Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 119 of 163
Found at i:38344602 original size:16 final size:16
Alignment explanation
Indices: 38344567--38344609 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
38344557 AATTCCTAGA
38344567 AAATTTGAGC-TAAAT
1 AAATTTGAGCTTAAAT
38344582 AAATTTGAGCTTAAA-
1 AAATTTGAGCTTAAAT
38344597 AGAATTTGAGCTT
1 A-AATTTGAGCTT
38344610 TAGCTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (16 bp):
AAATTTGAGCTTAAAT
Found at i:38346736 original size:16 final size:16
Alignment explanation
Indices: 38346702--38346737 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38346692 AATTTCATTC
* *
38346702 CATATATATATATATA
1 CATATATATATAAACA
38346718 CATATATATATAAACA
1 CATATATATATAAACA
38346734 CATA
1 CATA
38346738 ACCAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (16 bp):
CATATATATATAAACA
Found at i:38347536 original size:47 final size:47
Alignment explanation
Indices: 38347075--38347538 Score: 874
Period size: 47 Copynumber: 9.9 Consensus size: 47
38347065 TATACAAAAT
* * * *
38347075 TTGGATTGCATTTATACATTAAAATTTGGCAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
* *
38347122 TTGGACTGCATTTATACATCAAAATTTGACAGCATATACATAAATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347169 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347216 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347263 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347310 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347357 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347404 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347451 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
38347498 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACAT
1 TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACAT
38347539 TCATTTACTC
Statistics
Matches: 411, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 411 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (47 bp):
TTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAA
Found at i:38347815 original size:14 final size:15
Alignment explanation
Indices: 38347791--38347825 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
38347781 TATATACATT
38347791 ACCATATAAATACTA
1 ACCATATAAATACTA
38347806 ACCATA-AAATACTA
1 ACCATATAAATACTA
38347820 ATCCAT
1 A-CCAT
38347826 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:38355517 original size:31 final size:31
Alignment explanation
Indices: 38355455--38355517 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
38355445 TGAACTGTGA
* *
38355455 AAACCATCATTGCTGGACAATCCGAGGTGGT
1 AAACCATCATTCCTGGACAATCCGAGATGGT
* ** *
38355486 AAACCATCGTTCCTGGGTAATCTGAGATGGT
1 AAACCATCATTCCTGGACAATCCGAGATGGT
38355517 A
1 A
38355518 GGTCATCGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (31 bp):
AAACCATCATTCCTGGACAATCCGAGATGGT
Found at i:38355718 original size:111 final size:110
Alignment explanation
Indices: 38355399--38355710 Score: 335
Period size: 111 Copynumber: 2.8 Consensus size: 110
38355389 GAGAAATTTA
* *
38355399 GGATGGTAGGTCATCGTTTCTGAGCAA-CTCAAGATGACAGATTCGTTGAACTGTGAAAACCATC
1 GGATGGTAGGTCATCGTTTC-AAGCAACCT-GAGATGACAGATTCGTTGAACTGTGAAAACCATC
* * * * *
38355463 ATTG-CTGGACAATCCGAGGTGGTAAACCATC-GTTCCTGGGTAATCTG
64 ATTGTCAGG-CAATCCGAGGTGGTAAACCATCATTTTC-GGGCAATCCG
* * * * *
38355510 AGATGGTAGGTCATCGTTGTCAGGAAACCTGAGATGACAGATTTGTTGAATTGTGAAAACCATCA
1 GGATGGTAGGTCATCGTT-TCAAGCAACCTGAGATGACAGATTCGTTGAACTGTGAAAACCATCA
* ** * *
38355575 TCGTTGGGCAATCCAATGTGGTAAACCATCATTTTCGGGCAATCCG
65 TTGTCAGGCAATCCGAGGTGGTAAACCATCATTTTCGGGCAATCCG
* * * * *
38355621 GGATGGTAGGTCATCGTTCTCAAGCAACCTGGGATGATAGATTCATTGAACTATGAAAATCATCA
1 GGATGGTAGGTCATCGTT-TCAAGCAACCTGAGATGACAGATTCGTTGAACTGTGAAAACCATCA
*
38355686 TTGTCAGGCAATTCGAGGTGG-AAAC
65 TTGTCAGGCAATCCGAGGTGGTAAAC
38355711 TTATCATTGT
Statistics
Matches: 164, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
110 4 0.02
111 151 0.92
112 9 0.05
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (110 bp):
GGATGGTAGGTCATCGTTTCAAGCAACCTGAGATGACAGATTCGTTGAACTGTGAAAACCATCAT
TGTCAGGCAATCCGAGGTGGTAAACCATCATTTTCGGGCAATCCG
Found at i:38360792 original size:23 final size:23
Alignment explanation
Indices: 38360758--38360801 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
38360748 GCATAATATC
*
38360758 CAAATAATATTAAAAATGACACT
1 CAAATAAGATTAAAAATGACACT
38360781 CAAATAAGATTAAAAATGACA
1 CAAATAAGATTAAAAATGACA
38360802 GCTAAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (23 bp):
CAAATAAGATTAAAAATGACACT
Found at i:38360853 original size:23 final size:23
Alignment explanation
Indices: 38360827--38360881 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
38360817 AAACAATTGC
38360827 AAAACAACA-ATAAAATAGCACAA
1 AAAACAACACA-AAAATAGCACAA
* *
38360850 AAAACAACACCAAAAATAGTACCA
1 AAAACAACA-CAAAAATAGCACAA
38360874 AAAACAAC
1 AAAACAAC
38360882 CTGCAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.32
24 18 0.64
25 1 0.04
ACGTcount: A:0.67, C:0.22, G:0.04, T:0.07
Consensus pattern (23 bp):
AAAACAACACAAAAATAGCACAA
Found at i:38365843 original size:5 final size:5
Alignment explanation
Indices: 38365833--38365858 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38365823 TGAGCATTCG
38365833 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
38365859 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:38372472 original size:6 final size:6
Alignment explanation
Indices: 38372461--38372489 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38372451 AAAGAATGAG
38372461 AGGGAA AGGGAA AGGGAA AGGGAA AGGGA
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGA
38372490 GAGAACCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:38373154 original size:16 final size:16
Alignment explanation
Indices: 38373133--38373164 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38373123 GGATTATTTC
38373133 CTCATGGAATATGTAA
1 CTCATGGAATATGTAA
38373149 CTCATGGAATATGTAA
1 CTCATGGAATATGTAA
38373165 ACATCATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
CTCATGGAATATGTAA
Found at i:38379830 original size:12 final size:12
Alignment explanation
Indices: 38379815--38379847 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38379805 ATTAAAAGTT
*
38379815 AAAGTAAATATA
1 AAAGTAAAAATA
38379827 AAAGTAAAAATA
1 AAAGTAAAAATA
38379839 AAAG-AAAAA
1 AAAGTAAAAA
38379848 GATGACAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAGTAAAAATA
Found at i:38381038 original size:75 final size:75
Alignment explanation
Indices: 38380908--38381051 Score: 236
Period size: 75 Copynumber: 1.9 Consensus size: 75
38380898 AAGGAAAACC
* *
38380908 AGGATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATTATATTCTTTCC
1 AGGATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAAAAAAACGAATTATATTCTTTCC
38380973 AAAAAAATGT
66 AAAAAAATGT
* *
38380983 AGGATTGTTCCCTTATTAATAGAGAAGGCAAGTGGAAAGTTACAAAAAACG-ATTATATTCTTTC
1 AGGATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTA-AAAAAACGAATTATATTCTTTC
38381047 CAAAA
65 CAAAA
38381052 GAATATTAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 58 0.91
76 6 0.09
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (75 bp):
AGGATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAAAAAAACGAATTATATTCTTTCC
AAAAAAATGT
Found at i:38381180 original size:37 final size:37
Alignment explanation
Indices: 38381138--38381212 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
38381128 AATATATACA
*
38381138 ATTAATATTTTGTATGAAC-CAAATTCATATATTAATT
1 ATTAATAATTTGTATG-ACTCAAATTCATATATTAATT
38381175 ATTAATAATTTGTATGACTCAAATTCATATATTAATT
1 ATTAATAATTTGTATGACTCAAATTCATATATTAATT
38381212 A
1 A
38381213 AATTCTTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (37 bp):
ATTAATAATTTGTATGACTCAAATTCATATATTAATT
Found at i:38381238 original size:175 final size:176
Alignment explanation
Indices: 38381034--38381351 Score: 505
Period size: 175 Copynumber: 1.8 Consensus size: 176
38381024 ACAAAAAACG
* * *
38381034 ATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTT-GATCGAAATTAATTAA
1 ATTAAATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTGGCT-GAAATTAATTAA
* * *
38381098 TATAATTGTTTATATTAATAAATTCGGTAAAATA-TATACAATTAATATTTTGTATGAACCAAAT
65 TATAACTGTTAATACTAATAAATTCGGTAAAATATTATACAATTAATATTTTGTATGAACCAAAT
38381162 TCATATATTAATTATTAATAATTTGTATGACTCAAATTCATATATTA
130 TCATATATTAATTATTAATAATTTGTATGACTCAAATTCATATATTA
*
38381209 ATTAAATTCTTTCCAAAAGAATATTAATTTTCATGTCCTTTATATTTTGGCTGAAATTAATTAAT
1 ATTAAATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTGGCTGAAATTAATTAAT
* ** *
38381274 ATAACTGTTAATACTAATAAATTCGGTAAAATATTTATACTATTAATATTTTGTATGAATTAATT
66 ATAACTGTTAATACTAATAAATTCGGTAAAATA-TTATACAATTAATATTTTGTATGAACCAAAT
38381339 TCATATATTAATT
130 TCATATATTAATT
38381352 TTATCTATGT
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
175 88 0.68
176 2 0.02
177 39 0.30
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (176 bp):
ATTAAATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTGGCTGAAATTAATTAAT
ATAACTGTTAATACTAATAAATTCGGTAAAATATTATACAATTAATATTTTGTATGAACCAAATT
CATATATTAATTATTAATAATTTGTATGACTCAAATTCATATATTA
Found at i:38395537 original size:22 final size:23
Alignment explanation
Indices: 38395491--38395538 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
38395481 AATTATTAGC
*
38395491 TTACATTTCATATTCCAATTTATT
1 TTACATTT-ATATACCAATTTATT
*
38395515 TTACATTT-TATACCATTTTATT
1 TTACATTTATATACCAATTTATT
38395537 TT
1 TT
38395539 TTGAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (23 bp):
TTACATTTATATACCAATTTATT
Found at i:38397806 original size:3 final size:3
Alignment explanation
Indices: 38397800--38397904 Score: 203
Period size: 3 Copynumber: 35.3 Consensus size: 3
38397790 TCTGTTGTTC
38397800 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
38397848 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
38397895 CTT CTT CTT C
1 CTT CTT CTT C
38397905 ACTCAACCCA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 99 0.98
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:38400164 original size:3 final size:3
Alignment explanation
Indices: 38400156--38400196 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
38400146 TGGGCTGAGT
38400156 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA G
38400197 GGGAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38401338 original size:3 final size:3
Alignment explanation
Indices: 38401330--38402175 Score: 1683
Period size: 3 Copynumber: 282.0 Consensus size: 3
38401320 TTAGGTATAA
38401330 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401378 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401426 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401474 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401522 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401570 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401618 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401666 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401714 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401762 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401810 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401858 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401906 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38401954 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38402002 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38402050 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38402098 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
*
38402146 TGT TGT TGT TGT TGT TGT TGT TGT TAT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
38402176 GAGCTTCAGA
Statistics
Matches: 841, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 841 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:38402544 original size:15 final size:15
Alignment explanation
Indices: 38402526--38402565 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
38402516 ATGTGTACAA
38402526 GATTAGATTGGATTG
1 GATTAGATTGGATTG
38402541 GATTAGATTGGATTG
1 GATTAGATTGGATTG
*
38402556 GACTAGATTG
1 GATTAGATTG
38402566 AATCGTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.03, G:0.33, T:0.38
Consensus pattern (15 bp):
GATTAGATTGGATTG
Found at i:38402808 original size:5 final size:5
Alignment explanation
Indices: 38402798--38402847 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
38402788 NNNNNNNNNN
38402798 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
38402848 TAAGCTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:38403936 original size:3 final size:3
Alignment explanation
Indices: 38403928--38403967 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
38403918 TGGTCATATC
38403928 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38403968 AACCTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38404390 original size:22 final size:22
Alignment explanation
Indices: 38404365--38404407 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
38404355 TCTCCCTATT
38404365 TTGCTACCATTTTATTATTATG
1 TTGCTACCATTTTATTATTATG
* *
38404387 TTGCTACTATTTTATTGTTAT
1 TTGCTACCATTTTATTATTAT
38404408 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTATTATTATG
Found at i:38409575 original size:4 final size:4
Alignment explanation
Indices: 38409561--38409590 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
38409551 TTAAACCAAT
38409561 ATAA A-AA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
38409591 TATGTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:38415785 original size:89 final size:90
Alignment explanation
Indices: 38415662--38415854 Score: 361
Period size: 89 Copynumber: 2.2 Consensus size: 90
38415652 TATAGAACCA
* *
38415662 TTTTACGTTTACATGTTGCATACATATAAATAAATTGATGTATATATTTCTTTAAATATATATAT
1 TTTTATGTATACATGTTGCATACATATAAATAAATTGATGTATATATTTCTTTAAATATATATAT
38415727 ATATATAATTGAATCAAAATTAAAG
66 ATATATAATTGAATCAAAATTAAAG
38415752 TTTTATGTATACATGTTGCA-ACATATAAATAAATTGATGTATATATTTCTTTAAATATATATAT
1 TTTTATGTATACATGTTGCATACATATAAATAAATTGATGTATATATTTCTTTAAATATATATAT
38415816 ATATATAATTGAATCAAAATTAAAG
66 ATATATAATTGAATCAAAATTAAAG
38415841 TTTTATGTATACAT
1 TTTTATGTATACAT
38415855 TTGAACCATG
Statistics
Matches: 101, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
89 83 0.82
90 18 0.18
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (90 bp):
TTTTATGTATACATGTTGCATACATATAAATAAATTGATGTATATATTTCTTTAAATATATATAT
ATATATAATTGAATCAAAATTAAAG
Found at i:38418855 original size:14 final size:13
Alignment explanation
Indices: 38418821--38418860 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
38418811 ATGGATGGTT
*
38418821 TTATTTTGTTGGA
1 TTATTTTGATGGA
*
38418834 TCATTTTGATGGA
1 TTATTTTGATGGA
38418847 TGTATTTTGATGGA
1 T-TATTTTGATGGA
38418861 CGGTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.53
Consensus pattern (13 bp):
TTATTTTGATGGA
Found at i:38418866 original size:45 final size:45
Alignment explanation
Indices: 38418810--38418906 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
38418800 GTTAACATAC
* * * * *
38418810 GATGGATGGTTTTATTTTGTTGGATCATTTTGATGGATGTATTTT
1 GATGGACGGTTTAATTTTGTTGAATCATTCTGATGGATATATTTT
*
38418855 GATGGACGGTTTAATTTTGTTGAATCATTCTGATGGTTATATTTT
1 GATGGACGGTTTAATTTTGTTGAATCATTCTGATGGATATATTTT
38418900 GATGGAC
1 GATGGAC
38418907 AATTTATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (45 bp):
GATGGACGGTTTAATTTTGTTGAATCATTCTGATGGATATATTTT
Found at i:38425998 original size:50 final size:50
Alignment explanation
Indices: 38425883--38426124 Score: 344
Period size: 50 Copynumber: 4.8 Consensus size: 50
38425873 GATCATAACA
* * * ** *
38425883 TGCCAAAGCCATGTCCCGGACATAGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
38425934 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
38425984 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
38426034 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38426084 TGCCAACGCCATGTCCCAGACAGGGTCTTACAT-GGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
38426125 TTACCCAAAT
Statistics
Matches: 174, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
49 9 0.05
50 134 0.77
51 30 0.17
52 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:38429119 original size:35 final size:35
Alignment explanation
Indices: 38429073--38429168 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
38429063 ATTACCCCTA
*
38429073 AGGACTTGTATACCGTTTACACGATGTCACATCAT
1 AGGACTTGTATACCGTTTACACGATGTCACACCAT
* *
38429108 AGGACTTGTATACCATTTACAC-AGTGTCACCCCAT
1 AGGACTTGTATACCGTTTACACGA-TGTCACACCAT
*
38429143 AGGCCTATGTAT--CGTTTACACGATGT
1 AGGACT-TGTATACCGTTTACACGATGT
38429169 TGCTTTGAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
34 12 0.23
35 36 0.68
36 5 0.09
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (35 bp):
AGGACTTGTATACCGTTTACACGATGTCACACCAT
Found at i:38431054 original size:26 final size:26
Alignment explanation
Indices: 38431000--38431086 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
38430990 GGGTCTTCCA
* **
38431000 ACCAAATCAAACTCAAGGGACATTTG
1 ACCAACTCAAACTCAAGGGACATCGG
**
38431026 ACCAACTCAAACTCAAGGGTTATCGG
1 ACCAACTCAAACTCAAGGGACATCGG
* * * *
38431052 ACCCACTCAAACTCAAAGGACCTCTG
1 ACCAACTCAAACTCAAGGGACATCGG
38431078 A-CAACTCAA
1 ACCAACTCAA
38431087 GGGTCCTCGG
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 7 0.14
26 42 0.86
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.17
Consensus pattern (26 bp):
ACCAACTCAAACTCAAGGGACATCGG
Found at i:38434146 original size:19 final size:18
Alignment explanation
Indices: 38434104--38434146 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
38434094 CGACTCGCCC
*
38434104 TATTAATTTTTTTATATT
1 TATTAATTTTTATATATT
38434122 TATTAATATTTTATATTATT
1 TATTAAT-TTTTATA-TATT
38434142 T-TTAA
1 TATTAA
38434147 AAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTAATTTTTATATATT
Found at i:38446757 original size:17 final size:18
Alignment explanation
Indices: 38446730--38446814 Score: 59
Period size: 17 Copynumber: 4.7 Consensus size: 18
38446720 AAAATTATCA
38446730 AAATATTATAAAAA-ATAG
1 AAAT-TTATAAAAACATAG
* *
38446748 AAATTTATAAAAAAATCTAT
1 AAATTTATAAAAACA--TAG
*
38446768 AAATATTATAAAAACA-AA
1 AAAT-TTATAAAAACATAG
* **
38446786 AAATATATAAAAATTTAG
1 AAATTTATAAAAACATAG
38446804 -AATTTATAAAA
1 AAATTTATAAAA
38446815 TAATTATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
17 27 0.50
18 11 0.20
20 6 0.11
21 10 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTTATAAAAACATAG
Found at i:38446797 original size:55 final size:56
Alignment explanation
Indices: 38446729--38446835 Score: 148
Period size: 55 Copynumber: 1.9 Consensus size: 56
38446719 AAAAATTATC
*
38446729 AAAATATTATAAAAA-ATAGAAATTTATAAAAAAATCTATAAATAT-TATAAAAACAA
1 AAAATATTATAAAAATATAG-AATTTATAAAAAAAT-TATAAAAATATATAAAAACAA
* *
38446785 AAAATA-TATAAAAATTTAGAATTTATAAAATAATTATAAAAATATATAAAA
1 AAAATATTATAAAAATATAGAATTTATAAAAAAATTATAAAAATATATAAAA
38446836 TATAGAGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 8 0.17
55 29 0.63
56 9 0.20
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (56 bp):
AAAATATTATAAAAATATAGAATTTATAAAAAAATTATAAAAATATATAAAAACAA
Found at i:38446839 original size:28 final size:29
Alignment explanation
Indices: 38446731--38446839 Score: 75
Period size: 28 Copynumber: 3.9 Consensus size: 29
38446721 AAATTATCAA
* *
38446731 AATATTATAAAAA-ATAGAAATTTATAAAAA
1 AATA-TATAAAAATATAGAAA-ATATAAAAT
* * * *
38446761 AATCTATAAATAT-TATAAAA-ACAAAA-
1 AATATATAAAAATATAGAAAATATAAAAT
* **
38446787 AATATATAAAAATTTAGAATTTATAAAAT
1 AATATATAAAAATATAGAAAATATAAAAT
*
38446816 AAT-TATAAAAATATATAAAATATA
1 AATATATAAAAATATAGAAAATATA
38446840 GAGAAATTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
26 11 0.18
27 9 0.15
28 22 0.37
29 15 0.25
30 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
AATATATAAAAATATAGAAAATATAAAAT
Found at i:38453905 original size:21 final size:22
Alignment explanation
Indices: 38453880--38453928 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
38453870 GCTATTTCTG
* *
38453880 ATCTCACT-GCTGCAGTATCTA
1 ATCTCACTCGCTACAGTAACTA
*
38453901 ATCTC-GTCGCTACAGTAACTA
1 ATCTCACTCGCTACAGTAACTA
38453922 ATCTCAC
1 ATCTCAC
38453929 CGCCACTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (22 bp):
ATCTCACTCGCTACAGTAACTA
Found at i:38456990 original size:21 final size:21
Alignment explanation
Indices: 38456964--38457003 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38456954 GATCCGATTG
*
38456964 AAACACGGGAATTTTTTTTGA
1 AAACACGGAAATTTTTTTTGA
38456985 AAACACGGAAATTTTTTTT
1 AAACACGGAAATTTTTTTT
38457004 TGGAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
AAACACGGAAATTTTTTTTGA
Found at i:38457043 original size:17 final size:17
Alignment explanation
Indices: 38457000--38457075 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 17
38456990 CGGAAATTTT
38457000 TTTTTGGAAATAC-AAGAA
1 TTTTT-GAAATACGAA-AA
* *
38457018 TCTTAGAAATACGAAAA
1 TTTTTGAAATACGAAAA
*
38457035 TTTTTGAAAACACGAAAA
1 TTTTTG-AAATACGAAAA
* * *
38457053 TCTTTAAAATACGGGAAA
1 TTTTTGAAATAC-GAAAA
38457071 TTTTT
1 TTTTT
38457076 TTTGAAAACA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 18 0.40
18 27 0.60
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (17 bp):
TTTTTGAAATACGAAAA
Found at i:38457083 original size:22 final size:21
Alignment explanation
Indices: 38457068--38457118 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
38457058 AAAATACGGG
38457068 AAATTTTTTTTGAAAACACGA
1 AAATTTTTTTTGAAAACACGA
*
38457089 AAATTGTTTTTTTAAAACACGA
1 AAATT-TTTTTTGAAAACACGA
38457111 AAATTTTT
1 AAATTTTT
38457119 GAAACACGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (21 bp):
AAATTTTTTTTGAAAACACGA
Found at i:38457142 original size:42 final size:42
Alignment explanation
Indices: 38457095--38457218 Score: 141
Period size: 42 Copynumber: 3.0 Consensus size: 42
38457085 ACGAAAATTG
38457095 TTTTTTTAAAACACGAAAATTTTTGAAACACGAGAATTTTTA
1 TTTTTTTAAAACACGAAAATTTTTGAAACACGAGAATTTTTA
* * *
38457137 TTTTTTTTAAACACGAAGATTTTTG-AA-AC---AATTATTAA
1 TTTTTTTAAAACACGAAAATTTTTGAAACACGAGAATT-TTTA
* *
38457175 TTTTTTTGAAAACACGAAAAAATTTTAAAACACGAGAATTTTTA
1 TTTTTTT-AAAACACG-AAAATTTTTGAAACACGAGAATTTTTA
38457219 AGTTTTTCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
37 4 0.06
38 10 0.15
39 7 0.11
40 9 0.14
41 4 0.06
42 25 0.38
44 3 0.05
45 4 0.06
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (42 bp):
TTTTTTTAAAACACGAAAATTTTTGAAACACGAGAATTTTTA
Found at i:38457563 original size:1 final size:1
Alignment explanation
Indices: 38457559--38457611 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
38457549 GGCTTTTTCC
* * * * * *
38457559 TTTTTTTTCTTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38457612 GGCCTGTTGC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:38457570 original size:9 final size:9
Alignment explanation
Indices: 38457552--38457611 Score: 86
Period size: 9 Copynumber: 6.7 Consensus size: 9
38457542 CGACTCGGGC
*
38457552 TTTTTCCTT
1 TTTTTTCTT
38457561 TTTTTTCTT
1 TTTTTTCTT
*
38457570 TTTTCT-TT
1 TTTTTTCTT
38457578 TTTTTTCTT
1 TTTTTTCTT
38457587 TTTTTTCTT
1 TTTTTTCTT
38457596 TTTTTTCTCT
1 TTTTTTCT-T
38457606 TTTTTT
1 TTTTTT
38457612 GGCCTGTTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.15
9 32 0.70
10 7 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:38457580 original size:18 final size:18
Alignment explanation
Indices: 38457559--38457610 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
38457549 GGCTTTTTCC
38457559 TTTTTTTTCTTTTTTCTT
1 TTTTTTTTCTTTTTTCTT
*
38457577 TTTTTTTCTTTTTTTTCTT
1 TTTTTTT-TCTTTTTTCTT
*
38457596 TTTTTTCTCTTTTTT
1 TTTTTTTTCTTTTTT
38457611 TGGCCTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTCTT
Found at i:38457978 original size:3 final size:3
Alignment explanation
Indices: 38457970--38457996 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38457960 TCATTTTTCT
38457970 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
38457997 AAGCCCTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:38458405 original size:30 final size:28
Alignment explanation
Indices: 38458328--38458471 Score: 162
Period size: 30 Copynumber: 4.9 Consensus size: 28
38458318 TAATTTTGAG
* *
38458328 AAAATTTAGGGGTCATAAGGTAATTTCA
1 AAAATTTAGGGGTCAAAATGTAATTTCA
* *
38458356 AAAATTTTATGGGTTAAAATGTAATTTCAA
1 AAAA-TTTAGGGGTCAAAATGTAATTTC-A
* *
38458386 AAAAGTTTAGGGGTCAAAATATAATTTTA
1 AAAA-TTTAGGGGTCAAAATGTAATTTCA
*
38458415 GGAAAATTTAGGGGTCAAAATGCAATTTCA
1 --AAAATTTAGGGGTCAAAATGTAATTTCA
*
38458445 AAAAGTTTAGGGGCCAAAATGTAATTT
1 AAAA-TTTAGGGGTCAAAATGTAATTT
38458472 TTTAGGGGTA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
28 8 0.08
29 40 0.41
30 45 0.46
31 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (28 bp):
AAAATTTAGGGGTCAAAATGTAATTTCA
Found at i:38458411 original size:59 final size:58
Alignment explanation
Indices: 38458328--38458471 Score: 175
Period size: 59 Copynumber: 2.5 Consensus size: 58
38458318 TAATTTTGAG
* * * * *
38458328 AAAA-TTTAGGGGTCATAAGGTAATTTCA-AAAATTTTATGGGTTAAAATGTAATTTCAA
1 AAAAGTTTAGGGGTCAAAATGTAATTTCAGAAAA-TTTAGGGGTCAAAATGCAATTTC-A
* *
38458386 AAAAGTTTAGGGGTCAAAATATAATTTTAGGAAAATTTAGGGGTCAAAATGCAATTTCA
1 AAAAGTTTAGGGGTCAAAATGTAATTTCA-GAAAATTTAGGGGTCAAAATGCAATTTCA
*
38458445 AAAAGTTTAGGGGCCAAAATGTAATTT
1 AAAAGTTTAGGGGTCAAAATGTAATTT
38458472 TTTAGGGGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 4 0.05
59 46 0.62
60 20 0.27
61 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (58 bp):
AAAAGTTTAGGGGTCAAAATGTAATTTCAGAAAATTTAGGGGTCAAAATGCAATTTCA
Found at i:38458464 original size:89 final size:89
Alignment explanation
Indices: 38458306--38458471 Score: 235
Period size: 89 Copynumber: 1.9 Consensus size: 89
38458296 CAACACTTCT
* * * * **
38458306 GGGGCCAAAACATAATTTTGAGAAAATTTAGGGGTCATAAGGTAATTTCAAAAATTTTATGGGTT
1 GGGGCCAAAACATAATTTTGAGAAAATTTAGGGGTCAAAAGGCAATTTCAAAAAGTTTAGGGGCC
38458371 AAAATGTAATTTCAAAAAAGTTTA
66 AAAATGTAATTTCAAAAAAGTTTA
* * *
38458395 GGGGTCAAAATATAATTTT-AGGAAAATTTAGGGGTCAAAATGCAATTTCAAAAAGTTTAGGGGC
1 GGGGCCAAAACATAATTTTGA-GAAAATTTAGGGGTCAAAAGGCAATTTCAAAAAGTTTAGGGGC
38458459 CAAAATGTAATTT
65 CAAAATGTAATTT
38458472 TTTAGGGGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 1 0.01
89 66 0.99
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (89 bp):
GGGGCCAAAACATAATTTTGAGAAAATTTAGGGGTCAAAAGGCAATTTCAAAAAGTTTAGGGGCC
AAAATGTAATTTCAAAAAAGTTTA
Found at i:38458535 original size:22 final size:22
Alignment explanation
Indices: 38458507--38458550 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
38458497 AAATTTTGTC
* *
38458507 CATACATTCATGTTTGTAATCA
1 CATACATTCATATCTGTAATCA
38458529 CATACATTCATATCTGTAATCA
1 CATACATTCATATCTGTAATCA
38458551 TTAAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (22 bp):
CATACATTCATATCTGTAATCA
Found at i:38460885 original size:25 final size:27
Alignment explanation
Indices: 38460840--38460893 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
38460830 ACTTGAGAAG
*
38460840 CTTTAGTGGCGAAGTTATTTGGAAAGC
1 CTTTAGTGGCGAAGTCATTTGGAAAGC
38460867 CTTT-GTGGC-AAGTCATTTGGAAAGC
1 CTTTAGTGGCGAAGTCATTTGGAAAGC
38460892 CT
1 CT
38460894 ATATGACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.65
26 5 0.19
27 4 0.15
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (27 bp):
CTTTAGTGGCGAAGTCATTTGGAAAGC
Found at i:38473277 original size:22 final size:21
Alignment explanation
Indices: 38473252--38473298 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38473242 AAGCATGCAA
38473252 AATTCATCCAAAGAAATTTGAC
1 AATT-ATCCAAAGAAATTTGAC
* * *
38473274 AATTTTCCTAAGAAATTTGGC
1 AATTATCCAAAGAAATTTGAC
38473295 AATT
1 AATT
38473299 TTCCTAAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (21 bp):
AATTATCCAAAGAAATTTGAC
Found at i:38473286 original size:21 final size:21
Alignment explanation
Indices: 38473262--38473306 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
38473252 AATTCATCCA
38473262 AAGAAATTTGACAATTTTCCT
1 AAGAAATTTGACAATTTTCCT
*
38473283 AAGAAATTTGGCAATTTTCCT
1 AAGAAATTTGACAATTTTCCT
38473304 AAG
1 AAG
38473307 CACATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (21 bp):
AAGAAATTTGACAATTTTCCT
Found at i:38473644 original size:25 final size:25
Alignment explanation
Indices: 38473574--38473718 Score: 89
Period size: 25 Copynumber: 5.7 Consensus size: 25
38473564 TTCATATTCG
*
38473574 GGAATGCTCATGTGAGCACATA-AACG
1 GGAA-GCTCATGTGAGC-CATATAACA
*
38473600 GGAAGCCCTC-TCTCGAGCCATATAACA
1 GGAAG--CTCATGT-GAGCCATATAACA
*
38473627 GGAAGCTCATGTGAGCCATGTAACA
1 GGAAGCTCATGTGAGCCATATAACA
* ** * **
38473652 GGAAGCTTATCCGGGCTGTATAACA
1 GGAAGCTCATGTGAGCCATATAACA
** * *
38473677 GGAAGCTCATAAGAGTCATAT-TCA
1 GGAAGCTCATGTGAGCCATATAACA
* *
38473701 GGAAGCTTATGCGAGCCA
1 GGAAGCTCATGTGAGCCA
38473719 AAAACGGGCA
Statistics
Matches: 91, Mismatches: 23, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
24 16 0.18
25 48 0.53
26 12 0.13
27 15 0.16
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATGTGAGCCATATAACA
Found at i:38473875 original size:25 final size:26
Alignment explanation
Indices: 38473794--38473876 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 26
38473784 AGCGAGCCAT
*
38473794 ATCGGGAAACTTCGAAGAGCCAT-TA
1 ATCGGGAAGCTTCGAAGAGCCATATA
* * * *
38473819 ATCAGGAAGCTCACAAAGAGCC-TTTA
1 ATCGGGAAGCT-TCGAAGAGCCATATA
38473845 ATCGGGAAGCTTCGAAGAGCCATATA
1 ATCGGGAAGCTTCGAAGAGCCATATA
38473871 A-CGGGA
1 ATCGGGA
38473877 CGTTTATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 23 0.49
26 24 0.51
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (26 bp):
ATCGGGAAGCTTCGAAGAGCCATATA
Found at i:38476313 original size:17 final size:17
Alignment explanation
Indices: 38476271--38476436 Score: 69
Period size: 17 Copynumber: 9.6 Consensus size: 17
38476261 ATCTACAAGA
*
38476271 TAAATATTAAATTAAAT
1 TAAATATTTAATTAAAT
*
38476288 TAAATATTTAATTTAAT
1 TAAATATTTAATTAAAT
* * *
38476305 TTAATATTTATCTTGTAGA-
1 TAAATATTTA--AT-TAAAT
*
38476324 TAAATATTCT-ATTAATT
1 TAAATATT-TAATTAAAT
*
38476341 TAATAAATTTAA-T--AT
1 TAA-ATATTTAATTAAAT
*
38476356 TAAATTTATTAAATT-AA-
1 TAAA--TATTTAATTAAAT
*
38476373 TAGAATATTT-ATCTACAAGA
1 TA-AATATTTAAT-TA-AA-T
*
38476393 TAAATATTAAATTAAAT
1 TAAATATTTAATTAAAT
*
38476410 TAAATATTTAATTTAAT
1 TAAATATTTAATTAAAT
*
38476427 TTAATATTTA
1 TAAATATTTA
38476437 TCTTGTAGAT
Statistics
Matches: 111, Mismatches: 20, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
14 1 0.01
15 6 0.05
16 12 0.11
17 57 0.51
18 12 0.11
19 16 0.14
20 7 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TAAATATTTAATTAAAT
Found at i:38476356 original size:20 final size:20
Alignment explanation
Indices: 38476333--38476496 Score: 60
Period size: 20 Copynumber: 8.1 Consensus size: 20
38476323 ATAAATATTC
38476333 TATT-AATTTAATAAATTTAA
1 TATTAAATTTAATAAA-TTAA
*
38476353 TATTAAATTTATTAAATTAA
1 TATTAAATTTAATAAATTAA
* * *
38476373 TA-GAATATTTATCTACAAGATAAA
1 TATTAA-ATTTA---ATAA-ATTAA
38476397 TATTAAA--T--TAAATTAAA
1 TATTAAATTTAATAAATT-AA
*
38476414 TATTTAATTTAAT---TTAA
1 TATTAAATTTAATAAATTAA
** **
38476431 TATTTATCTTGTAGATAAATATTC
1 TA-TTAAATT-TA-ATAAAT-TAA
38476455 TATT-AATTTAATAAATTTAA
1 TATTAAATTTAATAAA-TTAA
*
38476475 TATTAAATTTATTAAATTAA
1 TATTAAATTTAATAAATTAA
38476495 TA
1 TA
38476497 GAATATTTAT
Statistics
Matches: 104, Mismatches: 19, Indels: 42
0.63 0.12 0.25
Matches are distributed among these distances:
16 2 0.02
17 14 0.13
18 6 0.06
19 5 0.05
20 33 0.32
21 24 0.23
22 3 0.03
23 5 0.05
24 10 0.10
25 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TATTAAATTTAATAAATTAA
Found at i:38476394 original size:69 final size:69
Alignment explanation
Indices: 38476278--38476429 Score: 163
Period size: 69 Copynumber: 2.3 Consensus size: 69
38476268 AGATAAATAT
* * ** *** ** *
38476278 TAAA-TTAA-ATTAAATAT-TTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAAT
1 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
38476340 TTAA
66 TTAA
38476344 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
1 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
38476409 TTAA
66 TTAA
*
38476413 -ATATTTAAT-TT-AATTTA
1 TAAATTTAATATTAAATTTA
38476430 ATATTTATCT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
66 10 0.14
67 6 0.08
68 16 0.22
69 40 0.56
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (69 bp):
TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
TTAA
Found at i:38476394 original size:122 final size:122
Alignment explanation
Indices: 38476222--38476546 Score: 650
Period size: 122 Copynumber: 2.7 Consensus size: 122
38476212 AGTATTAGAT
38476222 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
1 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
38476287 TTAAATATTTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAA
66 TTAAATATTTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAA
38476344 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
1 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
38476409 TTAAATATTTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAA
66 TTAAATATTTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAA
38476466 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
1 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
38476531 TTAAATATTTAATTTA
66 TTAAATATTTAATTTA
38476547 TTAATAATAT
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 203 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (122 bp):
TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
TTAAATATTTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAA
Found at i:38476437 original size:53 final size:56
Alignment explanation
Indices: 38476376--38476485 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 56
38476366 AAATTAATAG
*
38476376 AATATTTATCTACAAGATAAATATTAAATTAAATTAA-ATATTTAAT-TT-AATTT
1 AATATTTATCTACAAGATAAATATTAAATTAAATTAATAAATTTAATATTAAATTT
*** ** *
38476429 AATATTTATCTTGTAGATAAATATTCTATTAATTTAATAAATTTAATATTAAATTT
1 AATATTTATCTACAAGATAAATATTAAATTAAATTAATAAATTTAATATTAAATTT
38476485 A
1 A
38476486 TTAAATTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
53 31 0.66
54 8 0.17
55 2 0.04
56 6 0.13
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (56 bp):
AATATTTATCTACAAGATAAATATTAAATTAAATTAATAAATTTAATATTAAATTT
Found at i:38476529 original size:69 final size:68
Alignment explanation
Indices: 38476400--38476543 Score: 159
Period size: 69 Copynumber: 2.1 Consensus size: 68
38476390 AGATAAATAT
* ** *** ** *
38476400 TAAA-TTAA-ATTAAATATTTAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATT
1 TAAATTTAATATTAAATATTTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAAT
38476463 TAA
66 TAA
*
38476466 TAAATTTAATATTAAATTTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
1 TAAATTTAATATTAAATAT-TTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAA
38476531 TTAA
65 TTAA
*
38476535 -ATATTTAAT
1 TAAATTTAAT
38476544 TTATTAATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 4 0.06
67 4 0.06
68 16 0.25
69 40 0.62
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (68 bp):
TAAATTTAATATTAAATATTTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAAT
TAA
Found at i:38480199 original size:20 final size:21
Alignment explanation
Indices: 38480171--38480219 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
38480161 GCGAGGTGAT
*
38480171 AATTCATAAACCAC-AAT-ATA
1 AATTAATAAA-CACTAATAATA
38480191 AATTAATAAACACTAATAATA
1 AATTAATAAACACTAATAATA
*
38480212 AATGAATA
1 AATTAATA
38480220 CCAATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.48
21 10 0.40
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (21 bp):
AATTAATAAACACTAATAATA
Found at i:38486549 original size:17 final size:17
Alignment explanation
Indices: 38486527--38486561 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38486517 TTCTTATGTG
38486527 AATTCAGGTACTAGCTT
1 AATTCAGGTACTAGCTT
*
38486544 AATTCATGTACTAGCTT
1 AATTCAGGTACTAGCTT
38486561 A
1 A
38486562 TTGAAGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (17 bp):
AATTCAGGTACTAGCTT
Found at i:38489250 original size:18 final size:17
Alignment explanation
Indices: 38489227--38489279 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
38489217 GTACAATTCA
38489227 AATAATTTATTTTAATTT
1 AATAATTTA-TTTAATTT
* *
38489245 AATAATATATTTCATTT
1 AATAATTTATTTAATTT
* *
38489262 AATTATTTTACTTAATTT
1 AA-TAATTTATTTAATTT
38489280 TTTATTTCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
AATAATTTATTTAATTT
Found at i:38489363 original size:103 final size:104
Alignment explanation
Indices: 38489237--38489446 Score: 404
Period size: 103 Copynumber: 2.0 Consensus size: 104
38489227 AATAATTTAT
*
38489237 TTTAATTTAATAATATATTTCATTTAATTATTTTACTTAATTTTTTATTTCTAAAAAAATTACTA
1 TTTAATTTAATAATATATTTCATTTAATTATTGTACTTAATTTTTTATTTCTAAAAAAATTACTA
38489302 TTTTTTAATATCTTAGCTCCCTTTAATCAATTGTTAGGC
66 TTTTTTAATATCTTAGCTCCCTTTAATCAATTGTTAGGC
38489341 TTTAATTTAAT-ATATATTTCATTTAATTATTGTACTTAATTTTTTATTTCTAAAAAAATTACTA
1 TTTAATTTAATAATATATTTCATTTAATTATTGTACTTAATTTTTTATTTCTAAAAAAATTACTA
38489405 TTTTTTAATATCTTAGCTCCCTTTAATCAATTGTTAGGC
66 TTTTTTAATATCTTAGCTCCCTTTAATCAATTGTTAGGC
38489444 TTT
1 TTT
38489447 TCCCTATACT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 94 0.90
104 11 0.10
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.53
Consensus pattern (104 bp):
TTTAATTTAATAATATATTTCATTTAATTATTGTACTTAATTTTTTATTTCTAAAAAAATTACTA
TTTTTTAATATCTTAGCTCCCTTTAATCAATTGTTAGGC
Found at i:38493541 original size:88 final size:88
Alignment explanation
Indices: 38493437--38493688 Score: 285
Period size: 87 Copynumber: 2.8 Consensus size: 88
38493427 TCAAACTTAA
*
38493437 AAAAAAAGCAATTAAGCCCCTACTTTTTTT-ACACTCAATTAAGTACTTGAACTTTCAAAATGCA
1 AAAAAAAGCAATTAAGCCCCT-CTTTTTTTAAAACTCAATTAAGTACTTGAACTTTCAAAATGCA
* *
38493501 T-AAAAAGGCCCTCGAACTTTTTC
65 TCAAAAAGGCCCTCAAACTTTTCC
* **
38493524 AAATAAAAGCAACTAAGCCCCT-TTTTTTTAAAACTCAATTGGGTACTTGAACTTTCAAAATGCA
1 AAA-AAAAGCAATTAAGCCCCTCTTTTTTTAAAACTCAATTAAGTACTTGAACTTTCAAAATGCA
*
38493588 TCAAAAAGGCTCTCAAACTTTTCC
65 TCAAAAAGGCCCTCAAACTTTTCC
** *** * **
38493612 AAAAAAAAAAATTAAGCCCCTGCTTTTTTTTTTTACATCCAATTAGGTACTTGAACTGCCAAAAT
1 AAAAAAAGCAATTAAGCCCCT-C-TTTTTTTAAAAC-T-CAATTAAGTACTTGAACTTTCAAAAT
*
38493677 GTATCAAAAAGG
62 GCATCAAAAAGG
38493689 TCCTTTGACC
Statistics
Matches: 140, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
86 7 0.05
87 50 0.36
88 39 0.28
90 9 0.06
91 1 0.01
92 34 0.24
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.31
Consensus pattern (88 bp):
AAAAAAAGCAATTAAGCCCCTCTTTTTTTAAAACTCAATTAAGTACTTGAACTTTCAAAATGCAT
CAAAAAGGCCCTCAAACTTTTCC
Found at i:38493844 original size:20 final size:20
Alignment explanation
Indices: 38493821--38493869 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
38493811 AATAAAAGTT
*
38493821 ATAAAAATTATTAATTTTTA
1 ATAAAAATTATTAAATTTTA
*
38493841 ATAAAAAAT-TTAAATTTTA
1 ATAAAAATTATTAAATTTTA
*
38493860 TTAAAAATTA
1 ATAAAAATTA
38493870 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAAATTATTAAATTTTA
Found at i:38493918 original size:19 final size:18
Alignment explanation
Indices: 38493872--38493934 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
38493862 AAAAATTAGA
* *
38493872 AAAAAATTAAAAAATTGT
1 AAAAAATTATAAAATCGT
**
38493890 AAAATTTTATAAATATCGT
1 AAAAAATTATAAA-ATCGT
*
38493909 AAAAAATTATAAAATGCAT
1 AAAAAATTATAAAAT-CGT
38493928 AAAAAAT
1 AAAAAAT
38493935 CCCTTTAACC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 12 0.33
19 24 0.67
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAAATTATAAAATCGT
Found at i:38494130 original size:21 final size:21
Alignment explanation
Indices: 38494105--38494179 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 21
38494095 TTGATACGAT
38494105 AATTTTTATAATTTTTTTACG
1 AATTTTTATAATTTTTTTACG
*
38494126 AA-TTTTAT-ATTTCTTTAC-
1 AATTTTTATAATTTTTTTACG
* *
38494144 ATTTTTTATAATTTTCTTACG
1 AATTTTTATAATTTTTTTACG
* * *
38494165 ACTTTATAAAATTTT
1 AATTTTTATAATTTT
38494180 ATAATTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 1 0.02
19 15 0.34
20 14 0.32
21 14 0.32
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (21 bp):
AATTTTTATAATTTTTTTACG
Found at i:38494133 original size:20 final size:20
Alignment explanation
Indices: 38494108--38494179 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
38494098 ATACGATAAT
38494108 TTTTATAATTTTTTTACGAA
1 TTTTATAATTTTTTTACGAA
* *
38494128 TTTTAT-ATTTCTTTAC-ATT
1 TTTTATAATTTTTTTACGA-A
* *
38494147 TTTTATAATTTTCTTACGAC
1 TTTTATAATTTTTTTACGAA
*
38494167 TTTATAAAATTTT
1 TTT-TATAATTTT
38494180 ATAATTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.02
19 15 0.36
20 17 0.40
21 9 0.21
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAA
Found at i:38494187 original size:39 final size:38
Alignment explanation
Indices: 38494103--38494189 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 38
38494093 TATTGATACG
* *
38494103 ATAA-TTTTTATAATTTTTTTACGAATTTTATATTTCT
1 ATAATTTTTTATAATTTTCTTACGAATTTTAAATTTCT
* *
38494140 TTACATTTTTTATAATTTTCTTACGACTTTATAAAATTT-T
1 ATA-ATTTTTTATAATTTTCTTACGAATTT-T-AAATTTCT
38494180 ATAATTTTTT
1 ATAATTTTTT
38494190 TTACTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
37 2 0.05
38 1 0.02
39 29 0.71
40 4 0.10
41 5 0.12
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (38 bp):
ATAATTTTTTATAATTTTCTTACGAATTTTAAATTTCT
Found at i:38494338 original size:75 final size:78
Alignment explanation
Indices: 38494211--38494354 Score: 213
Period size: 76 Copynumber: 1.9 Consensus size: 78
38494201 ATAAAAAAAA
* * *
38494211 TTCTAATTTTTAATAATTTTTTAATATTTTTAATTAAAATTTAATCATTTTTATAACTTTTA-TG
1 TTCTAATTTTTAATAATTTTTTAATATTTTTAATCAAAATTTAATAATTTTTATAACTTCTATTG
38494275 ATTTCTATAATTT
66 ATTTCTATAATTT
* **
38494288 TTCT-ATTTTTAATATTTTTTTTCTATTTTT-ATCAAAATTTAATAATTTTTATAACTTCTATTG
1 TTCTAATTTTTAATAATTTTTTAATATTTTTAATCAAAATTTAATAATTTTTATAACTTCTATTG
38494351 ATTT
66 ATTT
38494355 TTATTTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 27 0.45
76 29 0.48
77 4 0.07
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (78 bp):
TTCTAATTTTTAATAATTTTTTAATATTTTTAATCAAAATTTAATAATTTTTATAACTTCTATTG
ATTTCTATAATTT
Found at i:38494633 original size:89 final size:89
Alignment explanation
Indices: 38494470--38494742 Score: 326
Period size: 89 Copynumber: 3.1 Consensus size: 89
38494460 TAACGGTCAA
* ** * *
38494470 AGGGCCGTTTTGATGCATTTTGGCAGTTCAAGTACCCAATTGGGTGCAAAAAAA-AAGGTGCTTA
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGAAGGGGCTTA
* *** *
38494534 ATTGCTTTTTTTTTTTTAAATTTTG
66 ATTGC-TTTTTCTTGAAAAAGTTTG
* * *
38494559 AGGGCCTTTTTGATGCATTTTGAAAGTTTAAGTACCTAATTGAGTGCAAAAAAAGCAGGGGGCTT
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAG-AAGGGGCTT
*
38494624 AGTTG-TTTTTCTTGAAAAAGTTTG
65 AATTGCTTTTTCTTGAAAAAGTTTG
*
38494648 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGC--AAAAA-AAGGGGCCTA
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGAAGGGGCTTA
* *
38494710 ATTGCATTTT-TTGAAAAATTTTG
66 ATTGCTTTTTCTTGAAAAAGTTTG
38494733 AGGG-CTTTTT
1 AGGGCCTTTTT
38494743 ACACCATTAA
Statistics
Matches: 160, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
84 6 0.04
85 27 0.17
86 4 0.03
87 5 0.03
89 107 0.67
91 11 0.07
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (89 bp):
AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGAAGGGGCTTA
ATTGCTTTTTCTTGAAAAAGTTTG
Found at i:38515134 original size:20 final size:21
Alignment explanation
Indices: 38515097--38515146 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
38515087 ATATAATAAT
38515097 AATTATATTAATAATTTTATTA
1 AATTATA-TAATAATTTTATTA
38515119 AATTATATAA-AATTTTATTA
1 AATTATATAATAATTTTATTA
38515139 AATTATAT
1 AATTATAT
38515147 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.64
21 3 0.11
22 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTATATAATAATTTTATTA
Found at i:38515147 original size:10 final size:10
Alignment explanation
Indices: 38515097--38515147 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
38515087 ATATAATAAT
38515097 AATTATATTAA
1 AATTATATT-A
*
38515108 TAATTTTATTA
1 -AATTATATTA
*
38515119 AATTATATAA
1 AATTATATTA
*
38515129 AATTTTATTA
1 AATTATATTA
38515139 AATTATATT
1 AATTATATT
38515148 TAATAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTATATTA
Found at i:38525976 original size:49 final size:49
Alignment explanation
Indices: 38525881--38525977 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
38525871 CAATGCGGAC
* ** * * * *
38525881 AAATATTGAAAGTTATCATTGCTAGGCAACCCGGGATGATAGAATAAAT
1 AAATATTAAAAGACATCATTGCTAGGCAACCCAGAATGACAAAATAAAT
* *
38525930 AAATATTAAAAGACATCGTTGCTAGGCAACCTAGAATGACAAAATAAA
1 AAATATTAAAAGACATCATTGCTAGGCAACCCAGAATGACAAAATAAA
38525978 GTATTCCTAG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (49 bp):
AAATATTAAAAGACATCATTGCTAGGCAACCCAGAATGACAAAATAAAT
Found at i:38526181 original size:2 final size:2
Alignment explanation
Indices: 38526169--38526203 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38526159 TTGATACTTG
*
38526169 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38526204 CTCGCTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:38529345 original size:24 final size:25
Alignment explanation
Indices: 38529286--38529349 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
38529276 TACATATGTT
*
38529286 TCTTACGAGCTTCCCAATTATTGGC
1 TCTTATGAGCTTCCCAATTATTGGC
* * *
38529311 TCTCT-TAAGCTTCCTATTTA-TGGC
1 TCT-TATGAGCTTCCCAATTATTGGC
38529335 TCTTATGAGCTTCCC
1 TCTTATGAGCTTCCC
38529350 GTTATACTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.03
24 15 0.48
25 14 0.45
26 1 0.03
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (25 bp):
TCTTATGAGCTTCCCAATTATTGGC
Found at i:38529440 original size:25 final size:25
Alignment explanation
Indices: 38529329--38529459 Score: 90
Period size: 25 Copynumber: 5.3 Consensus size: 25
38529319 GCTTCCTATT
**
38529329 TATGGCTCTTATGAGCTTCCCGTTA
1 TATGGCTCACATGAGCTTCCCGTTA
** * *
38529354 TACT-GCTCGGATAAGCTTCCCGATA
1 TA-TGGCTCACATGAGCTTCCCGTTA
* * *
38529379 T-TGGCTCACTTGAACTTCCTGATTA
1 TATGGCTCACATGAGCTTCCCG-TTA
* **
38529404 CA--GCTCTTATGAGCTTCCCGTTA
1 TATGGCTCACATGAGCTTCCCGTTA
* *
38529427 TATGGCTCACATGAGCTTTCCATTA
1 TATGGCTCACATGAGCTTCCCGTTA
38529452 TATGGCTC
1 TATGGCTC
38529460 GAAAGAGCTT
Statistics
Matches: 78, Mismatches: 22, Indels: 12
0.70 0.20 0.11
Matches are distributed among these distances:
23 5 0.06
24 25 0.32
25 47 0.60
26 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (25 bp):
TATGGCTCACATGAGCTTCCCGTTA
Found at i:38529444 original size:73 final size:74
Alignment explanation
Indices: 38529292--38529459 Score: 193
Period size: 73 Copynumber: 2.3 Consensus size: 74
38529282 TGTTTCTTAC
* **
38529292 GAGCTTCCCAATTATTGGCTCTCTTAAGCTTCCTATTTATGGCTCTTATGAGCTTCCCGTTATAC
1 GAGCTTCCCAATTATTGGCTCACTTAAGCTTCCTATTTACAGCTCTTATGAGCTTCCCGTTATAC
**
38529357 TGCTCGGAT
66 TGCTCACAT
* *
38529366 AAGCTTCCCGA-TATTGGCTCACTTGAA-CTTCCTGA-TTACAGCTCTTATGAGCTTCCCGTTAT
1 GAGCTTCCCAATTATTGGCTCACTT-AAGCTTCCT-ATTTACAGCTCTTATGAGCTTCCCGTTAT
38529428 A-TGGCTCACAT
64 ACT-GCTCACAT
*
38529439 GAGCTTTCC-ATTATATGGCTC
1 GAGCTTCCCAATTAT-TGGCTC
38529460 GAAAGAGCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
72 2 0.03
73 60 0.75
74 18 0.22
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (74 bp):
GAGCTTCCCAATTATTGGCTCACTTAAGCTTCCTATTTACAGCTCTTATGAGCTTCCCGTTATAC
TGCTCACAT
Found at i:38529467 original size:25 final size:25
Alignment explanation
Indices: 38529414--38529471 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
38529404 CAGCTCTTAT
* *
38529414 GAGCTTCCCGTTATATGGCTCACAT
1 GAGCTTCCCATTATATGGCTCACAA
*
38529439 GAGCTTTCCATTATATGGCTCGA-AA
1 GAGCTTCCCATTATATGGCTC-ACAA
38529464 GAGCTTCC
1 GAGCTTCC
38529472 TGTTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGCTCACAA
Found at i:38531439 original size:26 final size:26
Alignment explanation
Indices: 38531410--38531467 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
38531400 CCCGTTATGT
*
38531410 GGCTCTTCGTGAGCTT-CTCGATTAAA
1 GGCTCTTCGTAAGCTTCCT-GATTAAA
* *
38531436 GGCTCTTTGTAAGCTTCCTGATTAAT
1 GGCTCTTCGTAAGCTTCCTGATTAAA
38531462 GGCTCT
1 GGCTCT
38531468 CTAGAGCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
GGCTCTTCGTAAGCTTCCTGATTAAA
Found at i:38531658 original size:25 final size:25
Alignment explanation
Indices: 38531543--38531662 Score: 75
Period size: 25 Copynumber: 4.9 Consensus size: 25
38531533 TGGTTTTTCG
* *
38531543 GAGCTACCCATTGT-TGGCTCGCAT
1 GAGCTTCCCATTATATGGCTCGCAT
* **
38531567 GAGCTTCCCGA-T-TATGTCTCTTAT
1 GAGCTTCCC-ATTATATGGCTCGCAT
** ** *
38531591 GAGCTTCCTGTTATACAGCTCGGAT
1 GAGCTTCCCATTATATGGCTCGCAT
* * * * *
38531616 AAGCTTCCCGTCAAATGGCTCACAT
1 GAGCTTCCCATTATATGGCTCGCAT
38531641 GAGCTTCCCATTATATGGCTCG
1 GAGCTTCCCATTATATGGCTCG
38531663 AGAGAGTGCT
Statistics
Matches: 68, Mismatches: 24, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
23 1 0.01
24 25 0.37
25 42 0.62
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGCTCGCAT
Found at i:38536018 original size:25 final size:25
Alignment explanation
Indices: 38535990--38536093 Score: 90
Period size: 24 Copynumber: 4.2 Consensus size: 25
38535980 GGCTCTTACA
38535990 AGCTTCCCGATTATTGGCTCTCTTG
1 AGCTTCCCGATTATTGGCTCTCTTG
*
38536015 AGCTTCCCGTTTA-TGGCTCT-TATG
1 AGCTTCCCGATTATTGGCTCTCT-TG
* * **
38536039 AACTTCCTGATT-TATGGCTCTCCGG
1 AGCTTCCCGATTAT-TGGCTCTCTTG
* *
38536064 AGCTTCCCGA-TATTAGCTCACTTG
1 AGCTTCCCGATTATTGGCTCTCTTG
*
38536088 AACTTC
1 AGCTTC
38536094 TTGATTACAG
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
23 1 0.02
24 31 0.51
25 29 0.48
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (25 bp):
AGCTTCCCGATTATTGGCTCTCTTG
Found at i:38536057 original size:49 final size:50
Alignment explanation
Indices: 38535951--38536072 Score: 133
Period size: 49 Copynumber: 2.4 Consensus size: 50
38535941 GTCTCGATAT
*
38535951 TTGGCTCTCATGATCTTCCCGTTACATATGGCTCTTACAAGCTTCCCGATTA
1 TTGGCTCTCATGAGCTTCCCGTT--ATATGGCTCTTACAAGCTTCCCGATTA
* * *
38536003 TTGGCTCTCTTGAGCTTCCCGTT-TATGGCTCTTATGAA-CTTCCTGATT-
1 TTGGCTCTCATGAGCTTCCCGTTATATGGCTCTTA-CAAGCTTCCCGATTA
**
38536051 TATGGCTCTCCGGAGCTTCCCG
1 T-TGGCTCTCATGAGCTTCCCG
38536073 ATATTAGCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
48 1 0.02
49 38 0.61
50 2 0.03
52 21 0.34
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.38
Consensus pattern (50 bp):
TTGGCTCTCATGAGCTTCCCGTTATATGGCTCTTACAAGCTTCCCGATTA
Found at i:38536137 original size:25 final size:25
Alignment explanation
Indices: 38536109--38536169 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
38536099 TACAGCTCTT
*
38536109 ATGAGCTTCTCGTTACATGGCTCAC
1 ATGAGCTTCCCGTTACATGGCTCAC
*
38536134 ATGAGCTTCCCGTTATATGGCTCGA-
1 ATGAGCTTCCCGTTACATGGCTC-AC
*
38536159 AAGAGCTTCCC
1 ATGAGCTTCCC
38536170 ATTTATGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAC
Found at i:38536189 original size:25 final size:25
Alignment explanation
Indices: 38536109--38536189 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
38536099 TACAGCTCTT
* * *
38536109 ATGAGCTTCTCGTTACATGGCTC-A
1 ATGAGCTTCCCATTATATGGCTCGA
*
38536133 CATGAGCTTCCCGTTATATGGCTCGA
1 -ATGAGCTTCCCATTATATGGCTCGA
* *
38536159 AAGAGCTTCCCATT-TATGTGCTCGT
1 ATGAGCTTCCCATTATATG-GCTCGA
38536184 ATGAGC
1 ATGAGC
38536190 ATTTCCAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.08
25 43 0.90
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCATTATATGGCTCGA
Found at i:38538201 original size:28 final size:28
Alignment explanation
Indices: 38538155--38538211 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
38538145 CCAACCTATC
* *
38538155 TAAAACAAGTCTATTTATAATAAGAAAA
1 TAAAACAAGTCCATCTATAATAAGAAAA
38538183 TAAAACAAGTCCATCTATAATAAGAAAA
1 TAAAACAAGTCCATCTATAATAAGAAAA
38538211 T
1 T
38538212 GGAGGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (28 bp):
TAAAACAAGTCCATCTATAATAAGAAAA
Found at i:38540235 original size:3 final size:3
Alignment explanation
Indices: 38540227--38540264 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
38540217 ATCAAGGCAC
38540227 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T-A TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
38540265 AGCTTCATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:38542444 original size:23 final size:22
Alignment explanation
Indices: 38542405--38542450 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
38542395 AGTAATTATA
38542405 AAATAATTAGCTAAATAAACAAT
1 AAATAATTAGCTAAATAAA-AAT
*
38542428 AAATAATTA-CATCAATAAAAAT
1 AAATAATTAGC-TAAATAAAAAT
38542450 A
1 A
38542451 TTTAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAATTAGCTAAATAAAAAT
Found at i:38546988 original size:18 final size:17
Alignment explanation
Indices: 38546956--38546990 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
38546946 AAGGAAATAC
*
38546956 AAATGAAAAAGAGAAAT
1 AAATAAAAAAGAGAAAT
38546973 AAATAAAAAGAGAGAAAT
1 AAATAAAAA-AGAGAAAT
38546991 TATCATTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (17 bp):
AAATAAAAAAGAGAAAT
Found at i:38547221 original size:2 final size:2
Alignment explanation
Indices: 38547214--38547243 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38547204 NNNNCACATA
38547214 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
38547244 TAAGTGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38561730 original size:44 final size:44
Alignment explanation
Indices: 38561680--38561904 Score: 131
Period size: 44 Copynumber: 5.1 Consensus size: 44
38561670 GATAGTAGAT
* * *
38561680 CTTGCCTTCCTATACTGACAGAGAAGCAGATCGAAGACATCAGC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
* *** * * * * * * *
38561724 CTTGCCTCCCTGGGTTTACAGCGGAGTAGA-CTGAAAATAGCAGAT
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-C
38561769 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
* * * * *
38561813 CTTGCC-TCCTTGGGT-TTG-CAAC-AGAGCAGA-CTGAAGATAGCAGAT
1 CTTGCCTTCC-T--GTACTGACAGCGA-AGCAGATC-GAAGACACCAG-C
* * *
38561858 CTTGCTTTCCT-TACTGACAGCGAAGGAGATCGAAGGCACCAGC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
38561901 CTTG
1 CTTG
38561905 TCTCCCTGGG
Statistics
Matches: 130, Mismatches: 37, Indels: 29
0.66 0.19 0.15
Matches are distributed among these distances:
42 1 0.01
43 12 0.09
44 70 0.54
45 41 0.32
46 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.22
Consensus pattern (44 bp):
CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:38561915 original size:88 final size:89
Alignment explanation
Indices: 38561666--38561916 Score: 369
Period size: 89 Copynumber: 2.8 Consensus size: 89
38561656 AATAGATCAG
* * *
38561666 TGAAGATAGTAGATCTTGCCTTCCTATACTGACAGAGAAGCAGATCGAAGACATCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
38561731 CCCTGGGTTTACAGCGGAGTAGAC
66 CCCTGGGTTTACAACAGAGCAGAC
* *
38561755 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
38561820 CCTTGGGTTTGCAACAGAGCAGAC
66 CCCTGGGTTTACAACAGAGCAGAC
* * * *
38561844 TGAAGATAGCAGATCTTGCTTTCCT-TACTGACAGCGAAGGAGATCGAAGGCACCAGCCTTGTCT
1 TGAAGATAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
38561908 CCCTGGGTT
66 CCCTGGGTT
38561917 CGCAGTGGAG
Statistics
Matches: 146, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
88 44 0.30
89 102 0.70
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24
Consensus pattern (89 bp):
TGAAGATAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTTACAACAGAGCAGAC
Found at i:38563858 original size:21 final size:21
Alignment explanation
Indices: 38563832--38563872 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38563822 GAACTTTTTT
38563832 TATTATCATTGTAATTATTAA
1 TATTATCATTGTAATTATTAA
*
38563853 TATTATTATTGTAATTATTA
1 TATTATCATTGTAATTATTA
38563873 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
TATTATCATTGTAATTATTAA
Found at i:38575203 original size:6 final size:6
Alignment explanation
Indices: 38575194--38575224 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
38575184 TTGCGGTCGA
38575194 GGACGT GGACGT GGACGT GGACGT GGACGT G
1 GGACGT GGACGT GGACGT GGACGT GGACGT G
38575225 ACGAGGTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGACGT
Found at i:38579459 original size:18 final size:18
Alignment explanation
Indices: 38579415--38579459 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
38579405 TCAACTTTAA
38579415 CCTTA-AACCTTTCATCT
1 CCTTATAACCTTTCATCT
*
38579432 TCTT-TAAACCTTTCATCT
1 CCTTAT-AACCTTTCATCT
38579450 CCTTATAACC
1 CCTTATAACC
38579460 CCTTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 19 0.83
19 1 0.04
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.42
Consensus pattern (18 bp):
CCTTATAACCTTTCATCT
Found at i:38583667 original size:32 final size:32
Alignment explanation
Indices: 38583631--38583742 Score: 147
Period size: 32 Copynumber: 3.5 Consensus size: 32
38583621 CGCGTGGTTC
*
38583631 TGTGAAATGATAACAAATATCAGCTTTCATTT
1 TGTGAAATGATAACAAATATCAACTTTCATTT
*
38583663 TGTGAAATGGTAACAAAT-TACAAC-TTCAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTC-ATTT
* *
38583695 TGTGAAATAATAACAAATATCAACTTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTCATTT
*
38583727 TGTTAAATGATAACAA
1 TGTGAAATGATAACAA
38583743 TATTCCTCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.06
32 62 0.90
33 3 0.04
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTCATTT
Found at i:38583896 original size:33 final size:33
Alignment explanation
Indices: 38583849--38583917 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
38583839 GCCACATCGA
* *
38583849 GGTGGTTGACGGTTGCGTGCTAGATTCCTTCTT
1 GGTGCTTGACGGTTGCGCGCTAGATTCCTTCTT
38583882 GGTGCTTGACGGTTGCGCGCTAGATTCCTTCTT
1 GGTGCTTGACGGTTGCGCGCTAGATTCCTTCTT
38583915 GGT
1 GGT
38583918 TCAACCCTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.09, C:0.20, G:0.33, T:0.38
Consensus pattern (33 bp):
GGTGCTTGACGGTTGCGCGCTAGATTCCTTCTT
Found at i:38585914 original size:23 final size:23
Alignment explanation
Indices: 38585888--38586009 Score: 156
Period size: 23 Copynumber: 5.3 Consensus size: 23
38585878 ATAAGTGCCA
38585888 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
38585911 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* **
38585934 CACTGAAATGTAGTTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
38585957 CACTGACATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
38585980 CACTGA-ATTGTAGCCGAAGTTAC
1 CACTGATA-TGTAGCCGAAGCTAC
*
38586003 CTCTGAT
1 CACTGAT
38586010 CAATAACCCT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 84 0.99
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:38585955 original size:46 final size:46
Alignment explanation
Indices: 38585888--38586008 Score: 179
Period size: 46 Copynumber: 2.6 Consensus size: 46
38585878 ATAAGTGCCA
* *
38585888 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGACATGTAGCCGTAGCTAC
**
38585934 CACTGAAATGTAGTTGAAGCTACCACTGACATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGACATGTAGCCGTAGCTAC
* * *
38585980 CACTGAATTGTAGCCGAAGTTACCTCTGA
1 CACTGAAATGTAGCCGAAGCTACCACTGA
38586009 TCAATAACCC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGACATGTAGCCGTAGCTAC
Found at i:38586259 original size:18 final size:17
Alignment explanation
Indices: 38586233--38586271 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38586223 ATTTTCCTTC
38586233 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
38586250 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
38586268 CACA
1 CACA
38586272 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:38588704 original size:12 final size:13
Alignment explanation
Indices: 38588687--38588720 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
38588677 AAATATTTTC
38588687 AGAAAATATTAAT
1 AGAAAATATTAAT
*
38588700 AAAAAAT-TTAAT
1 AGAAAATATTAAT
38588712 AGAAAATAT
1 AGAAAATAT
38588721 AATTTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
AGAAAATATTAAT
Found at i:38589041 original size:30 final size:31
Alignment explanation
Indices: 38589005--38589062 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
38588995 TAAATATTTC
*
38589005 AAAAATCGGC-TTATTCTAGTAATTTAAAAA
1 AAAAATCAGCATTATTCTAGTAATTTAAAAA
* *
38589035 AAAAATCAGCATTTTTTTAGTAATTTAA
1 AAAAATCAGCATTATTCTAGTAATTTAA
38589063 TCAGAAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (31 bp):
AAAAATCAGCATTATTCTAGTAATTTAAAAA
Found at i:38592866 original size:18 final size:18
Alignment explanation
Indices: 38592840--38592874 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38592830 AGTGTAAAAG
*
38592840 TTGTTGAGTAAAATTAAT
1 TTGTGGAGTAAAATTAAT
*
38592858 TTGTGGAGTAGAATTAA
1 TTGTGGAGTAAAATTAA
38592875 CAATGAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
TTGTGGAGTAAAATTAAT
Found at i:38593139 original size:1 final size:1
Alignment explanation
Indices: 38593133--38593164 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
38593123 GTTTATCCCT
38593133 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
38593165 ACCTGCTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:38604814 original size:37 final size:37
Alignment explanation
Indices: 38604765--38604907 Score: 123
Period size: 37 Copynumber: 3.9 Consensus size: 37
38604755 CTTGGAAGAC
* *
38604765 AAAAGATAGAGATAAATAGAAGTAATTCTCTACAAAG
1 AAAAGACAGAGATGAATAGAAGTAATTCTCTACAAAG
* * **
38604802 AAAAGACGGAGATGAATAGTAA--AGATCCTCTATGAAG
1 AAAAGACAGAGATGAATAG-AAGTA-ATTCTCTACAAAG
* * *
38604839 AAAA-ATAGAGATGAACAGAAGTGATTCTCTACAAAG
1 AAAAGACAGAGATGAATAGAAGTAATTCTCTACAAAG
* * *
38604875 AAAAGAAAGAGATGAACAAGAA-CAATTCTCTAC
1 AAAAGACAGAGATGAA-TAGAAGTAATTCTCTAC
38604908 CCTCCAAAAA
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
35 2 0.02
36 26 0.31
37 49 0.59
38 6 0.07
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (37 bp):
AAAAGACAGAGATGAATAGAAGTAATTCTCTACAAAG
Found at i:38604869 original size:36 final size:37
Alignment explanation
Indices: 38604765--38604892 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 37
38604755 CTTGGAAGAC
* * *
38604765 AAAAGATAGAGATAAATAGAAGTAATTCTCTACAAAG
1 AAAAGATAGAGATGAACAGAAGTGATTCTCTACAAAG
** * * * **
38604802 AAAAGACGGAGATGAATAGTAA-AGATCCTCTATGAAG
1 AAAAGATAGAGATGAACAG-AAGTGATTCTCTACAAAG
38604839 AAAA-ATAGAGATGAACAGAAGTGATTCTCTACAAAG
1 AAAAGATAGAGATGAACAGAAGTGATTCTCTACAAAG
*
38604875 AAAAGAAAGAGATGAACA
1 AAAAGATAGAGATGAACA
38604893 AGAACAATTC
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
35 2 0.03
36 26 0.36
37 42 0.58
38 2 0.03
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.18
Consensus pattern (37 bp):
AAAAGATAGAGATGAACAGAAGTGATTCTCTACAAAG
Found at i:38610809 original size:37 final size:35
Alignment explanation
Indices: 38610763--38610840 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
38610753 AATTATTCTT
*
38610763 TGCAAAGAAAATACAAAGATGAATAGTAAAGATCCTC
1 TGCAAAGAAAA-A-AAAGATGAACAGTAAAGATCCTC
* * *
38610800 TGCATAGAAAAAAAAGATGAACAGTAACGATTCTC
1 TGCAAAGAAAAAAAAGATGAACAGTAAAGATCCTC
*
38610835 TTCAAA
1 TGCAAA
38610841 AATTCTCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 24 0.69
36 1 0.03
37 10 0.29
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (35 bp):
TGCAAAGAAAAAAAAGATGAACAGTAAAGATCCTC
Found at i:38610820 original size:35 final size:37
Alignment explanation
Indices: 38610723--38610840 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
38610713 AAGGGTGATT
* * * ** *
38610723 CTCTACAAAGAAAAGACAAAGATGGACA-TGAATTATT
1 CTCTGCAAAGAAAATACAAAGATGAACAGT-AAAGATC
* *
38610760 CTTTGCAAAGAAAATACAAAGATGAATAGTAAAGATC
1 CTCTGCAAAGAAAATACAAAGATGAACAGTAAAGATC
* * *
38610797 CTCTGCATAGAAAA-A-AAAGATGAACAGTAACGATT
1 CTCTGCAAAGAAAATACAAAGATGAACAGTAAAGATC
*
38610832 CTCTTCAAA
1 CTCTGCAAA
38610841 AATTCTCTCA
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
35 24 0.37
36 1 0.02
37 39 0.60
38 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.22
Consensus pattern (37 bp):
CTCTGCAAAGAAAATACAAAGATGAACAGTAAAGATC
Found at i:38613804 original size:43 final size:44
Alignment explanation
Indices: 38613688--38613816 Score: 160
Period size: 43 Copynumber: 3.0 Consensus size: 44
38613678 ATAGGATTCC
* *
38613688 ATTATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCATCG
1 ATTATGTGATTA-CATGTAAGACCACGTCTGGGATGTTGGCATCG
*
38613732 ACT-TGTGACTTACATGTAAGACC-CTGTCTGGGATAG-TGGCATCG
1 ATTATGTGA-TTACATGTAAGACCAC-GTCTGGGAT-GTTGGCATCG
38613776 -TTATGTGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 ATTATGTGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
38613817 TGTACGAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
42 1 0.01
43 35 0.47
44 34 0.46
45 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (44 bp):
ATTATGTGATTACATGTAAGACCACGTCTGGGATGTTGGCATCG
Found at i:38613951 original size:23 final size:23
Alignment explanation
Indices: 38613921--38613966 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38613911 AATGCTCAGG
38613921 TATGTACTCATACTAAGTTATGA
1 TATGTACTCATACTAAGTTATGA
38613944 TATGTACTCATACTAAGTTATGA
1 TATGTACTCATACTAAGTTATGA
38613967 AATTAAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (23 bp):
TATGTACTCATACTAAGTTATGA
Found at i:38616500 original size:37 final size:36
Alignment explanation
Indices: 38616451--38616569 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
38616441 TTGAAAGACT
38616451 AAAGACCAAGATGAACA-AAAGTGATTCTCTGAAAAGA
1 AAAGA-CAAGATGAACATAAA-TGATTCTCTGAAAAGA
* *
38616488 AAAGACAGAGATGAACATGAATGATTCTCTGTAAAGA
1 AAAGACA-AGATGAACATAAATGATTCTCTGAAAAGA
* * * *
38616525 AAAGACAAAGATGGATAGTAAA-GATTATCTGCAAAGA
1 AAAGAC-AAGATGAACA-TAAATGATTCTCTGAAAAGA
*
38616562 AAAAACAA
1 AAAGACAA
38616570 AGGTTAACAG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
36 4 0.06
37 60 0.86
38 6 0.09
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.18
Consensus pattern (36 bp):
AAAGACAAGATGAACATAAATGATTCTCTGAAAAGA
Found at i:38623590 original size:15 final size:15
Alignment explanation
Indices: 38623570--38623599 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38623560 AAAAACAACA
38623570 TAACTCTTAACCTTT
1 TAACTCTTAACCTTT
*
38623585 TAACTCTTGACCTTT
1 TAACTCTTAACCTTT
38623600 CACTTACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (15 bp):
TAACTCTTAACCTTT
Found at i:38631256 original size:29 final size:29
Alignment explanation
Indices: 38631212--38631267 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
38631202 AAATATAAAC
*
38631212 TATATTTTTTTATTTTAAAATATACTACA
1 TATATTTTTTTATTTTAAAATACACTACA
38631241 TATATTTTTTCT-TTTTAAAATACACTA
1 TATATTTTTT-TATTTTAAAATACACTA
38631268 TATTTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (29 bp):
TATATTTTTTTATTTTAAAATACACTACA
Found at i:38632876 original size:27 final size:27
Alignment explanation
Indices: 38632846--38632900 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
38632836 CTTCCATTTC
38632846 TGTTGCCCTTTCCAATTTAGTTATTAT
1 TGTTGCCCTTTCCAATTTAGTTATTAT
** *
38632873 TGTTGTTCTTTTCAATTTAGTTATTAT
1 TGTTGCCCTTTCCAATTTAGTTATTAT
38632900 T
1 T
38632901 TTATATATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (27 bp):
TGTTGCCCTTTCCAATTTAGTTATTAT
Found at i:38636856 original size:2 final size:2
Alignment explanation
Indices: 38636849--38636874 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38636839 ATTGAAATGA
38636849 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
38636875 GCAAATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38639378 original size:21 final size:21
Alignment explanation
Indices: 38639354--38639404 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
38639344 AACCGATATA
* *
38639354 AAAATTATCAAAAAATAAATT
1 AAAATTATCAAAAAAGAAAGT
* * *
38639375 AAAATCATAAAAAAAGAGAGT
1 AAAATTATCAAAAAAGAAAGT
38639396 AAAATTATC
1 AAAATTATC
38639405 GCAAATCTCA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (21 bp):
AAAATTATCAAAAAAGAAAGT
Found at i:38640189 original size:19 final size:17
Alignment explanation
Indices: 38640165--38640207 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
38640155 AAATTATAAA
*
38640165 ATAAATTATAGTAGTATCC
1 ATAAATTATA-AAGTAT-C
38640184 ATAAATTTATAAAGTATC
1 ATAAA-TTATAAAGTATC
38640202 ATAAAT
1 ATAAAT
38640208 CAAAATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 10 0.45
20 5 0.23
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (17 bp):
ATAAATTATAAAGTATC
Found at i:38646291 original size:15 final size:15
Alignment explanation
Indices: 38646273--38646307 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
38646263 TACAAATGCT
38646273 ACAATAATAAATACA
1 ACAATAATAAATACA
38646288 ACAATAATAAATACA
1 ACAATAATAAATACA
*
38646303 TCAAT
1 ACAAT
38646308 GGCATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:38646620 original size:182 final size:184
Alignment explanation
Indices: 38646294--38646667 Score: 711
Period size: 182 Copynumber: 2.0 Consensus size: 184
38646284 TACAACAATA
38646294 ATAA-ATA-CATCAATGGCATAAAAATAATATAAACAAATAAATAAACGAAACTAATATGCATAA
1 ATAATATACCATCAATGGCA-AAAAATAATATAAACAAATAAATAAACGAAACTAATATGCATAA
38646357 AAAAATAAACAATGACGATGCAAGAATATCAAATAAATAAACAAGATAAACAATAATATAAATGA
65 AAAAATAAACAATGACGATGCAAGAATATCAAATAAATAAACAAGATAAACAATAATATAAATGA
38646422 AAACACAAATTAATAAACAAATGAAAGAACTAAAT-AAAAAAGAATAAAAGGTAC
130 AAACACAAATTAATAAACAAATGAAAGAACTAAATAAAAAAAGAATAAAAGGTAC
38646476 ATAATATACCATCAATGGC-AAAAATAATATAAACAAATAAATAAACGAAACTAATATGCATAAA
1 ATAATATACCATCAATGGCAAAAAATAATATAAACAAATAAATAAACGAAACTAATATGCATAAA
38646540 AAAATAAACAATGACGATGCAAGAATATCAAATAAATAAACAAGATAAACAATAATATAAATGAA
66 AAAATAAACAATGACGATGCAAGAATATCAAATAAATAAACAAGATAAACAATAATATAAATGAA
38646605 AACACAAATTAATAAACAAATGAAAGAACTAAATAAAAAAAGAATAAAAGGTAC
131 AACACAAATTAATAAACAAATGAAAGAACTAAATAAAAAAAGAATAAAAGGTAC
38646659 ATAATATAC
1 ATAATATAC
38646668 ATATTGAACC
Statistics
Matches: 189, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
182 148 0.78
183 31 0.16
184 10 0.05
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.19
Consensus pattern (184 bp):
ATAATATACCATCAATGGCAAAAAATAATATAAACAAATAAATAAACGAAACTAATATGCATAAA
AAAATAAACAATGACGATGCAAGAATATCAAATAAATAAACAAGATAAACAATAATATAAATGAA
AACACAAATTAATAAACAAATGAAAGAACTAAATAAAAAAAGAATAAAAGGTAC
Found at i:38653041 original size:1 final size:1
Alignment explanation
Indices: 38653037--38653086 Score: 64
Period size: 1 Copynumber: 50.0 Consensus size: 1
38653027 AAAGTGAATC
****
38653037 TTTTTTTTTTTTTTTTTTTTTTTTGGAATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38653087 CTGTGTGAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.04, C:0.00, G:0.04, T:0.92
Consensus pattern (1 bp):
T
Found at i:38654994 original size:27 final size:23
Alignment explanation
Indices: 38654951--38655019 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
38654941 TTAAATTATA
38654951 AAAAAT-TATT-TTT-AAAAATT
1 AAAAATATATTATTTAAAAAATT
38654971 AAAGACATCATATTATTTAAAAAATAT
1 AAA-A-AT-ATATTATTTAAAAAAT-T
38654998 AAAAATATATT-TTTAAAAAATT
1 AAAAATATATTATTTAAAAAATT
38655020 TAAATTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 3 0.07
23 10 0.24
24 9 0.21
25 5 0.12
26 7 0.17
27 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (23 bp):
AAAAATATATTATTTAAAAAATT
Done.