Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 39
Found at i:5511598 original size:23 final size:22
Alignment explanation
Indices: 5511568--5511614 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
5511558 AACAAGACAG
5511568 TTGGATTAAAATCATATACTTTT
1 TTGGATTAAAATCATATA-TTTT
*
5511591 TTGGATTAAAATTATATATTTT
1 TTGGATTAAAATCATATATTTT
5511613 TT
1 TT
5511615 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (22 bp):
TTGGATTAAAATCATATATTTT
Found at i:5525899 original size:4 final size:4
Alignment explanation
Indices: 5525890--5525915 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5525880 AATGTGTTAA
5525890 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
5525916 TTATATACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:5526801 original size:16 final size:16
Alignment explanation
Indices: 5526780--5526818 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
5526770 TTCTTGATGG
5526780 TCTTTTAATAGTTTGA
1 TCTTTTAATAGTTTGA
5526796 TCTTTTAATAGTTTGA
1 TCTTTTAATAGTTTGA
5526812 TCTTTTA
1 TCTTTTA
5526819 TTGTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (16 bp):
TCTTTTAATAGTTTGA
Found at i:5527681 original size:15 final size:16
Alignment explanation
Indices: 5527659--5527696 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
5527649 TTATCATATT
5527659 TATTTATAAAAAAATA
1 TATTTATAAAAAAATA
*
5527675 T-TTTATATAAAAATA
1 TATTTATAAAAAAATA
5527690 TATTTAT
1 TATTTAT
5527697 TAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTATAAAAAAATA
Found at i:5527700 original size:15 final size:15
Alignment explanation
Indices: 5527659--5527700 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
5527649 TTATCATATT
5527659 TATTTA-TAAAAAAA
1 TATTTATTAAAAAAA
*
5527673 TATTTTATATAAAAATA
1 TA-TTTAT-TAAAAAAA
5527690 TATTTATTAAA
1 TATTTATTAAA
5527701 TTTTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
16 5 0.21
17 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTATTAAAAAAA
Found at i:5531473 original size:20 final size:20
Alignment explanation
Indices: 5531448--5531485 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5531438 TTACAACTAA
*
5531448 TCTCTCATAAAAATATTTAT
1 TCTCTCATAAAAAAATTTAT
*
5531468 TCTCTCTTAAAAAAATTT
1 TCTCTCATAAAAAAATTT
5531486 GTTGTCCACA
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:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
TCTCTCATAAAAAAATTTAT
Found at i:5536814 original size:66 final size:67
Alignment explanation
Indices: 5536723--5536870 Score: 185
Period size: 67 Copynumber: 2.2 Consensus size: 67
5536713 AATTATTTTA
* ** *
5536723 TAAAATAAACTAAA-TCTTCAAATATAATTTA-ATGATTATATATTACTTTATAATCAATTTAAA
1 TAAAATAAAATAAATTCTTCAAATATAATTTAGAAAAATATATATTACTTTATAATCAATTTAAA
5536786 CT
66 CT
* *
5536788 TAAAACTAAAATAAATTC-TCAAATATAATTTAGAAAAATATATATTATTTTATAATTAATTTAA
1 TAAAA-TAAAATAAATTCTTCAAATATAATTTAGAAAAATATATATTACTTTATAATCAATTTAA
*
5536852 ATT
65 ACT
*
5536855 TAAAAATGAAATAAAT
1 T-AAAATAAAATAAAT
5536871 CTTAATACCC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
65 5 0.07
66 22 0.31
67 40 0.56
68 4 0.06
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (67 bp):
TAAAATAAAATAAATTCTTCAAATATAATTTAGAAAAATATATATTACTTTATAATCAATTTAAA
CT
Found at i:5537509 original size:29 final size:29
Alignment explanation
Indices: 5537476--5537575 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
5537466 AGAGTGTCAT
*
5537476 AGTTTAGGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATATTCAAA
* * *
5537505 AGTTTAAGGACT-AATTTAGAATGGGAGTC-AT
1 AGTTTAAGGA-TGAAATTAGAAT---ATTCAAA
*
5537536 AGTTTAGGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATATTCAAA
5537565 AGTTTAAGGAT
1 AGTTTAAGGAT
5537576 CAATTTAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
28 3 0.05
29 29 0.52
30 2 0.04
31 19 0.34
32 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTAGAATATTCAAA
Found at i:5537525 original size:60 final size:60
Alignment explanation
Indices: 5537428--5537592 Score: 226
Period size: 60 Copynumber: 2.8 Consensus size: 60
5537418 TTTGGGAATA
* * * * * *
5537428 AAATTGGAAGATTCAAAGGTTTGAGGACTAATATAGAAAGAGTGTCATAGTTTAGGGATG
1 AAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTTTAGGGATG
* *
5537488 AAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGGGAGTCATAGTTTAGGGATG
1 AAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTTTAGGGATG
5537548 AAATTAGAATATTCAAAAGTTTAAGGA-TCAATTTA-AAATGAGAGT
1 AAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAGAAA-GAGAGT
5537593 TATTCTTTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 3 0.03
60 90 0.97
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (60 bp):
AAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTTTAGGGATG
Found at i:5537769 original size:55 final size:55
Alignment explanation
Indices: 5537685--5537794 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
5537675 TTTTCTAATT
5537685 TATGAAATAACATCTACATATTTTGTACTATAAAAGAGTAAAAATATAACTATTA
1 TATGAAATAACATCTACATATTTTGTACTATAAAAGAGTAAAAATATAACTATTA
5537740 TATGAAATAACATCTACATATTTTGTACTATAAAAGAGTAAAAATATAACTATTA
1 TATGAAATAACATCTACATATTTTGTACTATAAAAGAGTAAAAATATAACTATTA
5537795 AATTAAAGGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (55 bp):
TATGAAATAACATCTACATATTTTGTACTATAAAAGAGTAAAAATATAACTATTA
Found at i:5538179 original size:17 final size:18
Alignment explanation
Indices: 5538148--5538182 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5538138 AGTTTTCCAA
5538148 AAAAAATTATTAAAATATT
1 AAAAAATTA-TAAAATATT
5538167 AAAAAATTA-AAAATAT
1 AAAAAATTATAAAATAT
5538183 ATATGCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATTATAAAATATT
Found at i:5539315 original size:23 final size:24
Alignment explanation
Indices: 5539267--5539319 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
5539257 ATATTTTTTA
5539267 ATATTATAATAATATATACTCAATT
1 ATATTATAATAATATATACT-AATT
*
5539292 ATATTATAATAATATATAGT-ATT
1 ATATTATAATAATATATACTAATT
5539315 ATATT
1 ATATT
5539320 TTTACCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 8 0.30
25 19 0.70
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATTATAATAATATATACTAATT
Found at i:5539476 original size:23 final size:21
Alignment explanation
Indices: 5539450--5539495 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
5539440 ATGTATTAAA
5539450 TATTAATATAATATAACTAATAT
1 TATTAATATAATATAA-T-ATAT
* *
5539473 TATTATTTTAATATAATATAT
1 TATTAATATAATATAATATAT
5539494 TA
1 TA
5539496 ATCTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTAATATAATATAATATAT
Found at i:5539477 original size:30 final size:28
Alignment explanation
Indices: 5539404--5539497 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 28
5539394 TTTTCATAAA
*
5539404 AATAATATTATTGAATAATTAATA-AAGAAT
1 AATAATATTATT-AAT-ATTAATATAA-TAT
*
5539434 AATATTATGTATTAAATATTAATATAATAT
1 AATAATAT-TATT-AATATTAATATAATAT
*
5539464 AACTAATATTATT-ATTTTAATATAATAT
1 AA-TAATATTATTAATATTAATATAATAT
*
5539492 ATTAAT
1 AATAAT
5539498 CTTAATATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
27 4 0.07
28 15 0.27
30 22 0.40
31 14 0.25
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (28 bp):
AATAATATTATTAATATTAATATAATAT
Found at i:5539484 original size:14 final size:14
Alignment explanation
Indices: 5539467--5539508 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5539457 ATAATATAAC
*
5539467 TAATATTATTATTT
1 TAATATTAATATTT
*
5539481 TAATA-TAATATAT
1 TAATATTAATATTT
*
5539494 TAATCTTAATATTT
1 TAATATTAATATTT
5539508 T
1 T
5539509 TAATTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTAATATTT
Found at i:5539491 original size:19 final size:19
Alignment explanation
Indices: 5539449--5539505 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
5539439 TATGTATTAA
*
5539449 ATATTAAT-ATAATATAACT
1 ATATTAATCTTAATATAA-T
*
5539468 AATATTATTATTTTAATATAAT
1 -ATATTA--ATCTTAATATAAT
5539490 ATATTAATCTTAATAT
1 ATATTAATCTTAATAT
5539506 TTTTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 6 0.19
22 3 0.09
23 8 0.25
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTAATCTTAATATAAT
Found at i:5539509 original size:28 final size:28
Alignment explanation
Indices: 5539443--5539517 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
5539433 TAATATTATG
*
5539443 TATTAA-ATATTAATATAATATAACTAA
1 TATTAATATTTTAATATAATATAACTAA
* *
5539470 TATTATTATTTTAATATAATAT-ATTAA
1 TATTAATATTTTAATATAATATAACTAA
*
5539497 TCTTAATATTTTTAATTATAA
1 TATTAATA-TTTTAA-TATAA
5539518 AGTTGTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 15 0.38
28 20 0.50
29 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTAATATTTTAATATAATATAACTAA
Found at i:5539922 original size:31 final size:31
Alignment explanation
Indices: 5539887--5539962 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
5539877 ACATATTTAT
* *
5539887 TCACTCATCTATTACTTTCGTTCTATTTTGA
1 TCACTCAACTATTACTTTCATTCTATTTTGA
*
5539918 TCACTCAACTATTACTTTTATTCTATTTTGA
1 TCACTCAACTATTACTTTCATTCTATTTTGA
5539949 TCACTCAACTATTA
1 TCACTCAACTATTA
5539963 GTTTTTTTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.04, T:0.49
Consensus pattern (31 bp):
TCACTCAACTATTACTTTCATTCTATTTTGA
Found at i:5546747 original size:16 final size:16
Alignment explanation
Indices: 5546721--5546790 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
5546711 TTTTTGTAAA
5546721 TTTATAAAAATAATATT
1 TTTA-AAAAATAATATT
*
5546738 TTTAAAAAATAATAAT
1 TTTAAAAAATAATATT
* * * * *
5546754 GTTATAAAGT-TTTTT
1 TTTAAAAAATAATATT
5546769 TTTAAAAAATAA-AGTT
1 TTTAAAAAATAATA-TT
5546785 TTTAAA
1 TTTAAA
5546791 TATAAACATA
Statistics
Matches: 39, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
15 9 0.23
16 26 0.67
17 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
TTTAAAAAATAATATT
Found at i:5548268 original size:21 final size:21
Alignment explanation
Indices: 5548242--5548291 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
5548232 TCCAGATTTA
5548242 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
*
5548263 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTCGACTATCG
*
5548284 CAATGCGA
1 CAACGCGA
5548292 TTTACATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCG
Found at i:5548334 original size:21 final size:21
Alignment explanation
Indices: 5548300--5548642 Score: 273
Period size: 21 Copynumber: 16.6 Consensus size: 21
5548290 GATTTACATA
*
5548300 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
5548321 TTCGCGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
5548342 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
5548363 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
5548382 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
5548403 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
5548422 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
5548445 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
5548464 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
5548485 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
5548504 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
5548527 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
5548546 TTCGAGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCCAAG
5548569 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
5548588 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
5548611 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
5548630 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
5548643 TTATTCCAAA
Statistics
Matches: 248, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
19 79 0.32
21 136 0.55
23 33 0.13
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:5548450 original size:82 final size:84
Alignment explanation
Indices: 5548325--5548667 Score: 563
Period size: 82 Copynumber: 4.2 Consensus size: 84
5548315 TCCAAGTTCG
* *
5548325 CGTTGTGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
5548388 TTGCGA-TT-TTCCAAATT
66 TTGCGATTTATTCCAAATT
*
5548405 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
5548470 TTGCGA-TT-TTCCAAATT
66 TTGCGATTTATTCCAAATT
*
5548487 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGAG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
*
5548552 TTGCGATTTATTCTAAATT
66 TTGCGATTTATTCCAAATT
* *
5548571 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCA
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
5548636 TTGCGATTTATTCCAAATT
66 TTGCGATTTATTCCAAATT
* *
5548655 TGTTACGATAGTC
1 CGTTGCGATAGTC
5548668 CAAAATCTCA
Statistics
Matches: 249, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
80 28 0.11
81 2 0.01
82 118 0.47
83 2 0.01
84 99 0.40
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (84 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
TTGCGATTTATTCCAAATT
Found at i:5548670 original size:42 final size:42
Alignment explanation
Indices: 5548325--5548667 Score: 563
Period size: 42 Copynumber: 8.3 Consensus size: 42
5548315 TCCAAGTTCG
*
5548325 CGTTGTGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
5548365 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
5548405 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
5548447 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
5548487 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
5548529 CGTTGCGATAGTCCAAGTTCGAGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
5548571 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
5548613 CGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
5548655 TGTTACGATAGTC
1 CGTTGCGATAGTC
5548668 CAAAATCTCA
Statistics
Matches: 290, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
40 106 0.37
41 6 0.02
42 178 0.61
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:5548771 original size:6 final size:6
Alignment explanation
Indices: 5548760--5548786 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5548750 GACACGTATT
5548760 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
5548787 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5549455 original size:42 final size:42
Alignment explanation
Indices: 5549393--5549625 Score: 340
Period size: 42 Copynumber: 5.5 Consensus size: 42
5549383 TGCGATTTTG
* *
5549393 GACTATCGCAACGAATTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
5549435 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
5549477 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * ** *
5549519 GACTATCGCAATGAACTTGGAATAAATCACAACATGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
5549561 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
5549603 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
5549626 CTATCACAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 161 0.95
44 9 0.05
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:5550311 original size:23 final size:22
Alignment explanation
Indices: 5550272--5550316 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5550262 TTATTATATT
*
5550272 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
5550295 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
5550317 ATATTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:5550323 original size:17 final size:18
Alignment explanation
Indices: 5550286--5550324 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5550276 ATATTTTGTA
5550286 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
5550304 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
5550321 TTTA
1 TTTA
5550325 CATATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:5552700 original size:34 final size:34
Alignment explanation
Indices: 5552619--5552700 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
5552609 TTCAGTTAAT
5552619 TTTGTTTA-TTACCATTTAATATCAGTTATTGTAA
1 TTTGTTTATTTACCATTTAATATCA-TTATTGTAA
*
5552653 TTTGGTATCATTTACCATTTAATA-C-TTATTGTAA
1 TTT-GT-TTATTTACCATTTAATATCATTATTGTAA
5552687 GTTTGTTGTATTTA
1 -TTTGTT-TATTTA
5552701 AAATTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
33 1 0.02
34 19 0.46
35 5 0.12
36 3 0.07
37 13 0.32
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.54
Consensus pattern (34 bp):
TTTGTTTATTTACCATTTAATATCATTATTGTAA
Found at i:5553728 original size:20 final size:21
Alignment explanation
Indices: 5553691--5553730 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5553681 AAATTAAGTT
5553691 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
5553712 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
5553731 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:5554016 original size:65 final size:63
Alignment explanation
Indices: 5553900--5554106 Score: 220
Period size: 65 Copynumber: 3.2 Consensus size: 63
5553890 ATTTGAGGTG
* * * * * *
5553900 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCAAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
5553964 C
63 C
* *
5553965 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
5554030 ATGCATCGATGCA-CACGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATCA--CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
5554094 ATGCATCGATGCA
1 ATGCACCGATGCA
5554107 CACTTGGTGC
Statistics
Matches: 123, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 83 0.67
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:5554125 original size:64 final size:65
Alignment explanation
Indices: 5553947--5554110 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
5553937 GAATTAATTG
* * * ** *
5553947 AAACATCAAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* * **
5554012 AAACATCGAATGCATTTGATGCATCGATGCACACGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
5554076 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
5554111 TGGTGCACCG
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 33 0.38
65 54 0.62
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:5562612 original size:65 final size:63
Alignment explanation
Indices: 5562496--5562702 Score: 229
Period size: 65 Copynumber: 3.2 Consensus size: 63
5562486 ATTTGAGGTG
* * * * *
5562496 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
5562560 C
63 C
* *
5562561 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
5562626 ATGCATCGATGCA-CACGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATCA--CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
5562690 ATGCATCGATGCA
1 ATGCACCGATGCA
5562703 CACTTGGTGC
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 84 0.68
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:5562721 original size:64 final size:65
Alignment explanation
Indices: 5562543--5562706 Score: 240
Period size: 65 Copynumber: 2.5 Consensus size: 65
5562533 GAATTAATTG
* * ** *
5562543 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* * **
5562608 AAACATCGAATGCATTTGATGCATCGATGCACACGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
5562672 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
5562707 TGGTGCACCG
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 33 0.38
65 55 0.62
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:5564011 original size:30 final size:29
Alignment explanation
Indices: 5563945--5564011 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
5563935 TCTACAAGCC
*
5563945 TTAGAAAAATTAGGGACAATTTCGTAAGT
1 TTAGAAAAATTAGGGACAATTTCGTAAAT
* * *
5563974 TTTGAAAAGTTGGGGATCAA-TTCGTAAAT
1 TTAGAAAAATTAGGGA-CAATTTCGTAAAT
5564003 TCTAGAAAA
1 T-TAGAAAA
5564012 TTGATGGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (29 bp):
TTAGAAAAATTAGGGACAATTTCGTAAAT
Found at i:5565091 original size:43 final size:46
Alignment explanation
Indices: 5565043--5565145 Score: 140
Period size: 47 Copynumber: 2.3 Consensus size: 46
5565033 GTAAGTATGC
*
5565043 AAATAAGCTTACGAGCTTATG-AA-T-AATGGCAAGTGTATTGATA
1 AAATAAGCTTACGAGCTTATGAAATTAAATGGCAAGTATATTGATA
* * *
5565086 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGAAA-TTAAATGGCAAGTATATTGATA
5565133 AAATAAGCTTACG
1 AAATAAGCTTACG
5565146 CTTATGGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 21 0.40
44 2 0.04
46 1 0.02
47 28 0.54
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGAAATTAAATGGCAAGTATATTGATA
Found at i:5565674 original size:13 final size:13
Alignment explanation
Indices: 5565658--5565696 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5565648 ATTCATCGTC
5565658 ACTGTTCACTATT
1 ACTGTTCACTATT
*
5565671 ACTGTTCACGGA-T
1 ACTGTTCAC-TATT
5565684 ACTGTTCACTATT
1 ACTGTTCACTATT
5565697 CATAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (13 bp):
ACTGTTCACTATT
Found at i:5568818 original size:14 final size:15
Alignment explanation
Indices: 5568787--5568825 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
5568777 TCAAATAATC
5568787 ATAATAAACAATAAGT
1 ATAATAAA-AATAAGT
5568803 ATAATAAAAA-AAGT
1 ATAATAAAAATAAGT
*
5568817 ATAACAAAA
1 ATAATAAAA
5568826 TTACCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (15 bp):
ATAATAAAAATAAGT
Found at i:5569296 original size:15 final size:15
Alignment explanation
Indices: 5569253--5569296 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
5569243 AAAGGCTGTT
*
5569253 AGATCAAAAAATATA
1 AGATCAATAAATATA
* *
5569268 ATAT-AATCAATATA
1 AGATCAATAAATATA
5569282 AGATCAATAAATATA
1 AGATCAATAAATATA
5569297 CCGATCACCG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (15 bp):
AGATCAATAAATATA
Found at i:5575366 original size:25 final size:25
Alignment explanation
Indices: 5575329--5575390 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
5575319 GAACTAAATT
*
5575329 AAAATAATTAAAACAACAAATAATA
1 AAAATAATAAAAACAACAAATAATA
* *
5575354 AAAATAGTAAAAACAACCAATAA-A
1 AAAATAATAAAAACAACAAATAATA
*
5575378 AATAAAAATAAAA
1 AA-AATAATAAAA
5575391 TAAATACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 3 0.10
25 28 0.90
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAATAATAAAAACAACAAATAATA
Found at i:5577166 original size:20 final size:20
Alignment explanation
Indices: 5577104--5577168 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5577094 GCCTGAGAGT
*
5577104 CTTATGGATGGCCCGAAGGA
1 CTTATAGATGGCCCGAAGGA
** * * *
5577124 CTTATCATCTTGCTCGAAAGA
1 CTTAT-AGATGGCCCGAAGGA
5577145 CTTATAGATGGCCCGAAGGA
1 CTTATAGATGGCCCGAAGGA
5577165 CTTA
1 CTTA
5577169 CTCATCAAGA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (20 bp):
CTTATAGATGGCCCGAAGGA
Found at i:5577317 original size:235 final size:235
Alignment explanation
Indices: 5576868--5577399 Score: 802
Period size: 235 Copynumber: 2.3 Consensus size: 235
5576858 CCTTGAAAAA
* * * * * * *
5576868 CTTATAAATAGCCTGAAGGACTTATGCATCATGCTCGAAAGACTTACTA-ATAGTCAGAAGGACT
1 CTTATAGATGGCCCGAAGGACTTAT-CATCTTGCTCGAAAGACTTA-TAGATGGCCCGAAGGACT
5576932 TACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAA
64 TACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAA
* * * *
5576997 ATTAGGCTTAGCTTTCTTTAAAAAATCTTTGGAGATAATTATCAAGAAACCCCTAAAAATCAAGC
129 ATTAGGCTTAGCTTCCTTTAAAAAATCTTTGAAAATAATCATCAAGAAACCCCTAAAAATCAAGC
*
5577062 TTAGTTTCTAAAAGCTCATTTGAAAACATCATGCCTG-AGAGT
194 TTAGTTTCTAAAAACTCATTTGAAAACATCATGCCTGAAG-GT
*
5577104 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTTA
1 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTTA
*
5577169 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTTTTAGTTGTCATCAAGGAACCCCTAAAAAT
66 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAAAT
* **
5577234 TAGGCTTAGCTTCCTTTTAAAAACTCTTTGAAAAT-ATCATCAAGAAACCCCTGGAAATC-AGTC
131 TAGGCTTAGCTTCC-TTTAAAAAATCTTTGAAAATAATCATCAAGAAACCCCTAAAAATCAAG-C
*
5577297 TTAGTTTCTAAAAACTCATTTGAAAACATCCTGCCTGAAGGT
194 TTAGTTTCTAAAAACTCATTTGAAAACATCATGCCTGAAGGT
* * *
5577339 CTTATAGATGGCCCGAAGGGCTTATCATCTTGCTCGAAAGACTTATAGAAGACCCGAAGGA
1 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGA
5577400 TTTAAGCATC
Statistics
Matches: 270, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
234 4 0.01
235 226 0.84
236 40 0.15
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (235 bp):
CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTTA
CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAAAT
TAGGCTTAGCTTCCTTTAAAAAATCTTTGAAAATAATCATCAAGAAACCCCTAAAAATCAAGCTT
AGTTTCTAAAAACTCATTTGAAAACATCATGCCTGAAGGT
Found at i:5577452 original size:42 final size:41
Alignment explanation
Indices: 5577339--5577452 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
5577329 GCCTGAAGGT
* * **
5577339 CTTATAGATGGCCCGAAGGGCTTATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTATCATCACGCTCGAAAGA
* * *
5577380 CTTATAGAAGACCCGAAGGATTTAAGCATCACGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTT-ATCATCACGCTCGAAAGA
5577422 CTTA-ATGATGACCCGAAGGACTTACTCATCA
1 CTTATA-GATGACCCGAAGGACTTA-TCATCA
5577453 AGAAACCCTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 21 0.35
42 39 0.65
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (41 bp):
CTTATAGATGACCCGAAGGACTTATCATCACGCTCGAAAGA
Found at i:5577605 original size:71 final size:72
Alignment explanation
Indices: 5577489--5577644 Score: 226
Period size: 71 Copynumber: 2.2 Consensus size: 72
5577479 TTCTTAATTG
* * *
5577489 TCATCAAGAAACCCCTACATATCACGCTGGTCCCTCGAGCTTAGTTTCTTAT-AAAAATTCATT-
1 TCATCAAGAAACCCCTACATATCACACTGGTCCCTCAAGCTTAGTTTCTTATAAAAAAATCATTG
5577552 AAAATTCA
66 AAAA-TCA
* * *
5577560 TCATCAAGGAACCCCTACATATCATATTGGTCCCTCAAGCTTAGTTTCTTATAAAAAAATCATTG
1 TCATCAAGAAACCCCTACATATCACACTGGTCCCTCAAGCTTAGTTTCTTATAAAAAAATCATTG
*
5577625 AAAATCG
66 AAAATCA
5577632 TCATCAAGAAACC
1 TCATCAAGAAACC
5577645 TCTAAAAATC
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
71 47 0.63
72 24 0.32
73 4 0.05
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (72 bp):
TCATCAAGAAACCCCTACATATCACACTGGTCCCTCAAGCTTAGTTTCTTATAAAAAAATCATTG
AAAATCA
Found at i:5577851 original size:24 final size:23
Alignment explanation
Indices: 5577824--5577883 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
5577814 GATTAAAATA
5577824 TATATTATATTTATTATTATATAC
1 TATATTATATTTATTATTAT-TAC
* *
5577848 TATAGTATGA-TTATTATTATTAT
1 TATATTAT-ATTTATTATTATTAC
5577871 TAATATTAT-TTTA
1 T-ATATTATATTTA
5577884 CAATATTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 6 0.20
24 23 0.77
25 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (23 bp):
TATATTATATTTATTATTATTAC
Found at i:5580301 original size:228 final size:227
Alignment explanation
Indices: 5579867--5580324 Score: 864
Period size: 227 Copynumber: 2.0 Consensus size: 227
5579857 GGGTTGTTAA
5579867 TGTCGAGATTTATTTTTATATTAAAGTTTTTTTTTAATTCAAAACAAATTTAGCTTCGATAAAAG
1 TGTCGAGATTTATTTTTATATTAAAGTTTTTTTTTAATTCAAAACAAATTTAGCTTCGATAAAAG
5579932 GACCATATTTTAACTTTATATTCGATTCAATATTTTTACTATTACAACGTGTAAGCGAAACAGTA
66 GACCATATTTTAACTTTATATTCGATTCAATATTTTTACTATTACAACGTGTAAGCGAAACAGTA
5579997 CCAATTTTGTGGGCTGTGGGGTGCTAATCCTTCCCCACGCGTAACCGACTCCCGAACCCGTTTTA
131 CCAATTTTGTGGGCTGTGGGGTGCTAATCCTTCCCCACGCGTAACCGACTCCCGAACCCGTTTTA
5580062 AACGAATCTTTGGTAAACGCAGACTAGTCTTT
196 AACGAATCTTTGGTAAACGCAGACTAGTCTTT
*
5580094 TGTCGAGATTTCTTTTTATATTAAAGTTTTTTTTTAATTCAAAACAAATTTAGCTTCGATAAAAG
1 TGTCGAGATTTATTTTTATATTAAAGTTTTTTTTTAATTCAAAACAAATTTAGCTTCGATAAAAG
5580159 GACCATATTTTAACTTTATATTCGATTCAATATTTTTACTATTACAACGTGTAAGCGAAACAGTA
66 GACCATATTTTAACTTTATATTCGATTCAATATTTTTACTATTACAACGTGTAAGCGAAACAGTA
* *
5580224 CTAATTTTG-GGCGTTGTGGGGGTGCTAATCCTTCCCCACGCGTAACCGACTCCCGAACCCGTTT
131 CCAATTTTGTGG-GCTGT-GGGGTGCTAATCCTTCCCCACGCGTAACCGACTCCCGAACCCGTTT
5580288 TAAACGAATCTTTGGTAAACGCAGACTAGTCTTT
194 TAAACGAATCTTTGGTAAACGCAGACTAGTCTTT
5580322 TGT
1 TGT
5580325 TTTTAAAAAT
Statistics
Matches: 226, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
226 2 0.01
227 141 0.62
228 83 0.37
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (227 bp):
TGTCGAGATTTATTTTTATATTAAAGTTTTTTTTTAATTCAAAACAAATTTAGCTTCGATAAAAG
GACCATATTTTAACTTTATATTCGATTCAATATTTTTACTATTACAACGTGTAAGCGAAACAGTA
CCAATTTTGTGGGCTGTGGGGTGCTAATCCTTCCCCACGCGTAACCGACTCCCGAACCCGTTTTA
AACGAATCTTTGGTAAACGCAGACTAGTCTTT
Found at i:5584826 original size:40 final size:41
Alignment explanation
Indices: 5584758--5584834 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
5584748 TGAAAAACAA
5584758 TTTTGCTTTGAGTAGGATCTACATGATCTATATTTTTGTAC
1 TTTTGCTTTGAGTAGGATCTACATGATCTATATTTTTGTAC
* *
5584799 TTTT-CTTTGAGTAGGATTTAC-TGGATCTGTATTTTT
1 TTTTGCTTTGAGTAGGATCTACAT-GATCTATATTTTT
5584835 TCATTGTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 1 0.03
40 28 0.85
41 4 0.12
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.52
Consensus pattern (41 bp):
TTTTGCTTTGAGTAGGATCTACATGATCTATATTTTTGTAC
Found at i:5588548 original size:3 final size:3
Alignment explanation
Indices: 5588540--5588569 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5588530 GAATAGGGTT
*
5588540 TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
5588570 ACTCTTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:5596198 original size:17 final size:16
Alignment explanation
Indices: 5596177--5596207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5596167 GCTTCTAATT
*
5596177 TTTTTTTAGTTCAAGC
1 TTTTTTGAGTTCAAGC
5596193 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
5596208 TTTCAATATT
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:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:5596330 original size:16 final size:16
Alignment explanation
Indices: 5596305--5596335 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5596295 CAAGTTCGAG
5596305 TCGAGCTCAACAATAC
1 TCGAGCTCAACAATAC
*
5596321 TCGAGTTCAACAATA
1 TCGAGCTCAACAATA
5596336 AAATTTTCGT
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:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (16 bp):
TCGAGCTCAACAATAC
Found at i:5596616 original size:4 final size:4
Alignment explanation
Indices: 5596607--5596638 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
5596597 ATTTACCGTT
5596607 TTTA TTTA TTTA TTTA TTTA TTTA TTTCA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTT
5596639 TTGACTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:5605274 original size:43 final size:43
Alignment explanation
Indices: 5605223--5605304 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
5605213 GTTTGTTAAC
* *
5605223 AAAAAACGCCGTAATAGGTAAAGATATATAGCGGCGTTTATTT
1 AAAAAACGCCGCAATAAGTAAAGATATATAGCGGCGTTTATTT
** *
5605266 AAAAAACGCCGCAATAAGTACTGATATTTAGCGGCGTTT
1 AAAAAACGCCGCAATAAGTAAAGATATATAGCGGCGTTT
5605305 GTTAAAGTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (43 bp):
AAAAAACGCCGCAATAAGTAAAGATATATAGCGGCGTTTATTT
Found at i:5605409 original size:43 final size:42
Alignment explanation
Indices: 5605317--5605434 Score: 103
Period size: 43 Copynumber: 2.7 Consensus size: 42
5605307 TAAAGTTCTG
* * * * *
5605317 ATATTTAGCGGCGTTTCTCT-TAAAAATGCCGCAATAGGTGTTG
1 ATATTTAGCAGCGTTT-T-TATCAAAACGCCGCAATAAGTGTTC
* *
5605360 AGATTTAGCAGCGTTTTTATCACAAACGCCGCAATAAGTTTTC
1 ATATTTAGCAGCGTTTTTATCA-AAACGCCGCAATAAGTGTTC
** *
5605403 ATATTTAGTTGCGTTTTTTATGAAAACGCCGC
1 ATATTTAGCAGCG-TTTTTATCAAAACGCCGC
5605435 TACTATTCTA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.02
42 3 0.05
43 49 0.80
44 8 0.13
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (42 bp):
ATATTTAGCAGCGTTTTTATCAAAACGCCGCAATAAGTGTTC
Found at i:5605503 original size:43 final size:42
Alignment explanation
Indices: 5605456--5605556 Score: 105
Period size: 43 Copynumber: 2.4 Consensus size: 42
5605446 TATTTAGCAA
* * *
5605456 CGTTTTTATGATAAAAAGTCGCTATAGGTCCGGTATATAGTGG
1 CGTTTTTATGATAAAAAGCCGCTAAAGGT-CGGTATATAGCGG
* * *
5605499 CGTTTTTAGGATACAAATGCCGCTAAAGGTTGGTATATAGCGG
1 CGTTTTTATGATA-AAAAGCCGCTAAAGGTCGGTATATAGCGG
*
5605542 CTTTTTTTAT-ATAAA
1 C-GTTTTTATGATAAA
5605557 CGCCGCAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.04
43 27 0.56
44 19 0.40
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (42 bp):
CGTTTTTATGATAAAAAGCCGCTAAAGGTCGGTATATAGCGG
Found at i:5606017 original size:21 final size:21
Alignment explanation
Indices: 5605970--5606021 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5605960 GCTGATATGT
* *
5605970 TGCTTCTCTCTGTGCTGTCGC
1 TGCTTCTCTTTGTGCTGTCAC
*
5605991 TACTTCTCTTTGTGCTG-CTAC
1 TGCTTCTCTTTGTGCTGTC-AC
5606012 TGCTTCTCTT
1 TGCTTCTCTT
5606022 GCTTCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.04, C:0.31, G:0.17, T:0.48
Consensus pattern (21 bp):
TGCTTCTCTTTGTGCTGTCAC
Found at i:5609194 original size:21 final size:21
Alignment explanation
Indices: 5609168--5609225 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
5609158 ACTAGTGGAA
5609168 GGTGCATAGATGCACTGCAGG
1 GGTGCATAGATGCACTGCAGG
*
5609189 GGTGCATGGATGCACTGCAGG
1 GGTGCATAGATGCACTGCAGG
5609210 GGTGCATAGATGCACT
1 GGTGCATAGATGCACT
5609226 TTGACACCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (21 bp):
GGTGCATAGATGCACTGCAGG
Found at i:5609467 original size:21 final size:21
Alignment explanation
Indices: 5609443--5609482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5609433 ATGTTTAATG
5609443 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
5609464 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
5609483 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:5610765 original size:114 final size:115
Alignment explanation
Indices: 5610550--5610765 Score: 278
Period size: 114 Copynumber: 1.9 Consensus size: 115
5610540 TTCAAATCGA
*
5610550 AATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCA
1 AATTTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAAGATTTCA
* *
5610615 TTTTGATTTTCAAAATCCATTTTTGTTTCTAGAAGAATTTTTTTAATTTG
66 TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAATTTTTTTAATTTG
* * * * *
5610665 AATTTT-TTTTTCAA-AGTTTTCAGATTTTATTTTTAAAAGCTCTAACTCCTT-TCTCAATATTT
1 AATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCT-TCAAGATTT
* * *
5610727 CATTTTGATTTTCCAAGTCTATTTTAGCTTTC-AAAAGAA
64 CATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
5610766 GATCATTTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
113 2 0.02
114 75 0.86
115 10 0.11
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.50
Consensus pattern (115 bp):
AATTTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAAGATTTCA
TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAATTTTTTTAATTTG
Found at i:5612033 original size:20 final size:20
Alignment explanation
Indices: 5612008--5612062 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
5611998 TTGCAACCTT
*
5612008 GGTGCATGGATGCACAGCAG
1 GGTGCATCGATGCACAGCAG
5612028 GGTGCATCGATGCACAGCAG
1 GGTGCATCGATGCACAGCAG
5612048 GGTGCATCGATGCAC
1 GGTGCATCGATGCAC
5612063 TAATTGCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (20 bp):
GGTGCATCGATGCACAGCAG
Found at i:5613871 original size:7 final size:7
Alignment explanation
Indices: 5613861--5613897 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
5613851 ACTTATACAG
5613861 ATCACAT
1 ATCACAT
5613868 ATCACAT
1 ATCACAT
5613875 ATCACAT
1 ATCACAT
5613882 ATCACAT
1 ATCACAT
5613889 ATCACAT
1 ATCACAT
5613896 AT
1 AT
5613898 ACCTTTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
ATCACAT
Found at i:5614078 original size:18 final size:18
Alignment explanation
Indices: 5614055--5614140 Score: 127
Period size: 18 Copynumber: 4.8 Consensus size: 18
5614045 GCGTAGAATT
* * *
5614055 TGTCCCGTAGAACCACTG
1 TGTCCCGAAGGACCACTA
5614073 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5614091 TGTTCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5614109 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
5614127 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
5614141 GCGTAGACCC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5623834 original size:21 final size:20
Alignment explanation
Indices: 5623810--5623863 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
5623800 GATGTTGAAG
*
5623810 GAAGAGGAAGAAGGTAAAAAA
1 GAAGAAGAAGAAGGT-AAAAA
5623831 GAAGAAGAAGAAGGTAAAAA
1 GAAGAAGAAGAAGGTAAAAA
5623851 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
5623864 AAGAAGGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (20 bp):
GAAGAAGAAGAAGGTAAAAA
Found at i:5623835 original size:3 final size:3
Alignment explanation
Indices: 5623829--5623869 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
5623819 GAAGGTAAAA
*
5623829 AAG AAG AAG AAG AAGG TAAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AA-G -AAG AAG AAG AAG AAG AAG AAG AAG
5623870 GAGGAGGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 31 0.91
4 1 0.03
5 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:5625547 original size:18 final size:18
Alignment explanation
Indices: 5625524--5625580 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
5625514 TATATTTTCC
*
5625524 AACAATTGGTATCTTTTT
1 AACAATTGATATCTTTTT
5625542 AACAATTGATATCATTTTGTT
1 AACAATTGATATC--TTT-TT
*
5625563 AACAATTGTTATCTTTTT
1 AACAATTGATATCTTTTT
5625581 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 14 0.41
19 3 0.09
20 3 0.09
21 14 0.41
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (18 bp):
AACAATTGATATCTTTTT
Found at i:5625566 original size:21 final size:19
Alignment explanation
Indices: 5625524--5625580 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
5625514 TATATTTTCC
*
5625524 AACAATTGGTATC-TTTTT
1 AACAATTGATATCTTTTTT
5625542 AACAATTGATATCATTTTGTT
1 AACAATTGATATC-TTTT-TT
*
5625563 AACAATTGTTATCTTTTT
1 AACAATTGATATCTTTTT
5625581 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.35
19 1 0.03
20 7 0.21
21 14 0.41
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (19 bp):
AACAATTGATATCTTTTTT
Found at i:5625881 original size:18 final size:18
Alignment explanation
Indices: 5625858--5625923 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
5625848 AATGCATAAA
5625858 GGGTATCCATACCCCCAG
1 GGGTATCCATACCCCCAG
5625876 GGGTATCCATA-CCCC--
1 GGGTATCCATACCCCCAG
* *
5625891 TGAT-TCCGATACCCCCAG
1 GGGTATCC-ATACCCCCAG
5625909 GGGTAT-CATACCCCC
1 GGGTATCCATACCCCC
5625924 TGACTGCAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
14 3 0.08
15 5 0.13
16 4 0.10
17 12 0.31
18 14 0.36
19 1 0.03
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.20
Consensus pattern (18 bp):
GGGTATCCATACCCCCAG
Found at i:5630791 original size:17 final size:16
Alignment explanation
Indices: 5630760--5630793 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5630750 CACGTGAGGA
5630760 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
5630776 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
5630793 T
1 T
5630794 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:5637161 original size:23 final size:23
Alignment explanation
Indices: 5637135--5637209 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 23
5637125 CTCCCAAATT
5637135 TTTAACTTTTTCTTTTCTCTTTC
1 TTTAACTTTTTCTTTTCTCTTTC
*
5637158 TTTATTCTTTTT-TTTTCTCTTTC
1 TTTA-ACTTTTTCTTTTCTCTTTC
* *
5637181 ATGTTAACTTTTACTTTTTCTCTCTC
1 -T-TTAACTTTTTC-TTTTCTCTTTC
5637207 TTT
1 TTT
5637210 TACTCATCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 15 0.35
24 14 0.33
25 4 0.09
26 10 0.23
ACGTcount: A:0.09, C:0.20, G:0.01, T:0.69
Consensus pattern (23 bp):
TTTAACTTTTTCTTTTCTCTTTC
Found at i:5641042 original size:17 final size:16
Alignment explanation
Indices: 5641011--5641044 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5641001 CACGTGAGGA
5641011 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
5641027 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
5641044 T
1 T
5641045 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:5643971 original size:43 final size:43
Alignment explanation
Indices: 5643911--5644252 Score: 328
Period size: 43 Copynumber: 8.0 Consensus size: 43
5643901 CAAACTGCTG
* ** *
5643911 TTGAATGTGTATTTAGCGGCGTTT-TCAAAGACAAATGCCGCTA
1 TTGACTGTGTATTTAGCGGCGTTTGTC-ATTACAAACGCCGCTA
* * **
5643954 TTGACTGTGTATTTAGCGGCGTTTGTAAATACAAACGAAGCTA
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
* * * * *
5643997 TTGACTGTGTATTTTGCGCCGCTTGTCTTTATAAACGCCGCTA
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
* * ***
5644040 TTGACTGTGTATTTAGCGGCGTTTATCTTTACAAACATTGCTA
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
* * * * *
5644083 TTGACTGTATATTTAGCGGTGTTTGTCTTTACAAACACTGCTA
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
* * * *
5644126 TTGACTATGTATTTAGCGACGTTTGTCATTACAAACTCCACTA
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
** * * *
5644169 TTGACTGTGTATTTAGCGGTATTTTTCTTTACAAACGCCACTA
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
* * * *
5644212 TTAACTGTGTATTTAGTGGCATTTGTAATTA-AAACCGCCGC
1 TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAA-CGCCGC
5644253 AAATAAGCCC
Statistics
Matches: 248, Mismatches: 49, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
42 3 0.01
43 244 0.98
44 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (43 bp):
TTGACTGTGTATTTAGCGGCGTTTGTCATTACAAACGCCGCTA
Found at i:5647719 original size:41 final size:41
Alignment explanation
Indices: 5647632--5647912 Score: 174
Period size: 41 Copynumber: 6.8 Consensus size: 41
5647622 AAACTTGTAC
* * * * * * **
5647632 TTTAGTGGCGTTTATGCTTAAAACGCCACTAATGTATGGGCC
1 TTTAGCGGCGTTT-TTCTAAAAACGCCACTAAAGTACGAGTA
* *
5647674 TTTAGCGGCGTTTTTCTAAAAACACCACTAAAGTACGTGTA
1 TTTAGCGGCGTTTTTCTAAAAACGCCACTAAAGTACGAGTA
* * * * * *
5647715 TTTAGTGGCGTTTGTATAAAAACGCCACTAAAATAAGAGTC
1 TTTAGCGGCGTTTTTCTAAAAACGCCACTAAAGTACGAGTA
* * * * * *
5647756 TTTAACGGTGTTTATATAAAAACGCCGCTAAA-TAC-ACTTA
1 TTTAGCGGCGTTTTTCTAAAAACGCCACTAAAGTACGA-GTA
* * * * * *
5647796 CTTTAGCTGCGTTTGTGCTTAAAATGCCAATAAAGTACGAGTG
1 -TTTAGCGGCGTTT-TTCTAAAAACGCCACTAAAGTACGAGTA
* *
5647839 TTTAGCGGCGTTTATAC-AAAAATGCCACTAAAGTACGAGTA
1 TTTAGCGGCGTTT-TTCTAAAAACGCCACTAAAGTACGAGTA
* * *
5647880 TTTA-CTAGCATTTGTTCAAAAAACGCCACTAAA
1 TTTAGC-GGCGTTT-TTCTAAAAACGCCACTAAA
5647913 AATGCCGCTA
Statistics
Matches: 184, Mismatches: 48, Indels: 14
0.75 0.20 0.06
Matches are distributed among these distances:
39 1 0.01
40 4 0.02
41 122 0.66
42 52 0.28
43 4 0.02
44 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCTAAAAACGCCACTAAAGTACGAGTA
Found at i:5647883 original size:165 final size:165
Alignment explanation
Indices: 5647607--5647913 Score: 390
Period size: 165 Copynumber: 1.9 Consensus size: 165
5647597 GGCATTTGTT
* * * *
5647607 TAAAAACGCCGCTAAAAACTTGTACTTTAGTGGCGTTTATGCTTAAAACGCCACTAATGTATGGG
1 TAAAAACGCCGCTAAAAACTTGTACTTTAGTGGCGTTTATGCTTAAAACGCCAATAAAGTACGAG
* * * * *
5647672 CCTTTAGCGGCGTTTTTCTAAAAACACCACTAAAGTACGTGTATTTAGTGGCGTTTG-TATAAAA
66 CCTTTAGCGGCGTTTTACTAAAAACACCACTAAAGTACGAGTATTTACTAGCATTTGTTA-AAAA
5647736 ACGCCACTAAAATAAGAGTCTTTAACGGTGTTTATA
130 ACGCCACTAAAATAAGAGTCTTTAACGGTGTTTATA
* *
5647772 TAAAAACGCCGCTAAATACAC-T-TACTTTAGCT-GCGTTTGTGCTTAAAATGCCAATAAAGTAC
1 TAAAAACGCCGCTAAA-A-ACTTGTACTTTAG-TGGCGTTTATGCTTAAAACGCCAATAAAGTAC
** **
5647834 GAGTGTTTAGCGGCGTTTATAC-AAAAATGCCACTAAAGTACGAGTATTTACTAGCATTTGTTCA
63 GAGCCTTTAGCGGCGTTT-TACTAAAAACACCACTAAAGTACGAGTATTTACTAGCATTTGTT-A
5647898 AAAAACGCCACTAAAA
126 AAAAACGCCACTAAAA
5647914 ATGCCGCTAA
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
165 96 0.79
166 22 0.18
167 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (165 bp):
TAAAAACGCCGCTAAAAACTTGTACTTTAGTGGCGTTTATGCTTAAAACGCCAATAAAGTACGAG
CCTTTAGCGGCGTTTTACTAAAAACACCACTAAAGTACGAGTATTTACTAGCATTTGTTAAAAAA
CGCCACTAAAATAAGAGTCTTTAACGGTGTTTATA
Found at i:5648002 original size:14 final size:14
Alignment explanation
Indices: 5647983--5648047 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
5647973 TTATCAAGAT
* *
5647983 TTTAGGGTTTAGGA
1 TTTAGGATTTAGGG
*
5647997 TTTAGGATTTATGG
1 TTTAGGATTTAGGG
* ** *
5648011 CTTAAAATTTAGAG
1 TTTAGGATTTAGGG
*
5648025 TTTATGATTTAGGG
1 TTTAGGATTTAGGG
5648039 TTTA-GATTT
1 TTTAGGATTT
5648048 CATTGTTCAA
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
13 5 0.13
14 34 0.87
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.48
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:5648105 original size:7 final size:8
Alignment explanation
Indices: 5648089--5648149 Score: 60
Period size: 8 Copynumber: 8.2 Consensus size: 8
5648079 TAGTTCATGA
*
5648089 TTTAAGGT
1 TTTATGGT
5648097 TTTA-GG-
1 TTTATGGT
5648103 TTTA-GGT
1 TTTATGGT
*
5648110 TTTATGAT
1 TTTATGGT
5648118 TTTATGG-
1 TTTATGGT
5648125 TTTA-GGT
1 TTTATGGT
*
5648132 TTTATGAT
1 TTTATGGT
5648140 TTTATGGT
1 TTTATGGT
5648148 TT
1 TT
5648150 AGAGATTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 8 0.18
7 14 0.31
8 23 0.51
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (8 bp):
TTTATGGT
Found at i:5648129 original size:22 final size:22
Alignment explanation
Indices: 5648096--5648151 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
5648086 TGATTTAAGG
5648096 TTTTA-GGTTTAGGTTTTATGA
1 TTTTATGGTTTAGGTTTTATGA
5648117 TTTTATGGTTTAGGTTTTATGA
1 TTTTATGGTTTAGGTTTTATGA
5648139 TTTTATGGTTTAG
1 TTTTATGGTTTAG
5648152 AGATTATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (22 bp):
TTTTATGGTTTAGGTTTTATGA
Found at i:5648158 original size:22 final size:22
Alignment explanation
Indices: 5648096--5648159 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
5648086 TGATTTAAGG
*
5648096 TTTTA-GGTTTAGGTTTTATGA
1 TTTTATGGTTTAGGTATTATGA
*
5648117 TTTTATGGTTTAGGTTTTATGA
1 TTTTATGGTTTAGGTATTATGA
5648139 TTTTATGGTTTAGAG-ATTATG
1 TTTTATGGTTTAG-GTATTATG
5648160 GTTTATGTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 5 0.12
22 34 0.85
23 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.56
Consensus pattern (22 bp):
TTTTATGGTTTAGGTATTATGA
Found at i:5650314 original size:17 final size:18
Alignment explanation
Indices: 5650278--5650318 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5650268 ATATTATGTA
*
5650278 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
5650296 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
5650313 TTTACT
1 TTTACT
5650319 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:5652669 original size:35 final size:33
Alignment explanation
Indices: 5652630--5652714 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
5652620 GTATTTCAGT
5652630 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
5652665 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
5652700 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
5652715 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:5659753 original size:11 final size:10
Alignment explanation
Indices: 5659732--5659789 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
5659722 CTCATATATT
5659732 TAAAAATCAA
1 TAAAAATCAA
5659742 TAAAAATACAA
1 TAAAAAT-CAA
*
5659753 TAAAAATGAA
1 TAAAAATCAA
*
5659763 TTAAAAATGAA
1 -TAAAAATCAA
*
5659774 TAAAATTCAA
1 TAAAAATCAA
5659784 TAAAAA
1 TAAAAA
5659790 ATGTAAAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.52
11 20 0.48
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:5659792 original size:21 final size:20
Alignment explanation
Indices: 5659732--5659789 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
5659722 CTCATATATT
*
5659732 TAAAAATCAATAAAAATACAA
1 TAAAAATCAATAAAAAT-GAA
*
5659753 TAAAAATGAATTAAAAATGAA
1 TAAAAATCAA-TAAAAATGAA
*
5659774 TAAAATTCAATAAAAA
1 TAAAAATCAATAAAAA
5659790 ATGTAAAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 6 0.19
21 19 0.59
22 7 0.22
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (20 bp):
TAAAAATCAATAAAAATGAA
Found at i:5661070 original size:59 final size:60
Alignment explanation
Indices: 5660993--5661125 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 60
5660983 AGAATGAAAT
* * * * * * *
5660993 TCATAGTTTGAGGATGAAATTGGAATTTTCAAAAGTTTAAGGA-CTAATT-TAATCTAGTA
1 TCATAATTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAAATTAAAAT-TAGAA
* *
5661052 TCATAATTTGGGGATGAAATTAGAATATTCTAAAGTTTAGGGACCAAATTAAAATTAGAA
1 TCATAATTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAAATTAAAATTAGAA
5661112 TCATAATTTGGGGA
1 TCATAATTTGGGGA
5661126 CATATAATGC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 37 0.59
60 23 0.37
61 3 0.05
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.35
Consensus pattern (60 bp):
TCATAATTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAAATTAAAATTAGAA
Found at i:5668111 original size:5 final size:5
Alignment explanation
Indices: 5668101--5668129 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5668091 TGGTCTCGTA
5668101 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
5668130 CAGTCCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:5671036 original size:8 final size:8
Alignment explanation
Indices: 5671023--5671067 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
5671013 TTATTGTTAC
5671023 ATTCACAT
1 ATTCACAT
5671031 ATTCACAT
1 ATTCACAT
5671039 ATTCACAT
1 ATTCACAT
5671047 ATTCACAT
1 ATTCACAT
*
5671055 ATTTACAT
1 ATTCACAT
*
5671063 TTTCA
1 ATTCA
5671068 TTTTGCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (8 bp):
ATTCACAT
Found at i:5674401 original size:17 final size:19
Alignment explanation
Indices: 5674362--5674403 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
5674352 TATTATACTT
5674362 GGAAAAAAAGAGAAAGAAA
1 GGAAAAAAAGAGAAAGAAA
5674381 --AAAAAAAGA-AAA-AAA
1 GGAAAAAAAGAGAAAGAAA
5674396 GGAAAAAA
1 GGAAAAAA
5674404 TTGAATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 3 0.14
16 3 0.14
17 15 0.71
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
GGAAAAAAAGAGAAAGAAA
Found at i:5678166 original size:45 final size:46
Alignment explanation
Indices: 5678025--5678205 Score: 292
Period size: 46 Copynumber: 3.9 Consensus size: 46
5678015 TGGACCTCTT
*
5678025 TCTGTAAGCCCTTCGGTGCATGATGTTTTCAAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCA
5678071 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCA
* * *
5678117 TCTGTAATCCATTCAGTGCATGATATTTTC-AAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCA
* *
5678162 TCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
5678206 AGCTTTTTGG
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
45 40 0.32
46 76 0.61
47 8 0.06
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (46 bp):
TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCA
Found at i:5678181 original size:91 final size:93
Alignment explanation
Indices: 5678025--5678205 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 93
5678015 TGGACCTCTT
* * * * *
5678025 TCTGTAAGCCCTTCGGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 TCTGTAAGCCATTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGACCTACAGTGC
5678090 ATGATGTTTTCAAAAA-CCTTCGGGTCA
66 ATGATGTTTTCAAAAAGCCTTCGGGTCA
*
5678117 TCTGTAATCCATTCAGTGCATGATATTTTC-AAAACCTTCGGGTCATCTGTAAGACCTACAGTGC
1 TCTGTAAGCCATTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGACCTACAGTGC
5678181 ATGATGTTTTCAAAAAGCCTTCGGG
66 ATGATGTTTTCAAAAAGCCTTCGGG
5678206 AGCTTTTTGG
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 48 0.59
92 34 0.41
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (93 bp):
TCTGTAAGCCATTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGACCTACAGTGC
ATGATGTTTTCAAAAAGCCTTCGGGTCA
Found at i:5678263 original size:74 final size:73
Alignment explanation
Indices: 5678142--5678278 Score: 240
Period size: 74 Copynumber: 1.9 Consensus size: 73
5678132 GTGCATGATA
5678142 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGA
1 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAA-CCTTCGGGA
5678207 GCTTTTTGG
65 GCTTTTTGG
*
5678216 TTTTCAAAACCTTCGGGTCATCTGTAA-ACCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGA-CCTACAGTGCATGATGTTTTCAAAAACCTTCGGG
5678279 TCATCTGTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
73 9 0.15
74 52 0.85
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (73 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCTTCGGGAG
CTTTTTGG
Found at i:5678266 original size:45 final size:46
Alignment explanation
Indices: 5678215--5678370 Score: 228
Period size: 46 Copynumber: 3.4 Consensus size: 46
5678205 GAGCTTTTTG
5678215 GTTTTC-AAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGAT
*
5678260 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGAT
* * * *
5678306 GTTTTC-TAAACATTCAGGTCATCTGTAAGA-CCTACAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAA-ACCCTTCAGTGCATGAT
5678351 GTTTTCAAAAAGCCTTCGGG
1 GTTTTCAAAAA-CCTTCGGG
5678371 AGCTTTTTGG
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
45 45 0.46
46 47 0.48
47 6 0.06
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (46 bp):
GTTTTCAAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGAT
Found at i:5678310 original size:120 final size:120
Alignment explanation
Indices: 5678095--5678311 Score: 373
Period size: 120 Copynumber: 1.8 Consensus size: 120
5678085 AGTGCATGAT
*
5678095 GTTTTCAAAAACCTTCGGGTCATCTGTAATCCATTCAGTGCATGATATTTTCAAAACCTTCGGGT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAACCATTCAGTGCATGATATTTTCAAAACCTTCGGGT
5678160 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
66 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
* *
5678215 GTTTTC-AAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAACCATTCAGTGCATGATATTTTC-AAAACCTTCGGG
* *
5678279 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
65 TCATCTGTAAGACCTACAGTGCATGATGTTTTC
5678312 TAAACATTCA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
119 42 0.46
120 49 0.54
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (120 bp):
GTTTTCAAAAACCTTCGGGTCATCTGTAAACCATTCAGTGCATGATATTTTCAAAACCTTCGGGT
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
Found at i:5678328 original size:165 final size:165
Alignment explanation
Indices: 5678049--5678535 Score: 832
Period size: 165 Copynumber: 2.9 Consensus size: 165
5678039 GGTGCATGAT
5678049 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
* * *
5678114 TCATCTGTAATCCATTCAGTGCATGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGT
65 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGT
5678179 GCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
130 GCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
*
5678215 GTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
5678280 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCTAAACATTCAGGTCATCTGTAAGACCTACAGTG
66 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTG
5678345 CATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
131 CATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
* *
5678380 GTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACCTTCGGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * * *
5678445 CATCTGTAAGCCCTTCAGTGCATGATGTTTACAAAAACCTTCGGGTCATCTGTAAGCCCTTCAAT
66 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGACCTACAGT
5678510 GCATGATGTTTTCAAAAA-CCTTCGGG
130 GCATGATGTTTTCAAAAAGCCTTCGGG
5678536 TCATCTGTAA
Statistics
Matches: 303, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
165 253 0.83
166 50 0.17
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (165 bp):
GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTG
CATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
Found at i:5678413 original size:119 final size:120
Alignment explanation
Indices: 5678260--5678489 Score: 365
Period size: 119 Copynumber: 1.9 Consensus size: 120
5678250 AGTGCATGAT
* * *
5678260 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-TAAACATTCAGG
1 GTTTTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACATTCAGG
*
5678324 TCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
66 TCATCTGTAAGACCTACAGTGCATGATGTTTACAAAAA-CCTTCGGGAGCTTTTTG
* *
5678380 GTTTTC-AAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACATTCAGG
* *
5678444 TCATCTGTAAGCCCTTCAGTGCATGATGTTTACAAAAACCTTCGGG
66 TCATCTGTAAGACCTACAGTGCATGATGTTTACAAAAACCTTCGGG
5678490 TCATCTGTAA
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
119 51 0.50
120 50 0.50
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (120 bp):
GTTTTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACATTCAGG
TCATCTGTAAGACCTACAGTGCATGATGTTTACAAAAACCTTCGGGAGCTTTTTG
Found at i:5678427 original size:74 final size:73
Alignment explanation
Indices: 5678306--5678443 Score: 204
Period size: 74 Copynumber: 1.9 Consensus size: 73
5678296 AGTGCATGAT
* * *
5678306 GTTTTCTAAACATTCAGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
1 GTTTTCAAAACATTCAGGTCATCTATAAGACCTACAATGCATGATGTTTTCAAAAA-CCTTCGGG
5678371 AGCTTTTTG
65 AGCTTTTTG
* * * *
5678380 GTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTCAAAACATTCAGGTCATCTATAAGACCTACAATGCATGATGTTTTCAAAAACCTTCGGG
5678444 TCATCTGTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
73 8 0.14
74 49 0.86
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (73 bp):
GTTTTCAAAACATTCAGGTCATCTATAAGACCTACAATGCATGATGTTTTCAAAAACCTTCGGGA
GCTTTTTG
Found at i:5678436 original size:46 final size:46
Alignment explanation
Indices: 5678380--5678798 Score: 702
Period size: 46 Copynumber: 9.2 Consensus size: 46
5678370 GAGCTTTTTG
* *
5678380 GTTTTC-AAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
5678425 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* *
5678471 GTTTACAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
5678517 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
5678563 GTTTTCAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
5678609 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
5678654 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
5678700 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * * ** * *
5678745 GTTCTC-AAAACCTCCAGGTCATCCATAAGACCTTCAGTGCAGGAT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
5678790 GTTTTCAAA
1 GTTTTCAAA
5678799 TGAGATTTTA
Statistics
Matches: 355, Mismatches: 16, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
45 132 0.37
46 223 0.63
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (46 bp):
GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
Found at i:5678663 original size:91 final size:91
Alignment explanation
Indices: 5678380--5678798 Score: 698
Period size: 91 Copynumber: 4.6 Consensus size: 91
5678370 GAGCTTTTTG
* *
5678380 GTTTTC-AAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGG
5678444 TCATCTGTAAGCCCTTCAGTGCATGAT
65 TCATCTGTAAGCCCTTCAGTGCATGAT
* *
5678471 GTTTACAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGG
5678536 TCATCTGTAAGCCCTTCAGTGCATGAT
65 TCATCTGTAAGCCCTTCAGTGCATGAT
*
5678563 GTTTTCAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
5678628 CATCTGTAAGCCCTTCAGTGCATGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
5678654 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
5678719 CATCTGTAAGCCCTTCAGTGCATGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
* * * ** * *
5678745 GTTCTC-AAAACCTCCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAA
1 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
5678799 TGAGATTTTA
Statistics
Matches: 314, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
90 42 0.13
91 139 0.44
92 133 0.42
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (91 bp):
GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
CATCTGTAAGCCCTTCAGTGCATGAT
Found at i:5679062 original size:3 final size:3
Alignment explanation
Indices: 5679054--5679121 Score: 73
Period size: 3 Copynumber: 21.3 Consensus size: 3
5679044 TTTTACTTTA
* * *
5679054 ATT ATT ATT ATT ATT TTT ATT ATT ATT ATTT AAT AAT ATCT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT AT-T ATT AT-T
5679102 ATCT ATT ATT ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
5679122 AATAAAGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 45 0.79
4 12 0.21
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5680123 original size:5 final size:5
Alignment explanation
Indices: 5680113--5680140 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5680103 GGTCTCGTAT
5680113 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
5680141 CAGTCCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:5680514 original size:16 final size:16
Alignment explanation
Indices: 5680493--5680540 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
5680483 AATATGTTTA
*
5680493 AATTATTAATTTATTT
1 AATTATTTATTTATTT
5680509 AATTATTTATTTATTT
1 AATTATTTATTTATTT
5680525 -ATTATTTATGTTATTT
1 AATTATTTAT-TTATTT
5680541 CACTAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
AATTATTTATTTATTT
Found at i:5680518 original size:4 final size:4
Alignment explanation
Indices: 5680495--5680540 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
5680485 TATGTTTAAA
* *
5680495 TTAT TAAT TTAT TTAA TTAT TTAT TTAT TTA- TTAT TTAT GTTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TT
5680541 CACTAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.08
4 29 0.81
5 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:5680824 original size:21 final size:21
Alignment explanation
Indices: 5680799--5680847 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
5680789 ATATTTTTAA
5680799 ATAAATAAATATCT-TACTTTT
1 ATAAATAAATAT-TGTACTTTT
5680820 ATAAATAAATATTGTACTTTT
1 ATAAATAAATATTGTACTTTT
5680841 ATAAATA
1 ATAAATA
5680848 TTATTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
ATAAATAAATATTGTACTTTT
Found at i:5682552 original size:2 final size:2
Alignment explanation
Indices: 5682545--5682604 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
5682535 TTCATGTAGA
5682545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5682587 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
5682605 TTATTAACAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5685913 original size:185 final size:185
Alignment explanation
Indices: 5685588--5685977 Score: 613
Period size: 185 Copynumber: 2.1 Consensus size: 185
5685578 TTTTATAATT
* * * *
5685588 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
5685652 ATTATAAAATAAAAATTTTATATAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
66 ATTATAAAATAAAAATTTTATATAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
* * *
5685717 TGGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGTACATATGTTA
131 TCGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAGCACATATGTTA
* *
5685772 TATATAATATATTTAATATTTT-TAATTCAGAAAAATAATTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
* * *
5685836 ATTATAAAATATAAATTTTATATAAATTTTTTAATTGATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAA-TTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
* * *
5685901 TTCGATCTTAAATTATTCATTGAGTTTTAAATGGTTTGGACTGAGCCCATATGTTA
130 TTCGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAGCACATATGTTA
*
5685957 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
5685978 AAAATTTTAT
Statistics
Matches: 188, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
184 70 0.37
185 118 0.63
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
TCGATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGACTGAGCACATATGTTA
Found at i:5686156 original size:2 final size:2
Alignment explanation
Indices: 5686149--5686179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5686139 GAACACCCCA
5686149 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 A
5686180 GTACTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5686703 original size:24 final size:24
Alignment explanation
Indices: 5686647--5686706 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
5686637 ATTTACATTA
**
5686647 AATTTAATCATAGTTTATACATAT
1 AATTTAAAGATAGTTTATACATAT
5686671 AATTTAAAGATAGTTTATACATAT
1 AATTTAAAGATAGTTTATACATAT
5686695 AATTTAAAGATA
1 AATTTAAAGATA
5686707 AAATTGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (24 bp):
AATTTAAAGATAGTTTATACATAT
Found at i:5690201 original size:25 final size:24
Alignment explanation
Indices: 5690161--5690211 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
5690151 CCTAAATGTG
5690161 TATTCATATAATTCATC-TTCCTA
1 TATTCATATAATTCATCTTTCCTA
*
5690184 TATTTATATATATATCATCTTTCCTA
1 TATTCATATA-AT-TCATCTTTCCTA
5690210 TA
1 TA
5690212 CTTGTATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 2 0.08
25 5 0.21
26 8 0.33
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTCATATAATTCATCTTTCCTA
Found at i:5691339 original size:20 final size:20
Alignment explanation
Indices: 5691314--5691351 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5691304 TTCTCCTTGA
5691314 AGTGCATCGATACATTCTGC
1 AGTGCATCGATACATTCTGC
*
5691334 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
5691352 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTGC
Found at i:5691367 original size:24 final size:24
Alignment explanation
Indices: 5691335--5691395 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
5691325 ACATTCTGCA
5691335 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
5691359 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
5691383 GTGCATCGATGCA
1 GTGCATCGATGCA
5691396 CTACCTATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:5691450 original size:63 final size:62
Alignment explanation
Indices: 5691383--5691543 Score: 182
Period size: 63 Copynumber: 2.5 Consensus size: 62
5691373 TCTTTAACAT
* *
5691383 GTGCATCGATGCACTACCTATGCATTGATACACAAAT-CACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATGCA--TTCGATGTTTCCATTTTTAAGGG
* * **
5691446 GTGCATCGATGCACTCCTTATGCATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATTG
1 GTGCATCGATGCACTCC-TATGCATCGATACAC-AAATGCATTCGATGTTTCCATTTTTAAGGG
* *
5691510 GTGCATCAATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
5691544 CTAAACAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
62 2 0.02
63 41 0.49
64 36 0.43
65 5 0.06
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATGCATTCGATGTTTCCATTTTTAAGGG
Found at i:5694128 original size:12 final size:13
Alignment explanation
Indices: 5694099--5694132 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5694089 TAAGATTTTC
5694099 TTTGAAAATAATT
1 TTTGAAAATAATT
5694112 TTTGAAAATAA-T
1 TTTGAAAATAATT
5694124 TTTGAAAAT
1 TTTGAAAAT
5694133 TACTATCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATAATT
Found at i:5696478 original size:44 final size:44
Alignment explanation
Indices: 5696416--5696534 Score: 168
Period size: 44 Copynumber: 2.7 Consensus size: 44
5696406 CGACGAGTGT
* * *
5696416 ATCGGTACAC-TGCATAGTGTATCAATGCACATTTAAAGAATGC
1 ATCGGTACACTTTCATAGTGTATCGATGCACATTCAAAGAATGC
* * *
5696459 ATCGGTGCACTTTCATAGTGTATCGATGCATATTCAAGGAATGC
1 ATCGGTACACTTTCATAGTGTATCGATGCACATTCAAAGAATGC
*
5696503 ATCGGTACACTTTCATATTGTATCGATGCACA
1 ATCGGTACACTTTCATAGTGTATCGATGCACA
5696535 GTGCACAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 9 0.14
44 57 0.86
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCGGTACACTTTCATAGTGTATCGATGCACATTCAAAGAATGC
Found at i:5696488 original size:21 final size:21
Alignment explanation
Indices: 5696411--5696533 Score: 56
Period size: 21 Copynumber: 5.7 Consensus size: 21
5696401 AAACCCGACG
* * *
5696411 AGTGTATCGGTACAC-TGCAT
1 AGTGTATCGATGCACTTTCAT
* *
5696431 AGTGTATCAATGCACATTT-AA
1 AGTGTATCGATGCAC-TTTCAT
* *
5696452 AGAATGCATCGGTGCACTTTCAT
1 AG--TGTATCGATGCACTTTCAT
5696475 AGTGTATCGATGCA-TATTCA-
1 AGTGTATCGATGCACT-TTCAT
* * *
5696495 AGGAATGCATCGGTACACTTTCAT
1 A-G--TGTATCGATGCACTTTCAT
*
5696519 ATTGTATCGATGCAC
1 AGTGTATCGATGCAC
5696534 AGTGCACAAA
Statistics
Matches: 74, Mismatches: 18, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
20 14 0.19
21 28 0.38
22 4 0.05
23 26 0.35
24 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (21 bp):
AGTGTATCGATGCACTTTCAT
Found at i:5700241 original size:20 final size:21
Alignment explanation
Indices: 5700202--5700241 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5700192 GAAGCTTTAA
* *
5700202 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
5700223 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
5700242 AACTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:5702405 original size:65 final size:64
Alignment explanation
Indices: 5702327--5702462 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 64
5702317 ACACTAATTA
* * * *
5702327 CATTCGATGTTTCAA-AAGAGCCAGGAGTTCATCGATGCAT-TATCTGTGCATCGATACATAAAA
1 CATTCGATATTTCAATAA-AACCAGGAGTGCATCGATGCATGT-T-TGTGCATCGATACACAAAA
*
5702390 TG
63 AG
* * *
5702392 CTTTCGATATTTCAATAAAATCAGGAGTGCATCGATGCATGTTTGTGCATCGGTACACAAAAAG
1 CATTCGATATTTCAATAAAACCAGGAGTGCATCGATGCATGTTTGTGCATCGATACACAAAAAG
5702456 CATTCGA
1 CATTCGA
5702463 ATTAGGGTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
64 24 0.40
65 33 0.55
66 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (64 bp):
CATTCGATATTTCAATAAAACCAGGAGTGCATCGATGCATGTTTGTGCATCGATACACAAAAAG
Found at i:5704102 original size:13 final size:13
Alignment explanation
Indices: 5704084--5704116 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5704074 GCCACCGTGG
5704084 GTGGTGGCCTGCA
1 GTGGTGGCCTGCA
*
5704097 GTGGTGGCCTGCG
1 GTGGTGGCCTGCA
5704110 GTGGTGG
1 GTGGTGG
5704117 AGTAAGGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.18, G:0.55, T:0.24
Consensus pattern (13 bp):
GTGGTGGCCTGCA
Found at i:5710666 original size:22 final size:24
Alignment explanation
Indices: 5710618--5710663 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5710608 ATTCTGCAAG
5710618 GATGATAGATTCTCTTTTTCAAAA
1 GATGATAGATTCTCTTTTTCAAAA
*
5710642 GATGATATATTCT-TTTTTCAAA
1 GATGATAGATTCTCTTTTTCAAA
5710664 GATAAGAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (24 bp):
GATGATAGATTCTCTTTTTCAAAA
Found at i:5713681 original size:36 final size:36
Alignment explanation
Indices: 5713629--5713731 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
5713619 ATTTGAGTAT
*
5713629 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
5713665 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
5713701 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
5713732 CCAGCACTGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:5722590 original size:44 final size:44
Alignment explanation
Indices: 5722453--5722612 Score: 121
Period size: 44 Copynumber: 3.6 Consensus size: 44
5722443 CATAAATTTT
** * * *
5722453 AACTCCACAAAAGAGTAGTGGAACATATTTTTTAGCAAAGTAT-A
1 AACTCCACAAAAGAGTAGTGGAACGCA-ATTTCAGCAAAATATCA
** * * * *
5722497 AAGCTCCACGGAAGAGTAGTGGAA-GCAAATTCAATCATAA-ATCTG
1 AA-CTCCACAAAAGAGTAGTGGAACGCAATTTC-AGCAAAATATC-A
*
5722542 AACTCCACAAAAGAGTAGTGGAACGGAATTTCAGCAAAATATCA
1 AACTCCACAAAAGAGTAGTGGAACGCAATTTCAGCAAAATATCA
** *
5722586 AACTCCACGGAATAGTAGTGGAA-GCAA
1 AACTCCACAAAAGAGTAGTGGAACGCAA
5722613 ATCCAACCTT
Statistics
Matches: 88, Mismatches: 22, Indels: 13
0.72 0.18 0.11
Matches are distributed among these distances:
43 7 0.08
44 51 0.58
45 30 0.34
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (44 bp):
AACTCCACAAAAGAGTAGTGGAACGCAATTTCAGCAAAATATCA
Found at i:5722644 original size:88 final size:89
Alignment explanation
Indices: 5722443--5722668 Score: 276
Period size: 88 Copynumber: 2.6 Consensus size: 89
5722433 AGAACAAAAT
* * ** * *
5722443 CATAAATTTTAACTCCACAAAAGAGTAGTGGAACATATTTTTTAGCAAAGTATAAAGCTCCACGG
1 CATAAATCTAAACTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAATATAAAGCTCCACGG
* *
5722508 AAGAGTAGTGGAAGCAAATTCAAT
66 AAGAGTAGTGGAAGCAAATCCAAC
* *
5722532 CATAAATCTGAACTCCACAAAAGAGTAGTGGAACGGA-ATTTCAGCAAAATATCAAA-CTCCACG
1 CATAAATCTAAACTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAATAT-AAAGCTCCACG
*
5722595 GAATAGTAGTGGAAGCAAATCCAAC
65 GAAGAGTAGTGGAAGCAAATCCAAC
* * * * **
5722620 CTTGAATTTAAACTTCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAA
1 CATAAATCTAAACTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAA
5722669 GTATGAAATC
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
88 71 0.61
89 46 0.39
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (89 bp):
CATAAATCTAAACTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAATATAAAGCTCCACGG
AAGAGTAGTGGAAGCAAATCCAAC
Found at i:5722863 original size:126 final size:125
Alignment explanation
Indices: 5722633--5722874 Score: 362
Period size: 126 Copynumber: 1.9 Consensus size: 125
5722623 GAATTTAAAC
*
5722633 TTCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAATCTTCACGAAAGAATAGTAAA
1 TTCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAATATGAAATCTTCACGAAAGAATAGTAAA
* * *
5722698 GTAATCCAATGATGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCGTTCAGTT
66 GTAATCCAATGATGAGTCTGAACTTCACAGAAGAGTAGTGAAA-CAGATTCTCGTTCAGTT
* * **
5722759 TTCATGGAAGAGTAGTGGAACGGATTTTTCAGCAAAATATGAGAA-CTTCACGGAAGAATAGTGG
1 TTCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAATATGA-AATCTTCACGAAAGAATAGTAA
*
5722823 AGTAATCCAA-GTTTGAGTCTGAACTTCACAGAAGAGTAGTGAAACAGATTCT
65 AGTAATCCAATG-ATGAGTCTGAACTTCACAGAAGAGTAGTGAAACAGATTCT
5722875 ATTCAAGTCA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
125 8 0.08
126 95 0.90
127 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (125 bp):
TTCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAATATGAAATCTTCACGAAAGAATAGTAAA
GTAATCCAATGATGAGTCTGAACTTCACAGAAGAGTAGTGAAACAGATTCTCGTTCAGTT
Found at i:5723207 original size:13 final size:15
Alignment explanation
Indices: 5723190--5723231 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5723180 TTATATACGT
5723190 TATTATATATA-ATA
1 TATTATATATATATA
5723204 -ATTATATTATATATA
1 TATTATA-TATATATA
*
5723219 TATTATTTATATA
1 TATTATATATATA
5723232 GCTCGAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 6 0.25
14 4 0.17
15 9 0.38
16 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATATATATATA
Found at i:5723218 original size:20 final size:20
Alignment explanation
Indices: 5723193--5723230 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5723183 TATACGTTAT
5723193 TATATATAATAATTATATTA
1 TATATATAATAATTATATTA
* *
5723213 TATATATATTATTTATAT
1 TATATATAATAATTATAT
5723231 AGCTCGAAGG
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATAATAATTATATTA
Found at i:5724374 original size:22 final size:22
Alignment explanation
Indices: 5724326--5724371 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5724316 TTGGTCCCGA
* * *
5724326 AATTAGGTTTTACATTTTTTTT
1 AATTTGGTTTTACATTTTGTAT
5724348 AATTTGGTTTTCACATTTTGTAT
1 AATTTGGTTTT-ACATTTTGTAT
5724371 A
1 A
5724372 TTTATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.59
Consensus pattern (22 bp):
AATTTGGTTTTACATTTTGTAT
Done.