Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004983.1 Kokia drynarioides strain JFW-HI SEQ_118728, 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: 365800
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 102 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:287265 original size:41 final size:41
Alignment explanation
Indices: 287208--287290 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
287198 GGTCTATAGA
287208 AGCATACTTTACAGGTCACATCCCTGTAGAATGGCGAGACG
1 AGCATACTTTACAGGTCACATCCCTGTAGAATGGCGAGACG
287249 AGCATACTTTACAGGTCACATCCCTGTAGAATGGCGAGACG
1 AGCATACTTTACAGGTCACATCCCTGTAGAATGGCGAGACG
287290 A
1 A
287291 ACTAAGGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (41 bp):
AGCATACTTTACAGGTCACATCCCTGTAGAATGGCGAGACG
Found at i:287805 original size:85 final size:86
Alignment explanation
Indices: 287650--287816 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 86
287640 CAAACCCCAT
* **
287650 CTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATAAGATACA
1 CTTCCTGATGAGATACAAAGAAGTGAATCAAAGCAATAAAGCGATCATCTTCCTGATAAGATACA
*
287715 GAGAAGTGGACCAAATTTGGC
66 GAGAAGTAGACCAAATTTGGC
* * * * *
287736 CTTCCTGATGAGATACAAAGAAGTGAATTAAATCAAT-AAGCGGTCATCTTCCTGATGAGATATA
1 CTTCCTGATGAGATACAAAGAAGTGAATCAAAGCAATAAAGCGATCATCTTCCTGATAAGATACA
287800 GAGAAGTAGACCAAATT
66 GAGAAGTAGACCAAATT
287817 AATGAAGTGA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 40 0.56
86 32 0.44
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (86 bp):
CTTCCTGATGAGATACAAAGAAGTGAATCAAAGCAATAAAGCGATCATCTTCCTGATAAGATACA
GAGAAGTAGACCAAATTTGGC
Found at i:287930 original size:208 final size:208
Alignment explanation
Indices: 287569--288345 Score: 1092
Period size: 208 Copynumber: 3.7 Consensus size: 208
287559 AACTTCAAAA
* * * *
287569 GGTCATCTTCCTGATGAGATACATAGAAGTAAACCAAATCAATAAAGTGAAGCTCAATACGAATG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATG
* * *
287634 AGACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATC
66 AGACTTCAAAACCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGACCATC
* * *
287699 TTCCTGATAAGATACAGAGAAGTGGACCAAATTTGGCCTTCCTGATGAGATACAAAGAAGTGAAT
131 TTCCTGATAAGATACAAAGAAGTGGACCAAA-TTCGCCTTCCTGATGAGATACAAAGAAGTGGAT
287764 TAAATCAAT-AAGC
195 TAAATCAATAAAGC
* * *
287777 GGTCATCTTCCTGATGAGATATAGAGAAGTAGACCAAATTAATGAAGTGAAGCTCAATACGAATG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATG
* * * **
287842 AGAATTCAAAACCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATC
66 AGACTTCAAAACCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGACCATC
* *
287907 TTCCTGATAAGATACAAAGAAGTGGACCAAATCCGCCTTCCTAATGAGATACAAAGAAGTGGATT
131 TTCCTGATAAGATACAAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAAGAAGTGGATT
*
287972 AAATTAATAAAGC
196 AAATCAATAAAGC
* * * *
287985 GGTCATCTTCCTGATAAGATACTGAGAAGTAGATCAAATCAATGAAGCGGAGCTCAATACGAATG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATG
* * *
288050 AGACTTCAAAACCCATCATT-CTAATGAGATACAGAAAAGTGGGTCAAAGAAATAAAGCGGCCAT
66 AGACTTCAAAACCCATC-TTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGACCAT
* * * * * *
288114 CTTCCTAATGAGATACAAAAAAGTAGACCAAATTCGTCTTCCTGATGAGATACAAAAAAGTGGAT
130 CTTCCTGATAAGATACAAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAAGAAGTGGAT
*
288179 TAAATCAATGAAGC
195 TAAATCAATAAAGC
* * * ** * *
288193 GTTCATCATCCTGATGAGATACAGAGAAATAGATAAAATCAATGAAGCAAAGTTCAATACGAATG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATG
**
288258 AGACTTC-AAACCCTATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAATGACCAT
66 AGACTTCAAAACCC-ATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGACCAT
* *
288322 CTTCCTGATGAGATACAGAGAAGT
130 CTTCCTGATAAGATACAAAGAAGT
288346 TGATTAAATC
Statistics
Matches: 510, Mismatches: 55, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
207 45 0.09
208 463 0.91
209 2 0.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (208 bp):
GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATG
AGACTTCAAAACCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGACCATC
TTCCTGATAAGATACAAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAAGAAGTGGATT
AAATCAATAAAGC
Found at i:288001 original size:85 final size:85
Alignment explanation
Indices: 287858--288024 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
287848 CAAAACCCAT
* * * *
287858 CTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATACA
1 CTTCCTAATGAGATACAAAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATACA
*
287923 AAGAAGTGGACCAAATCCGC
66 AAGAAGTAGACCAAATCCGC
* ** *
287943 CTTCCTAATGAGATACAAAGAAGTGGATTAAATTAATAAAGCGGTCATCTTCCTGATAAGATACT
1 CTTCCTAATGAGATACAAAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATACA
* *
288008 GAGAAGTAGATCAAATC
66 AAGAAGTAGACCAAATC
288025 AATGAAGCGG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (85 bp):
CTTCCTAATGAGATACAAAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATACA
AAGAAGTAGACCAAATCCGC
Found at i:288014 original size:48 final size:48
Alignment explanation
Indices: 287943--288034 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
287933 CCAAATCCGC
* * * *
287943 CTTCCTAATGAGATACAAAGAAGTGGATTAAATTAATAAAGCGGTCAT
1 CTTCCTAATAAGATACAAAGAAGTAGATCAAATCAATAAAGCGGTCAT
* ** *
287991 CTTCCTGATAAGATACTGAGAAGTAGATCAAATCAATGAAGCGG
1 CTTCCTAATAAGATACAAAGAAGTAGATCAAATCAATAAAGCGG
288035 AGCTCAATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (48 bp):
CTTCCTAATAAGATACAAAGAAGTAGATCAAATCAATAAAGCGGTCAT
Found at i:288371 original size:48 final size:48
Alignment explanation
Indices: 288272--288413 Score: 167
Period size: 48 Copynumber: 3.0 Consensus size: 48
288262 TTCAAACCCT
* * * * **
288272 ATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAATGACC
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGACC
* * **
288320 ATCTTCCTGATGAGATACAGAGAAGTTGATTAAATCAATGAAGCGGTC
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGACC
* * *
288368 ATCTTCCTGATGAGATATAGAGAAATGGACCAAATCAATGAAGCGA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGA
288414 AGCTCAATAC
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (48 bp):
ATCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGACC
Found at i:288435 original size:171 final size:171
Alignment explanation
Indices: 288150--288867 Score: 1050
Period size: 171 Copynumber: 4.2 Consensus size: 171
288140 ACCAAATTCG
* * *
288150 TCTTCCTGATGAGATACAAAAAAGTGGATTAAATCAATGAAGC-GTTCATCATCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAAAAGTGGATTAAATCAATGAAGCAG-TCATCTTCCTGATAAGATA
** * * *
288214 CAGAGAAA-TAGATAAAATCAATGAAGCAAAGTTCAATACGAATGAGACTTCAAACCCTATCTTC
65 CAGA-AAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACACTATCTTC
* ** **
288278 CTGATGAGATACAGA-AAAGTGGGTCAAAGCAATAAAATGACCA
129 CTGATGAGATACAGAGAAA-TGGGTCAAAACAATAAAGCGGTCA
* * * * *
288321 TCTTCCTGATGAGATACAGAGAAGTTGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATAT
1 TCTTCCTGATGAGATACAGAAAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATAC
* *
288386 AGAGAAA-TGGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACATTATCTTCC
66 AGA-AAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACACTATCTTCC
288450 TGATGAGATACAGAGAAATGGGTCAAAACAATAAAGCGGTCA
130 TGATGAGATACAGAGAAATGGGTCAAAACAATAAAGCGGTCA
*
288492 TCTTCCTGATGAGATACAGATAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATAC
1 TCTTCCTGATGAGATACAGAAAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATAC
*
288557 AGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACATTATCTTCCT
66 AGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACACTATCTTCCT
288622 GATGAGATACAGAGAAATGGGTCAAAACAATAAAGCGGTCA
131 GATGAGATACAGAGAAATGGGTCAAAACAATAAAGCGGTCA
*
288663 TCTTCCTGATGAGATACAGATAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATAC
1 TCTTCCTGATGAGATACAGAAAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATAC
* * *
288728 AGAAAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAAC-CTCATCTTCT
66 AGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACACT-ATCTTCC
* * * ** *
288792 TGATGAGATATAGAGAAGTGGGTTAAAGTAATAAAGTGGTCA
130 TGATGAGATACAGAGAAATGGGTCAAAACAATAAAGCGGTCA
* *
288834 TCTTCTTGATGAGATACAGAAAAGTGGATCAAAT
1 TCTTCCTGATGAGATACAGAAAAGTGGATTAAAT
288868 TCGTCTTCCT
Statistics
Matches: 507, Mismatches: 36, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
170 4 0.01
171 499 0.98
172 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (171 bp):
TCTTCCTGATGAGATACAGAAAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATAC
AGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACACTATCTTCCT
GATGAGATACAGAGAAATGGGTCAAAACAATAAAGCGGTCA
Found at i:288540 original size:48 final size:48
Alignment explanation
Indices: 288443--288582 Score: 183
Period size: 48 Copynumber: 2.9 Consensus size: 48
288433 TTCAAACATT
* * * *
288443 ATCTTCCTGATGAGATACAGAGAAA-TGGGTCAAAACAATAAAGCGGTC
1 ATCTTCCTGATGAGATACAGA-AAAGTGGATCAAATCAATGAAGCAGTC
* *
288491 ATCTTCCTGATGAGATACAGATAAGTGGATTAAATCAATGAAGCAGTC
1 ATCTTCCTGATGAGATACAGAAAAGTGGATCAAATCAATGAAGCAGTC
* * *
288539 ATCTTCCTGATAAGATACAGAAAAGTAGACCAAATCAATGAAGC
1 ATCTTCCTGATGAGATACAGAAAAGTGGATCAAATCAATGAAGC
288583 GAAGCTCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 2 0.03
48 78 0.98
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (48 bp):
ATCTTCCTGATGAGATACAGAAAAGTGGATCAAATCAATGAAGCAGTC
Found at i:288711 original size:48 final size:48
Alignment explanation
Indices: 288614--288751 Score: 179
Period size: 48 Copynumber: 2.9 Consensus size: 48
288604 TTCAAACATT
* * * *
288614 ATCTTCCTGATGAGATACAGAGAAA-TGGGTCAAAACAATAAAGCGGTC
1 ATCTTCCTGATGAGATACAGA-AAAGTGGATCAAATCAATGAAGCAGTC
* *
288662 ATCTTCCTGATGAGATACAGATAAGTGGATTAAATCAATGAAGCAGTC
1 ATCTTCCTGATGAGATACAGAAAAGTGGATCAAATCAATGAAGCAGTC
* * *
288710 ATCTTCCTGATAAGATACAGAAAAGTAGACCAAATCAATGAA
1 ATCTTCCTGATGAGATACAGAAAAGTGGATCAAATCAATGAA
288752 ACGAAGCTCA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 2 0.03
48 76 0.97
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (48 bp):
ATCTTCCTGATGAGATACAGAAAAGTGGATCAAATCAATGAAGCAGTC
Found at i:288952 original size:85 final size:85
Alignment explanation
Indices: 288786--288952 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
288776 TCAAACCTCA
* * ** ** *
288786 TCTTCTTGATGAGATATAGAGAAGTGGGTTAAAGTAATAAAGTGGTCATCTTCTTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGAATTAAAGTAATAAAGCAGTCATCTTCTTAATGAGATAC
* * *
288851 AGAAAAGTGGATCAAATTCG
66 AGAAAACTAGACCAAATTCG
*
288871 TCTTCCTGATGAGATACAGAGAAGTGAATTAAA-TCAATGAAGCAGTCATCTTCTTAATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGAATTAAAGT-AATAAAGCAGTCATCTTCTTAATGAGATA
*
288935 CAGAGAACTAGACCAAAT
65 CAGAAAACTAGACCAAAT
288953 CATTGAAGCG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 68 0.99
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGAATTAAAGTAATAAAGCAGTCATCTTCTTAATGAGATAC
AGAAAACTAGACCAAATTCG
Found at i:289021 original size:208 final size:208
Alignment explanation
Indices: 288661--289106 Score: 664
Period size: 208 Copynumber: 2.1 Consensus size: 208
288651 ATAAAGCGGT
* * *
288661 CATCTTCCTGATGAGATACAGATAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCCTAATAAGAT
*
288726 ACAGAAAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTC
66 ACAGAAAACTAGACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTC
* * * * *
288791 TTGATGAGATATAGAGAAGTGGGTTAAAGTAATAAAG-TGGTCATCTTCTTGATGAGATACAGAA
131 TTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCT-GTCATCTTCCTGATAAGATACAGAA
*
288855 AAGTGGATCAAATT
195 AAGTGGATCAAATC
* * *
288869 CGTCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCTTAATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCCTAATAAGAT
* * * *
288934 ACAGAGAACTAGACCAAATCATTGAAGCGAAGCTCAATACGAATGAGACTTCAAATCC-CATCTT
66 ACAGAAAACTAGACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAA-CCTCATCTT
288998 -TCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCTGTCATCTTCCTGATAAGATACAGA
130 CT-TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCTGTCATCTTCCTGATAAGATACAGA
*
289062 GAAGTGGATCAAATC
194 AAAGTGGATCAAATC
* *
289077 CACCTTCCTGATAAGATACAGAGAAGTGAA
1 CATCTTCCTGATGAGATACAGAGAAGTGAA
289107 CCAAATCTGC
Statistics
Matches: 214, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
207 1 0.00
208 210 0.98
209 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (208 bp):
CATCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCCTAATAAGAT
ACAGAAAACTAGACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTC
TTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCTGTCATCTTCCTGATAAGATACAGAAA
AGTGGATCAAATC
Found at i:289093 original size:37 final size:37
Alignment explanation
Indices: 289043--289150 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
289033 AAGCTGTCAT
*
289043 CTTCCTGATAAGATACAGAGAAGTGGATCAAATCCAC
1 CTTCCTGATAAGATACAGAGAAGTGAATCAAATCCAC
* **
289080 CTTCCTGATAAGATACAGAGAAGTGAACCAAATCTGC
1 CTTCCTGATAAGATACAGAGAAGTGAATCAAATCCAC
* *
289117 CTTCCTGATAAGATATAGAGAAGTGAATTAAATC
1 CTTCCTGATAAGATACAGAGAAGTGAATCAAATC
289151 AATGAAGCGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (37 bp):
CTTCCTGATAAGATACAGAGAAGTGAATCAAATCCAC
Found at i:289153 original size:245 final size:245
Alignment explanation
Indices: 288835--289349 Score: 732
Period size: 245 Copynumber: 2.1 Consensus size: 245
288825 AAGTGGTCAT
* * * * *
288835 CTTCTTGATGAGATACAGAAAAGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAAT
1 CTTCCTGATGAGATACAGAAAAGTGAACCAAATTCGCCTTCCTGATAAGATACAGAGAAGTGAAT
* * * *
288900 TAAATCAATGAAGCAGTCATCTTCTTAATGAGATACAGAGAACTAGACCAAATCATTGAAGCGAA
66 TAAATCAATGAAGCAGTCATCTTCCTAATGAGATACAAAGAACTAAACCAAATCAATGAAGCGAA
* * *
288965 GCTCAATACGAATGAGACTTCAAATCCC-ATCTTTCTGATGAGATACAGAGAAGTGGGTCAAAGC
131 GCTCAATACGAATGAGACTTCAAA-CCCTATCTTCCTGAAGAGATACAGAGAAATGGGTCAAAGC
* *
289029 AAT-AA-AGCTGTCATCTTCCTGATAAGATACAGAGAAGTGGATCAAATCCAC
195 AATAAATAGC--TCATCTTCCTGATAAGATACAGAGAAGTAGACCAAATCCAC
* * *
289080 CTTCCTGATAAGATACAGAGAAGTGAACCAAA-TCTGCCTTCCTGATAAGATATAGAGAAGTGAA
1 CTTCCTGATGAGATACAGAAAAGTGAACCAAATTC-GCCTTCCTGATAAGATACAGAGAAGTGAA
* * * *
289144 TTAAATCAATGAAGCGGTCATCTTCCTGATGAGATGCAAAGAAGTAAACCAAATCAATGAAGCGA
65 TTAAATCAATGAAGCAGTCATCTTCCTAATGAGATACAAAGAACTAAACCAAATCAATGAAGCGA
* *
289209 AGCTCAATGCGAATGAGACTTCAAACCCTATCTTCCTGAAGAGATATAGAGAAATGGGTCAAAGC
130 AGCTCAATACGAATGAGACTTCAAACCCTATCTTCCTGAAGAGATACAGAGAAATGGGTCAAAGC
* **
289274 AATAAATAGCTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGT
195 AATAAATAGCTCATCTTCCTGATAAGATACAGAGAAGTAGACCAAATCCAC
289325 CTTCCTGATGAGATACAGAAAAGTG
1 CTTCCTGATGAGATACAGAAAAGTG
289350 GATTAAATTA
Statistics
Matches: 238, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
244 5 0.02
245 228 0.96
246 2 0.01
247 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (245 bp):
CTTCCTGATGAGATACAGAAAAGTGAACCAAATTCGCCTTCCTGATAAGATACAGAGAAGTGAAT
TAAATCAATGAAGCAGTCATCTTCCTAATGAGATACAAAGAACTAAACCAAATCAATGAAGCGAA
GCTCAATACGAATGAGACTTCAAACCCTATCTTCCTGAAGAGATACAGAGAAATGGGTCAAAGCA
ATAAATAGCTCATCTTCCTGATAAGATACAGAGAAGTAGACCAAATCCAC
Found at i:289411 original size:48 final size:48
Alignment explanation
Indices: 289324--289416 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
289314 ACCAAATCCG
* ** *
289324 TCTTCCTGATGAGATACAGAAAAGTGGATTAAATTAATGAAGCGATCA
1 TCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCGATCA
*
289372 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGA
1 TCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCGA
289417 AGTTCAATGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAGAAAAGTAGACCAAATCAATGAAGCGATCA
Found at i:289440 original size:208 final size:208
Alignment explanation
Indices: 289080--289526 Score: 632
Period size: 208 Copynumber: 2.1 Consensus size: 208
289070 TCAAATCCAC
* * *
289080 CTTCCTGATAAGATACAGAGAAGT-GAACCAAATCTGCCTTCCTGATAAGATATAGAGAAGTGAA
1 CTTCCTGATAAGATACAGAGAAGTAG-ACCAAATCCGCCTTCCTGATAAGATACAGAAAAGTGAA
* *
289144 TTAAATCAATGAAGCGGTCATCTTCCTGATGAGATGCAAAGAAGTAAACCAAATCAATGAAGCGA
65 TTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGCGA
* * * *
289209 AGCTCAATGCGAATGAGACTTCAAA-CCCTATCTTCCTGAA-GAGATATAGAGAAATGGGTCAAA
130 AGCTCAATGCGAATGAAACTTCAAACCCCTATCTTCCT-AATGAGATACAAAGAAATAGGTCAAA
289272 GCAATAAATAGC-TCAT
194 GCAAT-AA-AGCGTCAT
* * * *
289288 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAAAAGTGGAT
1 CTTCCTGATAAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATAAGATACAGAAAAGTGAAT
* * *
289353 TAAATTAATGAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAA
66 TAAATCAATGAAGCGATCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGCGAA
* * * * *
289418 GTTCAATGCGAGTGAAACTTCAAACCCCTATCTTCCTAATGAGATACAAAGAAGTAGGTCGAAGT
131 GCTCAATGCGAATGAAACTTCAAACCCCTATCTTCCTAATGAGATACAAAGAAATAGGTCAAAGC
289483 AATAAAGCGTCAT
196 AATAAAGCGTCAT
*
289496 CTTCCTGATAAGATATAGAGAAGTAGACCAA
1 CTTCCTGATAAGATACAGAGAAGTAGACCAA
289527 GAAATAAAGC
Statistics
Matches: 212, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
207 3 0.01
208 174 0.82
209 35 0.17
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (208 bp):
CTTCCTGATAAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATAAGATACAGAAAAGTGAAT
TAAATCAATGAAGCGATCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGCGAA
GCTCAATGCGAATGAAACTTCAAACCCCTATCTTCCTAATGAGATACAAAGAAATAGGTCAAAGC
AATAAAGCGTCAT
Found at i:289510 original size:453 final size:453
Alignment explanation
Indices: 288664--289519 Score: 1263
Period size: 453 Copynumber: 1.9 Consensus size: 453
288654 AAGCGGTCAT
* * *
288664 CTTCCTGATGAGATACAGATAAGTGGATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATACA
1 CTTCCTGATAAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATACA
* *
288729 GAAAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTCTTG
66 GAAAAGTAAACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTCCTG
* * * * * *
288794 ATGAGATATAGAGAAGTGGGTTAAAGTAATAAAGTGGTCATCTTCTTGATGAGATACAGAAAAGT
131 AAGAGATATAGAGAAATGGGTCAAAGCAATAAAGTGCTCATCTTCCTGATGAGATACAGAAAAGT
* * * *
288859 GGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTC
196 AGACCAAATCCGTCTTCCTGATGAGATACAGAAAAGTGAATTAAATCAATGAAGCAGTCATCTTC
* * *
288924 TTAATGAGATACAGAGAACTAGACCAAATCATTGAAGCGAAGCTCAATACGAATGAGACTTCAAA
261 CTAATGAGATACAGAGAACTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAAACTTCAAA
* * * * *
288989 TCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCTGTCATCTTCCTGATAA
326 CCCCATCTTCCTAATGAGATACAAAGAAGTAGGTCAAAGCAATAAAGCTGTCATCTTCCTGATAA
289054 GATACAGAGAAGTGGATCAAATCCACCTTCCTGATAAGATACAGAGAAGTGAACCAAATCTGC
391 GATACAGAGAAGTGGATCAAATCCACCTTCCTGATAAGATACAGAGAAGTGAACCAAATCTGC
* * * *
289117 CTTCCTGATAAGATATAGAGAAGTGAATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATGCA
1 CTTCCTGATAAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATACA
* * *
289182 -AAGAAGTAAACCAAATCAATGAAGCGAAGCTCAATGCGAATGAGACTTCAAACC-CTATCTTCC
66 GAA-AAGTAAACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTC-ATCTTCC
*
289245 TGAAGAGATATAGAGAAATGGGTCAAAGCAATAAA-TAGCTCATCTTCCTGATGAGATACAGAGA
129 TGAAGAGATATAGAGAAATGGGTCAAAGCAATAAAGT-GCTCATCTTCCTGATGAGATACAGAAA
* *
289309 AGTAGACCAAATCCGTCTTCCTGATGAGATACAGAAAAGTGGATTAAATTAATGAAGC-GATCAT
193 AGTAGACCAAATCCGTCTTCCTGATGAGATACAGAAAAGTGAATTAAATCAATGAAGCAG-TCAT
* * * * *
289373 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGTTCAATGCGAGTGAAACTT
257 CTTCCTAATGAGATACAGAGAACTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAAACTT
* *
289438 CAAACCCCTATCTTCCTAATGAGATACAAAGAAGTAGGTCGAAGTAATAAAGC-GTCATCTTCCT
322 CAAACCCC-ATCTTCCTAATGAGATACAAAGAAGTAGGTCAAAGCAATAAAGCTGTCATCTTCCT
*
289502 GATAAGATATAGAGAAGT
386 GATAAGATACAGAGAAGT
289520 AGACCAAGAA
Statistics
Matches: 357, Mismatches: 41, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
452 5 0.01
453 314 0.88
454 38 0.11
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (453 bp):
CTTCCTGATAAGATACAGAGAAGTGAATTAAATCAATGAAGCAGTCATCTTCCTGATAAGATACA
GAAAAGTAAACCAAATCAATGAAACGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTCCTG
AAGAGATATAGAGAAATGGGTCAAAGCAATAAAGTGCTCATCTTCCTGATGAGATACAGAAAAGT
AGACCAAATCCGTCTTCCTGATGAGATACAGAAAAGTGAATTAAATCAATGAAGCAGTCATCTTC
CTAATGAGATACAGAGAACTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAAACTTCAAA
CCCCATCTTCCTAATGAGATACAAAGAAGTAGGTCAAAGCAATAAAGCTGTCATCTTCCTGATAA
GATACAGAGAAGTGGATCAAATCCACCTTCCTGATAAGATACAGAGAAGTGAACCAAATCTGC
Found at i:291571 original size:30 final size:29
Alignment explanation
Indices: 291485--291714 Score: 198
Period size: 30 Copynumber: 7.8 Consensus size: 29
291475 TCCAAATTTC
* *
291485 TCTAAAATTATA-TTTAACCCCTAAACTTT
1 TCTAAAATTACATTTTAACCCTTAAAC-TT
**
291514 TCTAAAATTACATTTT-AGTCTTCAAACTCT
1 TCTAAAATTACATTTTAACCCTT-AAACT-T
*
291544 TCTAAAATTATATTTTAACCCTTAAACTT
1 TCTAAAATTACATTTTAACCCTTAAACTT
* * * *
291573 ATCCAAAATTGCATTTTGACCCCTAAACTT
1 -TCTAAAATTACATTTTAACCCTTAAACTT
* *
291603 TCCAAAATTACATTTTAACCCCTAAACTTT
1 TCTAAAATTACATTTTAACCCTTAAAC-TT
* *
291633 TCTAAAATTGCATTTTTGA-CCTCTAAACTT
1 TCTAAAATTACA-TTTTAACCCT-TAAACTT
*
291663 TTTGAAAATTACATTTTAA-CCTTAAACTTT
1 TCT-AAAATTACATTTTAACCCTTAAAC-TT
* **
291693 TCCAAAATTATGTTTTAACCCT
1 TCTAAAATTACATTTTAACCCT
291715 AAAATTCTCC
Statistics
Matches: 165, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
29 59 0.36
30 84 0.51
31 22 0.13
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (29 bp):
TCTAAAATTACATTTTAACCCTTAAACTT
Found at i:291582 original size:60 final size:59
Alignment explanation
Indices: 291460--291702 Score: 267
Period size: 60 Copynumber: 4.1 Consensus size: 59
291450 ACTCTTTTAG
* * * * *
291460 AATTGCATTTTGACCTCCAAATTTCTCTAAAATTATA-TTTAACCCCTAAACTTTTCTAA
1 AATTACATTTTGACCTCTAAACTT-TCTAAAATTACATTTTAACCCCTAAACTTTTCCAA
* * * * *
291519 AATTACATTTTAGTCTTC-AAACTCTTCTAAAATTATATTTTAACCCTTAAACTTATCCAA
1 AATTACATTTT-GACCTCTAAACT-TTCTAAAATTACATTTTAACCCCTAAACTTTTCCAA
* * * *
291579 AATTGCATTTTGACCCCTAAACTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAA
1 AATTACATTTTGACCTCTAAACTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAA
* * *
291638 AATTGCATTTTTGACCTCTAAACTTTTTGAAAATTACATTTTAA-CCTTAAACTTTTCCAA
1 AATTACA-TTTTGACCTCTAAACTTTCT-AAAATTACATTTTAACCCCTAAACTTTTCCAA
291698 AATTA
1 AATTA
291703 TGTTTTAACC
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
59 67 0.43
60 74 0.47
61 15 0.10
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (59 bp):
AATTACATTTTGACCTCTAAACTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAA
Found at i:291686 original size:119 final size:119
Alignment explanation
Indices: 291460--291701 Score: 332
Period size: 119 Copynumber: 2.0 Consensus size: 119
291450 ACTCTTTTAG
*
291460 AATTGCATTTTGACCTCCAAATTTCTCTAAAATTATATTTAACCCCTAAACTTTTCTAAAATTAC
1 AATTGCATTTTGACCTCCAAATTTCTCTAAAATTACATTTAACCCCTAAACTTTTCTAAAATTAC
* * *
291525 ATTTTAGTCTTCAAACTCTTCTAAAATTATATTTTAACCCTTAAACTTATCCAA
66 ATTTTAGACCTCAAACTCTTCTAAAATTACATTTTAACCCTTAAACTTATCCAA
291579 AATTGCATTTTGACC-CCTAAACTTTC-C-AAAATTACATTTTAACCCCTAAACTTTTCTAAAAT
1 AATTGCATTTTGACCTCC-AAA-TTTCTCTAAAATTACA-TTTAACCCCTAAACTTTTCTAAAAT
* * * *
291641 TGCATTTTTGACCTCTAAACT-TTTTGAAAATTACATTTTAA-CCTTAAACTTTTCCAA
63 TACATTTTAGACCTC-AAACTCTTCT-AAAATTACATTTTAACCCTTAAACTTATCCAA
291698 AATT
1 AATT
291702 ATGTTTTAAC
Statistics
Matches: 110, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
118 10 0.09
119 77 0.70
120 23 0.21
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (119 bp):
AATTGCATTTTGACCTCCAAATTTCTCTAAAATTACATTTAACCCCTAAACTTTTCTAAAATTAC
ATTTTAGACCTCAAACTCTTCTAAAATTACATTTTAACCCTTAAACTTATCCAA
Found at i:291737 original size:29 final size:29
Alignment explanation
Indices: 291488--291737 Score: 218
Period size: 29 Copynumber: 8.4 Consensus size: 29
291478 AAATTTCTCT
* *
291488 AAAATTATA-TTTAACCCCTAAACTTTTCT
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
** * * *
291517 AAAATTACATTTTAGTCTTCAAACTCTTCT
1 AAAATTACATTTTAACCCT-AAACTTTTCC
* *
291547 AAAATTATATTTTAACCCTTAAACTTATCC
1 AAAATTACATTTTAACCC-TAAACTTTTCC
* *
291577 AAAATTGCATTTTGACCCCTAAAC-TTTCC
1 AAAATTACATTTT-AACCCTAAACTTTTCC
*
291606 AAAATTACATTTTAACCCCTAAACTTTTCT
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* * **
291636 AAAATTGCATTTTTGACCTCTAAACTTTTTG
1 AAAATTACA-TTTTAACC-CTAAACTTTTCC
*
291667 AAAATTACATTTTAACCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
** * *
291696 AAAATTATGTTTTAACCCTAAAATTCTCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
291725 AAAACTT-CATTTT
1 AAAA-TTACATTTT
291738 GGACCTCGTT
Statistics
Matches: 177, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.01
29 75 0.42
30 73 0.41
31 28 0.16
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:292971 original size:31 final size:31
Alignment explanation
Indices: 292913--292976 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
292903 AAGTTTCAAC
* *
292913 TTAAGAAAAAGTGTCAAACTTAGGTACCGAA
1 TTAAGAAAAAGTGTCAAACTTAAGTACCAAA
**
292944 TTAAGAAAAAGTGTCAATTTTAAGTACCAAA
1 TTAAGAAAAAGTGTCAAACTTAAGTACCAAA
292975 TT
1 TT
292977 GGACAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (31 bp):
TTAAGAAAAAGTGTCAAACTTAAGTACCAAA
Found at i:304970 original size:61 final size:62
Alignment explanation
Indices: 304856--304986 Score: 153
Period size: 61 Copynumber: 2.1 Consensus size: 62
304846 TTTAATAAAA
* * * *
304856 AAAATTAATCTTTCAATGTTTACACATTATATCAATTTGATCTTAAATTTAAAATATTCAAT
1 AAAATTAATCTTTCAATGTTTACAAATTATATCAATTTGATCTCAAATCTAAAAAATTCAAT
* * *
304918 AAAATTAA-CTTTCAATGTTTCCAAATTTTATC-ATTTTAGT-TCAAATACTAAAAAATTCAAT
1 AAAATTAATCTTTCAATGTTTACAAATTATATCAATTTGA-TCTCAAAT-CTAAAAAATTCAAT
304979 -AAATTAAT
1 AAAATTAAT
304987 TTTTTTCCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
60 17 0.29
61 34 0.58
62 8 0.14
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (62 bp):
AAAATTAATCTTTCAATGTTTACAAATTATATCAATTTGATCTCAAATCTAAAAAATTCAAT
Found at i:305625 original size:3 final size:3
Alignment explanation
Indices: 305617--305651 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
305607 ACCAAAAATA
305617 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
305652 ATGCCCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:307335 original size:30 final size:30
Alignment explanation
Indices: 307294--307380 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
307284 CAAATTATCT
*
307294 AAAATTTCATTTTGACCCAT-GAACTTTTTG
1 AAAATTACATTTTGACCC-TCGAACTTTTTG
**
307324 AAAATTACATTTTGACCCTCGATTTTTTTG
1 AAAATTACATTTTGACCCTCGAACTTTTTG
* *
307354 AAAATTACATTTTAACCC-CAAACTTTT
1 AAAATTACATTTTGACCCTCGAACTTTT
307381 CAATATTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 7 0.14
30 42 0.86
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCGAACTTTTTG
Found at i:319535 original size:49 final size:48
Alignment explanation
Indices: 319384--319746 Score: 209
Period size: 49 Copynumber: 7.4 Consensus size: 48
319374 CAGGTTTGGA
** * * * * *
319384 GGGAAAGGTTGAAGCTACAAAGGCGAACCTTGTACCTTAGAGATGTAAT
1 GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACC-TAGAGAAGTGAT
* * * * * *
319433 GGGAAAGATTGAGGCCGCAACGACGAATCTTGAACC-ACGAAGATA-TAGA-
1 GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACCTA-G-AGA-AGT-GAT
* * * *
319482 GGGAAAGGTTAAAGTCGCAACGATAAACCTTGTACCTCAGAGAAGTGAT
1 GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACCT-AGAGAAGTGAT
* * * * * *
319531 GGGAAAGATTGAAGCCACAACGGCGAATCC-TGTACCATAAAGATA-TGGA-
1 GGGAAAGGTTGAAGCCGCAATGAC-AAACCTTGTACC-TAGAGA-AGT-GAT
* * *
319580 GGGAAAGGTTAAAGCAGCAATGACAAACCTTGTACCTTAGAGAAGTAAT
1 GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACC-TAGAGAAGTGAT
* * * * * *
319629 GAGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCATAGAGATA-TGAA
1 GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACC-TAGAGA-AGTGAT
* * * *
319678 GAGAAAGGTTGAGGCCGCAATGGCAAACCTTGTACCTTAGAGATGTGAT
1 GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACC-TAGAGAAGTGAT
* *
319727 GGGAAAGATTGAAGCTGCAA
1 GGGAAAGGTTGAAGCCGCAA
319747 GGATGGATCT
Statistics
Matches: 240, Mismatches: 57, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
47 1 0.00
48 10 0.04
49 217 0.90
50 11 0.05
51 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (48 bp):
GGGAAAGGTTGAAGCCGCAATGACAAACCTTGTACCTAGAGAAGTGAT
Found at i:319714 original size:196 final size:196
Alignment explanation
Indices: 319380--319741 Score: 496
Period size: 196 Copynumber: 1.8 Consensus size: 196
319370 TCTACAGGTT
* * * * *
319380 TGGAGGGAAAGGTTGAAGCTACAAAGGCGAACCTTGTACCTTAGAGATGTAATGGGAAAGATTGA
1 TGGAGGGAAAGGTTAAAGCTACAAAGACAAACCTTGTACCTTAGAGAAGTAATGAGAAAGATTGA
* * * * *
319445 GGCCGCAACGACGAATCTTGAACCACGAAGATATAGAGGGAAAGGTTAAAGTCGCAACGATAAAC
66 AGCCGCAACGACGAATCTTGAACCAAGAAGATATAGAGAGAAAGGTTAAAGCCGCAACGACAAAC
319510 CTTGTACCTCAGAGAAGTGATGGGAAAGATTGAAGCCACAACGGCGAATCCTGTACCATAAAGAT
131 CTTGTACCTCAGAGAAGTGATGGGAAAGATTGAAGCCACAACGGCGAATCCTGTACCATAAAGAT
319575 A
196 A
*
319576 TGGAGGGAAAGGTTAAAGC-AGCAATGACAAACCTTGTACCTTAGAGAAGTAATGAGAAAGATTG
1 TGGAGGGAAAGGTTAAAGCTA-CAAAGACAAACCTTGTACCTTAGAGAAGTAATGAGAAAGATTG
* * * * * * *
319640 AAGCCGCAATGGCGAATCTTGTACCATAG-AGATAT-GAAGAGAAAGGTTGAGGCCGCAATGGCA
65 AAGCCGCAACGACGAATCTTGAACCA-AGAAGATATAG-AGAGAAAGGTTAAAGCCGCAACGACA
* *
319703 AACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
128 AACCTTGTACCTCAGAGAAGTGATGGGAAAGATTGAAGC
319742 TGCAAGGATG
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
195 2 0.01
196 140 0.98
197 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.19
Consensus pattern (196 bp):
TGGAGGGAAAGGTTAAAGCTACAAAGACAAACCTTGTACCTTAGAGAAGTAATGAGAAAGATTGA
AGCCGCAACGACGAATCTTGAACCAAGAAGATATAGAGAGAAAGGTTAAAGCCGCAACGACAAAC
CTTGTACCTCAGAGAAGTGATGGGAAAGATTGAAGCCACAACGGCGAATCCTGTACCATAAAGAT
A
Found at i:319757 original size:98 final size:98
Alignment explanation
Indices: 319409--319746 Score: 428
Period size: 98 Copynumber: 3.4 Consensus size: 98
319399 TACAAAGGCG
* * * * *
319409 AACCTTGTACCTTAGAGATGTAATGGGAAAGATTGAGGCCGCAACGACGAATCTTGAACCA-CGA
1 AACCTTGTACCTTAGAGAAGTAATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCATAG-
* * *
319473 AGATAT-AGAGGGAAAGGTTAAAGTCGCAACGATA
65 AGATATGA-AGGGAAAGGTTAAAGCCGCAATGACA
* * * * *
319507 AACCTTGTACCTCAGAGAAGTGATGGGAAAGATTGAAGCCACAACGGCGAATCCTGTACCATAAA
1 AACCTTGTACCTTAGAGAAGTAATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCATAGA
* *
319572 GATATGGAGGGAAAGGTTAAAGCAGCAATGACA
66 GATATGAAGGGAAAGGTTAAAGCCGCAATGACA
* *
319605 AACCTTGTACCTTAGAGAAGTAATGAGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCATAGA
1 AACCTTGTACCTTAGAGAAGTAATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCATAGA
* * * *
319670 GATATGAAGAGAAAGGTTGAGGCCGCAATGGCA
66 GATATGAAGGGAAAGGTTAAAGCCGCAATGACA
* * *
319703 AACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAA
1 AACCTTGTACCTTAGAGAAGTAATGGGAAAGATTGAAGCCGCAA
319747 GGATGGATCT
Statistics
Matches: 206, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
98 206 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (98 bp):
AACCTTGTACCTTAGAGAAGTAATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCATAGA
GATATGAAGGGAAAGGTTAAAGCCGCAATGACA
Found at i:321722 original size:30 final size:28
Alignment explanation
Indices: 321659--321764 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 28
321649 AGAAATTATG
* *
321659 TTTTGACCCTTAAACTATCTAAAATTTCA
1 TTTTGACCC-TAAACTTTCTAAAATTACA
321688 TTTTGACCCATAAACTTTCTAAAAGTTACA
1 TTTTGACCC-TAAACTTTCTAAAA-TTACA
* * * *
321718 TTTTGACCCTCAAATTTTTTGAAATTATA
1 TTTTGACCCT-AAACTTTCTAAAATTACA
*
321747 TTTTGACCCCAAACTTTC
1 TTTTGACCCTAAACTTTC
321765 AAATATTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.09
29 36 0.55
30 23 0.35
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (28 bp):
TTTTGACCCTAAACTTTCTAAAATTACA
Found at i:323881 original size:38 final size:37
Alignment explanation
Indices: 323815--323886 Score: 117
Period size: 38 Copynumber: 1.9 Consensus size: 37
323805 AAAATAAAAA
*
323815 AATTTAATAATATTTTAACATAATTATTATTAAATAC
1 AATTTAATAACATTTTAACATAATTATTATTAAATAC
*
323852 AATTTAATAACATTCTTAATATAATTATTATTAAA
1 AATTTAATAACATT-TTAACATAATTATTATTAAA
323887 AAATGAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (37 bp):
AATTTAATAACATTTTAACATAATTATTATTAAATAC
Found at i:346332 original size:24 final size:24
Alignment explanation
Indices: 346300--346345 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
346290 ACTCACATTG
*
346300 AAGTGTCTTTTATTAATGCAATTA
1 AAGTATCTTTTATTAATGCAATTA
346324 AAGTATCTTTTATTAATGCAAT
1 AAGTATCTTTTATTAATGCAAT
346346 GTCGTTGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (24 bp):
AAGTATCTTTTATTAATGCAATTA
Found at i:347623 original size:16 final size:17
Alignment explanation
Indices: 347591--347624 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
347581 GTTCCAGGCC
347591 TTTATGTAAGCATAAAA
1 TTTATGTAAGCATAAAA
*
347608 TTTATGT-AGTATAAAA
1 TTTATGTAAGCATAAAA
347624 T
1 T
347625 CCATATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTATGTAAGCATAAAA
Found at i:356535 original size:37 final size:37
Alignment explanation
Indices: 356492--356703 Score: 280
Period size: 37 Copynumber: 5.7 Consensus size: 37
356482 AAATTCAAGT
* *
356492 TTTGTGCCTAGTAGGCTTCGTGTCGGTGTTTTCAAGC
1 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
356529 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
1 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
* *
356566 TTTGTGCCTAGTAGGCTTCATGCCGGTGTTTTTAGGC
1 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
* * * *
356603 TTTGTCCCTAGTAGGCTTCATGTCAGTGTTTTCAGGC
1 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
* * * *
356640 TATGTGCCTAGTAGGCTTCGTGCCAGTGTATTCGGGC
1 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
* * * *
356677 TATGTGCCTAGCAAGCTTTGTGCCGGT
1 TTTGTGCCTAGTAGGCTTCGTGCCGGT
356704 AATCCAAGAA
Statistics
Matches: 157, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 157 1.00
ACGTcount: A:0.12, C:0.21, G:0.30, T:0.38
Consensus pattern (37 bp):
TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGC
Found at i:365754 original size:17 final size:16
Alignment explanation
Indices: 365711--365778 Score: 82
Period size: 17 Copynumber: 4.1 Consensus size: 16
365701 TGTCTAGACC
* *
365711 TATTGAAAATTGAATT
1 TATTTAAAATTAAATT
*
365727 TATTTAAATTTAAATT
1 TATTTAAAATTAAATT
*
365743 TATTTGAAATTTAAATT
1 TATTT-AAAATTAAATT
365760 TATTATAAAATTAAATT
1 TATT-TAAAATTAAATT
365777 TA
1 TA
365779 GAAAGTCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
16 18 0.39
17 27 0.59
18 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TATTTAAAATTAAATT
Done.