Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 17
Found at i:585324 original size:22 final size:22
Alignment explanation
Indices: 585295--585349 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
585285 ATCTACACTC
585295 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
585317 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
585339 TTCAAAGATGA
1 TTCAAAGATGA
585350 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:586143 original size:76 final size:76
Alignment explanation
Indices: 586017--586396 Score: 654
Period size: 76 Copynumber: 5.0 Consensus size: 76
586007 CTATTTCTCA
* ** *
586017 CATCTGTAAGCCCTTCAGTTTATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
586082 AGCCTTCGGGT
66 AGCCTTCGGGT
*
586093 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
586158 AGCCTTC-GGT
66 AGCCTTCGGGT
*
586168 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
586233 AGCCTTCGGGT
66 AGCCTTCGGGT
*
586244 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
586309 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
586320 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
586385 AAAGCCTTCGGG
64 AAAGCCTTCGGG
586397 ATCTTTTTGA
Statistics
Matches: 293, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
75 73 0.25
76 208 0.71
78 12 0.04
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:586296 original size:151 final size:152
Alignment explanation
Indices: 586017--586396 Score: 663
Period size: 151 Copynumber: 2.5 Consensus size: 152
586007 CTATTTCTCA
** *
586017 CATCTGTAAGCCCTTCAGTTTATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
586082 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
586147 GATGTTTTCAAAGCCTTC-GGT
131 GATGTTTTCAAAGCCTTCGGGT
* *
586168 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
586233 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
586298 GATGTTTTTAAAGCCTTCGGGT
131 GATGTTTTCAAAGCCTTCGGGT
*
586320 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
586385 AAAGCCTTCGGG
64 AAAGCCTTCGGG
586397 ATCTTTTTGA
Statistics
Matches: 216, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
151 141 0.65
152 63 0.29
154 12 0.06
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (152 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGT
Found at i:586377 original size:31 final size:31
Alignment explanation
Indices: 586342--586425 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
586332 CTTCAGTGCA
586342 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
586373 TGATGTTTCCAAAAAGCCTTCGGGATCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
586404 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
586426 TCATCTGTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 12 0.24
31 39 0.76
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:586384 original size:107 final size:106
Alignment explanation
Indices: 586266--586500 Score: 402
Period size: 107 Copynumber: 2.2 Consensus size: 106
586256 CTTCAGTGCA
*
586266 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
586331 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTT
* *
586373 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
*
586438 CCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGATCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTT
*
586479 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
586501 TCATCTGTAA
Statistics
Matches: 123, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
104 12 0.10
106 28 0.23
107 83 0.67
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (106 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
CCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTT
Found at i:586453 original size:76 final size:76
Alignment explanation
Indices: 586373--586914 Score: 1002
Period size: 76 Copynumber: 7.2 Consensus size: 76
586363 GGGAGCTTTT
586373 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586438 CCTTCAGTGCA
66 CCTTCAGTGCA
586449 TGATGTTTCC-AAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586513 CCTTCAGTGCA
66 CCTTCAGTGCA
586524 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586589 CCTTCAGTGCA
66 CCTTCAGTGCA
586600 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586665 CCTTCAGTGCA
66 CCTTCAGTGCA
586676 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586741 CCTTCAGTGCA
66 CCTTCAGTGCA
*
586752 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586817 CCTTCAGTGCA
66 CCTTCAGTGCA
* * *
586828 TGA-GTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586891 CCTTTC-GTGCA
66 CC-TTCAGTGCA
*
586902 TGATGTTTTCAAA
1 TGATGTTTCCAAA
586915 CATTTCCATC
Statistics
Matches: 458, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
74 62 0.14
75 89 0.19
76 307 0.67
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (76 bp):
TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCA
Found at i:586496 original size:258 final size:258
Alignment explanation
Indices: 586115--586652 Score: 983
Period size: 258 Copynumber: 2.1 Consensus size: 258
586105 CTTCAGTGCA
586115 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGTC
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGTC
*
586180 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTC
66 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
*
586245 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAA
131 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
586310 GCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
196 GCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
586373 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGT
*
586438 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGT
65 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
586502 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
130 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
586567 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTT
195 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
586631 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
586653 TCATCTGTAA
Statistics
Matches: 272, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
256 12 0.04
258 225 0.83
259 35 0.13
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (258 bp):
TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGTC
CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:586556 original size:182 final size:183
Alignment explanation
Indices: 586190--586576 Score: 690
Period size: 182 Copynumber: 2.1 Consensus size: 183
586180 CTTCAGTGCA
*
586190 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
*
586255 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
586320 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
131 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
586373 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
*
586438 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
* *
586502 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTT
131 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
586555 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
586577 TCATCTGTAA
Statistics
Matches: 197, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
180 12 0.06
182 101 0.51
183 84 0.43
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (183 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:586648 original size:334 final size:334
Alignment explanation
Indices: 586039--586728 Score: 1287
Period size: 334 Copynumber: 2.1 Consensus size: 334
586029 CTTCAGTTTA
586039 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586104 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGTC
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGTC
*
586169 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAA
131 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
586234 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
196 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
*
586299 ATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
261 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
586364 GGAGCTTTT
326 GGAGCTTTT
586373 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
586438 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTC-GGT
*
586502 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
130 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
586567 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
195 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
586632 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
260 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
586697 GGGATCTTTT
325 GGGAGCTTTT
*
586707 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
586729 TCATCTGTAA
Statistics
Matches: 348, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
332 12 0.03
333 39 0.11
334 297 0.85
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (334 bp):
TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGTC
ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
GGAGCTTTT
Found at i:587048 original size:3 final size:3
Alignment explanation
Indices: 587040--587107 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
587030 CATTTAAATT
* * *
587040 TTA TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
587086 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
587108 ATATATATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.02
3 52 0.93
4 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:593275 original size:30 final size:31
Alignment explanation
Indices: 593241--593309 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
593231 CTAAAAATTT
* * * *
593241 AATTAAGTCCTTAAACTT-TCCAAAAGAATC
1 AATTAAGCCCTCAAACTTAACCAAAAAAATC
* *
593271 AATTAGGCCCTCAAACTTAACTAAAAAAATC
1 AATTAAGCCCTCAAACTTAACCAAAAAAATC
593302 AATTAAGC
1 AATTAAGC
593310 TCATCTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (31 bp):
AATTAAGCCCTCAAACTTAACCAAAAAAATC
Found at i:593750 original size:27 final size:25
Alignment explanation
Indices: 593698--593750 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
593688 TAAGTTTATG
*
593698 TAATAAATTTTTAATGACTATATTT
1 TAATAAATTTTTAATAACTATATTT
* *
593723 TAATATAATTATTTAATAATTATTTTT
1 TAATA-AATT-TTTAATAACTATATTT
593750 T
1 T
593751 CATCTCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 4 0.17
27 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TAATAAATTTTTAATAACTATATTT
Found at i:595361 original size:38 final size:38
Alignment explanation
Indices: 595319--595395 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
595309 CTCATGTCTG
* *
595319 TGAGTTGTCACTAACATTAAGCGCACCTAAATCTAGTC
1 TGAGTTGTCACTAAAATTAAGCGCACCTAAATCCAGTC
*
595357 TGAGTTGTCCCTAAAATTAAGCGCACCTAAATCCAGTC
1 TGAGTTGTCACTAAAATTAAGCGCACCTAAATCCAGTC
595395 T
1 T
595396 TCCACACCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (38 bp):
TGAGTTGTCACTAAAATTAAGCGCACCTAAATCCAGTC
Found at i:600722 original size:42 final size:41
Alignment explanation
Indices: 600646--600759 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 41
600636 CATCCTACCC
* *
600646 AAAGGTCTTACAGATGGCCCGAAGGATTTATCATCTTGCTCT
1 AAAGG-CTTACAGATGGCCCGAAGGATTTATCATCATGCTCG
*
600688 AAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCG
1 AAAGGCTTACAGATGGCCCGAAGGATTT-ATCATCATGCTCG
* ** *
600730 AAAGACTTATTGATGGCCCGAAGGACTTAT
1 AAAGGCTTACAGATGGCCCGAAGGATTTAT
600760 AAATTGTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 24 0.38
42 39 0.62
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (41 bp):
AAAGGCTTACAGATGGCCCGAAGGATTTATCATCATGCTCG
Found at i:600942 original size:214 final size:215
Alignment explanation
Indices: 600480--601175 Score: 1103
Period size: 214 Copynumber: 3.2 Consensus size: 215
600470 GCTCGGAAGA
* *
600480 CTTACAAATGACCCGAATGATTTAAGCATCATGCTCAAAAGACTTACTGAAT-GCCCGAAGGACT
1 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTG-ATGGCCCGAAGGACT
* *
600544 TATAAATTGTGAAATTTTAAAAATCGTATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATC
65 TATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATC
* * * **
600609 ATTTTC--ATTTTCAAATTCATTTGAACACATCCTACCCAAAGGTCTTACAGATGGCCCGAAGGA
130 ATTTTCTTATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGA
*
600672 TTTATCATCTTGCTCTAAAGG
195 CTTATCATCTTGCTCTAAAGG
* * *
600693 CTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTT
1 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
* * *
600758 ATAAATTGTGAAATTTTGAAACTCGCATTCTTCATTTTCAAAAATTTCATCATCTTAAAACATCA
66 ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCA
*
600823 TTTTCTTATTTTCAAATTCA-ATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCTGAAGGAC
131 TTTTCTTATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGAC
600887 TTATCATCTTGCTCTAAAGG
196 TTATCATCTTGCTCTAAAGG
*
600907 CTTACAGATGACCCGAATGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
1 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
*
600972 ATAAATTATGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCA
66 ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCA
* * * * *
601037 TTTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATTGCCCAAAGGA
131 TTTTCTT-ATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGA
601102 CTTATCATCTTGCTCTAAAGG
195 CTTATCATCTTGCTCTAAAGG
* * *
601123 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGG
601176 AGTTGCTTCA
Statistics
Matches: 443, Mismatches: 35, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
212 2 0.00
213 122 0.28
214 185 0.42
215 26 0.06
216 108 0.24
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (215 bp):
CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCA
TTTTCTTATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGAC
TTATCATCTTGCTCTAAAGG
Found at i:601221 original size:37 final size:37
Alignment explanation
Indices: 601171--601576 Score: 341
Period size: 37 Copynumber: 11.1 Consensus size: 37
601161 AAGACTTATT
* **
601171 GATGGAGTTGCTTCACTACTCTTTGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
*
601208 GATGGAATTGCTTCACT-CATCTCCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTAC-TCTCCGGTGAAGGCTTAA
* *** *** * * * **
601245 GATTGCCCTG-AGGACTTAATCATCATGCTCAGAAGGCTTGCT
1 GATGGATTTGCTTCAC-TACTC-TC-CGGT--GAAGGCTT-AA
*
601287 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
* * * *
601324 GATTGAGTTGCTTCACTATTCTCCGGTGGAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
*
601361 GATGG---TGCTTCACTACTC-CTCTGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTC-CGGTGAAGGCTTAA
* * *
601395 GAT--A-GTGCTTCACTACTCTTCTGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
* * * * *
601429 GATTGAGTTGCTTTACTATTCTCCGGTAAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
* *
601466 GATGG-TTTGCTTCACTACTCTCCAGTGAAGGCTTCA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
*
601502 GAT-GATTTGCTTCACTATTCTCCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
* *
601538 GATGG-TTTGCTTTACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
601574 GAT
1 GAT
601577 TGACTTTCCC
Statistics
Matches: 294, Mismatches: 57, Indels: 37
0.76 0.15 0.10
Matches are distributed among these distances:
33 1 0.00
34 57 0.19
35 1 0.00
36 94 0.32
37 106 0.36
38 10 0.03
39 2 0.01
40 2 0.01
41 9 0.03
42 10 0.03
43 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (37 bp):
GATGGATTTGCTTCACTACTCTCCGGTGAAGGCTTAA
Found at i:601357 original size:116 final size:112
Alignment explanation
Indices: 601119--601470 Score: 360
Period size: 116 Copynumber: 3.1 Consensus size: 112
601109 TCTTGCTCTA
* * * * *
601119 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGAGTTGCTT
1 AAGGCTTA-AGATGGCCC-TAGGACTTAATCATCATGCTCG-AAGGCTTA-TGATGGA-TTGCTT
* * *
601184 CACTACTCTTTGGTGAAGGCTTAAGATGGAATTGCTTCACTCA-TCTCCGGTG
61 CACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACT-ATTCTCCGGTG
* *
601236 AAGGCTTAAGATTGCCCTGAGGACTTAATCATCATGCTCAGAAGGCTTGCTGATGGATTTGCTTC
1 AAGGCTTAAGATGGCCCT-AGGACTTAATCATCATGCTC-GAAGGCTT-ATGATGGA-TTGCTTC
601301 ACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
62 ACTACTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
* ** ** * * * *
601352 GAGGCTTAAGATGGTGCT-TCAC-TACTCCTC-TG-T-GAAGGCTTAAGAT--AGTGCTTCACTA
1 AAGGCTTAAGATGGCCCTAGGACTTAATCATCATGCTCGAAGGCTTATGATGGATTGCTTCACTA
* * *
601410 CTCTTCTGTGAAGGCTTAAGATTGAGTTGCTTTACTATTCTCCGGTA
66 CTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
601457 AAGGCTTAAGATGG
1 AAGGCTTAAGATGG
601471 TTTGCTTCAC
Statistics
Matches: 205, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
105 67 0.33
106 1 0.00
108 3 0.01
109 8 0.04
111 1 0.00
112 2 0.01
113 6 0.03
114 2 0.01
115 1 0.00
116 105 0.51
117 9 0.04
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (112 bp):
AAGGCTTAAGATGGCCCTAGGACTTAATCATCATGCTCGAAGGCTTATGATGGATTGCTTCACTA
CTCTTCGGTGAAGGCTTAAGATTGAGTTGCTTCACTATTCTCCGGTG
Found at i:601488 original size:36 final size:35
Alignment explanation
Indices: 601294--601576 Score: 329
Period size: 36 Copynumber: 7.9 Consensus size: 35
601284 GCTGATGGAT
*
601294 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGAG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGA-TG-G
* *
601331 TTGCTTCACTATTCTCCGGTGGAGGCTTAAGATGG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
* *
601366 -TGCTTCACTACTC-CTCTGTGAAGGCTTAAGATAG
1 TTGCTTCACTACTCTC-CGGTGAAGGCTTAAGATGG
* *
601400 -TGCTTCACTACTCTTCTGTGAAGGCTTAAGATTGAG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGA-TG-G
* * *
601436 TTGCTTTACTATTCTCCGGTAAAGGCTTAAGATGG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
* * *
601471 TTTGCTTCACTACTCTCCAGTGAAGGCTTCAGATGAT
1 -TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATG-G
*
601508 TTGCTTCACTATTCTCCGGTGAAGGCTTAAGATGG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
* *
601543 TTTGCTTTACTACTCTTCGGTGAAGGCTTAAGAT
1 -TTGCTTCACTACTCTCCGGTGAAGGCTTAAGAT
601577 TGACTTTCCC
Statistics
Matches: 211, Mismatches: 27, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
33 1 0.00
34 57 0.27
35 3 0.01
36 95 0.45
37 55 0.26
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (35 bp):
TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
Found at i:606548 original size:42 final size:42
Alignment explanation
Indices: 606501--606625 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 42
606491 CGCAAAAATA
606501 GTCTTCAT-GTCTTTGTGAATGGTCTTCTCATCTTTATGAATG
1 GTCTTC-TCGTCTTTGTGAATGGTCTTCTCATCTTTATGAATG
* *
606543 GTCTTCTCGTCTTTATGAATGGTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTGTGAATGGTCTTCTCATCTTTATGAATG
* *
606585 GTCTTTTCGTCCTTGTGAATGGTCTTCTCATCCTTT-TGAAT
1 GTCTTCTCGTCTTTGTGAATGGTCTTCTCAT-CTTTATGAAT
606626 AGTTATATAT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.01
42 70 0.93
43 4 0.05
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.48
Consensus pattern (42 bp):
GTCTTCTCGTCTTTGTGAATGGTCTTCTCATCTTTATGAATG
Found at i:606625 original size:21 final size:21
Alignment explanation
Indices: 606501--606613 Score: 165
Period size: 21 Copynumber: 5.4 Consensus size: 21
606491 CGCAAAAATA
*
606501 GTCTTCAT-GTCTTTGTGAATG
1 GTCTTC-TCGTCTTTATGAATG
*
606522 GTCTTCTCATCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
606543 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
606564 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
* * *
606585 GTCTTTTCGTCCTTGTGAATG
1 GTCTTCTCGTCTTTATGAATG
606606 GTCTTCTC
1 GTCTTCTC
606614 ATCCTTTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 1 0.01
21 83 0.99
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (21 bp):
GTCTTCTCGTCTTTATGAATG
Found at i:616879 original size:13 final size:13
Alignment explanation
Indices: 616861--616888 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
616851 TCCTTAAATG
616861 TGCTTTAGAGTTT
1 TGCTTTAGAGTTT
616874 TGCTTTAGAGTTT
1 TGCTTTAGAGTTT
616887 TG
1 TG
616889 TTTTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.54
Consensus pattern (13 bp):
TGCTTTAGAGTTT
Found at i:618549 original size:6 final size:6
Alignment explanation
Indices: 618538--618582 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
618528 GAGAGAGTTT
* * *
618538 TGATGG TGATGG TGATGG TGATGG TGAGGG TGAGGG TGAGGG TGA
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGA
618583 GGAAAGTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.00, G:0.56, T:0.27
Consensus pattern (6 bp):
TGATGG
Found at i:619116 original size:15 final size:16
Alignment explanation
Indices: 619096--619129 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
619086 TGTCAAAATG
619096 GTTTGACCTTTCAT-T
1 GTTTGACCTTTCATCT
619111 GTTTGACCTTTCATCT
1 GTTTGACCTTTCATCT
619127 GTT
1 GTT
619130 CGTCCCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.12, C:0.21, G:0.15, T:0.53
Consensus pattern (16 bp):
GTTTGACCTTTCATCT
Found at i:639974 original size:20 final size:21
Alignment explanation
Indices: 639948--639995 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
639938 TACTCAGGGG
639948 AGTATCGAAACCATAGA-AAA
1 AGTATCGAAACCATAGATAAA
* * *
639968 TGTATCGATACCCTAGATAAA
1 AGTATCGAAACCATAGATAAA
639989 AGTATCG
1 AGTATCG
639996 GTACTTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTATCGAAACCATAGATAAA
Found at i:644258 original size:24 final size:24
Alignment explanation
Indices: 644227--644291 Score: 91
Period size: 22 Copynumber: 2.8 Consensus size: 24
644217 TTTTAATATG
644227 AATATTTATTTTTTTAATAA-TTT
1 AATATTTATTTTTTTAATAAGTTT
644250 AAT-TTT-TTATTTTTAATAAGTTT
1 AATATTTATT-TTTTTAATAAGTTT
*
644273 TATATTTATTTTTTTAATA
1 AATATTTATTTTTTTAATA
644292 CTTAGATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 2 0.05
22 13 0.35
23 8 0.22
24 12 0.32
25 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
AATATTTATTTTTTTAATAAGTTT
Found at i:644262 original size:22 final size:23
Alignment explanation
Indices: 644228--644291 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 23
644218 TTTAATATGA
644228 ATATTTATTTTTTTAATAA-TTT
1 ATATTTATTTTTTTAATAAGTTT
*
644250 A-ATTTTTTATTTTTAATAAGTTTT
1 ATATTTATT-TTTTTAATAAG-TTT
644274 ATATTTATTTTTTTAATA
1 ATATTTATTTTTTTAATA
644292 CTTAGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
24 13 0.36
25 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATATTTATTTTTTTAATAAGTTT
Found at i:644303 original size:24 final size:21
Alignment explanation
Indices: 644215--644291 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 21
644205 ATTTTTAGTA
*
644215 TTTTTTAATATGAATATTTAT
1 TTTTTTAATATTAATATTTAT
644236 TTTTTTAATAATTTAAT-TTT-T
1 TTTTTTAAT-A-TTAATATTTAT
*
644257 TATTTTTAATAAGTTTTATATTTAT
1 T-TTTTTAAT-A--TTAATATTTAT
644282 TTTTTTAATA
1 TTTTTTAATA
644292 CTTAGATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
21 11 0.23
22 14 0.29
23 10 0.21
24 11 0.23
25 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTTTTAATATTAATATTTAT
Found at i:644865 original size:17 final size:17
Alignment explanation
Indices: 644843--644876 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
644833 ATGGATCTAT
644843 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
*
644860 TCTATCGGGTTATTTGA
1 TCTATCGAGTTATTTGA
644877 AGATGCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:644947 original size:17 final size:17
Alignment explanation
Indices: 644914--644958 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
644904 GTTTATTTGT
*
644914 GTTAT-TTATAATATTC
1 GTTATATTATTATATTC
*
644930 GTTATATTATTATTTTC
1 GTTATATTATTATATTC
*
644947 GTAATATTATTA
1 GTTATATTATTA
644959 ATGATATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (17 bp):
GTTATATTATTATATTC
Found at i:650120 original size:42 final size:42
Alignment explanation
Indices: 650073--650195 Score: 187
Period size: 41 Copynumber: 3.0 Consensus size: 42
650063 TGAACTAAAG
650073 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
1 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
* * *
650115 ATCAGTAATGCATCTAACAGTCTCT-GCCAAAGTACAG-AAAA
1 ATCAGTAATACATCTTACAGTCT-TGGCCAAAGTATAGCAAAA
*
650156 ATCAGTAATACATCTTACAGTCTTGGCCAAATTATAGCAA
1 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAA
650196 CGATATACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 35 0.49
42 34 0.48
43 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (42 bp):
ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
Found at i:656614 original size:31 final size:31
Alignment explanation
Indices: 656579--656646 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
656569 CAGTTACATC
656579 GGGGACCATATTGCAGACA-G-ACTAAATGTTG
1 GGGGACCATATTGCA-A-ATGAACTAAATGTTG
*
656610 GGGGACCATATTGCAAATGAATTAAATGTTG
1 GGGGACCATATTGCAAATGAACTAAATGTTG
656641 GGGGAC
1 GGGGAC
656647 TGTATTACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.03
30 2 0.06
31 31 0.91
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAATGAACTAAATGTTG
Found at i:661115 original size:3 final size:3
Alignment explanation
Indices: 661109--661182 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
661099 TTAATATATT
* **
661109 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA GGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
661157 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
661183 TGGATAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:661630 original size:113 final size:113
Alignment explanation
Indices: 661432--661859 Score: 802
Period size: 113 Copynumber: 3.8 Consensus size: 113
661422 TCTTGATGAG
*
661432 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
*
661497 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
66 GCAATGTTGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
661545 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
661610 GCAATGTTGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
66 GCAATGTTGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
*
661658 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
661723 GCAATGTTGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
66 GCAATGTTGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
*
661771 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
**
661836 GCAATGTTGATCCATTGAATGATG
66 GCAATGTTGATCCATCAAATGATG
661860 GATTTGAACT
Statistics
Matches: 310, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 310 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
GCAATGTTGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
Found at i:662184 original size:28 final size:28
Alignment explanation
Indices: 662151--662208 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
662141 TTAGAAGAAT
662151 TGTGGAACTCTTGTCGTAGTCAGAACTA
1 TGTGGAACTCTTGTCGTAGTCAGAACTA
662179 TGTGGAACTCTTGTCGTAGTCAGAACTA
1 TGTGGAACTCTTGTCGTAGTCAGAACTA
662207 TG
1 TG
662209 ACCTTGATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (28 bp):
TGTGGAACTCTTGTCGTAGTCAGAACTA
Found at i:662308 original size:22 final size:22
Alignment explanation
Indices: 662283--662337 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
662273 GATAAAGCTT
*
662283 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
662305 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
662327 TCATCTTTGAA
1 TCATCTTTGAA
662338 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:663893 original size:36 final size:34
Alignment explanation
Indices: 663849--663926 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 34
663839 TGCTCAATGT
663849 TATT-TATTG-AGATGAACCTCCAAGAATGCCCAAA
1 TATTCTATTGCAG-TGAACCTCCAA-AATGCCCAAA
* * * *
663883 TATTCATATTGCTGTGAGCCTTCAAAATGCCCTAA
1 TATTC-TATTGCAGTGAACCTCCAAAATGCCCAAA
663918 TATTCTATT
1 TATTCTATT
663927 TCTGGTTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
34 8 0.22
35 14 0.38
36 14 0.38
37 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (34 bp):
TATTCTATTGCAGTGAACCTCCAAAATGCCCAAA
Found at i:665200 original size:115 final size:114
Alignment explanation
Indices: 664886--665226 Score: 556
Period size: 114 Copynumber: 3.0 Consensus size: 114
664876 GATCATGCAG
* * * * * * *
664886 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
664951 ACACTTCCAGAAGATGCTATTGGGTCTTCATATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* * *
665000 TTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGAAAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
665065 ACACTTCTAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
665114 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
665179 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
665227 CATGGCACTT
Statistics
Matches: 210, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
114 125 0.60
115 85 0.40
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:670450 original size:14 final size:13
Alignment explanation
Indices: 670416--670467 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
670406 TTGTGCAATA
*
670416 CAAATGCAAAGATG
1 CAAATGTAAA-ATG
670430 CCAAATGTAAATATG
1 -CAAATGTAAA-ATG
670445 CAAATGTAAAATTG
1 CAAATGTAAAA-TG
*
670459 TAAATGTAA
1 CAAATGTAA
670468 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 1 0.03
14 20 0.61
15 12 0.36
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (13 bp):
CAAATGTAAAATG
Found at i:674118 original size:3 final size:3
Alignment explanation
Indices: 674112--674185 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
674102 TTAATATATT
* **
674112 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA GGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
674160 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
674186 TGGATAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:675710 original size:13 final size:13
Alignment explanation
Indices: 675692--675737 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
675682 TTTTTATTTG
675692 TATATTATTAAAA
1 TATATTATTAAAA
**
675705 TATATTATTTTAA
1 TATATTATTAAAA
675718 T-TATT-TTAAAA
1 TATATTATTAAAA
675729 TATTATTAT
1 TA-TATTAT
675738 ATTTGGATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 16 0.62
14 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATATTATTAAAA
Found at i:675722 original size:22 final size:26
Alignment explanation
Indices: 675685--675737 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
675675 TTATGAATTT
675685 TTATTTGTATATTA-TTAAAATA-TA
1 TTATTTGTATATTATTTAAAATATTA
675709 TTATTT-TA-ATTATTTTAAAATATTA
1 TTATTTGTATATTA-TTTAAAATATTA
675734 TTAT
1 TTAT
675738 ATTTGGATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.15
23 2 0.08
24 14 0.54
25 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATTTGTATATTATTTAAAATATTA
Found at i:680110 original size:22 final size:22
Alignment explanation
Indices: 680085--680129 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
680075 AATTTTATTA
680085 AAAATAAGA-AAAAATATTAAAT
1 AAAATAAGATAAAAAT-TTAAAT
*
680107 AAAATAATATAAAAATTTAAAT
1 AAAATAAGATAAAAATTTAAAT
680129 A
1 A
680130 TATGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATAAGATAAAAATTTAAAT
Found at i:689286 original size:21 final size:21
Alignment explanation
Indices: 689260--689303 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
689250 GCTAAGCATC
689260 TATGAGATGGTCTACTAGAGA
1 TATGAGATGGTCTACTAGAGA
689281 TATGAGATGGTCTACTAGAGA
1 TATGAGATGGTCTACTAGAGA
689302 TA
1 TA
689304 GGATTATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (21 bp):
TATGAGATGGTCTACTAGAGA
Found at i:689743 original size:22 final size:23
Alignment explanation
Indices: 689698--689744 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
689688 AACCCTAAAT
*
689698 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATATGCTA
* *
689721 AAGCCC-AGAATCGTATATTCTA
1 AAGCCCAAAAATCGTATATGCTA
689743 AA
1 AA
689745 CTCGCGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATATGCTA
Found at i:699370 original size:23 final size:23
Alignment explanation
Indices: 699344--699388 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
699334 ATTATTATAT
*
699344 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTATACGC
*
699367 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTATACG
699389 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTATACGC
Found at i:703331 original size:20 final size:20
Alignment explanation
Indices: 703308--703360 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
703298 TCCACAAAAG
703308 TTCAAATTAATCCATAATT-T
1 TTCAAATTAAT-CATAATTAT
*
703328 TTCAAAATAAAGTCATAATTAT
1 TTC-AAATTAA-TCATAATTAT
*
703350 TTTAAATTAAT
1 TTCAAATTAAT
703361 TTATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (20 bp):
TTCAAATTAATCATAATTAT
Found at i:704161 original size:16 final size:17
Alignment explanation
Indices: 704140--704172 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
704130 TTATTGAAAT
704140 AAAGCATAT-CGGGTAG
1 AAAGCATATCCGGGTAG
*
704156 AAAGCATGTCCGGGTAG
1 AAAGCATATCCGGGTAG
704173 GATTGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.18
Consensus pattern (17 bp):
AAAGCATATCCGGGTAG
Found at i:704820 original size:46 final size:46
Alignment explanation
Indices: 704765--704859 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
704755 ATCTCGAATA
*
704765 TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGGTATTCATAT
1 TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGATATTCATAT
* *
704811 TTGATGACTTTTGTCTTTAATGAAACTTGTTCTAGGATATTCATAT
1 TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGATATTCATAT
704857 TTG
1 TTG
704860 GGATCAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (46 bp):
TTGACGACTTTTGTCTTAAATGAAACTTGTTCTAGGATATTCATAT
Found at i:706275 original size:94 final size:94
Alignment explanation
Indices: 706114--706302 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
706104 AACAGAGGGT
706114 ATCAGTACTCCTATAGGTAGTATCGATACTTTCTTTATATTTTAAAATAAAACTAGCCGTTAACT
1 ATCAGTACTCCTATAGGTAGTATCGATACTTTCTTTATATTTTAAAATAAAACTAGCCGTTAACT
706179 AGTTGTTGGGCCTGACAGTATCGATACTA
66 AGTTGTTGGGCCTGACAGTATCGATACTA
706208 ATCAGTACTCCTATAGGTAGTATCGATACTTTCTTTATATTTTAAAATAAAACTAGCCGTTAACT
1 ATCAGTACTCCTATAGGTAGTATCGATACTTTCTTTATATTTTAAAATAAAACTAGCCGTTAACT
706273 AGTTGTTGGGCCTGACAGTATCGATACTA
66 AGTTGTTGGGCCTGACAGTATCGATACTA
706302 A
1 A
706303 GCCTATGGTA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (94 bp):
ATCAGTACTCCTATAGGTAGTATCGATACTTTCTTTATATTTTAAAATAAAACTAGCCGTTAACT
AGTTGTTGGGCCTGACAGTATCGATACTA
Found at i:709442 original size:18 final size:17
Alignment explanation
Indices: 709419--709452 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
709409 TTAAAGTATT
709419 ATTTTTTAAGTTTTTTTG
1 ATTTTTT-AGTTTTTTTG
*
709437 ATTTTTTTGTTTTTTT
1 ATTTTTTAGTTTTTTT
709453 AAATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (17 bp):
ATTTTTTAGTTTTTTTG
Found at i:712157 original size:24 final size:24
Alignment explanation
Indices: 712125--712175 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
712115 ACAACATTAA
712125 TTCCTCCTATATTTACTT-AAGTAG
1 TTCCTCCTATATTTACTTCAA-TAG
*
712149 TTCCTCCTATATTTGCTTCAATAG
1 TTCCTCCTATATTTACTTCAATAG
712173 TTC
1 TTC
712176 ATTCGATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCCTCCTATATTTACTTCAATAG
Found at i:712387 original size:19 final size:21
Alignment explanation
Indices: 712348--712387 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
712338 ATATAAAATT
*
712348 ATATTATTTAAATTATTGTTA
1 ATATTATTTAAAATATTGTTA
712369 ATATT-TTTAAAAT-TTGTTA
1 ATATTATTTAAAATATTGTTA
712388 TTAGGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATATTATTTAAAATATTGTTA
Found at i:714239 original size:19 final size:19
Alignment explanation
Indices: 714215--714253 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
714205 TCGAATGCAT
714215 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
714234 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
714253 T
1 T
714254 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:714270 original size:65 final size:64
Alignment explanation
Indices: 714152--714360 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
714142 TATTCAAAGG
* *
714152 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
714213 ATTC
61 ATTT
714217 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
714282 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
714346 CATGCATCGATGCAC
1 CATGCACCGATGCAC
714361 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 65 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:714378 original size:64 final size:65
Alignment explanation
Indices: 714201--714363 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
714191 GAATTAATTG
* * * *
714201 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
714266 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
714329 A
65 A
714330 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
714364 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:720676 original size:171 final size:173
Alignment explanation
Indices: 720391--720737 Score: 671
Period size: 171 Copynumber: 2.0 Consensus size: 173
720381 CATCTCCACA
*
720391 TTCTCCTCAATCCGAATTTTTCAAGGTATTTTTTTTACAAAAACTCTATTTTATTAATTTTTGAA
1 TTCTCCTCAATCCAAATTTTTCAAGGTATTTTTTTTACAAAAACTCTATTTTATTAATTTTTGAA
720456 CTTAGGACTAGTTTAGATTAGTTCTAGTTTAAAATAATTATCGGGCATTGGTTATATGATGATTC
66 CTTAGGACTAGTTTAGATTAGTTCTAGTTTAAAATAATTATCGGGCATTGGTTATATGATGATTC
720521 TAAACTAGTTTCTAC-ATGAATTTC-TCAAAAACGCATAATTT
131 TAAACTAGTTTCTACAATGAATTTCATCAAAAACGCATAATTT
720562 TTCTCCTCAATCCAAATTTTTCAAGGTATTTTTTTTACAAAAACTCTATTTTATTAATTTTTGAA
1 TTCTCCTCAATCCAAATTTTTCAAGGTATTTTTTTTACAAAAACTCTATTTTATTAATTTTTGAA
720627 CTTAGGACTAGTTTAGATTAGTTCTAGTTTAAAATAATTATCGGGCATTGGTTATATGATGATTC
66 CTTAGGACTAGTTTAGATTAGTTCTAGTTTAAAATAATTATCGGGCATTGGTTATATGATGATTC
720692 TAAACTAGTTTCTACAATGAATTTCATCAAAAACGCATAATTT
131 TAAACTAGTTTCTACAATGAATTTCATCAAAAACGCATAATTT
720735 TTC
1 TTC
720738 AAAATTGTTT
Statistics
Matches: 173, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
171 144 0.83
172 9 0.05
173 20 0.12
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (173 bp):
TTCTCCTCAATCCAAATTTTTCAAGGTATTTTTTTTACAAAAACTCTATTTTATTAATTTTTGAA
CTTAGGACTAGTTTAGATTAGTTCTAGTTTAAAATAATTATCGGGCATTGGTTATATGATGATTC
TAAACTAGTTTCTACAATGAATTTCATCAAAAACGCATAATTT
Found at i:721887 original size:19 final size:18
Alignment explanation
Indices: 721863--721900 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
721853 TCGAATGCAT
721863 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGC-CTC
*
721882 TCCATGCATCGATGCCTC
1 TCCATGCACCGATGCCTC
721900 T
1 T
721901 GAATATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.26
Consensus pattern (18 bp):
TCCATGCACCGATGCCTC
Found at i:722004 original size:63 final size:63
Alignment explanation
Indices: 721849--722007 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 63
721839 GAATTAATTG
* * *** *
721849 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCCTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCCTCAGAATATTTTC-A
* **
721913 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGC-CTCAGAATA-TTTTCA
721976 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
722008 CTGTGCACCG
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 31 0.37
64 46 0.55
65 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCCTCAGAATATTTTCA
Found at i:723035 original size:63 final size:63
Alignment explanation
Indices: 722981--723117 Score: 154
Period size: 63 Copynumber: 2.2 Consensus size: 63
722971 CACATTGAAT
* * *
722981 GTGCATCGATGTA-CTCTTT-AAA-GAAAACATCGAATGCAATTGGTGCATCGATGCATAGGA
1 GTGCATCGATGCATCCCTTTAAAATGAAAACATCGAATGCAATTGGTGCATCGATGCATAGAA
* * * * * * *
723041 GTGCATCGATGCATCCCTTTAAAATGAAAACATCGAAGGTAATTTGTGTATTGATGCATGGGTA
1 GTGCATCGATGCATCCCTTTAAAATGAAAACATCGAATGCAATTGGTGCATCGATGCAT-AGAA
723105 GTGCATCGATGCA
1 GTGCATCGATGCA
723118 CATGTTAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 12 0.19
61 5 0.08
62 3 0.05
63 29 0.45
64 15 0.23
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCATCCCTTTAAAATGAAAACATCGAATGCAATTGGTGCATCGATGCATAGAA
Found at i:723132 original size:23 final size:20
Alignment explanation
Indices: 723106--723160 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 20
723096 GCATGGGTAG
723106 TGCATCGATGCACATGTTAAGAA
1 TGCATCGATGCAC-TG-T-AGAA
723129 TGCATCGATG--CTGTAGAA
1 TGCATCGATGCACTGTAGAA
723147 TGCATCGATGCACT
1 TGCATCGATGCACT
723161 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 14 0.47
19 1 0.03
20 4 0.13
21 1 0.03
23 10 0.33
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:723936 original size:18 final size:18
Alignment explanation
Indices: 723906--723955 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
723896 GGGTCTACGC
723906 GTCCTTC-GGACATAGTG
1 GTCCTTCGGGACATAGTG
* *
723923 GTCTTTTGGGACATAGTG
1 GTCCTTCGGGACATAGTG
723941 GTCCTTCGGGACATA
1 GTCCTTCGGGACATA
723956 TGTGTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:727084 original size:20 final size:20
Alignment explanation
Indices: 727042--727195 Score: 195
Period size: 20 Copynumber: 7.7 Consensus size: 20
727032 GCAAATATGA
* *
727042 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
727062 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
727082 AAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
727102 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
727122 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
727142 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
727162 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
727183 AAATCGCAACGCG
1 AAATCGCAACGCG
727196 ATTTTTAAAG
Statistics
Matches: 116, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
20 97 0.84
21 19 0.16
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:727609 original size:33 final size:33
Alignment explanation
Indices: 727570--727640 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
727560 TTCACTTAGA
727570 TTTCATTTCGCGTT-ATGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGAT-ATTCTCTCGTTGCGAT
*
727603 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGATATTCTCTCGTTGCGAT
727636 TTTCA
1 TTTCA
727641 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGATATTCTCTCGTTGCGAT
Found at i:727745 original size:20 final size:20
Alignment explanation
Indices: 727720--727794 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
727710 TGCAGAAGAG
727720 TCGCAACGAGAGAAATGAAA
1 TCGCAACGAGAGAAATGAAA
* *
727740 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGA-AA
*
727760 TCTGCAACGAGAAAAATGAAA
1 TC-GCAACGAGAGAAATGAAA
727781 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
727795 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 6 0.13
20 24 0.51
21 11 0.23
22 6 0.13
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAAATGAAA
Found at i:727836 original size:19 final size:19
Alignment explanation
Indices: 727814--727937 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
727804 GAAACCAAAA
*
727814 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
727833 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
727849 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
727866 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
727880 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
727897 TCTCGTTGCGACAGTCATT
1 TCGCGTTGCGATTTTCATT
*
727916 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
727936 TC
1 TC
727938 AACCAAAAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
12 8 0.10
14 12 0.14
16 5 0.06
17 9 0.11
19 33 0.40
20 16 0.19
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:727887 original size:31 final size:32
Alignment explanation
Indices: 727819--727907 Score: 153
Period size: 33 Copynumber: 2.8 Consensus size: 32
727809 CAAAATCGCA
727819 TTGCGATTTTCATTTCGCGTTGCGATTCTATCG
1 TTGCGATTTTCATTTCGCGTTGCGATTC-ATCG
727852 TTGCGATTTTCATTTCGCGTTGCGATTC-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCATCG
*
727883 TTGCGATTTTCATTTCTCGTTGCGA
1 TTGCGATTTTCATTTCGCGTTGCGA
727908 CAGTCATTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 27 0.49
33 28 0.51
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCATCG
Found at i:729766 original size:92 final size:93
Alignment explanation
Indices: 729599--729821 Score: 412
Period size: 92 Copynumber: 2.4 Consensus size: 93
729589 TAGATTGCTT
* *
729599 AGTACATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
729664 TTTGTCTTTGTTTTGTCTTTTGG-TGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
729691 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
729756 TTTGTCTTTGTTTTGTCTTTTGGTTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGG-TTGAA
729785 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
729822 AATACCCTGA
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
92 86 0.68
94 41 0.32
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:729974 original size:33 final size:33
Alignment explanation
Indices: 729915--730038 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
729905 TAGTTTACTT
* * *
729915 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
* *
729949 TCGCAACGCGAAATGAAAATTGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
* *
729982 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
*
730015 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAATCAAAATCGCA
730039 TTGCAATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:730004 original size:19 final size:19
Alignment explanation
Indices: 729980--730038 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
729970 GCAACGACAG
729980 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
729999 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
730013 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
730032 AATCGCA
1 AATCGCA
730039 TTGCAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:730056 original size:19 final size:19
Alignment explanation
Indices: 730034--730205 Score: 148
Period size: 19 Copynumber: 9.6 Consensus size: 19
730024 GAAACCAAAA
* *
730034 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
730053 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
730067 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
730086 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
730102 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
730119 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
730138 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
730157 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
* *
730176 TCGCGTTGCGATTTTAAGT
1 TCGCGTTGCGATTTTCATT
*
730195 TCGTGTTGCGA
1 TCGCGTTGCGA
730206 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 8 0.06
19 91 0.73
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:730075 original size:14 final size:14
Alignment explanation
Indices: 730056--730112 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
730046 TTTCATTTCG
730056 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
730070 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
730087 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
730103 CGTTGCGATT
1 CGTTGCGATT
730113 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:730086 original size:33 final size:33
Alignment explanation
Indices: 730039--730131 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
730029 CAAAATCGCA
*
730039 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
730072 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
730105 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
730132 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:732174 original size:20 final size:18
Alignment explanation
Indices: 732133--732391 Score: 187
Period size: 19 Copynumber: 15.4 Consensus size: 18
732123 GATTCGCTCG
732133 TGCGATTTTCATTCGCAT
1 TGCGATTTTCATTCGCAT
*
732151 TGCGATTTTCATTTCCGTAT
1 TGCGATTTTCA-TT-CGCAT
*
732171 TGCGATTCTC--TCG--T
1 TGCGATTTTCATTCGCAT
732185 T-CGATTTTCATTCGCA-
1 TGCGATTTTCATTCGCAT
732201 TGCGATTTTCATTCG-AT
1 TGCGATTTTCATTCGCAT
732218 TGC-A---T--TTCG--T
1 TGCGATTTTCATTCGCAT
732228 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCA-TTCGCAT
*
732247 TGCGATTCTC--TCG--T
1 TGCGATTTTCATTCGCAT
732261 T-CGATTTTCATTTCGCAT
1 TGCGATTTTCA-TTCGCAT
732279 TGCGATTTTCATTTCCGCAT
1 TGCGATTTTCA-TT-CGCAT
*
732299 TGCGATTCTC--TCG--T
1 TGCGATTTTCATTCGCAT
732313 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCA-TTCGCAT
732332 TGCGATTTTCATTTCCGCAT
1 TGCGATTTTCA-TT-CGCAT
732352 TGCGATTTTCA-T-G--T
1 TGCGATTTTCATTCGCAT
*
732366 TGGGATTTTCATTTCGCAT
1 TGCGATTTTCA-TTCGCAT
732385 TGCGATT
1 TGCGATT
732392 CTCTCGTGTT
Statistics
Matches: 197, Mismatches: 9, Indels: 69
0.72 0.03 0.25
Matches are distributed among these distances:
10 4 0.02
11 5 0.03
13 15 0.08
14 26 0.13
15 3 0.02
16 15 0.08
17 26 0.13
18 14 0.07
19 46 0.23
20 43 0.22
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (18 bp):
TGCGATTTTCATTCGCAT
Found at i:732184 original size:51 final size:48
Alignment explanation
Indices: 732099--732253 Score: 189
Period size: 51 Copynumber: 3.2 Consensus size: 48
732089 ATGCGAATGA
*
732099 TCGCATGCGATTTTCATTCC-A-TGCGATTCGCTCGTGCGATTTTCAT
1 TCGCATGCGATTTTCATTCCGATTGCGATTCTCTCGTGCGATTTTCAT
*
732145 TCGCATTGCGATTTTCATTTCCGTATTGCGATTCTCTCGTTCGATTTTCAT
1 TCGCA-TGCGATTTTCA-TTCCG-ATTGCGATTCTCTCGTGCGATTTTCAT
732196 TCGCATGCGATTTTCATT-CGATTGC-A-T-T-TCGTTGCGATTTTCATT
1 TCGCATGCGATTTTCATTCCGATTGCGATTCTCTCG-TGCGATTTTCA-T
732241 TCGCATTGCGATT
1 TCGCA-TGCGATT
732254 CTCTCGTTCG
Statistics
Matches: 98, Mismatches: 3, Indels: 16
0.84 0.03 0.14
Matches are distributed among these distances:
43 3 0.03
44 11 0.11
45 7 0.07
46 13 0.13
47 16 0.16
48 6 0.06
49 2 0.02
50 12 0.12
51 28 0.29
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (48 bp):
TCGCATGCGATTTTCATTCCGATTGCGATTCTCTCGTGCGATTTTCAT
Found at i:732231 original size:27 final size:30
Alignment explanation
Indices: 732201--732286 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 30
732191 TTCATTCGCA
732201 TGCGATTTTCA-TTCG-ATTGC-ATTTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTCGT
732228 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGA-T-T-TCGT
732261 T-CGATTTTCATTTCGCATTGCGATTT
1 TGCGATTTTCATTTCGCATTGCGATTT
732287 TCATTTCCGC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
27 11 0.21
28 4 0.08
29 6 0.11
30 2 0.04
31 2 0.04
32 23 0.43
33 5 0.09
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (30 bp):
TGCGATTTTCATTTCGCATTGCGATTTCGT
Found at i:732261 original size:33 final size:33
Alignment explanation
Indices: 732224--732398 Score: 144
Period size: 33 Copynumber: 5.1 Consensus size: 33
732214 CGATTGCATT
732224 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
*
732257 TCGTT-CGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TC
* * *
732292 TCCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC
1 T-CG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTC
* * *
732328 GCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 TCGTTGCGATTTTCATTT-CGCATTGCGATTCTC
*
732362 AT-GTTGGGATTTTCATTTCGCATTGCGATTCTC
1 -TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
732395 TCGT
1 TCGT
732399 GTTGTAATTT
Statistics
Matches: 112, Mismatches: 14, Indels: 32
0.71 0.09 0.20
Matches are distributed among these distances:
31 4 0.04
32 29 0.26
33 33 0.29
34 19 0.17
35 3 0.03
36 3 0.03
38 4 0.04
39 5 0.04
40 3 0.03
41 9 0.08
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
Found at i:732373 original size:53 final size:51
Alignment explanation
Indices: 732186--732391 Score: 275
Period size: 53 Copynumber: 4.1 Consensus size: 51
732176 TTCTCTCGTT
* *
732186 CGATTTTCA-TTCGCA-TGCGATT-T-TCATTCGA-TTGCATTTCG--TTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTCGATTTTCATTTCGCATTG
732230 CGATTTTCATTTCGCATTGCGATTCTCTCGTTCGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTCGATTTTCATTTCGCATTG
732281 CGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 CGATTTTCATTT-CGCATTGCGATTCTCTCGTT-CGATTTTCATTTCGCATTG
* *
732334 CGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTG
1 CGATTTTCATTT-CGCATTGCGATTCTC-TCGTT-CGATTTTCATTTCGCATTG
732387 CGATT
1 CGATT
732392 CTCTCGTGTT
Statistics
Matches: 148, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
44 9 0.06
45 6 0.04
46 7 0.05
47 1 0.01
48 7 0.05
49 9 0.06
51 15 0.10
52 20 0.14
53 73 0.49
54 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (51 bp):
CGATTTTCATTTCGCATTGCGATTCTCTCGTTCGATTTTCATTTCGCATTG
Found at i:734671 original size:12 final size:12
Alignment explanation
Indices: 734654--734678 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
734644 TCTTCGGGGA
734654 CTTTTTCTTCTT
1 CTTTTTCTTCTT
734666 CTTTTTCTTCTT
1 CTTTTTCTTCTT
734678 C
1 C
734679 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:735683 original size:20 final size:20
Alignment explanation
Indices: 735591--735741 Score: 148
Period size: 20 Copynumber: 7.5 Consensus size: 20
735581 AAATTTCAGT
* * *
735591 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTATC
*
735611 GTTACGATTTACGGATTATC
1 GTTGCGATTTACGGATTATC
* *
735631 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTATC
735651 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTATC
*
735671 GTTGCGATTTACGGA-TACGC
1 GTTGCGATTTACGGATTA-TC
*
735691 GTTGCGATATACGGA-TA-C
1 GTTGCGATTTACGGATTATC
* *
735709 GCATTGCGGTTTACGGA-TACGC
1 G--TTGCGATTTACGGATTA-TC
735731 GTTGCGATTTA
1 GTTGCGATTTA
735742 TGTGTTCGCG
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 106 0.95
22 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATTATC
Found at i:735694 original size:60 final size:60
Alignment explanation
Indices: 735591--735761 Score: 168
Period size: 60 Copynumber: 2.9 Consensus size: 60
735581 AAATTTCAGT
* * * * * * *
735591 GTTGTGATTTACAGATTCTCGTTACGATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTATCGTTGCGATTTACGGA-TACGCGTTGCGATTTACAGATACGC
* *
735651 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATACGC
* * * * *
735711 ATTGCGGTTTACGGA-TACGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTA
1 GTTGCGATTTACGGATTA-TCGTTGCGATTTACG-GATACGCGTTGCGATTTA
735762 TGTGTTCGCG
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 4 0.04
60 88 0.95
61 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATACGC
Found at i:735751 original size:20 final size:20
Alignment explanation
Indices: 735728--735799 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
735718 TTTACGGATA
735728 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATGTGTT
735748 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATGTGTT
* *
735768 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-GTGTT
735788 CGCGTTGCGATT
1 CGCGTTGCGATT
735800 CTGAAAAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.11, C:0.18, G:0.28, T:0.43
Consensus pattern (20 bp):
CGCGTTGCGATTTATGTGTT
Found at i:735756 original size:40 final size:40
Alignment explanation
Indices: 735591--735799 Score: 188
Period size: 40 Copynumber: 5.2 Consensus size: 40
735581 AAATTTCAGT
* * * * * **
735591 GTTGTGATTTACAGATTCTCGTTACGATTTACGGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTCGC
* * * **
735631 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTCGC
* *
735671 GTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTCGC
* * *
735711 ATTGCGGTTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACG-GATTCGC
* * * **
735751 GTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGC
1 GTTGCGATTTACG-GATACGCGTTGCGATTTACGGATTCGC
735791 GTTGCGATT
1 GTTGCGATT
735800 CTGAAAAATC
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 142 0.99
41 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTCGC
Found at i:735776 original size:60 final size:60
Alignment explanation
Indices: 735591--735799 Score: 156
Period size: 60 Copynumber: 3.5 Consensus size: 60
735581 AAATTTCAGT
* * * * * * * * * *
735591 GTTGTGATTTACAGATTCTCGTTACGATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATATACGGATACGC
*
735651 GTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
* * * * * * *
735711 ATTGCGGTTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACG-GATACGCGTTGCGATATACG-GATACGC
* ** *
735771 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACGGATACGCGTTGCGATT
735800 CTGAAAAATC
Statistics
Matches: 121, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
59 4 0.03
60 114 0.94
61 3 0.02
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (60 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
Found at i:735860 original size:42 final size:43
Alignment explanation
Indices: 735767--735865 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
735757 ATTTATGTGT
* *
735767 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAAAA
** * *
735808 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTCAAAAA
*
735850 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
735866 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 8 0.17
42 35 0.76
43 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAAAA
Found at i:739708 original size:121 final size:119
Alignment explanation
Indices: 739506--739724 Score: 298
Period size: 121 Copynumber: 1.8 Consensus size: 119
739496 ATATTAATAT
* * * * *
739506 AAATAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGTTTTAAGACAGCTCTT
1 AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCATCCAGGTATTTTAAGACAGCTCCT
*
739571 TTCTTAGATATTAAAAAATAAATAATTAATTAAAAATAATTAATATATAATTTATA
66 TTCTTAGATATT-AAAAATAAATAAAT-ATTAAAAATAATTAATATATAATTTATA
* * * *
739627 AAATAGGATATTTATTTATTTAAAAATATCAGAAAATAGACATCCAGTTATTTTAAGACTGC-CC
1 AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGAG-CATCCAGGTATTTTAAGACAGCTCC
739691 TTTCTTA-ATATTGAAAAATAAATAAATATTAAAA
65 TTTCTTAGATATT-AAAAATAAATAAATATTAAAA
739725 CAAGATTAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
119 7 0.08
120 18 0.21
121 44 0.51
122 17 0.20
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (119 bp):
AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCATCCAGGTATTTTAAGACAGCTCCT
TTCTTAGATATTAAAAATAAATAAATATTAAAAATAATTAATATATAATTTATA
Found at i:739755 original size:19 final size:19
Alignment explanation
Indices: 739704--739758 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
739694 CTTAATATTG
*
739704 AAAAATAAATAAAT-A-TT
1 AAAAATAATTAAATAAGTT
739721 AAAACA-AGATTAAAATAAGTT
1 AAAA-ATA-ATT-AAATAAGTT
739742 AAAAATAATTAAATAAG
1 AAAAATAATTAAATAAG
739759 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.16
18 3 0.10
19 11 0.35
20 5 0.16
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAATAATTAAATAAGTT
Found at i:741121 original size:3 final size:3
Alignment explanation
Indices: 741113--741158 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
741103 TAATATTTAT
741113 TAA TAA TAA -AA TAA TAA TAA TAA TAA T-A TAAA TAA T-A TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TAA
741157 TA
1 TA
741159 TTCAAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.16
3 27 0.71
4 5 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:741968 original size:54 final size:54
Alignment explanation
Indices: 741874--742006 Score: 150
Period size: 54 Copynumber: 2.6 Consensus size: 54
741864 AGAATAGCAG
* * * * * *
741874 GTTCGTAAAACACTTGACAGCGCATTCATCATTTCCTGTGGCTTCTGTTCAGAT
1 GTTCGTAAAACACTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
* * *
741928 GTTCGTAAAACATTTGACAACACATTCTTCATCTCATGTGGTTTCAGCTCAGA-
1 GTTCGTAAAACACTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
741981 --T-GTAAAACACTTGACAACA-ATTCATC
1 GTTCGTAAAACACTTGACAACACATTCATC
742007 CTTTTCTGTG
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 6 0.09
50 17 0.25
51 1 0.01
54 44 0.65
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (54 bp):
GTTCGTAAAACACTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
Found at i:742022 original size:39 final size:40
Alignment explanation
Indices: 741979--742057 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
741969 TTTCAGCTCA
741979 GATGTAAAACACTTGACAACA-ATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
742018 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
742058 CTTCTGCTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 21 0.54
40 18 0.46
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
Found at i:742088 original size:54 final size:54
Alignment explanation
Indices: 742021--742124 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
742011 TCTGTGGGAT
* *
742021 GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTC
1 GTAAAACACTTGACAACAAATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTC
* * *
742075 GTAAAGCATTTGACAATAAATTCATCATTTTCTGTGGCTTCTGCTCAGAT
1 GTAAAACACTTGACAACAAATTCATCATTTTCTGTGGCTTCTGCTCAGAT
742125 TTCTCAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (54 bp):
GTAAAACACTTGACAACAAATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTC
Found at i:744470 original size:114 final size:114
Alignment explanation
Indices: 744270--744495 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 114
744260 GATCATGCAG
* * * * ** *
744270 TTCATCTTTCAATTTCAATGATTGGTTCTGGGGTTCCTACTGAACCAGATCAGATAACTCAAATA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
744335 ACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTATGAGAAGA
66 ACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTACGAGAAGA
* *
744384 TTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
744449 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTACGAGAA
66 ACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTACGAGAA
744496 CATGGCACTT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTTCTTATTTCTACTACGAGAAGA
Found at i:746625 original size:7 final size:7
Alignment explanation
Indices: 746613--746737 Score: 87
Period size: 7 Copynumber: 16.7 Consensus size: 7
746603 TCAATTTCTC
746613 TCTTTTT
1 TCTTTTT
746620 TCTTTTT
1 TCTTTTT
746627 TCTTTTT
1 TCTTTTT
*
746634 CCTTTTT
1 TCTTTTT
*
746641 CCTTTTT
1 TCTTTTT
746648 T-TTTCTT
1 TCTTT-TT
746655 TCTTTTT
1 TCTTTTT
746662 T-TTCTTT
1 TCTT-TTT
746669 CTCATTTTT
1 -TC-TTTTT
746678 TCTTTTT
1 TCTTTTT
746685 CATCTTTTT
1 --TCTTTTT
746694 T-TTTTCT
1 TCTTTT-T
746701 T-TTTTT
1 TCTTTTT
*
746707 CCTTTCTT
1 TCTTT-TT
746715 TGCTGAATTTT
1 T-CT---TTTT
746726 TCTTTTT
1 TCTTTTT
746733 TCTTT
1 TCTTT
746738 CTTTGATGGA
Statistics
Matches: 99, Mismatches: 4, Indels: 30
0.74 0.03 0.23
Matches are distributed among these distances:
6 10 0.10
7 60 0.61
8 8 0.08
9 12 0.12
10 4 0.04
11 3 0.03
12 2 0.02
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.78
Consensus pattern (7 bp):
TCTTTTT
Found at i:746712 original size:13 final size:13
Alignment explanation
Indices: 746636--746715 Score: 60
Period size: 13 Copynumber: 6.1 Consensus size: 13
746626 TTCTTTTTCC
746636 TTTTTCC-TT-TT
1 TTTTTCCTTTCTT
746647 TTTTT-CTTTCTT
1 TTTTTCCTTTCTT
*
746659 TTTTTTCTTTCTCAT
1 TTTTTCCTTTCT--T
*
746674 TTTTTCTTTTTCATCT
1 TTTTTC-CTTTC-T-T
*
746690 TTTTT-TTTTCTT
1 TTTTTCCTTTCTT
746702 TTTTTCCTTTCTT
1 TTTTTCCTTTCTT
746715 T
1 T
746716 GCTGAATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
10 1 0.02
11 7 0.12
12 13 0.23
13 14 0.25
14 5 0.09
15 6 0.11
16 10 0.18
17 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCCTTTCTT
Found at i:750396 original size:14 final size:15
Alignment explanation
Indices: 750362--750400 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
750352 CATAAAAATA
*
750362 CAAATGCAAAGATGC
1 CAAATGTAAAGATGC
*
750377 CAAATGTAAATATG-
1 CAAATGTAAAGATGC
750391 CAAATGTAAA
1 CAAATGTAAA
750401 AATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAATGTAAAGATGC
Found at i:750409 original size:14 final size:14
Alignment explanation
Indices: 750354--750409 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
750344 AAAGCAAACA
*
750354 TAAAAATACAAATG
1 TAAAAATGCAAATG
* *
750368 CAAAGATGCCAAATG
1 TAAAAATG-CAAATG
*
750383 TAAATATGCAAATG
1 TAAAAATGCAAATG
*
750397 TAAAAATGTAAAT
1 TAAAAATGCAAAT
750410 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.23
Consensus pattern (14 bp):
TAAAAATGCAAATG
Found at i:752038 original size:20 final size:19
Alignment explanation
Indices: 751993--752057 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
751983 TTAATACTTG
*
751993 AAAAATAAAATAAAACATTA-
1 AAAAAT-AAAT-AAATATTAT
752013 ATAAAATAATATAAATATTAT
1 A-AAAATAA-ATAAATATTAT
752034 AAAAAT-AATAAATATATAT
1 AAAAATAAATAAATAT-TAT
752053 AAAAA
1 AAAAA
752058 ATTTGGAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 8 0.20
19 9 0.22
20 15 0.38
21 8 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATAAATAAATATTAT
Found at i:752058 original size:20 final size:18
Alignment explanation
Indices: 751999--752059 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
751989 CTTGAAAAAT
*
751999 AAAATA-AAACATTAATAA
1 AAAATATAAATATT-ATAA
752017 AATAATATAAATATTAT-A
1 AA-AATATAAATATTATAA
752035 AAAATAATAAATATATATAA
1 AAAAT-ATAAATAT-TATAA
752055 AAAAT
1 AAAAT
752060 TTGGAAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
17 3 0.08
18 13 0.35
19 9 0.24
20 12 0.32
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATAAATATTATAA
Found at i:754213 original size:3 final size:3
Alignment explanation
Indices: 754207--754255 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
754197 TAATATTTAT
754207 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
754251 TAA TA
1 TAA TA
754256 TTCAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:758223 original size:13 final size:13
Alignment explanation
Indices: 758205--758232 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
758195 ATCCCCCAGC
758205 ACCAAACAAATTA
1 ACCAAACAAATTA
758218 ACCAAACAAATTA
1 ACCAAACAAATTA
758231 AC
1 AC
758233 TCTACTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.25, G:0.00, T:0.14
Consensus pattern (13 bp):
ACCAAACAAATTA
Found at i:760749 original size:7 final size:7
Alignment explanation
Indices: 760737--760777 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
760727 TGAGTCAGTA
760737 TGGACAC
1 TGGACAC
760744 TGGACAC
1 TGGACAC
760751 TGGACAC
1 TGGACAC
760758 TGGACAC
1 TGGACAC
760765 TGGACAC
1 TGGACAC
760772 TGGACA
1 TGGACA
760778 GTCTTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.15
Consensus pattern (7 bp):
TGGACAC
Found at i:761861 original size:38 final size:37
Alignment explanation
Indices: 761723--761973 Score: 236
Period size: 38 Copynumber: 6.6 Consensus size: 37
761713 GCAAACGATC
*
761723 TTTGAAAATACGTATATAATATATAGTTTTTAAAACATT
1 TTTGAAAATA--TATATAATATATAATTTTTAAAACATT
* * * *
761762 TTTGAAAA-CTATATAATATACAGTTTTTAAAAAAACGTT
1 TTTGAAAATATATATAATATATAATTTTT---AAAACATT
* *
761801 TTAGAAAATATAGATAATATATAATTTTTAAAATCATT
1 TTTGAAAATATATATAATATATAATTTTTAAAA-CATT
* *
761839 TTTG-AAATCTTATATAATATATAATTTTGAAAACATT
1 TTTGAAAAT-ATATATAATATATAATTTTTAAAACATT
*
761876 TTTGAAAATATATATAATATATAACTTTTAAAACATT
1 TTTGAAAATATATATAATATATAATTTTTAAAACATT
** * * * * *
761913 TTAAAAAATACATATATTATATAGTTTTTTGAAACGTT
1 TTTGAAAATATATATAATATATA-ATTTTTAAAACATT
* **
761951 TTTAAAAATACGTATAATATATA
1 TTTGAAAATATATATAATATATA
761974 GTTTAAAAAA
Statistics
Matches: 177, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
36 18 0.10
37 60 0.34
38 61 0.34
39 22 0.12
40 16 0.09
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (37 bp):
TTTGAAAATATATATAATATATAATTTTTAAAACATT
Found at i:761890 original size:37 final size:37
Alignment explanation
Indices: 761693--761973 Score: 212
Period size: 38 Copynumber: 7.4 Consensus size: 37
761683 TTTTATATAT
* * * *
761693 ATATATATATTATAT-AGTTTGCAAACGATCTTTGAAA
1 ATATATATAATATATAATTTTGAAAAC-ATTTTTGAAA
* *
761730 ATACGTATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATA--TATATAATATATAATTTTGAAAACATTTTTGAAA
* * * * * *
761769 A-CTATATAATATACAGTTTTTAAAAAAACGTTTTAGAAA
1 ATATATATAATATATA-ATTTT--GAAAACATTTTTGAAA
* *
761808 ATATAGATAATATATAATTTTTAAAATCATTTTTG-AA
1 ATATATATAATATATAATTTTGAAAA-CATTTTTGAAA
*
761845 ATCTTATATAATATATAATTTTGAAAACATTTTTGAAA
1 AT-ATATATAATATATAATTTTGAAAACATTTTTGAAA
**
761883 ATATATATAATATATAACTTTT-AAAACATTTTAAAAA
1 ATATATATAATATATAA-TTTTGAAAACATTTTTGAAA
* * * * *
761920 ATACATATATTATATAGTTTTTTG-AAACGTTTTTAAAA
1 ATATATATAATATATA--ATTTTGAAAACATTTTTGAAA
**
761958 ATACGTATAATATATA
1 ATATATATAATATATA
761974 GTTTAAAAAA
Statistics
Matches: 198, Mismatches: 32, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
36 12 0.06
37 64 0.32
38 65 0.33
39 39 0.20
40 18 0.09
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (37 bp):
ATATATATAATATATAATTTTGAAAACATTTTTGAAA
Found at i:761953 original size:75 final size:75
Alignment explanation
Indices: 761697--761973 Score: 262
Period size: 75 Copynumber: 3.7 Consensus size: 75
761687 ATATATATAT
* * *
761697 ATATATTATATAG---TTTGCAAACGATCTTTGAAAATACGTATATAATATATAGTTTTTAAAAC
1 ATATATTATATAGTTTTTTGAAAACG-TTTTTGAAAATA--TATATAATATATAATTTTTAAAAC
761759 ATTTTTGAAA-AC
63 ATTTTTGAAATAC
* * ** * *
761771 TATATAATATACAGTTTTTAAAAAAACGTTTTAGAAAATATAGATAATATATAATTTTTAAAATC
1 -ATATATTATATAGTTTTT-TGAAAACGTTTTTGAAAATATATATAATATATAATTTTTAAAA-C
761836 ATTTTTGAAAT-C
63 ATTTTTGAAATAC
* * * * *
761848 TTATATAATATA-TAATTTTGAAAACATTTTTGAAAATATATATAATATATAACTTTTAAAACAT
1 ATATATTATATAGT-TTTTTGAAAACGTTTTTGAAAATATATATAATATATAATTTTTAAAACAT
**
761912 TTTAAAAAATAC
65 TTT-TGAAATAC
* **
761924 ATATATTATATAGTTTTTTG-AAACGTTTTTAAAAATACGTATAATATATA
1 ATATATTATATAGTTTTTTGAAAACGTTTTTGAAAATATATATAATATATA
761974 GTTTAAAAAA
Statistics
Matches: 163, Mismatches: 29, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
74 6 0.04
75 79 0.48
76 48 0.29
77 13 0.08
78 12 0.07
79 5 0.03
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (75 bp):
ATATATTATATAGTTTTTTGAAAACGTTTTTGAAAATATATATAATATATAATTTTTAAAACATT
TTTGAAATAC
Found at i:761977 original size:38 final size:37
Alignment explanation
Indices: 761727--761973 Score: 153
Period size: 37 Copynumber: 6.5 Consensus size: 37
761717 ACGATCTTTG
* *
761727 AAAATACGTATATAATATATAGTTTTTAAAACATTTTT-
1 AAAATAC--ATATAATATATATTTTTTGAAACATTTTTA
* * ** * *
761765 GAAA-ACTATATAATATACAGTTTTTAAAAAAACGTTTTA
1 AAAATAC-ATATAATATATA-TTTTTTGAAACA-TTTTTA
* * * *
761804 GAAAATATAGATAATATATAATTTTTAAAATCATTTTT-
1 -AAAATACATATAATATATATTTTTTGAAA-CATTTTTA
* * *
761842 GAAAT-CTTATATAATATATA-ATTTTGAAAACATTTTTG
1 AAAATAC--ATATAATATATATTTTTTG-AAACATTTTTA
* ** * *
761880 AAAATATATATAATATATAACTTTTAAAACATTTTAA
1 AAAATACATATAATATATATTTTTTGAAACATTTTTA
* *
761917 AAAATACATATATTATATAGTTTTTTGAAACGTTTTTA
1 AAAATACATATAATATATA-TTTTTTGAAACATTTTTA
*
761955 AAAATACGTATAATATATA
1 AAAATACATATAATATATA
761974 GTTTAAAAAA
Statistics
Matches: 162, Mismatches: 34, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
36 12 0.07
37 64 0.40
38 59 0.36
39 12 0.07
40 14 0.09
41 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (37 bp):
AAAATACATATAATATATATTTTTTGAAACATTTTTA
Found at i:762040 original size:15 final size:14
Alignment explanation
Indices: 762020--762049 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
762010 CTTTTGAACA
762020 TTTTTTATTATTATT
1 TTTTTTATTA-TATT
762035 TTTTTTATTATATT
1 TTTTTTATTATATT
762049 T
1 T
762050 CTAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTATTATATT
Found at i:762386 original size:12 final size:12
Alignment explanation
Indices: 762369--762398 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
762359 GACGAAGGGA
762369 GAGGTATCATCG
1 GAGGTATCATCG
762381 GAGGTATCATCG
1 GAGGTATCATCG
762393 GAGGTA
1 GAGGTA
762399 CACAAAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (12 bp):
GAGGTATCATCG
Found at i:765369 original size:19 final size:19
Alignment explanation
Indices: 765345--765390 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
765335 ATTTAGACAT
765345 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
765364 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
765383 TTTGCATT
1 TTTGCATT
765391 CACATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:768896 original size:81 final size:81
Alignment explanation
Indices: 768712--768939 Score: 226
Period size: 81 Copynumber: 2.8 Consensus size: 81
768702 TGCAGCTTAG
* **
768712 CTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
1 CTCAAAGCCAGAAGGGCTATCTGCCA-CAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGGCA
* *
768777 CATCATTTGCAGAATAG
65 CATCATTTACAGAATAA
* * * * * * *
768794 CT-TAAGTCGAGAAGGGCTATCTGCCA-AAGACCCCCGAGTTCGATTTCGTTCAGCTTCGAGGGC
1 CTCAAAG-CCAGAAGGGCTATCTGCCACAAGACCCCCGAGTTCGACTACGCTCAGC-TCCAAGGC
*
768857 ACATCATTTACAGCATAA
64 ACATCATTTACAGAATAA
* * * **
768875 CTCAAAGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAAGCCAGAAGGGCTATC--TG-CCACAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGG
768940 TCAAGAAGGG
Statistics
Matches: 116, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
80 23 0.20
81 37 0.32
82 23 0.20
83 2 0.02
84 8 0.07
85 23 0.20
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (81 bp):
CTCAAAGCCAGAAGGGCTATCTGCCACAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGGCAC
ATCATTTACAGAATAA
Found at i:769056 original size:138 final size:140
Alignment explanation
Indices: 768803--769077 Score: 396
Period size: 138 Copynumber: 2.0 Consensus size: 140
768793 GCTTAAGTCG
* **
768803 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTTCGTTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* **
768868 AGCATAACTCAAAGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
66 AGCATAACTCAAAGCGAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
768933 TCCAAGGTCA
131 TCCAAGGTCA
** * *
768943 AGAAGGGCTATCTGCCAAAGACCTTCGAG-TCGATTACACTCATCTTCGA-GGCACATCATTTGC
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* *
769006 AGCATAACT-TAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTACGCTCA
66 AGCATAACTCAAAG-CGAGAAGGGTTATCTG-CAACCAAAAGACCTTCGAGTTCGACTACGCTCA
769069 GCTCCAAGG
129 GCTCCAAGG
769078 CACATCATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
137 3 0.02
138 72 0.60
139 19 0.16
140 27 0.22
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (140 bp):
AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
AGCATAACTCAAAGCGAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGTCA
Found at i:769091 original size:84 final size:84
Alignment explanation
Indices: 768957--769562 Score: 625
Period size: 84 Copynumber: 7.3 Consensus size: 84
768947 GGGCTATCTG
* * * *
768957 CCAAAGACCTTCGAG-TCGATTACACTCATCTTCGAGGCACATCATTTGCAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
769021 GAGAAGGGTTATCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* * * *
769040 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
769105 AAGAAGGGCTATCTG----
66 GAGAAGGGTTATCTGCCAA
* * *
769120 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
769185 CGAGAAGGGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * * * * *
769205 CCAATGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* ***
769270 TAGAAGGGTTATCT-ATGA
66 GAGAAGGGTTATCTGCCAA
* **
769288 CCAAAAGACCTTTGAGTTCGACTACGTTCAGCT-CAACGGCACATCATTTGCAGCATAGA-TTAA
1 CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATA-ACTTAA
*
769351 GTCGAGAAGGGCTATCTG----
63 GTCGAGAAGGGTTATCTGCCAA
** * * * * * * *
769369 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGTAGCACAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
* * *
769434 CTAGAAGGGTTGTCTGCTAA
65 CGAGAAGGGTTATCTGCCAA
* * * *
769454 CAAAAGACCTTTGAGTTCGACTACAATCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGT
*
769518 CGAGAAGGGCTATCTG----
65 CGAGAAGGGTTATCTGCCAA
* *
769534 CCAAAGACCCTCGAGTTCGATTACACTCA
1 CCAAAGACCTTCGAGTTCGACTACACTCA
769563 ACTTCGAGGT
Statistics
Matches: 430, Mismatches: 75, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
80 75 0.17
81 82 0.19
82 1 0.00
83 21 0.05
84 197 0.46
85 54 0.13
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
GAGAAGGGTTATCTGCCAA
Found at i:769223 original size:165 final size:161
Alignment explanation
Indices: 768930--769611 Score: 728
Period size: 165 Copynumber: 4.1 Consensus size: 161
768920 GACTACGCTC
* * *
768930 AGCTCCAAGGTCAAGAAGGGCTATCTGCC-AAAGACCTTCGAG-TCGATTACACTCATCTTCGA-
1 AGCT-CAA-GTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGACTACACTCAGC-TCAAC
* * *
768992 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTT
63 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTT
* * *
769057 CGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAAT
124 CGACTACACTCAGCTCCAAGGCATATCATTTACAGAAT
* * * *
769095 AGCTTAAGTCAAGAAGGGCTATCTGCC-AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGG
1 AGCTCAAGTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGACTACACTCAGC-TCAACGG
* *
769159 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAATGACCTTCGAGTTCG
65 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A--AA-GACCCTCGAGTTCG
* *
769224 ACTACGCTCAGCTCCAAGGCATATCATTTACAGCAT
126 ACTACACTCAGCTCCAAGGCATATCATTTACAGAAT
* * * * * **
769260 AACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTTGAGTTCGACTACGTTCAGCTCAAC
1 AGCTCAAGTCAAGAAGGGCTATC--TG-CCAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAC
*
769325 GGCACATCATTTGCAGCATAGA-TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGA
63 GGCACATCATTTGCAGCATA-ACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGA
* * * ** * *
769389 TTACACTCAGCTTCGAGGGCATATCATTTGTAGCAC
127 CTACACTCAGC-TCCAAGGCATATCATTTACAGAAT
* * * * * *
769425 AGCTTAAGTCTAGAAGGGTTGTCTGCTAACAAAAGACCTTTGAGTTCGACTACAATCAGCTCAAC
1 AGCTCAAGTCAAGAAGGGCTATCTGC---CAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAC
* *
769490 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGAT
63 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGAC
* * *
769555 TACACTCAACTTCGAGGTCATATCATTTACA-ACAT
128 TACACTCAGCTCCAAGG-CATATCATTTACAGA-AT
*
769590 AGCTCAAGGCAAGAAGGGCTAT
1 AGCTCAAGTCAAGAAGGGCTAT
769612 TTGTCGATAA
Statistics
Matches: 450, Mismatches: 49, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
161 2 0.00
162 2 0.00
163 35 0.08
164 48 0.11
165 286 0.64
167 3 0.01
168 48 0.11
169 26 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (161 bp):
AGCTCAAGTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGACTACACTCAGCTCAACGGC
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
ACTCAGCTCCAAGGCATATCATTTACAGAAT
Found at i:769442 original size:249 final size:248
Alignment explanation
Indices: 768957--769533 Score: 809
Period size: 249 Copynumber: 2.3 Consensus size: 248
768947 GGGCTATCTG
* * *
768957 CCAAAGACCTTCGAG-TCGATTACACTCATCTTCGAGGCACATCATTTGCAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCAAGGCACATCATTTGCAGCATAACTTAAGTC
*
769021 GAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
65 GAGAAGGGTTATCTGACAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* **
769086 TTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGC
130 TTGCAGAATAGATTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGC
*
769151 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
195 TTCGAGGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAA
* * * * * *
769205 CCAATGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCT-CAAGGCACATCATTTGCAGCATAACTTAAGTC
* ** *
769270 TAGAAGGGTTATCT-ATGACCAAAAGACCTTTGAGTTCGACTACGTTCAGCT-CAACGGCACATC
65 GAGAAGGGTTATCTGACAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
* *
769333 ATTTGCAGCATAGATTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
128 ATTTGCAGAATAGATTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * * *
769398 GCTTCGAGGGCATATCATTTGTAGCACAGCTTAAGTCTAGAAGGGTTGTCTGCTAA
193 GCTTCGAGGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAA
* * * *
769454 CAAAAGACCTTTGAGTTCGACTACAATCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAA-GGCACATCATTTGCAGCATAACTTAAGTC
*
769519 GAGAAGGGCTATCTG
65 GAGAAGGGTTATCTG
769534 CCAAAGACCC
Statistics
Matches: 285, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
248 24 0.08
249 261 0.92
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (248 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAGGCACATCATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGACAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGAATAGATTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAA
Found at i:770220 original size:38 final size:36
Alignment explanation
Indices: 770169--770260 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 36
770159 TTTATACATA
* * *
770169 TATATATTATATAGTTTGCAAACGATCTTTGAAATAC
1 TATATAATATATAGTTTGAAAAC-ATCTTTGAAAAAC
* *
770206 GTATATAATATATAGTTTTTAAAACATTTTTGAAAAAC
1 -TATATAATATATAG-TTTGAAAACATCTTTGAAAAAC
*
770244 TATATAATATACAGTTT
1 TATATAATATATAGTTT
770261 TTAAAAAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 3 0.06
37 13 0.28
38 24 0.51
39 7 0.15
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (36 bp):
TATATAATATATAGTTTGAAAACATCTTTGAAAAAC
Found at i:770260 original size:37 final size:38
Alignment explanation
Indices: 770196--770444 Score: 217
Period size: 37 Copynumber: 6.6 Consensus size: 38
770186 GCAAACGATC
*
770196 TTTG-AAATACGTATATAATATATAGTTTTTAAAACATT
1 TTTGAAAATAC-TATATAATATATAATTTTTAAAACATT
* * *
770234 TTTGAAAA-ACTATATAATATACAGTTTTTAAAAAAACGTT
1 TTTGAAAATACTATATAATATATAATTTTT---AAAACATT
* *
770274 TTAGAAAATA-TAGATAATATATAATTTTTAAAATCATT
1 TTTGAAAATACTATATAATATATAATTTTTAAAA-CATT
* ***
770312 TTTG-AAAT-CTTATATAATATATAATTTTGAAATTTTT
1 TTTGAAAATAC-TATATAATATATAATTTTTAAAACATT
*
770349 TTTGAAAATA-TATATAATATATAACTTTTAAAACATT
1 TTTGAAAATACTATATAATATATAATTTTTAAAACATT
** * * * *
770386 TTAAAAAATAC-ATATATTATATAGTTTTTTGAAACGTT
1 TTTGAAAATACTATATAATATATA-ATTTTTAAAACATT
*
770424 TTTGAAAATAC-GTATAATATA
1 TTTGAAAATACTATATAATATA
770445 GTTTAAAAAA
Statistics
Matches: 170, Mismatches: 29, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
37 73 0.43
38 63 0.37
39 3 0.02
40 30 0.18
41 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (38 bp):
TTTGAAAATACTATATAATATATAATTTTTAAAACATT
Found at i:770426 original size:75 final size:74
Alignment explanation
Indices: 770170--770444 Score: 222
Period size: 75 Copynumber: 3.6 Consensus size: 74
770160 TTATACATAT
* *
770170 ATATATTATATAG---TTTGCAAACGATCTTTG-AAATACGTATATAATATATAGTTTTTAAAAC
1 ATATATTATATAGTTTTTTG-AAACG-TTTTTGAAAATA--TATATAATATATAATTTTTAAAAC
*
770231 ATTTTTGAAAA-AC
62 A-TTTTAAAAATAC
* * ** * *
770244 TATATAATATACAGTTTTTAAAAAAACGTTTTAGAAAATATAGATAATATATAATTTTTAAAATC
1 -ATATATTATATAGTTTTT--TGAAACGTTTTTGAAAATATATATAATATATAATTTTTAAAA-C
**
770309 ATTTTTGAAAT-C
62 ATTTTAAAAATAC
* * * ** *
770321 TTATATAATATA-TAATTTTGAAATTTTTTTTGAAAATATATATAATATATAACTTTTAAAACAT
1 ATATATTATATAGT-TTTTTGAAA-CGTTTTTGAAAATATATATAATATATAATTTTTAAAACAT
770385 TTTAAAAAATAC
64 TTT-AAAAATAC
**
770397 ATATATTATATAGTTTTTTGAAACGTTTTTGAAAATACGTATAATATA
1 ATATATTATATAGTTTTTTGAAACGTTTTTGAAAATATATATAATATA
770445 GTTTAAAAAA
Statistics
Matches: 156, Mismatches: 31, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
74 9 0.06
75 69 0.44
76 30 0.19
77 30 0.19
78 8 0.05
79 10 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (74 bp):
ATATATTATATAGTTTTTTGAAACGTTTTTGAAAATATATATAATATATAATTTTTAAAACATTT
TAAAAATAC
Found at i:770511 original size:12 final size:12
Alignment explanation
Indices: 770494--770519 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
770484 TTTTGAACAT
770494 TTTTTATTATTA
1 TTTTTATTATTA
770506 TTTTTATTATTA
1 TTTTTATTATTA
770518 TT
1 TT
770520 ATATTTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:770862 original size:12 final size:12
Alignment explanation
Indices: 770845--770874 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
770835 GACGAAGGGA
770845 GAGGTATCATCG
1 GAGGTATCATCG
770857 GAGGTATCATCG
1 GAGGTATCATCG
770869 GAGGTA
1 GAGGTA
770875 CACAAAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (12 bp):
GAGGTATCATCG
Found at i:773670 original size:2 final size:2
Alignment explanation
Indices: 773663--773697 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
773653 TAACACCTTA
773663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
773698 AATTTGACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:773743 original size:21 final size:22
Alignment explanation
Indices: 773700--773745 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
773690 TATATATAAA
773700 TTTGACACCTCAAAATAATTTT
1 TTTGACACCTCAAAATAATTTT
773722 TTTGACACCTCAAAAT-ATTTT
1 TTTGACACCTCAAAATAATTTT
773743 TTT
1 TTT
773746 AAAAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTGACACCTCAAAATAATTTT
Found at i:776448 original size:24 final size:25
Alignment explanation
Indices: 776398--776457 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
776388 CAGTCGAAAA
*
776398 TGCCACGTAGAATTTTGCACCGAAG
1 TGCCACGTAGAATTATGCACCGAAG
* *
776423 TGCCACGTAGAA-TATGTACCGTAG
1 TGCCACGTAGAATTATGCACCGAAG
*
776447 TGCCACATAGA
1 TGCCACGTAGA
776458 TTTGTCTCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
TGCCACGTAGAATTATGCACCGAAG
Done.