Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008131.1 Hibiscus syriacus cultivar Beakdansim tig00110686_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: 310772
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:225157 original size:13 final size:13
Alignment explanation
Indices: 225110--225139 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
225100 ATGGGTCAAC
225110 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
225123 GGTCAATGGGTCG
1 GGTCAACGGGTCG
225136 GGTC
1 GGTC
225140 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:227337 original size:24 final size:23
Alignment explanation
Indices: 227310--227360 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
227300 GATATCAAAA
227310 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTC-AGT
* *
227334 ATCATATCAAAATCCAGGTCAGT
1 ATCAAAACAAAATCCAGGTCAGT
227357 ATCA
1 ATCA
227361 GATCAGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (23 bp):
ATCAAAACAAAATCCAGGTCAGT
Found at i:227387 original size:24 final size:24
Alignment explanation
Indices: 227327--227441 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
227317 CATAAATCAG
* * *
227327 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
227351 GTC-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* * *
227374 GTCAAGTATTAGATCATAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
227398 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
227422 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
227442 TCAAATCGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 22 0.28
24 54 0.69
25 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:227417 original size:48 final size:47
Alignment explanation
Indices: 227327--227437 Score: 159
Period size: 48 Copynumber: 2.3 Consensus size: 47
227317 CATAAATCAG
*
227327 GTCAAGTATCATATCAAAATCCAGGTCAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAGGTCAGTATCAGATCAGAATCCAA
* * * * *
227374 GTCAAGTATTAGATCATAATCTATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAGGTCAG-TATCAGATCAGAATCCAA
227422 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
227438 GAATTCAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
47 24 0.43
48 32 0.57
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (47 bp):
GTCAAGTATCAGATCAAAATCCAGGTCAGTATCAGATCAGAATCCAA
Found at i:227457 original size:48 final size:48
Alignment explanation
Indices: 227357--227459 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
227347 CCAGGTCAGT
* * ** *
227357 ATCAGATCAGAATCCAAGTCAAGTATTAGATCATAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
*
227405 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AA
227453 ATCAGAT
1 ATCAGAT
227460 AAAATATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:229131 original size:27 final size:27
Alignment explanation
Indices: 229092--229158 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
229082 TCCAGGGACA
* * * *
229092 ATTCTTATCATTTTACTACATAGGGGT
1 ATTCTCATAATTTTACCACATAGGAGT
* * *
229119 ATTTTCATAATTTTACCATATCGGAGT
1 ATTCTCATAATTTTACCACATAGGAGT
229146 ATTCTCATAATTT
1 ATTCTCATAATTT
229159 CTCATCCAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (27 bp):
ATTCTCATAATTTTACCACATAGGAGT
Found at i:229870 original size:8 final size:8
Alignment explanation
Indices: 229830--229902 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
229820 TCAAAGTTTT
229830 GGTCAACAG
1 GGTCAAC-G
229839 TGGTCAACG
1 -GGTCAACG
229848 CCGGTCAAC-
1 --GGTCAACG
*
229857 GGTCAATG
1 GGTCAACG
229865 GGTCAACG
1 GGTCAACG
229873 GGT---CG
1 GGTCAACG
229878 GGTCAACG
1 GGTCAACG
229886 GGT---CG
1 GGTCAACG
229891 GGTCAACG
1 GGTCAACG
229899 GGTC
1 GGTC
229903 GGGTCAATGG
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
5 10 0.19
7 6 0.12
8 21 0.40
9 1 0.02
10 14 0.27
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:229882 original size:13 final size:13
Alignment explanation
Indices: 229864--229919 Score: 103
Period size: 13 Copynumber: 4.3 Consensus size: 13
229854 AACGGTCAAT
229864 GGGTCAACGGGTC
1 GGGTCAACGGGTC
229877 GGGTCAACGGGTC
1 GGGTCAACGGGTC
229890 GGGTCAACGGGTC
1 GGGTCAACGGGTC
*
229903 GGGTCAATGGGTC
1 GGGTCAACGGGTC
229916 GGGT
1 GGGT
229920 TGGGTTGTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (13 bp):
GGGTCAACGGGTC
Found at i:232069 original size:24 final size:24
Alignment explanation
Indices: 232042--232141 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
232032 TATATCAAAA
232042 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
232066 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
232090 ATCATATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * * *
232114 ATCAGATCAGAATCCATGTCAAAT
1 ATCAAAACAAAATCCAGGTCAAGT
232138 ATCA
1 ATCA
232142 GATCAGAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.06
24 64 0.94
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:232142 original size:24 final size:24
Alignment explanation
Indices: 232059--232150 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
232049 CATAAATCAG
* * *
232059 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
*
232083 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
232107 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
232131 GTCAAATATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
232151 TCAAATCGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:232165 original size:24 final size:24
Alignment explanation
Indices: 232060--232168 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
232050 ATAAATCAGG
* * * **
232060 TCAAGTATCATATCAAAATCCAGG
1 TCAAATATCAGATCAGAATCCAAA
* * *
232084 TCAAGTATCATATCAGAATCCAAG
1 TCAAATATCAGATCAGAATCCAAA
* **
232108 TCAAGTATCAGATCAGAATCCATG
1 TCAAATATCAGATCAGAATCCAAA
*
232132 TCAAATATCAGATCAGAATTCAAA
1 TCAAATATCAGATCAGAATCCAAA
232156 TCGAAA-ATCAGAT
1 TC-AAATATCAGAT
232169 AAAATATTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
24 73 0.96
25 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
TCAAATATCAGATCAGAATCCAAA
Found at i:232166 original size:48 final size:48
Alignment explanation
Indices: 232060--232173 Score: 124
Period size: 48 Copynumber: 2.4 Consensus size: 48
232050 ATAAATCAGG
* * * * *
232060 TCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAG
1 TCAAGAATCAGATCAAAATCCAGGTCAAATATCAGATCAGAATCCAAA
* * * *
232108 TCAAGTATCAGATCAGAATCCATGTCAAATATCAGATCAGAATTCAAA
1 TCAAGAATCAGATCAAAATCCAGGTCAAATATCAGATCAGAATCCAAA
232156 TCGAA-AATCAGAT-AAAAT
1 TC-AAGAATCAGATCAAAAT
232174 ATTCATGTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
47 4 0.07
48 50 0.89
49 2 0.04
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (48 bp):
TCAAGAATCAGATCAAAATCCAGGTCAAATATCAGATCAGAATCCAAA
Found at i:233737 original size:24 final size:24
Alignment explanation
Indices: 233710--233809 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
233700 TATATCAAAA
233710 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
233734 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
233758 ATCATATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
233782 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
233806 ATCA
1 ATCA
233810 GATCATAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
23 4 0.06
24 65 0.94
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:233810 original size:24 final size:24
Alignment explanation
Indices: 233727--233814 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
233717 CATAAATCAG
* * *
233727 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
*
233751 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
233775 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
233799 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
233815 TAATTCAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:233834 original size:48 final size:48
Alignment explanation
Indices: 233728--233842 Score: 124
Period size: 48 Copynumber: 2.4 Consensus size: 48
233718 ATAAATCAGG
* * * *
233728 TCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAG
1 TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
* * * * *
233776 TCAAGTATCAGATCAGAATCCATGTCAAGTATCAGATCATAATTCAAA
1 TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
*
233824 TCGAA-AATCAGATAAAAAT
1 TC-AAGAATCAGATCAAAAT
233843 ATTCATGTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 54 0.96
49 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.25
Consensus pattern (48 bp):
TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
Found at i:236374 original size:18 final size:18
Alignment explanation
Indices: 236326--236375 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
236316 TCGGTTTAAT
*
236326 GGGTCGGGTCGGCTCAAC
1 GGGTCGGGTCGGGTCAAC
236344 GGGTCGGGTCGGGTCAAC
1 GGGTCGGGTCGGGTCAAC
236362 GGGTCGGGTCGGGT
1 GGGTCGGGTCGGGT
236376 TGTGCCGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.08, C:0.22, G:0.52, T:0.18
Consensus pattern (18 bp):
GGGTCGGGTCGGGTCAAC
Found at i:238580 original size:24 final size:24
Alignment explanation
Indices: 238552--238656 Score: 95
Period size: 24 Copynumber: 4.4 Consensus size: 24
238542 AACATAAATC
* *
238552 AGTATCATACCAAAATCCAGGTCA
1 AGTATCAGACCAAAATCCAAGTCA
* *
238576 AGTATCAGATCATAATCCAAGTCA
1 AGTATCAGACCAAAATCCAAGTCA
* * * *
238600 AGTATCAGATCAGAATCTATGTC-
1 AGTATCAGACCAAAATCCAAGTCA
* * *
238623 AGATATCAGATCAGAATCCATGTCA
1 AG-TATCAGACCAAAATCCAAGTCA
238648 AGTATCAGA
1 AGTATCAGA
238657 TCAGAATTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
23 2 0.03
24 67 0.94
25 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
AGTATCAGACCAAAATCCAAGTCA
Found at i:238657 original size:24 final size:24
Alignment explanation
Indices: 238565--238663 Score: 146
Period size: 24 Copynumber: 4.1 Consensus size: 24
238555 ATCATACCAA
* *
238565 AATCCAGGTCAAGTATCAGATCAT
1 AATCCATGTCAAGTATCAGATCAG
*
238589 AATCCAAGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
*
238613 AATCTATGTC-AGATATCAGATCAG
1 AATCCATGTCAAG-TATCAGATCAG
238637 AATCCATGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
238661 AAT
1 AAT
238664 TAAAATCGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
23 2 0.03
24 64 0.94
25 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
AATCCATGTCAAGTATCAGATCAG
Found at i:238679 original size:48 final size:48
Alignment explanation
Indices: 238579--238681 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 48
238569 CAGGTCAAGT
* ** *
238579 ATCAGATCATAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
*
238627 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TAAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AA
238675 ATCAGAT
1 ATCAGAT
238682 AAAATATTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 2 0.04
48 46 0.96
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:242474 original size:24 final size:24
Alignment explanation
Indices: 242447--242522 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
242437 TATATCAAAA
242447 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
242471 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
242495 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
242519 ATCA
1 ATCA
242523 GATCAGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:242523 original size:24 final size:24
Alignment explanation
Indices: 242464--242579 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
242454 CATAAATCAG
* * *
242464 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
242488 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
242512 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
*
242536 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
242560 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
242580 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:245055 original size:8 final size:8
Alignment explanation
Indices: 245035--245069 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
245025 TGTCAACACC
245035 GGTCAAC-
1 GGTCAACG
*
245042 GGTCAATG
1 GGTCAACG
245050 GGTCAACG
1 GGTCAACG
245058 GGTCAACG
1 GGTCAACG
245066 GGTC
1 GGTC
245070 GGGTCGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:247271 original size:24 final size:24
Alignment explanation
Indices: 247244--247319 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
247234 TATATCAAAA
247244 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
247268 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
247292 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
247316 ATCA
1 ATCA
247320 GATCAGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:247320 original size:24 final size:24
Alignment explanation
Indices: 247261--247400 Score: 176
Period size: 24 Copynumber: 5.8 Consensus size: 24
247251 CATAAATCAG
* * *
247261 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
247285 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
247309 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
* * *
247333 GTC-AGATATTATATCAGAATCTAT
1 GTCAAG-TATCAGATCAGAATCCAT
247357 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
247381 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
247401 TCAAATCGAA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
23 2 0.02
24 100 0.96
25 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:247349 original size:12 final size:12
Alignment explanation
Indices: 247321--247377 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
247311 CAAGTATCAG
247321 ATCAGAATCTAT
1 ATCAGAATCTAT
*
247333 GTCAGATAT-TAT
1 ATCAGA-ATCTAT
247345 ATCAGAATCTAT
1 ATCAGAATCTAT
* *
247357 GTCAGATATC-AG
1 ATCAGA-ATCTAT
247369 ATCAGAATC
1 ATCAGAATC
247378 CATGTCAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 5 0.14
12 27 0.73
13 5 0.14
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (12 bp):
ATCAGAATCTAT
Found at i:247416 original size:48 final size:47
Alignment explanation
Indices: 247261--247418 Score: 158
Period size: 48 Copynumber: 3.3 Consensus size: 47
247251 CATAAATCAG
* * * *
247261 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAA-TATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAA
* * * *
247309 GTCAAGTATCAGATCAGAATCTATGTC-AGATATTATATCAGAA-TCTAT
1 GTCAA-TATCAGATCAGAATCCATGTCAAG-TATCAGATCAGAATTC-AA
247357 GTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAA
1 GTCA-ATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAA
* *
247405 ATCGAAAATCAGAT
1 GTC-AATATCAGAT
247419 AAAATATTCA
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
47 3 0.03
48 81 0.90
49 6 0.07
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (47 bp):
GTCAATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAA
Found at i:247808 original size:15 final size:16
Alignment explanation
Indices: 247778--247811 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
247768 GGTCAACTGT
247778 GGTCAACGTCGGTCAAC
1 GGTCAACG-CGGTCAAC
247795 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
247810 GG
1 GG
247812 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:247815 original size:27 final size:28
Alignment explanation
Indices: 247768--247821 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
247758 TCAAAGTTTT
247768 GGTCAACTGTGGTCAACGTC-GGTCAAC
1 GGTCAACTGTGGTCAACGTCGGGTCAAC
247795 GGTCAAC-G-GGTCAACGGGTCGGGTCAA
1 GGTCAACTGTGGTCAAC--GTCGGGTCAA
247822 TGGGTCGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 1 0.04
27 10 0.42
28 6 0.25
ACGTcount: A:0.22, C:0.24, G:0.35, T:0.19
Consensus pattern (28 bp):
GGTCAACTGTGGTCAACGTCGGGTCAAC
Found at i:247819 original size:13 final size:13
Alignment explanation
Indices: 247801--247832 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
247791 CAACGGTCAA
247801 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
247814 CGGGTCAATGGGT
1 CGGGTCAACGGGT
247827 CGGGTC
1 CGGGTC
247833 GAGTCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:247827 original size:8 final size:8
Alignment explanation
Indices: 247768--247814 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
247758 TCAAAGTTTT
247768 GGTCAACTG
1 GGTCAAC-G
247777 TGGTCAACG
1 -GGTCAACG
247786 TCGGTCAAC-
1 --GGTCAACG
247795 GGTCAACG
1 GGTCAACG
247803 GGTCAACG
1 GGTCAACG
247811 GGTC
1 GGTC
247815 GGGTCAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 1 0.03
10 14 0.41
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (8 bp):
GGTCAACG
Found at i:247832 original size:18 final size:18
Alignment explanation
Indices: 247795--247854 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
247785 GTCGGTCAAC
247795 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
*
247816 GGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
247834 AGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
247852 GGT
1 GGT
247855 TGTGACCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 25 0.71
21 10 0.29
ACGTcount: A:0.15, C:0.20, G:0.47, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:250075 original size:16 final size:17
Alignment explanation
Indices: 250050--250085 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
250040 ATCACCTATC
250050 AAAAACAG-AAAGATGA
1 AAAAACAGAAAAGATGA
*
250066 AAAAAGAGAAAAGATGA
1 AAAAACAGAAAAGATGA
250083 AAA
1 AAA
250086 TGTGAGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAACAGAAAAGATGA
Found at i:256805 original size:21 final size:21
Alignment explanation
Indices: 256772--257092 Score: 138
Period size: 21 Copynumber: 15.6 Consensus size: 21
256762 GTTTCCAGAT
* *
256772 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
256793 TCACAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
256814 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
256835 TCGCAATGCGAA-TGTGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
256855 TCGCAATACGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
256876 TCGCAATGCGAA-TGTGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
256896 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
256917 TCGCAATGCGAA-TGTGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
256937 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
256958 TCGCAATGCGAA-TGTGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
256978 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* * *
256999 TCGCAATGAGAA-TGTGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
257019 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* * *
257040 TCGCAATGAGAA-TGTGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
257060 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
257081 TCGCAATGCGAA
1 TCGCAATGCGAA
257093 TGTGTAAATC
Statistics
Matches: 226, Mismatches: 56, Indels: 37
0.71 0.18 0.12
Matches are distributed among these distances:
20 88 0.39
21 138 0.61
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:257131 original size:21 final size:21
Alignment explanation
Indices: 257101--257175 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
257091 AATGTGTAAA
*
257101 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
257122 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
257143 TTGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
257163 ATCGCATTGCGAT
1 -TCGCATTGCGAT
257176 TTACATATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:257132 original size:41 final size:41
Alignment explanation
Indices: 256786--257118 Score: 553
Period size: 41 Copynumber: 8.1 Consensus size: 41
256776 AACGCGAACT
* * * *
256786 TCGACTATCACAATGCGAACT-TGGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGAA-TGTGTA-AATCGCAATGCGATA-G
* *
256828 TGGACTATCGCAATGCGAATGTGTAAATCGCAATACGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
256869 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
256910 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
256951 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
*
256992 TCGACTATCGCAATGAGAATGTGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
*
257033 TCGACTATCGCAATGAGAATGTGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
257074 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
257115 TCGA
1 TCGA
257119 AGTTCGCGTT
Statistics
Matches: 279, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
41 258 0.92
42 21 0.08
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (41 bp):
TCGACTATCGCAATGCGAATGTGTAAATCGCAATGCGATAG
Found at i:257189 original size:20 final size:20
Alignment explanation
Indices: 257164--257238 Score: 150
Period size: 20 Copynumber: 3.8 Consensus size: 20
257154 TAGTCGACTA
257164 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
257184 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
257204 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
257224 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
257239 TTCCAAATTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:257383 original size:41 final size:41
Alignment explanation
Indices: 257355--257534 Score: 326
Period size: 41 Copynumber: 4.4 Consensus size: 41
257345 GCGAACTTCG
*
257355 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCG
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
257396 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
257437 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
257478 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
*
257519 AAGT-TCGCATTGCGAT
1 -ACTATCGCATTGCGAT
257535 AGTCCAAGTT
Statistics
Matches: 136, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
41 134 0.99
42 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (41 bp):
ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
Found at i:257384 original size:20 final size:20
Alignment explanation
Indices: 257359--257513 Score: 174
Period size: 20 Copynumber: 7.6 Consensus size: 20
257349 ACTTCGACTA
257359 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
257379 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
257400 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
257420 TCGCATTGCGATAGTCCACTA-
1 TCGCATTGCGAT-TTACA-TAT
257441 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
257461 TCGCATTGCGATAGTCCACTA-
1 TCGCATTGCGAT-TTACA-TAT
257482 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
257502 TCGCATTGCGAT
1 TCGCATTGCGAT
257514 AGTCCAAGTT
Statistics
Matches: 114, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
19 6 0.05
20 57 0.50
21 45 0.39
22 6 0.05
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:257539 original size:21 final size:20
Alignment explanation
Indices: 257359--257554 Score: 166
Period size: 21 Copynumber: 9.6 Consensus size: 20
257349 ACTTCGACTA
* *
257359 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCA-AT
* *
257379 TCGCATTGCGATAGTCGACT
1 TCGCATTGCGATAGTCCAAT
* *
257399 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
*
257420 TCGCATTGCGATAGTCCACT
1 TCGCATTGCGATAGTCCAAT
* *
257440 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
*
257461 TCGCATTGCGATAGTCCACT
1 TCGCATTGCGATAGTCCAAT
* *
257481 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
257502 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
257523 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
*
257544 TCGCGTTGCGA
1 TCGCATTGCGA
257555 ATCTGGAAAC
Statistics
Matches: 142, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
20 60 0.42
21 82 0.58
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCCAAT
Found at i:257811 original size:15 final size:16
Alignment explanation
Indices: 257791--257823 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
257781 AAAATTATAT
*
257791 TTGAAA-ATCACATTA
1 TTGAAATATAACATTA
257806 TTGAAATATAACATTA
1 TTGAAATATAACATTA
257822 TT
1 TT
257824 ATTGGAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (16 bp):
TTGAAATATAACATTA
Found at i:258181 original size:16 final size:17
Alignment explanation
Indices: 258162--258198 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
258152 TAATATATTA
258162 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
258178 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
258195 TTTT
1 TTTT
258199 TCATCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:262231 original size:32 final size:31
Alignment explanation
Indices: 262172--262231 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
262162 TATTAACTCG
* * * *
262172 ACCCGAAATCAACTGATCTGGTGTTGACCCT
1 ACCCGAAACCAACCGATCTAGTATTGACCCT
262203 ACCCGAAAACCAACCGATCTAGTATTGAC
1 ACCCG-AAACCAACCGATCTAGTATTGAC
262232 GTGAGCCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 5 0.21
32 19 0.79
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.22
Consensus pattern (31 bp):
ACCCGAAACCAACCGATCTAGTATTGACCCT
Found at i:262319 original size:32 final size:32
Alignment explanation
Indices: 262272--262340 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
262262 AATCGACCTA
* * * * *
262272 AAAACCAACCAATCTGATTTTTACCCGACTCG
1 AAAACAAACCAATCTGATATTGACCCAACCCG
*
262304 AAAACAAACCGATCTGATATTGACCCAACCCG
1 AAAACAAACCAATCTGATATTGACCCAACCCG
262336 AAAAC
1 AAAAC
262341 CAATCGACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.19
Consensus pattern (32 bp):
AAAACAAACCAATCTGATATTGACCCAACCCG
Found at i:275819 original size:7 final size:8
Alignment explanation
Indices: 275802--275826 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
275792 TTGAAACTGT
275802 AAAAAGAA
1 AAAAAGAA
275810 AAAAAGAA
1 AAAAAGAA
275818 AAAAAGAA
1 AAAAAGAA
275826 A
1 A
275827 CCTTGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:288367 original size:12 final size:12
Alignment explanation
Indices: 288350--288381 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
288340 AAATATTAAA
288350 AATAAATAGTAG
1 AATAAATAGTAG
288362 AATAAATAGTAG
1 AATAAATAGTAG
288374 AATAAATA
1 AATAAATA
288382 CAAGGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (12 bp):
AATAAATAGTAG
Found at i:289787 original size:24 final size:24
Alignment explanation
Indices: 289736--289792 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
289726 CCCAGGTCGG
289736 GTTTGGTTT-GGGCATGGTTTAGA
1 GTTTGGTTTGGGGCATGGTTTAGA
*
289759 GTTTGGTTTGGGGTATGGTTT-GA
1 GTTTGGTTTGGGGCATGGTTTAGA
*
289782 GTTTTGTTTGG
1 GTTTGGTTTGG
289793 TTTGGGGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.09, C:0.02, G:0.40, T:0.49
Consensus pattern (24 bp):
GTTTGGTTTGGGGCATGGTTTAGA
Found at i:289790 original size:28 final size:27
Alignment explanation
Indices: 289759--289849 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
289749 ATGGTTTAGA
*
289759 GTTTGGTTTGGGGTATGGTTTGAGTTTT
1 GTTTGGTTTGGGGT-TGGTTTAAGTTTT
* * *
289787 GTTTGGTTTGGGGTCTAGTTCAAGTTTC
1 GTTTGGTTTGGGGT-TGGTTTAAGTTTT
289815 GTTTGGTTTGGGGCTTGGTTTAAGGTTTT
1 GTTTGGTTTGGGG-TTGGTTTAA-GTTTT
289844 GTTTGG
1 GTTTGG
289850 GGACTTGTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
28 42 0.79
29 11 0.21
ACGTcount: A:0.08, C:0.04, G:0.37, T:0.51
Consensus pattern (27 bp):
GTTTGGTTTGGGGTTGGTTTAAGTTTT
Found at i:289870 original size:23 final size:24
Alignment explanation
Indices: 289815--289873 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
289805 TTCAAGTTTC
289815 GTTTGGTTTGGGGCTTGGTTTAAG
1 GTTTGGTTTGGGGCTTGGTTTAAG
* **
289839 GTTTTGTTTGGGGACTT-G-TTCGG
1 GTTTGGTTTGGGG-CTTGGTTTAAG
289862 GTTTGGTTTGGG
1 GTTTGGTTTGGG
289874 CCCGGCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 14 0.47
24 13 0.43
25 3 0.10
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.47
Consensus pattern (24 bp):
GTTTGGTTTGGGGCTTGGTTTAAG
Found at i:304767 original size:136 final size:136
Alignment explanation
Indices: 304530--304781 Score: 348
Period size: 136 Copynumber: 1.9 Consensus size: 136
304520 CTGTTGACCG
* *
304530 TTGACTTTGACCAAAAAGTCAATTTTTTTGAAAAGTCGTATTTTATATTTCTGGACATCCTGAGT
1 TTGACTTTGACCAAAAAGTCAATTTTTTTGAAAAGTCATATTTCATATTTCTGGACATCCTGAGT
**
304595 CCGATTTCGAAGTTCGTTTCTCCAAATTCGAACCCAAAAGCCTCCAAATTGTCAGTCAAAACCGT
66 CCGATTTCGAAGCCCGTTTCTCCAAATTCGAACCCAAAAGCCTCCAAATTGTCAGTCAAAACCGT
304660 TGACTT
131 TGACTT
* * * *
304666 TTGACTTTGACCAAAAAGTCAATTTTTTTGAAAAGTCATATTTCATGTTTTTTGACGTCCTGAG-
1 TTGACTTTGACCAAAAAGTCAATTTTTTTGAAAAGTCATATTTCATATTTCTGGACATCCTGAGT
* * * *
304730 CTTGATTTTGAAGCCCGTTT-TACCAAATTC-ATTCCCAAAAGCCTCCGAATTG
66 C-CGATTTCGAAGCCCGTTTCT-CCAAATTCGA-ACCCAAAAGCCTCCAAATTG
304782 ACTCGTAAAC
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
135 3 0.03
136 98 0.97
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (136 bp):
TTGACTTTGACCAAAAAGTCAATTTTTTTGAAAAGTCATATTTCATATTTCTGGACATCCTGAGT
CCGATTTCGAAGCCCGTTTCTCCAAATTCGAACCCAAAAGCCTCCAAATTGTCAGTCAAAACCGT
TGACTT
Done.