAGATCATGATGCTT
Found at i:33231 original size:15 final size:15
Alignment explanation
Indices: 33207--33242 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
33197 GCATAAAATT
* *
33207 TAAAAATGAAACAAG
1 TAAAAGTGAAACAAA
33222 TAAAAGTGAAACAAA
1 TAAAAGTGAAACAAA
33237 TAAAAG
1 TAAAAG
33243 AAAATGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.06, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAGTGAAACAAA
Found at i:44655 original size:37 final size:38
Alignment explanation
Indices: 44614--44701 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
44604 GTACATGTTC
* *
44614 ATGCAACAACA-TTCTTGGGTGCAA-TTGAAGGATACTT
1 ATGCAACAACAGTT-TTGGATGCAATTTGAAGAATACTT
* * *
44651 ATGCAGCAATAGTTTTGGATGCAATTTGAAGAATATTT
1 ATGCAACAACAGTTTTGGATGCAATTTGAAGAATACTT
* *
44689 ATGTAGCAACAGT
1 ATGCAACAACAGT
44702 CTAGGCTGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 18 0.43
38 24 0.57
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (38 bp):
ATGCAACAACAGTTTTGGATGCAATTTGAAGAATACTT
Found at i:51433 original size:22 final size:22
Alignment explanation
Indices: 51408--51450 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
51398 GCTACTACTA
51408 CTGCAACCCAAGCTTGTTGCTG
1 CTGCAACCCAAGCTTGTTGCTG
* *
51430 CTGCAGCCCATGCTTGTTGCT
1 CTGCAACCCAAGCTTGTTGCT
51451 ACCCTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.33, G:0.23, T:0.30
Consensus pattern (22 bp):
CTGCAACCCAAGCTTGTTGCTG
Found at i:65080 original size:20 final size:20
Alignment explanation
Indices: 65055--65101 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
65045 ATTCCTTCTT
65055 ATTTTACAAATTTAGTTATA
1 ATTTTACAAATTTAGTTATA
*
65075 ATTTTACGAATTTAGTTATA
1 ATTTTACAAATTTAGTTATA
65095 ATTTTAC
1 ATTTTAC
65102 TTGAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTTACAAATTTAGTTATA
Found at i:73693 original size:61 final size:63
Alignment explanation
Indices: 73600--73716 Score: 211
Period size: 61 Copynumber: 1.9 Consensus size: 63
73590 AGATTGTCTG
*
73600 CAACATGCAAACAATGCTTTATATGTTAATAATATCCGTAGCAATTCTTATGGTAATTGTCCA
1 CAACATGCAAACAATACTTTATATGTTAATAATATCCGTAGCAATTCTTATGGTAATTGTCCA
73663 CAACATGC-AA-AATACTTTATATGTTAATAATATCCGTAGCAATTCTTATGGTAA
1 CAACATGCAAACAATACTTTATATGTTAATAATATCCGTAGCAATTCTTATGGTAA
73717 CTCTTACAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
61 43 0.81
62 2 0.04
63 8 0.15
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (63 bp):
CAACATGCAAACAATACTTTATATGTTAATAATATCCGTAGCAATTCTTATGGTAATTGTCCA
Found at i:76995 original size:92 final size:92
Alignment explanation
Indices: 76828--77012 Score: 253
Period size: 92 Copynumber: 2.0 Consensus size: 92
76818 GTTGCAGACC
* * * *
76828 ATCTGTCTCAACTAGAAGTTCGCAATGAAGATGGAAACATACTTCAAATTGTCAACGTATTCCCA
1 ATCTGTCTCAACTAGAAGTTAGCAATGAAGATGGAAACACACTTCAAACTGTCAACGCATTCCCA
* * *
76893 GATGAGAAGTTATTTACTGTAGATGCA
66 AATGAAAAGTTATTTACTCTAGATGCA
* * * * *
76920 ATCTGTCTCGACTGGAAGTTAGTAGTGAAGATGGAAACACACTTCAAACTGTCGACGCATTCCCA
1 ATCTGTCTCAACTAGAAGTTAGCAATGAAGATGGAAACACACTTCAAACTGTCAACGCATTCCCA
*
76985 AATGAAAAGTTATTTGCTCTAGATGCA
66 AATGAAAAGTTATTTACTCTAGATGCA
77012 A
1 A
77013 CTACATGGTA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
92 80 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (92 bp):
ATCTGTCTCAACTAGAAGTTAGCAATGAAGATGGAAACACACTTCAAACTGTCAACGCATTCCCA
AATGAAAAGTTATTTACTCTAGATGCA
Found at i:94348 original size:20 final size:21
Alignment explanation
Indices: 94312--94350 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
94302 ATTTTTGTTA
94312 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTATTTGTTTCACT
94333 TTTACTTTTA-TTGTTTCA
1 TTTACTTTTATTTGTTTCA
94351 AATTCCTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTACTTTTATTTGTTTCACT
Found at i:97256 original size:18 final size:18
Alignment explanation
Indices: 97217--97257 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
97207 CAGTCATTTG
* *
97217 AAAAAGAAACAAAATGAG
1 AAAAAGAAACAAAAAGAA
*
97235 AAAAAGAAAGAAAAAGAA
1 AAAAAGAAACAAAAAGAA
97253 AAAAA
1 AAAAA
97258 AATCTTGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAGAAACAAAAAGAA
Found at i:105517 original size:16 final size:18
Alignment explanation
Indices: 105496--105534 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
105486 ATTACAGTCA
*
105496 CACAATC-AGA-TGCAAC
1 CACAATCGAGATTACAAC
105512 CACAATCGAGATTACAAC
1 CACAATCGAGATTACAAC
105530 CACAA
1 CACAA
105535 CAGTTTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 10 0.50
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (18 bp):
CACAATCGAGATTACAAC
Found at i:131615 original size:17 final size:17
Alignment explanation
Indices: 131594--131640 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
131584 GAAATGTAAT
*
131594 GACAATGCAAATGCTAGA
1 GACAATGAAAATGC-AGA
*
131612 -ACAAAGAAAATGCAGA
1 GACAATGAAAATGCAGA
*
131628 GACAATAAAAATG
1 GACAATGAAAATG
131641 GAATGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (17 bp):
GACAATGAAAATGCAGA
Found at i:132069 original size:18 final size:18
Alignment explanation
Indices: 132042--132091 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
132032 CAACATCTTC
*
132042 TTCTTTTTCTTCCTTCTA
1 TTCTTCTTCTTCCTTCTA
* *
132060 TTCTTCTTCTT-CTTGTT
1 TTCTTCTTCTTCCTTCTA
132077 TTCTTACTTCTTCCT
1 TTCTT-CTTCTTCCT
132092 CTACCTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.33
18 16 0.59
19 2 0.07
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (18 bp):
TTCTTCTTCTTCCTTCTA
Found at i:132165 original size:21 final size:20
Alignment explanation
Indices: 132130--132169 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
132120 TATGCGTACT
132130 TCCACCACAGCAGCCTCTCAC
1 TCCACCACAGCAGCC-CTCAC
* *
132151 TCCACCATAGTAGCCCTCA
1 TCCACCACAGCAGCCCTCA
132170 AGTTGTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.47, G:0.10, T:0.17
Consensus pattern (20 bp):
TCCACCACAGCAGCCCTCAC
Found at i:138311 original size:24 final size:24
Alignment explanation
Indices: 138274--138328 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
138264 GTTAAGAGTA
*
138274 AAAACTGTCAGTGCAAAAGTAATAT
1 AAAA-TGTCAGTGCAAAAGTAACAT
* *
138299 AAAATGTTAGTGCAAATGTAACAT
1 AAAATGTCAGTGCAAAAGTAACAT
138323 AAAATG
1 AAAATG
138329 AATTGATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (24 bp):
AAAATGTCAGTGCAAAAGTAACAT
Found at i:141962 original size:26 final size:26
Alignment explanation
Indices: 141924--142000 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
141914 AATTCTAGAT
* *
141924 ACAATTTTGGACATGCTCATACAGCG
1 ACAATTCTAGACATGCTCATACAGCG
* * *
141950 ATAATTCTAGACATGTTCATGCAGCG
1 ACAATTCTAGACATGCTCATACAGCG
* *
141976 ACAATTTTGGACATGCTCATACAGC
1 ACAATTCTAGACATGCTCATACAGC
142001 AACATTAATA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (26 bp):
ACAATTCTAGACATGCTCATACAGCG
Found at i:152034 original size:26 final size:26
Alignment explanation
Indices: 151990--152095 Score: 140
Period size: 26 Copynumber: 4.1 Consensus size: 26
151980 ATTCTAGATG
** *
151990 CAATTCTGGATGTGCTCATGCAGCGA
1 CAATTCTGGACATGCTCATGCAACGA
*
152016 CAATTCTGGACATGTTCATGCAACGA
1 CAATTCTGGACATGCTCATGCAACGA
* *
152042 CAATTCTTGACATGTTCATGCAACGA
1 CAATTCTGGACATGCTCATGCAACGA
* *
152068 CAATTTTGGACATGCTCATACAACGA
1 CAATTCTGGACATGCTCATGCAACGA
152094 CA
1 CA
152096 TTAGTAGTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (26 bp):
CAATTCTGGACATGCTCATGCAACGA
Found at i:153418 original size:22 final size:23
Alignment explanation
Indices: 153386--153429 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
153376 AGTGAAAAGA
* *
153386 ACAAAATGAAACGAGT-AGAAAT
1 ACAAAAAGAAAAGAGTAAGAAAT
153408 ACAAAAAGAAAAGAGTAAGAAA
1 ACAAAAAGAAAAGAGTAAGAAA
153430 AAATGTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.66, C:0.07, G:0.18, T:0.09
Consensus pattern (23 bp):
ACAAAAAGAAAAGAGTAAGAAAT
Found at i:153595 original size:23 final size:25
Alignment explanation
Indices: 153549--153595 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
153539 TGATTTCCTA
153549 AAGGAAGAAATAAGGAAGGTGAGAG
1 AAGGAAGAAATAAGGAAGGTGAGAG
153574 AAGG-AGAAATAAGG-AGGTGAGA
1 AAGGAAGAAATAAGGAAGGTGAGA
153596 TGTAGTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.36
24 10 0.45
25 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (25 bp):
AAGGAAGAAATAAGGAAGGTGAGAG
Found at i:153871 original size:24 final size:24
Alignment explanation
Indices: 153838--153884 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
153828 GTTAAGAGCA
*
153838 AAAATTGTCAGTGCAAATGTAATAC
1 AAAATTGTCAGAGCAAAT-TAATAC
153863 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
153885 AAATATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAC
Found at i:160162 original size:24 final size:24
Alignment explanation
Indices: 160135--160187 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
160125 CAAATAACAT
160135 TTAGCCTACACAAGCCCAGAATGA
1 TTAGCCTACACAAGCCCAGAATGA
* ** * *
160159 TTAGCTTTTACGAGCCCAGAATGG
1 TTAGCCTACACAAGCCCAGAATGA
160183 TTAGC
1 TTAGC
160188 TATTACGATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
TTAGCCTACACAAGCCCAGAATGA
Found at i:160188 original size:24 final size:24
Alignment explanation
Indices: 160147--160202 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
160137 AGCCTACACA
*
160147 AGCCCAGAATGATTAGCTTTTACG
1 AGCCCAGAATGATTAGCTATTACG
*
160171 AGCCCAGAATGGTTAGCTATTACG
1 AGCCCAGAATGATTAGCTATTACG
*
160195 ATCCCAGA
1 AGCCCAGA
160203 TAGAGTTCAA
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:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (24 bp):
AGCCCAGAATGATTAGCTATTACG
Found at i:167327 original size:16 final size:16
Alignment explanation
Indices: 167306--167336 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
167296 ATAATGTGAA
167306 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
167322 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
167337 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:181440 original size:15 final size:15
Alignment explanation
Indices: 181395--181440 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
181385 ACTATTTACC
*
181395 ATTTACTTTTCTTGC
1 ATTTACTTTTCTTGT
**
181410 ATTTAAATTT-TTGT
1 ATTTACTTTTCTTGT
181424 ATTTACTTTTCTTGT
1 ATTTACTTTTCTTGT
181439 AT
1 AT
181441 CAAAACAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.63
Consensus pattern (15 bp):
ATTTACTTTTCTTGT
Found at i:189505 original size:7 final size:7
Alignment explanation
Indices: 189493--189517 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
189483 ACCAAGCTAC
189493 ATCACAT
1 ATCACAT
189500 ATCACAT
1 ATCACAT
189507 ATCACAT
1 ATCACAT
189514 ATCA
1 ATCA
189518 AGATATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
ATCACAT
Found at i:198291 original size:19 final size:19
Alignment explanation
Indices: 198265--198339 Score: 89
Period size: 19 Copynumber: 4.0 Consensus size: 19
198255 AGTCAATAAT
* *
198265 TCGCTCTTATGATCCAGTA
1 TCGCTCTTACGAGCCAGTA
*
198284 TTGCTCTTACGAGCCAGTA
1 TCGCTCTTACGAGCCAGTA
* *
198303 TCGCTCATA-GAGCAAGTA
1 TCGCTCTTACGAGCCAGTA
*
198321 TCGCTCTTACGATCCAGTA
1 TCGCTCTTACGAGCCAGTA
198340 CAATATATCG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
18 16 0.35
19 30 0.65
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (19 bp):
TCGCTCTTACGAGCCAGTA
Found at i:198320 original size:18 final size:19
Alignment explanation
Indices: 198280--198332 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
198270 CTTATGATCC
* * *
198280 AGTATTGCTCTTACGAGCC
1 AGTATCGCTCATACGAGCA
198299 AGTATCGCTCATA-GAGCA
1 AGTATCGCTCATACGAGCA
*
198317 AGTATCGCTCTTACGA
1 AGTATCGCTCATACGA
198333 TCCAGTACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (19 bp):
AGTATCGCTCATACGAGCA
Found at i:198396 original size:26 final size:26
Alignment explanation
Indices: 198319--198396 Score: 111
Period size: 26 Copynumber: 3.0 Consensus size: 26
198309 ATAGAGCAAG
* *
198319 TATCGCTCTTACGATCCAGTACAATA
1 TATCGCTCTTACGAGCCAGTACAGTA
*
198345 TATCGCTCTTACGAGCCGGTACAGTA
1 TATCGCTCTTACGAGCCAGTACAGTA
* *
198371 TATTGCTCTTACGAGCCAGTATAGTA
1 TATCGCTCTTACGAGCCAGTACAGTA
198397 ATCTCTTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (26 bp):
TATCGCTCTTACGAGCCAGTACAGTA
Done.