Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004394.1 Kokia drynarioides strain JFW-HI SEQ_117770, 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: 207404
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 274 characters in sequence are not A, C, G, or T
Found at i:73 original size:14 final size:14
Alignment explanation
Indices: 30--73 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20 ATTAATTTTA
30 TTTTTTGTATTATAT
1 TTTTTTGTATTAT-T
** *
45 TTTGGTGTATAATT
1 TTTTTTGTATTATT
59 TTTTTTGTATTATT
1 TTTTTTGTATTATT
73 T
1 T
74 ATGTCAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (14 bp):
TTTTTTGTATTATT
Found at i:239 original size:27 final size:27
Alignment explanation
Indices: 152--224 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
142 CTTTTGATGT
* *
152 CGCCTGGCAGGTAGGAACCACTAGTGC
1 CGCCTGTCAGGTAGGCACCACTAGTGC
*
179 TGCCTGTCAGGTAGGCACCACTAGTGC
1 CGCCTGTCAGGTAGGCACCACTAGTGC
206 CGCCTGTCAGGTAGGCACC
1 CGCCTGTCAGGTAGGCACC
225 TTTGGTGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.18
Consensus pattern (27 bp):
CGCCTGTCAGGTAGGCACCACTAGTGC
Found at i:4647 original size:16 final size:15
Alignment explanation
Indices: 4628--4658 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4618 TAATAAATTC
4628 ATTTATAATTAAAGCA
1 ATTTATAA-TAAAGCA
4644 ATTTATAATAAAGCA
1 ATTTATAATAAAGCA
4659 TATCTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
ATTTATAATAAAGCA
Found at i:11225 original size:28 final size:28
Alignment explanation
Indices: 11193--11249 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
11183 TATAATTTAA
* *
11193 TGTGTAATTGTATATATGAATTTTTGAT
1 TGTGTAATTGTATACATGAAATTTTGAT
* *
11221 TGTGTAATTTTATACGTGAAATTTTGAT
1 TGTGTAATTGTATACATGAAATTTTGAT
11249 T
1 T
11250 TGATTAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.02, G:0.18, T:0.53
Consensus pattern (28 bp):
TGTGTAATTGTATACATGAAATTTTGAT
Found at i:15082 original size:34 final size:34
Alignment explanation
Indices: 15039--15105 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
15029 ACAGAATGAG
*
15039 GTATATTTCAAAAGTTCGTAATATCGGTAATTCT
1 GTATATTTCAAAAGTTCGTAATATCAGTAATTCT
*
15073 GTATATTTCAAAAGTTTGTAATATCAGTAATTC
1 GTATATTTCAAAAGTTCGTAATATCAGTAATTC
15106 CTTTTTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (34 bp):
GTATATTTCAAAAGTTCGTAATATCAGTAATTCT
Found at i:18932 original size:33 final size:33
Alignment explanation
Indices: 18893--18960 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
18883 ACAACAAGGG
18893 AATGCATTAAATTTCTTCATGTAGGATGAGGCA
1 AATGCATTAAATTTCTTCATGTAGGATGAGGCA
18926 AATGCATTAAATTTCTTCATGTAGGATGAGGCA
1 AATGCATTAAATTTCTTCATGTAGGATGAGGCA
18959 AA
1 AA
18961 ATGATAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (33 bp):
AATGCATTAAATTTCTTCATGTAGGATGAGGCA
Found at i:24417 original size:8 final size:8
Alignment explanation
Indices: 24404--24433 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
24394 GATTATGTGT
24404 TAAAAGCA
1 TAAAAGCA
24412 TAAAAGCA
1 TAAAAGCA
*
24420 TAAAACCA
1 TAAAAGCA
24428 TAAAAG
1 TAAAAG
24434 TTGAAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (8 bp):
TAAAAGCA
Found at i:38281 original size:30 final size:30
Alignment explanation
Indices: 38241--38302 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
38231 GTTGATAATT
* *
38241 TACAATAATTAGATCAAATCAAAATTTCATG
1 TACAATAATTACACCAAATCAAAATTT-ATG
*
38272 TACAA-AATTACACCAAATTAAAATTTATG
1 TACAATAATTACACCAAATCAAAATTTATG
38301 TA
1 TA
38303 TACAATTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 18 0.64
31 5 0.18
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (30 bp):
TACAATAATTACACCAAATCAAAATTTATG
Found at i:44628 original size:145 final size:144
Alignment explanation
Indices: 44348--44638 Score: 474
Period size: 145 Copynumber: 2.0 Consensus size: 144
44338 TTAAAAGGTC
*
44348 ATTGAGTATGTCCGTAAACATCTTCTGGCCACTGTTTTACAACTGCAAGAAAGAAAGAATTATTG
1 ATTGAGTATGTCCGTAAACATCTTCTGGCCACTGTTATACAACTGCAAGAAAGAAAGAATTATTG
*
44413 TAAGTGGAAATTTTTTTAAGTTAAAATTAAATTTTATATTTTTATTATCGTAAAAATATTATTTT
66 TAAGGGGAAATTTTTTTAAGTTAAAATTAAATTTTATATTTTTATTATCGTAAAAATATTA-TTT
44478 ATTATTTTAATAAAT
130 ATTATTTTAATAAAT
* * *
44493 ATTGAGTATGTCCGTAAACTTTTTCTGGCCACTGTTATACAACTGCAAGAAAGAATGAATTATTG
1 ATTGAGTATGTCCGTAAACATCTTCTGGCCACTGTTATACAACTGCAAGAAAGAAAGAATTATTG
**
44558 TAAGGGGAGAATTTTTTTTTAAGTTGGAATTAAATTTTATATTTTTATTATCGTAAAAATATTAT
66 TAAGGGGA-AA--TTTTTTTAAGTTAAAATTAAATTTTATATTTTTATTATCGTAAAAATATTA-
44623 TTTATTATTTTAATAA
127 TTTATTATTTTAATAA
44639 TTTATATTTT
Statistics
Matches: 136, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
145 68 0.50
146 2 0.01
148 66 0.49
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (144 bp):
ATTGAGTATGTCCGTAAACATCTTCTGGCCACTGTTATACAACTGCAAGAAAGAAAGAATTATTG
TAAGGGGAAATTTTTTTAAGTTAAAATTAAATTTTATATTTTTATTATCGTAAAAATATTATTTA
TTATTTTAATAAAT
Found at i:44648 original size:15 final size:16
Alignment explanation
Indices: 44623--44656 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
44613 AAAATATTAT
44623 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
44639 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
44654 TTT
1 TTT
44657 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:70578 original size:132 final size:132
Alignment explanation
Indices: 70424--70692 Score: 511
Period size: 132 Copynumber: 2.0 Consensus size: 132
70414 AATATTAAAA
70424 TTTCATATTACCACTAATTAAAAATAAAATAATTAAATGATAATCAAATGAGATTTTTTTATAAA
1 TTTCATATTACCACTAATTAAAAATAAAATAATTAAATGATAATCAAATGAGATTTTTTTATAAA
* * *
70489 TAAATTAAAACATAATAACTTTTTTATGAAATTATTAATATATTTGAATCTAAATTTTAAAATTT
66 GAAATTAAAACATAATAACTTTTTTATGAAATTATTAATATATTTAAATCTAAATTTTAAAATTA
70554 AT
131 AT
70556 TTTCATATTACCACTAATTAAAAATAAAATAATTAAATGATAATCAAATGAGATTTTTTTATAAA
1 TTTCATATTACCACTAATTAAAAATAAAATAATTAAATGATAATCAAATGAGATTTTTTTATAAA
70621 GAAATTAAAACATAATAACTTTTTTATGAAATTATTAATATATTTAAATCTAAATTTTAAAATTA
66 GAAATTAAAACATAATAACTTTTTTATGAAATTATTAATATATTTAAATCTAAATTTTAAAATTA
70686 AT
131 AT
70688 TTTCA
1 TTTCA
70693 ACTCAAAATT
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (132 bp):
TTTCATATTACCACTAATTAAAAATAAAATAATTAAATGATAATCAAATGAGATTTTTTTATAAA
GAAATTAAAACATAATAACTTTTTTATGAAATTATTAATATATTTAAATCTAAATTTTAAAATTA
AT
Found at i:73059 original size:6 final size:6
Alignment explanation
Indices: 73048--73134 Score: 129
Period size: 6 Copynumber: 14.5 Consensus size: 6
73038 TGAGGGAATT
73048 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
* * * * *
73096 GAAGGA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAA
73135 ATCCGAAGCA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:92561 original size:21 final size:21
Alignment explanation
Indices: 92548--92591 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
92538 AAACAAAATA
92548 GAAAAAGAAAAAAAAAAAAAG
1 GAAAAAGAAAAAAAAAAAAAG
* *
92569 GAAAAAGAAAAATAATAAAAG
1 GAAAAAGAAAAAAAAAAAAAG
92590 GA
1 GA
92592 GATGAAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAAAAAAG
Found at i:99381 original size:17 final size:16
Alignment explanation
Indices: 99339--99394 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
99329 GAAGGAGCTT
99339 TTTTTTAATTGTGTTGGC
1 TTTTTTAA-TG-GTTGGC
*
99357 TATATTTAATGGTTGGAC
1 T-TTTTTAATGGTTGG-C
*
99375 TTTTTTAAT-GTTGGG
1 TTTTTTAATGGTTGGC
99390 TTTTT
1 TTTTT
99395 GTATGGGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 12 0.36
18 5 0.15
19 6 0.18
ACGTcount: A:0.16, C:0.04, G:0.21, T:0.59
Consensus pattern (16 bp):
TTTTTTAATGGTTGGC
Found at i:99852 original size:6 final size:6
Alignment explanation
Indices: 99815--99844 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
99805 TAAATCCTTC
99815 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
99845 CTTTTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:107636 original size:32 final size:30
Alignment explanation
Indices: 107600--107672 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
107590 TTATAATACG
*
107600 AAAATTAGATATATATTATAATGTAA-TTAATA
1 AAAATTAGATATATATT-T-A-GAAATTTAATA
* *
107632 AAAATTATATTTATATTTAGAAATTTAATA
1 AAAATTAGATATATATTTAGAAATTTAATA
107662 AAAA-TAGATAT
1 AAAATTAGATAT
107673 GATGATAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 8 0.23
30 11 0.31
31 1 0.03
32 15 0.43
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAATTAGATATATATTTAGAAATTTAATA
Found at i:113586 original size:12 final size:13
Alignment explanation
Indices: 113564--113592 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
113554 GTTATCATGT
113564 TTTTTAGTATGAA
1 TTTTTAGTATGAA
113577 TTTTTA-TATGAA
1 TTTTTAGTATGAA
113589 TTTT
1 TTTT
113593 CTGGGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TTTTTAGTATGAA
Found at i:117082 original size:21 final size:20
Alignment explanation
Indices: 117057--117105 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
117047 GGTGGGGTTA
*
117057 AAATTAATTACTGTAGTAATT
1 AAATTAA-TACTGTAGTAATG
* *
117078 AAATTGAATATTGTAGTAGTG
1 AAATT-AATACTGTAGTAATG
117099 AAATTAA
1 AAATTAA
117106 AAATAACGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (20 bp):
AAATTAATACTGTAGTAATG
Found at i:136683 original size:21 final size:23
Alignment explanation
Indices: 136652--136697 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
136642 ACATGGGCAG
136652 GTAGTGTACTT-T-CCAGCTTTTA
1 GTAGTGTACTTCTGCCA-CTTTTA
136674 GTAGT-TACTTCTGCCACTTTTA
1 GTAGTGTACTTCTGCCACTTTTA
136696 GT
1 GT
136698 TTTGGCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.23
22 14 0.64
23 3 0.14
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (23 bp):
GTAGTGTACTTCTGCCACTTTTA
Found at i:151513 original size:15 final size:14
Alignment explanation
Indices: 151480--151521 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
151470 TATCATTTGC
151480 ATATATAAATTAAA
1 ATATATAAATTAAA
151494 A-ATATCAAATTAAA
1 ATATAT-AAATTAAA
*
151508 ATATATAAACTAAA
1 ATATATAAATTAAA
151522 TACACAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (14 bp):
ATATATAAATTAAA
Found at i:151522 original size:13 final size:13
Alignment explanation
Indices: 151480--151523 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
151470 TATCATTTGC
151480 ATATATAAATTAA
1 ATATATAAATTAA
*
151493 AAATATCAAATTAAA
1 ATATAT-AAATT-AA
*
151508 ATATATAAACTAA
1 ATATATAAATTAA
151521 ATA
1 ATA
151524 CACAACTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 10 0.38
14 9 0.35
15 7 0.27
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATATAAATTAA
Found at i:154033 original size:17 final size:18
Alignment explanation
Indices: 154000--154034 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
153990 AAATTTAACA
154000 TTAAAAATAAATAATTTT
1 TTAAAAATAAATAATTTT
*
154018 TTAAAAATCAAT-ATTTT
1 TTAAAAATAAATAATTTT
154035 CTTTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAAATAAATAATTTT
Found at i:159043 original size:22 final size:23
Alignment explanation
Indices: 159015--159073 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
159005 GCAACAGTAG
159015 GCACACAAAGTGCTAAACAG-AA
1 GCACACAAAGTGCTAAACAGAAA
* * *
159037 GTACACACAGTGCTAAATAGAAA
1 GCACACAAAGTGCTAAACAGAAA
*
159060 GCACACATAGTGCT
1 GCACACAAAGTGCT
159074 GAATAAAGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (23 bp):
GCACACAAAGTGCTAAACAGAAA
Found at i:159071 original size:23 final size:22
Alignment explanation
Indices: 159015--159078 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 22
159005 GCAACAGTAG
*
159015 GCACACAAAGTGCTAAACAGAA
1 GCACACAAAGTGCTAAATAGAA
* *
159037 GTACACACAGTGCTAAATAGAAA
1 GCACACAAAGTGCTAAATAG-AA
* *
159060 GCACACATAGTGCTGAATA
1 GCACACAAAGTGCTAAATA
159079 AAGGGCACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (22 bp):
GCACACAAAGTGCTAAATAGAA
Found at i:159208 original size:24 final size:26
Alignment explanation
Indices: 159170--159217 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
159160 TCTACATGGG
159170 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
159196 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
159218 ACATTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:164509 original size:23 final size:21
Alignment explanation
Indices: 164483--164529 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
164473 AAAAAAATAA
*
164483 TTTATATTTAACATCTAAATTTT
1 TTTATA-TTAA-ATCAAAATTTT
*
164506 TTTATATTAAATGAAAATTTT
1 TTTATATTAAATCAAAATTTT
164527 TTT
1 TTT
164530 TTGGAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTATATTAAATCAAAATTTT
Found at i:181842 original size:16 final size:16
Alignment explanation
Indices: 181821--181854 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
181811 ATAATTTTTT
*
181821 AAAATATAATTCTAAA
1 AAAATAAAATTCTAAA
181837 AAAATAAAATTCTAAA
1 AAAATAAAATTCTAAA
181853 AA
1 AA
181855 TATGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAATTCTAAA
Found at i:183716 original size:23 final size:23
Alignment explanation
Indices: 183686--183731 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
183676 AATGTCTTTC
183686 TTGTTGTGTTTGCTTCATAGTTT
1 TTGTTGTGTTTGCTTCATAGTTT
183709 TTGTTGTGTTTGCTTCATAGTTT
1 TTGTTGTGTTTGCTTCATAGTTT
183732 GACAATTCAA
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:0.09, C:0.09, G:0.22, T:0.61
Consensus pattern (23 bp):
TTGTTGTGTTTGCTTCATAGTTT
Found at i:187243 original size:2 final size:2
Alignment explanation
Indices: 187236--187266 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
187226 AAATTATAAG
187236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
187267 TAAAAGCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:191283 original size:22 final size:22
Alignment explanation
Indices: 191215--191288 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
191205 TATTAAAAAA
191215 ATAAAGATATATTAAATATGTT-AT
1 ATAAA-AT-TATTAAATAT-TTAAT
* **
191239 A-AAAATTTCAGTAAATAAATAAT
1 ATAAAA-TT-ATTAAATATTTAAT
191262 ATAAAATTATTAAATATTTAAT
1 ATAAAATTATTAAATATTTAAT
191284 -TAAAA
1 ATAAAA
191289 CAATATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
21 5 0.12
22 14 0.35
23 16 0.40
24 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAAAATTATTAAATATTTAAT
Found at i:194251 original size:15 final size:16
Alignment explanation
Indices: 194222--194255 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
194212 GAGTATTATA
194222 TATTTTTAAAAAAAAT
1 TATTTTTAAAAAAAAT
*
194238 TATTTTTAATAAAAAT
1 TATTTTTAAAAAAAAT
194254 TA
1 TA
194256 ATCTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTTTAAAAAAAAT
Found at i:200236 original size:6 final size:6
Alignment explanation
Indices: 200199--200245 Score: 51
Period size: 6 Copynumber: 7.3 Consensus size: 6
200189 ATCCGCTATA
200199 TTTTTC TTTCTTC ATTTTCTC TTTTT- TATTTTC TTTTTC TTTTTC TT
1 TTTTTC TTT-TTC -TTTT-TC TTTTTC T-TTTTC TTTTTC TTTTTC TT
200246 CTAAACAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 1 0.03
6 21 0.58
7 9 0.25
8 5 0.14
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:200404 original size:27 final size:26
Alignment explanation
Indices: 200371--200426 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
200361 TTATTTATAA
*
200371 ATTTTTAAAAAATAAATTAAAAATTTT
1 ATTTTTAAAAAATAAAAT-AAAATTTT
* *
200398 ATTTTTAGAAAATAAAATATAATTTT
1 ATTTTTAAAAAATAAAATAAAATTTT
200424 ATT
1 ATT
200427 ATTACTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTTTTAAAAAATAAAATAAAATTTT
Done.