Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008028.1 Kokia drynarioides strain JFW-HI SEQ_122682, 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: 182405
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:8449 original size:2 final size:2
Alignment explanation
Indices: 8442--8479 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8432 GGTAAAGGAA
8442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8480 TTGTCTGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13254 original size:20 final size:21
Alignment explanation
Indices: 13206--13258 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
13196 TACAATAAAA
*
13206 TAAATAAATAACTCATGAAAT
1 TAAAAAAATAACTCATGAAAT
* *
13227 TAAAAAAATAACTC-TTAATT
1 TAAAAAAATAACTCATGAAAT
13247 TAATAAAAATAA
1 TAA-AAAAATAA
13259 ACGTAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAAAAATAACTCATGAAAT
Found at i:16915 original size:15 final size:13
Alignment explanation
Indices: 16881--16937 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
16871 TTTGCTTGGT
*
16881 AAAATGGAAAGA-
1 AAAATTGAAAGAG
*
16893 AAATTTGAAAGATG
1 AAAATTGAAAGA-G
16907 AAAGATTGAAAGAG
1 AAA-ATTGAAAGAG
*
16921 AAAATTGGAA-AG
1 AAAATTGAAAGAG
16933 AAAAT
1 AAAAT
16938 ATTTTTGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 17 0.45
13 6 0.16
14 7 0.18
15 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.18
Consensus pattern (13 bp):
AAAATTGAAAGAG
Found at i:37064 original size:132 final size:132
Alignment explanation
Indices: 36827--37090 Score: 422
Period size: 132 Copynumber: 2.0 Consensus size: 132
36817 GAAATGGGTC
* * *
36827 TGCTCACATGAGCTGTGGGTCGAGATGTTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCAAGATGCTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAA
* *
36892 TCCGTAACATATGCCGAGTCTTAGCCATCGGTAAGACATCTAAGACCAGCACCCATATAACATGT
66 TCCGTAACAAATGCCGAGTCTTAGCCATCGGTAAGACATCTAAGACCAACACCCATATAACATGT
36957 AA
131 AA
*
36959 TGCTCACACGAGCTGTGGGTCAAGATGCTAGGCTACACAATGCTGCTCACACGAGCTGTGGGGAA
1 TGCTCACACGAGCTGTGGGTCAAGATGCTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAA
* * * *
37024 TCCGTAACAAATGCCG-GATCTTAGCCATCGGTAGGACATCTATGACTAACACTCATATAACATG
66 TCCGTAACAAATGCCGAG-TCTTAGCCATCGGTAAGACATCTAAGACCAACACCCATATAACATG
37088 TAA
130 TAA
37091 ACCCCAAAAT
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
131 1 0.01
132 120 0.99
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (132 bp):
TGCTCACACGAGCTGTGGGTCAAGATGCTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAA
TCCGTAACAAATGCCGAGTCTTAGCCATCGGTAAGACATCTAAGACCAACACCCATATAACATGT
AA
Found at i:37211 original size:12 final size:12
Alignment explanation
Indices: 37194--37235 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
37184 CTTTCTTCAT
*
37194 TAAATATAAATA
1 TAAATATATATA
37206 TAAATATATATA
1 TAAATATATATA
*
37218 TATATATATATAA
1 TAAATATATAT-A
37231 TAAAT
1 TAAAT
37236 GAAATTCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATATATATA
Found at i:44510 original size:200 final size:200
Alignment explanation
Indices: 44167--44573 Score: 796
Period size: 200 Copynumber: 2.0 Consensus size: 200
44157 AAAATTGAAC
*
44167 TTAATTTACTTTAATTCTGCAGATGGTTGATCCATCTAACGTATTGGAAGATCTAATCTTTACGA
1 TTAATTTACTTTAATTCTGCAGATGGTTGATCCATCTAACATATTGGAAGATCTAATCTTTACGA
44232 ATTGAGTTTTTACCATAGGACTGAGTCTTTAACCATATAAATAGCAGGTTTTATAAATTGTATGG
66 ATTGAGTTTTTACCATAGGACTGAGTCTTTAACCATATAAATAGCAGGTTTTATAAATTGTATGG
44297 TGAAATTTAGATTGGCACTACTTCAGAATAGCTGGAACTTTGAACTAAATTCAAACGTCAAAGTT
131 TGAAATTTAGATTGGCACTACTTCAGAATAGCTGGAACTTTGAACTAAATTCAAACGTCAAAGTT
44362 TTATG
196 TTATG
44367 TTAATTTACTTTAATTCTGCAGATGGTTGATCCATCTAACATATTGGAAGATCTAATCTTTACGA
1 TTAATTTACTTTAATTCTGCAGATGGTTGATCCATCTAACATATTGGAAGATCTAATCTTTACGA
*
44432 ATTGAGTTTTTACCGTAGGACTGAGTCTTTAACCATATAAATAGCAGGTTTTATAAATTGTATGG
66 ATTGAGTTTTTACCATAGGACTGAGTCTTTAACCATATAAATAGCAGGTTTTATAAATTGTATGG
44497 TGAAATTTAGATTGGCACTACTTCAGAATAGCTGGAACTTTGAACTAAATTCAAACGTCAAAGTT
131 TGAAATTTAGATTGGCACTACTTCAGAATAGCTGGAACTTTGAACTAAATTCAAACGTCAAAGTT
44562 TTATG
196 TTATG
44567 TTAATTT
1 TTAATTT
44574 TGGCAAATGT
Statistics
Matches: 205, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 205 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (200 bp):
TTAATTTACTTTAATTCTGCAGATGGTTGATCCATCTAACATATTGGAAGATCTAATCTTTACGA
ATTGAGTTTTTACCATAGGACTGAGTCTTTAACCATATAAATAGCAGGTTTTATAAATTGTATGG
TGAAATTTAGATTGGCACTACTTCAGAATAGCTGGAACTTTGAACTAAATTCAAACGTCAAAGTT
TTATG
Found at i:51422 original size:12 final size:12
Alignment explanation
Indices: 51398--51437 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
51388 TTTACGTTTC
*
51398 CCCTCTCCCTCT
1 CCCTCTCCTTCT
*
51410 CCTTCTCCTTCT
1 CCCTCTCCTTCT
*
51422 CCCTATCCTTCT
1 CCCTCTCCTTCT
51434 CCCT
1 CCCT
51438 AGTAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (12 bp):
CCCTCTCCTTCT
Found at i:51424 original size:18 final size:18
Alignment explanation
Indices: 51401--51435 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
51391 ACGTTTCCCC
*
51401 TCTCCCTCTCCTTCTCCT
1 TCTCCCTATCCTTCTCCT
51419 TCTCCCTATCCTTCTCC
1 TCTCCCTATCCTTCTCC
51436 CTAGTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.54, G:0.00, T:0.43
Consensus pattern (18 bp):
TCTCCCTATCCTTCTCCT
Found at i:56989 original size:2 final size:2
Alignment explanation
Indices: 56948--56977 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56938 TAGTGATTTA
56948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56978 TTAACATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57769 original size:6 final size:6
Alignment explanation
Indices: 57759--57815 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
57749 TTGGTTTGTC
* * *
57759 ATGTGC ATGTGC ATGTGT ATGTGC ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
57807 ATGTGT ATG
1 ATGTGT ATG
57816 ATAGAAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.18, C:0.05, G:0.33, T:0.44
Consensus pattern (6 bp):
ATGTGT
Found at i:57782 original size:18 final size:18
Alignment explanation
Indices: 57759--57815 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
57749 TTGGTTTGTC
*
57759 ATGTGCATGTGCATGTGT
1 ATGTGCATGTGTATGTGT
57777 ATGTGCATGTGTATGTGT
1 ATGTGCATGTGTATGTGT
*
57795 ATGTGTATGTGTATGTGT
1 ATGTGCATGTGTATGTGT
57813 ATG
1 ATG
57816 ATAGAAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.18, C:0.05, G:0.33, T:0.44
Consensus pattern (18 bp):
ATGTGCATGTGTATGTGT
Found at i:58014 original size:44 final size:44
Alignment explanation
Indices: 57946--58036 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
57936 TTTTGATTAT
*
57946 TGTCTGTCATGTGCATGAAAGAAATGGATTTGTTTGTATTAAAG
1 TGTCTGTCAAGTGCATGAAAGAAATGGATTTGTTTGTATTAAAG
**
57990 TGTCTGTCAAGTGCATGACTGAAATGGATTTGTTTGTATTAAAG
1 TGTCTGTCAAGTGCATGAAAGAAATGGATTTGTTTGTATTAAAG
58034 TGT
1 TGT
58037 ATGACTTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (44 bp):
TGTCTGTCAAGTGCATGAAAGAAATGGATTTGTTTGTATTAAAG
Found at i:58048 original size:44 final size:44
Alignment explanation
Indices: 57953--58053 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
57943 TATTGTCTGT
* * *
57953 CATGTGCATGAAAGAAATGGATTTGTTTGTATTAAAGTGTCTGT
1 CATGTGCATGACAGAAATGGATTTGTTTGTATTAAAGTGTATGA
* *
57997 CAAGTGCATGACTGAAATGGATTTGTTTGTATTAAAGTGTATGA
1 CATGTGCATGACAGAAATGGATTTGTTTGTATTAAAGTGTATGA
*
58041 CTTGTGCATGACA
1 CATGTGCATGACA
58054 AAGTGTGATA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.37
Consensus pattern (44 bp):
CATGTGCATGACAGAAATGGATTTGTTTGTATTAAAGTGTATGA
Found at i:62553 original size:13 final size:13
Alignment explanation
Indices: 62535--62582 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
62525 AGTTTAGCAT
62535 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
62548 TGCTTTTAAAAAA
1 TGCTTTTGAAAAG
* *
62561 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
62574 TGCTTTTGA
1 TGCTTTTGA
62583 GAATTACTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:75692 original size:20 final size:20
Alignment explanation
Indices: 75667--75706 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
75657 ACAGCATTGA
*
75667 ATAGCTAATCTTTAGGGATT
1 ATAGCTAATCTTTAGAGATT
* *
75687 ATAGCTGATTTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
75707 CTAATTAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
ATAGCTAATCTTTAGAGATT
Found at i:80256 original size:18 final size:19
Alignment explanation
Indices: 80218--80255 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
80208 AAATTCAAAA
80218 TCCGATTATCCTTCTTTTT
1 TCCGATTATCCTTCTTTTT
80237 TCCGATTATCCTTCTTTTT
1 TCCGATTATCCTTCTTTTT
80256 CTTTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.05, T:0.58
Consensus pattern (19 bp):
TCCGATTATCCTTCTTTTT
Found at i:81201 original size:22 final size:22
Alignment explanation
Indices: 81166--81217 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
81156 TTTAAAATTT
*
81166 AATTTTATACTTTTACTTTTAA
1 AATTTAATACTTTTACTTTTAA
* *
81188 GAATTTAATATTTTTACTTTTTA
1 -AATTTAATACTTTTACTTTTAA
81211 AATTTAA
1 AATTTAA
81218 AAATTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTAATACTTTTACTTTTAA
Found at i:81210 original size:30 final size:28
Alignment explanation
Indices: 81148--81233 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 28
81138 TTACACTTTT
*
81148 TTTTTATATTTAAAATTTAAT-TTTATAC
1 TTTTTAT-TTTAAAATTTAATATTTTTAC
81176 -TTTTACTTTTAAGAATTTAATATTTTTAC
1 TTTTTA-TTTTAA-AATTTAATATTTTTAC
*
81205 TTTTTAAATTTAAAAATTTAATATTTTTA
1 TTTTT--ATTTTAAAATTTAATATTTTTA
81234 TTAACAATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
27 10 0.20
28 9 0.18
29 6 0.12
30 19 0.38
31 5 0.10
32 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTTTATTTTAAAATTTAATATTTTTAC
Found at i:82172 original size:31 final size:29
Alignment explanation
Indices: 82109--82172 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
82099 TTAGTCTTCA
* * * *
82109 TATTTTTATTTTTAAAATTTTAGTTTATT
1 TATTTTTATTTTCAAAATTTAAGTTGAAT
82138 TATTTTTCATATTTCAAAATTTAAGTTGAAT
1 TATTTTT-AT-TTTCAAAATTTAAGTTGAAT
82169 TATT
1 TATT
82173 AATACTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.24
30 2 0.07
31 20 0.69
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (29 bp):
TATTTTTATTTTCAAAATTTAAGTTGAAT
Found at i:82544 original size:23 final size:23
Alignment explanation
Indices: 82518--82561 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
82508 TGGAGATGTT
*
82518 AAAAATTTTAATTTTTTTCTCTC
1 AAAAATTTTAACTTTTTTCTCTC
82541 AAAAATTTTAACTTTTTTCTC
1 AAAAATTTTAACTTTTTTCTC
82562 CCGAAAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAAATTTTAACTTTTTTCTCTC
Found at i:87877 original size:22 final size:23
Alignment explanation
Indices: 87826--87880 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
87816 GACTAATAAT
*
87826 AATTTAACTAAAACAAATAAATA
1 AATTTAACTAAAACAAATAAACA
*
87849 AATTTTAA-TTAAA-AAATAAACA
1 AA-TTTAACTAAAACAAATAAACA
87871 GAATTTAACT
1 -AATTTAACT
87881 GAAAGATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 13 0.48
23 9 0.33
24 5 0.19
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
AATTTAACTAAAACAAATAAACA
Found at i:89279 original size:30 final size:30
Alignment explanation
Indices: 89231--89303 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
89221 TTGAATTCTG
* *
89231 GATCTTTGTATG-TTTTTTTTTCGAAAGAA
1 GATCTTTGTATGTTTTTTTTTTAGAAAAAA
*
89260 GATCTTTGTATGTTTTTTTTTTATAAAAAA
1 GATCTTTGTATGTTTTTTTTTTAGAAAAAA
89290 GATCTTTGTATGTT
1 GATCTTTGTATGTT
89304 GGGAATGGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 12 0.30
30 28 0.70
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.55
Consensus pattern (30 bp):
GATCTTTGTATGTTTTTTTTTTAGAAAAAA
Found at i:94910 original size:20 final size:20
Alignment explanation
Indices: 94885--94923 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
94875 TGAGGTGTCC
*
94885 TTATTATTGTCATCATTATA
1 TTATTATTATCATCATTATA
94905 TTATTATTATCATCATTAT
1 TTATTATTATCATCATTAT
94924 CACTCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (20 bp):
TTATTATTATCATCATTATA
Found at i:112874 original size:16 final size:16
Alignment explanation
Indices: 112850--112881 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
112840 GTTCAAATAT
112850 TTTCATTTTAAGTTTA
1 TTTCATTTTAAGTTTA
*
112866 TTTCTTTTTAAGTTTA
1 TTTCATTTTAAGTTTA
112882 GCTAGTGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTCATTTTAAGTTTA
Found at i:114320 original size:14 final size:15
Alignment explanation
Indices: 114297--114325 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
114287 TAAAATTTTA
114297 ACAATAAATTTATTT
1 ACAATAAATTTATTT
114312 ACAAT-AATTTATTT
1 ACAATAAATTTATTT
114326 GTTGTTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
ACAATAAATTTATTT
Found at i:117083 original size:26 final size:26
Alignment explanation
Indices: 117043--117101 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
117033 ATGAATTTGG
*
117043 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
117069 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
117095 AATTAAT
1 AATTAAT
117102 TAGTCTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:117116 original size:26 final size:26
Alignment explanation
Indices: 117061--117116 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
117051 ATGTTTAAAT
* * *
117061 TTGTATTTAATTAATAATTTTTATGT
1 TTGTATTTAATTAATAATCTCTATGA
*
117087 TTGTATTTAATTAATTAGTCTCTAT-A
1 TTGTATTTAATTAA-TAATCTCTATGA
117113 TTGT
1 TTGT
117117 TTGGTCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.59
Consensus pattern (26 bp):
TTGTATTTAATTAATAATCTCTATGA
Found at i:117274 original size:7 final size:7
Alignment explanation
Indices: 117263--117338 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
117253 AAAATTTTGG
117263 GGTTTAA
1 GGTTTAA
*
117270 AGTTT-A
1 GGTTTAA
117276 GGATTTAA
1 GG-TTTAA
*
117284 GGTCTATA
1 GGTTTA-A
117292 -GTTTAA
1 GGTTTAA
*
117298 GGCTTAA
1 GGTTTAA
117305 GAGTTTAA
1 G-GTTTAA
117313 GGTTTAA
1 GGTTTAA
*
117320 GGTTT-C
1 GGTTTAA
117326 GTGTTTAA
1 G-GTTTAA
117334 GGTTT
1 GGTTT
117339 TGGGTATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
6 4 0.07
7 39 0.72
8 11 0.20
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.43
Consensus pattern (7 bp):
GGTTTAA
Found at i:117311 original size:15 final size:15
Alignment explanation
Indices: 117291--117324 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
117281 TAAGGTCTAT
117291 AGTTTAAGGCTTAAG
1 AGTTTAAGGCTTAAG
*
117306 AGTTTAAGGTTTAAG
1 AGTTTAAGGCTTAAG
117321 -GTTT
1 AGTTT
117325 CGTGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (15 bp):
AGTTTAAGGCTTAAG
Found at i:117351 original size:21 final size:21
Alignment explanation
Indices: 117327--117380 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
117317 TAAGGTTTCG
*
117327 TGTTTAAGGTTTTGGGTATTA
1 TGTTTAAGGTTTTGGGTATAA
* *
117348 TGTTCAGGGTTTTGGGTATAA
1 TGTTTAAGGTTTTGGGTATAA
* *
117369 AGTTTTAGGTTT
1 TGTTTAAGGTTT
117381 AATTGTGTAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.50
Consensus pattern (21 bp):
TGTTTAAGGTTTTGGGTATAA
Found at i:117560 original size:28 final size:32
Alignment explanation
Indices: 117466--117555 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
117456 CCCCAAACAT
* *
117466 AAACATAAGCATAAATATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
*
117498 AAACATAAATATAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
*
117530 AAACATAAACATAAAAATAATTAATT
1 AAACATAAACATAAACATAATTAATT
117556 CCAAATTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.28
Consensus pattern (32 bp):
AAACATAAACATAAACATAATTAATTAAATAC
Found at i:119765 original size:20 final size:21
Alignment explanation
Indices: 119735--119773 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
119725 TTACAAAATT
119735 AAAAATAAATAATTTTATTGA
1 AAAAATAAATAATTTTATTGA
*
119756 AAAAAT-AATATTTTTATT
1 AAAAATAAATAATTTTATT
119774 TATTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
AAAAATAAATAATTTTATTGA
Found at i:120304 original size:21 final size:22
Alignment explanation
Indices: 120248--120302 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 22
120238 TAAAAAATTT
* *
120248 ATAAAATAAATGAAA-A-ACAA
1 ATAAAATATATAAAACATACAA
120268 A-AAAAT-TATAATAACATACAA
1 ATAAAATATATAA-AACATACAA
120289 ATAAAATATATAAA
1 ATAAAATATATAAA
120303 CACTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.11
19 7 0.25
20 2 0.07
21 5 0.18
22 6 0.21
23 5 0.18
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAAAATATATAAAACATACAA
Found at i:120487 original size:22 final size:20
Alignment explanation
Indices: 120424--120494 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 20
120414 TAATTTAAAC
120424 ATAAAATAAATTAATTAAAAAATTT
1 ATAAAATAAA-T-A-TAAAAAA--T
*
120449 ATAAAATAAATAAAAAAAAT
1 ATAAAATAAATATAAAAAAT
120469 ATAATAATAACATAT-AAAAAT
1 ATAA-AATAA-ATATAAAAAAT
120490 ATAAA
1 ATAAA
120495 CACTATAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 6 0.14
21 15 0.36
22 9 0.21
23 1 0.02
24 1 0.02
25 10 0.24
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAATAAATATAAAAAAT
Found at i:120583 original size:28 final size:29
Alignment explanation
Indices: 120535--120607 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 29
120525 CAATTAATAA
* *
120535 AAAATTAAATTATAACAAACAATATTTTT
1 AAAATTAAATTAAAACAAACAAAATTTTT
120564 AAAA-TAAATTAAAATC-AACAAAA--TTT
1 AAAATTAAATTAAAA-CAAACAAAATTTTT
*
120590 -AAATTAAAATAAAACAAA
1 AAAATTAAATTAAAACAAA
120608 ACCCTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 4 0.11
26 14 0.37
28 15 0.39
29 5 0.13
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (29 bp):
AAAATTAAATTAAAACAAACAAAATTTTT
Found at i:120593 original size:21 final size:22
Alignment explanation
Indices: 120568--120608 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
120558 ATTTTTAAAA
*
120568 TAAATTAAAAT-CAACAAAATT
1 TAAATTAAAATAAAACAAAATT
120589 TAAATTAAAATAAAACAAAA
1 TAAATTAAAATAAAACAAAA
120609 CCCTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAATTAAAATAAAACAAAATT
Found at i:122810 original size:63 final size:66
Alignment explanation
Indices: 122720--122858 Score: 230
Period size: 63 Copynumber: 2.2 Consensus size: 66
122710 TTATTTATTT
122720 ATTTATTTATTTATATTCATAAAATAATAAATAAAT-AA-TAA-AACAAAATTAATATTATTTTA
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAAATTAATAACAAAATTAATATTATTTTA
122782 C
66 C
* *
122783 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATTAATAATAAAATTAATATTATTTTA
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAAATTAATAACAAAATTAATATTATTTTA
*
122848 T
66 C
122849 ATTTATTTAT
1 ATTTATTTAT
122859 ATTTATAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
63 35 0.50
64 2 0.03
65 3 0.04
66 30 0.43
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.47
Consensus pattern (66 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAAATTAATAACAAAATTAATATTATTTTA
C
Found at i:122872 original size:63 final size:60
Alignment explanation
Indices: 122714--122875 Score: 193
Period size: 66 Copynumber: 2.6 Consensus size: 60
122704 GGTTTGTTAT
* *
122714 TTATTTATTTATTTATTTATATTCAT-AAAATAATAAATAAATAATAAAACAAAATTAATA
1 TTATTT-TATATTTATTTATATTTATAAAAATAATAAATAAATAATAAAACAAAATTAATA
* * *
122774 TTATTTTACATTTATTTAT-TTATATTCATACAATAATAAATAAATAAATTAATAATAAAATTAA
1 TTATTTTATATTTATTTATATT-TA-T-A-AAAATAATAAATAAAT-AA-TAA-AACAAAATTAA
122838 TA
59 TA
122840 TTATTTTATATTTATTTATATTTATAAAAATAATAA
1 TTATTTTATATTTATTTATATTTATAAAAATAATAA
122876 GAAAAATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
58 2 0.02
59 12 0.14
60 7 0.08
63 24 0.28
64 3 0.03
65 4 0.05
66 32 0.37
67 2 0.02
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (60 bp):
TTATTTTATATTTATTTATATTTATAAAAATAATAAATAAATAATAAAACAAAATTAATA
Found at i:123574 original size:13 final size:13
Alignment explanation
Indices: 123556--123593 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
123546 CATAAACCAA
123556 ACTTTTCAAAATT
1 ACTTTTCAAAATT
123569 ACTTTTCAAAATT
1 ACTTTTCAAAATT
123582 ACTTTTCCAAAA
1 ACTTTT-CAAAA
123594 CAATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (13 bp):
ACTTTTCAAAATT
Found at i:123600 original size:26 final size:26
Alignment explanation
Indices: 123571--123623 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
123561 TCAAAATTAC
** * *
123571 TTTTCAAAATTACTTTTCCAAAACAA
1 TTTTCAAAAACACTTATCAAAAACAA
*
123597 TTTTTAAAAACACTTATCAAAAACAA
1 TTTTCAAAAACACTTATCAAAAACAA
123623 T
1 T
123624 GCTAAACTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (26 bp):
TTTTCAAAAACACTTATCAAAAACAA
Found at i:128179 original size:16 final size:16
Alignment explanation
Indices: 128132--128179 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
128122 CAACTGGAAT
* *
128132 TCAAAGTGATCCAAAC
1 TCAAAATGATCCGAAC
* **
128148 TCCAAATGATTTGAAC
1 TCAAAATGATCCGAAC
128164 TCAAAATGATCCGAAC
1 TCAAAATGATCCGAAC
128180 ATGAGATGAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (16 bp):
TCAAAATGATCCGAAC
Found at i:128384 original size:58 final size:58
Alignment explanation
Indices: 128314--128430 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
128304 TATTACTAAA
*
128314 TAGGAATGTCAATCTGAATTGCGGATTTGAATACTTACAAATATTCAATCTGTTTTTT
1 TAGGAATGTCAATCTGAATTGCGGATTCGAATACTTACAAATATTCAATCTGTTTTTT
*
128372 TAGGAATGTCAATCTGAATTGCGGATTCGAATACTTACAAATATTCGATCTGTTTTTT
1 TAGGAATGTCAATCTGAATTGCGGATTCGAATACTTACAAATATTCAATCTGTTTTTT
128430 T
1 T
128431 TTTTTTACGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (58 bp):
TAGGAATGTCAATCTGAATTGCGGATTCGAATACTTACAAATATTCAATCTGTTTTTT
Found at i:131197 original size:2 final size:2
Alignment explanation
Indices: 131190--131218 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
131180 GGTTGACATA
131190 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
131219 GAATTCTTCA
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:133870 original size:16 final size:16
Alignment explanation
Indices: 133860--133890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
133850 ATATTTATAT
133860 TAAAATTTATTAATAG
1 TAAAATTTATTAATAG
*
133876 TAAAATTAATTAATA
1 TAAAATTTATTAATA
133891 ATAATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAATTTATTAATAG
Found at i:134266 original size:27 final size:27
Alignment explanation
Indices: 134214--134267 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
134204 AGTATGACAT
*
134214 AGTATTAATGAAATAATATATTTTATA
1 AGTATTAATGAAATAATATATATTATA
134241 AGTATTAAT-ATAATAACTAT-TATTATA
1 AGTATTAATGA-AATAA-TATATATTATA
134268 TTATAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 20 0.83
28 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (27 bp):
AGTATTAATGAAATAATATATATTATA
Found at i:135302 original size:20 final size:20
Alignment explanation
Indices: 135273--135312 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
135263 ATTTTAAAAT
* *
135273 CAAGTTAAAATGATTTTAAC
1 CAAGTCAAAATCATTTTAAC
135293 CAAGTCAAAATCATTTTAAC
1 CAAGTCAAAATCATTTTAAC
135313 ACATCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (20 bp):
CAAGTCAAAATCATTTTAAC
Found at i:138865 original size:11 final size:12
Alignment explanation
Indices: 138844--138868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
138834 GGATAGAAGC
138844 TTTCTTTTTTTT
1 TTTCTTTTTTTT
138856 TTTCTTTTTTTT
1 TTTCTTTTTTTT
138868 T
1 T
138869 GTTGTTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:144048 original size:20 final size:21
Alignment explanation
Indices: 143995--144049 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
143985 ACTCCAAACC
*
143995 CTCAACCTTGGACCTTGAACT
1 CTCAACCTTGAACCTTGAACT
* * * *
144016 ATTAACTTTGAACTTTGAA-T
1 CTCAACCTTGAACCTTGAACT
144036 CTCAACCTTGAACC
1 CTCAACCTTGAACC
144050 GAGGGTTCGG
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (21 bp):
CTCAACCTTGAACCTTGAACT
Found at i:145324 original size:13 final size:13
Alignment explanation
Indices: 145280--145327 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
145270 CCATGGATCT
145280 TGATTACACCATG
1 TGATTACACCATG
145293 TGATGATACGACACTATG
1 TGAT--TAC-AC-C-ATG
145311 TGATTACACCATG
1 TGATTACACCATG
145324 TGAT
1 TGAT
145328 CACTTGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 5 0.17
16 5 0.17
17 1 0.03
18 7 0.23
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (13 bp):
TGATTACACCATG
Found at i:147650 original size:21 final size:22
Alignment explanation
Indices: 147608--147659 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
147598 AATATATTGT
*
147608 TGTTTTGATGCTGTTATTTTAC
1 TGTTTTGGTGCTGTTATTTTAC
*
147630 TGTTTTGGTGTTGTT-TTTTAC
1 TGTTTTGGTGCTGTTATTTTAC
147651 TGTTTTGGT
1 TGTTTTGGT
147660 TTTTTTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.08, C:0.06, G:0.23, T:0.63
Consensus pattern (22 bp):
TGTTTTGGTGCTGTTATTTTAC
Found at i:147663 original size:16 final size:17
Alignment explanation
Indices: 147624--147674 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
147614 GATGCTGTTA
147624 TTTTACTGTTTTGGTGTTGTT
1 TTTTACTGTTTT-G-G-T-TT
147645 TTTTACTGTTTTGGTTT
1 TTTTACTGTTTTGGTTT
*
147662 TTTTATTGTTTTG
1 TTTTACTGTTTTG
147675 ATCGTGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 1 0.03
20 1 0.03
21 12 0.41
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.71
Consensus pattern (17 bp):
TTTTACTGTTTTGGTTT
Found at i:149383 original size:17 final size:19
Alignment explanation
Indices: 149361--149397 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
149351 TATTATCTTT
149361 AAAATTA-TAGA-AAATAC
1 AAAATTACTAGAGAAATAC
149378 AAAATTACTAGAGAAATAC
1 AAAATTACTAGAGAAATAC
149397 A
1 A
149398 TTATCCTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAATTACTAGAGAAATAC
Found at i:149448 original size:20 final size:22
Alignment explanation
Indices: 149415--149455 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
149405 AACTAGAAAT
*
149415 AAAAATTTTCTAAAAT-TAAAG
1 AAAAATTCTCTAAAATATAAAG
149436 AAAAATTCT-TAAAATATAAA
1 AAAAATTCTCTAAAATATAAA
149456 AAATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAAATTCTCTAAAATATAAAG
Found at i:149981 original size:10 final size:10
Alignment explanation
Indices: 149966--149990 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
149956 AATTTTCTAT
149966 AAAATCTAAA
1 AAAATCTAAA
149976 AAAATCTAAA
1 AAAATCTAAA
149986 AAAAT
1 AAAAT
149991 AATAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATCTAAA
Found at i:151075 original size:35 final size:35
Alignment explanation
Indices: 151029--151100 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
151019 TTTTTAAGAA
151029 AAAATTAAATCAGTTTTTTAACTGAATGACTGACT
1 AAAATTAAATCAGTTTTTTAACTGAATGACTGACT
151064 AAAATTAAATCAGTTTTTTAACTGAATGACTGACT
1 AAAATTAAATCAGTTTTTTAACTGAATGACTGACT
151099 AA
1 AA
151101 GGATGTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (35 bp):
AAAATTAAATCAGTTTTTTAACTGAATGACTGACT
Found at i:153619 original size:26 final size:26
Alignment explanation
Indices: 153588--153638 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
153578 CACATAGATT
**
153588 TTATTTATCAAATTAAAAATAATTTA
1 TTATTTAAAAAATTAAAAATAATTTA
*
153614 TTATTTAAAAAATTTAAAATAATTT
1 TTATTTAAAAAATTAAAAATAATTT
153639 TCATATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTATTTAAAAAATTAAAAATAATTTA
Found at i:163913 original size:21 final size:21
Alignment explanation
Indices: 163856--163914 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
163846 CCTATGTTTT
*
163856 TTAAAATTA-AAAAAAAACCTT
1 TTAAAATTATAAAAAAAA-CTA
**
163877 TTAAAATTAT-TGAAAAA-TAA
1 TTAAAATTATAAAAAAAACT-A
163897 TTAAAATTATAAAAAAAA
1 TTAAAATTATAAAAAAAA
163915 AAAAAAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 10 0.33
21 19 0.63
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (21 bp):
TTAAAATTATAAAAAAAACTA
Found at i:165889 original size:30 final size:32
Alignment explanation
Indices: 165855--165928 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
165845 TTTTTCACAT
* *
165855 GTGCTTAAATGATGG-TCAAA-CCTTTTAAAA
1 GTGCTTAAATAAAGGTTCAAATCCTTTTAAAA
* ** *
165885 GTGCTCAAATAAAGGTTCAAATTTTTTTGAAA
1 GTGCTTAAATAAAGGTTCAAATCCTTTTAAAA
165917 GTGCTTAAATAA
1 GTGCTTAAATAA
165929 TGACTTTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 12 0.34
31 5 0.14
32 18 0.51
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (32 bp):
GTGCTTAAATAAAGGTTCAAATCCTTTTAAAA
Found at i:174666 original size:76 final size:75
Alignment explanation
Indices: 174541--174683 Score: 223
Period size: 76 Copynumber: 1.9 Consensus size: 75
174531 GCTGCTATTC
* *
174541 TAGAATTATGCATATTATTTAATCCGTGGATGATAAAAGAAAGTGTTTTAGAACTTGTTGCATCT
1 TAGAATTATGCATATTATTTAATCCGTGGAAGAGAAAAGAAAGTGTTTTAGAACTTGTTGCATCT
174606 TATAAGGTGT
66 TATAAGGTGT
* * * *
174616 TAGAATTATGCATATTGTATTAATCTGTGGAAGGGAAAAGAATGTGTTTTAGAACTTGTTGCATC
1 TAGAATTATGCATATTAT-TTAATCCGTGGAAGAGAAAAGAAAGTGTTTTAGAACTTGTTGCATC
174681 TTA
65 TTA
174684 AGTTCTTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 17 0.28
76 44 0.72
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (75 bp):
TAGAATTATGCATATTATTTAATCCGTGGAAGAGAAAAGAAAGTGTTTTAGAACTTGTTGCATCT
TATAAGGTGT
Found at i:179900 original size:52 final size:52
Alignment explanation
Indices: 179844--179948 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
179834 TTGCTACTTA
179844 TTGGTATTGATTTTCAAAAGATATTTAATATTATTTATAAATATCAAATGGG
1 TTGGTATTGATTTTCAAAAGATATTTAATATTATTTATAAATATCAAATGGG
179896 TTGGTATTGATTTTCAAAAGATATTTAATATTATTTATAAATATCAAATGGG
1 TTGGTATTGATTTTCAAAAGATATTTAATATTATTTATAAATATCAAATGGG
179948 T
1 T
179949 AAGTTAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (52 bp):
TTGGTATTGATTTTCAAAAGATATTTAATATTATTTATAAATATCAAATGGG
Done.