Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008000.1 Kokia drynarioides strain JFW-HI SEQ_122652, 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: 45072
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:3184 original size:23 final size:23
Alignment explanation
Indices: 3158--3202 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3148 TTTTTTGAAT
**
3158 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
3181 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
3203 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:7903 original size:23 final size:23
Alignment explanation
Indices: 7829--7891 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
7819 TGGGGAAATT
7829 GTAAGCACACACAGTGCGAATCA
1 GTAAGCACACACAGTGCGAATCA
* *
7852 GTAAGCACATATAGTGCGAATCA
1 GTAAGCACACACAGTGCGAATCA
7875 GTAAGCACACACAGTGC
1 GTAAGCACACACAGTGC
7892 TGAGCAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
GTAAGCACACACAGTGCGAATCA
Found at i:12978 original size:30 final size:30
Alignment explanation
Indices: 12919--13135 Score: 244
Period size: 30 Copynumber: 7.3 Consensus size: 30
12909 CAATTGGTCC
*
12919 TTCCAAAATTATATTTTGACCCC-AAACTT
1 TTCCAAAATCATATTTTGACCCCTAAACTT
*
12948 TTTCAAAATCATATTTTGACCCCTAAACTT
1 TTCCAAAATCATATTTTGACCCCTAAACTT
* * *
12978 TTCCAAAATTACATTTTGACCCTTAAACTT
1 TTCCAAAATCATATTTTGACCCCTAAACTT
* * *
13008 TTCCAAAATCATATTTTAAACCTTAAACTT
1 TTCCAAAATCATATTTTGACCCCTAAACTT
* * *
13038 TTCC-AAATTACATTTTAACCCCTAAACTT
1 TTCCAAAATCATATTTTGACCCCTAAACTT
*
13067 TTCCAAAATCATATTTTAAACCCC-AAACTT
1 TTCCAAAATCATATTTT-GACCCCTAAACTT
* *
13097 TTCCAAAATCACAGTTTGA-CCCTAGAACTT
1 TTCCAAAATCATATTTTGACCCCTA-AACTT
* *
13127 CTCTAAAAT
1 TTCCAAAAT
13136 TTCATTTTTA
Statistics
Matches: 162, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.02
29 48 0.30
30 105 0.65
31 6 0.04
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
TTCCAAAATCATATTTTGACCCCTAAACTT
Found at i:13120 original size:59 final size:59
Alignment explanation
Indices: 12919--13135 Score: 285
Period size: 59 Copynumber: 3.6 Consensus size: 59
12909 CAATTGGTCC
* * * *
12919 TTCCAAAATTATATTTTGACCCCAAACTTTTTCAAAATCATATTTT-GACCCCTAAACTT
1 TTCCAAAATTACATTTTGACCCTAAACTTTTCCAAAATCATATTTTAAACCCC-AAACTT
**
12978 TTCCAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCATATTTTAAACCTTAAACTT
1 TTCCAAAATTACATTTTGACCC-TAAACTTTTCCAAAATCATATTTTAAACCCCAAACTT
*
13038 TTCC-AAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAAACCCCAAACTT
1 TTCCAAAATTACATTTTGA-CCCTAAACTTTTCCAAAATCATATTTTAAACCCCAAACTT
* * * *
13097 TTCCAAAATCACAGTTTGACCCTAGAACTTCTCTAAAAT
1 TTCCAAAATTACATTTTGACCCTA-AACTTTTCCAAAAT
13136 TTCATTTTTA
Statistics
Matches: 139, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
59 78 0.56
60 58 0.42
61 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (59 bp):
TTCCAAAATTACATTTTGACCCTAAACTTTTCCAAAATCATATTTTAAACCCCAAACTT
Found at i:13126 original size:89 final size:88
Alignment explanation
Indices: 12919--13135 Score: 247
Period size: 89 Copynumber: 2.4 Consensus size: 88
12909 CAATTGGTCC
* * * *
12919 TTCCAAAATTATATTTTGACCCCAAACTTTTTCAAAATCATATTTTGACCCCTAAACTTTTCCAA
1 TTCCAAAATCATATTTTGACCCTAAAC-TTTTCAAAATCACATTTTAACCCCTAAACTTTTCCAA
* * *
12984 AATTACATTTTGACCCTTAAACTT
65 AATCACATTTTAACCCTCAAACTT
* * * *
13008 TTCCAAAATCATATTTTAAACCTTAAACTTTTCCAAATTACATTTTAACCCCTAAACTTTTCCAA
1 TTCCAAAATCATATTTT-GACCCTAAACTTTTCAAAATCACATTTTAACCCCTAAACTTTTCCAA
*
13073 AATCATATTTTAAACCC-CAAACTT
65 AATCACATTTT-AACCCTCAAACTT
* * *
13097 TTCCAAAATCACAGTTTGACCCTAGAACTTCTCTAAAAT
1 TTCCAAAATCATATTTTGACCCTA-AACTTTTC-AAAAT
13136 TTCATTTTTA
Statistics
Matches: 106, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
88 5 0.05
89 86 0.81
90 15 0.14
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (88 bp):
TTCCAAAATCATATTTTGACCCTAAACTTTTCAAAATCACATTTTAACCCCTAAACTTTTCCAAA
ATCACATTTTAACCCTCAAACTT
Found at i:13247 original size:34 final size:34
Alignment explanation
Indices: 13204--13272 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
13194 TTCTCTTCAA
13204 TGTTCATACACCGAATTTAATTATCATTCTTTCG
1 TGTTCATACACCGAATTTAATTATCATTCTTTCG
13238 TGTTCATACACCGAATTTAATTATCATTCTTTCG
1 TGTTCATACACCGAATTTAATTATCATTCTTTCG
13272 T
1 T
13273 ATTTTGTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (34 bp):
TGTTCATACACCGAATTTAATTATCATTCTTTCG
Found at i:17267 original size:16 final size:16
Alignment explanation
Indices: 17241--17278 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
17231 ACACACTATT
17241 AAAAG-AGAAGATAAA-
1 AAAAGAAGAAGA-AAAG
17256 AAAAGAAGAAGAAAAG
1 AAAAGAAGAAGAAAAG
17272 AAAAGAA
1 AAAAGAA
17279 AGAAAATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAAGAAGAAGAAAAG
Found at i:17333 original size:5 final size:5
Alignment explanation
Indices: 17325--17374 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
17315 TTTAAAAATA
17325 AAAAG AAAA- AAGAA- AAAAG AAAAG AAAAG AAAAG AAGAAG AAAAAG
1 AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AA-AAG -AAAAG
17371 AAAA
1 AAAA
17375 AGGAAAAGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.10
5 29 0.71
6 6 0.15
7 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:17340 original size:6 final size:6
Alignment explanation
Indices: 17318--17382 Score: 64
Period size: 6 Copynumber: 11.0 Consensus size: 6
17308 GGCATCTTTT
* *
17318 AAAAAT AAAAAG AAAAAAG AAAAA- AGAAAAG -AAAAG -AAAAG AAGAAG
1 AAAAAG AAAAAG -AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG
*
17365 AAAAAG AAAAAG GAAAAG
1 AAAAAG AAAAAG AAAAAG
17383 TCAAGATGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 11 0.22
6 34 0.67
7 6 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:17360 original size:22 final size:22
Alignment explanation
Indices: 17332--17374 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17322 ATAAAAAGAA
17332 AAAAGAAAAA-AGAAAAGAAAAG
1 AAAAGAAAAAGA-AAAAGAAAAG
*
17354 AAAAGAAGAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAAAGAAAA
17375 AGGAAAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAGAAAAAGAAAAG
Found at i:17418 original size:96 final size:98
Alignment explanation
Indices: 17241--17418 Score: 256
Period size: 96 Copynumber: 1.8 Consensus size: 98
17231 ACACACTATT
*
17241 AAAAGAGAAGATAAAAAAAGAAGAAGAAAAGAAAAGAAAGAAAATGTCAAAAAGAAAACCTGCAA
1 AAAAGAAAAGATAAAAAAAGAAGAAGAAAAGAAAAGAAAGAAAATGTCAAAAAGAAAACCTGCAA
**
17306 AGGGCATCTTTTAAAAATAAAAAGAAAAAAGAA
66 AGGGCATCTTAAAAAAATAAAAAGAAAAAAGAA
* * *
17339 AAAAGAAAAGA-AAAGAAAAGAAGAAGAAAA-AGAAA-AAGGAAAA-GTCAAGATGAAAACCTGC
1 AAAAGAAAAGATAAA-AAAAGAAGAAGAAAAGA-AAAGAAAGAAAATGTCAAAAAGAAAACCTGC
17400 AAAGGGCATCTTAAAAAAA
64 AAAGGGCATCTTAAAAAAA
17419 ATCTCATTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
96 33 0.46
97 11 0.15
98 28 0.39
ACGTcount: A:0.66, C:0.07, G:0.19, T:0.09
Consensus pattern (98 bp):
AAAAGAAAAGATAAAAAAAGAAGAAGAAAAGAAAAGAAAGAAAATGTCAAAAAGAAAACCTGCAA
AGGGCATCTTAAAAAAATAAAAAGAAAAAAGAA
Found at i:18148 original size:18 final size:18
Alignment explanation
Indices: 18107--18150 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18097 GATTTCACCC
* *
18107 AAAAAAGAAAAATGAGGA
1 AAAAAAGAAAAACGAGAA
*
18125 AAAAAAGAAAAACGAAAA
1 AAAAAAGAAAAACGAGAA
18143 AGAAAAAG
1 A-AAAAAG
18151 GAGAGGTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAAAACGAGAA
Found at i:19241 original size:98 final size:98
Alignment explanation
Indices: 19044--19688 Score: 624
Period size: 98 Copynumber: 6.6 Consensus size: 98
19034 AGTTTTCATC
*
19044 ACCACAAGGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
* * * *
19109 GGGAAAGATTTAAGCCGCAACAGCGAATCCAGT
66 GGGAAAGATTTAAACTGCAAGAGTGAATCCAGT
** * ** *
19142 ACTGCAAAGATATGGAGGGAAATGTTTAAGTCGTAACGACGAATCTTGTACCTCAGAAGCATGAA
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
* **
19207 GGGAAAGATTTAAACTGCAATGACT-AATTTAGT
66 GGGAAAGATTTAAACTGCAA-GAGTGAATCCAGT
* ** * * * * * *
19240 ACCACGAAGATATTAAGGGAAAGATTTAAGCCACAACGACGAATCC-AGTACCAC-GAGGATATG
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAA-CCTTGTACCTCAGAAG-CATG
* * *
19303 GAGGGAAAGGTTTAAA-TCGCAACAGTGAATCCAGT
64 AAGGGAAAGATTTAAACT-GCAAGAGTGAATCCAGT
* * * * *
19338 ACCACAAGGATATAGAGGGAAAGGTTTAAGTCACAACGACGAACTTTGTACCCCGGAAGCATGAA
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
* *
19403 GGGAAAGATTTAAGCCGCAACG-GTGAATCCAGT
66 GGGAAAGATTTAAACTGCAA-GAGTGAATCCAGT
* *
19436 ACCACAAGGATATGGAGGGAAAGGTTTAAGTCATAAC-AGCGAACCTTGTACCTCAGAAGCATGA
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGA-CGAACCTTGTACCTCAGAAGCATGA
* *
19500 AGGGAAAGATTT-AAGTCGCAACG-GTGAATCTAGT
65 AGGGAAAGATTTAAACT-GCAA-GAGTGAATCCAGT
* * ** * * * *
19534 ACCACGAAGATATGGAGGGAAAGATTTAAGTTGCAACGGCGAGCCTTGTACCTTATAAGCATGAA
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
* * * *
19599 GGGAAAGATTTAAGCCGTAACG-GTGAATCTAGT
66 GGGAAAGATTTAAACTGCAA-GAGTGAATCCAGT
* * * * ** * * *
19632 ACCACGAAGATTTGAAGGGAAGGGTTTAAGTCGTAATGACGAACCTTATGCCTCAGA
1 ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGA
19689 TACATAAATG
Statistics
Matches: 447, Mismatches: 87, Indels: 26
0.80 0.16 0.05
Matches are distributed among these distances:
97 9 0.02
98 432 0.97
99 6 0.01
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (98 bp):
ACCACAAAGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
GGGAAAGATTTAAACTGCAAGAGTGAATCCAGT
Found at i:19570 original size:147 final size:147
Alignment explanation
Indices: 19059--19575 Score: 546
Period size: 147 Copynumber: 3.5 Consensus size: 147
19049 AAGGATATGG
* * * *
19059 AGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGATTTAAGTCACAACGACGAATCTAGTACCACAGAAGCATGAAGGGAAAGATTTAAGC
* ** * * *
19124 CGCAACAGCGAATCCAGTACTGCAAAGATATGGAGGGAAATGTTTAAGTCGTAAC-GACGAATCT
66 CGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTTAAGTCGTAACAG-CGAACCT
19188 TGTACCTCAGAAGCATGA
130 TGTACCTCAGAAGCATGA
* * * * * * *
19206 AGGGAAAGATTTAA-ACTGCAATGACTAATTTAGTACCAC-GAAGATATTAAGGGAAAGATTTAA
1 AGGGAAAGATTTAAGTC-ACAACGACGAATCTAGTACCACAGAAG-CATGAAGGGAAAGATTTAA
* * * * * *
19269 GCCACAACGACGAATCCAGTACCACGAGGATATGGAGGGAAAGGTTTAAATCGCAACAGTGAATC
64 GCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTTAAGTCGTAACAGCGAA-C
* * * *
19334 C-AGTA-C-CACAAGGATATA
128 CTTGTACCTCAGAAGCAT-GA
* * * *
19352 GAGGGAAAGGTTTAAGTCACAACGACGAA-CTTTGTACCCCGGAAGCATGAAGGGAAAGATTTAA
1 -AGGGAAAGATTTAAGTCACAACGACGAATC-TAGTACCACAGAAGCATGAAGGGAAAGATTTAA
* *
19416 GCCGCAACGGTGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTTAAGTCATAACAGCGAACC
64 GCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTTAAGTCGTAACAGCGAACC
19481 TTGTACCTCAGAAGCATGA
129 TTGTACCTCAGAAGCATGA
* ** * *
19500 AGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACCAC-GAAGATATGGAGGGAAAGATTTAAG
1 AGGGAAAGATTTAAGTCACAACGACGAATCTAGTACCACAGAAG-CATGAAGGGAAAGATTTAAG
**
19564 TTGCAACGGCGA
65 CCGCAACGGCGA
19576 GCCTTGTACC
Statistics
Matches: 296, Mismatches: 60, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
145 7 0.02
146 13 0.04
147 259 0.88
148 10 0.03
149 7 0.02
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (147 bp):
AGGGAAAGATTTAAGTCACAACGACGAATCTAGTACCACAGAAGCATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTTAAGTCGTAACAGCGAACCTT
GTACCTCAGAAGCATGA
Found at i:19612 original size:196 final size:194
Alignment explanation
Indices: 19044--19688 Score: 737
Period size: 196 Copynumber: 3.3 Consensus size: 194
19034 AGTTTTCATC
*
19044 ACCAC-AAGGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGA
1 ACCACGAA-GATATGAAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGA
* *
19108 AGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACTGCA-AAGATATGGAGGGAAATGTTTAAG
65 AGGGAAAGATTTAAGTCGCAACAGTGAATCCAGTAC--CACAAGATATGGAGGGAAA-GTTTAAG
* * * * * * *
19172 TCGTAACGACGAATCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAACTGCAATGACT-AATT
127 TCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACG-GTGAATC
19236 TAGT
191 TAGT
* * * * * * *
19240 ACCACGAAGATATTAAGGGAAAGATTTAAGCCACAACGACGAATCC-AGTACCAC-GAGGATATG
1 ACCACGAAGATATGAAGGGAAAGGTTTAAGTCACAACGACGAA-CCTTGTACCTCAGAAG-CATG
* * * *
19303 GAGGGAAAGGTTTAAATCGCAACAGTGAATCCAGTACCACAAGGATATAGAGGGAAAGGTTTAAG
64 AAGGGAAAGATTTAAGTCGCAACAGTGAATCCAGTACCACAA-GATATGGAGGGAAA-GTTTAAG
* * * * *
19368 TCACAACGACGAACTTTGTACCCCGGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC
127 TCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
19433 AGT
192 AGT
* *
19436 ACCAC-AAGGATATGGAGGGAAAGGTTTAAGTCATAAC-AGCGAACCTTGTACCTCAGAAGCATG
1 ACCACGAA-GATATGAAGGGAAAGGTTTAAGTCACAACGA-CGAACCTTGTACCTCAGAAGCATG
* *
19499 AAGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGATTTAAG
64 AAGGGAAAGATTTAAGTCGCAACAGTGAATCCAGTACCAC-AAGATATGGAGGGAAAG-TTTAAG
* * * * * *
19564 TTGCAACGGCGAGCCTTGTACCTTATAAGCATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCT
127 TCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
19629 AGT
192 AGT
* * ** * * *
19632 ACCACGAAGATTTGAAGGGAAGGGTTTAAGTCGTAATGACGAACCTTATGCCTCAGA
1 ACCACGAAGATATGAAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGA
19689 TACATAAATG
Statistics
Matches: 375, Mismatches: 60, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
194 2 0.01
195 12 0.03
196 349 0.93
197 12 0.03
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (194 bp):
ACCACGAAGATATGAAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAAGCATGAA
GGGAAAGATTTAAGTCGCAACAGTGAATCCAGTACCACAAGATATGGAGGGAAAGTTTAAGTCGC
AACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGT
Found at i:19667 original size:49 final size:49
Alignment explanation
Indices: 19044--19664 Score: 413
Period size: 49 Copynumber: 12.7 Consensus size: 49
19034 AGTTTTCATC
* * * * * *
19044 ACCAC-AAGGATATGGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGT
1 ACCACGAA-GATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * * * *
19093 ACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGT
1 ACCAC-GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
** * * * * *
19142 ACTGCAAAGATATGGAGGGAAATG-TTTAAGTCGTAACGACGAATCTTGT
1 ACCACGAAGATATGAAGGGAAA-GATTTAAGTCGCAACGGCGAATCTAGT
* * * * * * *
19191 ACCTCAGAAG-CATGAAGGGAAAGATTTAA-ACTGCAATGACTAATTTAGT
1 ACCAC-GAAGATATGAAGGGAAAGATTTAAGTC-GCAACGGCGAATCTAGT
* * * * *
19240 ACCACGAAGATATTAAGGGAAAGATTTAAGCCACAACGACGAATCCAGT
1 ACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * * * * * *
19289 ACCACGAGGATATGGAGGGAAAGGTTTAAATCGCAACAGTGAATCCAGT
1 ACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * * *
19338 ACCAC-AAGGATAT-AGAGGGAAAGGTTTAAGTCACAACGACGAA-CTTTGT
1 ACCACGAA-GATATGA-AGGGAAAGATTTAAGTCGCAACGGCGAATC-TAGT
* * * * *
19387 ACCCCGGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGT
1 ACCAC-GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * ** * * *
19436 ACCAC-AAGGATATGGAGGGAAAGGTTTAAGTCATAACAGCGAACCTTGT
1 ACCACGAA-GATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * *
19485 ACCTCAGAAG-CATGAAGGGAAAGATTTAAGTCGCAACGGTGAATCTAGT
1 ACCAC-GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * ** *
19534 ACCACGAAGATATGGAGGGAAAGATTTAAGTTGCAACGGCGAGCCTTGT
1 ACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * * * *
19583 ACCTTA-TAAG-CATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCTAGT
1 ACC--ACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
* * *
19632 ACCACGAAGATTTGAAGGGAAGGGTTTAAGTCG
1 ACCACGAAGATATGAAGGGAAAGATTTAAGTCG
19665 TAATGACGAA
Statistics
Matches: 431, Mismatches: 116, Indels: 50
0.72 0.19 0.08
Matches are distributed among these distances:
47 3 0.01
48 19 0.04
49 389 0.90
50 13 0.03
51 7 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (49 bp):
ACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGT
Found at i:20095 original size:42 final size:41
Alignment explanation
Indices: 20020--20161 Score: 169
Period size: 42 Copynumber: 3.4 Consensus size: 41
20010 GTTACGTCAC
* *
20020 CATCCAATCTCTTACCCAATCATGGGGTAGATTGAAAACAT
1 CATCCAATCTCTTACCCGATCATGGGGCAGATTGAAAACAT
* * *
20061 CATCCAATATCTTACCTCGATCATGGGGCAGATTG-CAGCTAT
1 CATCCAATCTCTTACC-CGATCATGGGGCAGATTGAAAAC-AT
* * *
20103 CATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAGACCT
1 CATCCAATCTCTTA-CCCGATCATGGGGCAGATTGAAAACAT
*
20145 CATCCAATCTTTTACCC
1 CATCCAATCTCTTACCC
20162 TTAAGTCAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 20 0.24
42 62 0.73
43 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (41 bp):
CATCCAATCTCTTACCCGATCATGGGGCAGATTGAAAACAT
Found at i:20202 original size:44 final size:42
Alignment explanation
Indices: 20147--20229 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
20137 GAAGACCTCA
* *
20147 TCCAATCTTTTACCCTTAAGTCAAAAAGGGTCAAATTGAAGAAT
1 TCCAATATTTTACCCTT-AGTC-AAAAGGGGCAAATTGAAGAAT
*
20191 TCCAATATTTTACCCTTAGTCAAGAGGGGCAAATTGAAG
1 TCCAATATTTTACCCTTAGTCAAAAGGGGCAAATTGAAG
20230 CCATCTTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 16 0.44
43 4 0.11
44 16 0.44
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (42 bp):
TCCAATATTTTACCCTTAGTCAAAAGGGGCAAATTGAAGAAT
Found at i:22557 original size:30 final size:30
Alignment explanation
Indices: 22517--22903 Score: 284
Period size: 30 Copynumber: 12.8 Consensus size: 30
22507 GTCTCTAAAA
* *
22517 TTTTTCAAAATTATATTTTGACCCCTTCAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
* **
22547 TTTTCTAAAATTATATTTTGACCCCAAAAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
* *
22577 TTTTCCAAAATTACATTTTGA-CCCTTAAAT
1 TTTTCCAAAATTATATTTTGACCCCTT-AAC
* * *
22607 TTTTTCAAAATTACATTTTGACCCCTAAAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
* * * *
22637 TTTTCCAAAATCATATGTTGATCCCTAAAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
* * * *
22667 TTTTCCAAAGTCACATTTT-AACCCTTAAAC
1 TTTTCCAAAATTATATTTTGACCCCTT-AAC
* * *
22697 TTTTACAAAA-TATATTTTAACCCCTAAAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
* * *
22726 TTTTCCAAAATCATATTTT-AACCCTTAAATT
1 TTTTCCAAAATTATATTTTGACCCCTT-AA-C
* * *
22757 TTTTTCAAAATCATATTTT-AACCCTTAAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
* *
22786 TTTTCC-AAATTACATTTTAACCCCTTGAAC
1 TTTTCCAAAATTATATTTTGACCCCTT-AAC
* * *
22816 TTTTCAAAAAAAAATCATATTTTGACCCCTAAAC
1 TTTTC----CAAAATTATATTTTGACCCCTTAAC
* * * * **
22850 TTTTTCAAAATCACATTTTAACCCCCAAAC
1 TTTTCCAAAATTATATTTTGACCCCTTAAC
*
22880 TTTTCCAAAATCACT-TTTTGACCC
1 TTTTCCAAAATTA-TATTTTGACCC
22904 TCGAACTTCT
Statistics
Matches: 289, Mismatches: 53, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.03
29 42 0.15
30 185 0.64
31 29 0.10
34 7 0.02
35 16 0.06
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTTCCAAAATTATATTTTGACCCCTTAAC
Found at i:22670 original size:90 final size:90
Alignment explanation
Indices: 22512--22903 Score: 430
Period size: 90 Copynumber: 4.3 Consensus size: 90
22502 AAAAGGTCTC
* * ** * * *
22512 TAAAATTTTTCAAAATTATATTTTGACCCCTTCACTTTTCTAAAATTATATTTTGACCCCAAAAC
1 TAAACTTTTTCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
* *
22577 TTTTCCAAAATTACATTTTGACCCT
66 TTTTCCAAAATCACATTTTAACCCT
* * *
22602 TAAATTTTTTCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATGTTGATCCCTAAAC
1 TAAACTTTTTCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
*
22667 TTTTCCAAAGTCACATTTTAACCCT
66 TTTTCCAAAATCACATTTTAACCCT
* * * * *
22692 TAAACTTTTACAAAA-TATATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAACCCTTAAAT
1 TAAACTTTTTCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAA-
* * *
22756 TTTTTTCAAAATCATATTTTAACCCT
65 CTTTTCCAAAATCACATTTTAACCCT
* * * *
22782 T-AAC-TTTTCCAAATTACATTTTAACCCCTTGAACTTTTCAAAAAAAAATCATATTTTGACCCC
1 TAAACTTTTTCAAAATTACATTTTGACCCC-TAAACTTTTC----CAAAATCATATTTTGACCCC
* *
22845 TAAACTTTTTCAAAATCACATTTTAACCCC
61 TAAACTTTTCCAAAATCACATTTTAACCCT
* * * *
22875 CAAACTTTTCCAAAATCACTTTTTGACCC
1 TAAACTTTTTCAAAATTACATTTTGACCC
22904 TCGAACTTCT
Statistics
Matches: 253, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
88 7 0.03
89 58 0.23
90 123 0.49
93 23 0.09
94 24 0.09
95 18 0.07
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (90 bp):
TAAACTTTTTCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
TTTTCCAAAATCACATTTTAACCCT
Found at i:22920 original size:60 final size:59
Alignment explanation
Indices: 22511--22920 Score: 344
Period size: 60 Copynumber: 6.8 Consensus size: 59
22501 CAAAAGGTCT
* * * ** * * *
22511 CTAAAATTTTTCAAAATTATATTTTGACCCCTTCACTTTTCTAAAATTATATTTTGACCC
1 CTAAACTTTTCCAAAATCATATTTTGA-CCCTAAACTTTTCTAAAATCACATTTTAACCC
* * * * * *
22571 CAAAACTTTTCCAAAATTACATTTTGACCCTTAAA-TTTTTTCAAAATTACATTTTGACCC
1 CTAAACTTTTCCAAAATCATATTTTGACCC-TAAACTTTTCT-AAAATCACATTTTAACCC
* * *
22631 CTAAACTTTTCCAAAATCATATGTTGATCCCTAAACTTTTCCAAAGTCACATTTTAACCC
1 CTAAACTTTTCCAAAATCATATTTTGA-CCCTAAACTTTTCTAAAATCACATTTTAACCC
* * * * *
22691 TTAAACTTTTACAAAAT-ATATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAACCC
1 CTAAACTTTTCCAAAATCATATTTTGA-CCCTAAACTTTTCTAAAATCACATTTTAACCC
* * * * * * *
22750 TTAAATTTTTTTCAAAATCATATTTTAACCCTTAACTTTTC-CAAATTACATTTTAACCC
1 CTAAA-CTTTTCCAAAATCATATTTTGACCCTAAACTTTTCTAAAATCACATTTTAACCC
* *
22809 CTTGAACTTTTCAAAAAAAAATCATATTTTGACCCCTAAACTTTT-TCAAAATCACATTTTAACC
1 C-TAAACTTTTC----CAAAATCATATTTTGA-CCCTAAACTTTTCT-AAAATCACATTTTAACC
22873 C
59 C
* * *
22874 CCAAACTTTTCCAAAATCACT-TTTTGACCCTCGAACTTCTCTAAAAT
1 CTAAACTTTTCCAAAATCA-TATTTTGACCCT-AAACTTTTCTAAAAT
22921 TTCATTTCAT
Statistics
Matches: 289, Mismatches: 44, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
59 73 0.25
60 148 0.51
61 18 0.06
63 14 0.05
64 19 0.07
65 17 0.06
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (59 bp):
CTAAACTTTTCCAAAATCATATTTTGACCCTAAACTTTTCTAAAATCACATTTTAACCC
Found at i:26102 original size:38 final size:38
Alignment explanation
Indices: 26051--26127 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
26041 TTTGTACATA
26051 TATTGTTATTATTAGTAGTTTCAAACCAAATGTTTCAT
1 TATTGTTATTATTAGTAGTTTCAAACCAAATGTTTCAT
26089 TATTGTTATTATTAGTAGTTTCAAACCAAATGTTTCAT
1 TATTGTTATTATTAGTAGTTTCAAACCAAATGTTTCAT
26127 T
1 T
26128 GTTTTACTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (38 bp):
TATTGTTATTATTAGTAGTTTCAAACCAAATGTTTCAT
Found at i:26763 original size:20 final size:20
Alignment explanation
Indices: 26738--26777 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
26728 TGATTAAGAT
26738 TGTTTTGTTGATTTTGGAGA
1 TGTTTTGTTGATTTTGGAGA
26758 TGTTTTGTTGATTTTGGAGA
1 TGTTTTGTTGATTTTGGAGA
26778 ACATATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (20 bp):
TGTTTTGTTGATTTTGGAGA
Done.