Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 159 of 163
Found at i:45101735 original size:14 final size:14
Alignment explanation
Indices: 45101716--45101743 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45101706 TTTTTTCATG
45101716 GCAGACCAAGTCCA
1 GCAGACCAAGTCCA
45101730 GCAGACCAAGTCCA
1 GCAGACCAAGTCCA
45101744 ACATATAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.21, T:0.07
Consensus pattern (14 bp):
GCAGACCAAGTCCA
Found at i:45123064 original size:28 final size:28
Alignment explanation
Indices: 45122986--45123064 Score: 65
Period size: 30 Copynumber: 2.7 Consensus size: 28
45122976 AAATATCTCT
*
45122986 AAAATAGTAGCAAAATTAATAACAAAACA
1 AAAATAGTAGCAATA-TAATAACAAAACA
*
45123015 AAAATTA-TA-CAATATCCAAATAATAACAA-A
1 AAAA-TAGTAGCAATAT---AATAACAA-AACA
45123045 AAAATAGTAGCAATATAATA
1 AAAATAGTAGCAATATAATA
45123065 GCGAAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
27 1 0.02
28 8 0.20
29 8 0.20
30 16 0.39
31 8 0.20
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (28 bp):
AAAATAGTAGCAATATAATAACAAAACA
Found at i:45126959 original size:20 final size:18
Alignment explanation
Indices: 45126920--45126982 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 18
45126910 GTTTAAATAG
45126920 ATTTAAATTTATTGTTAA
1 ATTTAAATTTATTGTTAA
45126938 ATTTAAATTTATTGCTTTAA
1 ATTTAAATTTATTG--TTAA
* * *
45126958 ATCTAAATTTAAT-TAAA
1 ATTTAAATTTATTGTTAA
45126975 ATTTAAAT
1 ATTTAAAT
45126983 CAATATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 10 0.26
18 14 0.36
20 15 0.38
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTAAATTTATTGTTAA
Found at i:45129094 original size:29 final size:29
Alignment explanation
Indices: 45129012--45129276 Score: 171
Period size: 29 Copynumber: 9.0 Consensus size: 29
45129002 CTCTAGTCCC
*
45129012 CAAACTTTCCAAAATTCCATTTTTAACACT
1 CAAACTTTCCAAAATTCCATTTTT-ACCCT
*
45129042 GAAAC-TTCCAAAAATTACCA-TTTTACCCT
1 CAAACTTTCC-AAAATT-CCATTTTTACCCT
* * *
45129071 CAACCTTTCCAAAATTTCATTTTTAACCT
1 CAAACTTTCCAAAATTCCATTTTTACCCT
*
45129100 C-GA-TTTCACCCAAAATTACCA-TTTTACCC-
1 CAAACTTT---CCAAAATT-CCATTTTTACCCT
45129129 CTAAACTTTCCAAAATTCCATTTTTAACCC-
1 C-AAACTTTCCAAAATTCCATTTTT-ACCCT
* *
45129159 C-AA-TTTCACCCAAAATTATCA-TTTTACCCC
1 CAAACTTT---CCAAAATT-CCATTTTTACCCT
*
45129189 CAAACTTTCCAAAATTTCATTTTTAACCC-
1 CAAACTTTCCAAAATTCCATTTTT-ACCCT
*
45129218 C-GA-TTTCACCAAAATTACCA-TTTTACCCT
1 CAAACTTT--CCAAAATT-CCATTTTTACCCT
*
45129247 CAAACTTTCCAAAATTCTATTTTTAACCCT
1 CAAACTTTCCAAAATTCCATTTTT-ACCCT
45129277 GAATTTTCTC
Statistics
Matches: 189, Mismatches: 16, Indels: 60
0.71 0.06 0.23
Matches are distributed among these distances:
27 9 0.05
28 17 0.09
29 81 0.43
30 63 0.33
31 13 0.07
32 6 0.03
ACGTcount: A:0.34, C:0.29, G:0.01, T:0.36
Consensus pattern (29 bp):
CAAACTTTCCAAAATTCCATTTTTACCCT
Found at i:45129115 original size:59 final size:59
Alignment explanation
Indices: 45129012--45129275 Score: 358
Period size: 59 Copynumber: 4.5 Consensus size: 59
45129002 CTCTAGTCCC
* * * * *
45129012 CAAACTTTCCAAAATTCCATTTTTAACACTGAAACTT--CCAAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAATTTCATTTTTAACCCCG--ATTTCACCCAAAATTACCATTTTACCCT
* *
45129071 CAACCTTTCCAAAATTTCATTTTTAACCTCGATTTCACCCAAAATTACCATTTTACCC-
1 CAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCT
* * * *
45129129 CTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCCAAAATTATCATTTTACCCC
1 C-AAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCT
45129189 CAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCT
45129247 CAAACTTTCCAAAA-TTCTATTTTTAACCC
1 CAAACTTTCCAAAATTTC-ATTTTTAACCC
45129276 TGAATTTTCT
Statistics
Matches: 184, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
57 6 0.03
58 45 0.24
59 132 0.72
60 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.36
Consensus pattern (59 bp):
CAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCT
Found at i:45129282 original size:118 final size:116
Alignment explanation
Indices: 45129009--45129299 Score: 417
Period size: 118 Copynumber: 2.5 Consensus size: 116
45128999 GCTCTCTAGT
* * * * *
45129009 CCCCAAACTTTCCAAAATTCCATTTTTAACACTGAAACTTCCAAAAATTACCATTTTACCCTCAA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCTG-AATTTCCCAAAATTATCATTTTACCCCCAA
* *
45129074 CCTTTCCAAAATTTCATTTTTAACCTCGATTTCACCCAAAATTACCATTTTA
65 ACTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
*
45129126 CCCCTAAACTTTCCAAAATTCCATTTTTAACCC-CAATTTCACCCAAAATTATCATTTTACCCCC
1 CCCC-AAACTTTCCAAAATTCCATTTTTAACCCTGAATTT--CCCAAAATTATCATTTTACCCCC
45129190 AAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTA
63 AAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
* *
45129243 CCCTCAAACTTTCCAAAATTCTATTTTTAACCCTGAATTTTCTCAAAATTAT-ATTTT
1 CCC-CAAACTTTCCAAAATTCCATTTTTAACCCTGAA-TTTCCCAAAATTATCATTTT
45129300 TGCCCCTCGA
Statistics
Matches: 157, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
116 9 0.06
117 61 0.39
118 84 0.54
119 3 0.02
ACGTcount: A:0.33, C:0.29, G:0.01, T:0.37
Consensus pattern (116 bp):
CCCCAAACTTTCCAAAATTCCATTTTTAACCCTGAATTTCCCAAAATTATCATTTTACCCCCAAA
CTTTCCAAAATTTCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
Found at i:45134005 original size:6 final size:6
Alignment explanation
Indices: 45133994--45134022 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
45133984 ATGTACCTAT
45133994 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
45134023 GAATAACCGT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:45134561 original size:22 final size:22
Alignment explanation
Indices: 45134536--45134585 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
45134526 TGTCTAAATA
*
45134536 ATAATAACT-AAATAATAGTAAC
1 ATAATAA-TGAAATAACAGTAAC
*
45134558 ATAATAATGAAATGACAGTAAC
1 ATAATAATGAAATAACAGTAAC
45134580 ATAATA
1 ATAATA
45134586 GTGGAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (22 bp):
ATAATAATGAAATAACAGTAAC
Found at i:45140349 original size:3 final size:3
Alignment explanation
Indices: 45140341--45140371 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
45140331 GTGGTCTGCT
45140341 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
45140372 ACTAGAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:45145376 original size:24 final size:24
Alignment explanation
Indices: 45145346--45145395 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
45145336 TTAGATTAAG
* *
45145346 ATTTTAAAATTTTAAAA-AATATTA
1 ATTTT-AAATTTAAAAATAATAATA
45145370 ATTTTAAATTTAAAAATAATAATA
1 ATTTTAAATTTAAAAATAATAATA
45145394 AT
1 AT
45145396 AGTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTTAAATTTAAAAATAATAATA
Found at i:45151254 original size:45 final size:45
Alignment explanation
Indices: 45151185--45151274 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
45151175 TTCATTGTTA
* *
45151185 GCAAGGTCCGTCAAAAGCTTTCAAGATGGGATGCAAAGAAACTAT
1 GCAAGGTCCGTCAAAAGCTCTCAAGATAGGATGCAAAGAAACTAT
*
45151230 GCAAGGTCTGTCAAAAGCTCTCAAGATAGGATGCAAAGAAACTAT
1 GCAAGGTCCGTCAAAAGCTCTCAAGATAGGATGCAAAGAAACTAT
45151275 CTCTGGCAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (45 bp):
GCAAGGTCCGTCAAAAGCTCTCAAGATAGGATGCAAAGAAACTAT
Found at i:45161964 original size:26 final size:26
Alignment explanation
Indices: 45161935--45161990 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
45161925 CTGAATTTAA
45161935 TTTTAATATTTAATTTAGTGA-TTGAG
1 TTTTAATATTTAATTTAGT-ACTTGAG
* * *
45161961 TTTTGATGTTTAATTTGGTACTTGAG
1 TTTTAATATTTAATTTAGTACTTGAG
45161987 TTTT
1 TTTT
45161991 TCTTTATCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.23, C:0.02, G:0.18, T:0.57
Consensus pattern (26 bp):
TTTTAATATTTAATTTAGTACTTGAG
Found at i:45162390 original size:6 final size:7
Alignment explanation
Indices: 45162371--45162396 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
45162361 TATTTTTTAA
45162371 TATTTTT
1 TATTTTT
45162378 TATTTTT
1 TATTTTT
45162385 TATTTTT
1 TATTTTT
45162392 TATTT
1 TATTT
45162397 ATTAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:45163921 original size:33 final size:34
Alignment explanation
Indices: 45163884--45163959 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
45163874 CTTCTTCTAC
45163884 TTAAAATA-AGTAAATTATTTTTTATATATTAGA
1 TTAAAATATAGTAAATTATTTTTTATATATTAGA
**
45163917 TT-AAATATTTTAAATTATTTTTTATATATTAGA
1 TTAAAATATAGTAAATTATTTTTTATATATTAGA
45163950 TTAAAATATA
1 TTAAAATATA
45163960 AAATGGTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 5 0.13
33 27 0.71
34 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (34 bp):
TTAAAATATAGTAAATTATTTTTTATATATTAGA
Found at i:45163952 original size:19 final size:19
Alignment explanation
Indices: 45163897--45163952 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
45163887 AAATAAGTAA
45163897 ATTATTTTTTATATATTAG
1 ATTATTTTTTATATATTAG
* * *
45163916 ATTA-----AATATTTTAA
1 ATTATTTTTTATATATTAG
45163930 ATTATTTTTTATATATTAG
1 ATTATTTTTTATATATTAG
45163949 ATTA
1 ATTA
45163953 AAATATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 10
0.62 0.14 0.24
Matches are distributed among these distances:
14 11 0.42
19 15 0.58
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
ATTATTTTTTATATATTAG
Found at i:45164646 original size:132 final size:132
Alignment explanation
Indices: 45164409--45164678 Score: 486
Period size: 132 Copynumber: 2.0 Consensus size: 132
45164399 TTGAACATTG
45164409 TATTCAAGGTTTTGGGTAATGTTCATGTTGTACATTTAAGTTATTTTCTCCATATTATACTATCA
1 TATTCAAGGTTTTGGGTAATGTTCATGTTGTACATTTAAGTTATTTTCTCCATATTATACTATCA
* *
45164474 TTTATTTACTCATTAGTGAAAAACTGAATCATCCTTTCCCCATGGCTTTTTATTCTCTTCGAAAA
66 TTTATTTACTCATTAGTGAAAAACCGAAACATCCTTTCCCCATGGCTTTTTATTCTCTTCGAAAA
45164539 GT
131 GT
*
45164541 TATTCAAGGTTTTGGGTAATGTTCATGTTGTACATTTAAGTTATTTTTTCCATATTATACTATCA
1 TATTCAAGGTTTTGGGTAATGTTCATGTTGTACATTTAAGTTATTTTCTCCATATTATACTATCA
* *
45164606 TTTGTTTACTCATTAGTGAAAAACCGAAACATCCTTTCCCCATGGTTTTTTATTCTCTTCGAAAA
66 TTTATTTACTCATTAGTGAAAAACCGAAACATCCTTTCCCCATGGCTTTTTATTCTCTTCGAAAA
45164671 GT
131 GT
*
45164673 TTTTCA
1 TATTCA
45164679 CATAAAATAC
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 132 1.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (132 bp):
TATTCAAGGTTTTGGGTAATGTTCATGTTGTACATTTAAGTTATTTTCTCCATATTATACTATCA
TTTATTTACTCATTAGTGAAAAACCGAAACATCCTTTCCCCATGGCTTTTTATTCTCTTCGAAAA
GT
Found at i:45166127 original size:29 final size:30
Alignment explanation
Indices: 45166069--45166130 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
45166059 ATCTCAAAAT
*
45166069 TATACATGAATTTTAATTTAATGTGTAATTA
1 TATACATGAATTTTAATTTAA-GTGCAATTA
* *
45166100 TATATATGAATTTTAATTTGA-TGCAATTA
1 TATACATGAATTTTAATTTAAGTGCAATTA
45166129 TA
1 TA
45166131 CACGTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.32
31 19 0.68
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (30 bp):
TATACATGAATTTTAATTTAAGTGCAATTA
Found at i:45166958 original size:20 final size:20
Alignment explanation
Indices: 45166905--45166966 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
45166895 TCAAAATTCG
45166905 ATAATTTAAATCATAATAAA
1 ATAATTTAAATCATAATAAA
** **
45166925 ATATATTT-TGTCATAATTGA
1 ATA-ATTTAAATCATAATAAA
45166945 ATAATTTAAATCATAATAAA
1 ATAATTTAAATCATAATAAA
45166965 AT
1 AT
45166967 TACAAAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (20 bp):
ATAATTTAAATCATAATAAA
Found at i:45175552 original size:2 final size:2
Alignment explanation
Indices: 45175545--45175576 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45175535 ACCATAAGTA
45175545 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
45175577 CAGTTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45179949 original size:14 final size:13
Alignment explanation
Indices: 45179927--45179965 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
45179917 TTTTTAAAAT
*
45179927 TTTTTTTATTAAA
1 TTTTATTATTAAA
45179940 TCTTTATTATTAAA
1 T-TTTATTATTAAA
*
45179954 TTTTTTTATTAA
1 TTTTATTATTAA
45179966 GTCAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTATTATTAAA
Found at i:45180855 original size:16 final size:18
Alignment explanation
Indices: 45180836--45180871 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
45180826 TTTAAATTTT
45180836 TTAAAAAA-TA-ATAAAA
1 TTAAAAAATTATATAAAA
45180852 TTAAAAAATTATATAAAA
1 TTAAAAAATTATATAAAA
45180870 TT
1 TT
45180872 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAAATTATATAAAA
Found at i:45188568 original size:30 final size:31
Alignment explanation
Indices: 45188526--45188606 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 31
45188516 ATTGTTTATA
* *
45188526 TTTTTA-TATTTTTAAATAAT-AAAATTAAT
1 TTTTTATTATTTTTAAAAAATAAAAAATAAT
45188555 TTTTTATTATTTTTAAAAAATAAAAAATAAT
1 TTTTTATTATTTTTAAAAAATAAAAAATAAT
45188586 TTTATTATTATTAATTTAAAA
1 TTT-TTATTATT--TTTAAAA
45188607 CTTTATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
29 6 0.13
30 13 0.29
31 11 0.24
32 8 0.18
34 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTTTATTATTTTTAAAAAATAAAAAATAAT
Found at i:45189959 original size:26 final size:25
Alignment explanation
Indices: 45189930--45189983 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
45189920 AATTCTAGAG
45189930 ATTTAAATATTGAAATTAAGAATTTA
1 ATTTAAATATTGAAATT-AGAATTTA
* * * *
45189956 ATTTAAGTATTTATATTATAATTTA
1 ATTTAAATATTGAAATTAGAATTTA
45189981 ATT
1 ATT
45189984 ATTTTATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTTAAATATTGAAATTAGAATTTA
Found at i:45192437 original size:21 final size:21
Alignment explanation
Indices: 45192412--45192451 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45192402 ATTTATCCGT
* *
45192412 TTGTATTTTGTAGTAATTTTA
1 TTGTACTTTATAGTAATTTTA
*
45192433 TTGTACTTTATAGTTATTT
1 TTGTACTTTATAGTAATTT
45192452 AATCATGTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (21 bp):
TTGTACTTTATAGTAATTTTA
Found at i:45194730 original size:18 final size:18
Alignment explanation
Indices: 45194690--45194731 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
45194680 TTATGTCATG
*
45194690 TTTTTTGTTCTTATTGTT
1 TTTTTTCTTCTTATTGTT
*
45194708 CTTTTTCTTCTTACTT-TT
1 TTTTTTCTTCTTA-TTGTT
45194726 TTTTTT
1 TTTTTT
45194732 TATAGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTCTTATTGTT
Found at i:45197620 original size:22 final size:23
Alignment explanation
Indices: 45197583--45197645 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
45197573 AAATTTACAA
* * *
45197583 ATTTTTTTATTGTTTTACT-GCT
1 ATTTTTTTGTTATTTTACTCACT
45197605 ATTTTTTTGTTATTTT-CTCACT
1 ATTTTTTTGTTATTTTACTCACT
**
45197627 ATTTTACTGTTATTTTACT
1 ATTTTTTTGTTATTTTACT
45197646 ATTATATTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.16, C:0.11, G:0.06, T:0.67
Consensus pattern (23 bp):
ATTTTTTTGTTATTTTACTCACT
Found at i:45197650 original size:11 final size:11
Alignment explanation
Indices: 45197626--45197673 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
45197616 ATTTTCTCAC
*
45197626 TATTTTACTGT
1 TATTTTACTAT
45197637 TATTTTACTAT
1 TATTTTACTAT
* *
45197648 TATATTGCTAT
1 TATTTTACTAT
*
45197659 TATTTTATTAT
1 TATTTTACTAT
45197670 TATT
1 TATT
45197674 ATTTAGATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (11 bp):
TATTTTACTAT
Found at i:45198787 original size:83 final size:83
Alignment explanation
Indices: 45198648--45198813 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
45198638 AAAGATAGAA
45198648 CCCACATGAGCAAAAATTCAGAGATTAGCATAAATATTCAATCCATTTCCATTGTTAGTCAATTC
1 CCCACATGAGCAAAAATTCAGAGATTAGCATAAATATTCAATCCATTTCCATTGTTAGTCAATTC
45198713 ATCCAATTAAATATAATT
66 ATCCAATTAAATATAATT
45198731 CCCACATGAGCAAAAATTCAGAGATTAGCATAAATATTCAATCCATTTCCATTGTTAGTCAATTC
1 CCCACATGAGCAAAAATTCAGAGATTAGCATAAATATTCAATCCATTTCCATTGTTAGTCAATTC
45198796 ATCCAATTAAATATAATT
66 ATCCAATTAAATATAATT
45198814 TTCAGTTAAG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (83 bp):
CCCACATGAGCAAAAATTCAGAGATTAGCATAAATATTCAATCCATTTCCATTGTTAGTCAATTC
ATCCAATTAAATATAATT
Found at i:45208804 original size:39 final size:39
Alignment explanation
Indices: 45208750--45208828 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
45208740 CAGTTTGACT
45208750 TTTAAACCCTACCTTTGAACCTTAGAAGTTAAAAAGACC
1 TTTAAACCCTACCTTTGAACCTTAGAAGTTAAAAAGACC
*
45208789 TTTAAACCCTACCTTTGAACCTTAGAAGTTAAAAGGACC
1 TTTAAACCCTACCTTTGAACCTTAGAAGTTAAAAAGACC
45208828 T
1 T
45208829 ATCATATTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (39 bp):
TTTAAACCCTACCTTTGAACCTTAGAAGTTAAAAAGACC
Found at i:45215775 original size:18 final size:18
Alignment explanation
Indices: 45215740--45215777 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
45215730 TATACATTAA
*
45215740 AGAACTAACTAACATAAC
1 AGAACTAACAAACATAAC
45215758 AGAACTAACCAAAC-TAAC
1 AGAACTAA-CAAACATAAC
45215776 AG
1 AG
45215778 CTAACTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.55, C:0.24, G:0.08, T:0.13
Consensus pattern (18 bp):
AGAACTAACAAACATAAC
Found at i:45221789 original size:3 final size:3
Alignment explanation
Indices: 45221781--45221829 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
45221771 AGATTTCTTT
45221781 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45221829 A
1 A
45221830 AACTATCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45223923 original size:29 final size:30
Alignment explanation
Indices: 45223891--45223956 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
45223881 ATTTATAATA
*
45223891 TTATATA-TAAATTTTGAT-TTGGTGTATTT
1 TTATATATTAAATTTTAATATTGGT-TATTT
*
45223920 TTATACATTAAATTTTAATATTGGTTATTT
1 TTATATATTAAATTTTAATATTGGTTATTT
45223950 TTCATAT
1 TT-ATAT
45223957 TTCACTAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 6 0.19
30 17 0.55
31 8 0.26
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (30 bp):
TTATATATTAAATTTTAATATTGGTTATTT
Found at i:45230346 original size:19 final size:20
Alignment explanation
Indices: 45230322--45230365 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
45230312 TCTCTCTCTC
45230322 AAAAAA-TAAAAATAATTT-T
1 AAAAAATTAAAAAT-ATTTAT
*
45230341 AAAAAATTCAAAATATTTAT
1 AAAAAATTAAAAATATTTAT
45230361 AAAAA
1 AAAAA
45230366 TTCCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATTAAAAATATTTAT
Found at i:45230366 original size:19 final size:18
Alignment explanation
Indices: 45230335--45230379 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
45230325 AAATAAAAAT
45230335 AATTTTA-AAAAATTCAA
1 AATTTTATAAAAATTCAA
*
45230352 AATATTTATAAAAATTCCA
1 AAT-TTTATAAAAATTCAA
45230371 AATTTTATA
1 AATTTTATA
45230380 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 10 0.40
19 12 0.48
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTTATAAAAATTCAA
Found at i:45234018 original size:19 final size:19
Alignment explanation
Indices: 45233994--45234033 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
45233984 TAATAGTGAA
45233994 ATAATAGTA-AAACAACAAC
1 ATAATAG-AGAAACAACAAC
45234013 ATAATAGAGTAAACAACAAC
1 ATAATAGAG-AAACAACAAC
45234033 A
1 A
45234034 AACAACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.05
19 7 0.37
20 11 0.58
ACGTcount: A:0.62, C:0.15, G:0.07, T:0.15
Consensus pattern (19 bp):
ATAATAGAGAAACAACAAC
Found at i:45238848 original size:16 final size:17
Alignment explanation
Indices: 45238827--45238860 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
45238817 ATAATTTTAT
*
45238827 TTTTATTAATT-TAAAA
1 TTTTATAAATTATAAAA
45238843 TTTTATAAATTATAAAA
1 TTTTATAAATTATAAAA
45238860 T
1 T
45238861 GCTTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTATAAATTATAAAA
Found at i:45251928 original size:17 final size:17
Alignment explanation
Indices: 45251906--45251962 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
45251896 ATTAATATAT
45251906 TTTAAAAATAAAATTAA
1 TTTAAAAATAAAATTAA
** **
45251923 TTTAAATTTAAAA-TGG
1 TTTAAAAATAAAATTAA
*
45251939 TTT-AAAATTAAATTAA
1 TTTAAAAATAAAATTAA
45251955 TTTAAAAA
1 TTTAAAAA
45251963 AATTTAAATT
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 6 0.21
16 8 0.28
17 15 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTAAAAATAAAATTAA
Found at i:45251958 original size:16 final size:16
Alignment explanation
Indices: 45251910--45251961 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
45251900 ATATATTTTA
*
45251910 AAAATAAAATTAATTT
1 AAAATTAAATTAATTT
* * **
45251926 AAATTTAAAATGGTTT
1 AAAATTAAATTAATTT
45251942 AAAATTAAATTAATTT
1 AAAATTAAATTAATTT
45251958 AAAA
1 AAAA
45251962 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
AAAATTAAATTAATTT
Found at i:45255068 original size:2 final size:2
Alignment explanation
Indices: 45255061--45255085 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45255051 TTAAATCAGT
45255061 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
45255086 TTTAAATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45255901 original size:27 final size:27
Alignment explanation
Indices: 45255855--45255921 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
45255845 CTTTAAATAG
*
45255855 GTTTAGGGTTTAAGTTCGAG-TTTAAA
1 GTTTAGGATTTAAGTTCGAGATTTAAA
* *
45255881 GTTTAGGATTTGATGTTCGAGATTTGAA
1 GTTTAGGATTT-AAGTTCGAGATTTAAA
45255909 GTTT-GGAGTTTAA
1 GTTTAGGA-TTTAA
45255922 AGTTTAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.29
27 12 0.35
28 12 0.35
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.43
Consensus pattern (27 bp):
GTTTAGGATTTAAGTTCGAGATTTAAA
Found at i:45258935 original size:75 final size:75
Alignment explanation
Indices: 45258826--45258989 Score: 274
Period size: 75 Copynumber: 2.2 Consensus size: 75
45258816 AACAACTACG
* * *
45258826 ATGGTAACAATGAGGCCTTGTTCACTGAGAAAGGATGGAGTACTAAGGAAAACCAGAACAGCAAC
1 ATGGTAACAATGAGGCCATATTCACTGAGAAAGGATGGAGTACTAAGGAAAACCAGAACAACAAC
45258891 AACTATTACA
66 AACTATTACA
*
45258901 ATGGTAACAATGAGGCCATATTCACTGAGAAAGGATGGAGTACTAAGGAAAACCGGAACAACAAC
1 ATGGTAACAATGAGGCCATATTCACTGAGAAAGGATGGAGTACTAAGGAAAACCAGAACAACAAC
45258966 AACTATTACA
66 AACTATTACA
* *
45258976 ATGCTAACAGTGAG
1 ATGGTAACAATGAG
45258990 CACAACAATG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (75 bp):
ATGGTAACAATGAGGCCATATTCACTGAGAAAGGATGGAGTACTAAGGAAAACCAGAACAACAAC
AACTATTACA
Found at i:45269294 original size:32 final size:32
Alignment explanation
Indices: 45269258--45269335 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
45269248 TTAACTTTTC
* * *
45269258 AAGTACAAGGACTAAATGTCATATTCTATAAA
1 AAGTACAAGGACTAAATCTCAAATTCAATAAA
* *
45269290 AAGTATAAGGACTAAATCTTAAATTCAATAAA
1 AAGTACAAGGACTAAATCTCAAATTCAATAAA
*
45269322 AA-TACAAAGACTAA
1 AAGTACAAGGACTAA
45269336 CAACATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.26
Consensus pattern (32 bp):
AAGTACAAGGACTAAATCTCAAATTCAATAAA
Found at i:45273245 original size:21 final size:23
Alignment explanation
Indices: 45273220--45273267 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
45273210 AATGCCATGT
*
45273220 ATATATAATATT-A-ATTTAAAC
1 ATATATAATATTCATATTTAAAA
*
45273241 ATATATGATATTCATATTTAAAA
1 ATATATAATATTCATATTTAAAA
45273264 ATAT
1 ATAT
45273268 TATTCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATATAATATTCATATTTAAAA
Found at i:45279362 original size:21 final size:21
Alignment explanation
Indices: 45279336--45279380 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
45279326 AATTATATTC
*
45279336 AATAAAAAAATTTAAA-TTTGT
1 AATAAAAAAATATAAACTTT-T
*
45279357 AATAAAATAATATAAACTTTT
1 AATAAAAAAATATAAACTTTT
45279378 AAT
1 AAT
45279381 TTGACCCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAAAAAAATATAAACTTTT
Found at i:45296391 original size:17 final size:17
Alignment explanation
Indices: 45296371--45296423 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
45296361 CATGTGTTAT
45296371 AAATTACAAATATATAA
1 AAATTACAAATATATAA
*
45296388 AAATAACATAATATA-AA
1 AAATTACA-AATATATAA
* *
45296405 ATATTACAAACAT-TAA
1 AAATTACAAATATATAA
45296421 AAA
1 AAA
45296424 CGAGCCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.28
17 15 0.52
18 6 0.21
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTACAAATATATAA
Found at i:45301343 original size:153 final size:152
Alignment explanation
Indices: 45301060--45301513 Score: 585
Period size: 153 Copynumber: 3.0 Consensus size: 152
45301050 CTTTTGACGC
* * * * * *
45301060 AACCTCACAACTCACT-AAACAACAACACGAAACACTCAATTCACGTTTTTAAAAAAACAGCCAA
1 AACCTCACAACTCACTGAAA-ATCAACACAAAACACTAAATTCAC--ATTTCAAAAACCAGCCAA
* * * * *
45301124 TCGACCAAACCACCAAAGCAAAAAAAAGTGAATCCTAAACTGAATTATAAAAAAAAAGACTCGTT
63 TCTACCAAATCACCAAAGC-GAAAAAA-CGAATCGTAAACTGAATTATAAAAAAAAAGACTCGTT
45301189 TATAAGAAGCTTAATAAAAACAAATGT
126 TATAAGAAGCTTAATAAAAACAAATGT
45301216 AAACCTCACAACTCACTGAAAATCAACACAAAACACTAAATTCACATTTCAAAAACCAGCCAATC
1 -AACCTCACAACTCACTGAAAATCAACACAAAACACTAAATTCACATTTCAAAAACCAGCCAATC
* *
45301281 TACCAAATCACCAAAGCGAGAAAACGAATCGTAAACTGAATTATAAAAAACAAGACTCGTTTATA
65 TACCAAATCACCAAAGCGAAAAAACGAATCGTAAACTGAATTATAAAAAAAAAGACTCGTTTATA
*
45301346 AGAAGCTTAATCAAAACAAATGT
130 AGAAGCTTAATAAAAACAAATGT
** *
45301369 AATTTGCACAACTCACTGAAAATCAACACAAAACACTAAATTCACATTCCAAAAACCAGCCAATC
1 AACCT-CACAACTCACTGAAAATCAACACAAAACACTAAATTCACATTTCAAAAACCAGCCAATC
* * *
45301434 TACCAAATCACGAAAGCGAAAAAAACGAATCGTAAA-T-TA-TA-AAAAAAATAAGACTTGTTTA
65 TACCAAATCACCAAAGCG-AAAAAACGAATCGTAAACTGAATTATAAAAAAA-AAGACTCGTTTA
* *
45301495 CAAGAAGCTTTAAAAAAAA
128 TAAGAAGC-TTAATAAAAA
45301514 TATGATTCAC
Statistics
Matches: 267, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
150 6 0.02
151 20 0.07
152 12 0.04
153 136 0.51
154 21 0.08
155 32 0.12
157 37 0.14
158 3 0.01
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.19
Consensus pattern (152 bp):
AACCTCACAACTCACTGAAAATCAACACAAAACACTAAATTCACATTTCAAAAACCAGCCAATCT
ACCAAATCACCAAAGCGAAAAAACGAATCGTAAACTGAATTATAAAAAAAAAGACTCGTTTATAA
GAAGCTTAATAAAAACAAATGT
Found at i:45303664 original size:58 final size:58
Alignment explanation
Indices: 45303552--45303687 Score: 139
Period size: 58 Copynumber: 2.3 Consensus size: 58
45303542 TTATTTTTTA
* * * * *
45303552 AATTTGGTATCTAAACTTATTTTGCCTAATTTGGTATTTGAACTTGATACTTTTTCTT-
1 AATTTGGTATCTAAA-TTTTTTTGCCTAATTTGATACTTAAACTTGACACTTTTTCTTC
* * * * *
45303610 AATTTGGTATCTAAATTTTTTTGGTCTAATTTGATGCTTAAATTTGACATTTTTTTTTCC
1 AATTTGGTATCTAAATTTTTTT-GCCTAATTTGATACTTAAACTTGACACTTTTTCTT-C
*
45303670 AAATTGGTATCTAAATTT
1 AATTTGGTATCTAAATTT
45303688 ATTAAATGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 6 0.09
58 41 0.64
60 17 0.27
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (58 bp):
AATTTGGTATCTAAATTTTTTTGCCTAATTTGATACTTAAACTTGACACTTTTTCTTC
Found at i:45309314 original size:31 final size:31
Alignment explanation
Indices: 45309279--45309377 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
45309269 TTAATATATT
*
45309279 ATTTGATATATGAATTTGGTTTCAATATTCA
1 ATTTGATATTTGAATTTGGTTTCAATATTCA
* * * *
45309310 ATTTGATATTTGAGTTT-GTTT--TTGTCCCA
1 ATTTGATATTTGAATTTGGTTTCAATAT-TCA
*
45309339 ATTTGAT-TCTTGAATTTGATTTCAATATTCA
1 ATTTGATAT-TTGAATTTGGTTTCAATATTCA
45309370 ATTTGATA
1 ATTTGATA
45309378 CCTAGACCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
28 3 0.06
29 16 0.31
30 7 0.13
31 24 0.46
32 2 0.04
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (31 bp):
ATTTGATATTTGAATTTGGTTTCAATATTCA
Found at i:45313052 original size:2 final size:2
Alignment explanation
Indices: 45313033--45313080 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
45313023 ATATACATGC
* *
45313033 AT AT AC AT AT AC 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
45313075 AT AT AT
1 AT AT AT
45313081 GAGAGATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:45313052 original size:16 final size:16
Alignment explanation
Indices: 45313021--45313080 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
45313011 CAACACATTG
**
45313021 ATATATACATGCATAT
1 ATATATACATATATAT
*
45313037 ACATATACATATATAT
1 ATATATACATATATAT
*
45313053 ATATATATATATATAT
1 ATATATACATATATAT
*
45313069 ATATATATATAT
1 ATATATACATAT
45313081 GAGAGATTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATACATATATAT
Found at i:45323029 original size:17 final size:17
Alignment explanation
Indices: 45323007--45323040 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45322997 TGGACATTCC
45323007 CATTAAATTACAGACTT
1 CATTAAATTACAGACTT
45323024 CATTAAATTACAGACTT
1 CATTAAATTACAGACTT
45323041 GTTAATCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
CATTAAATTACAGACTT
Found at i:45323260 original size:17 final size:17
Alignment explanation
Indices: 45323238--45323270 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45323228 CTCAAATTTT
*
45323238 ATATTTAGATCCAATTC
1 ATATTTACATCCAATTC
45323255 ATATTTACATCCAATT
1 ATATTTACATCCAATT
45323271 GTTGCATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATTTACATCCAATTC
Found at i:45323917 original size:31 final size:31
Alignment explanation
Indices: 45323820--45323920 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 31
45323810 TTATGCATAA
* *
45323820 TTTTGAAATTTTGAATTAGGTCCTTCAAAAT
1 TTTTTAAATTTTTAATTAGGTCCTTCAAAAT
* * ** * *
45323851 TTTTAAAAATTTTAATTAAATCATTCAAAAG
1 TTTTTAAATTTTTAATTAGGTCCTTCAAAAT
* * *
45323882 TTTTTAATTTTTTAATTAGGCCCTTCAATAT
1 TTTTTAAATTTTTAATTAGGTCCTTCAAAAT
45323913 TTTTTAAA
1 TTTTTAAA
45323921 ATTCTCCTCA
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTTTAAATTTTTAATTAGGTCCTTCAAAAT
Found at i:45325796 original size:1 final size:1
Alignment explanation
Indices: 45325790--45325816 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
45325780 TGTCTTTTAG
45325790 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
45325817 ACTTTAGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:45327404 original size:22 final size:23
Alignment explanation
Indices: 45327363--45327424 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
45327353 GCAATCTGAG
*
45327363 GAAAAATAAAAG-AAACAGAATT
1 GAAAAATAAAAGAAAATAGAATT
45327385 -AAAAATAAAAGAAAATAGAATT
1 GAAAAATAAAAGAAAATAGAATT
* *
45327407 GAAAGA-AATAGAAAATAG
1 GAAAAATAAAAGAAAATAG
45327425 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.31
22 20 0.57
23 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.15, T:0.15
Consensus pattern (23 bp):
GAAAAATAAAAGAAAATAGAATT
Found at i:45328255 original size:19 final size:19
Alignment explanation
Indices: 45328231--45328273 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
45328221 AAACATAAAT
45328231 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
45328250 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
45328269 TAAAT
1 TAAAT
45328274 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:45329047 original size:106 final size:109
Alignment explanation
Indices: 45328872--45329070 Score: 244
Period size: 106 Copynumber: 1.9 Consensus size: 109
45328862 TACATTGGAT
* * * * * * **
45328872 CTTTTGACGCGAAATTAAATGACACCCAAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTC
1 CTTTTGACGCCAAATGAAATGACAACCAAACACTCCACCCCGGTTACTAAGCCCAACACACTCTC
*
45328937 AATTT-TTT-CTTCT-TTTTTTTTTTTTATAGAATGTGTTAGCC
66 AATTTATTTACTTATATTTTTTTTTTTTATAGAATGTGTTAGCC
* * *
45328978 CTTTTGACGCCAAGTGAAATGACAACCAAACACTCCACCCCGGTTACTAAGTCTAACACACTC-C
1 CTTTTGACGCCAAATGAAATGACAACCAAACACTCCACCCCGGTTACTAAGCCCAACACACTCTC
*
45329042 GAATTTATTTATTTATATTTTTTTTTTTT
66 -AATTTATTTACTTATATTTTTTTTTTTT
45329071 TATTCGGGTT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
105 1 0.01
106 57 0.75
107 3 0.04
108 3 0.04
109 12 0.16
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (109 bp):
CTTTTGACGCCAAATGAAATGACAACCAAACACTCCACCCCGGTTACTAAGCCCAACACACTCTC
AATTTATTTACTTATATTTTTTTTTTTTATAGAATGTGTTAGCC
Found at i:45329852 original size:6 final size:6
Alignment explanation
Indices: 45329843--45329868 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45329833 AGAAAAATAA
45329843 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
45329869 TTGGGTTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:45329852 original size:8 final size:8
Alignment explanation
Indices: 45329809--45329868 Score: 57
Period size: 8 Copynumber: 7.0 Consensus size: 8
45329799 TTTCCTGAAC
45329809 AAAAATAA
1 AAAAATAA
*
45329817 ATAAATAA
1 AAAAATAA
*
45329825 AATAAGATAG
1 AA-AA-ATAA
45329835 AAAAATAA
1 AAAAATAA
45329843 AAAAATAA
1 AAAAATAA
*
45329851 AAATAAAAA
1 AAA-AATAA
45329860 TAAAAATAA
1 -AAAAATAA
45329869 TTGGGTTGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
8 22 0.52
9 12 0.29
10 8 0.19
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:45329864 original size:26 final size:26
Alignment explanation
Indices: 45329809--45329868 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
45329799 TTTCCTGAAC
* *
45329809 AAAAATAAATAAATAAAATAAGATAG
1 AAAAATAAAAAAATAAAATAAGAAAG
*
45329835 AAAAATAAAAAAATAAAAATAA-AAAT
1 AAAAATAAAAAAAT-AAAATAAGAAAG
45329861 AAAAATAA
1 AAAAATAA
45329869 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (26 bp):
AAAAATAAAAAAATAAAATAAGAAAG
Found at i:45333872 original size:21 final size:21
Alignment explanation
Indices: 45333830--45333884 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
45333820 CCTCAGTTTT
*
45333830 CTTTTGAAAATTCACAGTTTG
1 CTTTTGAAAATTCACAGATTG
*
45333851 CTTTTGAAAA-TCTATAGATTG
1 CTTTTGAAAATTC-ACAGATTG
*
45333872 CTGTTG-AAATTCA
1 CTTTTGAAAATTCA
45333885 AGAACATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (21 bp):
CTTTTGAAAATTCACAGATTG
Found at i:45335205 original size:21 final size:22
Alignment explanation
Indices: 45335181--45335221 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
45335171 CGATCTGAGG
45335181 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
45335202 AAAAATAAAAGAAAACAGAA
1 AAAAATAAAAGAAAACAGAA
45335222 CTGAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:45336860 original size:2 final size:2
Alignment explanation
Indices: 45336853--45336892 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
45336843 ATATGTTACC
45336853 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
45336893 TATTTCTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45339405 original size:22 final size:21
Alignment explanation
Indices: 45339359--45339409 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
45339349 GCGCAACTCA
45339359 TTTTTTTCTTCTTTTAATTTC
1 TTTTTTTCTTCTTTTAATTTC
** *
45339380 TTTTCTTTCTTCTTTTTTTTTT
1 TTTT-TTTCTTCTTTTAATTTC
45339402 TTTTTTTC
1 TTTTTTTC
45339410 CATTTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTTCTTCTTTTAATTTC
Found at i:45341484 original size:22 final size:22
Alignment explanation
Indices: 45341454--45341497 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
45341444 ATATATTATT
*
45341454 TTATTTAAATTT-AATTATAAAA
1 TTATATAAATTTGAA-TATAAAA
45341476 TTATATAAATTTGAATATAAAA
1 TTATATAAATTTGAATATAAAA
45341498 CTTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTATATAAATTTGAATATAAAA
Found at i:45342332 original size:12 final size:13
Alignment explanation
Indices: 45342317--45342345 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
45342307 ATTTGTTTTT
45342317 ATATAAAAAA-TA
1 ATATAAAAAATTA
45342329 ATATAAAAAATTA
1 ATATAAAAAATTA
45342342 ATAT
1 ATAT
45342346 GGGGCGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAAATTA
Found at i:45345306 original size:4 final size:4
Alignment explanation
Indices: 45345297--45345321 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
45345287 CTAACTCCAT
45345297 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
45345322 TTCTGCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:45348920 original size:16 final size:16
Alignment explanation
Indices: 45348897--45348941 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
45348887 TTTTTAACAA
*
45348897 TTTAATTTTTATTTTT
1 TTTAATTTTTATTTCT
* * *
45348913 TTTTATTTTTCTCTCT
1 TTTAATTTTTATTTCT
45348929 TTTAATTTTTATT
1 TTTAATTTTTATT
45348942 ATAAAAACAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTAATTTTTATTTCT
Found at i:45356421 original size:18 final size:19
Alignment explanation
Indices: 45356395--45356434 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
45356385 AATAGACTAA
*
45356395 TTTATAATTT-TAAATATT
1 TTTACAATTTATAAATATT
*
45356413 TTTACAATTTATATATATT
1 TTTACAATTTATAAATATT
45356432 TTT
1 TTT
45356435 TAATGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTACAATTTATAAATATT
Found at i:45359519 original size:30 final size:30
Alignment explanation
Indices: 45359464--45359522 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
45359454 GAGGAATTTT
*
45359464 TGTCATTACAGTCTCTATTCTTTTCAATTC
1 TGTCATTACAGTCTCTATTCGTTTCAATTC
*
45359494 TGTCATTACAGTC-CTTGTTCGTTTCAATT
1 TGTCATTACAGTCTC-TATTCGTTTCAATT
45359523 TTTGAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.19, C:0.22, G:0.10, T:0.49
Consensus pattern (30 bp):
TGTCATTACAGTCTCTATTCGTTTCAATTC
Found at i:45359678 original size:58 final size:58
Alignment explanation
Indices: 45359580--45359798 Score: 197
Period size: 59 Copynumber: 3.6 Consensus size: 58
45359570 ACTTGTTTTC
* * *
45359580 TTTCAATTTTTGAAA-TTAAGCCATTCTACTTTTACTTTGAGAATTTAGCCCCTATTAT
1 TTTCAATTTTTGAAATTTAATCC-TCCTACTTTTAATTTGAGAATTTAGCCCCTATTAT
* * * * *
45359638 TTTCCATTTTTGAAATTTAATCCTCCTACTTTTAAGTTGAGGAATTTAACCCTTCACTTGTTTT
1 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAATTTGA-GAATTT-AGCC--C-C-TATTAT
* * * * * * * * *
45359702 CTTTCAAATTTTAAAATTTAGTCATTCTACTTTTATTTTGAGAAATTTAGTCCCTGTTCT
1 -TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAATTTGAG-AATTTAGCCCCTATTAT
45359762 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAATT
1 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAATT
45359799 CAAGGAATTT
Statistics
Matches: 127, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
58 28 0.22
59 43 0.34
60 8 0.06
61 1 0.01
62 2 0.02
63 1 0.01
64 7 0.06
65 37 0.29
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (58 bp):
TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAATTTGAGAATTTAGCCCCTATTAT
Found at i:45359742 original size:123 final size:125
Alignment explanation
Indices: 45359515--45359813 Score: 453
Period size: 123 Copynumber: 2.4 Consensus size: 125
45359505 TCCTTGTTCG
* * *
45359515 TTTCAATTTTTGAAATTTAGTTCTCTTACTTTT-AGTTCGAGGAATTTAACCCTTCACTTGTTTT
1 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAAGTTCGAGGAATTTAACCCTTCACTTGTTTT
* *
45359579 CTTTCAATTTTTGAAATTAAGCCATTCTACTTTTACTTTGAG-AATTTAGCCCCTATTAT
66 CTTTCAAATTTTAAAATTAAGCCATTCTACTTTTACTTTGAGAAATTTAGCCCCTATTAT
*
45359638 TTTCCATTTTTGAAATTTAATCCTCCTACTTTTAAGTT-GAGGAATTTAACCCTTCACTTGTTTT
1 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAAGTTCGAGGAATTTAACCCTTCACTTGTTTT
* * * * * *
45359702 CTTTCAAATTTTAAAATTTAGTCATTCTACTTTTATTTTGAGAAATTTAGTCCCTGTTCT
66 CTTTCAAATTTTAAAATTAAGCCATTCTACTTTTACTTTGAGAAATTTAGCCCCTATTAT
*
45359762 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAA-TTCAAGGAATTTAACCC
1 TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAAGTTCGAGGAATTTAACCC
45359814 CGCCACTTGT
Statistics
Matches: 159, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
123 94 0.59
124 65 0.41
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (125 bp):
TTTCAATTTTTGAAATTTAATCCTCCTACTTTTAAGTTCGAGGAATTTAACCCTTCACTTGTTTT
CTTTCAAATTTTAAAATTAAGCCATTCTACTTTTACTTTGAGAAATTTAGCCCCTATTAT
Found at i:45369336 original size:12 final size:12
Alignment explanation
Indices: 45369314--45369404 Score: 66
Period size: 12 Copynumber: 7.9 Consensus size: 12
45369304 ATAACATCCA
*
45369314 AACAATAAAAAT
1 AACAACAAAAAT
*
45369326 AACAACCAAAAT
1 AACAACAAAAAT
* *
45369338 AGCAGCAAAAAT
1 AACAACAAAAAT
*
45369350 AACAGC---AA-
1 AACAACAAAAAT
*
45369358 AACAACATTAAA-
1 AACAACA-AAAAT
45369370 AACAACAAAAAT
1 AACAACAAAAAT
*
45369382 AGCAACAAAAAT
1 AACAACAAAAAT
*
45369394 AACAGCAAAAA
1 AACAACAAAAA
45369405 CAACTCAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
11 3 0.05
12 53 0.84
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:45369352 original size:44 final size:44
Alignment explanation
Indices: 45369300--45369417 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
45369290 AAAACGCATA
* * * * *
45369300 AAAAATAACATCCAAACAATA-AAAATAACAACCAAAATAGCAGC
1 AAAAATAACAGCAAAACAACATAAAA-AACAACAAAAATAGCAAC
*
45369344 AAAAATAACAGCAAAACAACATTAAAAACAACAAAAATAGCAAC
1 AAAAATAACAGCAAAACAACATAAAAAACAACAAAAATAGCAAC
*
45369388 AAAAATAACAGCAAAAACAAC-TCAAAAACA
1 AAAAATAACAGC-AAAACAACATAAAAAACA
45369418 GTAAACAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 54 0.83
45 11 0.17
ACGTcount: A:0.67, C:0.19, G:0.04, T:0.09
Consensus pattern (44 bp):
AAAAATAACAGCAAAACAACATAAAAAACAACAAAAATAGCAAC
Found at i:45369446 original size:20 final size:21
Alignment explanation
Indices: 45369423--45369515 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 21
45369413 AAACAGTAAA
45369423 CAAAACAATAAAAAA-AGCAT
1 CAAAACAATAAAAAATAGCAT
* * * *
45369443 CAAAATAGTAAAAAACAACA-
1 CAAAACAATAAAAAATAGCAT
** * *
45369463 CAAAACAGCAAAAAATGGCAAC
1 CAAAACAATAAAAAATAGC-AT
*
45369485 CAAAACAGTAAAAAAAATAGCAT
1 CAAAACA--ATAAAAAATAGCAT
45369508 CAAAACAA
1 CAAAACAA
45369516 CAATATAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
20 27 0.48
21 5 0.09
22 7 0.12
23 8 0.14
24 9 0.16
ACGTcount: A:0.67, C:0.17, G:0.08, T:0.09
Consensus pattern (21 bp):
CAAAACAATAAAAAATAGCAT
Found at i:45369511 original size:23 final size:22
Alignment explanation
Indices: 45369432--45369514 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
45369422 ACAAAACAAT
*
45369432 AAAAAAAGCATCAAAATAGTAA
1 AAAAAAAGCATCAAAACAGTAA
* *
45369454 AAAACAA-CA-CAAAACAG-CA
1 AAAAAAAGCATCAAAACAGTAA
** *
45369473 AAAAATGGCAACCAAAACAGTAA
1 AAAAAAAGC-ATCAAAACAGTAA
45369496 AAAAAATAGCATCAAAACA
1 AAAAAA-AGCATCAAAACA
45369515 ACAATATAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
19 5 0.11
20 8 0.17
21 3 0.07
22 14 0.30
23 14 0.30
24 2 0.04
ACGTcount: A:0.66, C:0.17, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAAAAAGCATCAAAACAGTAA
Found at i:45371386 original size:3 final size:3
Alignment explanation
Indices: 45371371--45371440 Score: 81
Period size: 3 Copynumber: 24.0 Consensus size: 3
45371361 CAATTTTTTC
* *
45371371 TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TCT GC- TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
45371418 TTT TTT TCT T-T TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT
45371441 CCTCTTAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
2 3 0.05
3 54 0.95
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:45371426 original size:20 final size:18
Alignment explanation
Indices: 45371365--45371440 Score: 86
Period size: 17 Copynumber: 4.4 Consensus size: 18
45371355 GCATCTCAAT
*
45371365 TTTTTC-TCTTCTCCTTC
1 TTTTTCTTCTTCTTCTTC
*
45371382 TTCTTCTTCTTCTTCTTC
1 TTTTTCTTCTTCTTCTTC
* *
45371400 TTCTTCTGC-TCTTCTTC
1 TTTTTCTTCTTCTTCTTC
*
45371417 TTTTTTTTCTT-TTCTTC
1 TTTTTCTTCTTCTTCTTC
45371434 TTTTTCT
1 TTTTTCT
45371441 CCTCTTAAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
17 31 0.62
18 19 0.38
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTTTCTTCTTCTTCTTC
Found at i:45382843 original size:13 final size:13
Alignment explanation
Indices: 45382825--45382849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45382815 TTGCGATCTC
45382825 AAATTCAACTCTG
1 AAATTCAACTCTG
45382838 AAATTCAACTCT
1 AAATTCAACTCT
45382850 ATTATTACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTCAACTCTG
Found at i:45386648 original size:30 final size:30
Alignment explanation
Indices: 45386609--45386665 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
45386599 ATAATTTTTA
45386609 AAAGATT-AAAT-TAAATTTTAATTTTTAATG
1 AAAGATTAAAATGT-AATTTT-ATTTTTAATG
*
45386639 AAAGGTTAAAATGTAATTTTATTTTTA
1 AAAGATTAAAATGTAATTTTATTTTTA
45386666 CTAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 13 0.54
31 10 0.42
32 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (30 bp):
AAAGATTAAAATGTAATTTTATTTTTAATG
Found at i:45391946 original size:20 final size:19
Alignment explanation
Indices: 45391927--45391962 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45391917 AATTTATTTA
45391927 AAGATTGAGTTATTTGTTT
1 AAGATTGAGTTATTTGTTT
*
45391946 AAGTTTGAGTT-TTTGTT
1 AAGATTGAGTTATTTGTT
45391963 CGGATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (19 bp):
AAGATTGAGTTATTTGTTT
Found at i:45392311 original size:127 final size:127
Alignment explanation
Indices: 45392085--45392341 Score: 505
Period size: 127 Copynumber: 2.0 Consensus size: 127
45392075 AAATTATCTA
45392085 TAGCCCTCCACAATCCAGAAATAGGAGGATAAAGCGCTTCGAATCCATGTTCTCTTGCATTAGTA
1 TAGCCCTCCACAATCCAGAAATAGGAGGATAAAGCGCTTCGAATCCATGTTCTCTTGCATTAGTA
45392150 ACAATACCCATGTCAATCGAGCTAGGACTCAATCGACTTATATTATTTATATTTTTATAATG
66 ACAATACCCATGTCAATCGAGCTAGGACTCAATCGACTTATATTATTTATATTTTTATAATG
45392212 TAGCCCTCCACAATCCAGAAATAGGAGGATAAAGCGCTTCGAATCCATGTTCTCTTGCATTAGTA
1 TAGCCCTCCACAATCCAGAAATAGGAGGATAAAGCGCTTCGAATCCATGTTCTCTTGCATTAGTA
*
45392277 ACAATACCTATGTCAATCGAGCTAGGACTCAATCGACTTATATTATTTATATTTTTATAATG
66 ACAATACCCATGTCAATCGAGCTAGGACTCAATCGACTTATATTATTTATATTTTTATAATG
45392339 TAG
1 TAG
45392342 ATTATATCAC
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 129 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (127 bp):
TAGCCCTCCACAATCCAGAAATAGGAGGATAAAGCGCTTCGAATCCATGTTCTCTTGCATTAGTA
ACAATACCCATGTCAATCGAGCTAGGACTCAATCGACTTATATTATTTATATTTTTATAATG
Found at i:45394379 original size:17 final size:17
Alignment explanation
Indices: 45394335--45394390 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
45394325 TTAGAAATAT
45394335 AAAACTAAATTTTATAAG
1 AAAACTAAA-TTTATAAG
**
45394353 AAAAAAAAATTTA-AATG
1 AAAACTAAATTTATAA-G
45394370 AAAACTAAATTGTATAA-
1 AAAACTAAATT-TATAAG
45394387 AAAA
1 AAAA
45394391 AGATGAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
16 2 0.06
17 18 0.58
18 9 0.29
19 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAACTAAATTTATAAG
Found at i:45399488 original size:13 final size:15
Alignment explanation
Indices: 45399461--45399494 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
45399451 AAACGGTGAA
45399461 AAAAATAAGTGAAAT
1 AAAAATAAGTGAAAT
45399476 AAAAATAA-T-AAAT
1 AAAAATAAGTGAAAT
45399489 AAAAAT
1 AAAAAT
45399495 CTAAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAAATAAGTGAAAT
Found at i:45400355 original size:6 final size:6
Alignment explanation
Indices: 45400341--45400371 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
45400331 ACTAGAAAAT
*
45400341 CGTCAC CGTCGC CGTCGC CGTCGC CGTCGC C
1 CGTCGC CGTCGC CGTCGC CGTCGC CGTCGC C
45400372 ATCACCGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.52, G:0.29, T:0.16
Consensus pattern (6 bp):
CGTCGC
Found at i:45401810 original size:36 final size:36
Alignment explanation
Indices: 45401763--45401838 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
45401753 CCATTGTGTC
45401763 AAGCCTAGTGTTGGGTCTTATTAGTATTATCAGGCA
1 AAGCCTAGTGTTGGGTCTTATTAGTATTATCAGGCA
45401799 AAGCCTAGTGTTGGGTCTTATTAGTATTATCAGGCA
1 AAGCCTAGTGTTGGGTCTTATTAGTATTATCAGGCA
45401835 AAGC
1 AAGC
45401839 TAAGTAAGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (36 bp):
AAGCCTAGTGTTGGGTCTTATTAGTATTATCAGGCA
Found at i:45409217 original size:31 final size:31
Alignment explanation
Indices: 45409176--45409234 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
45409166 ACCATTAAAT
* *
45409176 TATTTTAAAGT-TTTCATTTAAATCACTGAAC
1 TATTTGAAAGTATTT-ATTAAAATCACTGAAC
*
45409207 TATTTGAAAGTATTTATTAAAATTACTG
1 TATTTGAAAGTATTTATTAAAATCACTG
45409235 GATTGTTACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
TATTTGAAAGTATTTATTAAAATCACTGAAC
Found at i:45410245 original size:31 final size:31
Alignment explanation
Indices: 45410210--45410272 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
45410200 TTTTTTAGGG
* * *
45410210 TTAATATACTATTTGGTACGTGAGTTTGGTT
1 TTAATATACAATTTGATACGTGAGCTTGGTT
* * *
45410241 TTAATGTTCAATTTGATACTTGAGCTTGGTT
1 TTAATATACAATTTGATACGTGAGCTTGGTT
45410272 T
1 T
45410273 CTATGTTTAA
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:0.22, C:0.08, G:0.21, T:0.49
Consensus pattern (31 bp):
TTAATATACAATTTGATACGTGAGCTTGGTT
Found at i:45410279 original size:31 final size:31
Alignment explanation
Indices: 45410220--45410286 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
45410210 TTAATATACT
* *
45410220 ATTTGGTACGTGAGTTTGGTTTTAATGTTCA
1 ATTTGATACGTGAGCTTGGTTTTAATGTTCA
* *
45410251 ATTTGATACTTGAGCTTGGTTTCT-ATGTTTA
1 ATTTGATACGTGAGCTTGGTTT-TAATGTTCA
45410282 ATTTG
1 ATTTG
45410287 GTTCCCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.51
Consensus pattern (31 bp):
ATTTGATACGTGAGCTTGGTTTTAATGTTCA
Found at i:45410429 original size:31 final size:30
Alignment explanation
Indices: 45410391--45410471 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
45410381 TATCAATTTG
*
45410391 AAAAAACTCAGGTACTAAAATAGATATTGAA
1 AAAAAACTCAGGTACTAAAATAAATATT-AA
* * *
45410422 ACAAAACTCAAGTA-TCAAATTAAATATTAA
1 AAAAAACTCAGGTACT-AAAATAAATATTAA
45410452 AAATAAACTCAGGTACTAAA
1 AAA-AAACTCAGGTACTAAA
45410472 CAATATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 5 0.12
31 35 0.85
32 1 0.02
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (30 bp):
AAAAAACTCAGGTACTAAAATAAATATTAA
Found at i:45410480 original size:31 final size:28
Alignment explanation
Indices: 45410391--45410482 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 28
45410381 TATCAATTTG
45410391 AAAAAACTCAGGTACTAAAATAGATATTGAA
1 AAAAAACTCAGGTACTAAAA-A-ATATT-AA
* *
45410422 ACAAAACTCAAGTA-TCAAATTAAATATTAA
1 AAAAAACTCAGGTACT-AAA--AAATATTAA
45410452 AAATAAACTCAGGTACTAAACAATATATTAA
1 AAA-AAACTCAGGTACTAAA-AA-ATATTAA
45410483 CCTTTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
30 7 0.14
31 40 0.80
32 2 0.04
33 1 0.02
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (28 bp):
AAAAAACTCAGGTACTAAAAAATATTAA
Found at i:45412982 original size:2 final size:2
Alignment explanation
Indices: 45412931--45412962 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45412921 AGTTTATATA
45412931 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
45412963 CATACACGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:45438676 original size:29 final size:27
Alignment explanation
Indices: 45438644--45438742 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 27
45438634 AAATTTTAAA
*
45438644 TTAATAATGATAAAATTACATTTTAA-CTT
1 TTAA-AATAATAAAATTA-A-TTTAATCTT
45438673 TTAAAATAATAAAAATTAATTTAATCTT
1 TTAAAATAAT-AAAATTAATTTAATCTT
* * * *
45438701 TTAAAA-ATTATAAA--AATATAAACTA
1 TTAAAATAATA-AAATTAATTTAATCTT
45438726 TTAAAATAATAAAATTA
1 TTAAAATAATAAAATTA
45438743 TTTTTTATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
25 17 0.29
26 4 0.07
27 11 0.19
28 15 0.26
29 11 0.19
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (27 bp):
TTAAAATAATAAAATTAATTTAATCTT
Found at i:45438694 original size:28 final size:30
Alignment explanation
Indices: 45438637--45438717 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 30
45438627 ATTTATAAAA
45438637 TTTTAAATTAATAATGATAAAATTACATTTTAA-C
1 TTTTAAA--AATAAT-A-AAAATTACA-TTTAATC
45438671 TTTT-AAAATAATAAAAATTA-ATTTAATC
1 TTTTAAAAATAATAAAAATTACATTTAATC
*
45438699 TTTTAAAAATTATAAAAAT
1 TTTTAAAAATAATAAAAAT
45438718 ATAAACTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 5 0.11
28 6 0.14
29 20 0.45
30 1 0.02
31 6 0.14
33 2 0.05
34 4 0.09
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTTAAAAATAATAAAAATTACATTTAATC
Found at i:45440515 original size:5 final size:6
Alignment explanation
Indices: 45440501--45440547 Score: 67
Period size: 6 Copynumber: 7.3 Consensus size: 6
45440491 ATAATAATGC
45440501 AAAATA AAAATA AAAATA AAAATA AAATATA AAATATA AAAAGTA AA
1 AAAATA AAAATA AAAATA AAAATA AAA-ATA AAA-ATA AAAA-TA AA
45440548 TTACTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.56
7 17 0.44
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:45440758 original size:28 final size:29
Alignment explanation
Indices: 45440726--45440784 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
45440716 AAAATTATAT
45440726 TTTAATCTCTT-AAAAATATAAAAAATTA
1 TTTAATCTCTTCAAAAATATAAAAAATTA
* * * *
45440754 TTTAATTTTTTCAAAATTATAAAAATTTA
1 TTTAATCTCTTCAAAAATATAAAAAATTA
45440783 TT
1 TT
45440785 AAAATGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAATCTCTTCAAAAATATAAAAAATTA
Found at i:45453298 original size:29 final size:29
Alignment explanation
Indices: 45453264--45453319 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
45453254 ATTTGATTTT
*
45453264 TTTAATAGTATAGGGACTAAATTGATCCA
1 TTTAATAGTAGAGGGACTAAATTGATCCA
*
45453293 TTTAATAGTAGAGGGACTAATTTGATC
1 TTTAATAGTAGAGGGACTAAATTGATC
45453320 AGGTCCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (29 bp):
TTTAATAGTAGAGGGACTAAATTGATCCA
Found at i:45456193 original size:135 final size:135
Alignment explanation
Indices: 45455473--45456172 Score: 1116
Period size: 135 Copynumber: 5.2 Consensus size: 135
45455463 ACCGTGCCTC
45455473 CTGAAACCGGTCT-CCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTG
1 CTGAAACCGGT-TGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTG
* *
45455537 AGAACTATCACTACTAGATGATTCCAAAGGTTTATACTTTTTCAGCTCGCTATTAGTCATATTAC
65 AGAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTAC
*
45455602 TAGAAA
130 TAGAAG
45455608 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
* *
45455673 GAATTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGCCGTATTACT
66 GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
45455738 AGAAG
131 AGAAG
45455743 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
*
45455808 GAACTATCACTACTAGATGATTCCAAAAGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
66 GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
45455873 AGAAG
131 AGAAG
* *
45455878 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGTTTGACAAGAATTCCGA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
* * * * * * *
45455943 TAAGTATCACTGCTGGATGATTCCAAAGGTTCT-TCCTTTTTCAGCTCTCTATTAGTTGTATTAG
66 GAACTATCACTACTAGATGATTCCAAAGGTT-TATCCTTTTTCAGCTCGCTATTAGTCGTATTAC
*
45456007 AAGAAG
130 TAGAAG
* * **
45456013 CTGAAACCGGTTGCCATTTTTTCTTTACAGTTCTTGAATCCCCATTTGTTTGACAAGAATTCCAA
1 CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
* * * * * *
45456078 TAACTATCACTGCTGGATGCTTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTTGTATTAGT
66 GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
45456143 AGAAG
131 AGAAG
* *
45456148 CTGAAACCGGTCGCCATATTTGCTT
1 CTGAAACCGGTTGCCATTTTTGCTT
45456173 AGGGGCTGTA
Statistics
Matches: 534, Mismatches: 28, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
134 2 0.00
135 531 0.99
136 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (135 bp):
CTGAAACCGGTTGCCATTTTTGCTTTACAGTTCTTGAATCCCCATTTGCTTGACAAGAATTCTGA
GAACTATCACTACTAGATGATTCCAAAGGTTTATCCTTTTTCAGCTCGCTATTAGTCGTATTACT
AGAAG
Found at i:45465969 original size:21 final size:21
Alignment explanation
Indices: 45465944--45465983 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
45465934 AATCAACTAT
45465944 GATTTTCA-AGTTATGTTCACC
1 GATTTTCATAGTT-TGTTCACC
45465965 GATTTTCATAGTTTGTTCA
1 GATTTTCATAGTTTGTTCA
45465984 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (21 bp):
GATTTTCATAGTTTGTTCACC
Found at i:45490232 original size:40 final size:40
Alignment explanation
Indices: 45490177--45490254 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
45490167 ACATGGACTA
45490177 ATTTGTTTATTTTTAAAATAAAAAGGGTAAAATATAATGT
1 ATTTGTTTATTTTTAAAATAAAAAGGGTAAAATATAATGT
45490217 ATTTGTTTATTTTTAAAATAAAAAGGGTAAAATATAAT
1 ATTTGTTTATTTTTAAAATAAAAAGGGTAAAATATAAT
45490255 TTGACTCCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (40 bp):
ATTTGTTTATTTTTAAAATAAAAAGGGTAAAATATAATGT
Found at i:45494818 original size:4 final size:4
Alignment explanation
Indices: 45494809--45494833 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
45494799 TATTAACTAA
45494809 TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC T
45494834 CTATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:45494853 original size:4 final size:4
Alignment explanation
Indices: 45494846--45494872 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
45494836 ATATATATAT
45494846 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
45494873 AAATAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:45500283 original size:29 final size:29
Alignment explanation
Indices: 45500205--45500283 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
45500195 TAATTGGACT
45500205 TAAATTTTAAA-ATCTGAAAATTAAAAAGAC
1 TAAATTTTAAATAT-TG-AAATTAAAAAGAC
* * * *
45500235 TAAATTCATGAATATAGAAA-TATAAAGAC
1 TAAATT-TTAAATATTGAAATTAAAAAGAC
45500264 TAAATTTTAAATATGTGAAA
1 TAAATTTTAAATAT-TGAAA
45500284 AGTATAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 6 0.15
29 18 0.46
30 9 0.23
31 4 0.10
32 2 0.05
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (29 bp):
TAAATTTTAAATATTGAAATTAAAAAGAC
Found at i:45500534 original size:18 final size:19
Alignment explanation
Indices: 45500511--45500546 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45500501 AATTTTTTCA
45500511 GTAAATTATAA-TAATAAG
1 GTAAATTATAAGTAATAAG
*
45500529 GTAAATTTTAAGTAATAA
1 GTAAATTATAAGTAATAA
45500547 AAGTGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
GTAAATTATAAGTAATAAG
Found at i:45505491 original size:12 final size:12
Alignment explanation
Indices: 45505474--45505499 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45505464 TTTTAGTTAA
45505474 AAAATCAAATAG
1 AAAATCAAATAG
45505486 AAAATCAAATAG
1 AAAATCAAATAG
45505498 AA
1 AA
45505500 CTTGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAATCAAATAG
Found at i:45509739 original size:6 final size:6
Alignment explanation
Indices: 45509728--45509752 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45509718 AGTTAACCCC
45509728 CCGCCA CCGCCA CCGCCA CCGCCA C
1 CCGCCA CCGCCA CCGCCA CCGCCA C
45509753 GGCTCCCGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CCGCCA
Found at i:45509865 original size:4 final size:4
Alignment explanation
Indices: 45509856--45509882 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
45509846 ACTCTCACCA
45509856 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
45509883 TTGCCTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:45518486 original size:14 final size:14
Alignment explanation
Indices: 45518467--45518495 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
45518457 AATTTATATA
45518467 CATAATATTTTTTC
1 CATAATATTTTTTC
45518481 CATAATATTTTTTC
1 CATAATATTTTTTC
45518495 C
1 C
45518496 TTTAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (14 bp):
CATAATATTTTTTC
Found at i:45519140 original size:18 final size:18
Alignment explanation
Indices: 45519117--45519155 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
45519107 TTTCGAGTCT
45519117 TTTCCATCTTTAGCATCC
1 TTTCCATCTTTAGCATCC
*
45519135 TTTCCATCTTTAGCGTCC
1 TTTCCATCTTTAGCATCC
45519153 TTT
1 TTT
45519156 GCTGGAGCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.31, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTCCATCTTTAGCATCC
Found at i:45537996 original size:20 final size:19
Alignment explanation
Indices: 45537971--45538028 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
45537961 TTCAAATTAA
45537971 TTAATTGAATTATATTAAAT
1 TTAATT-AATTATATTAAAT
* *
45537991 TTAATTATTTAATTTTAAAT
1 TTAATTAATT-ATATTAAAT
45538011 TTAAATTTAATTA-ATTAA
1 TT-AA-TTAATTATATTAA
45538029 TTGAGTTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 20 0.65
21 3 0.10
22 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATTAATTATATTAAAT
Found at i:45540930 original size:37 final size:37
Alignment explanation
Indices: 45540889--45540960 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
45540879 ATTAAATTTG
45540889 TTTATTAACCTTATAAAGTGTCAAACTATTTTTTTAA
1 TTTATTAACCTTATAAAGTGTCAAACTATTTTTTTAA
*
45540926 TTTATTAACCTTATAAAGTGTCAAATTATTTTTTT
1 TTTATTAACCTTATAAAGTGTCAAACTATTTTTTT
45540961 TAATGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (37 bp):
TTTATTAACCTTATAAAGTGTCAAACTATTTTTTTAA
Found at i:45541107 original size:17 final size:16
Alignment explanation
Indices: 45541078--45541116 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
45541068 TGTTACATTA
45541078 ATAAATAATTTAAAATT
1 ATAAA-AATTTAAAATT
45541095 ATAAAAATATTAAAATT
1 ATAAAAAT-TTAAAATT
45541112 A-AAAA
1 ATAAAA
45541117 TTAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAATTTAAAATT
Found at i:45545150 original size:3 final size:3
Alignment explanation
Indices: 45545142--45545173 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
45545132 TCTACTAATT
45545142 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45545174 GTACAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:45546410 original size:24 final size:25
Alignment explanation
Indices: 45546374--45546424 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
45546364 TATTGAAAAT
45546374 AATTTTATTTTGAAAAATTAATTTG
1 AATTTTATTTTGAAAAATTAATTTG
*
45546399 AATTTT-TTTTGACAAATTAATTTG
1 AATTTTATTTTGAAAAATTAATTTG
45546423 AA
1 AA
45546425 AATTCTGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (25 bp):
AATTTTATTTTGAAAAATTAATTTG
Found at i:45546712 original size:59 final size:60
Alignment explanation
Indices: 45546630--45546754 Score: 198
Period size: 59 Copynumber: 2.1 Consensus size: 60
45546620 AATTTCATTT
*
45546630 TTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGTATTA
1 TTTATTATTTGTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGTATTA
* * * *
45546690 TTTATTA-TTGTATGATTTTAAATAAATAAATGTAAAATAATATTAATTTTGTTTTATTA
1 TTTATTATTTGTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGTATTA
45546749 TTTATT
1 TTTATT
45546755 TATTATTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 53 0.88
60 7 0.12
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (60 bp):
TTTATTATTTGTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGTATTA
Found at i:45546755 original size:63 final size:60
Alignment explanation
Indices: 45546626--45546793 Score: 196
Period size: 59 Copynumber: 2.8 Consensus size: 60
45546616 ATTCAATTTC
45546626 ATTT-TTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGT
1 ATTTATTTATTA-TTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGT
* * * * *
45546686 A-TTATTTATTATTGTATGATTTTAAATAAATAAATGTAAAATAATATTAATTTTGTTTTATT
1 ATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG--TT-GT
* * * *
45546748 ATTTATTTATTATTTTATGAGTATAGATAAGTAAATAAATAAATAA
1 ATTTATTTATTATTTTATGAATATAAATAAATAAATATA-AAATAA
45546794 CAAACCTAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 42 0.47
60 8 0.09
61 2 0.02
62 2 0.02
63 30 0.33
64 6 0.07
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (60 bp):
ATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTGT
Found at i:45548250 original size:10 final size:10
Alignment explanation
Indices: 45548235--45548272 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
45548225 TATCAATAAC
45548235 ATTAAAAATT
1 ATTAAAAATT
*
45548245 ATTAAAATATC
1 ATTAAAA-ATT
45548256 ATTAAAAATT
1 ATTAAAAATT
45548266 -TTAAAAA
1 ATTAAAAA
45548273 ATCATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.28
10 9 0.36
11 9 0.36
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:45548269 original size:20 final size:21
Alignment explanation
Indices: 45548229--45548277 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
45548219 ATTAAATATC
*
45548229 AATAACATTAAAAATTATTAA
1 AATATCATTAAAAATTATTAA
45548250 AATATCATTAAAAATT-TTAA
1 AATATCATTAAAAATTATTAA
*
45548270 AAAATCAT
1 AATATCAT
45548278 AAATAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATCATTAAAAATTATTAA
Found at i:45548842 original size:23 final size:23
Alignment explanation
Indices: 45548795--45548842 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
45548785 ACCAAATATA
* *
45548795 ATTATTTTTATTTAATATTACAT
1 ATTATTTTTATTAAATATTAAAT
45548818 ATTATATTTTATTAAAT-TTAAAT
1 ATTAT-TTTTATTAAATATTAAAT
45548841 AT
1 AT
45548843 ATAAGTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATTTTTATTAAATATTAAAT
Found at i:45548902 original size:21 final size:22
Alignment explanation
Indices: 45548877--45548922 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
45548867 AATTTAATTT
45548877 TTTAATTT-T-TATTTTCAAGAA
1 TTTAATTTATATATTTTCAA-AA
*
45548898 TTTAATTTATATATTTTTAAAA
1 TTTAATTTATATATTTTCAAAA
45548920 TTT
1 TTT
45548923 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTAATTTATATATTTTCAAAA
Done.