Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010931.1 Kokia drynarioides strain JFW-HI SEQ_125899, 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: 144993
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 95 characters in sequence are not A, C, G, or T
Found at i:3408 original size:16 final size:16
Alignment explanation
Indices: 3387--3425 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3377 TGAATGTTGA
*
3387 AGCTCGAGCCAAGCCT
1 AGCTCGAGCCAAACCT
3403 AGCTCGAGCCAAACCT
1 AGCTCGAGCCAAACCT
3419 AGCTCGA
1 AGCTCGA
3426 CCCCTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.23, T:0.13
Consensus pattern (16 bp):
AGCTCGAGCCAAACCT
Found at i:14209 original size:105 final size:105
Alignment explanation
Indices: 14025--14238 Score: 293
Period size: 105 Copynumber: 2.0 Consensus size: 105
14015 TTAGTAATGG
* * * * *
14025 TTAAATTTTAATTTTAATCCCTCTATTATGTCTAAATTTGAGATTTGATTTTTATAATTTAATTT
1 TTAAATTTTAATTTTAATACCTCTATTATGTCTAAATTTGAAATTTAATCTCTATAATTTAATTT
* * *
14090 CTAATATAATTTGATCCCTATATTTTTATATTGTTACTAA
66 CTAATATAACTTGATCCCTATATTTTTATAATATTACTAA
* * * *
14130 TTAAATTTTAGTTTTAATACTTTTATTATGTCTAAATTTGAAATTTAATCTCTATATTTTAATTT
1 TTAAATTTTAATTTTAATACCTCTATTATGTCTAAATTTGAAATTTAATCTCTATAATTTAATTT
* * *
14195 TTAATATAACTTGATCTCTATATTTTTATAATATTATTAA
66 CTAATATAACTTGATCCCTATATTTTTATAATATTACTAA
14235 TTAA
1 TTAA
14239 TCGAAATAGT
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 94 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (105 bp):
TTAAATTTTAATTTTAATACCTCTATTATGTCTAAATTTGAAATTTAATCTCTATAATTTAATTT
CTAATATAACTTGATCCCTATATTTTTATAATATTACTAA
Found at i:15884 original size:20 final size:21
Alignment explanation
Indices: 15859--15897 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15849 TATATATATC
15859 AAATAAAC-TTAAAAATATTA
1 AAATAAACATTAAAAATATTA
15879 AAATAAACATTAAAAATAT
1 AAATAAACATTAAAAATAT
15898 ATTAAAAATT
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:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAACATTAAAAATATTA
Found at i:15903 original size:23 final size:22
Alignment explanation
Indices: 15844--15904 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
15834 ACAAATTAAA
15844 AAAAATATATATATCAAATAAACTT
1 AAAAATATAT-TA--AAATAAACTT
15869 -AAAA-ATATTAAAATAAACATT
1 AAAAATATATTAAAATAAAC-TT
15890 AAAAATATATTAAAA
1 AAAAATATATTAAAA
15905 ATTTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 8 0.24
21 2 0.06
22 6 0.18
23 13 0.39
24 4 0.12
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATATATTAAAATAAACTT
Found at i:16046 original size:20 final size:20
Alignment explanation
Indices: 16020--16141 Score: 129
Period size: 20 Copynumber: 5.9 Consensus size: 20
16010 AAAAATACAT
*
16020 AAAAATAACATCCAAACAAC
1 AAAAATAACATCAAAACAAC
*
16040 CAAAATAACAATCAAAACAGCAAC
1 AAAAATAAC-ATC-AAA-A-CAAC
*
16064 AAAAATAACAACAAAACAAC
1 AAAAATAACATCAAAACAAC
*
16084 AAAAATAACAATAAAAACAAC
1 AAAAATAAC-ATCAAAACAAC
**
16105 AAAAATAACATCAAAACAGT
1 AAAAATAACATCAAAACAAC
*
16125 AAAAA-AAAATCAAAACA
1 AAAAATAACATCAAAACA
16142 GCAACCAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
19 11 0.13
20 34 0.39
21 22 0.25
22 5 0.06
23 3 0.03
24 12 0.14
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:16055 original size:12 final size:11
Alignment explanation
Indices: 16034--16120 Score: 65
Period size: 12 Copynumber: 7.9 Consensus size: 11
16024 ATAACATCCA
16034 AACAACCAAAAT
1 AACAA-CAAAAT
*
16046 AACAATCAAAAC
1 AACAA-CAAAAT
*
16058 AGCAACAAAAAT
1 AACAAC-AAAAT
*
16070 AACAACAAAAC
1 AACAACAAAAT
16081 AAC-A-AAAAT
1 AACAACAAAAT
*
16090 AACAA-TAAA-
1 AACAACAAAAT
16099 AACAACAAAAAT
1 AACAAC-AAAAT
*
16111 AACATCAAAA
1 AACAACAAAA
16121 CAGTAAAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 12 0.20
10 5 0.08
11 15 0.25
12 28 0.47
ACGTcount: A:0.71, C:0.20, G:0.01, T:0.08
Consensus pattern (11 bp):
AACAACAAAAT
Found at i:16068 original size:44 final size:44
Alignment explanation
Indices: 16020--16151 Score: 175
Period size: 44 Copynumber: 3.1 Consensus size: 44
16010 AAAAATACAT
* *
16020 AAAAATAACATCCAAACAACCAAAATAACAATCAAAACAGCAAC
1 AAAAATAACATCAAAACAACAAAAATAACAATCAAAACAGCAAC
*
16064 AAAAATAACAACAAAACAACAAAAATAACAAT-AAAA-A-CAAC
1 AAAAATAACATCAAAACAACAAAAATAACAATCAAAACAGCAAC
**
16105 AAAAATAACATCAAAACAGTAAAAA-AA-AATCAAAACAGCAAC
1 AAAAATAACATCAAAACAACAAAAATAACAATCAAAACAGCAAC
*
16147 CAAAA
1 AAAAA
16152 CAATAAAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
39 3 0.04
40 6 0.08
41 27 0.35
42 9 0.12
43 4 0.05
44 29 0.37
ACGTcount: A:0.70, C:0.20, G:0.02, T:0.08
Consensus pattern (44 bp):
AAAAATAACATCAAAACAACAAAAATAACAATCAAAACAGCAAC
Found at i:16151 original size:19 final size:19
Alignment explanation
Indices: 16049--16145 Score: 77
Period size: 21 Copynumber: 4.7 Consensus size: 19
16039 CCAAAATAAC
16049 AATCAAAACAGCAACAAAAATA
1 AATCAAAACAGC-A-AAAAA-A
* *
16071 ACAACAAAACAACAAAAATAA
1 A-ATCAAAACAGCAAAAA-AA
* *
16092 CAATAAAAACAACAAAAATAA
1 -AATCAAAACAGCAAAAA-AA
* *
16113 CATCAAAACAGTAAAAAAA
1 AATCAAAACAGCAAAAAAA
16132 AATCAAAACAGCAA
1 AATCAAAACAGCAA
16146 CCAAAACAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 14 0.23
20 13 0.21
21 22 0.35
22 4 0.06
23 9 0.15
ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08
Consensus pattern (19 bp):
AATCAAAACAGCAAAAAAA
Found at i:16165 original size:18 final size:19
Alignment explanation
Indices: 16144--16214 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 19
16134 TCAAAACAGC
*
16144 AACCAAAACA-ATAAAAAA
1 AACCAAAACAGAAAAAAAA
16162 AACCAAAACAGAAAAAAAA
1 AACCAAAACAGAAAAAAAA
*
16181 AACACTAAAGCAGTAAAAAAATA
1 AAC-C-AAAACAG-AAAAAAA-A
16204 ACACCAAAACA
1 A-ACCAAAACA
16215 ATAAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
18 10 0.23
19 10 0.23
20 1 0.02
21 6 0.14
22 12 0.27
23 3 0.07
24 2 0.05
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.06
Consensus pattern (19 bp):
AACCAAAACAGAAAAAAAA
Found at i:16178 original size:17 final size:18
Alignment explanation
Indices: 16144--16180 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
16134 TCAAAACAGC
*
16144 AACCAAAACAATAAAAAA
1 AACCAAAACAAGAAAAAA
16162 AACCAAAAC-AGAAAAAA
1 AACCAAAACAAGAAAAAA
16179 AA
1 AA
16181 AACACTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.78, C:0.16, G:0.03, T:0.03
Consensus pattern (18 bp):
AACCAAAACAAGAAAAAA
Found at i:16181 original size:22 final size:21
Alignment explanation
Indices: 16156--16214 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
16146 CCAAAACAAT
16156 AAAAAAA-ACCAAAACAGAAA
1 AAAAAAACACCAAAACAGAAA
* *
16176 AAAAAAACACTAAAGCAGTAAA
1 AAAAAAACACCAAAACAG-AAA
*
16198 AAAATAACACCAAAACA
1 AAAAAAACACCAAAACA
16215 ATAAATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 7 0.22
21 8 0.25
22 17 0.53
ACGTcount: A:0.73, C:0.17, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAAAACACCAAAACAGAAA
Found at i:16219 original size:22 final size:21
Alignment explanation
Indices: 16145--16219 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
16135 CAAAACAGCA
16145 ACCAAAACAAT--AAAAAAA-
1 ACCAAAACAATAAAAAAAAAC
16163 ACCAAAACAGA-AAAAAAAAAC
1 ACCAAAACA-ATAAAAAAAAAC
* * *
16184 ACTAAAGCAGTAAAAAAATAAC
1 ACCAAAACAATAAAAAAA-AAC
16206 ACCAAAACAATAAA
1 ACCAAAACAATAAA
16220 TTTTTTTACT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.20
19 1 0.02
20 7 0.16
21 14 0.31
22 14 0.31
ACGTcount: A:0.72, C:0.17, G:0.04, T:0.07
Consensus pattern (21 bp):
ACCAAAACAATAAAAAAAAAC
Found at i:18338 original size:15 final size:15
Alignment explanation
Indices: 18308--18340 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
18298 GAAATTAAAT
18308 TTTAATTTTTAGTAA
1 TTTAATTTTTAGTAA
18323 TTTATATTTTTA-TAA
1 TTTA-ATTTTTAGTAA
18338 TTT
1 TTT
18341 TTAAAGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTAATTTTTAGTAA
Found at i:39255 original size:18 final size:19
Alignment explanation
Indices: 39224--39262 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
39214 CAATTCTTAA
*
39224 TATTGTATTTTTTACTTTT
1 TATTGTATTATTTACTTTT
*
39243 TATT-TATTATTTATTTTT
1 TATTGTATTATTTACTTTT
39261 TA
1 TA
39263 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (19 bp):
TATTGTATTATTTACTTTT
Found at i:39430 original size:7 final size:7
Alignment explanation
Indices: 39408--39444 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
39398 AACATAAATT
*
39408 TAAATAT
1 TAAATAA
*
39415 TATATAA
1 TAAATAA
39422 TAAATAA
1 TAAATAA
39429 TAAATAA
1 TAAATAA
39436 TAAATAA
1 TAAATAA
39443 TA
1 TA
39445 TAAAAAGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
TAAATAA
Found at i:39789 original size:27 final size:27
Alignment explanation
Indices: 39759--39820 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
39749 ATTTTTATTG
* *
39759 TAAATTTTAAATTATTTATGTATTTAA
1 TAAATTTTAAATTATTTACGTAATTAA
***
39786 TAAAAAATAAATTATTTACGTAATTAA
1 TAAATTTTAAATTATTTACGTAATTAA
*
39813 TTAATTTT
1 TAAATTTT
39821 TTTAGGTTAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (27 bp):
TAAATTTTAAATTATTTACGTAATTAA
Found at i:40067 original size:36 final size:34
Alignment explanation
Indices: 40027--40120 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 34
40017 ATTTATAAAA
40027 TTTTAAATTAATAATAAAAAAATTATTTTAACTTTT
1 TTTTAAATT-ATAATAAAAAAATTATTTTAA-TTTT
* *
40063 TTTT-AA-TACAAT--AAAAATTAATTTAATTTT
1 TTTTAAATTATAATAAAAAAATTATTTTAATTTT
* *
40093 TTTAAAATTATAAAAAATATAAATTATT
1 TTTTAAATTATAATAAA-A-AAATTATT
40121 AAAACGATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
30 7 0.15
31 15 0.33
32 4 0.09
33 4 0.09
34 2 0.04
35 3 0.07
36 11 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (34 bp):
TTTTAAATTATAATAAAAAAATTATTTTAATTTT
Found at i:40105 original size:29 final size:30
Alignment explanation
Indices: 40044--40108 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
40034 TTAATAATAA
* *
40044 AAAAATTATTTTAACTTTTTTTTAATACAAT
1 AAAAATTAATTTAAC-TTTTTTTAAAACAAT
**
40075 AAAAATTAATTTAA-TTTTTTTAAAATTAT
1 AAAAATTAATTTAACTTTTTTTAAAACAAT
40104 AAAAA
1 AAAAA
40109 ATATAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.57
31 13 0.43
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAAATTAATTTAACTTTTTTTAAAACAAT
Found at i:40377 original size:15 final size:16
Alignment explanation
Indices: 40343--40380 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
40333 ATTTTGAACT
*
40343 TTAATTTATTTATAATA
1 TTAA-TTATTAATAATA
40360 TTAATTATTAAT-ATA
1 TTAATTATTAATAATA
40375 TTAATT
1 TTAATT
40381 TTATTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 7 0.35
17 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTATTAATAATA
Found at i:44009 original size:23 final size:24
Alignment explanation
Indices: 43931--44010 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 24
43921 ACACTAGAGC
* *
43931 GCTCTTTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTGT-GT
43954 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
* * * *
43979 ACTATCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
44002 GCTCTCTGT
1 GCTCTCTGT
44011 TGCCCAGCAC
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
23 26 0.58
24 1 0.02
25 15 0.33
26 3 0.07
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:50215 original size:16 final size:17
Alignment explanation
Indices: 50194--50226 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
50184 GAAATTTAAC
*
50194 TTTTACTAATT-TAAAA
1 TTTTACAAATTATAAAA
50210 TTTTACAAATTATAAAA
1 TTTTACAAATTATAAAA
50227 AATTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTACAAATTATAAAA
Found at i:60237 original size:2 final size:2
Alignment explanation
Indices: 60230--60255 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60220 GATTTAATTT
60230 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
60256 AAATAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62829 original size:45 final size:45
Alignment explanation
Indices: 62667--62821 Score: 274
Period size: 45 Copynumber: 3.4 Consensus size: 45
62657 TTGTGCTCTG
62667 TAATACTTGATGTTGATTATGATTGATTCGAATATGTATAGTTTA
1 TAATACTTGATGTTGATTATGATTGATTCGAATATGTATAGTTTA
* *
62712 TAATGCTTGATTTTGATTATGATTGATTCGAATATGTATAGTTTA
1 TAATACTTGATGTTGATTATGATTGATTCGAATATGTATAGTTTA
62757 TAATACTTGATGTTGATTATGATTGATTCGAATATGTATAGTTTA
1 TAATACTTGATGTTGATTATGATTGATTCGAATATGTATAGTTTA
* *
62802 TAATGCTTGATTTTGATTAT
1 TAATACTTGATGTTGATTAT
62822 AGCTGATTTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (45 bp):
TAATACTTGATGTTGATTATGATTGATTCGAATATGTATAGTTTA
Found at i:65846 original size:32 final size:32
Alignment explanation
Indices: 65787--65854 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
65777 GTGTCGATCC
** * *
65787 GAGCTCGAAAAAACCTTAGCTTAAAAAAGCTT
1 GAGCTCGAAAAAACCCAAGCTCAAAAAAGCCT
* *
65819 GAGCTCGACAAAACCCAAGCTCGAAAAAGCCT
1 GAGCTCGAAAAAACCCAAGCTCAAAAAAGCCT
65851 GAGC
1 GAGC
65855 CCATAACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (32 bp):
GAGCTCGAAAAAACCCAAGCTCAAAAAAGCCT
Found at i:68518 original size:21 final size:22
Alignment explanation
Indices: 68475--68518 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
68465 TAAATCATGG
**
68475 TTATTTTTATAAATTATGGTTT
1 TTATTTTTATAAATTATCATTT
*
68497 TTATTTTTA-AAATTTTCATTT
1 TTATTTTTATAAATTATCATTT
68518 T
1 T
68519 GAACATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
TTATTTTTATAAATTATCATTT
Found at i:69593 original size:41 final size:40
Alignment explanation
Indices: 69509--69595 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
69499 AAGTAAACAT
*
69509 TAAAATAATGTTAATATGATTATATAAAAATAATAATAAA
1 TAAAATAATGTTAAGATGATTATATAAAAATAATAATAAA
* *
69549 TAAAA-AATGTATAAGATTATTAATATTAAAATAAT--TAAA
1 TAAAATAATGT-TAAGATGATT-ATATAAAAATAATAATAAA
69588 TATAAATA
1 TA-AAATA
69596 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
39 11 0.28
40 16 0.40
41 13 0.32
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (40 bp):
TAAAATAATGTTAAGATGATTATATAAAAATAATAATAAA
Found at i:82687 original size:29 final size:29
Alignment explanation
Indices: 82643--82701 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
82633 ATCTATTAAC
*
82643 ATTTGTTTGATCTGTTAACACTGTTTGGG
1 ATTTGTTTGATCTGTTAACACTATTTGGG
*
82672 ATTTGTTTGATTTGTTAACACTATTTGGG
1 ATTTGTTTGATCTGTTAACACTATTTGGG
82701 A
1 A
82702 GTTAAGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (29 bp):
ATTTGTTTGATCTGTTAACACTATTTGGG
Found at i:82820 original size:13 final size:13
Alignment explanation
Indices: 82802--82831 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
82792 TTACAGATAC
*
82802 ATATGCTTTATAT
1 ATATGCTCTATAT
82815 ATATGCTCTATAT
1 ATATGCTCTATAT
82828 ATAT
1 ATAT
82832 TGCCTAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (13 bp):
ATATGCTCTATAT
Found at i:84938 original size:11 final size:11
Alignment explanation
Indices: 84895--84944 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
84885 TTCTGACTTG
84895 TATGTTGTG-TT
1 TATGTTG-GCTT
84906 T-TGTTGGCTT
1 TATGTTGGCTT
* *
84916 TATGATGACTT
1 TATGTTGGCTT
84927 TATGTTGGCTT
1 TATGTTGGCTT
84938 TAATGTT
1 T-ATGTT
84945 TTATATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 1 0.03
10 8 0.25
11 18 0.56
12 5 0.16
ACGTcount: A:0.14, C:0.06, G:0.24, T:0.56
Consensus pattern (11 bp):
TATGTTGGCTT
Found at i:85841 original size:12 final size:12
Alignment explanation
Indices: 85814--85848 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
85804 ATTATTGTTC
*
85814 TGAACTATTT-T
1 TGAACTTTTTGT
85825 TGAACTTTTTGT
1 TGAACTTTTTGT
85837 TGAACTTTTTGT
1 TGAACTTTTTGT
85849 AAAGTTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (12 bp):
TGAACTTTTTGT
Found at i:94800 original size:19 final size:20
Alignment explanation
Indices: 94763--94800 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
94753 TCTGTTAAAT
94763 CTTTTACAATTTTTATGAAC
1 CTTTTACAATTTTTATGAAC
*
94783 CTTTTATAATTTTT-TGAA
1 CTTTTACAATTTTTATGAA
94801 TTTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (20 bp):
CTTTTACAATTTTTATGAAC
Found at i:96153 original size:2 final size:2
Alignment explanation
Indices: 96146--96174 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96136 GATCTAGGGG
96146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96175 ATGGAGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:97035 original size:28 final size:30
Alignment explanation
Indices: 96983--97045 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
96973 TTTAAACCCA
*
96983 AAAAACAAAATGACTAAATTCTTAAAAAT-
1 AAAAACAAAAAGACTAAATTCTTAAAAATG
* * *
97012 AAAAATAAAAAGACT-AATTTTTAAATATG
1 AAAAACAAAAAGACTAAATTCTTAAAAATG
97041 AAAAA
1 AAAAA
97046 ACTATAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAACAAAAAGACTAAATTCTTAAAAATG
Found at i:105243 original size:4 final size:4
Alignment explanation
Indices: 105236--105265 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
105226 CCAATGTATG
105236 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
105266 TAAATATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:135157 original size:17 final size:19
Alignment explanation
Indices: 135131--135166 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
135121 AAATTTACTT
135131 AACAGAAAAATGTT-AAAG
1 AACAGAAAAATGTTCAAAG
135149 AACAG-AAAATGTTCAAAG
1 AACAGAAAAATGTTCAAAG
135167 TTCAAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.08, G:0.17, T:0.17
Consensus pattern (19 bp):
AACAGAAAAATGTTCAAAG
Found at i:137207 original size:19 final size:19
Alignment explanation
Indices: 137179--137226 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
137169 ACTATTTAAT
*
137179 TCAAAATTTGAATTTTTTA
1 TCAAATTTTGAATTTTTTA
137198 TCAAATTTTGAATTTTTTA
1 TCAAATTTTGAATTTTTTA
137217 TCAAATTTTG
1 TCAAATTTTG
137227 CTCACTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.54
Consensus pattern (19 bp):
TCAAATTTTGAATTTTTTA
Done.