Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011704.1 Kokia drynarioides strain JFW-HI SEQ_126698, 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: 58726
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3232 original size:22 final size:21
Alignment explanation
Indices: 3189--3232 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
3179 ATTAGTTGAA
*
3189 ATCCAAATATAAATTTAAATT
1 ATCCAAATATAAATCTAAATT
*
3210 ATCCAAATAATAAATCTAGATT
1 ATCCAAAT-ATAAATCTAAATT
3232 A
1 A
3233 ATTCAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (21 bp):
ATCCAAATATAAATCTAAATT
Found at i:4251 original size:18 final size:19
Alignment explanation
Indices: 4228--4265 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4218 ATTAGAAGTA
4228 AAATAA-AT-GCAAATAATT
1 AAATAACATGGCAAA-AATT
4246 AAATAACATGGCAAAAATT
1 AAATAACATGGCAAAAATT
4265 A
1 A
4266 GAATGTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATAACATGGCAAAAATT
Found at i:6346 original size:21 final size:21
Alignment explanation
Indices: 6322--6377 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
6312 GATAATAGCA
6322 AAATCCAAATATAAAGTTTAG
1 AAATCCAAATATAAAGTTTAG
*
6343 AAATCCAAACATAAAGTTTAG
1 AAATCCAAATATAAAGTTTAG
6364 AAATCCAAAT-TAAA
1 AAATCCAAATATAAA
6378 TAACCCAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (21 bp):
AAATCCAAATATAAAGTTTAG
Found at i:7668 original size:13 final size:13
Alignment explanation
Indices: 7652--7685 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
7642 AAATAAAGAA
7652 AAGAAAAAAAATG
1 AAGAAAAAAAATG
*
7665 AAGAAAAGAAATG
1 AAGAAAAAAAATG
*
7678 ATGAAAAA
1 AAGAAAAA
7686 GCTATAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (13 bp):
AAGAAAAAAAATG
Found at i:17545 original size:3 final size:3
Alignment explanation
Indices: 17537--17565 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17527 CTTTAAAGTT
17537 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
17566 TCTTAGGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:17703 original size:2 final size:2
Alignment explanation
Indices: 17696--17727 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17686 ACCTCCCTCC
*
17696 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17728 TTAAACTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:21813 original size:26 final size:28
Alignment explanation
Indices: 21784--21855 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 28
21774 ATTATTTTTT
21784 ATAATTTTGGTTAA-A-AGTTAAATATG
1 ATAATTTTGGTTAATAGAGTTAAATATG
21810 ATAATTTT--TTAATAGAGTTAAATATG
1 ATAATTTTGGTTAATAGAGTTAAATATG
* *
21836 GTAA-TTTGGTTAATTGAGTT
1 ATAATTTTGGTTAATAGAGTT
21856 TGTGTTTGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.10
25 4 0.10
26 22 0.55
27 10 0.25
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (28 bp):
ATAATTTTGGTTAATAGAGTTAAATATG
Found at i:22275 original size:23 final size:24
Alignment explanation
Indices: 22244--22291 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
22234 GGTCGAAATT
22244 AAATAGTAATTTTTAAAATAATAA
1 AAATAGTAATTTTTAAAATAATAA
*
22268 AAAT-GTAATTTTTAAAATATTAA
1 AAATAGTAATTTTTAAAATAATAA
22291 A
1 A
22292 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATAGTAATTTTTAAAATAATAA
Found at i:22299 original size:22 final size:23
Alignment explanation
Indices: 22251--22299 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
22241 ATTAAATAGT
**
22251 AATTTTTAAAATAATAAAAATGT
1 AATTTTTAAAATAATAAAAATAA
* *
22274 AATTTTTAAAAT-ATTAAATTAA
1 AATTTTTAAAATAATAAAAATAA
22296 AATT
1 AATT
22300 ATATCATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTTTAAAATAATAAAAATAA
Found at i:24768 original size:12 final size:12
Alignment explanation
Indices: 24751--24777 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24741 CAAAAGGGAA
24751 GAATATGAAGAT
1 GAATATGAAGAT
24763 GAATATGAAGAT
1 GAATATGAAGAT
24775 GAA
1 GAA
24778 GAAGAGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.22
Consensus pattern (12 bp):
GAATATGAAGAT
Found at i:25023 original size:29 final size:30
Alignment explanation
Indices: 24981--25050 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
24971 AAATAATAAC
* * *
24981 ATAAGTGACGAAAACGTAATAT-TTCAAAT
1 ATAAGTGACTAAAACGTAACATAGTCAAAT
*
25010 ATAAGTGACTAAAATGTAACATGAGTCAAAT
1 ATAAGTGACTAAAACGTAACAT-AGTCAAAT
25041 A-AAGTGACTA
1 ATAAGTGACTA
25051 TTTTGTAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.54
30 9 0.26
31 7 0.20
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.26
Consensus pattern (30 bp):
ATAAGTGACTAAAACGTAACATAGTCAAAT
Found at i:31056 original size:24 final size:24
Alignment explanation
Indices: 31029--31083 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
31019 TAAGAATTTG
*
31029 ATTGAAACAACTAAACAAAGTTTA
1 ATTGAAACAAATAAACAAAGTTTA
*
31053 ATTGAAACAAATAAACAGAGTTTA
1 ATTGAAACAAATAAACAAAGTTTA
*
31077 ACTGAAA
1 ATTGAAA
31084 GATTATTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (24 bp):
ATTGAAACAAATAAACAAAGTTTA
Found at i:33048 original size:24 final size:24
Alignment explanation
Indices: 33019--33073 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
33009 TAAGAATTTG
*
33019 ACTGAAACAACTAAACAAAGTTTA
1 ACTGAAACAAATAAACAAAGTTTA
* *
33043 ATTGAAACAAATAAACAGAGTTTA
1 ACTGAAACAAATAAACAAAGTTTA
33067 ACTGAAA
1 ACTGAAA
33074 GATTATTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.22
Consensus pattern (24 bp):
ACTGAAACAAATAAACAAAGTTTA
Found at i:33270 original size:15 final size:15
Alignment explanation
Indices: 33250--33280 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33240 AATTTAATTA
*
33250 GATTAATTAAATCAT
1 GATTAATTAAACCAT
33265 GATTAATTAAACCAT
1 GATTAATTAAACCAT
33280 G
1 G
33281 TTACATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (15 bp):
GATTAATTAAACCAT
Found at i:33528 original size:16 final size:16
Alignment explanation
Indices: 33507--33541 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33497 AAGGTGTCTA
33507 AAATTAGAATTTTTAT
1 AAATTAGAATTTTTAT
* *
33523 AAATTATAATTTTTTT
1 AAATTAGAATTTTTAT
33539 AAA
1 AAA
33542 AGATAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AAATTAGAATTTTTAT
Found at i:34259 original size:21 final size:21
Alignment explanation
Indices: 34217--34259 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
34207 CAAAAAATAA
*
34217 ATAATAAAAACATTTTTAAAT
1 ATAATAAAAACATTTATAAAT
*
34238 ATAATATAAAA-ATTTATCAAT
1 ATAATA-AAAACATTTATAAAT
34259 A
1 A
34260 GTTTTGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATAAAAACATTTATAAAT
Found at i:35993 original size:22 final size:23
Alignment explanation
Indices: 35960--36004 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
35950 GTGATGTCAT
35960 TATTTTTCTTTTCTTTATTTTTA
1 TATTTTTCTTTTCTTTATTTTTA
*
35983 TATTTTT-TTTTCTTTTTTTTTA
1 TATTTTTCTTTTCTTTATTTTTA
36005 ACCTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (23 bp):
TATTTTTCTTTTCTTTATTTTTA
Found at i:37210 original size:10 final size:10
Alignment explanation
Indices: 37185--37246 Score: 61
Period size: 10 Copynumber: 5.6 Consensus size: 10
37175 AGCTTTTTAT
37185 TTTAAGATTGGA
1 TTTAA-ATT-GA
37197 TTTAAATTGA
1 TTTAAATTGA
37207 TTTAAATTGA
1 TTTAAATTGA
*
37217 TTTTTAAATTTAAA
1 --TTTAAA-TT-GA
37231 TTTAAATTGA
1 TTTAAATTGA
37241 TTTAAA
1 TTTAAA
37247 ATTTAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 19 0.43
11 5 0.11
12 17 0.39
13 2 0.05
14 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (10 bp):
TTTAAATTGA
Found at i:37237 original size:24 final size:23
Alignment explanation
Indices: 37206--37252 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
37196 ATTTAAATTG
*
37206 ATTTAAATTGATTTTTAAATTTAA
1 ATTTAAATTGA-TTTAAAATTTAA
37230 ATTTAAATTGATTTAAAATTTAA
1 ATTTAAATTGATTTAAAATTTAA
37253 TAATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTAAATTGATTTAAAATTTAA
Found at i:37259 original size:23 final size:24
Alignment explanation
Indices: 37209--37261 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
37199 TAAATTGATT
* *
37209 TAAATTGATTTTTAAATTTAAATT
1 TAAATTGATTTTAAAATTTAAATA
37233 TAAATTGA-TTTAAAATTT-AATAA
1 TAAATTGATTTTAAAATTTAAAT-A
37256 TAAATT
1 TAAATT
37262 AAAAGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TAAATTGATTTTAAAATTTAAATA
Found at i:37264 original size:34 final size:34
Alignment explanation
Indices: 37196--37261 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
37186 TTAAGATTGG
* **
37196 ATTTAAATTGATTTAAATTGATTTTTAAATTTAA
1 ATTTAAATTGATTTAAATTGAATAATAAATTTAA
*
37230 ATTTAAATTGATTTAAAATTTAATAATAAATT
1 ATTTAAATTGATTT-AAATTGAATAATAAATT
37262 AAAAGTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 14 0.52
35 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (34 bp):
ATTTAAATTGATTTAAATTGAATAATAAATTTAA
Found at i:39218 original size:87 final size:85
Alignment explanation
Indices: 39069--39311 Score: 243
Period size: 87 Copynumber: 2.8 Consensus size: 85
39059 CTAAACTCTC
* * * * * *
39069 CAAAAATTACATTTTTAACCTCGAACTTCCAAAAATTCCATTTTGACCTCAAAACTTCCAAAAAT
1 CAAAAATTACA-TTTTAACCCCGAACTT-CAAAAATTACATTTTTACCCCTAAACTTTCAAAAAT
* **
39134 TACATTTTTACACTTTAACTTT
64 TACATTTTAACACTAAAACTTT
* *
39156 CAAAAATTATATTTTAACCCCAAAACTTCTAAAAATTACATTTTTACCCCTAAACTTTCAAAAAT
1 CAAAAATTACATTTTAACCCC-GAACTTC-AAAAATTACATTTTTACCCCTAAACTTTCAAAAAT
* *
39221 TCCATTTTAACCCTAAAACTTT
64 TACATTTTAACACTAAAACTTT
* * * * * * *
39243 CAAAAATTACATTTTTACCCTTGAATTTGCAAAAATTTCTTTTTTAACCTTGAAACTTTCAAAAA
1 CAAAAATTACATTTTAACCC-CGAACTT-CAAAAATTACATTTTTACCCCT-AAACTTTCAAAAA
39308 TTAC
63 TTAC
39312 CCTTTTACCT
Statistics
Matches: 128, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
86 10 0.08
87 101 0.79
88 17 0.13
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.37
Consensus pattern (85 bp):
CAAAAATTACATTTTAACCCCGAACTTCAAAAATTACATTTTTACCCCTAAACTTTCAAAAATTA
CATTTTAACACTAAAACTTT
Found at i:39318 original size:59 final size:58
Alignment explanation
Indices: 39069--39338 Score: 289
Period size: 58 Copynumber: 4.6 Consensus size: 58
39059 CTAAACTCTC
* * * * * *
39069 CAAAAATTACATTTTTAACCTCGAACTTCCAAAAATTCCATTTTGA-CCTCAAAACTTC
1 CAAAAATTACATTTTTACCCTTGAACTTTCAAAAATTCTATTTTAACCCT-AAAACTTT
* * * *
39127 CAAAAATTACATTTTTACACTTTAACTTTCAAAAATTATATTTTAACCCCAAAAC-TT
1 CAAAAATTACATTTTTACCCTTGAACTTTCAAAAATTCTATTTTAACCCTAAAACTTT
* * *
39184 CTAAAAATTACATTTTTACCCCTAAACTTTCAAAAATTCCATTTTAACCCTAAAACTTT
1 C-AAAAATTACATTTTTACCCTTGAACTTTCAAAAATTCTATTTTAACCCTAAAACTTT
* * *
39243 CAAAAATTACATTTTTACCCTTGAA-TTTGCAAAAATTTCTTTTTTAACCTTGAAACTTT
1 CAAAAATTACATTTTTACCCTTGAACTTT-CAAAAA-TTCTATTTTAACCCTAAAACTTT
**
39302 CAAAAATTACCCTTTTA-CCTTCGAA-TGTTCAAAAATT
1 CAAAAATTACATTTTTACCCTT-GAACT-TTCAAAAATT
39339 TTGTTTTTGA
Statistics
Matches: 181, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
57 5 0.03
58 125 0.69
59 49 0.27
60 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCTTGAACTTTCAAAAATTCTATTTTAACCCTAAAACTTT
Found at i:39322 original size:29 final size:30
Alignment explanation
Indices: 39069--39311 Score: 209
Period size: 29 Copynumber: 8.3 Consensus size: 30
39059 CTAAACTCTC
* *
39069 CAAAAATTACATTTTTAACCTCG-AACTTC
1 CAAAAATTACATTTTTAACCTTGAAACTTT
* * ** *
39098 CAAAAATTCCA-TTTTGACCTCAAAACTTC
1 CAAAAATTACATTTTTAACCTTGAAACTTT
*
39127 CAAAAATTACATTTTT-ACACTT-TAACTTT
1 CAAAAATTACATTTTTAAC-CTTGAAACTTT
* ***
39156 CAAAAATTATA-TTTTAACCCCAAAAC-TT
1 CAAAAATTACATTTTTAACCTTGAAACTTT
* *
39184 CTAAAAATTACATTTTTACCCCT-AAACTTT
1 C-AAAAATTACATTTTTAACCTTGAAACTTT
* * *
39214 CAAAAATTCCA-TTTTAACCCTAAAACTTT
1 CAAAAATTACATTTTTAACCTTGAAACTTT
*
39243 CAAAAATTACATTTTTACCCTTG-AA-TTT
1 CAAAAATTACATTTTTAACCTTGAAACTTT
* *
39271 GCAAAAATTTCTTTTTTAACCTTGAAACTTT
1 -CAAAAATTACATTTTTAACCTTGAAACTTT
39302 CAAAAATTAC
1 CAAAAATTAC
39312 CCTTTTACCT
Statistics
Matches: 177, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
28 29 0.16
29 109 0.62
30 36 0.20
31 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAAAATTACATTTTTAACCTTGAAACTTT
Found at i:53478 original size:206 final size:205
Alignment explanation
Indices: 52954--53545 Score: 968
Period size: 205 Copynumber: 2.9 Consensus size: 205
52944 TGAATCCCAT
52954 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGGTACAGAGAAGCGGAT
1 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGGTACAGAGAAGCGGAT
* *
53019 TGAAACAAACGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATTAAACTCACGC
66 TGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGC
* * * *
53084 TCGATATGAGCAAATCTTCGAATCTCAGCTTCCTGATAAGATACTGAGAAGCAGGGCGAAGCAAT
131 TCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAAT
53149 AAAAGGTTAG
196 AAAAGGTTAG
* * * *
53159 CTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTAATGAGGTACAGAGAAGCAGAT
1 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGGTACAGAGAAGCGGAT
* *
53224 TGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGCGC
66 TGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGC
* *
53289 TTGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAAT
131 TCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAAT
*
53354 AAAATTGTTAG
196 AAAA-GGTTAG
* * *
53365 CTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGGTACAGAGAAGCGGAT
* * *
53430 TGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACTCACGC
66 TGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGC
* *
53495 TCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
131 TCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
53546 TGGATCAAAT
Statistics
Matches: 356, Mismatches: 30, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
205 185 0.52
206 171 0.48
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (205 bp):
CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGGTACAGAGAAGCGGAT
TGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGC
TCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAAT
AAAAGGTTAG
Found at i:53546 original size:158 final size:158
Alignment explanation
Indices: 53363--53703 Score: 549
Period size: 158 Copynumber: 2.2 Consensus size: 158
53353 TAAAATTGTT
*
53363 AGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
1 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
* *
53428 ATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACTC-A
66 ATTGAAACAAGAGATACGGTCACCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAA-TCAA
53492 CGCTCAATACGAGCAAATCTTCGAACCCC
130 CGCTCAATACGAGCAAATCTTCGAACCCC
* * * *
53521 AGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGATATAGAGAGGCGG
1 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
* *
53586 ATTGAAACAAGAGATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCAAC
66 ATTGAAACAAGAGATACGGTCACCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAATCAAC
* *
53651 GCTCTATGCGAGCAAATCTTCGAACCCC
131 GCTCAATACGAGCAAATCTTCGAACCCC
* *
53679 ACCTTCCTAATGAGATACTGAGAAG
1 AGCTTCCTGATGAGATACTGAGAAG
53704 CGAGTCGAAG
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
157 2 0.01
158 167 0.99
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (158 bp):
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
ATTGAAACAAGAGATACGGTCACCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAATCAAC
GCTCAATACGAGCAAATCTTCGAACCCC
Found at i:53826 original size:364 final size:364
Alignment explanation
Indices: 53157--53836 Score: 1085
Period size: 364 Copynumber: 1.9 Consensus size: 364
53147 ATAAAAGGTT
* *
53157 AGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTAATGAGGTACAGAGAAGCAG
1 AGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAG
* **
53222 ATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGC
66 ATTGAAACAAACGATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCAAC
* * *
53287 GCTTGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCA
131 GCTTGATACGAGCAAATCTTCGAACCCCACCTTCCTAATGAGATACTGAGAAGCAAGTCGAAGCA
*
53352 ATAAAATTGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
196 ATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
*
53417 CAGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
261 CAGAGAAGCAGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
53482 ATCAAACTCACGCTCAATACGAGCAAATCTTCGAACCCC
326 ATCAAACTCACGCTCAATACGAGCAAATCTTCGAACCCC
* * * * * *
53521 AGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGATATAGAGAGGCGG
1 AGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAG
*
53586 ATTGAAACAAGA-GATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCAA
66 ATTGAAACAA-ACGATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCAA
* *
53650 CGCTCT-ATGCGAGCAAATCTTCGAACCCCACCTTCCTAATGAGATACTGAGAAGCGAGTCGAAG
130 CGCT-TGATACGAGCAAATCTTCGAACCCCACCTTCCTAATGAGATACTGAGAAGCAAGTCGAAG
* * *
53714 TAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGA
194 CAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
* * * * *
53779 TATAGGGAAGCAGATTGAAACAAGTGATGCGGTCATCTTCTTAATGAGATACTGAGAA
259 TACAGAGAAGCAGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAA
53837 AAATGCCAAG
Statistics
Matches: 287, Mismatches: 27, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
364 285 0.99
365 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (364 bp):
AGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAG
ATTGAAACAAACGATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCAAC
GCTTGATACGAGCAAATCTTCGAACCCCACCTTCCTAATGAGATACTGAGAAGCAAGTCGAAGCA
ATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCAGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
ATCAAACTCACGCTCAATACGAGCAAATCTTCGAACCCC
Found at i:54183 original size:12 final size:12
Alignment explanation
Indices: 54175--54256 Score: 73
Period size: 11 Copynumber: 7.0 Consensus size: 12
54165 CAAATTTATT
54175 TTTAAATTTAAA
1 TTTAAATTTAAA
54187 TTT--ATCTTAAA
1 TTTAAAT-TTAAA
**
54198 TTTAAATTTATCT
1 TTTAAATTTA-AA
54211 TTTAAATTTAAA
1 TTTAAATTTAAA
**
54223 TTT-GCTTTAAA
1 TTTAAATTTAAA
54234 TTTAAATTT-AA
1 TTTAAATTTAAA
*
54245 TTAAAATTTAAA
1 TTTAAATTTAAA
54257 CTGATTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 2 0.04
11 27 0.49
12 14 0.25
13 12 0.22
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:54184 original size:6 final size:6
Alignment explanation
Indices: 54175--54256 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
54165 CAAATTTATT
**
54175 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATCT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
** *
54223 TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
54257 CTGATTTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 2 0.03
5 9 0.15
6 43 0.72
7 6 0.10
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:54198 original size:17 final size:17
Alignment explanation
Indices: 54166--54256 Score: 96
Period size: 17 Copynumber: 5.2 Consensus size: 17
54156 AAATTGATTC
*
54166 AAATTTATTTTTAAATTT
1 AAATTTA-TCTTAAATTT
54184 AAATTTATCTTAAATTT
1 AAATTTATCTTAAATTT
54201 AAATTTATCTTTTAAATTT
1 AAATTTATC--TTAAATTT
*
54220 AAATTT-GCTTTAAATTT
1 AAATTTATC-TTAAATTT
*
54237 AAATTTAAT-TAAAATTT
1 AAATTT-ATCTTAAATTT
54254 AAA
1 AAA
54257 CTGATTTAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
17 43 0.66
18 8 0.12
19 14 0.22
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
AAATTTATCTTAAATTT
Found at i:54217 original size:36 final size:35
Alignment explanation
Indices: 54166--54256 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 35
54156 AAATTGATTC
*
54166 AAATTTATTTTTAAATTTAAATTT-ATCTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTGCT-TTAAATTT
54201 AAATTTATCTTTTAAATTTAAATTTGCTTTAAATTT
1 AAATTTAT-TTTTAAATTTAAATTTGCTTTAAATTT
* *
54237 AAATTTA-ATTAAAATTTAAA
1 AAATTTATTTTTAAATTTAAA
54257 CTGATTTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
34 11 0.22
35 8 0.16
36 31 0.61
37 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTGCTTTAAATTT
Found at i:56073 original size:29 final size:29
Alignment explanation
Indices: 56040--56294 Score: 202
Period size: 29 Copynumber: 8.8 Consensus size: 29
56030 CTAAACTGTC
*
56040 CAAAAATTACATTTTTACCCTCGAACTTT
1 CAAAAATTACATTTTTACCCTCAAACTTT
* * *
56069 CAAAAATT-CTATTTTGACCC-AAAACTTC
1 CAAAAATTAC-ATTTTTACCCTCAAACTTT
*
56097 CAAAAATTACATTTTTACCCTTAAAC-TT
1 CAAAAATTACATTTTTACCCTCAAACTTT
*
56125 CTAAAAATT-CATTTTTTAACCCTAAAAC-TT
1 C-AAAAATTACA-TTTTT-ACCCTCAAACTTT
56155 CTAAAAATTACATTTTTA-CCTCCAAAC-TT
1 C-AAAAATTACATTTTTACCCT-CAAACTTT
* * * *
56184 CACAAAAATCCATTTTGA-CCTCGAAACTTC
1 CA-AAAATTACATTTTTACCCTC-AAACTTT
* * *
56214 CAAAAATTATATTTTTACTCTCAAATTTT
1 CAAAAATTACATTTTTACCCTCAAACTTT
* * *
56243 CAAATATTCCATTTTTAACCTCAAAACTTT
1 CAAAAATTACATTTTTACCCTC-AAACTTT
* **
56273 AAAAAATTACCCTTTTACCCTC
1 CAAAAATTACATTTTTACCCTC
56295 GAATGTCCAA
Statistics
Matches: 181, Mismatches: 32, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
28 32 0.18
29 94 0.52
30 53 0.29
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCAAACTTT
Found at i:56174 original size:59 final size:59
Alignment explanation
Indices: 56028--56294 Score: 257
Period size: 59 Copynumber: 4.6 Consensus size: 59
56018 CCTTAGAGGT
* *
56028 CCCT-AAACTGTCCAAAAATTACATTTTTACCCTCGAACTT-TCAAAAATTC-TATTTTGA
1 CCCTAAAACT-TCCAAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTCAT-TTTTAA
*
56086 CCC-AAAACTTCCAAAAATTACATTTTTACCCTTAAACTTCT-AAAAATTCATTTTTTAA
1 CCCTAAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTCA-TTTTTAA
* * * *
56144 CCCTAAAACTTCTAAAAATTACATTTTTA-CCTCCAAACTTCACAAAAATCCA-TTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTTTACCCT-CAAACTTCTCAAAAATTCATTTTTAA
* * * * *
56202 -CCTCGAAACTTCCAAAAATTATATTTTTACTCTCAAA-TTTTCAAATATTCCATTTTTAA
1 CCCT-AAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCTCAAAAATT-CATTTTTAA
** **
56261 -CCTCAAAACTTTAAAAAATTACCCTTTTACCCTC
1 CCCT-AAAACTTCCAAAAATTACATTTTTACCCTC
56295 GAATGTCCAA
Statistics
Matches: 174, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
57 47 0.27
58 53 0.30
59 66 0.38
60 8 0.05
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTCATTTTTAA
Found at i:56258 original size:117 final size:116
Alignment explanation
Indices: 56028--56294 Score: 305
Period size: 117 Copynumber: 2.3 Consensus size: 116
56018 CCTTAGAGGT
* * * *
56028 CCCT-AAACTGTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTCTATTTTGACCCAAA
1 CCCTAAAACT-TCTAAAAATTACATTTTTACCCTCAAACTTTCAAAAAATCCATTTTGACCCAAA
*
56092 ACTTCCAAAAATTACATTTTTACCCTTAAACTTCTAAAAATTCATTTTTTAA
65 ACTTCCAAAAATTACATTTTTACCCTCAAACTTCTAAAAATTCATTTTTTAA
*
56144 CCCTAAAACTTCTAAAAATTACATTTTTA-CCTCCAAAC-TTCACAAAAATCCATTTTGACCTCG
1 CCCTAAAACTTCTAAAAATTACATTTTTACCCT-CAAACTTTCA-AAAAATCCATTTTGACC-CA
* * * *
56207 AAACTTCCAAAAATTATATTTTTACTCTCAAA-TTTTCAAATATTCCA-TTTTTAA
63 AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCT-AAAAATT-CATTTTTTAA
**
56261 -CCTCAAAACTT-TAAAAAATTACCCTTTTACCCTC
1 CCCT-AAAACTTCT-AAAAATTACATTTTTACCCTC
56295 GAATGTCCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
115 7 0.05
116 48 0.37
117 70 0.54
118 5 0.04
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (116 bp):
CCCTAAAACTTCTAAAAATTACATTTTTACCCTCAAACTTTCAAAAAATCCATTTTGACCCAAAA
CTTCCAAAAATTACATTTTTACCCTCAAACTTCTAAAAATTCATTTTTTAA
Done.