Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006103.1 Hibiscus syriacus cultivar Beakdansim tig00014463_pilon, 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: 206028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:154689 original size:102 final size:102
Alignment explanation
Indices: 154528--154712 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
154518 ATAGTTTACC
* * *
154528 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGAC
1 TTGAAACAAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGAAATAAATTTTGTCTCTCTTGAGAC
*
154593 AATTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
66 AATTTCCCTTAAAACAAAATATTTGAATATGTTTTCT
** * *
154630 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 TTGAAACAAAATTTCGTCTCCCTTGAGACAGTTGCCCTT-GAAATAAATTTTGTCTCTCTTGAGA
* *
154694 CAGTTTCTCTTAAAACAAA
65 CAATTTCCCTTAAAACAAA
154713 TTTCGTCTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 26 0.36
102 46 0.64
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (102 bp):
TTGAAACAAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGAAATAAATTTTGTCTCTCTTGAGAC
AATTTCCCTTAAAACAAAATATTTGAATATGTTTTCT
Found at i:154733 original size:36 final size:36
Alignment explanation
Indices: 154625--154748 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
154615 TTGAATATGT
*
154625 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * * *
154660 TTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
154697 TTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
154733 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
154749 ATCTTTAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
35 4 0.05
36 40 0.55
37 29 0.40
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:154805 original size:63 final size:67
Alignment explanation
Indices: 154704--154861 Score: 198
Period size: 63 Copynumber: 2.4 Consensus size: 67
154694 CAGTTTCTCT
* ** * * *
154704 TAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTAAA-TTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
154766 CC
66 CC
*
154768 TAAAAC-AATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
*
154832 CT
66 CC
*
154834 TAAAACATAATTTTGTTTCCCTTGAGAC
1 TAAAACA-AATTTTGTCTCCCTTGAGAC
154862 CGGTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
63 25 0.31
64 8 0.10
65 13 0.16
66 15 0.19
68 19 0.24
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
CC
Found at i:155713 original size:105 final size:107
Alignment explanation
Indices: 155481--155937 Score: 647
Period size: 105 Copynumber: 4.3 Consensus size: 107
155471 GCCATCCGCG
* *
155481 ATTTCAACTCCACAACGGAGGATATCGTGGCAC-TCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTTCGAGACAACACAAGTTCAACTTCACAACGA
* * * *
155545 AGGGACGGCTGGTTGTCAACAAAAAACTTCTCAATTTCAGAGCCA
63 AGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
155590 ATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
155654 GACCGCTGCTTGTCAA-AAACAACTTCCCAATTTCAGAGCCA
66 GACCGCTGCTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* ** *
155695 ATTTCAACTTCACAACGAAGGATATTGGAC-TCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
*
155759 GACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
66 GACCGCTGCTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
155800 ATTTCAACTTCACGACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * * ** *
155864 GACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 GACCGCTGCTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
155906 ATTTCAACTTCACGACGGAGGATATTGGACTT
1 ATTTCAACTTCACAACGAAGGATATTGGACTT
155938 GGAACAATGC
Statistics
Matches: 320, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
104 2 0.01
105 196 0.61
106 93 0.29
107 6 0.02
109 23 0.07
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (107 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
GACCGCTGCTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:155826 original size:210 final size:212
Alignment explanation
Indices: 155481--155936 Score: 666
Period size: 211 Copynumber: 2.1 Consensus size: 212
155471 GCCATCCGCG
* *
155481 ATTTCAACTCCACAACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGGAGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACAACGAA
* * * *
155546 GGGACGGCTGGTTGTCAACAAAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAACAAAAAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
155611 ATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-AAAC
128 ATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAAC
*
155674 AACTTCCCAATTTCAGAGCCA
192 AACTTCCCAATTCCAGAGCCA
* ** *
155695 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
155760 ACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACGACGAAGGATA
66 ACCGCTGCTTGTCAACAAAAAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* * *
155824 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATT
131 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACT
**
155889 TCCCGGTTCCAGAGCCA
196 TCCCAATTCCAGAGCCA
*
155906 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGGAGGATATTGGACT
155937 TGGAACAATG
Statistics
Matches: 218, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
209 2 0.01
210 93 0.43
211 97 0.44
212 3 0.01
214 23 0.11
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (212 bp):
ATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
ACCGCTGCTTGTCAACAAAAAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACT
TCCCAATTCCAGAGCCA
Found at i:156528 original size:34 final size:37
Alignment explanation
Indices: 156484--156585 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
156474 TTTCGTCCTA
*
156484 CTAGGATTCAAACTCCTAAAAATATGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
156519 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
156554 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
156586 GTTCTACTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.46
35 3 0.05
37 28 0.46
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:156569 original size:37 final size:35
Alignment explanation
Indices: 156484--156619 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
156474 TTTCGTCCTA
*
156484 CTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
156519 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
156554 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
156591 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
156620 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
33 1 0.01
34 28 0.32
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:157036 original size:53 final size:53
Alignment explanation
Indices: 156979--157079 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
156969 ATATGAATAT
*
156979 TTTCATTTATTTTTATTA-T-TCATGTTATTATTATATGTATATATATATAATTA
1 TTTCATTTATTTTT-TTACTAT-ATGTTATTATTATATATATATATATATAATTA
*
157032 TTTCATTTATTTTTTTACTATATTTTATTATTATATATATATATATAT
1 TTTCATTTATTTTTTTACTATATGTTATTATTATATATATATATATAT
157080 TTATTTAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 3 0.07
53 40 0.91
54 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (53 bp):
TTTCATTTATTTTTTTACTATATGTTATTATTATATATATATATATATAATTA
Found at i:157277 original size:9 final size:9
Alignment explanation
Indices: 157263--157304 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
157253 TATAACTTTA
157263 TATTATTTT
1 TATTATTTT
157272 TATTATTTT
1 TATTATTTT
*
157281 TGTT-TTTT
1 TATTATTTT
*
157289 TATTCATTAT
1 TATT-ATTTT
157299 TATTAT
1 TATTAT
157305 ATTATTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.25
9 14 0.50
10 7 0.25
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTATTTT
Found at i:157508 original size:2 final size:2
Alignment explanation
Indices: 157501--157548 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
157491 TAATACTTTG
157501 AT AT 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 AT AT
157543 AT AT AT
1 AT AT AT
157549 TCTTTTTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160348 original size:16 final size:16
Alignment explanation
Indices: 160309--160340 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
160299 TGACGCTAAT
160309 ATAATATAATGTATAC
1 ATAATATAATGTATAC
160325 ATAATATAATGTATAC
1 ATAATATAATGTATAC
160341 TTCTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
ATAATATAATGTATAC
Found at i:161457 original size:42 final size:42
Alignment explanation
Indices: 161410--161492 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
161400 GAAGTGCCAA
* * * *
161410 GTTTGTATACGATTGTCCTTGATCATATGTGTGAACAAGTTC
1 GTTTGTAAACGAGTGTCCTTCATCATATATGTGAACAAGTTC
* *
161452 GTTTGTAAACGAGTGTGCTTCATCTTATATGTGAACAAGTT
1 GTTTGTAAACGAGTGTCCTTCATCATATATGTGAACAAGTT
161493 GTCTTCAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (42 bp):
GTTTGTAAACGAGTGTCCTTCATCATATATGTGAACAAGTTC
Found at i:165267 original size:20 final size:20
Alignment explanation
Indices: 165232--165269 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
165222 TTACACCAAA
* *
165232 TTCTCTCAATTTCTCTTAAC
1 TTCTCTCAAATACTCTTAAC
165252 TTCTCTCAAATACTCTTA
1 TTCTCTCAAATACTCTTA
165270 TAATCTCTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (20 bp):
TTCTCTCAAATACTCTTAAC
Found at i:165315 original size:21 final size:23
Alignment explanation
Indices: 165301--165353 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 23
165291 TTATTATATT
165301 TTTAATATTTTTTATTTAATTTA
1 TTTAATATTTTTTATTTAATTTA
*
165324 TTTAATATTTTACTTATTTTAATTTT
1 TTTAATATTTT--TTA-TTTAATTTA
165350 TTTA
1 TTTA
165354 CAGATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.42
25 3 0.12
26 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTAATATTTTTTATTTAATTTA
Found at i:166970 original size:16 final size:16
Alignment explanation
Indices: 166949--166982 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
166939 AATATGAATT
166949 AATATGATATT-ATATA
1 AATATGA-ATTAATATA
166965 AATATGAATTAATATA
1 AATATGAATTAATATA
166981 AA
1 AA
166983 ATAATATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AATATGAATTAATATA
Found at i:166989 original size:26 final size:26
Alignment explanation
Indices: 166935--166989 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
166925 CTTTTTTCTT
* * *
166935 TATAAATATGAATTAATATGATATTA
1 TATAAATATGAATTAATATAAAATAA
166961 TATAAATATGAATTAATATAAAATAA
1 TATAAATATGAATTAATATAAAATAA
166987 TAT
1 TAT
166990 CTGTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
TATAAATATGAATTAATATAAAATAA
Found at i:168054 original size:15 final size:15
Alignment explanation
Indices: 168031--168093 Score: 99
Period size: 15 Copynumber: 4.2 Consensus size: 15
168021 CGTAGGACTC
168031 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
168046 CTACGTCCCGAAGAA
1 CTACATCCCGAAGGA
168061 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
168076 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
168091 CTA
1 CTA
168094 TTATACCCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.32, C:0.33, G:0.21, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:168067 original size:30 final size:30
Alignment explanation
Indices: 168031--168093 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
168021 CGTAGGACTC
168031 CTACATCCCGAAGGACTACGTCCCGAAGAA
1 CTACATCCCGAAGGACTACGTCCCGAAGAA
*
168061 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGAA
168091 CTA
1 CTA
168094 TTATACCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.33, G:0.21, T:0.14
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGAA
Found at i:168220 original size:29 final size:29
Alignment explanation
Indices: 168178--168255 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
168168 TTTCATATGT
168178 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
168206 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
168235 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
168256 ATATCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:168301 original size:12 final size:12
Alignment explanation
Indices: 168267--168301 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
168257 TATCATGTTC
**
168267 TCATATCACAGG
1 TCATATCACATA
168279 TCATATCACATA
1 TCATATCACATA
168291 TCATATCACAT
1 TCATATCACAT
168302 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:168730 original size:64 final size:64
Alignment explanation
Indices: 168622--168783 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 64
168612 TAATGAAGAT
* * * * * **
168622 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTAGTACTATTAATGGG
* * ** **
168686 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTAGTACTATTAATGGG
168750 ATGCATCGATGCACTACTTATGCATCGATGCACA
1 ATGCATCGATGCACTACTTATGCATCGATGCACA
168784 TTCATACAAT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTAGTACTATTAATGGG
Found at i:169718 original size:10 final size:10
Alignment explanation
Indices: 169703--169732 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
169693 TTAGAATTAA
169703 TTATATATTT
1 TTATATATTT
*
169713 TTATATTTTT
1 TTATATATTT
169723 TTATATATTT
1 TTATATATTT
169733 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATATATTT
Found at i:185132 original size:2 final size:2
Alignment explanation
Indices: 185125--185192 Score: 76
Period size: 2 Copynumber: 37.0 Consensus size: 2
185115 CCGCCCCGAT
185125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
185165 TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
185193 AAATATTTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:187655 original size:17 final size:18
Alignment explanation
Indices: 187635--187669 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
187625 ATAAAGCTAA
187635 AAATAAA-AAAAAATATT
1 AAATAAACAAAAAATATT
187652 AAATAAATCAAAAAATAT
1 AAATAAA-CAAAAAATAT
187670 ATATAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAACAAAAAATATT
Found at i:187659 original size:21 final size:24
Alignment explanation
Indices: 187634--187687 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 24
187624 AATAAAGCTA
187634 AAAATAAAAAAAAATAT-TAA-AT
1 AAAATAAAAAAAAATATATAAGAT
* *
187656 -AAATCAAAAAATATATATAAGAT
1 AAAATAAAAAAAAATATATAAGAT
187679 AAAATAAAA
1 AAAATAAAA
187688 TACAAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.54
22 3 0.12
23 2 0.08
24 7 0.27
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAAAAAAAATATATAAGAT
Found at i:189068 original size:17 final size:16
Alignment explanation
Indices: 189040--189074 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
189030 GGAAAAAAAC
*
189040 AAAAAAAGAAATTAAT
1 AAAAAAAGAAATAAAT
189056 AAAAAAAGAAAATAAAT
1 AAAAAAAG-AAATAAAT
189073 AA
1 AA
189075 TAATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAAAAAGAAATAAAT
Found at i:189238 original size:38 final size:37
Alignment explanation
Indices: 189155--189541 Score: 352
Period size: 38 Copynumber: 10.5 Consensus size: 37
189145 AAAAAAAATC
**
189155 AAAACTATATATTATAT-AGTTTTC-AAAAT-TAATA
1 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTA
*
189189 TAAAA--A-ATATTATATAAGTTTTCAAAAAATGTTTTT
1 -AAAACTATATATTATATAAGTTTTC-AAAAATGTTTTA
* * *
189225 AAAACCATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTA
*
189262 AAAACTATATATTATATAACTTTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATAA--GTTTTCAAAAATGTTTTA
189301 AAAACTATATATTATATAAGTTTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATAAG--TTTTCAAAAATGTTTTA
189340 AAAACTATATATTATATAAGTTTTCAAAAATTGTTTTA
1 AAAACTATATATTATATAAGTTTTCAAAAA-TGTTTTA
* * *
189378 AAAACTATATATTATATACA-TATTTCCAAAATGATTTC
1 AAAACTATATATTATATA-AGT-TTTCAAAAATGTTTTA
* * *
189416 AAAACTATATATTAAATATA-TTTTCAAAAGCA-CTTTCA
1 AAAACTATATATTATATA-AGTTTTCAAAA--ATGTTTTA
* * * **
189454 AAAATTATACATTATATATG-TTTC-AAAAT-TTTCC
1 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTA
* * *
189488 AAAACTATATAATATATATA-TTTTC-GAAATGTTTTT
1 AAAACTATATATTATATA-AGTTTTCAAAAATGTTTTA
* *
189524 GAAACTATATAGTATATA
1 AAAACTATATATTATATA
189542 TATTTTAGAA
Statistics
Matches: 300, Mismatches: 31, Indels: 41
0.81 0.08 0.11
Matches are distributed among these distances:
32 9 0.03
33 8 0.03
34 20 0.07
35 21 0.07
36 24 0.08
37 52 0.17
38 83 0.28
39 83 0.28
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAACTATATATTATATAAGTTTTCAAAAATGTTTTA
Found at i:189298 original size:39 final size:37
Alignment explanation
Indices: 189155--189547 Score: 353
Period size: 39 Copynumber: 10.6 Consensus size: 37
189145 AAAAAAAATC
* **
189155 AAAACTATATATTATAT-AGTTTTC-AAAAT-TAATA
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTA
* *
189189 TAAAA--A-ATATTATATAAGTTTTCAAAAAATGTTTTT
1 -AAAACTATATATTATATAATTTTTC-AAAAATGTTTTA
* *
189225 AAAACCATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTA
189262 AAAACTATATATTATATAACTTTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATAA--TTTTTCAAAAATGTTTTA
189301 AAAACTATATATTATATAAGTTTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATAA--TTTTTCAAAAATGTTTTA
*
189340 AAAACTATATATTATATAAGTTTTCAAAAATTGTTTTA
1 AAAACTATATATTATATAATTTTTCAAAAA-TGTTTTA
* * * *
189378 AAAACTATATATTATATACATATTTCCAAAATGATTTC
1 AAAACTATATATTATATA-ATTTTTCAAAAATGTTTTA
* * *
189416 AAAACTATATATTAAAT-ATATTTTCAAAAGCA-CTTTCA
1 AAAACTATATATTATATAAT-TTTTCAAAA--ATGTTTTA
* * * **
189454 AAAATTATACATTATAT-ATGTTTC-AAAAT-TTTCC
1 AAAACTATATATTATATAATTTTTCAAAAATGTTTTA
* * *
189488 AAAACTATATAATATAT-ATATTTTC-GAAATGTTTTT
1 AAAACTATATATTATATAAT-TTTTCAAAAATGTTTTA
* *
189524 GAAACTATATAGTATATATATTTT
1 AAAACTATATATTATATA-ATTTT
189548 AGAAAACCGT
Statistics
Matches: 305, Mismatches: 34, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
32 9 0.03
33 8 0.03
34 21 0.07
35 21 0.07
36 25 0.08
37 55 0.18
38 82 0.27
39 84 0.28
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATAATTTTTCAAAAATGTTTTA
Found at i:190262 original size:84 final size:84
Alignment explanation
Indices: 190138--191015 Score: 733
Period size: 84 Copynumber: 10.5 Consensus size: 84
190128 GACAATTTTA
* * * ** ** * * * * *
190138 TTGGCAGATAACCCTTCTTGCGTTTAACTATGTTGTAAATGATTTGCCTTGGAACTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTGCCTTCGAACTGAGTGTAAT
* **
190203 AGAACTCGAATATCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * *
190222 TTGGAAGATAACCCTTCTAGCCTTGAGTTATACAGCAAATGATATGCCCTCGAAGCTAAGTGTAA
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTGCCTTCGAA-CTGAGTGTAA
* *
190287 TCGAACTCG-AGG---GTGT
65 TCGAACTCGAAGGTCTTTGG
* * * * *
190303 TTGGCAGATAGCCCTTCTAGCATTGAGTTATACCGCAAATGATGTGTCGTT-GAGA-TGAGTGTA
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTG-CCTTCGA-ACTGAGTGTA
* *
190366 ATCGAACTCAAAGGT-TTTTG
64 ATCGAACTCGAAGGTCTTTGG
* * * * * *
190386 TTGACAGATAACCCTTCTAGCCTTGAGTTTTGCTA-CAAATGATGTGCCCTCGAAGTTGATTATA
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGC-AGCAAATGATGTGCCTTCGAA-CTGAGTGTA
190450 ATCGAACTCGAAGGTCTTTGG
64 ATCGAACTCGAAGGTCTTTGG
* * * * * * * *
190471 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCCA-CAAATGATGTGCCTTTGAGCTGAGTGTAG
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATG-CAGCAAATGATGTGCCTTCGAACTGAGTGTAA
* *
190535 TCAAACTCGAAGGTCTAT-G
65 TCGAACTCGAAGGTCTTTGG
* * * *
190554 TTGGTAGATAACCCTTCTAGCCTTAAGTTATGCTGCACAA-GATGTGCCCTCGAAGCTGAGTGTA
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCA-AATGATGTGCCTTCGAA-CTGAGTGTA
* *
190618 ATCGAACTTGAAGGTTTTTGG
64 ATCGAACTCGAAGGTCTTTGG
* * * * * * * * * *
190639 TTGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATAATGTGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTGCCTTCGAACTGAGTGTAAT
*
190704 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTGG
* * * * * * *
190723 TTGGTAGATAACCC-TCTTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTC-TAGCCTTGAGTTATGCAGCAAATGATGTGCCTTCGAACTGAGTGTAA
*
190787 TCGAACTCGAAGGTCTTTTG
65 TCGAACTCGAAGGTCTTTGG
* * * * * * * * * * * *
190807 TTAGCATATAGCCATTCTAGCCTTTAGCTATGCTAG-AAATGTTGCGCCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGC-AGCAAATGATGTGCCTTCGAACTGAGTGTAA
**
190871 TCGAACTCGAAGAACTTTTGG
65 TCGAACTCGAAGGTC-TTTGG
* * *
190892 -TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTA-CAAATGATTTGCCCTCAAAGCTGAGTGTA
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGC-AGCAAATGATGTGCCTTCGAA-CTGAGTGTA
*
190955 ATCGAACTCGAAGGTCTTTTG
64 ATCGAACTCGAAGGTCTTTGG
*
190976 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAAT
191016 AAATGAAGAA
Statistics
Matches: 640, Mismatches: 129, Indels: 49
0.78 0.16 0.06
Matches are distributed among these distances:
80 16 0.03
81 48 0.08
82 7 0.01
83 85 0.13
84 313 0.49
85 170 0.27
86 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTGCCTTCGAACTGAGTGTAAT
CGAACTCGAAGGTCTTTGG
Found at i:190577 original size:168 final size:168
Alignment explanation
Indices: 190174--190995 Score: 897
Period size: 168 Copynumber: 4.9 Consensus size: 168
190164 ACTATGTTGT
* * * * ** *
190174 AAATGATTTGCCTTGGAACTGAGCGTAGTAGAACTCGAATATCTTTGGTTGGAAGATAACCCTTC
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTC
* * *
190239 TAGCCTTGAGTTATAC-AGCAAATGATATGCCCTCGAAGCTAAGTGTAATCGAACTCG-AGG---
65 TAGCCTTGAGTTATGCTA-CAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * * *
190299 GTGTTTGGCAGATAGCCCTTCTAG-CATTGAGTTATACCGC
129 TTGGTTGGCAGATAGCCCTTCTAGAC-TTAAGCTATGCCAC
* * * * * * * *
190339 AAATGATGTGTCGTTGAGATGAGTGTAATCGAACTCAAAGGTTTTTGTTGACAGATAACCCTTCT
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
* * * *
190404 AGCCTTGAGTTTTGCTACAAATGATGTGCCCTCGAAGTTGATTATAATCGAACTCGAAGGTCTTT
66 AGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT
*
190469 GGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCCAC
131 GGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* * * *
190507 AAATGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTATGTTGGTAGATAACCCTTCT
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
* * * *
190572 AGCCTTAAGTTATGCTGCACAA-GATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTTTT
66 AGCCTTGAGTTATGCTACA-AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTT
* * * * **
190636 TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATTCTGC
130 TGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* *
190675 AAATAATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGATAACCC-TC
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTC
* * * * * *
190739 TTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCT
65 -TAGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * * * * *
190803 TTTGTTAGCATATAGCCATTCTAGCCTTTAGCTATGCTAG
129 TTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
* * * ** *
190843 AAATGTTGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGAACTTTTGGTGGCAGATAACCCTTC
1 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTC
* *
190908 TAGCCTTGAGTTATGCTACAAATGATTTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTCTT
65 TAGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTT
* *
190973 TTGTTGGCAGATAACCCTTCTAG
130 TGGTTGGCAGATAGCCCTTCTAG
190996 CCTTGAGTTA
Statistics
Matches: 549, Mismatches: 96, Indels: 20
0.83 0.14 0.03
Matches are distributed among these distances:
164 64 0.12
165 37 0.07
168 352 0.64
169 96 0.17
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (168 bp):
AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
AGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT
GGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCCAC
Found at i:190710 original size:252 final size:247
Alignment explanation
Indices: 190174--191006 Score: 809
Period size: 252 Copynumber: 3.3 Consensus size: 247
190164 ACTATGTTGT
* * * * * ** *
190174 AAATGATTTGCCTTGGAACTGAGCGTAGTAGAACTCGAATATCTTTGGTTGGAAGATAACCCTTC
1 AAATGATGTGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * * * *
190239 TAGCCTTGAGTTATACAGCAAATGATATGCCCTCGAAGCTAAGTGTAATCGAACTCGAGGGT-GT
66 TAGCCTTGAGTTATCCA-CAAATGATGTGCCTTAG-AGCTGAGTGTAGTCGAACTCGAAGGTCTT
* * * * * * * * *
190303 TTGGCAGATAGCCCTTCTAGCATTGAGTTATACCGCAAATGATGTGTCGTTGAGATGAGTGTAAT
129 TTGGTAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAA-GATGTGCCCTTGAGCTGAGTGTAAT
* *
190368 CGAACTCAAAGGTTTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTT-TTGCTAC
193 CGAACTCGAAGGTTTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATT-CTAC
* * * *** *
190422 AAATGATGTGCCCTCGAAGTTGATTATAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTT
1 AAATGATGTGCCTTAG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
* * * * * *
190487 CTCGACTTAAGCTATGCCACAAATGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTA
65 CTAGCCTTGAGTTAT-CCACAAATGATGTGCCTTAGAGCTGAGTGTAGTCGAACTCGAAGGTCT-
*
190552 TGTTGGTAGATAACCCTTCTAGCCTTAAGTTATGCTGCACAAGATGTGCCCTCGAAGCTGAGTGT
128 T-TTGGTAGATAACCCTTCTAGCCTTAAGTTATGCTGCA-AAGATGTGCCCTTG-AGCTGAGTGT
* * * * *
190617 AATCGAACTTGAAGGTTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATTCTGC
190 AATCGAACTCGAAGGTTTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATTCTAC
* * * * *
190675 AAATAATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGATAACCC-TC
1 AAATGATGTGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
** *
190739 TTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 -TAGCCTTGAGTTAT-CCACAAATGATGTGCCTTAGAGCTGAGTGTAGTCGAACTCGAAGGTCTT
* * * *
190804 TTGTTAGCATATAGCCATTCTAGCCTTTAGCTATGCT--AGAA-ATGTTGCGCCTTGGAGCTGAG
129 TTGGTAG-ATA-A-CCCTTCTAGCCTTAAGTTATGCTGCA-AAGATG-TGC-CCTT-GAGCTGAG
* * ** *
190866 CGTAGTCGAACTCGAAGAACTTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTAC
187 TGTAATCGAACTCGAAG-GTTTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATTCTAC
* * * * *
190927 AAATGATTTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT
1 AAATGATGTG-CCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
190992 CTAGCCTTGAGTTAT
65 CTAGCCTTGAGTTAT
191007 GCTGCAAATA
Statistics
Matches: 477, Mismatches: 89, Indels: 33
0.80 0.15 0.06
Matches are distributed among these distances:
248 35 0.07
249 62 0.13
250 12 0.03
251 52 0.11
252 183 0.38
253 129 0.27
254 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (247 bp):
AAATGATGTGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
TAGCCTTGAGTTATCCACAAATGATGTGCCTTAGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTT
GGTAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAAGATGTGCCCTTGAGCTGAGTGTAATCGA
ACTCGAAGGTTTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATTCTAC
Found at i:192319 original size:95 final size:93
Alignment explanation
Indices: 192130--192390 Score: 319
Period size: 95 Copynumber: 2.7 Consensus size: 93
192120 GACTAGCTGG
* * *
192130 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGATAGCTCAATATCATTGTATAG-AT
1 ATCCATAAAGCCG-GGCGTTTAACCAATTGCTCTAGAGGGA-AACTC-A-AGC-TT-TATTGTAT
*
192194 ATTATAATCACCTTTATCAAGCTAGTTGAATATT
60 ATTATAATCACCTTTATCAAGCTAGCTGAATATT
* * *
192228 ATCCATAGAGCCAGGGCGTTTAACCAATTGCTCTAGCGGGACAACTCGAGCTTTATTGTATATTA
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGA-AACTCAAGCTTTATTGTATATTA
* *
192293 TAATCACCTTTATCAGGCTAGCTGAATCTT
64 TAATCACCTTTATCAAGCTAGCTGAATATT
* *
192323 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGAAAGCTCAAGCTTTATTGTATA-TA
1 ATCCATAAAGC-CGGGCGTTTAACCAATTGCTCTAGAGGGAAA-CTCAAGCTTTATTGTATATTA
192387 TAAT
64 TAAT
192391 ATTATAATCT
Statistics
Matches: 144, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
94 12 0.08
95 88 0.61
96 2 0.01
98 41 0.28
99 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (93 bp):
ATCCATAAAGCCGGGCGTTTAACCAATTGCTCTAGAGGGAAACTCAAGCTTTATTGTATATTATA
ATCACCTTTATCAAGCTAGCTGAATATT
Found at i:195192 original size:19 final size:19
Alignment explanation
Indices: 195165--195203 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
195155 AATAATAAAT
* *
195165 TTAAGGGAAATAGAAATAA
1 TTAAAGGAAAAAGAAATAA
*
195184 TTAAAGGAAAAAGTAATAA
1 TTAAAGGAAAAAGAAATAA
195203 T
1 T
195204 GATAAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (19 bp):
TTAAAGGAAAAAGAAATAA
Found at i:195261 original size:19 final size:18
Alignment explanation
Indices: 195205--195276 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 18
195195 AGTAATAATG
*
195205 ATAAAAAATATTAAATAA
1 ATAAAAAATAATAAATAA
*
195223 GAT-GAAAATAATACAA-AA
1 -ATAAAAAATAATA-AATAA
195241 ATAAAAAAGTAATAAATAA
1 ATAAAAAA-TAATAAATAA
195260 ATAATAATAATAATAAA
1 ATAA-AA-AATAATAAA
195277 GAATTATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 2 0.05
18 16 0.36
19 15 0.34
20 9 0.20
21 2 0.05
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (18 bp):
ATAAAAAATAATAAATAA
Found at i:195810 original size:31 final size:31
Alignment explanation
Indices: 195758--195840 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 31
195748 TTATATAATA
*
195758 TAAACTATATAATATATATTTTAAAAA-TATTTT
1 TAAACTATAT-AT-TATATTTTAAAAAGT-TTTC
195791 TAAACTATATATTATATTTTTTAAAAAGTTTTC
1 TAAACTATATATTATA--TTTTAAAAAGTTTTC
*
195824 AAAACTATATATTATAT
1 TAAACTATATATTATAT
195841 AGTTTTCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
31 5 0.11
32 2 0.04
33 37 0.82
34 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (31 bp):
TAAACTATATATTATATTTTAAAAAGTTTTC
Found at i:195965 original size:39 final size:37
Alignment explanation
Indices: 195759--196141 Score: 402
Period size: 39 Copynumber: 10.5 Consensus size: 37
195749 TATATAATAT
* *
195759 AAACTATATAATATAT-A-TTTT-AAAAATATTTTT-
1 AAACTATATATTATATAATTTTTCAAAAATGTTTTTA
*
195792 AAACTATATATTATAT--TTTTT-AAAAA-GTTTTCA
1 AAACTATATATTATATAATTTTTCAAAAATGTTTTTA
* *
195825 AAACTATATATTATAT-AGTTTTC-AAAAT-TAATTT-
1 AAACTATATATTATATAATTTTTCAAAAATGT-TTTTA
*
195859 AAA--A-ATATTATATAAGTTTTCAAAAAATGTTTTTA
1 AAACTATATATTATATAATTTTTC-AAAAATGTTTTTA
* *
195894 AAACCAT-CATTATATAATTTTTCAAAAATGTTTTTA
1 AAACTATATATTATATAATTTTTCAAAAATGTTTTTA
*
195930 AAACTATATATTATATAAATTTTTTCAAAAATGTTTTGA
1 AAACTATATATTATAT-AA-TTTTTCAAAAATGTTTTTA
*
195969 AAACTATATATTATATAAGCTTTTTCAAAAATGTTTTAA
1 AAACTATATATTATATAA--TTTTTCAAAAATGTTTTTA
*
196008 AAACTATATATTATATAAGCTTTTTCAAAAATGTTTTAA
1 AAACTATATATTATATAA--TTTTTCAAAAATGTTTTTA
* *
196047 AAACTATATATTATATAAGTTTTCAAAAAATGTTTTAA
1 AAACTATATATTATATAATTTTTC-AAAAATGTTTTTA
* * *
196085 AAACTATATATTATATATATATATTTCCAAAATGATTTCA
1 AAACTATATATTATATA-AT-T-TTTCAAAAATGTTTTTA
196125 AAACTATATATTATATA
1 AAACTATATATTATATA
196142 TATATATATA
Statistics
Matches: 309, Mismatches: 19, Indels: 37
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.03
32 12 0.04
33 40 0.13
34 20 0.06
35 6 0.02
36 19 0.06
37 27 0.09
38 34 0.11
39 110 0.36
40 28 0.09
41 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
AAACTATATATTATATAATTTTTCAAAAATGTTTTTA
Found at i:196141 original size:2 final size:2
Alignment explanation
Indices: 196129--196158 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
196119 ATTTCAAAAC
196129 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196159 TCAAAAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:196164 original size:48 final size:49
Alignment explanation
Indices: 196089--196192 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 49
196079 TTTTAAAAAC
*
196089 TATATATTATATATATATATTTCCAAAATG-A-TTTC-AAAACTATATAT
1 TATATATTATATATATATATTTCCAAAA-GCACTTTCAAAAACTATACAT
196136 TATATATATATATATATATATATT-CAAAAGCACTTTCAAAAACTATACAT
1 TATATAT-TATATATATATAT-TTCCAAAAGCACTTTCAAAAACTATACAT
196186 TATATAT
1 TATATAT
196193 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
47 8 0.16
48 19 0.37
49 6 0.12
50 18 0.35
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (49 bp):
TATATATTATATATATATATTTCCAAAAGCACTTTCAAAAACTATACAT
Found at i:199430 original size:41 final size:41
Alignment explanation
Indices: 199385--199654 Score: 347
Period size: 41 Copynumber: 6.6 Consensus size: 41
199375 ATTCGCGTTG
199385 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
199426 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
199467 CATTTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
199508 CATTTCGCGTTGCGACAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
199549 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
* * * *
199590 CAAATT--CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTC
1 C-ATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
* *
199631 CAAATT--CGTTGCGATAGTTAAAAA
1 C-ATTTCGCGTTGCGATAGTTGAAAA
199655 AAGATTTTGT
Statistics
Matches: 213, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
40 20 0.09
41 189 0.89
42 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:199438 original size:20 final size:20
Alignment explanation
Indices: 199410--199564 Score: 121
Period size: 20 Copynumber: 7.6 Consensus size: 20
199400 TAGTTGAAAA
199410 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
199430 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
199451 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
199471 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
199492 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** ** **
199512 TCGCGTTGCGACAGTTGAAAA
1 TCGCGTTGCGA-TTTTCCATT
199533 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
199553 TCGCGTTGCGAT
1 TCGCGTTGCGAT
199565 AGTCTACAAT
Statistics
Matches: 96, Mismatches: 36, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
20 54 0.56
21 42 0.44
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:199735 original size:6 final size:6
Alignment explanation
Indices: 199724--199762 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
199714 GACACGTATT
199724 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
199763 CAAGCCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:200308 original size:20 final size:20
Alignment explanation
Indices: 200283--200536 Score: 241
Period size: 20 Copynumber: 12.6 Consensus size: 20
200273 TTTTTTAACT
*
200283 ATCGCAATGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
200303 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
* * *
200323 ATTGCAACACGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
200343 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
200363 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
*
200383 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
200402 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
*
200424 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
200443 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
*
200465 ATCGCAACGCTAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
200485 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
* *
200505 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
* *
200525 ATTGTAACGCGA
1 ATCGCAACGCGA
200537 TTTTCAACTA
Statistics
Matches: 194, Mismatches: 26, Indels: 28
0.78 0.10 0.11
Matches are distributed among these distances:
18 4 0.02
19 23 0.12
20 133 0.69
21 7 0.04
22 27 0.14
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:200438 original size:41 final size:41
Alignment explanation
Indices: 200383--200493 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
200373 GAAATGGAAA
200383 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
200424 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
*
200465 ATCGCAACGCTAA-CTGGAAAATCGCAACG
1 ATCGCAACG--AATTTGGAAAATCGCAACG
200494 CGAAATGGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 50 0.75
42 15 0.22
43 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
Found at i:200480 original size:22 final size:22
Alignment explanation
Indices: 200402--200473 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
200392 AATTTGGAAA
200402 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
200424 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
200443 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
200465 ATCGCAACG
1 ATCGCAACG
200474 CTAACTGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:200556 original size:21 final size:21
Alignment explanation
Indices: 200530--200578 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
200520 GGAAAATTGT
200530 AACGCGATTTTCAACTATCAC
1 AACGCGATTTTCAACTATCAC
* *
200551 AACGCGATTTTCAATTATCGC
1 AACGCGATTTTCAACTATCAC
200572 AACGCGA
1 AACGCGA
200579 AATGCAACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (21 bp):
AACGCGATTTTCAACTATCAC
Found at i:202010 original size:63 final size:63
Alignment explanation
Indices: 201897--202032 Score: 143
Period size: 63 Copynumber: 2.2 Consensus size: 63
201887 TTCAATGTGT
* *
201897 ATCGATGCACTCTCAAATAAATAAACATCGAATGCAATTAATGCATCGATGCATAAGGA-A-TGC
1 ATCGATGCACTCCCAAATAAATAAACATCGAATGCAATTAATGCACCGATG--TAAGGATAGTGC
** * ** * *
201960 ATCGATGCACTCCCTTA-AAATGAAACATCGAATGTAATTTGTGTACCGATGTATGGATAGTGC
1 ATCGATGCACTCCCAAATAAAT-AAACATCGAATGCAATTAATGCACCGATGTAAGGATAGTGC
202023 ATCGATGCAC
1 ATCGATGCAC
202033 ATGTTAAGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
61 5 0.08
62 5 0.08
63 51 0.84
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (63 bp):
ATCGATGCACTCCCAAATAAATAAACATCGAATGCAATTAATGCACCGATGTAAGGATAGTGC
Found at i:202764 original size:32 final size:30
Alignment explanation
Indices: 202723--202844 Score: 102
Period size: 32 Copynumber: 3.9 Consensus size: 30
202713 AGTCGAGGGT
202723 TTACCTATGTTCTACGGAACATATGGATAGAA
1 TTACCTATG-TCTACGGAACATATGGA-AGAA
* *
202755 TTACCTATGTCTTTCGGGACATATGGACAGAA
1 TTACCTATGTC-TACGGAACATATGGA-AGAA
*** *
202787 TTACCTATGTCTTTTGAGACATATGG-ACAA
1 TTACCTATGTCTACGGA-ACATATGGAAGAA
* *
202817 TATATCTATGTTCTAAGGAACATATGGA
1 T-TACCTATG-TCTACGGAACATATGGA
202845 CAGTTTACAT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
30 4 0.05
31 20 0.27
32 50 0.68
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (30 bp):
TTACCTATGTCTACGGAACATATGGAAGAA
Done.