Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007985.1 Hibiscus syriacus cultivar Beakdansim tig00110430_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: 2235968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1414493 original size:31 final size:31
Alignment explanation
Indices: 1414435--1414494 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1414425 TAGTTGTATG
*
1414435 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
1414466 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
1414495 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:1415408 original size:228 final size:227
Alignment explanation
Indices: 1415006--1415453 Score: 790
Period size: 228 Copynumber: 2.0 Consensus size: 227
1414996 GTAAATTATC
* * *
1415006 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1415071 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1415136 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1415201 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
1415234 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1415299 TTAATATTGTTAAATTTAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1415363 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
1415428 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1415454 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 4 0.02
228 151 0.72
229 55 0.26
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1415542 original size:20 final size:19
Alignment explanation
Indices: 1415519--1415564 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1415509 CGATATACCA
1415519 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1415539 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1415559 GGTAAA
1 GGTAAA
1415565 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1418003 original size:21 final size:21
Alignment explanation
Indices: 1417956--1418020 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1417946 AAGACAATCA
* *
1417956 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
1417978 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
1417998 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
1418019 AG
1 AG
1418021 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:1418096 original size:33 final size:34
Alignment explanation
Indices: 1418054--1418120 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1418044 AAATAGATGG
*
1418054 AGTGGTGAAAGAAG-TAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTAGAGGTGTTAAGGGGTGA
* *
1418087 AGTGGTGAAAGAAGTTGGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTAGAGGTGTTAAGGGGTGA
1418121 TATTAGGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.28, C:0.00, G:0.49, T:0.22
Consensus pattern (34 bp):
AGTGGTGAAAGAAGTTAGAGGTGTTAAGGGGTGA
Found at i:1419923 original size:19 final size:19
Alignment explanation
Indices: 1419899--1419947 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1419889 AATGTAGGGT
1419899 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1419918 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1419937 TATTTTTGTAT
1 TAATTTTGTAT
1419948 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1420703 original size:198 final size:198
Alignment explanation
Indices: 1420072--1421152 Score: 1992
Period size: 198 Copynumber: 5.5 Consensus size: 198
1420062 GGCCAAAAGG
*
1420072 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
1420137 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
*
1420202 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCTAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1420267 AAT
196 AAT
*
1420270 ATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
1420335 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAAGAATGAATGGAAAACAAGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
1420400 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
130 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1420465 TAAT
195 TAAT
1420469 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1420534 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
1420599 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
130 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1420663 TAAT
195 TAAT
*
1420667 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
1420732 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
1420796 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1420861 AAT
196 AAT
* * *
1420864 ATGTAATTTTTTAATCTAACCGATACAATTATACCGGTTTTATATGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1420929 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
1420994 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1421059 AAT
196 AAT
*
1421062 ATGTAATTTTTCAATCTAACCGGTACAATTATACCAGTTTTATGTGAG-A-ATGTCT-AATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
1421124 TGTCGACACTAATAGAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
1421153 CTAATTTAAA
Statistics
Matches: 859, Mismatches: 21, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
195 35 0.04
196 29 0.03
197 201 0.23
198 345 0.40
199 249 0.29
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (198 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AAT
Found at i:1420962 original size:395 final size:397
Alignment explanation
Indices: 1420072--1421152 Score: 1987
Period size: 395 Copynumber: 2.7 Consensus size: 397
1420062 GGCCAAAAGG
1420072 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA-GAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT-ATGAGAATATGTCTAAATAAT
*
1420136 GTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
65 GTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
*
1420201 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCTAACCCAAAAGTATAATG
130 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1420266 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGTGAGAATATGTCTAAAT
195 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAAT
*
1420331 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAAGAATGAATGGAAAACAAGGTG
260 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAAGGTG
1420396 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
325 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
1420461 AATGTAAT
390 AATGTAAT
*
1420469 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATATGAGAATATGTCTAAATAATG
1420534 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
1420599 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
130 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1420663 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
195 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAAT
* *
1420728 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTG
260 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAAGGTG
1420792 CA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
325 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
1420856 AATGTAAT
390 AATGTAAT
* *
1420864 ATGTAATTTTTTAATCTAACCGATACAATTATACCGGTTTTATATGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATATGAGAATATGTCTAAATAATG
1420929 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
1420994 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
1421059 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCAGTTTTATGTGAG-A-ATGTCT-AATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
*
1421121 ATGTGTCGACACTAATAGAGTTTGTGTCGATA
261 ATGTGTCGACACTAATATAGTTTGTGTCGATA
1421153 CTAATTTAAA
Statistics
Matches: 667, Mismatches: 14, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
392 35 0.05
393 6 0.01
394 58 0.09
395 253 0.38
396 30 0.04
397 229 0.34
398 56 0.08
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (397 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATATGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAAGGTGC
ACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAAT
Found at i:1422625 original size:18 final size:18
Alignment explanation
Indices: 1422604--1422665 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1422594 AGCGGTCGCA
1422604 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
1422622 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
1422640 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
1422658 GAAGATGA
1 GAAGATGA
1422666 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1422628 original size:6 final size:6
Alignment explanation
Indices: 1422604--1422689 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
1422594 AGCGGTCGCA
* * * * * *
1422604 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
1422652 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1422690 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:1422639 original size:3 final size:3
Alignment explanation
Indices: 1422619--1422693 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
1422609 TGAAGCTGAC
* * * * * ** *
1422619 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1422667 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1422694 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1422658 original size:36 final size:36
Alignment explanation
Indices: 1422607--1422685 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
1422597 GGTCGCAGAA
*
1422607 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
1422643 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
1422679 GATGAAG
1 GATGAAG
1422686 ATGATGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:1422693 original size:12 final size:12
Alignment explanation
Indices: 1422607--1422689 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
1422597 GGTCGCAGAA
*
1422607 GATGAAGCTGAC
1 GATGAAGATGAC
1422619 GATGAAGATGAC
1 GATGAAGATGAC
*
1422631 GATGATGATGAC
1 GATGAAGATGAC
* *
1422643 GATGAAGCTGGC
1 GATGAAGATGAC
*
1422655 GATGAAGATGAT
1 GATGAAGATGAC
* * *
1422667 GACGATGATGAT
1 GATGAAGATGAC
1422679 GATGAAGATGA
1 GATGAAGATGA
1422690 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1424669 original size:183 final size:183
Alignment explanation
Indices: 1424152--1424815 Score: 1249
Period size: 183 Copynumber: 3.6 Consensus size: 183
1424142 CTTTCAACAT
** * * *
1424152 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
1424217 GGTCTACAACCTATATTGACACTTTTTAATATTGTATCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1424282 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
1424335 ATTATAATGTAATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1424399 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1424464 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
1424517 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1424582 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1424647 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
1424700 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1424765 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
1424816 TAAAATGTGT
Statistics
Matches: 471, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
182 180 0.38
183 291 0.62
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:1427346 original size:25 final size:25
Alignment explanation
Indices: 1427312--1427376 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
1427302 TTATCATTAA
1427312 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
**** *
1427337 ATTTAGGTATGTTTGTTAACTATAT
1 ATTTAGGTATGTACAATAACTACAT
*
1427362 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1427377 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1427706 original size:22 final size:23
Alignment explanation
Indices: 1427658--1427706 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1427648 AAATTACATA
1427658 ACTTTTTAAAAAAAATATCGATC
1 ACTTTTTAAAAAAAATATCGATC
* * *
1427681 -CTTTTTATAAAAAGTATGGA-C
1 ACTTTTTAAAAAAAATATCGATC
1427702 ACTTT
1 ACTTT
1427707 CAATATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (23 bp):
ACTTTTTAAAAAAAATATCGATC
Found at i:1427755 original size:23 final size:23
Alignment explanation
Indices: 1427724--1427787 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1427714 ATAGGTAAAC
*
1427724 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1427747 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1427770 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1427788 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1427794 original size:23 final size:23
Alignment explanation
Indices: 1427724--1427796 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1427714 ATAGGTAAAC
* **
1427724 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1427747 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1427770 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1427793 ATAT
1 ATAT
1427797 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1428834 original size:7 final size:7
Alignment explanation
Indices: 1428822--1428846 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1428812 AACTAATTGG
1428822 CTTCGAC
1 CTTCGAC
1428829 CTTCGAC
1 CTTCGAC
1428836 CTTCGAC
1 CTTCGAC
1428843 CTTC
1 CTTC
1428847 AGGAAGCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.12, T:0.32
Consensus pattern (7 bp):
CTTCGAC
Found at i:1429012 original size:57 final size:58
Alignment explanation
Indices: 1428909--1429026 Score: 175
Period size: 57 Copynumber: 2.0 Consensus size: 58
1428899 GCCATCACTG
*
1428909 CCTCCTTCCACTGACAAAAACTCAAAGTCTCTTAAATTGTTTCAGGTTCTTTATCTGTA
1 CCTCCTTCCACTGACAAAAACTC-AAGTCTCTTAAATTGTTTCAGGTTCTTTATCTATA
* ** *
1428968 CCTCCTTTCACTGACTGAAACTC-AGTCTCTTGAATTGTTTCAGGTTCTTTATCTATA
1 CCTCCTTCCACTGACAAAAACTCAAGTCTCTTAAATTGTTTCAGGTTCTTTATCTATA
1429025 CC
1 CC
1429027 CATAGAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 34 0.63
59 20 0.37
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (58 bp):
CCTCCTTCCACTGACAAAAACTCAAGTCTCTTAAATTGTTTCAGGTTCTTTATCTATA
Found at i:1429360 original size:18 final size:18
Alignment explanation
Indices: 1429337--1429374 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1429327 ACTGAATTGC
*
1429337 CCTGCAATTACACCACTT
1 CCTGCAATTACACAACTT
*
1429355 CCTGCAATTCCACAACTT
1 CCTGCAATTACACAACTT
1429373 CC
1 CC
1429375 AAGGCTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.42, G:0.05, T:0.26
Consensus pattern (18 bp):
CCTGCAATTACACAACTT
Found at i:1431120 original size:16 final size:17
Alignment explanation
Indices: 1431099--1431136 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1431089 TGACCCTATA
*
1431099 GAGTCC-GGTCGAGTCG
1 GAGTCCGGGTCAAGTCG
*
1431115 GAGTCCGGGTCAAGTTG
1 GAGTCCGGGTCAAGTCG
1431132 GAGTC
1 GAGTC
1431137 AGGATCTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.16, C:0.21, G:0.42, T:0.21
Consensus pattern (17 bp):
GAGTCCGGGTCAAGTCG
Found at i:1436586 original size:20 final size:20
Alignment explanation
Indices: 1436563--1436639 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
1436553 ATTATTTTTT
1436563 ATAAAAATATATTAATTATA
1 ATAAAAATATATTAATTATA
* *
1436583 ATAAAAAT-TATAAAATA-A
1 ATAAAAATATATTAATTATA
*
1436601 TATAAAAATATTTTTAA-TATCA
1 -ATAAAAATA-TATTAATTAT-A
1436623 A-ATAAAATATATTAATT
1 ATA-AAAATATATTAATT
1436640 TTATAAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
18 1 0.02
19 15 0.33
20 16 0.36
21 12 0.27
22 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAATATATTAATTATA
Found at i:1436712 original size:28 final size:25
Alignment explanation
Indices: 1436680--1436749 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
1436670 AAGTTAAAAG
1436680 ATTAAGGAATAAAAATAATAATGTATTA
1 ATTAA-GAATAAAAATAAT-ATGT-TTA
* *
1436708 ATTAA-AATATAAATTATATGTTTA
1 ATTAAGAATAAAAATAATATGTTTA
*
1436732 ATTAAGAAATAAATATAA
1 ATTAAG-AATAAAAATAA
1436750 AATTATATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 8 0.23
25 4 0.11
26 18 0.51
28 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (25 bp):
ATTAAGAATAAAAATAATATGTTTA
Found at i:1438124 original size:46 final size:49
Alignment explanation
Indices: 1438031--1438157 Score: 127
Period size: 47 Copynumber: 2.6 Consensus size: 49
1438021 CCCTTAGCAG
* * *
1438031 GAAAGCGCGCCCCTGAACCGCGCTATATGCTGATTTGGCACCACGTGGA
1 GAAAGCGCGCCCCTGAACCGCGCTATACGCTGACTGGGCACCACGTGGA
* * *
1438080 GAAA-CGC-CCCCTGAACCGCGCTATGCGCTGACTGGGTA-CACGTGGG
1 GAAAGCGCGCCCCTGAACCGCGCTATACGCTGACTGGGCACCACGTGGA
* *
1438126 GTATAGCGCCCCCCCTGATA-CGCGCTATACGC
1 G-AAAGCG-CGCCCCTGA-ACCGCGCTATACGC
1438158 CACGTAGGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
46 8 0.12
47 28 0.43
48 5 0.08
49 5 0.08
50 18 0.28
51 1 0.02
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.17
Consensus pattern (49 bp):
GAAAGCGCGCCCCTGAACCGCGCTATACGCTGACTGGGCACCACGTGGA
Found at i:1442690 original size:31 final size:31
Alignment explanation
Indices: 1442632--1442696 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1442622 AGAGTCGAGG
* *
1442632 GTTTACCTATGTCTTTCGAGACATATGGATA
1 GTTTACCTAGGTCTTTCGAGACATATGGACA
* *
1442663 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGACA
1442694 GTT
1 GTT
1442697 ACCGATGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGACA
Found at i:1442747 original size:29 final size:30
Alignment explanation
Indices: 1442682--1442750 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1442672 GGTTCTTCGG
* *
1442682 GACCTATGGACAGTTACCGATGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
1442712 GACCTCTGGACAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1442741 GACCTCTGGA
1 GACCTCTGGA
1442751 TAGGTCATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1444204 original size:111 final size:111
Alignment explanation
Indices: 1444064--1444285 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
1444054 ATTATAAAAA
* *
1444064 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATCAATCAACTAAATATTACTAATAATTTAAATTA
* * *
1444129 AATTAAAACATTAAAATGTTACCGTATTAGTAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* *
1444175 TTAATTCTTAATCTAATAATCATGTATTAAATCAATCAACTAAATGTTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATCAATCAACTAAATATTACTAATAATTTAAATTA
*
1444240 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1444286 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATCAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:1444685 original size:11 final size:12
Alignment explanation
Indices: 1444657--1444708 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
1444647 TATTTAAACG
1444657 GGTATTGGGCCA
1 GGTATTGGGCCA
*
1444669 GGTATTGGGTC-
1 GGTATTGGGCCA
**
1444680 GGTATTGGGCTG
1 GGTATTGGGCCA
* *
1444692 GGAATCGGGCCA
1 GGTATTGGGCCA
1444704 GGTAT
1 GGTAT
1444709 ATATATATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.15, C:0.13, G:0.44, T:0.27
Consensus pattern (12 bp):
GGTATTGGGCCA
Found at i:1444766 original size:24 final size:25
Alignment explanation
Indices: 1444706--1444766 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
1444696 TCGGGCCAGG
1444706 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
1444729 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
1444753 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
1444767 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:1445179 original size:50 final size:50
Alignment explanation
Indices: 1445109--1445218 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
1445099 ACGCGGATCA
* * * * * *
1445109 GGGGCGCACTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGGCAG
1 GGGGCGCGCTATACCCACGTGGAGCCAAATCAACATATAGCGCGGGGCAG
* * * **
1445159 GGGGCGCGCTATATCTACGTGGAGTCAAATCAACATATAGCGCGGTTCAG
1 GGGGCGCGCTATACCCACGTGGAGCCAAATCAACATATAGCGCGGGGCAG
1445209 GGGGCGCGCT
1 GGGGCGCGCT
1445219 TTTCTATTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.21, C:0.27, G:0.35, T:0.17
Consensus pattern (50 bp):
GGGGCGCGCTATACCCACGTGGAGCCAAATCAACATATAGCGCGGGGCAG
Found at i:1448885 original size:6 final size:6
Alignment explanation
Indices: 1448876--1448905 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1448866 TGATGATGGT
*
1448876 GAAGAG GAAGAG GAAGAG GAAGCG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
1448906 ACCTCTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:1449717 original size:17 final size:18
Alignment explanation
Indices: 1449685--1449722 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
1449675 TTTTTAAAAA
1449685 AATTAAAAGCAGATTTTTT
1 AATTAAAA-CAGATTTTTT
1449704 AATTAAAA-AGATTTTTT
1 AATTAAAACAGATTTTTT
1449721 AA
1 AA
1449723 AAAAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (18 bp):
AATTAAAACAGATTTTTT
Found at i:1450919 original size:8 final size:8
Alignment explanation
Indices: 1450888--1450928 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1450878 CACACACACA
*
1450888 GAGAGAGA
1 GAGAGAGG
1450896 GAGAGAGAG
1 GAGAGAG-G
1450905 G-GAGAGG
1 GAGAGAGG
1450912 GAGAGAGG
1 GAGAGAGG
1450920 GA-AGAGG
1 GAGAGAGG
1450927 GA
1 GA
1450929 CAACATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 9 0.30
8 20 0.67
9 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:1470828 original size:28 final size:28
Alignment explanation
Indices: 1470788--1470844 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
1470778 AATATCAAAA
*
1470788 TAGTCACTCAATTATTTTATTTATGTTT
1 TAGTCACTCAATTATTTTATTTATATTT
1470816 TAGTCA-TCTAATTATTTTATTTATATTT
1 TAGTCACTC-AATTATTTTATTTATATTT
1470844 T
1 T
1470845 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (28 bp):
TAGTCACTCAATTATTTTATTTATATTT
Found at i:1470845 original size:73 final size:73
Alignment explanation
Indices: 1470725--1470906 Score: 346
Period size: 73 Copynumber: 2.5 Consensus size: 73
1470715 CACATTATCT
*
1470725 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATGTTTTTAAAAAAATATCAAAATA
1 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTAAAAAAATATCAAAATA
1470790 GTCACTCA
66 GTCACTCA
*
1470798 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTTAAAAAATATCAAAATA
1 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTAAAAAAATATCAAAATA
1470863 GTCACTCA
66 GTCACTCA
1470871 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTT
1 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTT
1470907 TTTCAAAATC
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 107 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.54
Consensus pattern (73 bp):
ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTAAAAAAATATCAAAATA
GTCACTCA
Found at i:1476710 original size:29 final size:28
Alignment explanation
Indices: 1476668--1476760 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 28
1476658 GGAACATGTG
* *
1476668 AATAGTTGGAGGACCATTTTATAAGTTTC
1 AATAGTT-GAGGACCATTTTATAACTTTT
*
1476697 AATAGTATGAGGACCATTTTGTAACTTTT
1 AATAGT-TGAGGACCATTTTATAACTTTT
* *
1476726 AATAGTCGAAGGATCATTTTATAACTTTT
1 AATAGTTG-AGGACCATTTTATAACTTTT
1476755 AATAGT
1 AATAGT
1476761 CAAGTAACTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 54 0.96
30 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (28 bp):
AATAGTTGAGGACCATTTTATAACTTTT
Found at i:1478828 original size:60 final size:59
Alignment explanation
Indices: 1478694--1478829 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 59
1478684 ATTTTAGGCT
* ** *
1478694 AAAG-TACACAAATGATCCCCCGATTATAGGTATTATTTTGTTGAGTCCCTTGATTATTA
1 AAAGTTACA-AAATGATCTCCTAATTATAGGTATTATTTTGTTGAGTCCCTTGACTATTA
* ** * *
1478753 GAAGTTACAGGATGATCTCCTAATTATATGGTGTTGTTTTGTTGAGTCCCTCT-ACTATTA
1 AAAGTTACAAAATGATCTCCTAATTATA-GGTATTATTTTGTTGAGTCCCT-TGACTATTA
*
1478813 AAAGTTATAAAATGATC
1 AAAGTTACAAAATGATC
1478830 ACCCGACTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
59 17 0.28
60 43 0.70
61 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (59 bp):
AAAGTTACAAAATGATCTCCTAATTATAGGTATTATTTTGTTGAGTCCCTTGACTATTA
Found at i:1481420 original size:41 final size:41
Alignment explanation
Indices: 1481364--1481451 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
1481354 CGAAATCCCG
*
1481364 TGTTTGTTTCCCGTAATTCGTTTTCCAGAAAATGTTTATCA
1 TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
* * *
1481405 TGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTTTTTCA
1 TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
*
1481446 TATTTG
1 TGTTTG
1481452 GTTGGAGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (41 bp):
TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
Found at i:1481639 original size:24 final size:23
Alignment explanation
Indices: 1481612--1481658 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1481602 TTTATGAATC
1481612 TAATATTAAT-AATAATATTTAATT
1 TAATATTAATCAA-AATA-TTAATT
*
1481636 TAATTTTAATCAAAATATTAATT
1 TAATATTAATCAAAATATTAATT
1481659 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 13 0.62
25 2 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTAATCAAAATATTAATT
Found at i:1481715 original size:18 final size:19
Alignment explanation
Indices: 1481673--1481718 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1481663 AAATATTTAA
*
1481673 AATATATTATATTTCTAAT
1 AATATAATATATTTCTAAT
1481692 AATATAATATATTT-TAAT
1 AATATAATATATTTCTAAT
*
1481710 ATTATAATA
1 AATATAATA
1481719 AAATAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATAATATATTTCTAAT
Found at i:1481723 original size:28 final size:28
Alignment explanation
Indices: 1481692--1481778 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
1481682 TATTTCTAAT
*
1481692 AATATAATATATTTTAATATTATAATAA
1 AATATAATATATTTTAATAATATAATAA
* * *
1481720 AATAATCAATTATATTATAATAATATAAGAT
1 AAT-AT-AA-TATATTTTAATAATATAATAA
* *
1481751 ATTATATTATATTTTAATAATATAATAA
1 AATATAATATATTTTAATAATATAATAA
1481779 TTATTAATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
28 21 0.45
29 3 0.06
30 4 0.09
31 19 0.40
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (28 bp):
AATATAATATATTTTAATAATATAATAA
Found at i:1481734 original size:23 final size:23
Alignment explanation
Indices: 1481676--1481761 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 23
1481666 TATTTAAAAT
* * *
1481676 ATATTATATTTCTAATAATATAAT
1 ATATTATA-TTATAATAAAATAAC
1481700 ATATTTTAATATTATAATAAAATAATC
1 ATA--TT-ATATTATAATAAAATAA-C
* *
1481727 A-ATTATATTATAATAATATAAG
1 ATATTATATTATAATAAAATAAC
1481749 ATATTATATTATA
1 ATATTATATTATA
1481762 TTTTAATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
22 1 0.02
23 27 0.52
24 5 0.10
26 15 0.29
27 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (23 bp):
ATATTATATTATAATAAAATAAC
Found at i:1481774 original size:18 final size:19
Alignment explanation
Indices: 1481669--1481801 Score: 71
Period size: 18 Copynumber: 7.1 Consensus size: 19
1481659 ATTAAAATAT
1481669 TTAA-AATATATTATATT-
1 TTAATAATATATTATATTA
*
1481686 TCTAATAATATAATATATT-
1 T-TAATAATATATTATATTA
* * * *
1481705 TTAATATTATAATAAAATAA
1 TTAATAATAT-ATTATATTA
* * * *
1481725 TCAATTATATTATAATAATA
1 TTAATAATA-TATTATATTA
* *
1481745 TAAGATATTATATTATATT-
1 TTA-ATAATATATTATATTA
*
1481764 TTAATAATATAATA-ATTA
1 TTAATAATATATTATATTA
*
1481782 TTAATAAAAT-TTATATTA
1 TTAATAATATATTATATTA
1481800 TT
1 TT
1481802 TGTTAATTTC
Statistics
Matches: 86, Mismatches: 22, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
17 6 0.07
18 35 0.41
19 19 0.22
20 21 0.24
21 5 0.06
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (19 bp):
TTAATAATATATTATATTA
Found at i:1481794 original size:28 final size:28
Alignment explanation
Indices: 1481737--1481794 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
1481727 AATTATATTA
* * *
1481737 TAATAATATAAGATATTATATTATATTT
1 TAATAATATAAGATATTATAATAAAATT
*
1481765 TAATAATATAATA-ATTATTAATAAAATT
1 TAATAATATAAGATATTA-TAATAAAATT
1481793 TA
1 TA
1481795 TATTATTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TAATAATATAAGATATTATAATAAAATT
Found at i:1481855 original size:19 final size:18
Alignment explanation
Indices: 1481831--1481901 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 18
1481821 ATACTATTAA
1481831 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1481850 ATTATTTATATATATTTAAT
1 ATTATTAATA-ATA-ATAAT
1481870 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1481892 ATT-TTAATAA
1 ATTATTAATAA
1481902 AGATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 16 0.38
20 10 0.24
21 3 0.07
22 11 0.26
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1481922 original size:23 final size:23
Alignment explanation
Indices: 1481896--1481940 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1481886 AATAATATTT
1481896 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1481919 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1481941 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1482297 original size:15 final size:14
Alignment explanation
Indices: 1482267--1482296 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1482257 TCTAAAATAT
*
1482267 AATTTATTTTTCAA
1 AATTTAATTTTCAA
1482281 AATTTAATTTTCAA
1 AATTTAATTTTCAA
1482295 AA
1 AA
1482297 ACAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAATTTTCAA
Found at i:1483180 original size:16 final size:17
Alignment explanation
Indices: 1483138--1483180 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1483128 ATAAATACTA
1483138 TAAAATCTTATAAAATT
1 TAAAATCTTATAAAATT
*
1483155 TAAAA-GTTATAAAA-T
1 TAAAATCTTATAAAATT
*
1483170 TAAAATTTTAT
1 TAAAATCTTAT
1483181 GTATAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATCTTATAAAATT
Found at i:1484710 original size:34 final size:34
Alignment explanation
Indices: 1484667--1484747 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
1484657 TCCCTTCAAG
1484667 TATTATATTATTAGTAACTTTCATACT-TTCGAAT
1 TATTATATTATTAGTAACTTTCATA-TATTCGAAT
* * **
1484701 TATTATATTATTATTAATTTTCATATATTTTAAT
1 TATTATATTATTAGTAACTTTCATATATTCGAAT
*
1484735 TATTATATCATTA
1 TATTATATTATTA
1484748 AAATTATACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 1 0.02
34 40 0.98
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (34 bp):
TATTATATTATTAGTAACTTTCATATATTCGAAT
Found at i:1486007 original size:33 final size:34
Alignment explanation
Indices: 1485932--1486111 Score: 328
Period size: 34 Copynumber: 5.4 Consensus size: 34
1485922 TTATAAAAAA
1485932 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1485966 GGCATTTATATGAGCTTGAGTTAATATTAAGG-G
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1485999 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
*
1486033 GGCATTTATATGAGCTTGA-TTACTATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
*
1486066 GGCATTTATATGAGCTTGAGTTACTATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1486100 GGCATTTATATG
1 GGCATTTATATG
1486112 GAGGTATTAA
Statistics
Matches: 143, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
33 65 0.45
34 78 0.55
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (34 bp):
GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
Found at i:1486040 original size:67 final size:67
Alignment explanation
Indices: 1485932--1486111 Score: 326
Period size: 67 Copynumber: 2.7 Consensus size: 67
1485922 TTATAAAAAA
1485932 GGCATTTATATGAGCTTGAGTTAATATTAAGGCGGGCATTTATATGAGCTTGAGTTAATATTAAG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCGGGCATTTATATGAGCTTGA-TTAATATTAAG
1485997 G-G
65 GCG
*
1485999 GGCATTTATATGAGCTTGAGTTAATATTAAGGCGGGCATTTATATGAGCTTGATTACTATTAAGG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCGGGCATTTATATGAGCTTGATTAATATTAAGG
1486064 CG
66 CG
*
1486066 GGCATTTATATGAGCTTGAGTTACTATTAAGGCGGGCATTTATATG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCGGGCATTTATATG
1486112 GAGGTATTAA
Statistics
Matches: 110, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 11 0.10
67 99 0.90
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (67 bp):
GGCATTTATATGAGCTTGAGTTAATATTAAGGCGGGCATTTATATGAGCTTGATTAATATTAAGG
CG
Found at i:1486606 original size:25 final size:25
Alignment explanation
Indices: 1486568--1486616 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1486558 ATCCCCGCGG
** *
1486568 TTTTTTAAGTGGGGACGGGTACGGA
1 TTTTTTAAACGGGGACGGGGACGGA
1486593 TTTTTTAAACGGGGACGGGGACGG
1 TTTTTTAAACGGGGACGGGGACGG
1486617 GGGGACTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.29
Consensus pattern (25 bp):
TTTTTTAAACGGGGACGGGGACGGA
Found at i:1500670 original size:39 final size:39
Alignment explanation
Indices: 1500627--1500712 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 39
1500617 ACCCTTTCAT
* *
1500627 TAAATCTTTTTAT-ATTTTCAATTTTGTAAAAAAAATATA
1 TAAAT-TTTTTATGAATTTAAATTTTGTAAAAAAAATATA
* *
1500666 TAAA--TTTTATGAATTTAAATTTTTTAAAGAAAATATA
1 TAAATTTTTTATGAATTTAAATTTTGTAAAAAAAATATA
*
1500703 TAAATATTTT
1 TAAATTTTTT
1500713 CCAACTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 6 0.15
37 26 0.65
39 8 0.20
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (39 bp):
TAAATTTTTTATGAATTTAAATTTTGTAAAAAAAATATA
Found at i:1502257 original size:29 final size:28
Alignment explanation
Indices: 1502215--1502307 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 28
1502205 GGAACATGTG
* *
1502215 AATAGTTGGAGGACCATTTTATAAGTTTC
1 AATAGTT-GAGGACCATTTTATAACTTTT
*
1502244 AATAGTATGAGGACCATTTTGTAACTTTT
1 AATAGT-TGAGGACCATTTTATAACTTTT
* *
1502273 AATAGTCGAAGGATCATTTTATAACTTTT
1 AATAGTTG-AGGACCATTTTATAACTTTT
1502302 AATAGT
1 AATAGT
1502308 CAAGTAACTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 54 0.96
30 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (28 bp):
AATAGTTGAGGACCATTTTATAACTTTT
Found at i:1506992 original size:41 final size:41
Alignment explanation
Indices: 1506936--1507013 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1506926 CGAAATCCCG
*
1506936 TGTTTGTTTCCCGTAATTCGTTTTCCAGAAAATGTTTATCA
1 TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
* *
1506977 TGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTTT
1 TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
1507014 TTCAGTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (41 bp):
TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
Found at i:1507282 original size:22 final size:22
Alignment explanation
Indices: 1507257--1507305 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1507247 ATATATTTAT
1507257 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
1507279 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
1507301 AAATA
1 TAATA
1507306 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:1507320 original size:23 final size:23
Alignment explanation
Indices: 1507290--1507343 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1507280 AATATTTTTA
1507290 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
* *
1507313 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAACATATT
1507336 ATATTATA
1 ATATTATA
1507344 TTTTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:1507352 original size:23 final size:23
Alignment explanation
Indices: 1507310--1507393 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
1507300 AAAATAATCA
* *
1507310 ATTATATTATAATAAT-ATAAGAT
1 ATTATATTATATTATTAATAA-AT
1507333 ATTATATTATATT-TTAAT-AAT
1 ATTATATTATATTATTAATAAAT
* *
1507354 A-TATAATAAATTATTAATAAA-
1 ATTATATTATATTATTAATAAAT
*
1507375 ATTTATATTAT-TTGTTAAT
1 A-TTATATTATATTATTAAT
1507394 TTCATAGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
20 9 0.18
21 9 0.18
22 11 0.22
23 20 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTATATTATATTATTAATAAAT
Found at i:1507360 original size:53 final size:53
Alignment explanation
Indices: 1507266--1507367 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
1507256 TTAATATTTC
* * *
1507266 TAATAATATAATATAATATTTTTAATATTATAATAAAATAATCAATTATATTA
1 TAATAATATAAGATAATATTATTAATATTATAATAAAATAATAAATTATATTA
* *
1507319 TAATAATATAAGATATTA-TATT-ATATTTTAATAATATATAATAAATTAT
1 TAATAATATAAGATAATATTATTAATATTATAATAA-A-ATAATAAATTAT
1507368 TAATAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 11 0.26
52 4 0.10
53 27 0.64
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (53 bp):
TAATAATATAAGATAATATTATTAATATTATAATAAAATAATAAATTATATTA
Found at i:1507369 original size:28 final size:28
Alignment explanation
Indices: 1507266--1507356 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
1507256 TTAATATTTC
* * *
1507266 TAATAATATAATATAATAT-TTTTAATA
1 TAATAATATAAGATAATATATTATATTA
*
1507293 TTATAATA-AA-ATAATCA-ATTATATTA
1 TAATAATATAAGATAAT-ATATTATATTA
* *
1507319 TAATAATATAAGATATTATATTATATTT
1 TAATAATATAAGATAATATATTATATTA
1507347 TAATAATATA
1 TAATAATATA
1507357 TAATAAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 5 0.09
26 16 0.30
27 10 0.19
28 22 0.42
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATAATATAAGATAATATATTATATTA
Found at i:1507440 original size:19 final size:18
Alignment explanation
Indices: 1507416--1507486 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 18
1507406 ATACTATTAA
1507416 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1507435 ATTATTTATATATATTTAAT
1 ATTATTAATA-ATA-ATAAT
1507455 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1507477 ATT-TTAATAA
1 ATTATTAATAA
1507487 AGATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 16 0.38
20 10 0.24
21 3 0.07
22 11 0.26
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1507507 original size:23 final size:22
Alignment explanation
Indices: 1507481--1507524 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1507471 AATAATATTT
1507481 TAATAAAGATATTTAAAATATAC
1 TAATAAAGAT-TTTAAAATATAC
* *
1507504 TAATTAATATTTTAAAATATA
1 TAATAAAGATTTTAAAATATA
1507525 ATATAACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TAATAAAGATTTTAAAATATAC
Found at i:1507885 original size:15 final size:14
Alignment explanation
Indices: 1507855--1507884 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1507845 CTAAAAATAT
*
1507855 AATTTATTTTTCAA
1 AATTTAATTTTCAA
1507869 AATTTAATTTTCAA
1 AATTTAATTTTCAA
1507883 AA
1 AA
1507885 AACAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAATTTTCAA
Found at i:1508548 original size:22 final size:22
Alignment explanation
Indices: 1508497--1508548 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1508487 CTAAATTTAG
* *
1508497 AATATAAAAATATTAAAAAATA
1 AATATAAAAATACTAAAAAACA
1508519 AATATAAAAATACTAAAAATACA
1 AATATAAAAATACTAAAAA-ACA
1508542 AAT-TAAA
1 AATATAAA
1508549 TTACTAGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (22 bp):
AATATAAAAATACTAAAAAACA
Found at i:1508776 original size:16 final size:17
Alignment explanation
Indices: 1508734--1508776 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1508724 ATAAATACTA
1508734 TAAAATCTTATAAAATT
1 TAAAATCTTATAAAATT
*
1508751 TAAAA-GTTATAAAA-T
1 TAAAATCTTATAAAATT
*
1508766 TAAAATTTTAT
1 TAAAATCTTAT
1508777 GTATAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATCTTATAAAATT
Found at i:1510007 original size:2 final size:2
Alignment explanation
Indices: 1510000--1510031 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1509990 AGTTATCATA
1510000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1510032 TAATTACGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1510298 original size:35 final size:36
Alignment explanation
Indices: 1510259--1510334 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
1510249 TATAATTGGA
1510259 TCATATCCCTTC-AAGTATTATATTATT-AGTAACTT
1 TCATAT-CCTTCGAAGTATTATATTATTAAGTAACTT
* * * *
1510294 TCATA-CTTTCGAATTATTATATTATTAATTAATTT
1 TCATATCCTTCGAAGTATTATATTATTAAGTAACTT
1510329 TCATAT
1 TCATAT
1510335 ATTTTAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
33 4 0.12
34 14 0.41
35 16 0.47
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (36 bp):
TCATATCCTTCGAAGTATTATATTATTAAGTAACTT
Found at i:1510344 original size:35 final size:35
Alignment explanation
Indices: 1510274--1510356 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
1510264 TCCCTTCAAG
1510274 TATTATATTATT-AGTAACTTTCATACTTTCGAAT
1 TATTATATTATTAAGTAACTTTCATACTTTCGAAT
* * **
1510308 TATTATATTATTAATTAATTTTCATA-TATTTTAAT
1 TATTATATTATTAAGTAACTTTCATACT-TTCGAAT
*
1510343 TATTATATCATTAA
1 TATTATATTATTAA
1510357 AATTATACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 13 0.31
35 29 0.69
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (35 bp):
TATTATATTATTAAGTAACTTTCATACTTTCGAAT
Found at i:1510350 original size:16 final size:17
Alignment explanation
Indices: 1510305--1510355 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
1510295 CATACTTTCG
1510305 AATTATTATATTATTAATT
1 AATTATTATA-TATT-ATT
1510324 AATT-TTCATATATT-TT
1 AATTATT-ATATATTATT
1510340 AATTATTATATCATTA
1 AATTATTATAT-ATTA
1510356 AAATTATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 10 0.36
17 5 0.18
18 6 0.21
19 7 0.25
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTATTATATATTATT
Found at i:1511586 original size:34 final size:34
Alignment explanation
Indices: 1511548--1511729 Score: 346
Period size: 34 Copynumber: 5.4 Consensus size: 34
1511538 TTATAAAAAA
1511548 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1511582 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1511616 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
*
1511650 GGCATTTATATGAGCTTGAGTTACTATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
*
1511684 GGCATTTATATGAGCTTGAGTTACTATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1511718 GGCATTTATATG
1 GGCATTTATATG
1511730 GAGGTATTAA
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 147 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (34 bp):
GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
Found at i:1512232 original size:25 final size:25
Alignment explanation
Indices: 1512194--1512242 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1512184 ATCCCCGCGG
** *
1512194 TTTTTTAAGTGGGGACGGGTACGGA
1 TTTTTTAAACGGGGACGGGGACGGA
1512219 TTTTTTAAACGGGGACGGGGACGG
1 TTTTTTAAACGGGGACGGGGACGG
1512243 GGGGACTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.29
Consensus pattern (25 bp):
TTTTTTAAACGGGGACGGGGACGGA
Found at i:1526388 original size:39 final size:39
Alignment explanation
Indices: 1526345--1526430 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 39
1526335 ACCCTTTCAT
* *
1526345 TAAATCTTTTTAT-ATTTTCAATTTTGTAAAAAAAATATA
1 TAAAT-TTTTTATGAATTTAAATTTTGTAAAAAAAATATA
* *
1526384 TAAA--TTTTATGAATTTAAATTTTTTAAAGAAAATATA
1 TAAATTTTTTATGAATTTAAATTTTGTAAAAAAAATATA
*
1526421 TAAATATTTT
1 TAAATTTTTT
1526431 CCAACTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 6 0.15
37 26 0.65
39 8 0.20
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (39 bp):
TAAATTTTTTATGAATTTAAATTTTGTAAAAAAAATATA
Found at i:1527985 original size:29 final size:28
Alignment explanation
Indices: 1527943--1528035 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 28
1527933 GGAACATGTG
* *
1527943 AATAGTTGGAGGACCATTTTATAAGTTTC
1 AATAGTT-GAGGACCATTTTATAACTTTT
*
1527972 AATAGTATGAGGACCATTTTGTAACTTTT
1 AATAGT-TGAGGACCATTTTATAACTTTT
* *
1528001 AATAGTCGAAGGATCATTTTATAACTTTT
1 AATAGTTG-AGGACCATTTTATAACTTTT
1528030 AATAGT
1 AATAGT
1528036 CAAGTAACTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 54 0.96
30 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (28 bp):
AATAGTTGAGGACCATTTTATAACTTTT
Found at i:1532705 original size:41 final size:41
Alignment explanation
Indices: 1532649--1532726 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1532639 CGAAATCCCG
*
1532649 TGTTTGTTTCCCGTAATTCGTTTTCCAGAAAATGTTTATCA
1 TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
* *
1532690 TGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTTT
1 TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
1532727 TTCAGTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (41 bp):
TGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTATCA
Found at i:1532995 original size:22 final size:22
Alignment explanation
Indices: 1532970--1533018 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1532960 ATATATTTAT
1532970 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
1532992 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
1533014 AAATA
1 TAATA
1533019 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:1533033 original size:23 final size:23
Alignment explanation
Indices: 1533003--1533056 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1532993 AATATTTTTA
1533003 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
* *
1533026 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAACATATT
1533049 ATATTATA
1 ATATTATA
1533057 TTTTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:1533065 original size:23 final size:23
Alignment explanation
Indices: 1533023--1533106 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
1533013 AAAATAATCA
* *
1533023 ATTATATTATAATAAT-ATAAGAT
1 ATTATATTATATTATTAATAA-AT
1533046 ATTATATTATATT-TTAAT-AAT
1 ATTATATTATATTATTAATAAAT
* *
1533067 A-TATAATAAATTATTAATAAA-
1 ATTATATTATATTATTAATAAAT
*
1533088 ATTTATATTAT-TTGTTAAT
1 A-TTATATTATATTATTAAT
1533107 TTCATAGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
20 9 0.18
21 9 0.18
22 11 0.22
23 20 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTATATTATATTATTAATAAAT
Found at i:1533073 original size:53 final size:53
Alignment explanation
Indices: 1532979--1533080 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
1532969 TTAATATTTC
* * *
1532979 TAATAATATAATATAATATTTTTAATATTATAATAAAATAATCAATTATATTA
1 TAATAATATAAGATAATATTATTAATATTATAATAAAATAATAAATTATATTA
* *
1533032 TAATAATATAAGATATTA-TATT-ATATTTTAATAATATATAATAAATTAT
1 TAATAATATAAGATAATATTATTAATATTATAATAA-A-ATAATAAATTAT
1533081 TAATAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 11 0.26
52 4 0.10
53 27 0.64
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (53 bp):
TAATAATATAAGATAATATTATTAATATTATAATAAAATAATAAATTATATTA
Found at i:1533082 original size:28 final size:28
Alignment explanation
Indices: 1532979--1533069 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
1532969 TTAATATTTC
* * *
1532979 TAATAATATAATATAATAT-TTTTAATA
1 TAATAATATAAGATAATATATTATATTA
*
1533006 TTATAATA-AA-ATAATCA-ATTATATTA
1 TAATAATATAAGATAAT-ATATTATATTA
* *
1533032 TAATAATATAAGATATTATATTATATTT
1 TAATAATATAAGATAATATATTATATTA
1533060 TAATAATATA
1 TAATAATATA
1533070 TAATAAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 5 0.09
26 16 0.30
27 10 0.19
28 22 0.42
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATAATATAAGATAATATATTATATTA
Found at i:1533216 original size:23 final size:23
Alignment explanation
Indices: 1533190--1533234 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1533180 TAATAATATT
1533190 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1533213 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1533235 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1533595 original size:15 final size:14
Alignment explanation
Indices: 1533565--1533594 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1533555 CTAAAAATAT
*
1533565 AATTTATTTTTCAA
1 AATTTAATTTTCAA
1533579 AATTTAATTTTCAA
1 AATTTAATTTTCAA
1533593 AA
1 AA
1533595 AACAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAATTTTCAA
Found at i:1534261 original size:21 final size:21
Alignment explanation
Indices: 1534205--1534246 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1534195 CTAAATTTAG
*
1534205 AATATAAAAATATTAAAAATA
1 AATATAAAAATACTAAAAATA
1534226 AATATAAAAATACTAAAAATA
1 AATATAAAAATACTAAAAATA
1534247 CAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AATATAAAAATACTAAAAATA
Found at i:1534482 original size:16 final size:17
Alignment explanation
Indices: 1534440--1534482 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1534430 ATAAATACTA
1534440 TAAAATCTTATAAAATT
1 TAAAATCTTATAAAATT
*
1534457 TAAAA-GTTATAAAA-T
1 TAAAATCTTATAAAATT
*
1534472 TAAAATTTTAT
1 TAAAATCTTAT
1534483 GTATAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATCTTATAAAATT
Found at i:1543631 original size:17 final size:17
Alignment explanation
Indices: 1543611--1543648 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1543601 AGATATGATG
*
1543611 TTTGTTTGTA-TATATTA
1 TTTGTTTGAATTAT-TTA
1543628 TTTGTTTGAATTATTTA
1 TTTGTTTGAATTATTTA
1543645 TTTG
1 TTTG
1543649 AGCTTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (17 bp):
TTTGTTTGAATTATTTA
Found at i:1552407 original size:15 final size:15
Alignment explanation
Indices: 1552381--1552423 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1552371 TAATATATAA
1552381 TTATATATTTAATGTC
1 TTATA-ATTTAATGTC
*
1552397 TTATAATTTAATGTT
1 TTATAATTTAATGTC
*
1552412 TTATAAATTAAT
1 TTATAATTTAAT
1552424 TTAATGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATAATTTAATGTC
Found at i:1554103 original size:16 final size:16
Alignment explanation
Indices: 1554082--1554112 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1554072 GTCGAGCGTG
*
1554082 GATGAGTACCGTTAAC
1 GATGAGTACCATTAAC
1554098 GATGAGTACCATTAA
1 GATGAGTACCATTAA
1554113 ATTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (16 bp):
GATGAGTACCATTAAC
Found at i:1555982 original size:22 final size:23
Alignment explanation
Indices: 1555947--1555994 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1555937 CATTTAAATT
1555947 TTTAACTAATTTATAA-TTATACG
1 TTTAACTAATTTATAATTTA-ACG
*
1555970 TTTAA-TACTTTATAATTTAACG
1 TTTAACTAATTTATAATTTAACG
1555992 TTT
1 TTT
1555995 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACG
Found at i:1564767 original size:14 final size:13
Alignment explanation
Indices: 1564731--1564757 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1564721 ACAAATTGTC
1564731 GACTCAAAAAACT
1 GACTCAAAAAACT
1564744 GACTCAAAAAACT
1 GACTCAAAAAACT
1564757 G
1 G
1564758 TAGTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (13 bp):
GACTCAAAAAACT
Found at i:1565059 original size:30 final size:30
Alignment explanation
Indices: 1565024--1565091 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1565014 ACCCTAACCC
1565024 GACGGGGAAAAACCGTTTATACTAAACGGG
1 GACGGGGAAAAACCGTTTATACTAAACGGG
**
1565054 GACGGGGAAAAACCGTTTATGTTAAACGGG
1 GACGGGGAAAAACCGTTTATACTAAACGGG
*
1565084 GATGGGGA
1 GACGGGGA
1565092 CGGGGACGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.35, T:0.18
Consensus pattern (30 bp):
GACGGGGAAAAACCGTTTATACTAAACGGG
Found at i:1565245 original size:41 final size:42
Alignment explanation
Indices: 1565173--1565253 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
1565163 AAAAATAATT
* *
1565173 ATTATATATATATATATATTTTAATAAATTTAAATTAAATTAA
1 ATTATAAATATATATAAATTTTAAT-AATTTAAATTAAATTAA
*
1565216 ATTATAAATATATATAAATATTT-AT-ATTTAATTTAAAT
1 ATTATAAATATATATAAAT-TTTAATAATTTAAATTAAAT
1565254 ATATACCTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 12 0.35
43 19 0.56
44 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
ATTATAAATATATATAAATTTTAATAATTTAAATTAAATTAA
Found at i:1574671 original size:21 final size:21
Alignment explanation
Indices: 1574632--1574671 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1574622 ATCTAATTCC
*
1574632 AGTATCAATACTCCTTGAATA
1 AGTATCAATACTACTTGAATA
1574653 AGTATCAATAC-ACTATGAA
1 AGTATCAATACTACT-TGAA
1574672 AGTTTTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (21 bp):
AGTATCAATACTACTTGAATA
Found at i:1575874 original size:2 final size:2
Alignment explanation
Indices: 1575867--1575891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1575857 TGATAAAGTA
1575867 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1575892 ATTTTACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1577197 original size:21 final size:21
Alignment explanation
Indices: 1577171--1577212 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1577161 GATCTTCAGC
1577171 TTAGTAATACGAATTAATCAT
1 TTAGTAATACGAATTAATCAT
1577192 TTAGTAATACGAATTAATCAT
1 TTAGTAATACGAATTAATCAT
1577213 AGAAGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAGTAATACGAATTAATCAT
Found at i:1589836 original size:60 final size:59
Alignment explanation
Indices: 1589755--1589870 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 59
1589745 AGTCAGGTGA
* *
1589755 TCATTTTATAACTTTTAATAGTCGGAA-GACTCAATAAAATAACGTTCTATAGTCGGATGG
1 TCATTTTATAACTTTTAATAGTC--AAGGACTCAACAAAATAACGTCCTATAGTCGGATGG
* *
1589815 TCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAATAATGTCCTATAGTCGG
1 TCATTTTATAACTTTTAATAGTCAA-GGACTCAACAAAATAACGTCCTATAGTCGG
1589871 GGACGACCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 2 0.04
60 48 0.96
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (59 bp):
TCATTTTATAACTTTTAATAGTCAAGGACTCAACAAAATAACGTCCTATAGTCGGATGG
Found at i:1591542 original size:19 final size:20
Alignment explanation
Indices: 1591518--1591571 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1591508 AATGACCAAT
1591518 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1591537 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1591557 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1591572 GCTGAGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1591562 original size:20 final size:20
Alignment explanation
Indices: 1591518--1591625 Score: 110
Period size: 20 Copynumber: 5.4 Consensus size: 20
1591508 AATGACCAAT
* *
1591518 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1591537 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* *
1591557 AAAATCGCAACGCGAGCTGAG
1 AAAATCGCAACGCGA-TTTAG
* * * *
1591578 AGAATCGCATCGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
1591598 AGAATTGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1591618 AAAATCGC
1 AAAATCGC
1591626 TTTGTTTCTT
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.23
20 42 0.56
21 16 0.21
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1591701 original size:6 final size:6
Alignment explanation
Indices: 1591690--1591830 Score: 282
Period size: 6 Copynumber: 23.5 Consensus size: 6
1591680 GACACGTATT
1591690 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1591738 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1591786 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1591831 CGAGACGAGA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 135 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1592541 original size:6 final size:6
Alignment explanation
Indices: 1592520--1592592 Score: 132
Period size: 6 Copynumber: 12.5 Consensus size: 6
1592510 TCTCGTCTCG
1592520 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1592566 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1592593 AATACGTGTC
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.15
6 57 0.85
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1592703 original size:20 final size:20
Alignment explanation
Indices: 1592680--1592977 Score: 143
Period size: 20 Copynumber: 14.6 Consensus size: 20
1592670 TTCTTTTGAC
1592680 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1592700 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1592720 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1592740 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
1592760 CATTGCGAATCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1592780 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
1592803 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
1592823 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
1592843 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1592866 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1592887 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
1592905 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1592927 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1592947 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1592966 CGTTGCGATTTT
1 CGTTGCGATTTT
1592978 ATTGGTCATT
Statistics
Matches: 225, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 160 0.71
21 14 0.06
22 5 0.02
23 27 0.12
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1592726 original size:40 final size:40
Alignment explanation
Indices: 1592682--1592852 Score: 216
Period size: 40 Copynumber: 4.2 Consensus size: 40
1592672 CTTTTGACCG
* * *
1592682 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* *
1592722 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * *
1592762 TTGCGAATCTCTCAGTCGCATTGCGATTCTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGATTCTC-TC--AATCGCA
* **
1592805 TTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
1592845 TTGCGATT
1 TTGCGATT
1592853 TTCTTCTAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
40 78 0.68
41 2 0.02
42 2 0.02
43 32 0.28
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:1592830 original size:63 final size:63
Alignment explanation
Indices: 1592680--1592873 Score: 259
Period size: 63 Copynumber: 3.1 Consensus size: 63
1592670 TTCTTTTGAC
* * * *
1592680 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTC-TC--AGTCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
* * * *
1592740 CATTGCGATTCTCTCAGTCGCATTGCGAATCTCTCAGTCGCATTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
* ** *
1592803 CGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
1592866 CGTTGCGA
1 CGTTGCGA
1592874 ACTTGGAAGC
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
60 46 0.40
61 2 0.02
63 67 0.58
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (63 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
Found at i:1592967 original size:19 final size:20
Alignment explanation
Indices: 1592927--1592977 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1592917 TTCTTTTTAA
*
1592927 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1592947 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1592966 CGTTGCGATTTT
1 CGTTGCGATTTT
1592978 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1597833 original size:37 final size:36
Alignment explanation
Indices: 1597758--1597833 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1597748 TTTTTATATT
*
1597758 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1597794 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1597831 TTT
1 TTT
1597834 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1597998 original size:18 final size:19
Alignment explanation
Indices: 1597975--1598011 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1597965 CCAGTAATCA
1597975 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
1597993 TATTCCTACTGGTAATCTT
1 TATTCC-ACTGGTAATCTT
1598012 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:1598017 original size:20 final size:20
Alignment explanation
Indices: 1597981--1598018 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1597971 ATCATATTCC
**
1597981 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
1598001 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1598019 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:1606973 original size:19 final size:20
Alignment explanation
Indices: 1606925--1606988 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 20
1606915 TGGTATATCT
*
1606925 AAACTTTTAAAAATTTATTTTAA
1 AAAC-TTTAAAAA--TATATTAA
*
1606948 AATCTTTAAAAATATA-TAA
1 AAACTTTAAAAATATATTAA
* *
1606967 AAACTTTGAAACTATATTAA
1 AAACTTTAAAAATATATTAA
1606987 AA
1 AA
1606989 TTAGAAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 16 0.46
20 8 0.23
22 8 0.23
23 3 0.09
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (20 bp):
AAACTTTAAAAATATATTAA
Found at i:1608766 original size:353 final size:353
Alignment explanation
Indices: 1607846--1608901 Score: 2073
Period size: 353 Copynumber: 3.0 Consensus size: 353
1607836 GGGGTGATAA
1607846 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1607911 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
66 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
1607976 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
131 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
1608041 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
196 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
1608106 GTGCAGAATATATAATTTGCAAAC-TGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
261 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
1608170 CAAGCCCACTATTATTCATTGCTAAGGT
326 CAAGCCCACTATTATTCATTGCTAAGGT
1608198 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1608263 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
66 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
1608328 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
131 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
1608393 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
196 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
1608458 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
261 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
1608523 CAAGCCCACTATTATTCATTGCTAAGGT
326 CAAGCCCACTATTATTCATTGCTAAGGT
1608551 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1608616 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
66 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
1608681 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
131 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
*
1608746 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGCACTGAAGGGA
196 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
*
1608811 GTGCA-TA-ATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
261 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
1608874 CAAGCCCACTATTATTCATTGCTAAGGT
326 CAAGCCCACTATTATTCATTGCTAAGGT
1608902 GAGTAACATA
Statistics
Matches: 701, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
351 84 0.12
352 285 0.41
353 332 0.47
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (353 bp):
TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
CAAGCCCACTATTATTCATTGCTAAGGT
Found at i:1626257 original size:17 final size:17
Alignment explanation
Indices: 1626235--1626272 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1626225 TACATACACG
*
1626235 TATTTTCTTATTTTAT-T
1 TATTTTATT-TTTTATAT
1626252 TATTTTATTTTTTATAT
1 TATTTTATTTTTTATAT
1626269 TATT
1 TATT
1626273 ACTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTATTTTTTATAT
Found at i:1626271 original size:21 final size:22
Alignment explanation
Indices: 1626235--1626288 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1626225 TACATACACG
*
1626235 TATTTTCTTATTTTATTTA-TTT
1 TATTTTCTTATATTA-TTACTTT
1626257 TATTTT-TTATATTATTACTTT
1 TATTTTCTTATATTATTACTTT
1626278 TATTTTGCTTA
1 TATTTT-CTTA
1626289 CAAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 6 0.21
23 3 0.11
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTCTTATATTATTACTTT
Found at i:1626307 original size:10 final size:10
Alignment explanation
Indices: 1626292--1626347 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
1626282 TTGCTTACAA
1626292 ATTATTATAT
1 ATTATTATAT
1626302 ATTATTATAT
1 ATTATTATAT
1626312 A-TATATATAT
1 ATTAT-TATAT
*
1626322 ATATATAACTAT
1 AT-TATTA-TAT
1626334 ATTATTAT-T
1 ATTATTATAT
1626343 ATTAT
1 ATTAT
1626348 CTTTTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 9 0.22
10 18 0.45
11 5 0.12
12 8 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTATTATAT
Found at i:1626312 original size:2 final size:2
Alignment explanation
Indices: 1626297--1626328 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1626287 TACAAATTAT
1626297 TA TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1626329 ACTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1637164 original size:11 final size:12
Alignment explanation
Indices: 1637132--1637175 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
1637122 CCTAAATTGA
1637132 AAAAGAAAAAAG
1 AAAAGAAAAAAG
1637144 AAAAGAAAAAAG
1 AAAAGAAAAAAG
1637156 AAAAG-AAAAAG
1 AAAAGAAAAAAG
*
1637167 AAGAGAAAA
1 AAAAGAAAA
1637176 TAAGGTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:1638102 original size:105 final size:105
Alignment explanation
Indices: 1637916--1638920 Score: 1676
Period size: 105 Copynumber: 9.7 Consensus size: 105
1637906 AGGTTTTACC
*
1637916 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTCCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1637981 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1638021 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1638086 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1638126 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1638191 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
1638231 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1638296 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1638336 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1638401 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
1638442 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1638507 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1638547 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1638612 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
1638652 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1638717 GCGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * * *
1638758 CAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1638823 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1638856 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
1638915 CGACGA
64 CGACGA
1638921 GGATGTCATT
Statistics
Matches: 864, Mismatches: 32, Indels: 19
0.94 0.03 0.02
Matches are distributed among these distances:
94 55 0.06
95 1 0.00
96 2 0.00
98 7 0.01
103 1 0.00
105 602 0.70
106 196 0.23
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:1638589 original size:316 final size:315
Alignment explanation
Indices: 1637916--1638920 Score: 1687
Period size: 316 Copynumber: 3.2 Consensus size: 315
1637906 AGGTTTTACC
*
1637916 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTCCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1637981 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAAATTCAGGGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTCAGAGCCAATTTCAACTTCACAACG
1638046 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
130 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
1638111 AAC-ATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
195 AACAATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
1638175 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
260 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1638231 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1638296 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGAATTCCGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTCAGAGCCAATTTCAACTTCACAACG
1638361 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
130 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
1638426 AACAATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
195 AACAATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
1638491 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
260 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1638547 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1638612 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACATCG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACG
* *
1638677 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAACA
130 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
* * * * * *
1638742 AACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCCAGACAACA
195 AACAATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
1638807 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
260 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1638856 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
1638915 CGACGA
64 CGACGA
1638921 GGATGTCATT
Statistics
Matches: 661, Mismatches: 25, Indels: 18
0.94 0.04 0.03
Matches are distributed among these distances:
305 57 0.09
306 1 0.00
307 2 0.00
309 7 0.01
314 1 0.00
315 195 0.30
316 398 0.60
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (315 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTCAGAGCCAATTTCAACTTCACAACGA
AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
ACAATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1640372 original size:42 final size:45
Alignment explanation
Indices: 1640326--1640409 Score: 111
Period size: 42 Copynumber: 1.9 Consensus size: 45
1640316 TTGCTTACAA
1640326 ATTATTATATATTATTTTA-T-ATATATATATATA-ACTATTATT
1 ATTATTATATATTATTTTACTCATATATATATATATACTATTATT
* * * *
1640368 ATTATTATCTTTTTTTTTACTCATTTATATATATATACTATT
1 ATTATTATATATTATTTTACTCATATATATATATATACTATT
1640410 TATATATACG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 16 0.46
43 1 0.03
44 12 0.34
45 6 0.17
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (45 bp):
ATTATTATATATTATTTTACTCATATATATATATATACTATTATT
Found at i:1640465 original size:13 final size:13
Alignment explanation
Indices: 1640424--1640469 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1640414 TATACGTTTC
*
1640424 TTTATTTTTTTTA
1 TTTATTTTTTTTG
* *
1640437 TTTATTGTTTTCG
1 TTTATTTTTTTTG
1640450 TTTATTTTTTTTG
1 TTTATTTTTTTTG
1640463 TTT-TTTT
1 TTTATTTT
1640470 AAACATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTATTTTTTTTG
Found at i:1643656 original size:107 final size:107
Alignment explanation
Indices: 1643468--1643680 Score: 417
Period size: 107 Copynumber: 2.0 Consensus size: 107
1643458 GTCCATTCTA
1643468 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
1 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
*
1643533 AAATCAGAAAATAGTTTAATAATCCCCTTCAAATGAGAGAAG
66 AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAAG
1643575 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
1 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
1643640 AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAA
66 AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAA
1643681 ATATGAGAAA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (107 bp):
CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAAG
Found at i:1646375 original size:34 final size:34
Alignment explanation
Indices: 1646332--1646398 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1646322 TTTGCAGTTG
1646332 GAAATAATTTAATTAGTGAACTTTTTATATATAC
1 GAAATAATTTAATTAGTGAACTTTTTATATATAC
*
1646366 GAAATAATTTAATTAGTGAATTTTTTATATATA
1 GAAATAATTTAATTAGTGAACTTTTTATATATA
1646399 AATATAGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (34 bp):
GAAATAATTTAATTAGTGAACTTTTTATATATAC
Found at i:1647617 original size:22 final size:21
Alignment explanation
Indices: 1647592--1647667 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1647582 CAGTAGAGCG
* * *
1647592 CTACTTAAAATGTTATTTTTTT
1 CTACTTAAAATATTA-ATTTAT
**
1647614 CTACTGGAAATATTAATTTAT
1 CTACTTAAAATATTAATTTAT
* *
1647635 CTACTTGAAATATTAATTTCT
1 CTACTTAAAATATTAATTTAT
1647656 CTACTTAAAATA
1 CTACTTAAAATA
1647668 AATATTTCCG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
21 34 0.74
22 12 0.26
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
CTACTTAAAATATTAATTTAT
Done.