Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014179.1 Kokia drynarioides strain JFW-HI SEQ_129212, 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: 29306
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--38 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39 GGCTTTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10197 original size:24 final size:23
Alignment explanation
Indices: 10160--10209 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
10150 TTTTAAGTAT
* *
10160 TAAATGTCTGTTAATATTAATAA
1 TAAATGTCTATTAATAATAATAA
*
10183 TAAATGTGCTATTAATAATGATAA
1 TAAATGT-CTATTAATAATAATAA
10207 TAA
1 TAA
10210 TAATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (23 bp):
TAAATGTCTATTAATAATAATAA
Found at i:10231 original size:24 final size:25
Alignment explanation
Indices: 10196--10270 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 25
10186 ATGTGCTATT
10196 AATAA-TGATAATAATAATAATAATA
1 AATAATTG-TAATAATAATAATAATA
* * *
10221 AAT-CTTGTAATAATGATAATATTA
1 AATAATTGTAATAATAATAATAATA
*
10245 AATAATTGTAATATTAAT-ATAA-A
1 AATAATTGTAATAATAATAATAATA
10268 AAT
1 AAT
10271 TAAAATCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 4 0.10
24 21 0.51
25 16 0.39
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (25 bp):
AATAATTGTAATAATAATAATAATA
Found at i:11397 original size:29 final size:29
Alignment explanation
Indices: 11285--11392 Score: 164
Period size: 29 Copynumber: 3.7 Consensus size: 29
11275 GGTCTCTAAC
*
11285 CTTCCAAAAATTGCATTTTT-ACCCTCAAA
1 CTTCCAAAAATTCCATTTTTGACCC-CAAA
*
11314 CTTTCAAAAATTCCATTTTTGACCCCAAA
1 CTTCCAAAAATTCCATTTTTGACCCCAAA
11343 CTTCCAAAAATTCCATTTTTGACCCCAAAA
1 CTTCCAAAAATTCCATTTTTGACCCC-AAA
11373 CTTCCAAAAATTACCATTTT
1 CTTCCAAAAATT-CCATTTT
11393 GCCCCCGGAT
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
29 47 0.64
30 19 0.26
31 7 0.10
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTTGACCCCAAA
Found at i:11551 original size:28 final size:28
Alignment explanation
Indices: 11494--11556 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
11484 CTAAATTTTC
* *
11494 CCAAAATTGCCATTTCACCCTCGAGAAT
1 CCAAAATTACCATTTCACCCTCAAGAAT
* *
11522 CCAAAATTACCATTTTACCCTCAAGTAT
1 CCAAAATTACCATTTCACCCTCAAGAAT
11550 CCGAAAA
1 CC-AAAA
11557 GCCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (28 bp):
CCAAAATTACCATTTCACCCTCAAGAAT
Found at i:13821 original size:29 final size:29
Alignment explanation
Indices: 13779--13839 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
13769 GGTATGGTTT
13779 CCTATCAGTACTTGTCTAAAGATTACTCC
1 CCTATCAGTACTTGTCTAAAGATTACTCC
13808 CCTATCAGTACTTGTCTAAAGATTACTCC
1 CCTATCAGTACTTGTCTAAAGATTACTCC
13837 CCT
1 CCT
13840 TTGAAAGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (29 bp):
CCTATCAGTACTTGTCTAAAGATTACTCC
Found at i:23573 original size:205 final size:203
Alignment explanation
Indices: 23209--23810 Score: 913
Period size: 205 Copynumber: 3.0 Consensus size: 203
23199 GCGATTATCC
*
23209 ACAAACGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
23274 --G-CAAATCTTCGAACCCTAGCTTCCTGATGAGACACTTAGAAGCAGGTCGAAGCAATAAAAGG
66 TGGACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGG
*
23336 TTAGATTCCTGATAAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
131 TTAGATTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
23401 GAATTGAA
196 GAATTGAA
* *
23409 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATTAAACCCACGCTTGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * *
23474 TGTGAACAAATATTCGAACCCCAGCTTCTTGATGGGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 TG-G-ACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * * *
23539 GATTAGCTTCCTGATGAGATACTGAGAAGTGGACCGAATTCGTCTTCCTAATGAGATACAGAGAA
129 GGTTAGATTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
*
23604 GTGAATTGAA
194 GCGAATTGAA
23614 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * *
23679 TGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAA
66 TG-GA-CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * * * * * * *
23744 CGGTTAGATTCCTGATGAAATACAGGGAAGTGAACCAAAATCATCTTCCTGATGAAACACAGAGA
129 -GGTTAGATTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGA
23809 AG
193 AG
23811 TGGATCAAAA
Statistics
Matches: 360, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
200 62 0.17
203 1 0.00
204 1 0.00
205 242 0.67
206 54 0.15
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (203 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGGACAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGG
TTAGATTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
GAATTGAA
Found at i:24194 original size:11 final size:11
Alignment explanation
Indices: 24180--24257 Score: 79
Period size: 11 Copynumber: 6.9 Consensus size: 11
24170 CCCCCTTTTT
*
24180 AATTTATTTTA
1 AATTTAATTTA
24191 AATTTAGATTT-
1 AATTTA-ATTTA
*
24202 ATTTTAAATTTA
1 AATTT-AATTTA
24214 AA-TTAATCTTA
1 AATTTAAT-TTA
24225 AATTTAAATTTA
1 AATTT-AATTTA
*
24237 ATTTTAATTTA
1 AATTTAATTTA
24248 AATTTAATTT
1 AATTTAATTT
24258 CAAAATTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
10 3 0.05
11 36 0.64
12 14 0.25
13 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:24201 original size:6 final size:6
Alignment explanation
Indices: 24187--24267 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
24177 TTTAATTTAT
* *
24187 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
24233 TTT-AA TTTTAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
24268 AAAGTCCGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
4 2 0.03
5 15 0.24
6 38 0.61
7 7 0.11
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:24203 original size:17 final size:17
Alignment explanation
Indices: 24180--24267 Score: 106
Period size: 17 Copynumber: 5.1 Consensus size: 17
24170 CCCCCTTTTT
24180 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
24197 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
24214 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
24231 AATTTAATTTT-AATTTA
1 AATTT-ATTTTAAATTTA
* *
24248 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
24266 AA
1 AA
24268 AAAGTCCGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
17 50 0.82
18 11 0.18
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:24997 original size:24 final size:23
Alignment explanation
Indices: 24960--25009 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
24950 TTTTAAGTAT
* *
24960 TAAATGTCTGTTAATATTAATAA
1 TAAATGTCTATTAATAATAATAA
*
24983 TAAATGTGCTATTAATAATGATAA
1 TAAATGT-CTATTAATAATAATAA
25007 TAA
1 TAA
25010 TAATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (23 bp):
TAAATGTCTATTAATAATAATAA
Found at i:26070 original size:29 final size:28
Alignment explanation
Indices: 26022--26181 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 28
26012 AGAGGTCCAG
26022 AAACTTCCAAAAATTCCATTTTT-ACCCTC
1 AAACTTCCAAAAA-TCCATTTTTGACCC-C
* *
26051 GAACTTCCAAAAATCACATTTTTGACCCT
1 AAACTTCCAAAAATC-CATTTTTGACCCC
26080 AAACTTCCAAAAATTCCATTTTT-ACCCC
1 AAACTTCCAAAAA-TCCATTTTTGACCCC
* *
26108 AAACTTCCAAAATTTTCATTTTTGACCCC
1 AAACTTCCAAAA-ATCCATTTTTGACCCC
*
26137 AAAACTTCCAAAAATCACATTTTTCACCCC
1 -AAACTTCCAAAAATC-CATTTTTGACCCC
*
26167 TAAACTTCAAAAAAT
1 -AAACTTCCAAAAAT
26182 TCCACTTTCA
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
28 26 0.23
29 44 0.39
30 43 0.38
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATCCATTTTTGACCCC
Found at i:26142 original size:58 final size:58
Alignment explanation
Indices: 26022--26224 Score: 232
Period size: 58 Copynumber: 3.5 Consensus size: 58
26012 AGAGGTCCAG
* * *
26022 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGA-CCCT
1 AAACTTCCAAAAATTCCATTTTTACCC-CAAACTTCCAAAAATTACATTTTTGACCCCA
* *
26080 AAACTTCCAAAAATTCCATTTTTACCCCAAACTTCCAAAATTTTCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCAAACTTCCAAAAATTACATTTTTGACCCCA
* * * ** **
26138 AAACTTCCAAAAA-TCACATTTTTCACCCCTAAACTTCAAAAAATTCCACTTTCAACCTAA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCC-AAACTTCCAAAAATTACATTTTTGACCCCA
26198 AAACTTCCAAAAATTACCA-TTTTACCC
1 AAACTTCCAAAAATT-CCATTTTTACCC
26225 TCGGGTGTCC
Statistics
Matches: 126, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
57 24 0.19
58 50 0.40
59 9 0.07
60 39 0.31
61 3 0.02
62 1 0.01
ACGTcount: A:0.37, C:0.30, G:0.01, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAACTTCCAAAAATTACATTTTTGACCCCA
Found at i:26190 original size:29 final size:30
Alignment explanation
Indices: 26022--26220 Score: 200
Period size: 30 Copynumber: 6.7 Consensus size: 30
26012 AGAGGTCCAG
26022 AAACTTCCAAAAATTCCATTTTT-A-CCCT
1 AAACTTCCAAAAATTCCATTTTTCACCCCT
* *
26050 CGAACTTCCAAAAA-TCACATTTTTGA-CCCT
1 -AAACTTCCAAAAATTC-CATTTTTCACCCCT
26080 AAACTTCCAAAAATTCCATTTTT-ACCCC-
1 AAACTTCCAAAAATTCCATTTTTCACCCCT
* * * *
26108 AAACTTCCAAAATTTTCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTCACCCCT
26138 AAACTTCCAAAAA-TCACATTTTTCACCCCT
1 AAACTTCCAAAAATTC-CATTTTTCACCCCT
* * *
26168 AAACTTCAAAAAATTCCA-CTTTCA-ACCT
1 AAACTTCCAAAAATTCCATTTTTCACCCCT
26196 AAAAACTTCCAAAAATTACCATTTT
1 --AAACTTCCAAAAATT-CCATTTT
26221 ACCCTCGGGT
Statistics
Matches: 145, Mismatches: 13, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
28 27 0.19
29 52 0.36
30 59 0.41
31 5 0.03
32 2 0.01
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTCACCCCT
Found at i:26297 original size:58 final size:59
Alignment explanation
Indices: 26022--26316 Score: 193
Period size: 58 Copynumber: 5.0 Consensus size: 59
26012 AGAGGTCCAG
* *
26022 AAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAA-TCACATTTTTGACCCT--
1 AAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAATTC-CA-TTTTCAACCTAA
* * * ** **
26080 AAACTTCCAAAAATT-CCATTTTTACCC-CAAACT-TCCAAAATTTTCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAATTCCATTTTCAACCTAA
* * * *
26138 AAACTTCCAAAAATCA-CATTTTTCACCC-CTAAACT-TCAAAAAATTCCACTTTCAACCTAA
1 AAACTTCCAAAAATTACCA-TTTT-ACCCTC-GAA-TGTCCAAAAATTCCATTTTCAACCTAA
** * **
26198 AAACTTCCAAAAATTACCATTTTACCCTCGGGTGTCCAAAAACTCCATTTTCAACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTCAACCTAA
* * * *
26257 AAAC-TCTC-AAATTTACCTTTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACTCTAA
1 AAACTTC-CAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTCAAC-CTAA
26316 A
1 A
26317 TTTTCCTAAA
Statistics
Matches: 192, Mismatches: 34, Indels: 21
0.78 0.14 0.09
Matches are distributed among these distances:
56 6 0.03
57 14 0.07
58 91 0.47
59 37 0.19
60 42 0.22
61 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTCAACCTAA
Found at i:26306 original size:29 final size:30
Alignment explanation
Indices: 26206--26308 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 30
26196 AAAAACTTCC
** *
26206 AAAAATTACCA-TTTTACCCTCGGGTGTCC
1 AAAAATTACCATTTTTACCCTCGAATGTCT
* * * **
26235 AAAAACT-CCATTTTCAACCTCGAAACTCT
1 AAAAATTACCATTTTTACCCTCGAATGTCT
* *
26264 CAAATTTACC-TTTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTTACCCTCGAATGTCT
26293 AAAAATT-CCATTTTTA
1 AAAAATTACCATTTTTA
26309 ACTCTAAATT
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
28 5 0.09
29 47 0.87
30 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (30 bp):
AAAAATTACCATTTTTACCCTCGAATGTCT
Found at i:27835 original size:30 final size:28
Alignment explanation
Indices: 27790--27923 Score: 90
Period size: 29 Copynumber: 4.6 Consensus size: 28
27780 AAAGAATTCG
**
27790 GGGTTAAAACATAATTATGTAAAAGTTTA
1 GGGTTAAAATGTAATT-TGTAAAAGTTTA
* *
27819 GCGGTAAAAATGTAATTT-TAGGAAAGTTTG
1 G-GGTTAAAATGTAATTTGTA--AAAGTTTA
* *
27849 GGGTTAAAATGTGATTTTGTGAAAGTTTA
1 GGGTTAAAATGT-AATTTGTAAAAGTTTA
* * * **
27878 GGGTTAAAATATGATTTTTGGCAAGTTTA
1 GGGTTAAAATGTAATTTGT-AAAAGTTTA
* *
27907 GGGTCAAAATGTGATTT
1 GGGTTAAAATGTAATTT
27924 TGGGAAAGTT
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
28 6 0.07
29 53 0.63
30 24 0.29
31 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (28 bp):
GGGTTAAAATGTAATTTGTAAAAGTTTA
Found at i:27855 original size:59 final size:58
Alignment explanation
Indices: 27789--27915 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
27779 CAAAGAATTC
*
27789 GGGGTTAAAACATAATTATGTAAAAGTTTAGCGGTAAAAATGTAATTTTAGGAAAGTTT
1 GGGGTTAAAACATAATTATGTAAAAGTTTAG-GGTAAAAATATAATTTTAGGAAAGTTT
** * * * * * * *
27848 GGGGTTAAAATGTGATTTTGTGAAAGTTTAGGGTTAAAATATGATTTTTGGCAAGTTT
1 GGGGTTAAAACATAATTATGTAAAAGTTTAGGGTAAAAATATAATTTTAGGAAAGTTT
* *
27906 AGGGTCAAAA
1 GGGGTTAAAA
27916 TGTGATTTTG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
58 30 0.54
59 26 0.46
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
GGGGTTAAAACATAATTATGTAAAAGTTTAGGGTAAAAATATAATTTTAGGAAAGTTT
Found at i:27866 original size:29 final size:28
Alignment explanation
Indices: 27811--27945 Score: 153
Period size: 29 Copynumber: 4.6 Consensus size: 28
27801 TAATTATGTA
* *
27811 AAAGTTTAGCGGTAAAAATGTAATTTTAGG
1 AAAGTTTAG-GGTTAAAATGTGATTTT-GG
*
27841 AAAGTTTGGGGTTAAAATGTGATTTTGTG
1 AAAGTTTAGGGTTAAAATGTGATTTTG-G
*
27870 AAAGTTTAGGGTTAAAATATGATTTTTGG
1 AAAGTTTAGGGTTAAAATGTGA-TTTTGG
* *
27899 CAAGTTTAGGGTCAAAATGTGATTTTGGG
1 AAAGTTTAGGGTTAAAATGTGATTTT-GG
*
27928 AAAGTTTAGAGATTAAAA
1 AAAGTTTAG-GGTTAAAA
27946 CAAGAACACT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.06
29 66 0.73
30 19 0.21
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAGTTTAGGGTTAAAATGTGATTTTGG
Found at i:27916 original size:58 final size:59
Alignment explanation
Indices: 27811--27945 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 59
27801 TAATTATGTA
* * * * * *
27811 AAAGTTTAGCGGTAAAAATGTAATTTTAGGAAAGTTTGGGGTTAAAATGTGATTTTGTG
1 AAAGTTTAGAGGTTAAAATATAATTTTAGGAAAGTTTAGGGTCAAAATGTGATTTTGGG
* * *
27870 AAAGTTTAG-GGTTAAAATATGATTTTTGGCAAGTTTAGGGTCAAAATGTGATTTTGGG
1 AAAGTTTAGAGGTTAAAATATAATTTTAGGAAAGTTTAGGGTCAAAATGTGATTTTGGG
*
27928 AAAGTTTAGAGATTAAAA
1 AAAGTTTAGAGGTTAAAA
27946 CAAGAACACT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 50 0.76
59 16 0.24
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (59 bp):
AAAGTTTAGAGGTTAAAATATAATTTTAGGAAAGTTTAGGGTCAAAATGTGATTTTGGG
Done.